Compositions and methods for the targeting of PCSK9

Provided herein are gene repressor systems comprising fusion proteins, such as fusion proteins comprising a DNA binding domain such as a TALE, zinc finger or catalytically-dead CRISPR protein and guide nucleic acid (gRNA), which are useful in the repression of a proprotein convertase subtilisin/kexin Type 9 (PCSK9) gene. Also provided are methods of using such systems to repress transcription of PCSK9.

1. 11. A system comprising a repressor fusion protein and a guide ribonucleic acid (gRNA), wherein the repressor fusion protein comprises: (a) a catalytically-dead CasX protein (dCasX); (b) a repressor domain (RD1) comprising the sequence of any one of SEQ ID NOS: 130, 131, 135 and 143; (c) a DNA methyltransferase (DNMT) 3A ATRX-DNMT3-DNMT3L domain (ADD) comprising the sequence of SEQ ID NO: 125; (d) a DNMT3A catalytic domain comprising the sequence of SEQ ID NO: 126; and (e) a DNMT3L comprising the sequence of SEQ ID NO: 127, wherein the gRNA comprises a scaffold capable of binding to the dCasX and a targeting sequence complementary to a proprotein convertase subtilisin/kexin Type 9 (PCSK9) gene target nucleic acid sequence, wherein the targeting sequence comprises the sequence of any one of SEQ ID NOS: 1844, 1852, 1853, 1855, 1858, 1859, 1867, 1869, and 1870, wherein the repressor fusion protein is capable of forming a ribonucleoprotein (RNP) with the gRNA, and wherein the RNP is capable of repressing transcription of the PCSK9 gene upon binding to the PCSK9 gene target nucleic acid sequence.
2. 22. The system of claim 1, wherein the ADD is fused to the N-terminus of the DNMT3A catalytic domain.
3. 33. The system of claim 1, wherein the repressor fusion protein comprises, from N- to C-terminus: (a) the ADD; (b) the DNMT3A catalytic domain; (c) the DNMT3L; (d) the dCasX; and (e) the RD1, or wherein the repressor fusion protein comprises, from N- to C-terminus: (a) the ADD; (b) the DNMT3A catalytic domain; (c) the DNMT3L; (d) the RD1; and (e) the dCasX.
4. 44. The system of claim 1, wherein the dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 4-29.
5. 55. The system of claim 1, wherein the PCSK9 gene target nucleic acid sequence is: (a) within the 5′ untranslated region of the PCSK9 gene; or (b) within an exon of the PCSK9 gene.
6. 66. The system of claim 1, wherein the scaffold comprises the sequence of SEQ ID NO: 1746, or a sequence having at least 95% sequence identity to the full-length sequence of SEQ ID NO: 1746.

CROSS REFERENCE TO RELATED APPLICATIONS
This application is a continuation of PCT/US2023/067987, filed on Jun. 6, 2023, which claims priority to, and benefit of, U.S. Provisional Application Nos. 63/349,981 filed on Jun. 7, 2022, 63/492,923, filed on Mar. 29, 2023, and 63/505,823, filed on Jun. 2, 2023, the contents of each of which are incorporated by reference herein in their entireties.


REFERENCE TO AN ELECTRONIC SEQUENCE LISTING
The contents of the electronic sequence listing (SCRB_055_03US_SubSeqList_ST26.xml; Size: 4,366,818 bytes; and Date of Creation: Aug. 15, 2024) are herein incorporated by reference in their entirety.
BACKGROUND
In mammals, cholesterol is transported within lipoproteins via emulsification. The lipoprotein particles are classified based on their density: low-density lipoproteins (LDL), very low-density lipoproteins (VLDL), high-density lipoproteins (HDL), and chylomicrons. Surface LDL receptors are internalized during cholesterol absorption. A cell with abundant cholesterol will have its LDL receptor synthesis blocked to prevent new cholesterol in LDL particles from being taken up. Conversely, LDL receptor synthesis is promoted when a cell is deficient in cholesterol. When the process is unregulated, excess LDL particles will travel in the blood without uptake by an LDL receptor. LDL particles in the blood are oxidized and taken up by macrophages, which then become engorged and form foam cells. These foam cells can become trapped in the walls of blood vessels and contribute to atherosclerotic plaque formation, which is one of the main causes of heart attacks, strokes, and other serious medical problems.
The liver protein proprotein convertase subtilisin/kexin Type 9 (PCSK9) is a secreted, globular, auto-activating serine protease that binds to the low-density lipoprotein receptor (LDL-R) during endocytosis of LDL particles, preventing recycling of the LDL-R to the cell surface and leading to reduction of LDL-cholesterol clearance. PCSK9 binds to the LDL-R (through the EGF-A domain), preventing the conformational change of the receptor-ligand complex, which redirects the LDL-R to the lysosome instead. As the receptor for low-density lipoprotein particles (LDL) typically transports thousands of fat molecules (including cholesterol) per particle within extracellular fluid, blocking or inhibiting the function of PCSK9 to boost LDL-R-mediated clearance of LDL cholesterol can lower LDL particle concentrations. PCSK9 is expressed mainly in the liver, the intestine, the kidney, and the central nervous system, but is also highly expressed in arterial walls such as endothelium, smooth muscle cells, and macrophages, with a local effect that can regulate vascular homeostasis and atherosclerosis.
PCSK9 is a member of the proprotein convertase (PC) family and its gene is mutated in 2% to 3% of individuals with familial hypercholesterolemia (FH) (Sepideh Mikaeeli, S., et al. Functional analysis of natural PCSK9 mutants in modern and archaic humans. FEBS J. 2019 Aug. 6. doi: 10.1111/febs.15036). Researchers have identified several PCSK9 mutations that cause an inherited form of high cholesterol (hypercholesterolemia). These mutations change a single amino acid in the PCSK9 protein. Researchers describe the mutations responsible for hypercholesterolemia as “gain-of-function” because they appear to enhance the activity of the PCSK9 protein or give the protein a new, atypical function (Blesa, S., et al. A New PCSK9 Gene Promoter Variant Affects Gene Expression and Causes Autosomal Dominant Hypercholesterolemia. J. Clin. Endocrinol. & Metab. 93:3577(2008)). The overactive PCSK9 protein substantially reduces the number of low-density lipoprotein receptors on the surface of liver cells. With fewer receptors to remove low-density lipoproteins from the blood, people with gain-of-function mutations in the PCSK9 gene have very high blood cholesterol levels. Autosomal dominant hypercholesterolemia (ADH) is a genetic disorder characterized by increased low-density lipoprotein (LDL)-cholesterol levels, leading to high risk of premature cardiovascular disease. Approximately 10 mutations in PCSK9 have been identified as a cause of the disease in different populations. All known mutations in PCSK9 causing hypercholesterolemia produce an increase in the enzymatic activity of this protease (Bleasa, S., 2008). In addition, mutations in PCSK9 can lead to autosomal dominant familial hypobetalipoproteinemia, which can lead to hepatic steatosis, cirrhosis, and other disorders.
The advent of CRISPR/Cas systems, and the programmable nature of these minimal systems, has facilitated their use as a versatile technology for genomic manipulation and engineering. However, current methods of generating PCSK9 protective variants and loss-of-function mutants in vivo have been ineffective due to the large number of cells that need to be modified to modulate cholesterol levels. Other concerns involve off-target effects, genome instability, or oncogenic modifications that may be caused by genome editing, as well as a lack of safe delivery modalities for gene-repression systems. Additionally, in certain disease indications, gene silencing, or repression, is preferable to gene editing. The ability to render CRISPR nucleases such as Cas9 and CasX catalytically-inactive has been demonstrated (WO2020247882A1 and US20200087641A1, incorporated by reference herein), which makes these systems an attractive platform for the generation of fusion proteins with repressor domains capable of gene silencing. While certain repressor systems have been described, there remains a need for additional gene repressor systems that have been optimized and/or offer improvements over earlier generations of gene repressor systems, such as those based on Cas9, for utilization in a variety of therapeutic, diagnostic, and research applications. Thus, there remains a need for improved compositions and methods to regulate PCSK9.
SUMMARY
The present disclosure provides systems comprising or encoding repressor fusion proteins comprising DNA-binding and linked repressor domains used in the repression and/or epigenetic modification of proprotein convertase subtilisin/kexin Type 9 (PCSK9) gene target nucleic acid sequences. In some cases, the repressor fusion protein comprises a DNA-binding protein comprising a zinc finger (ZF) or a transcription-activator-like effector (TALE) protein complementary to the PCSK9 gene target nucleic acid sequence and one or more linked repressor domains. In some cases, the repressor fusion protein comprises a DNA-binding protein comprising a catalytically-dead CRISPR protein and one or more linked repressor domains, and a guide nucleic acid comprising a targeting sequence complementary to the PCSK9 gene target nucleic acid sequence. The proteins and guide nucleic acids can be modified for passive entry into target cells and are useful in a variety of methods for repression of PCSK9, which methods are also provided. The present disclosure also provides vectors and lipid nanoparticles (LNP) encoding or encapsulating the repressor fusion proteins and guide nucleic acids components for the delivery of the systems to cells for the transcriptional repression of the PCSK9 target nucleic acid sequence.
The disclosure provides pharmaceutical compositions comprising the systems, nucleic acids, LNP and vectors described herein.
The present disclosure also provides methods for treating subjects having a PCSK9-related disease. In some embodiments, the compositions and methods have utility in subjects having a metabolic disorder such as, but not limited to, familial hypercholesterolemia, familial hypobetalipoproteinemia, or elevated cholesterol levels.
In another aspect, provided herein are systems comprising PCRK9 repressor systems, or vectors comprising or encoding PCSK9 repressor systems for use in the manufacture of a medicament for the treatment of a PCSK9-related disease in a subject in need thereof.
The present disclosure provides compositions for use in methods of treating subjects having a PCSK9-related disease. In some embodiments, the composition comprises repressor fusion proteins comprising a catalytically-dead CRISPR protein and one or more linked repressor domains, and a guide nucleic acid comprising a targeting sequence complementary to the PCSK9 gene target nucleic acid sequence for use in the transcriptional repression of PCSK9 gene target nucleic acid sequences in a subject. In some embodiments, the composition comprises systems, nucleic acids, LNP, vectors and/or pharmaceutical compositions described herein.
In some embodiments, the PCSK9 gene comprises one or more mutations, for example amino acid substitutions selected from the group consisting of S127R, D129G, F216L, D374H, and D374Y relative to the sequence of SEQ ID NO: 1823.
The disclosure provides methods of repressing transcription of a PCSK9 gene in a population of cells, the method comprising introducing into cells of the population the systems, nucleic acids, LNP, vectors and/or pharmaceutical compositions described herein.
In some embodiments, the catalytically-dead CRISPR protein and guide nucleic acid for use in the PCSK9 repressor systems comprise catalytically-dead CasX variant proteins and/or CasX variant guide nucleic acids as described herein.
Further features and advantages of certain embodiments of the present disclosure will become more fully apparent in the following description of embodiments and drawings thereof, and from the claims.



BRIEF DESCRIPTION OF THE DRAWINGS
The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:
FIG. 1 illustrates the schematics of five configurations of long-term repressor protein (LTRP, also referred to herein as “repressor fusion proteins”) fusion proteins with repressor molecules linked to catalytically-dead CasX. D3A and D3L denote DNA methyltransferase 3 alpha (DNMT3A) and DNMT3A-like protein (DNMT3L), respectively. L1-L4 are linkers. NLS is the nuclear localization signal.
FIG. 2 illustrates schematics of various configurations of LTRP fusion proteins with the DNMT3A ADD domain incorporated. “D3A ADD”, “D3A CD”, and “D3L ID” denote the ADD domain of DNMT3A, the catalytic domain of DNMT3A, and the interaction domain of DNMT3L, respectively. L1-L3 are linkers. NLS is the nuclear localization signal.
FIG. 3 is a dot plot graph showing the correlation between secreted PCSK9 protein and PCSK9 mRNA levels in human hepatocytes that were transiently transfected with LTRPs, as described in Example 1. PCSK9 mRNA levels were normalized to the housekeeping gene RPLP0. Secreted PCSK9 protein levels were normalized to secreted human serum albumin (HSA). Samples were normalized to a non-targeting (NT) control.
FIG. 4 is a bar plot showing the percentage of mouse Hepa1-6 cells, treated with either dXR1 or LTRP1-ZIM3 mRNA paired with the indicated PCSK9-targeting gRNAs, that stained negative for intracellular PCSK9 at day 6, as described in Example 2. Spacer 6.7 targeting the human PCSK9 locus served as a non-targeting control.
FIG. 5 is a time course plot showing the percentage of mouse Hepa1-6 cells, treated with dXR1 mRNA paired with the indicated PCSK9-targeting gRNAs, that stained negative for intracellular PCSK9 at 6, 13, and 25 days post-delivery, as described in Example 2. Spacer 6.7 targeting the human PCSK9 locus served as a non-targeting control, and treatment with water served as a negative control.
FIG. 6 is a time course plot showing the percentage of mouse Hepa1-6 cells, treated with LTRP1-ZIM3 mRNA paired with the indicated PCSK9-targeting gRNAs, that stained negative for intracellular PCSK9 at 6, 13, and 25 days post-delivery, as described in Example 2. Spacer 6.7 targeting the human PCSK9 locus served as a non-targeting control, and treatment with water served as a negative control.
FIG. 7 is a time course plot showing the percentage of mouse Hepa1-6 cells, treated with IVT-produced LTRP1-ZIM3 vs. LTRP5-ZIM5 mRNA paired with the indicated PCSK9-targeting gRNAs, that stained negative for intracellular PCSK9 at the indicated timepoints days post-delivery, as described in Example 2.
FIG. 8 is a time course plot showing the percentage of mouse Hepa1-6 cells, treated with third-party-produced LTRP1-ZIM3 vs. dCas9-ZNF10-DNMT3A/3L mRNA paired with the indicated PCSK9-targeting gRNAs, that stained negative for intracellular PCSK9 at the indicated timepoints post-delivery, as described in Example 2.
FIG. 9 is a bar graph showing the quantification of secreted PCSK9 levels at 6, 18, 36, and 87 days post-transfection in Huh7 cells lipofected with mRNA encoding for CasX 676, dXR1, or LTRP5-ADD-ZIM3 when paired with the indicated targeting gRNAs, as described in Example 3. Secreted PCSK9 levels were normalized to total cell count. Naïve, untreated cells served as an experimental control.
FIG. 10A is a time course plot showing the percentage of mouse Hepa1-6 cells, treated with LTRP5-ZIM3 or LTRP5-ADD-ZIM3 mRNA paired with the PCSK9-targeting gRNA with spacer 27.88, that stained negative for intracellular PCSK9 at 4, 12, 18, 24, 41, and 53 days post-delivery, as described in Example 4. A non-targeting (NT) spacer was used as an experimental control.
FIG. 10B is a time course plot showing the percentage of mouse Hepa1-6 cells, treated with LTRP5-ZIM3 or LTRP5-ADD-ZIM3 mRNA paired with the PCSK9-targeting gRNA with spacer 27.94, that stained negative for intracellular PCSK9 at 4, 12, 18, 24, 41, and 53 days post-delivery, as described in Example 4. A non-targeting (NT) spacer was used as an experimental control.
FIG. 11A is a bar plot showing the quantification of normalized secreted PCSK9 levels at 4 days post-transfection in HepG2 cells lipofected with mRNA encoding for CasX 676, dXR1, or LTRP5-ADD-ZIM3 when paired with the indicated targeting gRNAs, as described in Example 5. Secreted PCSK9 levels were normalized to total cell count. Naïve, untreated cells served as experimental controls.
FIG. 11B is a bar plot showing the quantification of normalized secreted PCSK9 levels at 4 days post-transfection in Huh7 cells lipofected with mRNA encoding for CasX 676, dXR1, or LTRP5-ADD-ZIM3 when paired with the indicated targeting gRNAs, as described in Example 5. Secreted PCSK9 levels were normalized to total cell count. Naïve, untreated cells served as experimental controls.
FIG. 11C is a bar plot showing the quantification of normalized secreted PCSK9 levels at 4 days post-transfection in Hep3B cells lipofected with mRNA encoding for CasX 676, dXR1, or LTRP5-ADD-ZIM3 when paired with the indicated targeting gRNAs, as described in Example 5. Secreted PCSK9 levels were normalized to total cell count. Naïve, untreated cells served as experimental controls.
FIG. 12 is a bar plot showing the quantification of secreted PCSK9 levels at 4, 14, and 27 days post-transfection in Huh7 cells lipofected with mRNA encoding for CasX 676, dXR1, or LTRP5-ADD-ZIM3 when paired with the indicated targeting gRNAs, as described in Example 5. Quantification of secreted PCSK9 levels is shown as relative to the secreted levels detected in the naïve, untreated cells at the day 4 timepoint.
FIG. 13 is a violin plot showing the distribution of secreted PCSK9 levels in HepG2 cells transfected with CasX 676 mRNA #2 and a gRNA with the indicated PCSK9-targeting spacer, as described in Example 6. Naïve, untreated cells and cells transfected with CasX 676 mRNA only served as experimental controls.
FIG. 14 is a pair of representative western blots showing the levels of pro-PCSK9 and processed PCSK9 protein (top western blot) in HepG2 cells transfected with CasX 676 mRNA and a gRNA with the indicated PCSK9-targeting spacer, as described in Example 6. Naïve, untreated cells and cells transfected with CasX 676 mRNA only served as experimental controls. Lysate from HEK293T cells, which do not express the PCSK9 protein, and a cynomolgus macaque recombinant PCSK9 protein control were used as western blot controls. The bottom western blot shows the total protein loading control.
FIG. 15 is a bar plot showing the western blot quantification for pro-PCSK9, processed PCSK9, and total PCSK9 levels for each of the indicated spacers assessed when transfected with CasX 676 mRNA into HepG2 cells, as described in Example 6. Naïve, untreated cells and cells transfected with CasX 676 mRNA only served as experimental controls. PCSK9 levels were normalized to total PCSK9 levels from the naïve condition.
FIG. 16A is a schematic illustrating versions 1-3 of chemical modifications made to gRNA scaffold variant 235, as described in Example 7. Structural motifs are highlighted. Standard ribonucleotides are depicted as open circles, and 2′OMe-modified ribonucleotides are depicted as black circles. Phosphorothioate bonds are indicated with * below or beside the bond. For the v2 profile, the addition of three 3′ uracils (3′UUU) is annotated with “U”s in the relevant circles.
FIG. 16B is a schematic illustrating versions 4-6 of chemical modifications made to gRNA scaffold variant 235, as described in Example 7. Structural motifs are highlighted. Standard ribonucleotides are depicted as open circles, and 2′OMe-modified ribonucleotides are depicted as black circles. Phosphorothioate bonds are indicated with * below or beside the bond.
FIG. 17 is a plot illustrating the quantification of percent knockout of B2M in HepG2 cells co-transfected with 100 ng of CasX 491 mRNA and with the indicated doses of end-modified (v1) or unmodified (v0) B2M-targeting gRNAs with spacer 7.37, as described in Example 7. Editing level was determined by flow cytometry as the population of cells with loss of surface presentation of the HLA complex due to successful editing at the B2M locus.
FIG. 18 is a schematic illustrating versions 7-9 of chemical modifications made to gRNA scaffold variant 316, as described in Example 7. Structural motifs are highlighted. Standard ribonucleotides are depicted as open circles, and 2′OMe-modified ribonucleotides are depicted as black circles. Phosphorothioate bonds are indicated with * below or beside the bond.
FIG. 19A is a schematic of gRNA scaffold variant 174 (SEQ ID NO: 1744), as described in Example 7. Structural motifs are highlighted.
FIG. 19B is a schematic of gRNA scaffold variant 235 (SEQ ID NO: 1745), as described in Example 7. Highlighted structural motifs are the same as in FIG. 19A. The differences between variant 174 and variant 235 lie in the extended stem motif and several single-nucleotide changes (indicated with asterisks). Variant 316 maintains the shorter extended stem from variant 174 but harbors the four substitutions found in scaffold 235.
FIG. 19C is a schematic of gRNA scaffold variant 316 (SEQ ID NO: 1746), as described in Example 7. Highlighted structural motifs are the same as in FIG. 19A. Variant 316 maintains the shorter extended stem from variant 174 (FIG. 19A) but harbors the four substitutions found in scaffold 235 (FIG. 19B).
FIG. 20 is a plot displaying a correlation between indel rate (depicted as edit fraction) at the PCSK9 locus as measured by next-generation sequencing (NGS) (x-axis) and secreted PCSK9 levels (ng/mL) detected by enzyme-linked immunosorbent assay (ELISA) (y-axis) in HepG2 cells lipofected with CasX 491 mRNA and PCSK9-targeting gRNAs containing the indicated scaffold variant and spacer combination, as described in Example 7.
FIG. 21A is a plot depicting the results of an editing assay measured as indel rate detected by NGS at the human B2M locus in HepG2 cells treated with the indicated doses of LNPs formulated with CasX 491 mRNA and the indicated B2M-targeting gRNA, as described in Example 7.
FIG. 21B is a plot illustrating the quantification of percent knockout of B2M in HepG2 cells treated with the indicated doses of LNPs formulated with CasX 491 mRNA and the indicated B2M-targeting gRNA, as described in Example 7. Editing level was determined by flow cytometry as population of cells that did not have surface presentation of the HLA complex due to successful editing at the B2M locus.
FIG. 22A is a plot depicting the results of an editing assay measured as indel rate detected by NGS at the mouse ROSA26 locus in Hepa1-6 cells treated with the indicated doses of LNPs formulated with CasX 676 mRNA #2 and the indicated ROSA26-targeting gRNA with either the v1 or v5 modification profile, as described in Example 7.
FIG. 22B is a plot illustrating the quantification of percent editing measured as indel rate detected by NGS at the ROSA26 locus in mice treated with LNPs formulated with CasX 676 mRNA #2 and the indicated chemically-modified ROSA26-targeting gRNA, as described in Example 7.
FIG. 23 is a bar graph showing the results of an editing assay measured as indel rate detected by NGS at the mouse PCSK9 locus in mice treated with LNPs formulated with CasX 676 mRNA #1 and the indicated chemically-modified PCSK9-targeting gRNA, as described in Example 7. Untreated mice served as experimental control.
FIG. 24 is a schematic illustrating versions 1-3 of chemical modifications made to gRNA scaffold variant 316, as described in Example 7. Structural motifs are highlighted. Standard ribonucleotides are depicted as open circles, and 2′OMe-modified ribonucleotides are depicted as black circles. Phosphorothioate bonds are indicated with * below or beside the bond.
FIG. 25 is a schematic illustrating versions 4-6 of chemical modifications made to gRNA scaffold variant 316, as described in Example 7. Structural motifs are highlighted. Standard ribonucleotides are depicted as open circles, and 2′OMe-modified ribonucleotides are depicted as black circles. Phosphorothioate bonds are indicated with * below or beside the bond.
FIG. 26 is a bar graph showing the quantification of percent editing measured as indel rate detected by NGS at the mouse PCSK9 locus in Hepa1-6 cells transfected with the indicated engineered CasX mRNAs and targeting spacers and harvested at 20 hours post-transfection, as described in Example 8.
FIG. 27A is a diagram of the secondary structure of guide RNA scaffold 235 (SEQ ID NO: 1745), noting the regions with CpG motifs, as described in Example 12. CpG motifs in (1) the pseudoknot stem, (2) the scaffold stem, (3) the extended stem bubble, (4) the extended step, and (5) the extended stem loop are labeled on the structure.
FIG. 27B is a diagram of the CpG-reducing mutations that were introduced into each of the five regions in the coding sequence of the guide RNA scaffold, as described in Example 12. The substitute bubble from scaffold 174 has a sequence of AGCUCCCUCUUCGGAGGGAGCA (SEQ ID NO: 3442).
FIG. 28 provides the results of an editing experiment in which AAV vectors with various CpG-reduced or CpG-depleted guide RNA scaffolds were used to edit the B2M locus in induced neurons, as described in Example 12. The AAV vectors were administered at a multiplicity of infection (MOI) of 4e3. The bars show the mean±the SD of two replicates per sample. “No Tx” indicates a non-transduced control, and “NT” indicates a control with a non-targeting spacer.
FIG. 29 provides the results of an editing experiment in which AAV vectors with various CpG-reduced or CpG-depleted guide RNA scaffolds were used to edit the B2M locus in induced neurons, as described in Example 12. The AAV vectors were administered at an MOI of 3e3. The bars show the mean±the SD of two replicates per sample. “No Tx” indicates a non-transduced control.
FIG. 30 provides the results of an editing experiment in which AAV vectors with various CpG-reduced or CpG-depleted guide RNA scaffolds were used to edit the B2M locus in induced neurons, as described in Example 12. The AAV vectors were administered at an MOI of 1e3. The bars show the mean±the SD of two replicates per sample. “No Tx” indicates a non-transduced control.
FIG. 31 provides the results of an editing experiment in which AAV vectors with various CpG-reduced or CpG-depleted guide RNA scaffolds were used to edit the B2M locus in induced neurons, as described in Example 12. The AAV vectors were administered at an MOI of MOI=3e2. The bars show the mean±the SD of two replicates per sample. “No Tx” indicates a non-transduced control.
FIG. 32A presents the results of a time-course experiment comparing beta-2-microglobulin (B2M) repression activities (represented as percentage of HLA-negative cells) of LTRP proteins Nos. 1-3, as described in Example 13. Data are presented as mean with standard deviation, N=3.
FIG. 32B presents the results of the same time-course experiment shown in FIG. 32A but illustrates the B2M repression activities of LTRP proteins Nos. 1-3 containing the ZIM3-KRAB domain, benchmarked against the same experimental controls, as described in Example 13. Data are presented as mean with standard deviation, N=3.
FIG. 33A presents the results of a time-course experiment comparing B2M silencing activities (represented as percentage of HLA-negative cells) of LTRP proteins #1, #4, and #5, as described in Example 13. Data are presented as mean with standard deviation, N=3.
FIG. 33B presents the results of the same time-course experiment shown in FIG. 33A but illustrates the B2M silencing activities of LTRP proteins #1, #4, and #5 containing the ZIM3-KRAB domain, benchmarked against the same experimental controls, as described in Example 13. Data are presented as mean with standard deviation, N=3.
FIG. 34 is a violin plot of percent CpG methylation for CpG sites around the transcription start site of the B2M locus for each indicated experimental condition as described in Example 13.
FIG. 35 is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 21) versus specificity (percentage of off-target CpG methylation at the B2M locus quantified at day 5) for LTRP proteins #1-3, benchmarked against catalytically-active CasX 491 and dCas9-ZNF10-DNMT3A/L, as described in Example 13.
FIG. 36 is a violin plot of percent CpG methylation for CpG sites downstream of the transcription start site of the VEGFA locus for each indicated experimental condition as described in Example 13.
FIG. 37A is a violin plot of percent CpG methylation for CpG sites around the transcription start site of the VEGFA locus for each indicated experimental condition assessing LTRP #1, 4, and 5 with the B2M-targeting spacer as described in Example 13.
FIG. 37B is a violin plot of percent CpG methylation for CpG sites around the transcription start site of the VEGFA locus for each indicated experimental condition assessing LTRP #1, 4, and 5 with the non-targeting spacer as described in Example 13.
FIG. 38 is a scatterplot showing the relative activity (average percentage of HLA-negative cells at day 21) versus specificity (median percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for LTRP proteins #1-5 harboring either the ZNF10- or ZIM-KRAB domain, and the LTRP proteins were benchmarked against catalytically-active CasX 491 and dCas9-ZNF10-DNMT3A/L, as described in Example 13.
FIG. 39 presents the results of a time-course experiment comparing B2M repression activities (represented as percentage of HLA-negative cells) of the indicated LTRP-ZIM3 and its variants with B2M-targeting gRNA using spacer 7.37, as described in Example 14. Data are presented as mean with standard deviation, N=3. CD=catalytic domain of DNMT3A.
FIG. 40 presents the results of the same time-course experiment shown in FIG. 39 but shows B2M repression activities of the indicated LTRP-ZIM3 variants with B2M-targeting gRNA using spacer 7.160, as described in Example 14. Data are presented as mean with standard deviation, N=3.
FIG. 41 presents the results of the same time-course experiment shown in FIG. 39 but shows B2M repression activities of the indicated LTRP-ZIM3 variants with B2M-targeting gRNA using spacer 7.165, as described in Example 14. Data are presented as mean with standard deviation, N=3.
FIG. 42 presents the results of the same time-course experiment shown in FIG. 39 but shows B2M repression activities of the indicated LTRP-ZIM3 variants with a non-targeting gRNA, as described in Example 14. Data are presented as mean with standard deviation, N=3.
FIG. 43 is a violin plot of percent CpG methylation for CpG sites downstream of the transcription start site of the VEGFA locus for each indicated LTRP-ZIM3 variant for the three B2M-targeting gRNA and non-targeting gRNA, as described in Example 14.
FIG. 44 is a scatterplot showing the relative activity (average percentage of HLA-negative cells at day 21 for spacer 7.160) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 7 for spacer 7.160) for the indicated LTRP5-ZIM3 variants, as described in Example 14.
FIG. 45 illustrates the schematics of the various LTRP #5 architectures, where the additional DNMT3A domains were incorporated, as described in Example 14. The additional DNMT3A domains were the ADD domain of DNMT3A (“D3A ADD”) and the PWWP domain of DNMT3A (“D3A PWWP”). “D3A endo” encodes for an endogenous sequence that occurs between DNMT3A PWWP and ADD domains. “D3A CD” and “D3L ID” denote the catalytic domain of DNMT3A and the interaction domain of DNMT3L respectively. “L1-L3” are linkers. “NLS” is the nuclear localization signal. See Table 12 for exemplary sequences.
FIG. 46 illustrates the schematics of the general architectures of the LTRP molecules with the ADD domain for LTRP configuration #1, #4, and #5 tested in Example 15. “D3A ADD”, “D3A CD” and “D3L ID” denote the ADD domain of DNMT3A, the catalytic domain of DNMT3A, and the interaction domain of DNMT3L respectively, as described in Example 15. “L1-L4” are linkers. “NLS” is the nuclear localization signal. See Table 17 for exemplary sequences.
FIG. 47A presents the results of a time-course experiment comparing B2M repression activities (represented as percentage of HLA-negative cells) of LTRPs with the ZIM3-KRAB domain having configuration #1, #4, or #5 with or without the DNMT3A ADD domain when paired with the B2M-targeting gRNA with spacer 7.160, as described in Example 15. Data are presented as mean with standard deviation, N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 47B is a plot showing the results of the same time-course experiment shown in FIG. 47A but illustrates B2M repression activities for LTRP #5 with the ZNF10 or ZIM3-KRAB domain, with or without the DNMT3A ADD domain, paired with the B2M-targeting gRNA with spacer 7.160, as described in Example 15. Data are presented as mean with standard deviation, N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 47C is a plot showing the results of the same time-course experiment shown in FIG. 47A but illustrates B2M repression activities for LTRP5-ZIM3 with or without the DNMT3A ADD domain paired with a B2M-targeting gRNA with the indicated spacers, as described in Example 15. Data are presented as mean with standard deviation, N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 48A is a plot illustrating the results of B2M repression activities on day 27 post-transfection for LTRPs with either the ZNF10 or ZIM3-KRAB domain having configuration #1 with or without the DNMT3A ADD domain for the indicated gRNAs, as described in Example 15. Data are presented as mean with standard deviation, N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 48B is a plot illustrating the results of B2M repression activities on day 27 post-transfection for LTRPs with either the ZNF10 or ZIM3-KRAB domain having configuration #4 with or without the DNMT3A ADD domain for the indicated gRNAs, as described in Example 15. Data are presented as mean with standard deviation, N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 48C is a plot illustrating the results of B2M repression activities on day 27 post-transfection for LTRPs with either the ZNF10 or ZIM3-KRAB domain having configuration #5 with or without the DNMT3A ADD domain for the indicated gRNAs, as described in Example 15. Data are presented as mean with standard deviation, N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 49A is a plot illustrating the results of bisulfite sequencing used to determine off-target methylation at the VEGFA locus on day 5 post-transfection for LTRPs with either the ZNF10 or ZIM3-KRAB domain having configuration #1 with or without the DNMT3A ADD domain for the indicated gRNAs, as described in Example 15. Data are presented as mean percentage of CpG methylation for CpG sites near the VEGFA locus; standard error of the mean is also presented; N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 49B is a plot illustrating the results of bisulfite sequencing used to determine off-target methylation at the VEGFA locus on day 5 post-transfection for LTRPs with either the ZNF10 or ZIM3-KRAB domain having configuration #4 with or without the DNMT3A ADD domain for the indicated gRNAs, as described in Example 15. Data are presented as mean percentage of CpG methylation for CpG sites near the VEGFA locus; standard error of the mean is also presented; N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 49C is a plot illustrating the results of bisulfite sequencing used to determine off-target methylation at the VEGFA locus on day 5 post-transfection for LTRPs with either the ZNF10 or ZIM3-KRAB domain having configuration #5 with or without the DNMT3A ADD domain for the indicated gRNAs, as described in Example 15. Data are presented as mean percentage of CpG methylation for CpG sites near the VEGFA locus; standard error of the mean is also presented; N=3. “NT” is a gRNA with a non-targeting spacer.
FIG. 50A is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 27) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for the LTRP molecules with the ZIM3-KRAB domain having configurations #1, #4, and #5, for B2M-targeting gRNA with spacer 7.160, as described in Example 15.
FIG. 50B is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 27) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for the LTRP molecules with the ZNF10-KRAB domain having configurations #1, #4, and #5, for B2M-targeting gRNA with spacer 7.160, as described in Example 15.
FIG. 51A is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 27) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for the LTRP molecules with the ZIM3-KRAB domain having configurations #1, #4, and #5, for B2M-targeting gRNA with spacer 7.37, as described in Example 15.
FIG. 51B is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 27) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for the LTRP molecules with the ZNF10-KRAB domain having configurations #1, #4, and #5, for B2M-targeting gRNA with spacer 7.37, as described in Example 15.
FIG. 52A is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 27) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for the LTRP molecules with the ZIM3-KRAB domain having configurations #1, #4, and #5, for B2M-targeting gRNA with spacer 7.165, as described in Example 15.
FIG. 52B is a dot plot showing the relative activity (average percentage of HLA-negative cells at day 27) versus specificity (percentage of off-target CpG methylation at the VEGFA locus quantified at day 5) for the LTRP molecules with the ZNF10-KRAB domain having configurations #1, #4, and #5, for B2M-targeting gRNA with spacer 7.165, as described in Example 15.
FIG. 53 shows the dose response results of the diphtheria toxin titration for cells transduced with either catalytically active CasX editors with gRNAs targeting the gene encoding the Heparin Binding EGF-like Growth Factor (HBEGF), i.e., CasX-34.19 and CasX-34.21; a catalytically-dead CasX (dCasX) protein linked to a repressor domain as a fusion protein targeted to HBEGF (dXR fusion proteins, i.e., dXR1-34.28); or a non-targeting dXR molecule (CasX-NT or dXR-NT), as described in Example 16. Data represent the mean and standard deviation of two biological replicates.
FIG. 54 provides violin plots showing the log 2 (fold change) of sequences before and after selection for their ability to support dXR repression of the HBEGF locus, as described in Example 17. The plots show the results for the entire library, a negative control set of sequences, a positive control set of known KRAB repressors, the top 1597 enhanced domains tested with log 2(fold change)>2 and p-values<0.01, and the top 95 enhanced domains tested.
FIG. 55 shows B2M silencing activities (represented as percentage of HLA-negative cells) of dXR proteins with various repressor domains, as described in Example 17. Data are presented as mean with standard deviation, N=3.
FIG. 56 shows B2M silencing activities (represented as percentage of HLA-negative cells) of dXR proteins with various repressor domains, as described in Example 17. Data are presented as mean with standard deviation, N=3.
FIG. 57A provides the logo of repressor domain motif 1, as described in Example 17.
FIG. 57B provides the logo of repressor domain motif 2, as described in Example 17.
FIG. 57C provides the logo of repressor domain motif 3 (SEQ ID NO: 1727), as described in Example 17. The logo corresponds to SEQ ID NO: 1727.
FIG. 57D provides the logo of repressor domain motif 4 (SEQ ID NO: 1728), as described in Example 17. The logo corresponds to SEQ ID NO: 1728.
FIG. 57E provides the logo of repressor domain motif 5, as described in Example 17.
FIG. 57F provides the logo of repressor domain motif 6 (SEQ ID NO: 1729), as described in Example 17. The logo corresponds to SEQ ID NO: 1729.
FIG. 57G provides the logo of repressor domain motif 7 (SEQ ID NO: 1730), as described in Example 17. The logo corresponds to SEQ ID NO: 1730.
FIG. 57H provides the logo of repressor domain motif 8, as described in Example 17.
FIG. 57I provides the logo of repressor domain motif 9, as described in Example 17.
FIG. 58A provides the logo of alternative repressor domain motif 1 (SEQ ID NO: 2945), as described in Example 19. The logo corresponds to SEQ ID NO: 2945.
FIG. 58B provides the logo of alternative repressor domain motif 2, as described in Example 19.
FIG. 58C provides the logo of alternative repressor domain motif 3, as described in Example 19.
FIG. 58D provides the logo of alternative repressor domain motif 4, as described in Example 19.
FIG. 58E provides the logo of alternative repressor domain motif 5 (SEQ ID NO: 2946), as described in Example 19. The logo corresponds to SEQ ID NO: 2946.
FIG. 59 is a plot illustrating percentage of HEK293T cells, transfected with a plasmid encoding the indicated CasX or LTRP:gRNA construct, that expressed B2M six days post-treatment with the DNMT1 inhibitor 5-azadC at varying concentrations, as described in Example 20.
FIG. 60 is a plot that juxtaposes the quantification of B2M repression in HEK293T cells transfected with a plasmid encoding the indicated CasX or LTRP:gRNA construct and cultured for 58 days, with the quantification of B2M reactivation upon treatment of transfected cells with 5-azadC, as described in Example 20.
FIG. 61 is a plot illustrating the percent of secreted PCSK9, normalized to baseline PCSK9 secretion levels, at 4 days post-treatment, for primary cynomolgus macaque (CM) hepatocytes from the BJE lot. CM hepatocytes were treated with the indicated doses of LNPs formulated with CasX 515 or LTRP5-ADD-ZIM3 mRNA and a PCSK9-targeting gRNA with spacer 6.1, as described in Example 10. The dashed line represents the lower limit of quantitation (LLOQ).
FIG. 62 is a plot illustrating the percent of secreted PCSK9, normalized to baseline PCSK9 secretion levels, at 4 days post-treatment, for primary CM hepatocytes from the VDU lot. CM hepatocytes were treated with the indicated doses of LNPs formulated with CasX 515 or LTRP5-ADD-ZIM3 mRNA and a PCSK9-targeting gRNA with spacer 6.1, as described in Example 10. The dashed line represents the lower limit of quantitation (LLOQ).
FIG. 63 is a plot illustrating the percent of secreted PCSK9, normalized to baseline PCSK9 secretion levels, at 11 days post-treatment, for primary CM hepatocytes from the BJE lot. CM hepatocytes were treated with the indicated doses of LNPs formulated with CasX 515 or LTRP5-ADD-ZIM3 mRNA and a PCSK9-targeting gRNA with spacer 6.1, as described in Example 10. The dashed line represents the lower limit of quantitation (LLOQ).
FIG. 64 is a plot illustrating the percent of secreted PCSK9, normalized to baseline PCSK9 secretion levels, at 11 days post-treatment, for primary CM hepatocytes from the VDU lot. CM hepatocytes treated with the indicated doses of LNPs formulated with CasX 515 or LTRP5-ADD-ZIM3 mRNA and a PCSK9-targeting gRNA with spacer 6.1, as described in Example 10. The dashed line represents the lower limit of quantitation (LLOQ).
FIG. 65A is a volcano plot showing the differential gene expression analysis (log 2 fold changes (log 2FC) of read counts) comparing LTRP5-ADD-ZIM3 paired with a non-targeting (NT) spacer with the untreated, naïve control at 6 days post-transfection. The horizontal dotted line shows the adjusted p<0.001.
FIG. 65B is a volcano plot showing the differential gene expression analysis (log 2FC of read counts) comparing LTRP5-ADD-ZIM3 paired with a non-targeting (NT) spacer with the untreated, naïve control at 26 days post-transfection. The horizontal dotted line shows the adjusted p<0.001, and the vertical lines show the |log 2FCJ>2 threshold. Black dots are the identified differentially regulated off-target genes after applying the two significance thresholds.
FIG. 66A is a volcano plot showing the differential gene expression analysis (log 2FC of read counts) comparing LTRP5-ADD-ZIM3 paired with spacer TG-06-154 with the untreated, naïve control at 6 days post-transfection. The horizontal dotted line shows the adjusted p<0.001, and the vertical lines show the |log 2FCJ>2 threshold. Black dots (except for PCSK9) are the identified differentially regulated off-target genes after applying the two significance thresholds.
FIG. 66B is a volcano plot showing the differential gene expression analysis (log 2FC of read counts) comparing LTRP5-ADD-ZIM3 paired with spacer TG-06-154 with the untreated, naïve control at 26 days post-transfection. The horizontal dotted line shows the adjusted p<0.001, and the vertical lines show the |log 2FCJ>2 threshold. Black dots (except for PCSK9) are the identified differentially regulated off-target genes after applying the two significance thresholds.
FIG. 67A is a volcano plot is a volcano plot showing the differential gene expression analysis (log 2FC of read counts) comparing LTRP5-ADD-ZIM3 paired with spacer TG-06-133 with the untreated, naïve control at 6 days post-transfection. The horizontal dotted line shows the adjusted p<0.001, and the vertical lines show the |log 2FCJ>2 threshold. Black dots (except for PCSK9) are the identified differentially regulated off-target genes after applying the two significance thresholds.
FIG. 67B is a volcano plot showing the differential gene expression analysis (log 2FC of read counts) comparing LTRP5-ADD-ZIM3 paired with spacer TG-06-133 with the untreated, naïve control at 26 days post-transfection. The horizontal dotted line shows the adjusted p<0.001, and the vertical lines show the |log 2FCJ>2 threshold. Black dots (except for PCSK9) are the identified differentially regulated off-target genes after applying the two significance thresholds.
FIG. 68 is a bar graph showing the quantification of percent knockout of B2M in HEK293 cells transfected with CpG-depleted AAV plasmids containing the indicated gRNA scaffolds with spacer 7.37, as described in Example 24. The dotted line indicates ˜41% transfection efficiency.
FIG. 69A is a bar plot showing percent editing at the AAVS1 locus in human induced neurons (iNs) transduced with AAVs expressing the CasX:gRNA system using the indicated gRNA scaffolds (AAV construct ID #262-274) at the MOI of 3E4 vg/cell, as described in Example 24.
FIG. 69B is a bar plot showing percent editing at the AAVS1 locus in human iNs transduced with AAVs expressing the CasX:gRNA system using the indicated gRNA scaffolds (AAV construct ID #262-274) at the MOI of 1E4 vg/cell, as described in Example 24.
FIG. 69C is a bar plot showing percent editing at the AAVS1 locus in human iNs transduced with AAVs expressing the CasX:gRNA system using the indicated gRNA scaffolds (AAV construct ID #262-274) at the MOI of 3E3 vg/cell, as described in Example 24.
FIG. 70A is a bar plot showing the quantification of percent knockout of B2M in HEK293 cells transfected with CpG-depleted AAV plasmids containing the indicated gRNA scaffolds with spacer 7.37 (AAV construct ID #275-289) at the MOI of 1E4 vg/cell, as described in Example 24.
FIG. 70B is a bar plot showing the quantification of percent knockout of B2M in HEK293 cells transfected with CpG-depleted AAV plasmids containing the indicated gRNA scaffolds with spacer 7.37 (AAV construct ID #275-289) at the MOI of 3E3 vg/cell, as described in Example 24.
FIG. 70C is a bar plot showing the quantification of percent knockout of B2M in HEK293 cells transfected with CpG-depleted AAV plasmids containing the indicated gRNA scaffolds with spacer 7.37 (AAV construct ID #275-289) at the MOI of 1E3 vg/cell, as described in Example 24.



DETAILED DESCRIPTION
While exemplary embodiments have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the inventions claimed herein. It should be understood that various alternatives to the embodiments described herein may be employed in practicing the embodiments of the disclosure. It is intended that the claims define the scope of the invention and that methods and structures within the scope of these claims and their equivalents be covered thereby.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present embodiments, suitable methods and materials are described below. In case of conflict, the patent specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and not intended to be limiting. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the invention.
Definitions
“Hybridizable” or “complementary” are used interchangeably to mean that a nucleic acid (e.g., RNA, DNA) comprises a sequence of nucleotides that enables it to non-covalently bind, i.e., form Watson-Crick base pairs and/or G/U base pairs, “anneal”, or “hybridize,” to another nucleic acid in a sequence-specific, antiparallel, manner (i.e., a nucleic acid specifically binds to a complementary nucleic acid) under the appropriate in vitro and/or in vivo conditions of temperature and solution ionic strength. It is understood that the sequence of a polynucleotide need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable; it can have at least about 70%, at least about 80%, or at least about 90%, or at least about 95% sequence identity and still hybridize to the target nucleic acid. Moreover, a polynucleotide may hybridize over one or more segments such that intervening or adjacent segments are not involved in the hybridization event (e.g., a loop structure or hairpin structure, a ‘bulge’, ‘bubble’ and the like). Thus, the skilled artisan will understand that while individual bases within a sequence may not be complementary to another sequence, the sequence as a whole is still considered to be complementary.
A “gene,” for the purposes of the present disclosure, includes a DNA region encoding a gene product (e.g., a protein, RNA), as well as all DNA regions which regulate the production of the gene product, whether or not such regulatory sequences are adjacent to coding and/or transcribed sequences. Accordingly, a gene may include accessory element sequences including, but not necessarily limited to, promoter sequences, terminators, translational regulatory sequences such as ribosome binding sites and internal ribosome entry sites, enhancers, silencers, insulators, boundary elements, replication origins, matrix attachment sites and locus control regions. Coding sequences encode a gene product upon transcription or transcription and translation; the coding sequences of the disclosure may comprise fragments and need not contain a full-length open reading frame. A gene can include both the strand that is transcribed as well as the complementary strand containing the anticodons.
The term “downstream” refers to a nucleotide sequence that is located 3′ to a reference nucleotide sequence. In certain embodiments, downstream nucleotide sequences relate to sequences that follow the starting point of transcription. For example, the translation initiation codon of a gene is located downstream of the start site of transcription.
The term “upstream” refers to a nucleotide sequence that is located 5′ to a reference nucleotide sequence. In certain embodiments, upstream nucleotide sequences relate to sequences that are located on the 5′ side of a coding region or starting point of transcription. For example, most promoters are located upstream of the start site of transcription.
The term “adjacent to” with respect to polynucleotide or amino acid sequences refers to sequences that are next to, or adjoining each other in a polynucleotide or polypeptide. The skilled artisan will appreciate that two sequences can be considered to be adjacent to each other and still encompass a limited amount of intervening sequence, e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 nucleotides or amino acids.
The term “regulatory element” is used interchangeably herein with the term “regulatory sequence,” and is intended to include promoters, enhancers, and other expression regulatory elements. It will be understood that the choice of the appropriate regulatory element will depend on the encoded component to be expressed (e.g., protein or RNA) or whether the nucleic acid comprises multiple components that require different polymerases or are not intended to be expressed as a fusion protein.
The term “accessory element” is used interchangeably herein with the term “accessory sequence,” and is intended to include, inter alia, polyadenylation signals (poly(A) signal), enhancer elements, introns, posttranscriptional regulatory elements (PTREs), nuclear localization signals (NLS), deaminases, DNA glycosylase inhibitors, additional promoters, factors that stimulate CRISPR-mediated homology-directed repair (e.g. in cis or in trans), self-cleaving sequences, and fusion domains, for example a fusion domain fused to a CRISPR protein. It will be understood that the choice of the appropriate accessory element or elements will depend on the encoded component to be expressed (e.g., protein or RNA) or whether the nucleic acid comprises multiple components that require different polymerases or are not intended to be expressed as a fusion protein.
The term “promoter” refers to a DNA sequence that contains a transcription start site and additional sequences to facilitate polymerase binding and transcription. Exemplary eukaryotic promoters include elements such as a TATA box, and/or B recognition element (BRE) and assists or promotes the transcription and expression of an associated transcribable polynucleotide sequence and/or gene (or transgene). A promoter can be synthetically produced or can be derived from a known or naturally occurring promoter sequence or another promoter sequence. A promoter can also include a chimeric promoter comprising a combination of two or more heterologous sequences to confer certain properties. A promoter of the present disclosure can include variants of promoter sequences that are similar in composition, but not identical to, other promoter sequence(s) known or provided herein. A promoter can be classified according to criteria relating to the pattern of expression of an associated coding or transcribable sequence or gene operably linked to the promoter, such as constitutive, developmental, tissue-specific, inducible, etc. A promoter can also be classified according to its strength. As used in the context of a promoter, “strength” refers to the rate of transcription of the gene controlled by the promoter. A “strong” promoter means the rate of transcription is high, while a “weak” promoter means the rate of transcription is relatively low.
A promoter of the disclosure can be a Polymerase II (Pol II) promoter. Polymerase II transcribes all protein coding and many non-coding genes. A representative Pol II promoter includes a core promoter, which is a sequence of about 100 base pairs surrounding the transcription start site, and serves as a binding platform for the Pol II polymerase and associated general transcription factors. The promoter may contain one or more core promoter elements such as the TATA box, BRE, Initiator (INR), motif ten element (MTE), downstream core promoter element (DPE), downstream core element (DCE), although core promoters lacking these elements are known in the art. All Pol II promoters are envisaged as within the scope of the instant disclosure.
A promoter of the disclosure can be a Polymerase III (Pol III) promoter. Pol III transcribes DNA to synthesize small ribosomal RNAs such as the 5S rRNA, tRNAs, and other small RNAs. Representative Pol III promoters use internal control sequences (sequences within the transcribed section of the gene) to support transcription, although upstream elements such as the TATA box are also sometimes used. All Pol III promoters are envisaged as within the scope of the instant disclosure.
The term “enhancer” refers to regulatory DNA sequences that, when bound by specific proteins called transcription factors, regulate the expression of an associated gene. Enhancers may be located in the intron of the gene, or 5′ or 3′ of the coding sequence of the gene. Enhancers may be proximal to the gene (i.e., within a few tens or hundreds of base pairs (bp) of the promoter), or may be located distal to the gene (i.e., thousands of bp, hundreds of thousands of bp, or even millions of bp away from the promoter). A single gene may be regulated by more than one enhancer, all of which are envisaged as within the scope of the instant disclosure.
As used herein, a “post-transcriptional regulatory element (PTRE, or TRE),” such as a hepatitis PTRE, refers to a DNA sequence that, when transcribed creates a tertiary structure capable of exhibiting post-transcriptional activity to enhance or promote expression of an associated gene operably linked thereto.
In the context of the present disclosure and with respect to a gene, “repress”, “repression”, “repressing”, “inhibition of gene expression”, “downregulation”, and “silencing” are used interchangeably herein to refer to the inhibition or blocking of transcription of a gene or a portion thereof. Accordingly, repression of a gene can result in a decrease in production of a gene product. Examples of gene repression processes which decrease transcription include, but are not limited to, those which inhibit formation of a transcription initiation complex, those which decrease transcription initiation rate, those which decrease transcription elongation rate, those which decrease processivity of transcription and those which antagonize transcriptional activation (by, for example, blocking the binding of a transcriptional activator). Gene repression can constitute, for example, prevention of activation as well as inhibition of expression below an existing level. Transcriptional repression includes both reversible and irreversible inactivation of gene transcription; the latter can result from epigenetic modification of the gene.
“Repressor” or “repressor domain” are used interchangeably to refer to polypeptide factors that act as regulatory elements on DNA that inhibit, repress, or block transcription of DNA, resulting in repression of gene expression. In the context of the present disclosure, the linking of a repressor domain to DNA-binding protein that can, when bound to the target nucleic acid, prevent transcription from a promoter or otherwise inhibit the expression of a gene. Without wishing to be bound by theory, it is thought that transcriptional repressors can function by a variety of mechanisms, including physically blocking RNA polymerase passage by steric hindrance, altering the polymerase's post-translational modification state, modifying the epigenetic state of the nascent RNA, changing the epigenetic state of the DNA through methylation, changing the epigenetic state of the DNA through histone deacetylation or modulating nucleosome remodeling, or preventing enhancer-promoter interactions, thereby leading to gene silencing or a reduction in the level of gene expression.
“Long-term repressor protein” or “LTRP” is used interchangeably herein with “repressor fusion protein” and refers to a fusion protein comprising a DNA binding protein (or DNA binding domain of a protein) fused to one or more domains capable of repressing transcription of a target nucleic acid sequence. Optionally, the repressor fusion proteins of the disclosure may contain additional elements, such as linkers between any of the domains of the fusion protein, nuclear localization signals, nuclear export signals, as well as additional protein domains that confer additional activities upon the repressor fusion protein.
As used herein a “repressor fusion protein:gRNA system” is a system for transcriptional repression and comprises a repressor fusion protein comprising a catalytically-dead CRISPR protein and one or more linked repressor domains, and a guide nucleic acid (gRNA) that binds to the catalytically-dead CRISPR protein. For clarity, the system also includes any encoding DNA, RNA or vectors and the like that can be used to produce the repressor fusion proteins and gRNA components of the system.
As used herein, a DNA-binding protein refers to a protein, or domain of a protein, capable of binding to DNA. Exemplary DNA-binding proteins include zinc finger (ZF) proteins, TALEs, and CRISPR proteins. The skilled artisan will appreciate that in multi-functional proteins that are capable of both binding DNA and carrying out another activity such as DNA cleavage, such as, e.g., CRISPR proteins, the DNA binding function can be separated from the other functions of the protein, leading to catalytically-dead DNA binding proteins.
As used herein a “catalytically-dead CRISPR protein” refers to a CRISPR protein that lacks endonuclease activity. The skilled artisan will appreciate that a CRISPR protein can be catalytically-dead, and still able to carry out additional protein functions, such as DNA binding. Similarly, a “catalytically-dead CasX” refers to a CasX protein that lacks endonuclease activity but is still able to carry out additional protein functions, such as DNA binding.
“Recombinant,” as used herein, means that a particular nucleic acid (DNA or RNA) is the product of various combinations of cloning, restriction, and/or ligation steps resulting in a construct having a structural coding or non-coding sequence distinguishable from endogenous nucleic acids found in natural systems. Generally, DNA sequences encoding the structural coding sequence can be assembled from cDNA fragments and short oligonucleotide linkers, or from a series of synthetic oligonucleotides, to provide a synthetic nucleic acid which is capable of being expressed from a recombinant transcriptional unit contained in a cell or in a cell-free transcription and translation system. Such sequences can be provided in the form of an open reading frame uninterrupted by internal non-translated sequences, or introns, which are typically present in eukaryotic genes. Genomic DNA comprising the relevant sequences can also be used in the formation of a recombinant gene or transcriptional unit. Sequences of non-translated DNA may be present 5′ or 3′ from the open reading frame, where such sequences do not interfere with manipulation or expression of the coding regions, and may indeed act to modulate production of a desired product by various mechanisms (see “enhancers” and “promoters”, above).
The term “recombinant polynucleotide” or “recombinant nucleic acid” refers to one which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of sequence through human intervention. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques. Such is usually done to replace a codon with a redundant codon encoding the same or a conservative amino acid, while typically introducing or removing a sequence recognition site. Alternatively, it is performed to join together nucleic acid segments of desired functions to generate a desired combination of functions. This artificial combination is often accomplished by either chemical synthesis means, or by the artificial manipulation of isolated segments of nucleic acids, e.g., by genetic engineering techniques.
Similarly, the term “recombinant polypeptide” or “recombinant protein” refers to a polypeptide or protein which is not naturally occurring, e.g., is made by the artificial combination of two otherwise separated segments of amino sequence through human intervention. Thus, e.g., a protein that comprises a heterologous amino acid sequence is recombinant.
As used herein, “lipoprotein”, such as VLDL, LDL and HDL, refers to a group of proteins found in the serum, plasma and lymph and are important for lipid transport. The chemical composition of each lipoprotein differs, for example, in that the HDL has a higher proportion of protein versus lipid, whereas the VLDL has a lower proportion of protein versus lipid.
As used herein, “atherosclerosis” means a hardening of the arteries affecting large and medium-sized arteries and is characterized by the presence of fatty deposits. The fatty deposits are called “atheromas” or “plaques,” which consist mainly of cholesterol and other fats, calcium and scar tissue, and damage the lining of arteries.
As used herein, “coronary heart disease (CHD)” means a narrowing of the small blood vessels that supply blood and oxygen to the heart, which is often a result of atherosclerosis.
As used herein, “dyslipidemia” refers to a disorder of lipid and/or lipoprotein metabolism, including lipid and/or lipoprotein overproduction or deficiency. Dyslipidemias can be manifested by elevation of lipids such as chylomicron, cholesterol and triglycerides as well as lipoproteins such as low-density lipoprotein (LDL) cholesterol.
As used herein, “high density lipoprotein-C” or “HDL-C” means cholesterol associated with high-density lipoprotein particles. Concentration of HDL-C in serum (or plasma) is typically quantified in mg/dL or nmol/L. “Serum HDL-C” and “plasma HDL-C” mean HDL-C in serum and plasma, respectively.
As used herein, “low density lipoprotein-cholesterol (LDL-C)” means cholesterol carried in low density lipoprotein particles. Concentration of LDL-C in serum (or plasma) is typically quantified in mg/dL or nmol/L. “Serum LDL-C” and “plasma LDL-C” mean LDL-C in the serum and plasma, respectively.
As used herein, “hypercholesterolemia” means a condition characterized by elevated cholesterol or circulating (plasma) cholesterol, LDL-cholesterol and VLDL-cholesterol, as per the guidelines of the Expert Panel Report of the National Cholesterol Educational Program (NCEP) of Detection, Evaluation of Treatment of high cholesterol in adults (see, Arch. Int. Med. 148: 36 (1988)).
As used herein, “hyperlipidemia” or “hyperlipemia” is a condition characterized by elevated serum lipids or circulating (plasma) lipids. This condition manifests an abnormally high concentration of fats. The lipid fractions in the circulating blood are cholesterol, low-density lipoproteins, very low density lipoproteins, chylomicrons and triglycerides. The Fredrickson classification of hyperlipidemias is based on the pattern of TG and cholesterol-rich lipoprotein particles, as measured by electrophoresis or ultracentrifugation and is commonly used to characterize primary causes of hyperlipidemias such as hypertriglyceridemia.
As used herein, “triglyceride” or “TG” means a lipid or neutral fat consisting of glycerol combined with three fatty acid molecules.
As used herein, “hypertriglyceridemia” means a condition characterized by elevated triglyceride levels. Its etiology includes primary (i.e. genetic causes) and secondary (other underlying causes such as diabetes, metabolic syndrome/insulin resistance, obesity, physical inactivity, cigarette smoking, excess alcohol and a diet very high in carbohydrates) factors or, most often, a combination of both
As used herein, “diabetes mellitus” or “diabetes” is a syndrome characterized by disordered metabolism and abnormally high blood sugar (hyperglycemia) resulting from insufficient levels of insulin or reduced insulin sensitivity. The characteristic symptoms are excessive urine production (polyuria) due to high blood glucose levels, excessive thirst and increased fluid intake (polydipsia) attempting to compensate for increased urination, blurred vision due to high blood glucose effects on the eye's optics, unexplained weight loss, and lethargy.
As used herein, “diabetic dyslipidemia” or “type 2 diabetes with dyslipidemia” means a condition characterized by Type 2 diabetes, reduced HDL-C, elevated triglycerides (TG), and elevated small, dense LDL particles.
As used herein, “lipid nanoparticle” refers to particles having at least one dimension on the order of nanometers (e.g., 1-1,000 nm) comprising one or more lipids (e.g., cationic lipids, non-cationic lipids, and PEG-modified lipids). In some embodiments, lipid nanoparticles are included in a formulation that can be used to deliver an active agent or therapeutic agent, such as a nucleic acid (e.g., mRNA) to a target site of interest (e.g., cell, tissue, organ, tumor, and the like). In some embodiments, the lipid nanoparticles of the disclosure comprise a nucleic acid. Such lipid nanoparticles typically comprise neutral lipids, charged lipids, steroids and polymer conjugated lipids. In some embodiments, the active agent or therapeutic agent, such as a nucleic acid, may be encapsulated in the lipid portion of the lipid nanoparticle or an aqueous space enveloped by some or all of the lipid portion of the lipid nanoparticle, thereby protecting it from enzymatic degradation or other undesirable effects induced by the mechanisms of the host organism or cells e.g. an adverse immune response.
As used herein, “lipid encapsulated” refers to a lipid nanoparticle that provides an active agent or therapeutic agent, such as a nucleic acid (e.g., mRNA), with full encapsulation, partial encapsulation, or both. In an embodiment, the nucleic acid (e.g., mRNA) is fully encapsulated in the lipid nanoparticle.
As used herein, the term “contacting” means establishing a physical connection between two or more entities. For example, contacting a target nucleic acid with a guide nucleic acid means that the target nucleic acid and the guide nucleic acid are made to share a physical connection; e.g., can hybridize if the sequences share sequence similarity.
“Dissociation constant”, or “Kd”, are used interchangeably and mean the affinity between a ligand “L” and a protein “P”; i.e., how tightly a ligand binds to a particular protein. It can be calculated using the formula Kd=[L][P]/[LP], where [P], [L] and [LP] represent molar concentrations of the protein, ligand and complex, respectively.
The disclosure provides compositions and methods useful for modifying a target nucleic acid. As used herein “editing” is used interchangeably with “modifying” and “modification” and includes but is not limited to cleaving, nicking, editing, deleting, knocking in, knocking out, and the like. Modifying can also encompass epigenetic modifications to a nucleic acid, or chromatin containing the nucleic acid, such as, but not limited to, changes in DNA methylation, and histone methylation and acetylation.
By “cleavage” it is meant the breakage of the covalent backbone of a target nucleic acid molecule (e.g., RNA, DNA). Cleavage can be initiated by a variety of methods including, but not limited to, enzymatic or chemical hydrolysis of a phosphodiester bond. Both single-stranded cleavage and double-stranded cleavage are possible, and double-stranded cleavage can occur as a result of two distinct single-stranded cleavage events.
The term “knock-down” as used herein refers to reduction in the expression of a gene or its gene product(s). As a result of a gene knock-down, the protein activity or function may be attenuated or the protein levels may be reduced or eliminated.
A polynucleotide or polypeptide has a certain percent “sequence similarity” or “sequence identity” to another polynucleotide or polypeptide, meaning that, when aligned, that percentage of bases or amino acids are the same, and in the same relative position, when comparing the two sequences. Sequence similarity (sometimes referred to as percent similarity, percent identity, or homology) can be determined in a number of different manners. To determine sequence similarity, sequences can be aligned using the methods and computer programs that are known in the art, including BLAST, available over the world wide web at ncbi.nlm.nih.gov/BLAST. Percent complementarity between particular stretches of nucleic acid sequences within nucleic acids can be determined using any convenient method. Example methods include BLAST programs (basic local alignment search tools) and PowerBLAST programs (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656) or by using the Gap program (Wisconsin Sequence Analysis Package, Version 8 for Unix, Genetics Computer Group, University Research Park, Madison Wis.), e.g., using default settings, which uses the algorithm of Smith and Waterman (Adv. Appl. Math., 1981, 2, 482-489).
The terms “polypeptide,” and “protein” are used interchangeably herein, and refer to a polymeric form of amino acids of any length, which can include coded and non-coded amino acids, chemically or biochemically modified or derivatized amino acids, and polypeptides having modified peptide backbones. The term includes fusion proteins, including, but not limited to, fusion proteins with a heterologous amino acid sequence.
A “vector” or “expression vector” is a replicon, such as plasmid, phage, virus, or cosmid, to which another DNA segment, i.e., an expression cassette, may be attached so as to bring about the replication or expression of the attached segment in a cell.
The term “naturally-occurring” or “unmodified” or “wild type” as used herein as applied to a nucleic acid, a polypeptide, a cell, or an organism, refers to a nucleic acid, polypeptide, cell, or organism that is found in nature.
As used herein, a “mutation” refers to an insertion, deletion, substitution, duplication, or inversion of one or more amino acids or nucleotides as compared to a wild-type or reference amino acid sequence or to a wild-type or reference nucleotide sequence.
As used herein the term “isolated” is meant to describe a polynucleotide, a polypeptide, or a cell that is in an environment different from that in which the polynucleotide, the polypeptide, or the cell naturally occurs. An isolated genetically modified host cell may be present in a mixed population of genetically modified host cells.
A “host cell,” as used herein, denotes a eukaryotic cell, a prokaryotic cell, or a cell from a multicellular organism (e.g., a cell line) cultured as a unicellular entity, which eukaryotic or prokaryotic cells are used as recipients for a nucleic acid (e.g., an AAV vector), and include the progeny of the original cell which has been genetically modified by the nucleic acid. It is understood that the progeny of a single cell may not necessarily be completely identical in morphology or in genomic or total DNA complement as the original parent, due to natural, accidental, or deliberate mutation. A “recombinant host cell” (also referred to as a “genetically modified host cell”) is a host cell into which has been introduced a heterologous nucleic acid, e.g., an AAV vector.
The term “conservative amino acid substitution” refers to the interchangeability in proteins of amino acid residues having similar side chains. For example, a group of amino acids having aliphatic side chains consists of glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains consists of serine and threonine; a group of amino acids having amide-containing side chains consists of asparagine and glutamine; a group of amino acids having aromatic side chains consists of phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains consists of lysine, arginine, and histidine; and a group of amino acids having sulfur-containing side chains consists of cysteine and methionine. Exemplary conservative amino acid substitution groups are: valine-leucine-isoleucine, phenylalanine-tyrosine, lysine-arginine, alanine-valine, and asparagine-glutamine.
As used herein, “treatment” or “treating,” are used interchangeably herein and refer to an approach for obtaining beneficial or desired results, including but not limited to a therapeutic benefit and/or a prophylactic benefit. By therapeutic benefit is meant eradication or amelioration of the underlying disorder or disease being treated. A therapeutic benefit can also be achieved with the eradication or amelioration of one or more of the symptoms or an improvement in one or more clinical parameters associated with the underlying disease such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder.
The terms “therapeutically effective amount” and “therapeutically effective dose”, as used herein, refer to an amount of a drug or a biologic, alone or as a part of a composition, that is capable of having any detectable, beneficial effect on any symptom, aspect, measured parameter or characteristics of a disease state or condition when administered in one or repeated doses to a subject such as a human or an experimental animal. Such effect need not be absolute to be beneficial.
As used herein, “administering” means a method of giving a dosage of a compound (e.g., a composition of the disclosure) or a composition (e.g., a pharmaceutical composition) to a subject.
A “subject” is a mammal. Mammals include, but are not limited to, domesticated animals, non-human primates, humans, dogs, rabbits, mice, rats and other rodents.
The term “low-density lipoprotein (LDL)” refers to one of the five major groups of lipoprotein, from least dense (lower weight-volume ratio particles) to most dense (larger weight-volume ratio particles): chylomicrons, very low-density lipoproteins (VLDL), low-density lipoproteins (LDL), intermediate-density lipoproteins (IDL), and high-density lipoproteins (HDL). Lipoproteins transfer lipids (fats) around the body in the extracellular fluid thereby facilitating the transfer of fats to the cells body via receptor-mediated endocytosis. An LDL particle is about 220-275 angstroms in diameter.
“Low-density lipoprotein (LDL) receptor” refers to a receptor protein of 839 amino acids (after removal of 21-amino acid signal peptide) that mediates the endocytosis of cholesterol-rich LDL particles. It is a cell-surface receptor that recognizes the apoprotein B100 and apoE protein found in chylomicron remnants and VLDL remnants (IDL) resulting in the binding and endocytosis of LDL-cholesterol. This process occurs in all nucleated cells, but mainly in the liver which removes approximately 70% of LDL from the circulation. The human LDLR gene is described in part in the NCBI database (ncbi.nlm.nih.gov) as Reference Sequence NG_009060.1, which is incorporated by reference herein.
All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference. The contents of WO 2020/247882, filed on Jun. 5, 2020, WO 2020/247883, filed Jun. 5, 2020, WO 2021/050593, filed on Sep. 9, 2020, WO 2021/050601, filed on Sep. 9, 2021, WO 2021/142342, filed on Jan. 8, 2021, WO 2021/113763, filed on Dec. 4, 2020, WO 2021/113769, filed on Dec. 4, 2020, WO 2021/113772, filed on Dec. 4, 2020, WO 2021/188729, filed on Dec. 4, 2020, WO 2022/120095, filed Dec. 2, 2021, WO 2022/120094, filed on Dec. 2, 2021, WO 2022/125843, filed on Dec. 9, 2021, WO 2022/120089, filed on Dec. 2, 2021, WO 2022/261150, filed on Jun. 7, 2022, WO 2023/049742, filed on Sep. 21, 2022, WO 2022/261149, filed on Jun. 7, 2022, and PCT/US2023/067791, filed on Jun. 1, 2023, which disclose CasX variants and gRNA variants, and methods of delivering same, are hereby incorporated by reference in their entirety.
I. General Methods
The practice of the present invention employs, unless otherwise indicated, conventional techniques of immunology, biochemistry, chemistry, molecular biology, microbiology, cell biology, genomics and recombinant DNA, which can be found in such standard textbooks as Molecular Cloning: A Laboratory Manual, 3rd Ed. (Sambrook et al., Harbor Laboratory Press 2001); Short Protocols in Molecular Biology, 4th Ed. (Ausubel et al. eds., John Wiley & Sons 1999); Protein Methods (Bollag et al., John Wiley & Sons 1996); Nonviral Vectors for Gene Therapy (Wagner et al. eds., Academic Press 1999); Viral Vectors (Kaplift & Loewy eds., Academic Press 1995); Immunology Methods Manual (I. Lefkovits ed., Academic Press 1997); and Cell and Tissue Culture: Laboratory Procedures in Biotechnology (Doyle & Griffiths, John Wiley & Sons 1998), the disclosures of which are incorporated herein by reference.
Where a range of values is provided, it is understood that endpoints are included and that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
It must be noted that as used herein and in the appended claims, the singular forms “a,” “an,” and “the” include plural referents unless the context clearly dictates otherwise.
It will be appreciated that certain features of the disclosure, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. In other cases, various features of the disclosure, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. It is intended that all combinations of the embodiments pertaining to the disclosure are specifically embraced by the present disclosure and are disclosed herein just as if each and every combination was individually and explicitly disclosed. In addition, all sub-combinations of the various embodiments and elements thereof are also specifically embraced by the present disclosure and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.
II. Systems for Epigenetic Modification and Repression of PCSK9 Genes
In a first aspect, the present disclosure provides systems comprising or encoding a fusion protein comprising a DNA-binding protein and linked repressor domains capable of binding a target nucleic acid sequence of a PCSK9 gene targeted for transcriptional repression, silencing, and/or epigenetic modification (collectively, long-term repressor proteins, referred to herein as “LTRP” or “LTRP fusion protein” or “repressor fusion protein”; a reflection of the long-term repression effects that can be achieved on the targeted gene). As used herein, a “system” is used interchangeably with “composition”. The disclosure also provides nucleic acids encoding the systems provided herein. Also provided herein are methods of making the systems, as well as methods of using the systems, including methods of gene repression and/or epigenetic modification and methods of treatment of PCSK9-related diseases.
In some embodiments, the DNA-binding proteins comprise zinc finger (ZF) or TALE (transcription-activator-like effector) proteins, or DNA binding domains thereof, also referred to herein as a DNA-binding protein, that bind but do not cleave the target nucleic acid. The DNA-binding domain of a TALE is comprised of a tandem array of 33-34 amino acid (aa)-long customizable monomers that theoretically can be assembled to recognize any genetic sequence following a one-repeat-binds-one-base-pair recognition code (Jain, S., et al. TALE outperforms Cas9 in editing heterochromatin target sites. Nat. Commun. 12:606 (2021)). The specificity of TALEs for binding DNA arises from two polymorphic amino acids, the so-called repeat variable diresidues (RVDs) located at positions 12 and 13 of a repeated unit. By re-arranging the repeats, the DNA binding specificities of TALE can be changed at will. Zinc finger proteins are transcription factors, where each finger recognizes 3-4 bases of DNA. By mixing and matching these finger modules, the ZFs can be customized for the sequence to be targeted. Exemplary ZFs that are capable of binding the PCSK9 gene are described in WO2018049009A2.
In some embodiments, the DNA-binding protein is a catalytically-dead Class 1 or Class 2 CRISPR protein. Catalytically-dead CRISPR proteins are also referred to in the art as “catalytically inactive” CRISPR proteins. In some embodiments, the Class 2, Type II protein is a catalytically-dead Cas9. In other embodiments, the Class 2 CRISPR protein is selected from the group consisting of a Type II, Type V, or Type VI protein. In one embodiment, the Class 2 Type V protein is selected from the group consisting of Cas12a (Cpf1), Cas12b (C2c1), Cas12c (C2c3), Cas12d (CasY), Cas12e (CasX), Cas12f, Cas12g, Cas12h, Cas12i, Cas12j, Cas12k, Cas14, and/or CasΦ, in each case rendered catalytically-dead by specific mutations, as described herein. In some embodiments, the CasX protein is a catalytically-dead CasX variant (dCasX), wherein the dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 4-29, or a sequence having at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity thereto, wherein the fusion protein comprising the dCasX retains the ability to form an RNP with a gRNA. In some embodiments, the dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 4-29. In some embodiments, the dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 3281-3441, comprising a RuvC domain with one or more mutations that inactivates the cleavage activity of the RuvC domain, thereby rendering the CasX protein catalytically dead. In a particular embodiment, the dCasX comprises a sequence of SEQ ID NO: 4.
The CRISPR-based systems further comprise a guide nucleic acid (gNA), for example a guide ribonucleic acid (gRNA) with a targeting sequence complementary to the target sequence of a gene. Upon binding of the target sequence by the CRISPR-based system, (the CRISPR protein and linked repressor domains) and the gRNA, transcription the gene is repressed.
The present disclosure provides systems for transcriptional repression of a PCSK9 gene. In some embodiments, the system comprises a repressor fusion protein comprising a catalytically-dead CasX protein and linked repressor domains, and a guide ribonucleic acid (gRNA) comprising a targeting sequence complementary to a target nucleic acid sequence of a PCSK9 gene targeted for repression, silencing, or downregulation (a repressor fusion protein:gRNA system). In some embodiments, the system comprises nucleic acids encoding the repressor fusion protein, for example a dCasX and linked repressor domains, and gRNA. In some embodiments, the system comprises a repressor fusion protein and a gRNA as gene repressor pairs that are capable of forming a ribonucleoprotein (RNP) complex and binding a PCSK9 target nucleic acid in a eukaryotic cell. In other cases, the disclosure provides systems of nucleic acids encoding the repressor fusion protein and gRNA, or a gRNA and an mRNA encoding the repressor fusion protein for use in certain particle formulations (e.g., an LNP) described herein.
Also provided herein are methods of making repressor fusion proteins and gRNAs, as well as methods of using the repressor fusion protein:gRNA systems, including methods of gene repression and/or epigenetic modification, and methods of treatment. The DNA-binding proteins (e.g., dCasX) and linked repressor domain(s) and gRNA components of the systems and their features, as well as the delivery modalities and the methods of using the systems for the repression, down-regulation or silencing of a PCSK9 gene are described more fully, below.
The disclosure provides systems specifically designed to repress or silence transcription of the PCSK9 gene. In some cases, the system is designed to repress transcription of the PCSK9 gene in eukaryotic cells having a gain of function mutation. In some cases, the system is designed to repress transcription of the wild-type PCSK9 gene in eukaryotic cells. In the alternative, the system is designed to repress transcription of a mutant allele of the PCSK9 gene in eukaryotic cells. Generally, any portion of the PCSK9 gene can be targeted using the programable systems and methods provided herein, described more fully, herein.
The PCSK9 gene encodes proprotein convertase subtilisin/kexin Type 9 (“PCSK9”), a protein that binds to the receptor for low-density lipoprotein particles (LDL) for transport of LDL into the cell. The PCSK9 gene encompasses the sequence that spans chr1:55,039,476-55,064,853 of the human genome (GRCh38/hg38) (the notation refers to the chromosome 1 (chr1), starting at the 55,039,476 bp to 55,064,853 bp on chromosome 1 (Homo sapiens Updated Annotation Release 109.20190905, GRCh38.p13) (NCBI). The human PCSK9 gene is described in part in the NCBI database (ncbi.nlm.nih.gov) as Reference Sequence NG_009061.1, which is incorporated by reference herein. The PCSK9 locus has 12 exons that produces an mRNA of 3636 bp encoding a 692-amino acid protein that, following its synthesis, undergoes an autocatalytic cleavage reaction that clips off the prodomain, resulting in an activated protein having 540 amino acids. The prodomain remains attached to the catalytic and resistin-like domains, likely because the prodomain serves as a chaperone and facilitates folding and secretion (Seidah, N G et al., Proc Natl Acad Sci USA 100(3):928 (2003)). The secretory proprotein convertase neural apoptosis-regulated convertase 1 (NARC-1): liver regeneration and neuronal differentiation (Seidah N G, et al.). This protein, also called neural apoptosis regulated convertase, is a serine protease belonging to the protease K subfamily of subtilases.
The human PCSK9 gene (HGNC:20001) encodes a protein (Q8NBP7) having the sequence








(SEQ ID NO: 1823)



MGTVSSRRSWWPLPLLLLLLLLLGPAGARAQEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDP



 


WRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDY


 


IEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDG


 


TRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLV


 


VLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNERDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNF


 


GRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINE


 


AWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAVARCAPDEELLSCSSFSRSGKRRG


 


ERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEV


 


EDLGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALP


 


GTSHVLGAYAVDNTCVVRSRDVSTTGSTSEGAVTAVAICCRSRHLAQASQELQ.






III. Catalytically-Dead Proteins for Use in the Repressor Systems

In some embodiments, the DNA-binding proteins for use in the fusion proteins, systems and methods of the disclosure are zinc finger (ZF) or TALE (transcription-activator-like effector) proteins that can bind, but not cleave, a PCSK9 target nucleic acid.
In some embodiments, the DNA-binding protein is a catalytically-dead Class 1 or Class 2 CRISPR protein. In one embodiment, the Class 2, Type II protein is a catalytically-dead Cas9. In another embodiment, the Class 2 CRISPR protein is selected from the group consisting of a Type II, Type V, or Type VI protein. In one embodiment, the Class 2 CRISPR Type V protein is selected from the group consisting of Cas12a (Cpf1), Cas12b (C2c1), Cas12c (C2c3), Cas12d (CasY), Cas12e (CasX), Cas12f, Cas12g, Cas12h, Cas12i, Cas12j, Cas12k, Cas14, and/or CasΦ, in each case rendered catalytically-dead by specific mutations, as described herein. In some embodiments, the CasX protein is a catalytically-dead CasX variant (dCasX).
The term “CasX protein”, as used herein, refers to a family of proteins, and encompasses all naturally-occurring CasX proteins (“reference CasX”), as well as engineered CasX proteins with multiple sequence modifications, in addition to those rendering the CasX catalytically-dead (dCasX), that possess one or more improved characteristics relative to a reference CasX protein, described more fully, below. CasX proteins of the disclosure comprise the following domains: a non-target strand binding (NTSB) domain, a target strand loading (TSL) domain, a helical I domain, a helical II domain, an oligonucleotide binding domain (OBD), and a RuvC domain, and, in some cases, domains can be further divided into subdomains, as listed in Table 1.
In the context of the present disclosure, the CasX for use in the repressor fusion proteins, systems and methods are catalytically-dead (dCasX); achieved by mutations introduced at select locations in the RuvC sequence, described below.
a. Reference CasX Proteins
The disclosure provides naturally-occurring CasX proteins (referred to herein as a “reference CasX protein”), which were subsequently modified to create the engineered dCasX of the disclosure. For example, reference CasX proteins can be isolated from naturally occurring prokaryotes, such as Deltaproteobacteria, Planctomycetes, or Candidatus Sungbacteria species. A reference CasX protein (interchangeably referred to herein as a reference CasX polypeptide) is a Class 2, Type V CRISPR/Cas endonuclease belonging to the CasX (interchangeably referred to as Cas12e) family of proteins that interacts with a guide RNA to form a ribonucleoprotein (RNP) complex.
In some cases, a reference CasX protein is isolated or derived from Deltaproteobacter having a sequence of:








(SEQ ID NO: 1)










1
MEKRINKIRK KLSADNATKP VSRSGPMKTL LVRVMTDDLK KRLEKRRKKP EVMPQVISNN



 


61
AANNLRMLLD DYTKMKEAIL QVYWQEFKDD HVGLMCKFAQ PASKKIDQNK LKPEMDEKGN


 


121
LTTAGFACSQ CGQPLFVYKL EQVSEKGKAY TNYFGRCNVA EHEKLILLAQ LKPEKDSDEA


 


181
VTYSLGKFGQ RALDFYSIHV TKESTHPVKP LAQIAGNRYA SGPVGKALSD ACMGTIASFL


 


241
SKYQDIIIEH QKVVKGNQKR LESLRELAGK ENLEYPSVTL PPQPHTKEGV DAYNEVIARV


 


301
RMWVNLNLWQ KLKLSRDDAK PLLRLKGFPS FPVVERRENE VDWWNTINEV KKLIDAKRDM


 


361
GRVFWSGVTA EKRNTILEGY NYLPNENDHK KREGSLENPK KPAKRQFGDL LLYLEKKYAG


 


421
DWGKVEDEAW ERIDKKIAGL TSHIEREEAR NAEDAQSKAV LIDWLRAKAS FVLERLKEMD


 


481
EKEFYACEIQ LQKWYGDLRG NPFAVEAENR VVDISGFSIG SDGHSIQYRN LLAWKYLENG


 


541
KREFYLLMNY GKKGRIRFTD GTDIKKSGKW QGLLYGGGKA KVIDLTFDPD DEQLIILPLA


 


601
FGTRQGREFI WNDLLSLETG LIKLANGRVI EKTIYNKKIG RDEPALFVAL TFERREVVDP


 


661
SNIKPVNLIG VDRGENIPAV IALTDPEGCP LPEFKDSSGG PTDILRIGEG YKEKQRAIQA


 


721
AKEVEQRRAG GYSRKFASKS RNLADDMVRN SARDLFYHAV THDAVLVFEN LSRGFGRQGK


 


781
RTFMTERQYT KMEDWLTAKL AYEGLISKTY LSKTLAQYTS KTCSNCGFTI TTADYDGMLV


 


841
RLKKTSDGWA TILNNKELKA EGQITYYNRY KRQTVEKELS AELDRLSEES GNNDISKWTK


 


901
GRRDEALFLL KKRFSHRPVQ EQFVCLDCGH EVHADEQAAL NIARSWLFLN SNSTEFKSYK


 


961
SGKQPFVGAW QAFYKRRLKE VWKPNA.






In some cases, a reference CasX protein is isolated or derived from Planctomycetes having a sequence of:








(SEQ ID NO: 2)










1
MQEIKRINKI RRRLVKDSNT KKAGKTGPMK TLLVRVMTPD LRERLENLRK KPENIPQPIS



 


61
NTSRANLNKL LTDYTEMKKA ILHVYWEEFQ KDPVGLMSRV AQPAPKNIDQ RKLIPVKDGN


 


121
ERLTSSGFAC SQCCQPLYVY KLEQVNDKGK PHTNYFGRCN VSEHERLILL SPHKPEANDE


 


181
LVTYSLGKFG QRALDFYSIH VTRESNHPVK PLEQIGGNSC ASGPVGKALS DACMGAVASF


 


241
LTKYQDIILE HQKVIKKNEK RLANLKDIAS ANGLAFPKIT LPPQPHTKEG IEAYNNVVAQ


 


301
IVIWVNLNLW QKLKIGRDEA KPLQRLKGFP SFPLVERQAN EVDWWDMVCN VKKLINEKKE


 


361
DGKVFWQNLA GYKRQEALLP YLSSEEDRKK GKKFARYQFG DLLLHLEKKH GEDWGKVYDE


 


421
AWERIDKKVE GLSKHIKLEE ERRSEDAQSK AALTDWLRAK ASFVIEGLKE ADKDEFCRCE


 


481
LKLQKWYGDL RGKPFAIEAE NSILDISGFS KQYNCAFIWQ KDGVKKLNLY LIINYFKGGK


 


541
LRFKKIKPEA FEANRFYTVI NKKSGEIVPM EVNENFDDPN LIILPLAFGK RQGREFIWND


 


601
LLSLETGSLK LANGRVIEKT LYNRRTRQDE PALFVALTFE RREVLDSSNI KPMNLIGIDR


 


661
GENIPAVIAL TDPEGCPLSR FKDSLGNPTH ILRIGESYKE KQRTIQAAKE VEQRRAGGYS


 


721
RKYASKAKNL ADDMVRNTAR DLLYYAVTQD AMLIFENLSR GFGRQGKRTF MAERQYTRME


 


781
DWLTAKLAYE GLPSKTYLSK TLAQYTSKTC SNCGFTITSA DYDRVLEKLK KTATGWMTTI


 


841
NGKELKVEGQ ITYYNRYKRQ NVVKDLSVEL DRLSEESVNN DISSWTKGRS GEALSLLKKR


 


901
FSHRPVQEKF VCLNCGFETH ADEQAALNIA RSWLFLRSQE YKKYQTNKTT GNTDKRAFVE


 


961
TWQSFYRKKL KEVWKPAV.






In some cases, a reference CasX protein is isolated or derived from Candidatus Sungbacteria having a sequence of








(SEQ ID NO: 3)










1
MDNANKPSTK SLVNTTRISD HFGVTPGQVT RVFSFGIIPT KRQYAIIERW FAAVEAARER



 


61
LYGMLYAHFQ ENPPAYLKEK FSYETFFKGR PVLNGLRDID PTIMTSAVFT ALRHKAEGAM


 


121
AAFHTNHRRL FEEARKKMRE YAECLKANEA LLRGAADIDW DKIVNALRTR LNTCLAPEYD


 


181
AVIADFGALC AFRALIAETN ALKGAYNHAL NQMLPALVKV DEPEEAEESP RLRFENGRIN


 


241
DLPKFPVAER ETPPDTETII RQLEDMARVI PDTAEILGYI HRIRHKAARR KPGSAVPLPQ


 


301
RVALYCAIRM ERNPEEDPST VAGHELGEID RVCEKRRQGL VRTPEDSQIR ARYMDIISER


 


361
ATLAHPDRWT EIQFLRSNAA SRRVRAETIS APFEGFSWTS NRINPAPQYG MALAKDANAP


 


421
ADAPELCICL SPSSAAFSVR EKGGDLIYMR PTGGRRGKDN PGKEITWVPG SFDEYPASGV


 


481
ALKLRLYFGR SQARRMLINK TWGLLSDNPR VFAANAELVG KKRNPQDRWK LFFHMVISGP


 


541
PPVEYLDFSS DVRSRARTVI GINRGEVNPL AYAVVSVEDG QVLEEGLLGK KEYIDQLIET


 


601
RRRISEYQSR EQTPPRDLRQ RVRHLQDIVL GSARAKIHSL IAFWKGILAI ERLDDQFHGR


 


661
EQKIIPKKTY LANKTGFMNA LSFSGAVRVD KKGNPWGGMI EIYPGGISRT CTQCGTVWLA


 


721
RRPKNPGHRD AMVVIPDIVD DAAATGEDNV DCDAGTVDYG ELFTLSREWV RLTPRYSRVM


 


781
RGTLGDLERA IRQGDDRKSR QMLELALEPQ PQWGQFFCHR CGENGQSDVL AATNLARRAI


 


841
SLIRRLPDTD TPPTP.






b. Catalytically-Dead CasX Variant Proteins

In the repressor fusion proteins and systems comprising same of the disclosure, the CasX protein is catalytically-dead (dCasX) in that it is unable to cleave DNA, but retains the ability to bind a target nucleic acid when complexed with a guide RNA (gRNA). The present disclosure provides catalytically-dead variants (interchangeably referred to herein as “dCasX variant” or “dCasX variant protein”), wherein the catalytically-dead CasX variants comprise multiple modifications in select domains relative to the catalytically-dead versions of sequences of SEQ ID NOS:1-3 (described, supra). An exemplary catalytically-dead CasX protein comprises one or more mutations in the active site of the RuvC domain of the CasX protein. In some embodiments, a catalytically-dead reference CasX protein comprises substitutions at residues 672, 769 and/or 935 with reference to SEQ ID NO: 1. In some embodiments, a catalytically-dead reference CasX protein comprises substitutions of D672A, E769A and/or D935A with reference to SEQ ID NO: 1. In other embodiments, a catalytically-dead reference CasX protein comprises substitutions at amino acids 659, 756 and/or 922 with reference to SEQ ID NO: 2. In some embodiments, a catalytically-dead reference CasX protein comprises D659A, E756A and/or D922A substitutions with reference to of SEQ ID NO: 2. An exemplary RuvC domain of the dCasX of the disclosure comprises amino acids 661-824 and 935-986 of SEQ ID NO: 1, or amino acids 648-812 and 922-978 of SEQ ID NO: 2, with one or more amino acid modifications relative to said RuvC cleavage domain sequence, wherein the dCasX variant exhibits one or more improved characteristics compared to the reference dCasX. In further embodiments, a catalytically-dead CasX variant protein comprises deletions of all or part of the RuvC domain of the reference CasX protein. It will be understood that the same foregoing substitutions or deletions can similarly be introduced into CasX variants known in the art, resulting in a dCasX variant (see, e.g., WO2022120095A1 and U.S. Pat. No. 11,560,555, incorporated by reference herein, for exemplary sequences).
In some embodiments, the dCasX variant with linked repressor domains exhibits at least one improved characteristic compared to the reference dCasX protein with linked repressor domains configured in a comparable fashion. All dCasX variants that improve one or more functions or characteristics of the dCasX variant protein with linked repressor domain compared to a reference dCasX protein with linked repressor domain described herein are envisaged as being within the scope of the disclosure. In some embodiments, the modification is a mutation in one or more amino acids of the reference dCasX other than those rendering the dCasX catalytically-dead. For example, dCasX variants can comprise one or more amino acid substitutions, insertions, deletions, or swapped domains, or any combinations thereof, relative to a reference dCasX protein sequence. Any amino acid can be substituted for any other amino acid in the substitutions described herein. The substitution can be a conservative substitution (e.g., a basic amino acid is substituted for another basic amino acid). The substitution can be a non-conservative substitution (e.g., a basic amino acid is substituted for an acidic amino acid or vice versa). For example, a proline in a reference dCasX protein can be substituted for any of arginine, histidine, lysine, aspartic acid, glutamic acid, serine, threonine, asparagine, glutamine, cysteine, glycine, alanine, isoleucine, leucine, methionine, phenylalanine, tryptophan, tyrosine or valine to generate a dCasX variant protein of the disclosure. In some embodiments, the dCasX variant exhibits an improved characteristic compared to a reference dCasX. Exemplary improved characteristics of the dCasX variant embodiments include, but are not limited to improved folding of the variant, increased binding affinity to the gRNA, increased binding affinity to the target nucleic acid, improved ability to utilize a greater spectrum of PAM sequences in the repression and/or binding of target nucleic acid, improved unwinding of the target DNA, increased target strand loading, increased binding of the non-target strand of DNA, improved protein stability, increased ability to complex with gRNA, improved protein:gRNA (RNP) complex stability, and, with linked repressor domains and when complexed as an RNP, increased repressor activity, improved repressor specificity for the target nucleic acid, decreased off-target repression, increased percentage of a eukaryotic genome that can be efficiently repressed and/or epigenetically modified. In some embodiments, an improved characteristic of the dCasX variant is at least about 1.1 to about 100,000-fold improved relative to the reference dCasX protein. In some embodiments, an improved characteristic of the dCasX variant is at least about 1.1 to about 10,000-fold improved, at least about 1.1 to about 1,000-fold improved, at least about 1.1 to about 500-fold improved, at least about 1.1 to about 400-fold improved, at least about 1.1 to about 300-fold improved, at least about 1.1 to about 200-fold improved, at least about 1.1 to about 100-fold improved, at least about 1.1 to about 50-fold improved, at least about 1.1 to about 40-fold improved, at least about 1.1 to about 30-fold improved, at least about 1.1 to about 20-fold improved, at least about 1.1 to about 10-fold improved, at least about 1.1 to about 9-fold improved, at least about 1.1 to about 8-fold improved, at least about 1.1 to about 7-fold improved, at least about 1.1 to about 6-fold improved, at least about 1.1 to about 5-fold improved, at least about 1.1 to about 4-fold improved, at least about 1.1 to about 3-fold improved, at least about 1.1 to about 2-fold improved, at least about 1.1 to about 1.5-fold improved, at least about 1.5 to about 3-fold improved, at least about 1.5 to about 4-fold improved, at least about 1.5 to about 5-fold improved, at least about 1.5 to about 10-fold improved, at least about 5 to about 10-fold improved, at least about 10 to about 20-fold improved, at least 10 to about 30-fold improved, at least 10 to about 50-fold improved or at least 10 to about 100-fold improved relative to the reference dCasX protein. In some embodiments, an improved characteristic of the dCasX variant is at least about 10 to about 1000-fold improved relative to the reference dCasX protein. Additional disclosure on improved characteristics is described herein, below.
In other embodiments, the modification is a substitution of one or more domains of the reference dCasX with one or more domains from a different CasX. In some embodiments, insertion includes the insertion of a part or all of a domain from a different CasX protein. Mutations can be placed in any one or more domains of the dCasX variant, and may include, for example, deletion of part or all of one or more domains, or one or more amino acid substitutions, deletions, or insertions in any domain. The domains of dCasX proteins include the non-target strand binding (NTSB) domain, the target strand loading (TSL) domain, the helical I domain, the helical II domain, the oligonucleotide binding domain (OBD), and the RuvC DNA cleavage domain, which can further comprise subdomains, described below.
Suitable mutagenesis methods for generating dCasX variant proteins of the disclosure may include, for example, Deep Mutational Evolution (DME), deep mutational scanning (DMS), error prone PCR, cassette mutagenesis, random mutagenesis, staggered extension PCR, gene shuffling, or domain swapping. In some embodiments, the dCasX variants are designed, for example by selecting one or more desired mutations in a reference dCasX. In certain embodiments, the activity of a reference dCasX protein is used as a benchmark against which the activity of one or more dCasX variants are compared, thereby measuring improvements in function of the dCasX variants.
In some embodiments, the dCasX variant protein comprises between 700 and 1200 amino acids, between 800 and 1100 amino acids or between 900 and 1000 amino acids.
The dCasX and linked repressor domains of the disclosure have an enhanced ability to efficiently bind target nucleic acid, when complexed with a gRNA as an RNP, utilizing and binding to a PAM TC motif, including PAM sequences selected from TTC, ATC, GTC, or CTC, compared to an RNP of a reference dCasX protein and reference gRNA in a comparable assay system. In the foregoing, the PAM sequence is located at least 1 nucleotide 5′ to the non-target strand of the protospacer having identity with the targeting sequence of the gRNA.
In some embodiments, an RNP comprising the dCasX variant protein with linked repressor domains and a gRNA of the disclosure, at a concentration of 20 pM or less, is capable of binding a double stranded DNA target with an efficiency of at least 70%, at least 80%, at least 85%, at least 90% or at least 95%. In one embodiment, an RNP of a dCasX variant with linked repressor domains and a gRNA variant exhibits greater binding of a target sequence in the target nucleic acid compared to an RNP comprising a reference dCasX protein with linked repressor domains and a reference gRNA in a comparable assay system, wherein the PAM sequence of the target nucleic acid is TTC. In another embodiment, an RNP of a dCasX variant with linked repressor domains and gRNA variant exhibits greater binding affinity of a target sequence in the target nucleic acid compared to an RNP comprising a reference dCasX protein with linked repressor domains and a reference gRNA in a comparable assay system, wherein the PAM sequence of the target nucleic acid is ATC. In another embodiment, an RNP of a dCasX variant with linked repressor domains and gRNA variant exhibits greater binding affinity of a target sequence in the target nucleic acid compared to an RNP comprising a reference dCasX protein with linked repressor domains and a reference gRNA in a comparable assay system, wherein the PAM sequence of the target nucleic acid is CTC. In another embodiment, an RNP of a dCasX variant with linked repressor domains and gRNA variant exhibits greater binding affinity of a target sequence in the target nucleic acid compared to an RNP comprising a reference dCasX protein with linked repressor domains and a reference gRNA in a comparable assay system, wherein the PAM sequence of the target nucleic acid is GTC. In the foregoing embodiments, the increased binding affinity for the one or more PAM sequences is at least 1.5-fold greater or more compared to the binding affinity of an RNP of any one of the reference dCasX proteins (modified from SEQ ID NOS: 1-3) with linked repressor domains and the gRNA of SEQ ID NOS: 1731-1743 of Table 6 for the PAM sequences.
c. dCasX Variant Proteins with Domains from Multiple Source Proteins
Also contemplated within the scope of the disclosure are chimeric dCasX proteins. As used herein, a “chimeric dCasX” protein refers to both a dCasX protein containing at least two domains from different sources, as well a dCasX protein containing at least one domain that itself is chimeric. Accordingly, in some embodiments, a chimeric dCasX protein is one that includes at least two domains isolated or derived from different sources, such as from two different naturally occurring CasX proteins, (e.g., from two different CasX reference proteins), or from two different engineered CasX proteins. In some embodiments, the helical I-I domain and NTSB domain of the dCasX variant derived from SEQ ID NO: 2 is replaced with the corresponding helical I-I and NTSB sequences from SEQ ID NO: 1, resulting in a chimeric dCasX protein. As another example of the foregoing, the chimeric RuvC domain comprises amino acids 660 to 823 of SEQ ID NO: 1 and amino acids 921 to 978 of SEQ ID NO: 2. As an alternative example of the foregoing, a chimeric RuvC domain comprises amino acids 647 to 810 of SEQ ID NO: 2 and amino acids 934 to 986 of SEQ ID NO: 1.
In other embodiments, the chimeric dCasX protein is one that contains at least one domain that is a chimeric domain, e.g., in some embodiments, part of a domain comprises a substitution from a different CasX protein (from a reference CasX protein, or another engineered CasX protein). In some embodiments, the at least one chimeric domain can be any of the NTSB, TSL, helical I, helical II, OBD or RuvC domains as described herein. In some embodiments, the helical I-I domain (sometimes referred to as helical I-a) of the dCasX variant derived from SEQ ID NO: 2 is replaced with the corresponding helical I-I sequence from SEQ ID NO: 1, resulting in a chimeric dCasX protein.
Sequences of Table 2 having the NTSB domain and helical I-II domain from SEQ ID NO: 1 and a helical I-I domain from SEQ ID NO: 2 include dCasX 491, 515, 516, 518-520, 522-527, 532, 593, 676 (with a L169K substitution in the NTSB domain), and 812 (see Table 2 for SEQ ID NOS). Coordinates of CasX domains in the reference CasX proteins of SEQ ID NO: 1 and SEQ ID NO: 2 are provided in Table 1 below. The skilled artisan will understand that the domain boundaries indicated in Table 1 below are approximate, and that protein fragments whose boundaries differ from those given in the table below by 1, 2, or 3 amino acids may have the same activity as the domains described below. In some embodiments, the disclosure provides the CasX proteins of SEQ ID NOS: 3281-3441, or 3444-3446 having the NTSB domain and helical I-II domain from SEQ ID NO: 1 and a helical I-I domain from SEQ ID NO: 2, wherein the CasX have additional amino acid changes (i.e., 1, 2, 3, 4, or 5 mismatches) at select locations relative to the domains of the reference CasX, and that are rendered catalytically dead by introducing one or more mutations that inactivates the cleavage activity of the RuvC domain.







TABLE 1







Domain coordinates in Reference CasX proteins












Coordinates in
Coordinates in



Domain Name
SEQ ID NO: 1*
SEQ ID NO: 2*







OBD-I
 1-55
 1-57



helical I-I
56-99
 58-101



NTSB
100-190
102-191



helical I-II
191-331
192-332



helical II
332-508
333-500



OBD-II
509-659
501-646



RuvC-I
660-823
647-810



TSL
824-933
811-920



RuvC-II
934-986
921-978







*amino acid position






In some embodiments, a dCasX variant protein utilized in the fusion proteins of the disclosure comprises a sequence of SEQ ID NOS: 4-29 as set forth in Table 2. In other embodiments, a dCasX variant protein utilized in the fusion proteins of the disclosure comprises a sequence at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical to a sequence of SEQ ID NOS: 4-29 as set forth in Table 2. In a particular embodiment, the dCasX variant protein utilized in the fusion protein of the gene repressor systems of the disclosure comprises a sequence of SEQ ID NO: 4 (dCasX 491). In another particular embodiment, the dCasX variant protein utilized in the fusion protein of the gene repressor systems of the disclosure comprises a sequence of SEQ ID NO: 6 (dCasX 515). In another particular embodiment, the dCasX variant protein utilized in the fusion protein of the gene repressor systems of the disclosure comprises a sequence of SEQ ID NO: 29 (dCasX 812).







TABLE 2







dCasX Variant Sequences









SEQ




ID




NO
dCasX
Amino Acid Sequence





 4
dCasX491
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSREKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


 5
dCasX514
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTIHTSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


 6
dCasX515
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




7KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMITINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


 7
dCasX516
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNHNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


 8
dCasX517
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGAPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLELRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


 9
dCasX518
RQEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPI




SNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMD




EKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEK




DSDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


10
dCasX519
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNEDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHIQLRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


11
dCasX520
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTTQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


12
dCasX522
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKRSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


13
dCasX523
QEIKRINKIRRRLVKDSNTKKAGKTYPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


14
dCasX524
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTIHSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


15
dCasX525
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAATQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMITINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


16
dCasX526
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAA




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVLE




KLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSWT




KGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKYQ




TNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


17
dCasX527
QEIKRINKIRRRLVKDSNTKKAGKTRGPMKTLLVRVMTPDLRERLENLRKKPENIPQPI




SNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMD




EKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEK




DSDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


18
dCasX528
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASYPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGESKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMITINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


19
dCasX529
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASNPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


20
dCasX530
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGWGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


21
dCasX531
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGYGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


22
dCasX532
QEIKRINKIRRRLVKDSNTKKAGKTRGPMKTLLVRVMTPDLRERLENLRKKPENIPQPI




SNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMD




EKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEK




DSDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


23
dCasX533
QEIKRINKIRRRLVKDSNTKKAGKTRGPMKTLLVRVMTPDLRERLENLRKKPENIPQPI




SNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMD




EKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEK




DSDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASYPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLELRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


24
dCasX535
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASSPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNFNFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


25
dCasX593
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRWWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


26
dCasX668
QEIKRINKIRRRLVKDSNTKKAGKTRGPMKTLLVRVMTPDLRERLENLRKKPENIPQPI




SNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMD




EKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEK




DSDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASSPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


27
dCasX672
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLIKLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASSPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


28
dCasX676
QEIKRINKIRRRLVKDSNTKKAGKTRGPMKTLLVRVMTPDLRERLENLRKKPENIPQPI




SNTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMD




EKGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLIKLAQLKPEK




DSDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASSPVGKALSDACMG




TIASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAY




NEVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKGFPSFPLVERQANEVDWWDMVCNVKK




LINEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGE




DWGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEA




DKDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLY




LIINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFG




KRQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSS




NIKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQA




KKEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQG




KRTEMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRV




LEKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISS




WTKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKK




YQTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV


 


29
dCasX812
QEIKRINKIRRRLVKDSNTKKAGKTGPMKTLLVRVMTPDLRERLENLRKKPENIPQPIS




NTSRANLNKLLTDYTEMKKAILHVYWEEFQKDPVGLMSRVAQPASKKIDQNKLKPEMDE




KGNLTTAGFACSQCGQPLFVYKLEQVSEKGKAYTNYFGRCNVAEHEKLILLAQLKPEKD




SDEAVTYSLGKFGQRALDFYSIHVTKESTHPVKPLAQIAGNRYASGPVGKALSDACMGT




IASFLSKYQDIIIEHQKVVKGNQKRLESLRELAGKENLEYPSVTLPPQPHTKEGVDAYN




EVIARVRMWVNLNLWQKLKLSRDDAKPLLRLKKFPSFPLVERQANEVDWWDMVCNVKKL




INEKKEDGKVFWQNLAGYKRQEALRPYLSSEEDRKKGKKFARYQLGDLLLHLEKKHGED




WGKVYDEAWERIDKKVEGLSKHIKLEEERRSEDAQSKAALTDWLRAKASFVIEGLKEAD




KDEFCRCELKLQKWYGDLRGKPFAIEAENSILDISGFSKQYNCAFIWQKDGVKKLNLYL




IINYFKGGKLRFKKIKPEAFEANRFYTVINKKSGEIVPMEVNENFDDPNLIILPLAFGK




RQGREFIWNDLLSLETGSLKLANGRVIEKTLYNRRTRQDEPALFVALTFERREVLDSSN




IKPMNLIGVARGENIPAVIALTDPEGCPLSRFKDSLGNPTHILRIGESYKEKQRTIQAK




KEVEQRRAGGYSRKYASKAKNLADDMVRNTARDLLYYAVTQDAMLIFANLSRGFGRQGK




RTFMAERQYTRMEDWLTAKLAYEGLPSKTYLSKTLAQYTSKTCSNCGFTITSADYDRVL




EKLKKTATGWMTTINGKELKVEGQITYYNRYKRQNVVKDLSVELDRLSEESVNNDISSW




TKGRSGEALSLLKKRFSHRPVQEKFVCLNCGFETHAAEQAALNIARSWLFLRSQEYKKY




QTNKTTGNTDKRAFVETWQSFYRKKLKEVWKPAV









In some embodiments, a dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 4-29, or a sequence having or a sequence having at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity thereto. In some embodiments, a dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 4-29. In some embodiments, a dCasX comprises a sequence selected from the group consisting of SEQ ID NOS: 3281-3441 and 3444-3446, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity thereto, wherein the sequence further comprises one or mutations in the RuvC domain that render the dCasX capable of binding DNA, but is otherwise catalytically dead. In some embodiments, the one or more mutations are in the RuvC domain and render the RuvC catalytically inactive (i.e. not capable of cleaving DNA). In some embodiments, the one or more mutations comprise D659A, E756A and/or D922A substitutions corresponding to a sequence of SEQ ID NO: 2. The repressor fusion protein comprising the dCasX retains the ability to form an RNP with a gRNA. In some embodiments, the repressor fusion protein comprising the dCasX retains one or more functions of a CasX protein, including but not limited to, affinity for the gRNA, binding to the target nucleic acid, specificity for the target nucleic acid, unwinding of the target nucleic acid, target strand loading, or any combination thereof.
d. Affinity for the gRNA
In some embodiments, a dCasX with linked repressor domains has improved affinity for the gRNA relative to a reference dCasX protein, leading to the formation of the ribonucleoprotein complex. Increased affinity of the repressor fusion protein for the gRNA may, for example, result in a lower Kd for the generation of a RNP complex, which can, in some cases, result in a more stable ribonucleoprotein complex formation. In some embodiments, the Kd of a repressor fusion protein for a gRNA is increased relative to a reference dCasX protein and linked repressor domains by a factor of at least about 1.1, at least about 1.2, at least about 1.3, at least about 1.4, at least about 1.5, at least about 1.6, at least about 1.7, at least about 1.8, at least about 1.9, at least about 2, at least about 3, at least about 4, at least about 5, at least about 6, at least about 7, at least about 8, at least about 9, at least about 10, at least about 15, at least about 20, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, or at least about 100. In some embodiments, the dCasX variant has about 1.1 to about 10-fold increased binding affinity to the gRNA compared to the catalytically-dead variant of reference CasX protein of SEQ ID NO: 2.
In some embodiments, increased affinity of the dCasX with linked repressor domains for the gRNA results in increased stability of the ribonucleoprotein complex when delivered to mammalian cells, including in vivo delivery to a subject. This increased stability can affect the function and utility of the complex in the cells of a subject, as well as result in improved pharmacokinetic properties in blood, when delivered to a subject. In some embodiments, increased affinity of the repressor fusion protein, and the resulting increased stability of the ribonucleoprotein complex, allows for a lower dose of the repressor fusion protein to be delivered to the subject or cells while still having the desired activity; for example in vivo or in vitro gene repression and/or epigenetic modification. The increased ability to form RNP and keep them in stable form can be assessed using in vitro assays known in the art.
In some embodiments, a higher affinity (tighter binding) of a dCasX variant protein and linked repressor domain to a gRNA allows for a greater amount of repression and/or epigenetic modification events when both the dCasX variant protein and the gRNA remain in an RNP complex. Increased repression events can be assessed using assays described herein.
Methods of measuring repressor fusion protein binding affinity for a gRNA include in vitro methods using purified an repressor fusion protein and a gRNA. The binding affinity for the repressor fusion protein can be measured by fluorescence polarization if the gRNA or the repressor fusion protein is tagged with a fluorophore. Alternatively, or in addition, binding affinity can be measured by biolayer interferometry, electrophoretic mobility shift assays (EMSAs), or filter binding. Additional standard techniques to quantify absolute affinities of RNA binding proteins such as the reference dCasX and variant proteins of the disclosure for specific gRNAs such as reference gRNAs and variants thereof include, but are not limited to, isothermal calorimetry (ITC), and surface plasmon resonance (SPR).
e. Improved Specificity for a Target Nucleic Acid Sequence
In some embodiments, a repressor fusion protein comprising a dCasX variant protein with linked repressor domains has improved specificity for a target nucleic acid sequence that is complementary to the targeting sequence of the gRNA relative to a reference dCasX protein with linked repressor domains. As used herein, “specificity,” sometimes referred to as “target specificity,” refers to the degree to which a CRISPR/Cas system ribonucleoprotein complex binds off-target sequences that are similar, but not identical to the target nucleic acid sequence; e.g., a repressor fusion protein RNP with a higher degree of specificity would exhibit reduced off-target methylation of sequences relative to an RNP of a reference dCasX with linked repressor domains. The specificity, and the reduction of potentially deleterious off-target effects, of repressor fusion proteins can be vitally important in order to achieve an acceptable therapeutic index for use in mammalian subjects.
Without wishing to be bound by theory, it is possible that amino acid changes in the helical I and II domains that increase the specificity of the repressor fusion protein for the target nucleic acid strand can increase the specificity of the repressor fusion protein for the target nucleic acid overall. In some embodiments, amino acid changes that increase specificity of repressor fusion proteins for target nucleic acid may also result in decreased affinity of repressor fusion proteins for DNA, but the overall benefit and safety of the composition is enhanced.
f. Repressor fusion proteins with Additional Heterologous Proteins
Also contemplated within the scope of the disclosure are repressor fusion proteins comprising one or more heterologous proteins fused to the repressor fusion protein. This includes repressor fusion proteins comprising N-terminal or C-terminal fusions to a heterologous protein or domain thereof. In some embodiments, the repressor fusion protein is fused to one or more proteins or domains thereof that has a different activity of interest.
In some cases, a heterologous polypeptide (a fusion partner) for use with a repressor fusion protein provides for subcellular localization, i.e., the heterologous polypeptide contains a subcellular localization sequence (e.g., a nuclear localization signal (NLS) for targeting to the nucleus, a sequence to keep the fusion protein out of the nucleus, a nuclear export sequence (NES), a sequence to keep the fusion protein retained in the cytoplasm, a mitochondrial localization signal for targeting to the mitochondria, a chloroplast localization signal for targeting to a chloroplast, an ER retention signal, and the like).
In some cases, a repressor fusion protein includes (is fused to) a nuclear localization signal (NLS). In some cases, a repressor fusion protein is fused to 2 or more, 3 or more, 4 or more, or 5 or more 6 or more, 7 or more, 8 or more NLSs. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus and/or the C-terminus of the repressor fusion protein. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the N-terminus of the repressor fusion protein. In some cases, one or more NLSs (2 or more, 3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) the C-terminus of the repressor fusion protein. In some cases, one or more NLSs (3 or more, 4 or more, or 5 or more NLSs) are positioned at or near (e.g., within 50 amino acids of) both the N-terminus and the C-terminus of the repressor fusion protein. In some cases, a single NLS is positioned at the N-terminus and a single NLS is positioned at the C-terminus of the repressor fusion protein. The person of ordinary skill in the art will understand that an NLS at or near the N- or C-terminus of a protein can be within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19 or 20 amino acids of the N- or C-terminus. In some embodiments, the NLS linked to the N-terminus of the dCasX or the repressor fusion protein are identical to the NLS linked to the C-terminus. In other embodiments, the NLS linked to the N-terminus of the dCasX or the repressor fusion protein are different to the NLS linked to the C-terminus. Representative configurations of repressor fusion proteins with NLS are shown in FIG. 1 and FIG. 2. In some embodiments, NLSs suitable for use with a repressor fusion protein in the systems of the disclosure comprise sequences having at least about 85%, at least about 90%, or at least about 95% identity or are identical to sequences derived from: the NLS of the simian virus 40 (SV40) virus large T-antigen, having the amino acid sequence PKKKRKV (SEQ ID NO: 30); the NLS from nucleoplasmin (e.g., the nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK (SEQ ID NO: 31); the c-MYC NLS having the amino acid sequence PAAKRVKLD (SEQ ID NO: 32) or RQRRNELKRSP (SEQ ID NO: 33). In some embodiments, the NLS linked to the N-terminus of the repressor fusion protein is selected from the group consisting of the N-terminal sequences as set forth in Table 3. In some embodiments, the NLS linked to the C-terminus of the repressor fusion protein is selected from the group consisting of the C-terminal sequences as set forth in Table 4. In some embodiments, NLSs suitable for use with a repressor fusion protein in the systems of the disclosure include sequences having at least about 80%, at least about 90%, or at least about 95% identity or are identical to one or more sequences of Table 3 or Table 4. The skilled artisan will understand that Tables 3 and 4 present NLS sequences as N-terminal or C-terminal as exemplary embodiments. Any of the NLS in Table 3 or 4 can be fused to either the N or C terminal of a repressor fusion protein described herein.







TABLE 3







N-terminal NLS Amino Acid Sequences









SEQ


NLS Amino Acid Sequence*
ID NO





PKKKRKVSR
34


 


PKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKVSR
35


 


PKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKV
36


SR



 


PAAKRVKLDSR
37


 


PAAKRVKLDGGSPAAKRVKLDSR
38


 


PAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLDSR
39


 


PAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLD
40


GGSPAAKRVKLDSR



 


KRPAATKKAGQAKKKKSR
41


 


KRPAATKKAGQAKKKKGGSKRPAATKKAGQAKKKKSR
42


 


PAAKRVKLDGGSPKKKRKVSR
43


 


PAAKKKKLDGGSPKKKRKVSR
44


 


PAAKKKKLDSR
45


 


PAAKKKKLDGGSPAAKKKKLDGGSPAAKKKKLDSR
46


 


PAAKKKKLDGGSPAAKKKKLDGGSPAAKKKKLDGGSPAAKKKKLDSR
47


 


PAKRARRGYKCSR
48


 


PAKRARRGYKCGSPAKRARRGYKCSR
49


 


PRRKREESR
50


 


PYRGRKESR
51


 


PLRKRPRRSR
52


 


PLRKRPRRGSPLRKRPRRSR
53


 


PAAKRVKLDGGKRTADGSEFESPKKKRKVGGS
54


 


PAAKRVKLDGGKRTADGSEFESPKKKRKVPPPPG
55


 


PAAKRVKLDGGKRTADGSEFESPKKKRKVGIHGVPAAPG
56


 


PAAKRVKLDGGKRTADGSEFESPKKKRKVGGGSGGGSPG
57


 


PAAKRVKLDGGKRTADGSEFESPKKKRKVPGGGSGGGSPG
58


 


PAAKRVKLDGGKRTADGSEFESPKKKRKVAEAAAKEAAAKEAAAKAPG
59


 


PAAKRVKLDGGSPKKKRKVGGS
60


 


PAAKRVKLDPPPPKKKRKVPG
61


 


PAAKRVKLDPG
62


 


PAAKRVKLDGGGSGGGSGGGS
63


 


PAAKRVKLDPPP
64


 


PAAKRVKLDGGGSGGGSGGGSPPP
65


 


PKKKRKVPPP
66


 


PKKKRKVGGS
67





*Residues in bold are NLS residues, while unbolded residues are linkers.













TABLE 4







C-terminal NLS Amino Acid Sequences









SEQ ID


NLS Amino Acid Sequence
NO





GSPKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKV
68


 


GSPKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKKRKVGGSPKKK
69


RKV



 


GSPAAKRVKLDGGSPAAKRVKLD
70


 


GSPAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLDGGSPAAKRVKLD
71


 


GSKRPAATKKAGQAKKKK
72


 


KRPAATKKAGQAKKKKGGSKRPAATKKAGQAKKKK
73


 


GSKLGPRKATGRWGS
74


 


GSKRKGSPERGERKRHWGS
75


 


GSPKKKRKVGSGSKRPAATKKAGQAKKKKLE
76


 


GPKRTADSQHSTPPKTKRKVEFEPKKKRKV
77


 


GGGSGGGSKRTADSQHSTPPKTKRKVEFEPKKKRKV
78


 


AEAAAKEAAAKEAAAKAKRTADSQHSTPPKTKRKVEFEPKKKRKV
79


 


GPPKKKRKVGGSKRTADSQHSTPPKTKRKVEFEPKKKRKV
80


 


GPAEAAAKEAAAKEAAAKAPAAKRVKLD
81


 


GPGGGSGGGSGGGSPAAKRVKLD
82


 


GPPAAKRVKLD
83


 


VGSKRPAATKKAGQAKKKK
84


 


TGGGPGGGAAAGSGSPKKKRKVGSGSKRPAATKKAGQAKKKKLE
85


 


TGGGPGGGAAAGSGSPKKKRKVGSGS
86


 


PPPPKKKRKVPPP
87


 


GGSPKKKRKVPPP
88


 


PPPPKKKRKV
89


 


GGSPKKKRKV
90


 


GGSPKKKRKVGGSGGSGGS
91


 


GGSPKKKRKVGGSPKKKRKV
92


 


GGSGGSGGSPKKKRKVGGSPKKKRKV
93


 


VGGGSGGGSGGGSPAAKRVKLD
94


 


VPPPPAAKRVKLD
95


 


VPPPGGGSGGGSGGGSPAAKRVKLD
96


 


VGSPAAKRVKLD
97









In some embodiments, the one or more NLSs are linked to the repressor fusion protein or to adjacent NLS with a linker peptide wherein the linker peptide is selected from the group consisting of SR, GS, GP, VGS, GGS, (G)n (SEQ ID NO: 98), (GS)n (SEQ ID NO: 99), (GSGGS)n (SEQ ID NO: 100), (GGSGGS)n (SEQ ID NO: 101), (GGGS)n (SEQ ID NO: 102), GGSG (SEQ ID NO: 103), GGSGG (SEQ ID NO: 104), GSGSG (SEQ ID NO: 105), GSGGG (SEQ ID NO: 106), GGGSG (SEQ ID NO: 107), GSSSG (SEQ ID NO: 108), GPGP (SEQ ID NO: 109), GGP, PPP, VPPP, PPAPPA (SEQ ID NO: 110), PPPG (SEQ ID NO: 111), PPPGPPP (SEQ ID NO: 112), PPP(GGGS)n (SEQ ID NO: 113), (GGGS)nPPP (SEQ ID NO: 114), AEAAAKEAAAKEAAAKA (SEQ ID NO: 115), VPPPGGGSGGGSGGGS (SEQ ID NO: 116), TGGGPGGGAAAGSGS (SEQ ID NO: 117), GGGSGGGSGGGSPPP (SEQ ID NO: 118), TPPKTKRKVEFE (SEQ ID NO: 119), GGSGGGS (SEQ ID NO: 120), GSGSGGG (SEQ ID NO: 121), SSGNSNANSRGPSFSSGLVPLSLRGSH (SEQ ID NO: 122), GGPSSGAPPPSGGSPAGSPTSTEEGTSESATPESGPGTSTEPSEGSAPGSPAGSPTSTEEGTSTE PSEGSAPGTSTEPSE (SEQ ID NO: 123), and GGSGGG (SEQ ID NO: 124), where n is 1 to 5.
In general, NLS (or multiple NLSs) are of sufficient strength to drive accumulation of a LTRP fusion protein in the nucleus of a eukaryotic cell. Detection of accumulation in the nucleus may be performed by any suitable technique. For example, a detectable marker may be fused to a LTRP fusion protein such that location within a cell may be visualized. Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry, Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly.
IV. Repressor Domains
In some embodiments, the disclosure provides repressor fusion proteins and systems comprising same, the repressor fusion proteins comprising a DNA-binding protein linked to multiple repressor domains (repressor fusion proteins), wherein the system is capable of binding to a target nucleic acid of PCSK9 and repressing transcription of a PCSK9 target nucleic acid, including by epigenetic modification of the target nucleic acid. Exemplary DNA-binding proteins for use in the repressor fusion proteins include zinc finger (ZF), TALE (transcription-activator-like effector) proteins, and DNA-binding proteins such as catalytically-dead CRISPR proteins.
In some embodiments, the disclosure provides repressor fusion proteins comprising a catalytically-dead CRISPR protein, such as a dCasX, linked to multiple repressor domains. When the repressor fusion protein is complexed with a guide ribonucleic acid (gRNA) comprising a targeting sequence complementary to a target nucleic acid sequence of PCSK9, the system is capable of binding to the target nucleic acid of PCSK9 and repressing transcription and/or epigenetic modification of the PCSK9 target nucleic acid. Examples of gene repression processes which decrease transcription include, but are not limited to, those which inhibit formation of a transcription initiation complex, those which decrease transcription initiation rate, those which decrease transcription elongation rate, those which decrease processivity of transcription and those which antagonize transcriptional activation (by, for example, blocking the binding of a transcriptional activator). Gene repression can constitute, for example, prevention of activation as well as inhibition of expression below an existing level. Transcriptional repression includes both reversible and irreversible inactivation of gene transcription; the latter can result from epigenetic modification of the target nucleic acid.
Amongst repressor domains that have the ability to repress, or silence genes, the Krüppel-associated box (KRAB) repressor domain is amongst the most powerful in human genome systems (Alerasool, N., et al. An efficient KRAB domain for CRISPRi applications. Nat. Methods 17:1093 (2020)). KRAB domains are present in approximately 400 human zinc finger protein-based transcription factors that upon binding of the linked dCasX to the target nucleic acid, is capable of recruiting additional repressor domains such as, but not limited to, Trim28 (also known as Kap1 or Tif1-beta) that, in turn, assembles a protein complex with chromatin regulators such as CBX5/HP1α and SETDB1 that induce repression of transcription of the gene, but do so in a limited, temporal fashion. Representative, non-limiting examples of KRAB domains suitable for use in the systems of the disclosure include ZIM3 (SEQ ID NO: 128) and ZNF10 (SEQ ID NO: 129). The disclosure provides additional repressor domains that are from human and non-human sources that have been found to result in enhanced activity compared to ZIM3 and ZNF10 when incorporated in a repressor fusion proteins, described herein.
In some embodiments, the disclosure provides systems in which the modification imparted by use of the repressor fusion protein:gRNA system is epigenetic, and hence the silencing of the PCSK9 gene is heritable by mechanisms other than by replication of a target nucleic acid that has been edited. As used herein “epigenetic modification” means a modification to either DNA or histones associated with DNA, other than a change in the DNA sequence itself (e.g., a substitution, deletion or rearrangement), wherein the modification is either a direct modification by a component of the system or is indirect by the recruitment of one or more additional cellular components, but in which the DNA target nucleic acid sequence itself is not edited to change the sequence. For example, DNA methyltransferase 3A (DNMT3A) (or its catalytic domain) directly modifies the DNA by methylating it, whereas KRAB recruits KAP-1/TIF13 corepressor complexes that act as potent transcriptional repressors and can further recruit factors associated with DNA methylation and formation of repressive chromatin, such as heterochromatin protein 1 (HP1), histone deacetylases and histone methyltransferases (Ying, Y., et al. The Krüppel-associated box repressor domain induces reversible and irreversible regulation of endogenous mouse genes by mediating different chromatin states. Nucleic Acids Res. 43(3): 1549 (2015)). Further, the catalytically inactive DNMT3L cofactor helps establish a heritable methylation pattern after DNA replication, together with endogenous DNMT1 of the cell. The ATRX-DNMT3-DNMT3L domain (ADD) of DNMT3A is known to have two key functions: 1) it allosterically regulates the catalytic activity of DNMT3A by serving as a methyltransferase auto-inhibitory domain, and 2) it specifically interacts with histone H3 tails that are unmethylated at lysine (K)4, leading to the preferential methylation of DNA bound to chromatin H3 tails that are unmethylated at K4 (Zhang, Y., et al. Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Research 38:4246 (2010)).
In some embodiments, the repressor fusion protein (or the mRNA encoding the repressor fusion protein) comprises a DNA-binding protein linked to a first, second, third, and fourth repressor domain, wherein each of the repressor domains are different. In some embodiments, the DNA-binding protein is a TALE that can bind but not cleave the target nucleic acid. In some embodiments, the DNA-binding protein is a zinc-finger protein that can bind but not cleave the target nucleic acid. In some embodiments, the DNA-binding protein is a catalytically dead CRISPR protein that can bind but not cleave the target nucleic acid. In some embodiments, the repressor fusion protein (or the mRNA encoding the repressor) comprises a catalytically-dead CasX sequence, a first repressor domain (herein after referred to as “RD1”), a DNMT3A catalytic domain (herein after referred to as “DNMT3A”) as the second domain, a DNMT3L interaction domain (herein after referred to as “DNMT3L”) as the third domain, and an ATRX-DNMT3-DNMT3L domain (herein after referred to as “ADD”) as the fourth domain. In some embodiments, the ADD is fused to the N-terminus of the DNMT3A. In some embodiments, the repressor fusion protein comprises a first and a second NLS and one or more linker peptides described herein, and the fusion protein is capable of forming an RNP with a gRNA of the system that binds to the target nucleic acid.
It has been discovered that the use of the foregoing domains, when configured in select orientations relative to a dCasX in a repressor fusion protein, results in pronounced epigenetic modification of a PCSK9 target nucleic acid when complexed with a gRNA with a targeting sequence complementary to defined regions of the PCSK9 gene, and that the combination of the repressor domains work in synchrony, resulting in an additive or synergistic effect on transcriptional silencing of the targeted gene, depending on the configuration. In one embodiment of the foregoing, the dCasX of the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 4-29, or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the first repressor domain (RD1) of the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 128-1726, or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the RD1 of the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 130-224 or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the first repressor domain (RD1) of the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 130-138 or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the RD1 of the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 135 or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the RD1 of the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 131 or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the second repressor domain of the repressor fusion protein is a DNMT3A, comprising a sequence of SEQ ID NO: 126, or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the third repressor domain of the repressor fusion protein is a DNMT3L, comprising a sequence of SEQ ID NO: 127, or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In another embodiment of the foregoing, the fourth repressor domain of the repressor fusion protein is an ADD, comprising a sequence of SEQ ID NO: 125, or a sequence having at least about 80%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% identity thereto. In a surprising finding, it has been discovered that the addition of the ADD to the repressor fusion proteins comprising the RD1, DNMT3A, and DNMT3L greatly enhances or increases the long-term repression and/or epigenetic modification of the target nucleic acid, as well as the specificity of the repression, in comparison to repressor fusion proteins lacking the ADD. Exemplary data for the improved repression and specificity of repressor fusion proteins comprising the ADD are presented in the Examples. Exemplary configurations of repressor fusion proteins comprising the ADD are presented in FIG. 2.
In some embodiments, the present disclosure provides a system of an repressor fusion protein comprising a first, a second, a third, and a fourth repressor domain operably linked to a dCasX comprising the sequence of SEQ ID NO: 4, or a sequence having at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, wherein the RD1 comprises one or more motifs selected from the group consisting of a) PX1X2X3X4X5X6EX7, wherein X1 is A, D, E, or N, X2 is L or V, X3 is I or V, X4 is S, T, or F, X5 is H, K, L, Q, R or W, X6 is L or M, and X7 is G, K, Q, or R; b) X1X2X3X4GX5X6X7X8X9, wherein X1 is L or V, X2 is A, G, L, T or V, X3 is A, F, or S, X4 is L or V, X5 is C, F, H, I, L or Y, X6 is A, C, P, Q, or S, X7 is A, F, G, I, S, or V, X8 is A, P, S, or T, and X9 is K or R; c) QX1X2LYRX3VMX4 (SEQ ID NO: 1727), wherein X1 is K or R, X2 is A, D, E, G, N, S, or T, X3 is D, E, or S, and X4 is L or R; d) X1X2X3FX4DVX5X6X7FX8X9X10X11 (SEQ ID NO: 1728), wherein X1 is A, L, P, or S, X2 is L or V, X3 is S or T, X4 is A, E, G, K, or R, X5 is A or T, X6 is I or V, X7 is D, E, N, or Y, X8 is S or T, X9 is E, P, Q, R, or W, X10 is E or N, and X11 is E or Q; e) X1X2X3PX4X5X6X7X8X9X10, wherein X1 is E, G, or R, X2 is E or K, X3 is A, D, or E, X4 is C or W, X5 is I, K, L, M, T, or V, X6 is I, L, P, or V, X7 is D, E, K, or V, X8 is E, G, K, P, or R, X9 is A, D, R, G, K, Q, or V, and X10 is D, E, G, I, L, R, S, or V; f) LYX1X2VMX3EX4X5X6X7X8X9X10 (SEQ ID NO: 1729), wherein X1 is K or R, X2 is D or E, X3 is L, Q, or R, X4 is N or T, X5 is F or Y, X6 is A, E, G, Q, R, or S, X7 is H, L, or N, X8 is L or V, X9 is A, G, I, L, T, or V, and X10 is A, F, or S; g) FX1DVX2X3X4FX5X6X7EWX8 (SEQ ID NO: 1730), wherein X1 is A, E, G, K, or R, X2 is A, S, or T, X3 is I or V, X4 is D, E, N, or Y, X5 is S or T, X6 is E, L, P, Q, R, or W, X7 is D or E, and X8 is A, E, G, Q, or R; h) X1PX2X3X4X5 X6LEX7X8X9X10X11X12, wherein X1 is K or R, X2 is A, D, E, or N, X3 is I, L, M, or V, X4 is I or V, X5 is F, S, or T, X6 is H, K, L, Q, R, or W, X7 is K, Q, or R, X8 is E, G, or R, X9 is D, E, or K, X10 is A, D, or E, X1I is L or P, and X12 is C or W; and i) X1LX2X3X4QX5X6, wherein X1 is C, H, L, Q, or W, X2 is D, G, N, R, or S, X3 is L, P, S, or T, X4 is A, S, or T, X5 is K or R, and X6 is A, D, E, K, N, S, or T; or comprises a first and a second motif wherein the first amino acid sequence motif comprises a) LYX1X2VMX3EX4X5X6X7X8X9X10 (SEQ ID NO: 1729), wherein (i) X1 is K or R, (ii) X2 is D or E, (iii) X3 is L, Q, or R, (iv) X4 is N or T, (v) X5 is F or Y, (vi) X6 is A, E, G, Q, R, or S, (vii) X7 is H, L, or N, (viii) X8 is L or V, (ix) X9 is A, G, I, L, T, or V, and (x) X10 is A, F, or S; and b) the second amino acid sequence motif comprises FX1DVX2X3X4FX5X6X7EWX8 (SEQ ID NO: 1730), wherein (i) X1 is A, E, G, K, or R, (ii) X2 is A, S, or T, (iii) X3 is I or V, (iv) X4 is D, E, N, or Y, (iv) X5 is S or T, (v) X6 is E, L, P, Q, R, or W, (vi) X7 is D or E, and (vii) X8 is A, E, G, Q, or R; or comprises an amino acid sequence motif selected from the group consisting of: a) DVAVYFSPEEWGCL (SEQ ID NO: 2945); b) X1X2X3QX4X5LY, wherein (i) X1 is A, D, G, N, R, or S, (ii) X2 is P, S, or T, (iii) X3 is A, S, or T, (iv) X4 is K or R, and (v) X5 is A, D, K, N, S, or T; c) X1KPX2X3X4X5X6, wherein (i) X1 is A, P, or S, (ii) X2 is A, D, or E, (iii) X3 is L, M, or V, (iv) X4 is I or V, (v) X5 is F, S, or T, and (vi) X6 is H, K, L, Q, R, or W; d) LEX1X2X3X4X5X6, wherein (i) X1 is E, K, Q or R, (ii) X2 is E, G, or R, (iii) X3 is A, D, E, or K, (iv) X4 is A, D, or E, (v) X5 is L or P, and (vi) X6 is C or W; and e) X1VMLEX2YX3X4X5X6SX7X8X9 (SEQ ID NO: 2946), wherein (i) X1 is D or E, (ii) X2 is N or T, (iii) X3 is A, E, G, Q, R, or S, (iv) X4 is H or N, (v) X5 is L, M, or V, (vi) X6 is A, L, or V, (vii) X7 is L or V, (ix) X8 is A, G, or V, and (x) X9 is C, F, or L, and the second repressor domain is a DNMT3A sequence comprises the sequence of SEQ ID NO: 126, or sequence variants having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, the third repressor is a DNMT3L comprising the sequence of SEQ ID NO: 127, or a sequence variant having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, and the fourth repressor is an ADD comprising the sequence of SEQ ID NO: 125, or a sequence variant having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, wherein the fusion protein comprises one or more linker peptides described herein, and wherein the fusion protein is capable of forming an RNP with a gRNA of the system that binds to the target nucleic acid. In some embodiments of the foregoing, the RD1 comprises a sequence selected from the group consisting of SEQ ID NOS: 130-1726, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, and the second repressor domain is a DNMT3A sequence comprises the sequence of SEQ ID NO: 126, or sequence variants having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, the third repressor is a DNMT3L comprising the sequence of SEQ ID NO: 127, or a sequence variant having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, and the fourth repressor is an ADD comprising the sequence of SEQ ID NO: 125, or a sequence variant having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto, wherein the fusion protein comprises one or more linker peptides described herein, and wherein the fusion protein is capable of forming an RNP with a gRNA of the system that binds to the target nucleic acid. In other embodiments of the foregoing, the first RD1 comprises a sequence selected from the group consisting of SEQ ID NOS: 130-224, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto. In other embodiments of the foregoing, the first RD1 comprises a sequence selected from the group consisting of SEQ ID NOS: 130-138, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto. In other embodiments of the foregoing, the first RD1 comprises the sequence of SEQ ID NO: 135, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto. In other embodiments of the foregoing, the first RD1 comprises the sequence of SEQ ID NO: 131, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90% at least about 91%, at least about 92%, at least about 93% at least about 94% at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% identity thereto. In the foregoing embodiments, the fusion protein can comprise a first and a second NLS comprising a sequence selected from the group consisting of SEQ ID NOS: 30-97, and one or more linker peptides comprising a sequence selected from the group consisting of SEQ ID NOS: 98-124, as set forth in Table 5. In the foregoing embodiments of the paragraph, the repressor fusion protein is capable of forming an RNP complex with a gRNA of the system that is capable of binding to the gene target nucleic acid.
The skilled artisan will understand that RD1 proteins comprising the motifs described supra, with one or more conservative substitutions to the motif, may also function as RD1 domains and are envisaged as within the scope of the instant disclosure.
In some embodiments, the repressor fusion protein comprises, from N- to C-terminus, an RD1, an ADD, a DNMT3A, a DNMT3L, and a DNA-binding protein. In some embodiments, the repressor fusion protein comprises, from N- to C-terminus, an RD1, an ADD, a DNMT3A, a DNMT3L, and a catalytically-dead CRISPR protein. In some embodiments, the repressor fusion protein comprises, from N- to C-terminus, an RD1, an ADD, a DNMT3A, a DNMT3L, and a dCasX.
In some embodiments, the repressor fusion protein comprises, from N- to C-terminus, an ADD, a DNMT3A, a DNMT3L, an RD1, and a DNA-binding protein. In some embodiments, the repressor fusion protein comprises, from N- to C-terminus, an ADD, a DNMT3A, a DNMT3L, an RD1, and a catalytically-dead CRISPR protein. In some embodiments, the repressor fusion protein comprises, from N- to C-terminus, an ADD, a DNMT3A, a DNMT3L, an RD1, and a dCasX.
In some embodiments, the repressor fusion protein has a configuration of, N-terminal to C-terminal of NLS-ADD-DNMT3A-DNMT3L-dCasX-RD1-NLS, NLS-dCasX-RD1-NLS-ADD-DNMT3A-DNMT3L, NLS-dCasX-ADD-DNMT3A-DNMT3L-RD1-NLS), NLS-RD-ADD-DNMT3A-DNMT3L-dCasX-NLS, or NLS-ADD-DNMT3A-DNMT3L-RD1-dCasX-NLS. In any of the foregoing, a linker peptide may be inserted between one or more of the ADD, DNMT3A, DNMT3L, RD1 or dCasX domains.
In some embodiments, the repressor fusion protein has a configuration of, N-terminal to C-terminal, of configuration 1 (NLS-ADD-DNMT3A-Linker2-DNMT3L-Linker1-Linker3A-dCasX-Linker3B-RD1-NLS), configuration 2 (NLS-Linker3A-dCasX-Linker3B-RD1-NLS-Linker1-ADD-DNMT3A-Linker2-DNMT3L), configuration 3 (NLS-Linker3A-dCasX-Linker1-ADD-DNMT3A-Linker2-DNMT3L-Linker3B-RD1-NLS), configuration 4 (NLS-RD1-Linker3A-ADD-DNMT3A-Linker2-DNMT3L-Linker1-dCasX-Linker3B-NLS), or configuration 5 (NLS-ADD-DNMT3A-Linker2-DNMT3L-Linker3A-RD1-Linker1-dCasX-Linker3B-NLS). In some embodiments, the repressor fusion protein has a configuration of, N-terminal to C-terminal, of configuration 1′ (NLS-DNMT3A-Linker2-DNMT3L-Linker1-Linker3A-dCasX-Linker3B-RD1-NLS), configuration 2′ (NLS-Linker3A-dCasX-Linker3B-RD1-NLS-Linker1-DNMT3A-Linker2-DNMT3L), configuration 3′ (NLS-Linker3A-dCasX-Linker1-DNMT3A-Linker2-DNMT3L-Linker3B-RD1-NLS), configuration 4′ (NLS-RD1-Linker3A-DNMT3A-Linker2-DNMT3L-Linker1-dCasX-Linker3B-NLS), or configuration 5′ (NLS-DNMT3A-Linker2-DNMT3L-Linker3A-RD1-Linker1-dCasX-Linker3B-NLS). The skilled artisan will appreciate that configurations 1′-5′ correspond to configurations 1-5 without the ADD domain. In some embodiments of the system, the fusion protein components of the system are configured as schematically portrayed in FIG. 1 or FIG. 2. In the foregoing embodiment of configurations 1-5 or 1′-5′, the NLS comprise a sequence selected from the group consisting of SEQ ID NOS: 30-97 and the linker sequences are independently selected from the group consisting of SEQ ID NOS: 98-124 as set forth in Table 5. In some embodiments, the linker sequences are independently selected from the group consisting of SEQ ID NOS 120-123. In some embodiments, Linker 1 comprises a sequence of SEQ ID NOS: 123. In some embodiments, Linker 2 comprises a sequence of SEQ ID NO: 122. In some embodiments, Linker 3A and/or Linker 3B comprise a sequence of SEQ ID NO: 120. In some embodiments, Linker 4 comprises a sequence of SEQ ID NO: 121.







TABLE 5







Exemplary linker amino acid sequences for LTRP fusion proteins









SEQ ID


Amino Acid Sequence*
NO





(G)n
 98


 


(GS)n
 99


 


(GSGGS)n
100


 


(GGSGGS)n
101


 


(GGGS)n
102


 


GGSG
103


 


GGSGG
104


 


GSGSG
105


 


GSGGG
106


 


GGGSG
107


 


GSSSG
108


 


GPGP
109


 


PPAPPA
110


 


PPPG
111


 


PPPGPPP
112


 


PPP(GGGS)n
113


 


(GGGS)nPPP
114


 


AEAAAKEAAAKEAAAKA
115


 


VPPPGGGSGGGSGGGS
116


 


TGGGPGGGAAAGSGS
117


 


GGGSGGGSGGGSPPP
118


 


TPPKTKRKVEFE
119


 


GGSGGGS
120


 


GSGSGGG
121


 


SSGNSNANSRGPSFSSGLVPLSLRGSH
122


 


GGPSSGAPPPSGGSPAGSPTSTEEGTSESATPESGPGTSTE
123


PSEGSAPGSPAGSPTSTEEGTSTEPSEGSAPGTSTEPSE



 


GGSGGG
124





*n is 1 to 5






In some embodiments of the repressor fusion proteins and systems comprising same, the repressor fusion protein comprises a DNA-binding protein, a first, second, third, and fourth repressor domain configured as a configuration selected from the group consisting of configuration 1, configuration 2, configuration 3, configuration 4, configuration 5, configuration 1′, configuration 2′, configuration 3,′ configuration 4′, and configuration 5′, described supra, upon binding of an RNP of the repressor fusion protein and the gRNA with a targeting sequence complementary to the PCSK9 target nucleic acid in a cell, the target nucleic acid is epigenetically-modified and transcription of the PCSK9 gene is repressed. In some embodiments, transcription of the PCSK9 gene is repressed by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, or at least 99%, when assayed in an in vitro assay, including cell-based assays, when compared to untreated cells or cells treated with a comparable system comprising a non-targeting spacer. Most preferably, PCSK9 gene repression results in complete inhibition of gene expression, such that no gene product is detectable. In some embodiments, transcription of the PCSK9 gene of at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, or at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60% or more of cells of a population targeted by the repressor fusion protein:gRNA system are repressed.
In some embodiments, the repression of transcription of the PCSK9 gene is sustained for at least about 8 hours, at least about 1 day, at least about 7 days, at least 2 weeks, at least about 3 weeks, at least about 1 month, or at least about 2 months, when assayed in an in vitro assay, including cell-based assays. In some embodiments, the repression of transcription of the PCSK9 gene is sustained for at least about 7 days, at least 2 weeks, at least about 3 weeks, at least about 1 month, at least about 2 months, at least about 3 months, at least about 4 months, at least about 5 months, or at least about 6 months in targeted cells of a subject when the composition is administered as a therapeutically effective dose, wherein the subject is selected from the group consisting of mouse, rat, pig, non-human primate, and human. In a particular embodiment, repressor fusion proteins configurations 4 and 5, or 4′ and 5′, when used in the repressor fusion protein:gRNA system, result in less off-target methylation or off-target activity in an in vitro assay compared to configuration 1. In some embodiments, use of the repressor fusion protein configurations 4 and 5, or 4′ and 5′, when used in a repressor fusion protein:gRNA system, results in off-target methylation or off-target activity that is less than about 10%, less than about 9%, less than about 8%, less than about 7%, less than about 6%, less than about 5%, less than about 4%, less than about 3%, less than about 2%, less than about 1%, less that 0.5%, or less than 0.1% in the cells.
a. mRNA Compositions Encoding LTRP Fusion Proteins
In another aspect, the disclosure relates to messenger RNA (mRNA) compositions comprising sequences that encode DNA-binding protein (e.g., dCasX) and linked repressor domain fusion proteins (repressor fusion proteins) of the disclosure. The mRNA compositions can be used in the repressor fusion protein:gRNA systems of the disclosure, and in certain delivery formulations; e.g., particles such as lipid nanoparticles (LNP). In some embodiments, the compositions have been designed to result in one or more of improved expression, reduced immunogenicity, increased stability, and enhanced manufacturability of the repressor fusion protein relative to repressor fusion proteins encoded by unmodified mRNAs. In some embodiments, the repressor fusion proteins are designed to result in heritable repression, wherein the repression of the PCKS9 gene persists for at least 1, 2, 3, 4, 5, or 6 or more cell divisions. In some embodiments, the repressor fusion proteins result in repression of transcription of the PCSK9 gene that is sustained for at least about 8 hours, at least about 1 day, at least about 7 days, at least 2 weeks, at least about 3 weeks, at least about 1 month, or at least about 2 months, when assayed in an in vitro assay. The disclosure also provides methods utilized to design the compositions, and formulations to deliver the compositions.
Modifications to an mRNA sequence can affect mRNA stability, protein translation and expression levels, and immunogenicity, and therefore can have a significant impact on the efficacy of mRNA-based delivery. Optimization of coding sequences and untranslated regions (UTRs) may be particularly significant when delivering an mRNA encoding a protein of interest, as opposed to a DNA template that would be transcribed into an mRNA. DNA templates are long-lived, can replicate, and can produce many RNA transcripts over their lifetimes. For DNA templates, efficiency of transcription and pre-mRNA processing are major determinants of protein expression levels. In contrast, mRNAs generally have a much shorter half-life, on the order of hours, as they are vulnerable to degradation in the cytoplasm, and cannot produce more copies of themselves. As such, mRNA stability and translation efficiency are determinants of protein expression levels for mRNA-based delivery, and the specific sequences of UTRs and coding sequences that dictate mRNA stability and translation efficiency can therefore be enhanced to improve the efficacy of mRNA-based delivery.
In some embodiments, the disclosure provides an mRNA encoding dCasX 515 (SEQ ID NO: 6) for incorporation into an mRNA encoding a repressor fusion protein, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or having at least about 99% sequence identity thereto. In some embodiments, the disclosure provides an mRNA encoding dCasX 812 (SEQ ID NO: 29) for incorporation into an mRNA encoding a repressor fusion protein, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or having at least about 99% sequence identity thereto. In some embodiments, the disclosure provides an mRNA sequence encoding dCasX 491 (SEQ ID NO: 4) for incorporation into an mRNA encoding a repressor fusion protein of the disclosure, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or having at least about 99% sequence identity thereto. In some embodiments, the disclosure provides an mRNA encoding dCasX 676 (SEQ ID NO: 28) for incorporation into an mRNA encoding a repressor fusion protein, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or having at least about 99% sequence identity thereto. In some embodiments, the disclosure provides an mRNA encoding a repressor fusion protein comprising dCasX 491 comprising a sequence of SEQ ID NO: 3122.
Various naturally-occurring or modified nucleosides may be used to produce mRNA according to the present disclosure. In some embodiments, an mRNA is or comprises natural nucleosides (e.g., adenosine, guanosine, cytidine, uridine); nucleoside analogs (e.g., 2-aminoadenosine, 2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine, 5-methylcytidine, C-5 propynyl-cytidine, C-5 propynyl-uridine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine, C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine, C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine, 8-oxoguanosine, 0(6)-methylguanine, pseudouridine, (e.g., N-1-methyl-pseudouridine), 2-thiouridine, and 2-thiocytidine); chemically modified bases; biologically modified bases (e.g., methylated bases); intercalated bases; modified sugars (e.g., 2′-fluororibose, ribose, 2′-deoxyribose, arabinose, and hexose); and/or modified phosphate groups (e.g., phosphorothioates and 5′-N-phosphoramidite linkages). In some embodiments, the mRNA comprises one or more nonstandard nucleotide residues. The nonstandard nucleotide residues may include, e.g., 5-methyl-cytidine (“5 mC”), pseudouridine (“WU”), and/or 2-thio-uridine (“2sU”). In a particular embodiment, one or more of the uridine residues of the mRNA of the disclosure are replaced with N1-methyl-pseudouridine. See, e.g., U.S. Pat. No. 8,278,036 or WO2011012316, incorporated by reference herein, for a discussion of such residues and their incorporation into mRNA. In some embodiments, the mRNA encoding CasX 515 has N1-methyl-pseudouridine nucleosides replacing one or more, or all uridines in the sequence. In some embodiments, the mRNA encoding CasX 812 has N1-methyl-pseudouridine nucleosides replacing one or more, or all uridines in the sequence.
In some embodiments, the mRNA sequence encoding the repressor fusion protein comprises a 5′ UTR and a 3′ UTR sequence. The person of ordinary skill in the art will be able to select appropriate UTR sequences. In some embodiments, the 3′ UTR comprises a sequence of SEQ ID NOS: 3189, 3205-3209 or 3278. In some embodiments, the 5′ UTR comprises a sequence of SEQ ID NOS: 3200-3204 or 3274.
V. Guide Nucleic Acids of the Systems
In another aspect, the disclosure relates to guide ribonucleic acids (gRNA) comprising a scaffold and a linked targeting sequence complementary to (and are therefore able to hybridize with) a target nucleic acid sequence of a PCSK9 gene that have utility in repression of transcription of the PCSK9 target nucleic acid in a eukaryotic cell. As used herein, the term “gRNA” covers naturally-occurring molecules and gRNA variants, including chimeric gRNA variants comprising domains from different gRNA. gRNAs of the disclosure comprise a scaffold and a targeting sequence complementary to a target nucleic acid of a cell.
In some embodiments, the disclosure provides systems comprising an mRNA encoding a repressor fusion protein comprising a dCasX protein, and one or more gRNAs as a repressor fusion protein:gRNA system designed, upon expression of the dCasX protein in a transfected cell, to form a ribonucleoprotein (RNP) complex with the gRNA. The RNP targets and binds to specific locations in the target nucleic acid sequence of the cell for repression of transcription. The gRNA provides target specificity to the RNP complex by including a targeting sequence (or “spacer”) comprising a nucleotide sequence that is complementary to a sequence of the target nucleic acid sequence. The repressor fusion protein of the system provides the site-specific activity, such as the binding and repression of the target sequence, and is guided to a target site (e.g., stabilized at a target site) within a target nucleic acid sequence by virtue of its association with the gRNA in the RNP.
Embodiments of gRNAs and formulations of mRNAs and gRNAs for use in the repression and/or epigenetic modification of PCSK9 target nucleic acids are described herein, below.
A. Reference gRNA and gRNA Variants
As used herein, a “reference gRNA” refers to a CRISPR guide ribonucleic acid comprising a wild-type sequence of a naturally-occurring gRNA. In some embodiments, a gRNA scaffold of the disclosure may be subjected to one or more mutagenesis methods, such as the mutagenesis methods described in WO2022120095A1 and WO2020247882A1, incorporated by reference herein, which may include Deep Mutational Evolution (DME), deep mutational scanning (DMS), error prone PCR, cassette mutagenesis, random mutagenesis, staggered extension PCR, gene shuffling, domain swapping, or chemical modification to generate one or more gRNA variants with enhanced or varied properties relative to the gRNA scaffold that was modified. The activity of the gRNA scaffold from which a gRNA variant was derived may be used as a benchmark against which the activity of the gRNA variant is compared, thereby measuring improvements in function or other characteristics of the gRNA scaffold.
Table 6 provides the sequences of reference gRNA tracr and scaffold sequences. In some embodiments, the disclosure provides gRNA sequences wherein the gRNA has a scaffold comprising a sequence having one or more nucleotide modifications relative to a reference gRNA sequence of any one of SEQ ID NOS: 1731-1743 of Table 6.







TABLE 6







Reference gRNA tracr and scaffold sequences








SEQ ID NO.
Nucleotide Sequence





1731
ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCG



UAUGGACGAAGCGCUUAUUUAUCGGAGAGAAACCGAUAAGUAAAACGCAUCAA



AG


 


1732
UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGU



AUGGGUAAAGCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGCAUCAA



AG


 


1733
ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCG



UAUGGACGAAGCGCUUAUUUAUCGGAGA


 


1734
ACAUCUGGCGCGUUUAUUCCAUUACUUUGGAGCCAGUCCCAGCGACUAUGUCG



UAUGGACGAAGCGCUUAUUUAUCGG


 


1735
UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGU



AUGGGUAAAGCGCUUAUUUAUCGGAGA


 


1736
UACUGGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGU



AUGGGUAAAGCGCUUAUUUAUCGG


 


1737
GUUUACACACUCCCUCUCAUAGGGU


 


1738
GUUUACACACUCCCUCUCAUGAGGU


 


1739
UUUUACAUACCCCCUCUCAUGGGAU


 


1740
GUUUACACACUCCCUCUCAUGGGGG


 


1741
CCAGCGACUAUGUCGUAUGG


 


1742
GCGCUUAUUUAUCGGAGAGAAAUCCGAUAAAUAAGAAGC


 


1743
GGCGCUUUUAUCUCAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAUGG



GUAAAGCGCUUAUUUAUCGGA









b. gRNA Domains and their Functions

The gRNAs of the disclosure comprise two segments: a targeting sequence and a protein-binding segment. The targeting segment of a gRNA includes a nucleotide sequence (referred to interchangeably as a spacer, a targeter, or a targeting sequence) that is complementary to (and therefore hybridizes with) a specific sequence (a target site) within the target nucleic acid sequence (e.g., a strand of a double stranded target DNA, a target ssRNA, a target ssDNA, etc.), described more fully below. The targeting sequence of a gRNA is capable of binding to a target nucleic acid sequence, including, in the context of the present disclosure, a coding sequence, a complement of a coding sequence, a non-coding sequence, and to accessory elements. The protein-binding segment (or “activator” or “protein-binding sequence”) of the gRNA interacts with (e.g., binds to) a CasX protein as a complex, forming an RNP (described more fully, below). As used herein, “scaffold” refers to all parts to the guide with the exception of the targeting sequence, which is comprised of several regions, described more fully, below. The properties and characteristics of CasX gRNA, both wild-type and variants, are described in WO2020247882A1, US20220220508A1, and WO2022120095A1, incorporated by reference herein.
In the case of a reference gRNA, the gRNA occurs naturally as a dual guide RNA (dgRNA), wherein the targeter and the activator portions each have a duplex-forming segment that have complementarity with one another and hybridize to one another to form a double stranded duplex (dsRNA duplex for a gRNA). The term “targeter” or “targeter RNA” is used herein to refer to a crRNA-like molecule (crRNA: “CRISPR RNA”) of a CasX dual guide RNA (and therefore of a CasX single guide RNA when the “activator” and the “targeter” are linked together, e.g., by intervening nucleotides). The crRNA has a 5′ region that anneals with the tracrRNA followed by the nucleotides of the targeting sequence. In the case of the gRNA for use in the systems of the disclosure, the scaffolds are designed such that the activator and targeter portions are covalently linked to one another (rather than hybridizing to one another) and comprise a single molecule, and can be referred to as a “single-molecule gRNA,” “single guide RNA”, a “single-molecule guide RNA,” a “one-molecule guide RNA”, or a “sgRNA”. The gRNA variants of the disclosure for use in the systems are all single molecule versions.
Collectively, the assembled gRNAs of the disclosure comprise distinct structured regions, or domains: the RNA triplex, the scaffold stem loop, the extended stem loop, the pseudoknot, and the targeting sequence that, in the embodiments of the disclosure is specific for a target nucleic acid and is located on the 3′ end of the gRNA. The RNA triplex, the scaffold stem loop, the pseudoknot and the extended stem loop, together with the unstructured triplex loop that bridges portions of the triplex, together, are referred to as the “scaffold” of the gRNA. In some cases, the scaffold stem further comprises a bubble. In other cases, the scaffold further comprises a triplex loop region. In still other cases, the scaffold further comprises a 5′ unstructured region. In some embodiments, the gRNA scaffolds of the disclosure for use in the repressor fusion protein:gRNA systems comprise a scaffold stem loop having the sequence of CCAGCGACUAUGUCGUAGUGG (SEQ ID NO: 1822), or a sequence with at least 1, 2, 3, 4 or 5 mismatches thereto.
Each of the structured domains are critical to establish the global RNA fold of the guide and retain functionality of the guide; particularly the ability to properly complex with the dCasX protein. For example, the guide scaffold stem interacts with the helical I domain of dCasX protein, while residues within the triplex, triplex loop, and pseudoknot stem interact with the OBD of the dCasX protein. Together, these interactions confer the ability of the guide to bind and form an RNP with the dCasX that retains stability, while the spacer (or targeting sequence) directs and defines the specificity of the RNP for binding a specific sequence of DNA.
Site-specific binding of a target nucleic acid sequence (e.g., genomic DNA) by the dCasX protein can occur at one or more locations (e.g., a sequence of a target nucleic acid) determined by base-pairing complementarity between the targeting sequence of the gRNA and the target nucleic acid sequence. Thus, for example, the gRNA of the disclosure have sequences complementarity to and therefore can hybridize with the target nucleic acid that is adjacent to a sequence complementary to a TC protospacer adjacent motif (PAM) motif or a PAM sequence, such as ATC, CTC, GTC, or TTC. Because the targeting sequence of a guide sequence hybridizes with a sequence of a target nucleic acid sequence, a targeting sequence can be modified by a user to hybridize with a specific target nucleic acid sequence, so long as the location of the PAM sequence is considered. In some embodiments, for design of a targeting sequence, the target nucleic acid comprises a PAM sequence located 5′ of the targeting sequence with at least a single nucleotide separating the PAM from the first nucleotide of the target nucleic acid complementary to that of the targeting sequence. In some embodiments, the PAM is located on the non-targeted strand of the target region, i.e., the strand that is complementary to the target nucleic acid. In some embodiments, the targeting sequence of the gRNA is complementary to a target nucleic acid sequence one nucleotide from an ATC PAM sequence. In some embodiments, the targeting sequence of the gRNA is complementary to a target nucleic acid sequence one nucleotide from an CTC PAM sequence. In some embodiments, the targeting sequence of the gRNA is complementary to a target nucleic acid sequence one nucleotide from an GTC PAM sequence. In some embodiments, the targeting sequence of the gRNA is complementary to a target nucleic acid sequence one nucleotide from an TTC PAM sequence. By selection of the targeting sequences of the gRNA, defined regions of the target nucleic acid sequence or sequences bracketing a particular location within the target nucleic acid can be repressed using the repressor fusion protein:gRNA systems described herein. In some embodiments, the targeting sequence of the gRNA has between 15 and 20 consecutive nucleotides. In some embodiments, the targeting sequence has 15, 16, 17, 18, 19, and 20 consecutive nucleotides. In some embodiments, the targeting sequence consists of 20 consecutive nucleotides. In some embodiments, the targeting sequence consists of 19 consecutive nucleotides. In some embodiments, the targeting sequence consists of 18 consecutive nucleotides. In some embodiments, the targeting sequence consists of 17 consecutive nucleotides. In some embodiments, the targeting sequence consists of 16 consecutive nucleotides. In some embodiments, the targeting sequence consists of 15 consecutive nucleotides. By selection of the targeting sequences of the gRNA, defined regions of the target nucleic acid sequence can be repressed and/or epigenetically modified using the repressor fusion protein:gRNA systems described herein.
The gene repressor systems of the present disclosure can be designed to target any region of, or proximal to, a PCSK9 gene or region of a PCSK9 gene for which repression of transcription is sought. When the entirety of the gene is to be repressed, designing a guide with a targeting sequence complementary to a sequence encompassing or proximal to the transcription start site (TSS) is contemplated by the disclosure. The TSS selection occurs at different positions within the promoter region, depending on promoter sequence and initiating-substrate concentration. The core promoter serves as a binding platform for the transcription machinery, which comprises Pol II and its associated general transcription factors (GTFs) (Haberle, V. et al. Eukaryotic core promoters and the functional basis of transcription initiation (Nat Rev Mol Cell Biol. 19(10):621 (2018)). Variability in TSS selection has been proposed to involve DNA ‘scrunching’ and ‘anti-scrunching,’ the hallmarks of which are: (i) forward and reverse movement of the RNA polymerase leading edge, but not trailing edge, relative to DNA, and (ii) expansion and contraction of the transcription bubble. In some embodiments, the target nucleic acid sequence bound by an RNP of the repressor fusion protein:gRNA system is within 1 kb of a transcription start site (TSS) in the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 20 bp, 50 bp, 100 bp, 150 bp, 200 bp, 250 bp, 500 bps, 1 kb, or 1.5 kb upstream of a TSS of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 20 bp, 50 bp, 100 bp, 150 bp, 200 bp, 250 bp, 500 bps, 1 kb, or 1.5 kb downstream of a TSS of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 1.5 kb upstream to 1.5 downstream, 1 kb upstream to 1 kb downstream, 500 bps upstream to 500 bps downstream, or 300 bps upstream to 300 bps downstream, or 100 bps upstream to 100 bps downstream of a TSS of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 20 bp, 50 bp, 100 bp, 150 bp, 200 bp, 250 bp, 500 bps, 1 kb, or 1.5 kb of an enhancer of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system of the disclosure is within 1 kb 3′ to a 5′ untranslated region of the PCSK9 gene. In other embodiments, the target nucleic acid sequence bound by an RNP of the system is within the open reading frame of the PCSK9 gene, inclusive of introns (if any). In some embodiments, the targeting sequence of a gRNA of the system of the disclosure is designed to be specific for an exon of the PCSK9 gene. In a particular embodiment, the targeting sequence of a gRNA of the system of the disclosure is designed to be specific for exon 1 of the PCSK9 gene. In other embodiments, the targeting sequence of a gRNA of the system of the disclosure is designed to be specific for an intron of the PCSK9 gene. In other embodiments, the targeting sequence of the gRNA of the system of the disclosure is designed to be specific for an intron-exon junction of the PCSK9 gene. In other embodiments, the targeting sequence of the gRNA of the system of the disclosure is designed to be specific for a regulatory element of the PCSK9 gene. In other embodiments, the targeting sequence of the gRNA of the system of the disclosure is designed to be complementary to a sequence of an intergenic region of the PCSK9 gene. In other embodiments, the targeting sequence of a gRNA of the system of the disclosure is specific for a junction of the exon, an intron, and/or a regulatory element of the PCSK9 gene. In those cases where the targeting sequence is specific for a regulatory element, such regulatory elements include, but are not limited to promoter regions, enhancer regions, intergenic regions, 5′ untranslated regions (5′ UTR), 3′ untranslated regions (3′ UTR), conserved elements, and regions comprising cis-regulatory elements. The promoter region is intended to encompass nucleotides within 5 kb of the initiation point of the encoding sequence or, in the case of gene enhancer elements or conserved elements, can be thousands of bp, hundreds of thousands of bp, or even millions of bp away from the encoding sequence of the PCSK9 gene. In the foregoing, the targets are those in which the encoding PCSK9 gene of the target is intended to be repressed such that the PCSK9 gene product is not expressed or is expressed at a lower level in a cell. In some embodiments, upon binding of the RNP of the system of the disclosure to the binding location of the target nucleic acid, the system is capable of repressing transcription of the PCSK9 gene 5′ to the binding location of the RNP. In other embodiments, upon binding of the RNP of the system to the binding location of the target nucleic acid, the system is capable of repressing transcription of the PCSK9 gene 3′ to the binding location of the RNP.
In some embodiments, the target nucleic acid comprises a PAM sequence located 5′ of the targeting sequence with at least a single nucleotide separating the PAM from the first nucleotide of the targeting sequence. In some embodiments, the PAM is located on the non-targeted strand of the target region, i.e. the strand that is complementary to the target nucleic acid. Representative, but non-limiting examples of targeting sequences to wild-type PCSK9 nucleic acid are presented as SEQ ID NOS: 1824-2944, and are shown below as Table 7, representing targeting sequences for PCSK9 target nucleic acid for linkage to the gRNA scaffolds of the disclosure; e.g., gRNA 174, 235, 316, or chemically-modified versions thereof. In some embodiments, the targeting sequence of the gRNA comprises a sequence having at least about 65%, at least about 75%, at least about 85%, or at least about 95% identity to a sequence selected from the group consisting of SEQ ID NOS: 1824-2944. In some embodiments, the PAM sequence is TTC. In some embodiments, a targeting sequences for a TTC PAM comprises SEQ ID NOS: 1824-2944, or a sequence that is at least 50% identical, at least 55% identical, at least 60% identical, at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, at least 95% identical, or at least 99% identical to SEQ ID NOS: 1824-2944. In some embodiments, a targeting sequence for a TTC PAM is selected from the group consisting of SEQ ID NOS: 1824-2944.
In some embodiments, the targeting sequence of the gRNA for use in the repressor fusion protein:gRNA systems of the disclosure comprises a sequence selected from the group consisting of SEQ ID NO: 1824-2545. In a particular embodiment, the targeting sequence of the gRNA for use in the repressor fusion protein:gRNA systems of the disclosure consists of a sequence selected from the group consisting of SEQ ID NOS: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714. In some embodiments, the targeting sequence consists of SEQ ID NO: 1834. In some embodiments, the targeting sequence consists of SEQ ID NO: 2009. In some embodiments, the targeting sequence consists of SEQ ID NO: 2341. In some embodiments, the targeting sequence consists of SEQ ID NO: 1841. In some embodiments, the targeting sequence consists of SEQ ID NO: 1842. In some embodiments, the targeting sequence consists of SEQ ID NO: 1844. In some embodiments, the targeting sequence consists of SEQ ID NO: 1845. In some embodiments, the targeting sequence consists of SEQ ID NO: 2672. In some embodiments, the targeting sequence consists of SEQ ID NO: 1884. In some embodiments, the targeting sequence consists of SEQ ID NO: 1851. In some embodiments, the targeting sequence consists of SEQ ID NO: 1849. In some embodiments, the targeting sequence consists of SEQ ID NO: 1852. In some embodiments, the targeting sequence consists of SEQ ID NO: 1853. In some embodiments, the targeting sequence consists of SEQ ID NO: 1855. In some embodiments, the targeting sequence consists of SEQ ID NO: 1856. In some embodiments, the targeting sequence consists of SEQ ID NO: 1857. In some embodiments, the targeting sequence consists of SEQ ID NO: 1858. In some embodiments, the targeting sequence consists of SEQ ID NO: 1859. In some embodiments, the targeting sequence consists of SEQ ID NO: 1860. In some embodiments, the targeting sequence consists of SEQ ID NO: 1862. In some embodiments, the targeting sequence consists of SEQ ID NO: 1863. In some embodiments, the targeting sequence consists of SEQ ID NO: 1867. In some embodiments, the targeting sequence consists of SEQ ID NO: 1869. In some embodiments, the targeting sequence consists of SEQ ID NO: 1870. In some embodiments, the targeting sequence consists of SEQ ID NO: 1872. In some embodiments, the targeting sequence consists of SEQ ID NO: 1875. In some embodiments, the targeting sequence consists of SEQ ID NO: 1830. In any of the foregoing, the targeting sequence may have 1, 2, 3, 4, or 5 nucleotides removed from the 3′ end of the targeting sequence.







TABLE 7







Targeting Sequences Specific to PCSK9










SEQ ID NO:
PAM Sequence







1824-2944
TTC

















TABLE 8







Exemplary Targeting Sequences of PCSK9










SEQ ID NO:
PAM Sequence







1824-1890, 1910, 1925, 2672, 2675,
TTC



2694, and 2714










c. gRNA Modifications

In another aspect, the disclosure relates to gRNAs (sometimes referred to as gRNA variants herein) which comprise modifications relative to a reference gRNA from which the gRNAs were derived. The gRNAs can be used in the systems of the disclosure. In some embodiments, a gRNA variant comprises one or more nucleotide substitutions, insertions, deletions, or swapped or replaced domains relative to a reference gRNA sequence that improve a characteristic relative to the reference gRNA. Exemplary regions for modifications and swapped regions or domains include the RNA triplex, the pseudoknot, the scaffold stem loop, and the extended stem loop. In some embodiments, the gRNA variant comprises at least a first swapped region from a different gRNA, resulting in a chimeric gRNA. A representative example of such a chimeric gRNA is guide 316 (SEQ ID NO: 1746), in which the extended stem loop of gRNA scaffold 235 is replaced with the extended stem loop of gRNA scaffold 174, wherein the resulting 316 variant retains the ability to form an RNP with an repressor fusion protein and exhibits an improved characteristic compared to the parent 235, when assessed in an in vitro or in vivo assay under comparable conditions.
All gRNAs that have one or more improved functions, characteristics, or add one or more new functions when the gRNA scaffold variant is compared to a gRNA scaffold from which it was derived, while retaining the functional properties of being able to complex with the repressor fusion protein and guide the ribonucleoprotein holo RNP complex to the target nucleic acid are envisaged as within the scope of the disclosure. In some embodiments, the gRNA has an improved characteristic selected from the group consisting of increased pseudoknot stem stability, increased triplex region stability, increased scaffold stem stability, extended stem stability, reduced off-target folding intermediates, increased binding affinity to a repressor fusion protein, and increased repression activity when complexed with a repressor fusion protein, or any combination thereof. In some cases of the foregoing, the improved characteristic is assessed in an in vitro assay, including the assays of the Examples. In other cases of the foregoing, the improved characteristic is assessed in vivo.
Table 9 provides exemplary gRNA variant scaffold sequences for the generation of the gRNAs. The gRNAs can be used in the repressor fusion protein:gRNA systems of the disclosure. In some embodiments, the gRNA variant scaffold comprises any one of the sequences listed in Table 9, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto, wherein the gRNA variant retains the ability to form an RNP with a dCasX of the disclosure. In other embodiments, the gRNA variant scaffold comprises any one of the sequences listed in Table 9, wherein the gRNA variant retains the ability to form an RNP with an repressor fusion protein of the disclosure. It will be understood that in those embodiments wherein a vector comprises a DNA encoding sequence for a gRNA, that thymine (T) bases can be substituted for the uracil (U) bases of any of the gRNA sequence embodiments described herein. In some embodiments, the disclosure provides gRNA variants of Table 9 that are chemically-modified, described below.







TABLE 9







gRNA Scaffold Sequences










Scaffold



SEQ ID
variant



NO:
ID
Nucleotide sequence





1744
174
ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAU




GUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAG


 


1745
235
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAU




GUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUCCGUAAGAGGCAU




CAGAG


 


1746
316
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAU




GUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGAG









Additional gRNA scaffold variants contemplated for use in the gRNAs, and in the repressor fusion protein:gRNA systems of the disclosure are selected from the group consisting of SEQ ID NOS: 1747-1821.
d. gRNA Scaffold 316
Guide scaffolds can be made by several methods, including recombinantly or by solid-phase RNA synthesis. However, the length of the scaffold can affect the manufacturability when using solid-phase RNA synthesis, with longer lengths resulting in increased manufacturing costs, decreased purity and yield, and higher rates of synthesis failure. For use in particle formulations, such as lipid nanoparticle (LNP) formulations, solid-phase RNA synthesis of the scaffold is preferred to generate the quantities needed for commercial development. While previous experiments had identified gRNA scaffold 235 as having enhanced properties relative to gRNA scaffold 174, its increased length (in nucleotides) rendered its use for LNP formulations problematic due to synthetic manufacturing constraints. Accordingly, alternative sequences were sought. In some embodiments, the disclosure provides gRNA variant scaffolds having improved manufacturability compared to the gRNA scaffold from which it was derived. In some embodiments, the disclosure provides a gRNA wherein the gRNA scaffold and linked targeting sequence has a sequence that is less than about 115 nucleotides, less than about 110 nucleotides, or less than about 100 nucleotides.
In some embodiments, a gRNA scaffold was designed wherein the scaffold 174 (SEQ ID NO: 1744) sequence was modified by introducing one or more mutations at positions selected from the group consisting of U11, U24, A29, and A87. In some embodiments, the gRNA comprises a sequence of SEQ ID NO: 1744, or a sequence having at least about 70% sequence identity thereto, comprising an extended stem loop sequence of SEQ ID NO: 49739 and one or more mutations at positions selected from the group consisting of U11, U24, A29, and A87. In one embodiment of the foregoing, the mutations consist of U11C, U24C, A29C, and A87G, resulting in the sequence of SEQ ID NO: 1746.
In another embodiment, the 316 gRNA scaffold was designed wherein the scaffold 235 sequence was modified by a domain swap in which the extended stem loop of scaffold 174 replaced the extended stem loop of the 235 scaffold, resulting in the chimeric gRNA scaffold 316 (SEQ ID NO: 1746), having 89 nucleotides, compared with the 99 nucleotides of gRNA scaffold 235. The resulting 316 scaffold had the further advantage in that the extended stem loop does not contain CpG motifs; an enhanced property conferring reduced potential to elicit an immune response. In some embodiments, the shorter sequence length of the 316 scaffold confers the improvements of a higher fidelity in the ability to create the guide synthetically with the correct and complete sequence, as well as an enhanced ability to be successfully incorporated into an LNP. In some embodiments, the disclosure provides gRNA 316 variants that are chemically-modified, described below.
e. Chemically-Modified gRNAs
In some embodiments, the gRNAs have one or more chemical modifications. In some embodiments, the chemical modification is the addition of a 2′O-methyl group to one or more nucleotides of the sequence. In some embodiments, the chemical modification is substitution of a phosphorothioate bond between two or more nucleosides of the sequence. In some embodiments, the first 1, 2, or 3 nucleosides of the 5′ end of the scaffold (i.e., A, C, and U in the case of gRNA 174, 235, and 316) are modified by the addition of a 2′O-methyl group and each of the modified nucleosides is linked to the adjoining nucleoside by a phosphorothioate bond. Similarly, the last 1, 2, or 3 nucleotides of the 3′ end of the targeting sequence linked to the 3′ end of the scaffold are similarly modified. In some embodiments, the disclosure provides gRNA with chemical modifications selected from the group consisting of the sequences of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976, as set forth in Table 25, or a sequence having at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto. In some embodiments, the gRNA with chemical modifications comprises a scaffold of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976, i.e., a sequence of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976 without the spacer represented in the foregoing sequences as undefined nucleotides. The skilled artisan will understand the 20 3′ terminal undefined sequences in the foregoing represent non-targeting sequences, and can be substituted with any suitable targeting sequence complementary to a target nucleic acid of the PCSK9 gene; for example a targeting sequence selected from the group consisting of SEQ ID NOS: 1824-2944. In some embodiments, the chemically modified gRNA comprises the sequence of SEQ ID NO: 2968. A schematic of the structure of gRNA variants 174, 235, and 316 are shown in FIGS. 19A-19C, respectively. In some embodiments, the gRNA with chemical modifications exhibit improved stability compared to gRNA without chemical modifications.
f. Complex Formation with Repressor Fusion Proteins
Upon delivery or expression of the components of the system in a target cell, the gRNA variant is capable of complexing as an RNP with a repressor fusion protein comprising a catalytically-dead CRISPR protein and binding to the target nucleic acid of the PCSK9 gene. In some embodiments, a gRNA variant has an improved ability to form an RNP complex with a repressor fusion protein when compared to a reference gRNA or another gRNA variant from which it was derived. Improving ribonucleoprotein complex formation may, in some embodiments, improve the efficiency with which functional RNPs are assembled. In some embodiments, greater than 90%, greater than 93%, greater than 95%, greater than 96%, greater than 97%, greater than 98% or greater than 99% of RNPs comprising a gRNA variant and its targeting sequence are competent for gene repression of a target nucleic acid.
VI. Polynucleotides and Vectors
In another aspect, the present disclosure relates to polynucleotides encoding the repressor fusion proteins, and, in some embodiments, gRNAs, that have utility in the repression and epigenetic modification of the PCSK9 gene.
A repressor fusion protein or an mRNA encoding the repressor fusion protein of the disclosure may be prepared by in vitro synthesis, using conventional methods as known in the art. Various commercial synthetic apparatuses are available, for example, automated synthesizers by Applied Biosystems, Inc., Beckman, etc. By using synthesizers, naturally occurring amino acids or nucleotides (as applicable) may be substituted with unnatural amino acids or nucleotides. The particular sequence and the manner of preparation will be determined by convenience, economics, purity required, and the like. A gRNA can also be produced synthetically; for example by use of a T7 RNA polymerase system known in the art.
The repressor fusion protein and/or the gRNA may also be prepared by recombinantly producing a polynucleotide sequence coding for the repressor or gRNA of any of the embodiments described herein using standard recombinant techniques known in the art and incorporating the encoding gene into an expression vector appropriate for a host cell. For production of the encoded repressor fusion protein and/or gRNA, the methods include transforming an appropriate host cell with an expression vector comprising the encoding polynucleotide, and culturing the host cell under conditions causing or permitting the resulting repressor or gRNA to be expressed or transcribed in the transformed host cell, which are recovered by methods described herein or by standard purification methods known in the art, or as described in the Examples. Standard recombinant techniques in molecular biology are used to make the polynucleotides and expression vectors of the present disclosure.
A repressor fusion protein and/or a gRNA of the disclosure may also be isolated and purified in accordance with conventional methods of recombinant synthesis. A lysate may be prepared of the expression host and the lysate purified using high performance liquid chromatography (HPLC), exclusion chromatography, gel electrophoresis, affinity chromatography, or other purification technique. For the most part, the compositions which are used will comprise 50% or more by weight of the desired product, more usually 75% or more by weight, preferably 95% or more by weight, and for therapeutic purposes, usually 99.5% or more by weight, in relation to contaminants related to the method of preparation of the product and its purification. Usually, the percentages will be based upon total protein. Thus, in some cases, a repressor fusion protein or gRNA of the present disclosure is at least 80% pure, at least 85% pure, at least 90% pure, at least 95% pure, at least 98% pure, or at least 99% pure (e.g., free of contaminants or other macromolecules, etc.).
Additionally, the disclosure provides vectors comprising polynucleotides encoding the repressor fusion proteins and, in some cases, the gRNAs described herein. In some cases, the vectors are utilized for the expression and recovery of the CasX and gRNA components of the repressor fusion protein:gRNA system. In other cases, the vectors are utilized for the delivery of the encoding polynucleotides to target cells for the repression and/or epigenetic modification of the target nucleic acid, as described more fully, below. In some embodiments, sequences encoding the repressor fusion protein and the gRNA are encoded by the same vector. In some embodiments, sequences encoding the repressor fusion protein and a gRNA are encoded by sequences on different vectors. Suitable vectors are described, for example, in WO2022120095A1 and WO2020247882A1, incorporated by reference herein. As described in WO2022120095A1 and WO2020247882A1, depending on the host/vector system utilized, any of a number of suitable transcription and translation control elements, including constitutive and inducible promoters, transcription enhancer elements, transcription terminators, etc. may be used in the expression vector.
In some embodiments, the disclosure provides polynucleotide sequences encoding repressor fusion proteins, including the repressor fusion proteins of SEQ ID NOS: 3131-3132 as set forth in Table 20, or sequences having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity thereto. In some embodiments, the disclosure provides an isolated polynucleotide sequence encoding a gRNA variant. In some embodiments, the disclosure provides polynucleotides encoding a gRNA comprising a scaffold sequence of SEQ ID NOS: 1744-1746 and 2947-2976, or a sequence having at least about 50%, at least about 60%, at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto, wherein the expressed gRNA variant retains the ability to form an RNP with an repressor fusion protein. In some embodiments, the disclosure provides polynucleotide sequences encoding gRNAs comprising targeting sequences of SEQ ID NOS: 1824-2944, or sequences having at least about 65%, at least about 75%, at least about 85%, or at least about 95% identity thereto. In some embodiments, the disclosure provides polynucleotide sequences encoding gRNAs comprising targeting sequences of SEQ ID NOS: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714, or sequences having at least about 65%, at least about 75%, at least about 85%, or at least about 95% identity thereto.
In some embodiments, the disclosure relates to methods to produce polynucleotide sequences encoding the repressor fusion proteins or the gRNAs, including variants thereof, as well as methods to express the proteins or RNA transcribed by the polynucleotide sequences. In general, the methods include producing a polynucleotide sequence coding for the repressor fusion protein or the gRNA of any of the embodiments described herein and incorporating the encoding gene into an expression vector. In some embodiments, the vector is designed for transduction of cells for repression and/or epigenetic modification of the PCSK9 target nucleic acid. Such vectors can include a retroviral vector, a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, a herpes simplex virus (HSV) vector, a plasmid, a minicircle, a nanoplasmid, a DNA vector, and an RNA vector. In other embodiments, the expression vector is designed for production of a repressor fusion protein, mRNA encoding the repressor fusion protein, or gRNA in either a cell-free system or in a host cell. For production of the encoded repressor fusion protein or the gRNA of any of the embodiments described herein in a host cell, the methods include transforming an appropriate host cell with an expression vector comprising the encoding polynucleotide, and culturing the host cell under conditions causing or permitting the resulting repressor fusion protein or the gRNA of any of the embodiments described herein to be expressed or transcribed in the transformed host cell, thereby producing the repressor fusion protein or the gRNA, which are recovered by methods described herein (e.g., in the Examples, below) or by standard purification methods known in the art. Standard recombinant techniques in molecular biology are used to make the polynucleotides and expression vectors of the present disclosure.
In accordance with the disclosure, nucleic acid sequences that encode the repressor fusion protein or the gRNA of any of the embodiments described herein are used to generate recombinant DNA molecules that direct the expression in appropriate host cells. Several cloning strategies are suitable for performing the present disclosure, many of which are used to generate a construct that comprises a gene coding for a composition of the present disclosure, or its complement. In some embodiments, the cloning strategy is used to create a gene that encodes a construct that comprises nucleotides encoding the repressor fusion protein or the gRNA that is used to transform a host cell for expression of the composition.
In one approach, a construct is first prepared containing the DNA sequence encoding a repressor fusion protein or a gRNA. Exemplary methods for the preparation of such constructs are described in the Examples. The construct is then used to create an expression vector suitable for transforming a host cell, such as a prokaryotic or eukaryotic host cell for the expression and recovery of the protein construct, in the case of the repressor fusion protein, or the gRNA. Where desired, the host cell is an E. coli. In other embodiments, the host cell is a eukaryotic cell. The eukaryotic host cell can be selected from Baby Hamster Kidney fibroblast (BHK) cells, human embryonic kidney 293 (HEK293), human embryonic kidney 293T (HEK293T), NSO cells, SP2/0 cells, YO myeloma cells, P3X63 mouse myeloma cells, PER cells, PER.C6® cells, hybridoma cells, NIH3T3 cells, CV-1 (simian) in Origin with SV40 genetic material (COS), HeLa, Chinese hamster ovary (CHO), yeast cells, or other eukaryotic cells known in the art suitable for the production of recombinant products. Exemplary methods for the creation of expression vectors, the transformation of host cells and the expression and recovery of the repressor fusion protein or the gRNA are described in the Examples.
The gene encoding the repressor fusion protein or the gRNA construct can be made in one or more steps, either fully synthetically or by synthesis combined with enzymatic processes, such as restriction enzyme-mediated cloning, PCR and overlap extension, including methods more fully described in the Examples. The methods disclosed herein can be used, for example, to ligate sequences of polynucleotides encoding the various components into a gene of a desired sequence. Genes encoding polypeptide compositions are assembled from oligonucleotides using standard techniques of gene synthesis.
In some embodiments, the nucleotide sequence encoding an repressor fusion protein is codon optimized. This type of optimization can entail a mutation of an encoding nucleotide sequence to mimic the codon preferences of the intended host organism or cell while encoding the same protein. Thus, the codons can be changed, but the encoded protein remains unchanged. For example, if the intended target cell of the repressor fusion protein was a human cell, a human codon-optimized repressor fusion protein-encoding nucleotide sequence could be used. As another non-limiting example, if the intended host cell were a mouse cell, then a mouse codon-optimized repressor fusion protein-encoding nucleotide sequence could be generated. The gene design can be performed using algorithms that optimize codon usage and amino acid composition appropriate for the host cell utilized in the production of the repressor fusion protein or the gRNA. In one method of the disclosure, a library of polynucleotides encoding the components of the constructs is created and then assembled, as described above. The resulting genes are then assembled and the resulting genes used to transform a host cell and produce and recover the repressor fusion protein or the gRNA compositions for evaluation of its properties or for use in the modification of the PCSK9 target nucleic acid, as described herein.
In some embodiments, a nucleotide sequence encoding a gRNA is operably linked to a control element, e.g., a transcriptional control element, such as a promoter. In some embodiments, a nucleotide sequence encoding a repressor fusion protein is operably linked to a control element, e.g., a transcriptional control element, such as a promoter. In some cases, the promoter is a constitutively active promoter. In some cases, the promoter is a regulatable promoter. In some cases, the promoter is an inducible promoter. In some cases, the promoter is a tissue-specific promoter. In some cases, the promoter is a cell type-specific promoter. In some cases, the transcriptional control element (e.g., the promoter) is functional in a targeted cell type or targeted cell population. For example, in some cases, the transcriptional control element can be functional in eukaryotic cells, e.g., hepatocytes or a liver sinusoidal endothelial cell.
Non-limiting examples of Pol II promoters operably linked to the polynucleotide encoding the repressor fusion protein of the disclosure include, but are not limited to EF-1alpha, EF-1alpha core promoter, Jens Tornoe (JeT), promoters from cytomegalovirus (CMV), CMV immediate early (CMVIE), CMV enhancer, herpes simplex virus (HSV) thymidine kinase, early and late simian virus 40 (SV40), the SV40 enhancer, long terminal repeats (LTRs) from retrovirus, mouse metallothionein-I, adenovirus major late promoter (Ad MLP), CMV promoter full-length promoter, the minimal CMV promoter, the chicken β-actin promoter (CBA), CBA hybrid (CBh), chicken β-actin promoter with cytomegalovirus enhancer (CB7), chicken beta-Actin promoter and rabbit beta-Globin splice acceptor site fusion (CAG), the rous sarcoma virus (RSV) promoter, the HIV-Ltr promoter, the hPGK promoter, the HSV TK promoter, a 7SK promoter, the Mini-TK promoter, the human synapsin I (SYN) promoter which confers neuron-specific expression, beta-actin promoter, super core promoter 1 (SCP1), the Mecp2 promoter for selective expression in neurons, the minimal IL-2 promoter, the Rous sarcoma virus enhancer/promoter (single), the spleen focus-forming virus long terminal repeat (LTR) promoter, the TBG promoter, promoter from the human thyroxine-binding globulin gene (Liver specific), the PGK promoter, the human ubiquitin C promoter (UBC), the UCOE promoter (Promoter of HNRPA2B1-CBX3), the synthetic CAG promoter, the Histone H2 promoter, the Histone H3 promoter, the U1a1 small nuclear RNA promoter (226 nt), the U1a1 small nuclear RNA promoter (226 nt), the U1b2 small nuclear RNA promoter (246 nt) 26, the GUSB promoter, the CBh promoter, rhodopsin (Rho) promoter, silencing-prone spleen focus forming virus (SFFV) promoter, a human H1 promoter (H1), a POL1 promoter, the TTR minimal enhancer/promoter, the b-kinesin promoter, mouse mammary tumor virus long terminal repeat (LTR) promoter, the human eukaryotic initiation factor 4A (EIF4A1) promoter, the ROSA26 promoter, the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) promoter, tRNA promoters, and truncated versions and sequence variants of the foregoing. In a particular embodiment, the Pol II promoter is EF-1alpha, wherein the promoter enhances transfection efficiency, the transgene transcription or expression of the CRISPR nuclease, the proportion of expression-positive clones and the copy number of the episomal vector in long-term culture.
Non-limiting examples of Pol III promoters operably linked to the polynucleotide encoding the gRNA variants of the disclosure include, but are not limited to U6, mini U6, U6 truncated promoters, 7SK, and H1 variants, BiH1 (Bidrectional H1 promoter), BiU6, Bi7SK, BiH1 (Bidirectional U6, 7SK, and H1 promoters), gorilla U6, rhesus U6, human 7SK, human H1 promoters, and truncated versions and sequence variants thereof. In the foregoing embodiment, the pol III promoter enhances the transcription of the gRNA. In a particular embodiment, the Pol III promoter is U6, wherein the promoter enhances expression of the gRNA. In another particular embodiment, the promoter linked to the gene encoding the tropism factor is CMV promoter. Experimental details and data for the use of such promoters are provided in the Examples.
Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art, as it related to controlling expression. The expression vector may also contain a ribosome binding site for translation initiation, and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression. The expression vector may also include nucleotide sequences encoding protein tags (e.g., 6×His tag, hemagglutinin tag, fluorescent protein, etc.) that can be fused to the repressor fusion protein, thus resulting in a chimeric protein that are used for purification or detection.
Recombinant expression vectors of the disclosure can also comprise elements that facilitate robust expression of the proteins and the gRNAs of the disclosure. For example, recombinant expression vectors can include one or more of a polyadenylation signal (poly(A)), an intronic sequence or a post-transcriptional regulatory element such as a woodchuck hepatitis post-transcriptional regulatory element (WPRE). Exemplary poly(A) sequences include hGH poly(A) signal (short), HSV TK poly(A) signal, synthetic polyadenylation signals, SV40 poly(A) signal, (3-globin poly(A) signal and the like (for example, SEQ ID NO: 3459). A person of ordinary skill in the art will be able to select suitable elements to include in the recombinant expression vectors described herein.
The polynucleotides encoding the repressor fusion protein or the gRNA sequences can be individually cloned into an expression vector. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art, as it relates to controlling expression, e.g., for repressing expression and/or epigenetic modification of the PCSK9 gene. The expression vector may also contain a ribosome binding site for translation initiation and a transcription terminator. The expression vector may also include appropriate sequences for amplifying expression.
The nucleic acid sequence is inserted into the vector by a variety of procedures. In general, DNA is inserted into an appropriate restriction endonuclease site(s) using techniques known in the art. Vector components generally include, but are not limited to, one or more of a signal sequence, an origin of replication, one or more marker genes, an enhancer element, a promoter, and a transcription termination sequence. Construction of suitable vectors containing one or more of these components employs standard ligation techniques which are known to the skilled artisan. Such techniques are well known in the art and well described in the scientific and patent literature. Various vectors are publicly available. The vector may, for example, be in the form of a plasmid, cosmid, viral particle, or phage that may conveniently be subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which it is to be introduced. Thus, the vector may be an autonomously replicating vector, i.e., a vector, which exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid. Alternatively, the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome(s) into which it has been integrated. Once introduced into a suitable host cell, expression of the repressor fusion protein can be determined using any nucleic acid or protein assay known in the art. For example, the presence of transcribed mRNA of the repressor fusion protein can be detected and/or quantified by conventional hybridization assays (e.g., Northern blot analysis), amplification procedures (e.g., RT-PCR), SAGE (U.S. Pat. No. 5,695,937), and array-based technologies (see e.g., U.S. Pat. Nos. 5,405,783, 5,412,087 and 5,445,934), using probes complementary to any region of CasX polynucleotide.
In some embodiments, a vector is created for the transcription of the repressor fusion protein gene and expression and recovery of the resulting encoding mRNA. In some embodiments, the mRNA is generated by in vitro transcription (IVT) using a PCR product or linearized plasmid DNA template and a T7 RNA polymerase, wherein the plasmid contains a T7 promoter. If using a PCR product, DNA sequences encoding candidate mRNAs will be cloned into a plasmid containing a T7 promoter, wherein the plasmid DNA template will be linearized and then used to perform IVT reactions for expression of the mRNA. Exemplary methods for the generation of such vectors and the production and recovery of the mRNA are provided in the Examples, below.
VII. Particles for Delivery of Repressor Fusion Proteins
In another aspect, the present disclosure provides particle compositions for delivery of the repressor fusion proteins to cells or to subjects for the modification of the PCSK9 gene. In some embodiments, the particle composition delivers a repressor fusion protein:gRNA system, e.g., when the repressor fusion protein comprises a catalytically dead CRISPR protein such as a dCasX, to cells or to subjects for the repression of the PCSK9 gene. In some embodiments, the disclosure provides synthetic nanoparticles that encapsulate gRNA variants and mRNAs encoding a repressor fusion proteins comprising a dCasX protein of any of the embodiments described herein. In some embodiments, materials for the creation of biodegradable polymeric nanoparticles (PNP) include polylactide, poly (lactic-co-glycolic acid) (PLGA), poly(ethyl cyanoacrylate), poly(butyl cyanoacrylate), poly(isobutyl cyanoacrylate), and poly(isohexyl cyanoacrylate), polyglutamic acid (PGA), poly (ε-caprolactone) (PCL), cyclodextrin, and natural polymers for instance chitosan, albumin, gelatin, and alginate are the most utilized polymers for the synthesis of PNP (Production and clinical development of nanoparticles for gene delivery. Molecular Therapy-Methods & Clinical Development 3:16023; doi:10.1038 (2016)). In some embodiments, the disclosure provides virus-like particles for delivery of the repressor fusion proteins comprising a dCasX protein and gRNA variants (see, WO2021113772A1, incorporated by reference herein). In other embodiments, the disclosure provides lipid nanoparticles that encapsulate gRNA variants and mRNAs encoding repressor fusion proteins comprising a dCasX protein of any of the embodiments described herein, described more fully, below.
a. Lipid Nanoparticles (LNP)
In another aspect, the present disclosure provides lipid nanoparticles (LNP) for delivery of the repressor fusion protein:gRNA systems of the disclosure to cells or to subjects for the transcriptional repression of the PCSK9 gene. In some embodiments, the LNPs of the disclosure are tissue- or organ-specific (e.g., the liver), have excellent biocompatibility, and can deliver the systems with high efficiency, and thus can be usefully used for the repression of the PCSK9 gene.
In their native forms, nucleic acid polymers are unstable in biological fluids and cannot penetrate into the cytoplasm of target cells, thus requiring delivery systems. Lipid nanoparticles (LNP) have proven useful for both the protection and delivery of nucleic acids to tissues and cells. Furthermore, the use of mRNA in LNPs to encode the CRISPR nuclease eliminates the possibility of undesirable genome integration compared to DNA vectors. Moreover, mRNA efficiently translates into protein in both mitotic and non-mitotic cells, as it does not require to enter into the nucleus since it exerts its function in the cytoplasmic compartment. LNPs as a delivery platform offers the additional advantage of being able to co-formulate both the mRNA encoding the nuclease and the gRNA into single LNP particles.
Accordingly, in various embodiments, the disclosure encompasses lipid nanoparticles and compositions that may be used for a variety of purposes, including the delivery of encapsulated or associated (e.g., complexed) therapeutic agents such as nucleic acids to cells, both in vitro and in vivo. In certain embodiments, the disclosure encompasses methods of treating or preventing diseases or disorders in a subject in need thereof by contacting the subject with a lipid nanoparticle that encapsulates or is associated with a suitable therapeutic agent complexed through various physical, chemical or electrostatic interactions between one or more of the lipid components used in the compositions to make LNPs. In some embodiments, the suitable therapeutic agent comprises a repressor fusion protein:gRNA system as described herein.
In certain embodiments, the lipid nanoparticles are useful for the delivery of nucleic acids, including, e.g., the mRNA encoding the repressor fusion proteins of the disclosure, and the gRNA variants of the disclosure, including the sequences of SEQ ID NOS: 1744-1746 and 2947-2976. In some embodiments, the present disclosure provides LNP in which the gRNA and mRNA encoding the repressor fusion proteins are incorporated into single LNP particles. In other embodiments, the present disclosure provides LNP in which the gRNA and mRNA encoding the repressor fusion proteins are incorporated into separate populations of LNPs, which can be formulated together in varying ratios for administration. In some embodiments, the mRNA for incorporation into the LNP of the disclosure encode any of the repressor fusion proteins described herein. In some embodiments, the gRNA for use in the LNP comprises a sequence of SEQ ID NOS: 1744-1746 and 2947-2976.
The lipid nanoparticles and systems of certain embodiments of the disclosure may be used to induce expression of a desired protein both in vitro and in vivo by contacting cells with a lipid nanoparticle comprising one or more novel ionizable cationic lipids or permanently charged cationic lipids described herein, wherein the lipid nanoparticle encapsulates or is associated with a nucleic acid that is expressed to produce the desired protein (e.g., a messenger RNA encoding the CasX protein). In some embodiments, the lipid nanoparticles and systems may be used to decrease the expression of the PCKS9 target gene both in vitro and in vivo by contacting cells with a lipid nanoparticle comprising one or more novel ionizable/cationic lipids described herein, wherein the lipid nanoparticle encapsulates or is associated with nucleic acids of the CasX:gRNA system that reduces target gene expression. The lipid nanoparticles and systems of embodiments of the disclosure may also be used for co-delivery of different nucleic acids (e.g., mRNA, gRNA, siRNA, saRNA, mcDNA and plasmid DNA) separately or in combination, such as may be useful to provide an effect requiring colocalization of different nucleic acids (e.g. mRNA encoding for a suitable gene modifying enzyme and gRNA for targeting of the target nucleic acid).
In some embodiments, LNPs and LNP compositions described herein include at least one cationic lipid, at least one conjugated lipid, at least one steroid or derivative thereof, at least one helper lipid, or any combination thereof. Alternatively, the lipid compositions of the disclosure can include an ionizable lipid, such as an ionizable cationic lipid, a helper lipid (usually a phospholipid), cholesterol, and a polyethylene glycol-lipid conjugate (PEG-lipid) to improve the colloidal stability in biological environments by, for example, reducing a specific absorption of plasma proteins and forming a hydration layer over the nanoparticles. Such lipid compositions can be formulated at typical mole ratios of 50:10:37-39:1-3 or 20-50:8-65:15-70:1-3.0 of IL:HL:Sterol:PEG-lipid, with variations made to include or exclude one or more of the components to the traditional 4-component system in the LNP and to adjust individual properties.
The LNPs and LNP compositions of the present disclosure are configured to protect and deliver an encapsulated payload of the systems of the disclosure to tissues and cells, both in vitro and in vivo. Various embodiments of the LNPs and LNP compositions of the present disclosure are described in further detail herein.
Cationic Lipid
In some embodiments, the LNPs and LNP compositions of the present disclosure include at least one cationic lipid. The term “cationic lipid,” refers to a lipid species that has a net positive charge. In some embodiments, the cationic lipid is an ionizable cationic lipid that has a net positive charge at a selected pH<pKa of the ionizable lipid. In some embodiments, the ionizable cationic lipid has a pKa less than about 7 such that the LNPs and LNP compositions achieve efficient encapsulation of the payload at a relatively low pH below the pKa of the respective lipid. In some embodiments, the cationic lipid has a pKa of about 5 to about 8, about 5.5 to about 7.5, about 6 to about 7, or about 6.5 to about 7. In some embodiments, the cationic lipid may be protonated at a pH below the pKa of the cationic lipid, and it may be substantially neutral at a pH over the pKa. The LNPs and LNP compositions may be safely delivered to a target organ (for example, the liver, lung, heart, spleen, as well as to tumors) and/or cell(hepatocyte, LSEC, cardiac cell, cancer cell, etc.) in vivo, and during endocytosis, exhibit a positive charge when pH drops below the ionizable lipid pKa to release the encapsulated payload through electrostatic interaction with an anionic lipids of the endosomal membrane.
Early formulations of LNP utilizing permanently cationic lipids resulted in LNPs with positive surface charge that proved toxic in vivo, plus were rapidly cleared by phagocytic cells. By changing to ionizable cationic lipids bearing tertiary amines, especially those with pKa<7, results in LNP achieving efficient encapsulation of nucleic acid polymers at low pH by interacting electrostatically with the negative charges of the phosphate backbone of mRNA, that also result in largely neutral systems at physiological pH values, thus alleviating problems associated with permanently-charged cationic lipids.
As used herein, “ionizable lipid” means an amine-containing lipid which can be easily protonated, and, for example, it may be a lipid of which charge state changes depending on the surrounding pH. The ionizable lipid may be protonated (positively charged) at a pH below the pKa of a cationic lipid, and it may be substantially neutral at a pH over the pKa. In one example, the LNP may comprise a protonated ionizable lipid and/or an ionizable lipid showing neutrality. In some embodiments, the LNP has a pKa of 5 to 8, 5.5 to 7.5, 6 to 7, or 6.5 to 7. The pKa of the LNP is important for in vivo stability and release of the nucleic acid payload of the LNP in the target cell or organ. In some embodiments, the LNP having the foregoing pKa ranges may be safely delivered to a target organ (for example, the liver, lung, heart, spleen, as well as to tumors) and/or target cell (hepatocyte, LSEC, cardiac cell, cancer cell, etc.) in vivo, and inside endosomes, exhibit a positive charge to release the encapsulated payload through electrostatic interaction with an anionic lipids of the endosome membrane.
The ionizable lipid is an ionizable compound having characteristics similar to lipids generally, and through electrostatic interaction with a nucleic acid (for example, an mRNA of the disclosure), may play a role of encapsulating the nucleic acid payloads within the LNP with high efficiency.
According to the type of the amine and the tail group comprised in the ionizable lipid, (i) the nucleic acid encapsulation efficiency, (ii) PDI (polydispersity index) and/or (iii) the nucleic acid delivery efficiency to tissue and/or cells constituting an organ (for example, hepatocytes or liver sinusoidal endothelial cells in the liver) of the LNP may be different. In certain embodiments, the ionizable lipid is an ionizable cationic lipid, and comprises from about 25 mol % to about 66 mol % of the total lipid present in the particle.
The LNP comprising an ionizable lipid comprising an amine may have one or more kinds of the following characteristics: (1) the ability to encapsulate a nucleic acid with high efficiency; (2) uniform size of prepared particles (or having a low PDI value); and/or (3) excellent nucleic acid delivery efficiency to organs such as liver, lung, heart, spleen, bone marrow, as well as to tumors, and/or cells constituting such organs (for example, hepatocytes, LSEC, cardiac cells, cancer cells, etc.).
In particular embodiments, the cationic lipid form plays a crucial role both in nucleic acid encapsulation through electrostatic interactions and intracellular release by disrupting endosomal membranes. The nucleic acid payloads are encapsulated within the LNP by the ionic interactions they form with the positively charged cationic lipid. Non-limiting examples of ionizable cationic lipid components utilized in the LNP of the disclosure are selected from DLin-MC3-DMA (heptatriaconta-6,9,28,31-tetraen-19-yl4-(dimethylamino)butanoate), DLin-KC2-DMA (2,2-dilinoleyl-4-(2-dimethylaminoethyl)-[1,3]-dioxolane), and TNT (1,3,5-triazinane-2,4,6-trione) and TT (N1,N3,N5-tris(2-aminoethyl)benzene-1,3,5-tricarboxamide). Non-limiting examples of helper lipids utilized in the LNP of the disclosure are selected from DSPC (1,2-distearoyl-sn-glycero-3-phosphocholine), POPC (2-Oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine) and DOPE (1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine), 1,2-dioleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) DOPG, 1,2-Dimyristoyl-sn-glycero-3-phosphoethanolamine (DMPE), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), sphingolipid, and ceramide. Cholesterol and PEG-DMG ((R)-2,3-bis(octadecyloxy)propyl-1-(methoxy polyethylene glycol 2000) carbamate), PEG-DSG (1,2-Distearoyl-rac-glycero-3-methylpolyoxyethylene glycol 2000), or DSPE-PEG2k (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[amino(polyethylene glycol)-2000]), are components utilized in the LNP of the disclosure for the stability, circulation, and size of the LNP.
In some embodiments, the cationic lipid in the LNP of the disclosure comprises a tertiary amine. In some embodiments, the tertiary amine includes alkyl chains connected to N of the tertiary amine with ether linkages. In some embodiments, the alkyl chains comprise C12-C30 alkyl chains having 0 to 3 double bonds. In some embodiments, the alkyl chains comprise C16-C22 alkyl chains. In some embodiments, the alkyl chains comprise C18 alkyl chains. A number of cationic lipids and related analogs have been described in U.S. Patent Publication Nos. 20060083780, 20060240554, 20110117125, 20190336608, 20190381180 and 20200121809; U.S. Pat. Nos. 5,208,036; 5,264,618; 5,279,833; 5,283,185; 5,753,613; 5,785,992; 9,738,593; 10,106,490; 10,166,298; 10,221,127; and 11,219,634; and PCT Publication No. WO 96/10390, the disclosures of which are herein incorporated by reference in their entirety.
In some embodiments, the cationic lipid in the LNP of the disclosure may comprise, for example, one or more ionizable cationic lipids wherein the ionizable cationic lipid is a dialkyl lipid. In other embodiments, the ionizable cationic lipid is a tetraalkyl lipid.
In some embodiments, the cationic lipid in the LNP of the disclosure is selected from 1,2-dilinoleyloxy-N,N-dimethylaminopropane (DLinDMA), 1,2-dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA), 2,2-dilinoleyl-4-(2-dimethylaminoethyl)-[1,3]-dioxolane (DLin-K-C2-DMA), 2,2-dilinoleyl-4-(3-dimethylaminopropyl)-[1,3]-dioxolane (DLin-K-C3-DMA), 2,2-dilinoleyl-4-(4-dimethylaminobutyl)-[1,3]-dioxolane (DLin-K-C4-DMA), 2,2-dilinoleyl-5-dimethylaminomethyl-[1,3]-dioxane (DLin-K6-DMA), 2,2-dilinoleyl-4-N-methylpepiazino-[1,3]-dioxolane (DLin-K-MPZ), 2,2-dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane (DLin-K-DMA), 1,2-dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLin-C-DAP), 1,2-dilinoleyoxy-3-(dimethylamino)acetoxypropane (DLin-DAC), 1,2-dilinoleyoxy-3-morpholinopropane (DLin-MA), 1,2-dilinoleoyl-3-dimethylaminopropane (DLinDAP), 1,2-dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA), 1-linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP), 1,2-dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.Cl), 1,2-dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.Cl), 1,2-dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ), 3-(N,N-dilinoleylamino)-1,2-propanediol (DLinAP), 3-(N,N-dioleylamino)-1,2-propanedio (DOAP), 1,2-dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA), N,N-dioleyl-N,N-dimethylammonium chloride (DODAC), 1,2-dioleyloxy-N,N-dimethylaminopropane (DODMA), 1,2-distearyloxy-N,N-dimethylaminopropane (DSDMA), N-(1-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA), N,N-distearyl-N,N-dimethylammonium bromide (DDAB), N-(1-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP), 3-(N-(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol (DC-Chol), N-(1,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammonium bromide (DMRIE), 2,3-dioleyloxy-N-[2(spermine-carboxamido)ethyl]-N,N-dimethyl-1-propanaminiumtrifluoroacetate (DOSPA), dioctadecylamidoglycyl spermine (DOGS), 3-dimethylamino-2-(cholest-5-en-3-beta-oxybutan-4-oxy)-1-(cis,cis-9,12-octadecadienoxy)propane (CLinDMA), 2-[5′-(cholest-5-en-3-beta-oxy)-3′-oxapentoxy)-3-dimethyl-1-(cis,cis-9′,1-2′-octadecadienoxy)propane (CpLinDMA), N,N-dimethyl-3,4-dioleyloxybenzylamine (DMOBA), 1,2-N,N′-dioleylcarbamyl-3-dimethylaminopropane (DOcarbDAP), 1,2-N,N′-dilinoleylcarbamyl-3-dimethylaminopropane (DLincarbDAP), and any combination of the forgoing.
In some embodiments, the cationic lipid in the LNP of the disclosure is selected from heptatriaconta-6,9,28,31-tetraen-19-yl4-(dimethylamino)butanoate (DLin-MC3-DMA), 2,2-dilinoleyl-4-(2-dimethylaminoethyl)-[1,3]-dioxolane (DLin-KC2-DMA), (1,3,5-triazinane-2,4,6-trione) (TNT), N1,N3,N5-tris(2-aminoethyl)benzene-1,3,5-tricarboxamide (TT), and any combination of the forgoing.
In some embodiments, the N/P ratio (nitrogen from the cationic/ionizable lipid and phosphate from the nucleic acid) in the LNP of the disclosure is in the range of is about 3:1 to 7:1, or about 4:1 to 6:1, or is 3:1, or is 4:1, or is 5:1, or is 6:1, or is 7:1, or is 8:1, or is 9:1.
Conjugated Lipid
In some embodiments, the LNPs and LNP compositions of the present disclosure include at least one conjugated lipid. In some embodiments, the conjugated lipid may be selected from a polyethyleneglycol (PEG)-lipid conjugate, a polyamide (ATTA)-lipid conjugate, a cationic-polymer-lipid conjugate (CPL), and any combination of the foregoing. In some cases, conjugated lipids can inhibit aggregation of the LNPs of the disclosure.
In some embodiments, the conjugated lipid of the LNP of the disclosure comprises a pegylated lipid. The terms “polyethyleneglycol (PEG)-lipid conjugate,” “pegylated lipid” “lipid-PEG conjugate”, “lipid-PEG”, “PEG-lipid”, “PEG-lipid”, or “lipid-PEG” are used interchangeably herein and refer to a lipid attached to a polyethylene glycol (PEG) polymer which is a hydrophilic polymer. The pegylated lipid contributes to the stability of the LNPs and LNP compositions and reduces aggregation of the LNPs. In other embodiments, the lipid of the LNP comprises peptide modified PEG lipids that are used for targeting cell surface receptors Ex: DSPE-PEG-RGD, DSPE-PEG-Transferrin, DSPE-PEG-cholesterol.
As the PEG-lipid can form the surface lipid, the size of the LNP can be readily varied by varying the proportion of surface (PEG) lipid to the core (ionizable cationic) lipids. In some embodiments, the PEG-lipid of the LNP of the disclosure can be varied from ˜1 to 5 mol % to modify particle properties such as size, stability, and circulation time.
The lipid-PEG conjugate contributes to the particle stability in serum of the nanoparticle within the LNP, and plays a role of preventing aggregation between nanoparticles. In addition, the lipid-PEG conjugate may protect nucleic acids, such as mRNAs encoding the repressor fusion proteins of the disclosure, or gRNAs of the disclosure, from degrading enzymes during in vivo delivery of the nucleic acids and enhance the stability of the nucleic acids in vivo and increase the half-life of the delivered nucleic acids encapsulated in the nanoparticle. Examples of PEG-lipid conjugates include, but are not limited to, PEG-DAG conjugates, PEG-DAA conjugates, and mixtures thereof. In certain embodiments, the PEG-lipid conjugate is selected from the group consisting of a PEG-diacylglycerol (PEG-DAG) conjugate, a PEG-dialkyloxypropyl (PEG-DAA) conjugate, a PEG-phospholipid conjugate, a PEG-ceramide (PEG-Cer) conjugate, and a mixture thereof.
In some embodiments, the pegylated lipid of the LNP of the disclosure is selected from a PEG-ceramide, a PEG-diacylglycerol, a PEG-dialkyloxypropyl, a PEG-dialkoxypropylcarbamate, a PEG-phosphatidylethanoloamine, a PEG-phospholipid, a PEG-succinate diacylglycerol, and any combination of the foregoing.
In some embodiments, the pegylated lipid of the LNP of the disclosure is a PEG-dialkyloxypropyl. In some embodiments, the pegylated lipid is selected from PEG-didecyloxypropyl (C10), PEG-dilauryloxypropyl (C12), PEG-dimyristyloxypropyl (C14), PEG-dipalmityloxypropyl (C16), PEG-distearyloxypropyl (C18), and any combination of the foregoing.
In other embodiments, the lipid-PEG conjugate of the LNP of the disclosure may be PEG bound to phospholipid such as phosphatidylethanolamine (PEG-PE), PEG conjugated to ceramide (PEG-CER, ceramide-PEG conjugate, ceramide-PEG, cholesterol or PEG conjugated to derivative thereof, PEG-c-DOMG, PEG-DMG, PEG-DLPE, PEG-DMPE, PEG-DPPC, PEG-DSPE(DSPE-PEG), and a mixture thereof, and for example, may be C16-PEG2000 ceramide (N-palmitoyl-sphingosine-1-{succinyl[methoxy(polyethylene glycol)2000]}), DMG-PEG 2000, 14:0 PEG2000 PE.
In some embodiments, the pegylated lipid of the LNP of the disclosure is selected from 1-(monomethoxy-polyethyleneglycol)-2,3-dimyristoylglycerol, 4-O-(2′,3′-di(tetradecanoyloxy)propyl-1-O-(o-methoxy(polyethoxy)ethyl)butanedioate (PEG-S-DMG), o-methoxy(polyethoxy)ethyl-N-(2,3-di(tetradecanoxy)propyl)carbamate, 2,3-di(tetradecanoxy)propyl-N-(o-methoxy(polyethoxy)ethyl)carbamate, and any combination of the foregoing.
In some embodiments, the pegylated lipid of the LNP of the disclosure is selected from mPEG2000-1,2-di-O-alkyl-sn3-carbomoylglyceride (PEG-C-DOMG), 1-[8′-(1,2-dimyristoyl-3-propanoxy)-carboxamido-3′,6′-dioxaoctanyl]carbamoyl-w-methyl-poly(ethylene glycol) (2 KPEG-DMG), and any combination of the foregoing.
In some embodiments, the PEG is directly attached to the lipid of the pegylated lipid. In other embodiments, the PEG is attached to the lipid of the pegylated lipid by a linker moiety selected from an ester-free linker moiety or an ester-containing linker moiety. Non-limiting examples of the ester-free linker moiety include amido (—C(O)NH—), amino (—NR—), carbonyl (—C(O)—), carbamate (—NHC(O)O—), urea (—NHC(O)NH—), disulfide (—S—S—), ether (—O—), succinyl (—(O)CCH2CH2C(O)—), succinamidyl (—NHC(O)CH2CH2C(O)NH—), ether, disulfide and combinations thereof. For example, the linker may contain a carbamate linker moiety and an amido linker moiety. Non-limiting examples of the ester-containing linker moiety include carbonate (—OC(O)O—), succinoyl, phosphate ester (—O—(O)POH—O—), sulfonate ester, and combinations thereof.
The PEG moiety of the pegylated lipid of the LNP of the disclosure described herein may have an average molecular weight ranging from about 550 daltons to about 10,000 daltons. In certain embodiments, the PEG moiety has an average molecular weight of from about 750 daltons to about 5,000 daltons, about 1,000 daltons to about 4,000 daltons, about 1,500 daltons to about 3,000 daltons, about 750 daltons to about 3,000 daltons, or about 1750 daltons to about 2,000 daltons.
In some embodiments, the conjugated lipid (e.g., pegylated lipid) comprises from about 1 mol % to about 60 mol %, from about 2 mol % to about 50 mol %, from about 5 mol % to about 40 mol %, or from about 5 mol % to about 20 mol % of the total lipid present in the LNPs and/or LNP compositions. In certain embodiments, the conjugated lipid comprises from about 0.5 mol % to about 3 mol % of the total lipid present in the particle.
In additional embodiments, the conjugated lipid (e.g., pegylated lipid) of the LNP of the disclosure comprises at least about 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 mol %, or an intermediate range of any of the foregoing, of the total lipid present in the LNPs and/or LNP compositions.
For the lipid in the lipid-PEG conjugate of the LNP of the disclosure, any lipid capable of binding to polyethyleneglycol may be used without limitation, and the phospholipid and/or cholesterol which are other elements of the LNP may be also used. In some embodiments, the lipid in the lipid-PEG conjugate may be ceramide, dimyristoylglycerol (DMG), succinoyl-diacylglycerol (s-DAG), distearoylphosphatidylcholine (DSPC), distearoylphosphatidylethanolamine (DSPE), or cholesterol, but not limited thereto.
In the lipid-PEG conjugate of the LNP of the disclosure, the PEG may be directly conjugated to the lipid or linked to the lipid via a linker moiety. Any linker moiety suitable for binding PEG to the lipid may be used, and for example, includes an ester-free linker moiety and an ester-containing linker moiety. The ester-free linker moiety includes not only amido (—C(O)NH—), amino (—NR—), carbonyl (—C(O)—), carbamate (—NHC(O)O—), urea (—NHC(O)NH—), disulfide (—S—S—), ether (—O—), succinyl (—(O)CCH2CH2C(O)—), succinamidyl (—NHC(O)CH2CH2C(O)NH—), ether, disulfide but also combinations thereof (for example, a linker containing both a carbamate linker moiety and an amido linker moiety), but not limited thereto. The ester-containing linker moiety includes for example, carbonate (—OC(O)O—), succinoyl, phosphate ester (—O—(O)POH—O—), sulfonate ester, and combinations thereof, but not limited thereto.
Steroids
In some embodiments, the LNPs and LNP compositions of the present disclosure include at least one steroid or derivative thereof. In some embodiments, the steroid comprises cholesterol. In some embodiments, the LNPs and LNP compositions comprise a cholesterol derivative selected from cholestanol, cholestanone, cholestenone, coprostanol, cholesteryl-2′-hydroxyethyl ether, cholesteryl-4′-hydroxybutyl ether, and any combination of the foregoing.
In some embodiments, the steroid (e.g., cholesterol) of the LNP of the disclosure comprises from about 1 mol % to about 65 mol %, from about 2 mol % to about 50 mol %, from about 5 mol % to about 40 mol %, or from about 5 mol % to about 20 mol % of the total lipid present in the LNPs and/or LNP compositions. In other embodiments, the steroid (e.g., cholesterol) of the LNP of the disclosure comprises at least about 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 mol %, or an intermediate range of any of the foregoing, of the total lipid present in the LNPs and/or LNP compositions.
Helper Lipid/Helper Lipid or Structural Lipid
In some embodiments, the LNPs and LNP compositions of the present disclosure include at least one helper lipid. In some embodiments, the helper lipid is non-cationic lipid selected from an anionic lipid, a neutral lipid, or both. In some embodiments, the helper lipid comprises at least one phospholipid. In some embodiments, the phospholipid is selected from an anionic phospholipid, a neutral phospholipid, or both. The phospholipid of the elements of the LNPs and LNP compositions can play a role in covering and protecting a core of the LNP formed by interaction of the cationic lipid and nucleic acid in the LNP, and may facilitate cell membrane permeation and endosomal escape during intracellular delivery of the nucleic acid by binding to the phospholipid bilayer of a target cell. A phospholipid which can promote fusion of the LNP to a cell may include without limitation, any of the phospholipids selected from the group described below.
In some embodiments, the LNPs and LNP compositions comprise at least one phospholipid selected from, but not limited to, dipalmitoyl-phosphatidylcholine (DPPC), distearoylphosphatidylcholine (DSPC), dioleoyl-phosphatidylethanolamine (DOPE), dioleoyl-phosphatidylcholine (DOPC), dioleoyl-phosphatidylglycerol (DOPG), palmitoyloleoyl-phosphatidylcholine (POPC), palmitoyloleoyl-phosphatidylethanolamine (POPE), palmitoyloleyol-phosphatidylglycerol (POPG), dipalmitoyl-phosphatidylethanolamine (DPPE), dipalmitoyl-phosphatidylglycerol (DPPG), dimyristoyl-phosphatidylethanolamine (DMPE), distearoylphosphatidylethanolamine (DSPE), monomethyl-phosphatidylethanolamine, dimethyl-phosphatidylethanolamine, dielaidoyl-phosphatidylethanolamine (DEPE), stearoyloleoyl-phosphatidylethanolamine (SOPE), egg phosphatidylcholine (EPC), phosphatidylethanolamine (PE), 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1,2-dioleoyl-sn-glycero-3-[phospho-L-serine](DOPS), 1,2-dioleoyl-sn-glycero-3-[phospho-L-serine], and any combination of the foregoing. In one example, the LNP comprising DOPE may be effective in mRNA delivery (excellent drug delivery efficacy).
In some embodiments, the helper lipid (e.g., phospholipid) of the LNP of the disclosure comprises from about 1 mol % to about 60 mol %, from about 2 mol % to about 50 mol %, from about 5 mol % to about 40 mol %, or from about 5 mol % to about 20 mol % of the total lipid present in the LNPs and/or LNP compositions. In other embodiments, the helper lipid (e.g., phospholipid) of the LNP of the disclosure comprises at least about 1, 2, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, or 60 mol %, or an intermediate range of any of the foregoing, of the total lipid present in the LNPs and/or LNP compositions.
It will be appreciated that the total lipid present in the LNPs and/or LNP compositions comprises the lipids as individual or in combination of the cationic lipid or ionizable cationic lipid, the conjugated lipid, (e.g., pegylated lipid), the peptide conjugated PEG lipid, the steroid (e.g., cholesterol), peptide conjugated-structural lipid (Ex: DSPE-cRGD) and the structural lipid (e.g., phospholipid), leading from LNP formulation containing one to multi-component but not limited to one, two, three, four or five components in an LNP formulation.
The LNPs and/or LNP compositions may be prepared by dissolving the total lipids (or a portion thereof) in an organic solvent (e.g., ethanol) followed by mixing through a micromixer with the payload (e.g., nucleic acids of the systems) dissolved in an acidic buffer (e.g., pH between 1.0-6.5). At this pH the ionizable cationic lipid is positively charged and interacts with the negatively-charged nucleic acid polymers. The resulting nanostructures containing the nucleic acids are then converted to neutral LNPs when dialyzed against a neutral buffer which also includes removal of the organic solvent (e.g., ethanol) during the exchange of LNPs into physiologically relevant buffer. The LNPs and/or LNP compositions thus formed have a distinct electron-dense nanostructured core where the cationic lipids are organized into inverted micelles around the encapsulated payload, as opposed to traditional bilayer liposomal structures. In another embodiment, the LNP may form a bleb-like structure with nucleic acids in aqueous pockets along the non-electron dense lipid core.
b. Lipid Nanoparticle Properties
The LNPs and/or LNP compositions may be prepared by dissolving the total lipids (or a portion thereof) in an organic solvent (e.g., ethanol) followed by mixing through a micromixer with the payload (e.g., nucleic acids of the systems) dissolved in an acidic buffer (e.g., pH between 1.0-6.5). At this pH the ionizable cationic lipid is positively charged and interacts with the negatively-charged nucleic acid polymers. The resulting nanostructures containing the nucleic acids are then converted to neutral LNPs when dialyzed against a neutral buffer which also includes removal of the organic solvent (e.g., ethanol) during the exchange of LNPs into physiologically relevant buffer. The LNPs and/or LNP compositions thus formed have a distinct electron-dense nanostructured core where the cationic lipids are organized into inverted micelles around the encapsulated payload, as opposed to traditional bilayer liposomal structures. In another embodiment, the LNP may form a bleb-like structure with nucleic acids in aqueous pockets along the non-electron dense lipid core.
In some embodiments, the LNPs and/or LNP compositions of the disclosure comprise cationic lipid:helper lipid (e.g., phospholipid):steroid (e.g., cholesterol):conjugated lipid, (e.g., pegylated lipid) at a molar ratio of 20 to 50:10 to 30:30 to 60:0.5 to 5, at a molar ratio of 25 to 45:10 to 25:40 to 50:0.5 to 3, at a molar ratio of 25 to 45:10 to 20:40 to 55:0.5 to 3, or at a molar ratio of 25 to 45:10 to 20:40 to 55:1.0 to 1.5.
In some embodiments, the LNPs and/or LNP compositions of the disclosure have a total lipid:payload ratio (mass/mass) of from about 1 to about 100. In some embodiments, the total lipid:payload ratio is about 1 to about 50, from about 2 to about 25, from about 3 to about 20, from about 4 to about 15, or from about 5 to about 10. In some embodiments, the total lipid:payload ratio is about 5 to about 15, e.g., about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, or an intermediate range of any of the foregoing.
In certain embodiments, the LNPs of the disclosure comprise a total lipid:nucleic acid mass ratio of from about 5:1 to about 15:1. In some embodiments, the weight ratio of the cationic lipid and nucleic acid comprised in the LNP may be 1 to 20:1, 1 to 15:1, 1 to 10:1, 5 to 20:1, 5 to 15:1, 5 to 10:1, 7.5 to 20:1, 7.5 to 15:1, or 7.5 to 10:1.
In some embodiments, the LNP of the disclosure may comprise the cationic lipid of 20 to 50 parts by weight, the phospholipid of 10 to 30 parts by weight, cholesterol of 20 to 60 parts by weight (or 20 to 60 parts by weight), and lipid-PEG conjugate of 0.1 to 10 parts by weight (or 0.25 to 10 parts by weight, 0.5 to 5 parts by weight). Alternatively, the LNP may comprise the cationic lipid of 20 to 50% by weight, phospholipid of 10 to 60% by weight, cholesterol of 20 to 60% by weight (or 30 to 60% by weight), and lipid-PEG conjugate of 0.1 to 10% by weight (or 0.25 to 10% by weight, 0.5 to 5% by weight) based on the total nanoparticle weight. As a further alternative, the LNP may comprise the cationic lipid of 25 to 50% by weight, phospholipid of 10 to 20% by weight, cholesterol of 35 to 55% by weight, and lipid-PEG conjugate of 0.1 to 10% by weight (or 0.25 to 10% by weight, 0.5 to 5% by weight), based on the total nanoparticle weight.
In some embodiments, the LNPs of the present disclosure have a mean diameter of from about 20 to 200 nm, 20 to 180 nm, 20 to 170 nm, 20 to 150 nm, 20 to 120 nm, 20 to 100 nm, 20 to 90 nm, 30 to 200 nm, 30 to 180 nm, 30 to 170 nm, 30 to 150 nm, 30 to 120 nm, 30 to 100 nm, 30 to 90 nm, 40 to 200 nm, 40 to 180 nm, 40 to 170 nm, 40 to 150 nm, 40 to 120 nm, 40 to 100 nm, 40 to 90 nm, 40 to 80 nm, 40 to 70 nm, 50 to 200 nm, 50 to 180 nm, 50 to 170 nm, 50 to 150 nm, 50 to 120 nm, 50 to 100 nm, 50 to 90 nm, 60 to 200 nm, 60 to 180 nm, 60 to 170 nm, 60 to 150 nm, 60 to 120 nm, 60 to 100 nm, 60 to 90 nm, 70 to 200 nm, 70 to 180 nm, 70 to 170 nm, 70 to 150 nm, 70 to 120 nm, 70 to 100 nm, 70 to 90 nm, 80 to 200 nm, 80 to 180 nm, 80 to 170 nm, 80 to 150 nm, 80 to 120 nm, 80 to 100 nm, 80 to 90 nm, 90 to 200 nm, 90 to 180 nm, 90 to 170 nm, 90 to 150 nm, 90 to 120 nm, or 90 to 100 nm, or an intermediate range of any of the foregoing.
In some embodiments, the LNPs and/or LNP compositions of the disclosure have a positive charge at acidic pH and may encapsulate the payload (e.g., therapeutic agent) through electrostatic interaction produced by negative charges of the payload (e.g., therapeutic agent). The term “encapsulation,” refers to the mixture of lipids surrounding and embedding the payload (e.g., therapeutic agent) at physiological conditions, forming the LNPs. The term “encapsulation efficiency,” as used herein is the percent amount of payload (e.g., therapeutic agent) encapsulated by the LNPs. It is a measure of payload (e.g., therapeutic agent) in bulk before disruption of LNPs divided by the total amount of payload (e.g., therapeutic agent) measured in bulk post-disruption of LNPs using a surfactant based reagent such as 1-2% Triton™ X-100. The encapsulation efficiency of the LNPs and/or LNP compositions may be 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 91% or more, 92% or more, 94% or more, or 95% or more. In other embodiments, the encapsulation efficiency of the LNPs and/or LNP compositions is about 80% to 99%, about 85% to 98%, about 88% to 95%, about 90% to 95%, or the payload (e.g., nucleic acids of the systems) may be fully encapsulated within the lipid portion of the LNPs compositions, and thereby protected from enzymatic degradation. In some embodiments, the payload (e.g., therapeutic agent) is not substantially degraded after exposure of the LNPs and/or LNP compositions to a nuclease at 37° C. for at least about 20, 30, 45, or 60 minutes or at least about 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, or 36 hours. In some embodiments, the payload (e.g., nucleic acids of the systems) is complexed with the lipid portion of the LNPs and/or LNP compositions. The LNPs and/or LNP compositions of the present disclosure are non-toxic to mammals such as humans.
The term “fully encapsulated” indicates that the payload (e.g., the nucleic acids of the system) in the LNPs and/or LNP compositions is not significantly degraded after exposure to conditions that significantly degrade free DNA, RNA, or protein. In a fully encapsulated system, less than about 25%, more preferably less than about 10%, and most preferably less than about 5% of the payload (e.g., nucleic acids of the system) in the LNPs and/or LNP compositions is degraded by conditions that would degrade 100% of a non-encapsulated payload. “Fully encapsulated” also indicates that the LNPs and/or LNP compositions are serum-stable, and do not decompose into their component parts immediately upon exposure to serum proteins post in vivo administration and protects the cargo until endosomal escape and release into cytoplasm of the cell.
In some embodiments, the amount of the LNPs and/or LNP compositions having the payload (e.g., therapeutic agent), encapsulated therein is from about 30% to about 100%, from about 40% to about 100%, from about 50% to about 100%, from about 60% to about 100%, from about 70% to about 100%, from about 80% to about 100%, from about 90% to about 100%, from about 30% to about 95%, from about 40% to about 95%, from about 50% to about 95%, from about 60% to about 95%, %, from about 70% to about 95%, from about 80% to about 95%, from about 85% to about 95%, from about 90% to about 95%, from about 30% to about 90%, from about 40% to about 90%, from about 50% to about 90%, from about 60% to about 90%, from about 70% to about 90%, from about 80% to about 90%, or at least about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or an intermediate range of any of the foregoing.
In some embodiments, the amount of the payload (e.g., the nucleic acids), encapsulated within the LNPs and/or LNP compositions is from about 30% to about 100%, from about 40% to about 100%, from about 50% to about 100%, from about 60% to about 100%, from about 70% to about 100%, from about 80% to about 100%, from about 90% to about 100%, from about 30% to about 95%, from about 40% to about 95%, from about 50% to about 95%, from about 60% to about 95%, %, from about 70% to about 95%, from about 80% to about 95%, from about 85% to about 95%, from about 90% to about 95%, from about 30% to about 90%, from about 40% to about 90%, from about 50% to about 90%, from about 60% to about 90%, from about 70% to about 90%, from about 80% to about 90%, or at least about 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or an intermediate range of any of the foregoing.
In some embodiments, the nucleic acids of the disclosure, such as the mRNA encoding the repressor fusion protein, and/or the gRNA, may be provided in a solution to be mixed with a lipid solution such that the nucleic acids may be encapsulated in the lipid nanoparticles. A suitable nucleic acid solution may be any aqueous solution containing the nucleic acid to be encapsulated at various concentrations. For example, a suitable nucleic acid solution may contain the nucleic acid (or nucleic acids) at a concentration of or greater than about 0.01 mg/ml, 0.05 mg/ml, 0.06 mg/ml, 0.07 mg/ml, 0.08 mg/ml, 0.09 mg/ml, 0.1 mg/ml, 0.15 mg/ml, 0.2 mg/ml, 0.3 mg/ml, 0.4 mg/ml, 0.5 mg/ml, 0.6 mg/ml, 0.7 mg/ml, 0.8 mg/ml, 0.9 mg/ml, 1.0 mg/ml, 1.25 mg/ml, 1.5 mg/ml, 1.75 mg/ml, or 2.0 mg/ml. In some embodiments, the nucleic acid comprises an mRNA encoding a repressor fusion protein, and a suitable mRNA solution may contain the mRNA at a concentration ranging from about 0.01-2.0 mg/ml, 0.01-1.5 mg/ml, 0.01-1.25 mg/ml, 0.01-1.0 mg/ml, 0.01-0.9 mg/ml, 0.01-0.8 mg/ml, 0.01-0.7 mg/ml, 0.01-0.6 mg/ml, 0.01-0.5 mg/ml, 0.01-0.4 mg/ml, 0.01-0.3 mg/ml, 0.01-0.2 mg/ml, 0.01-0.1 mg/ml, 0.05-1.0 mg/ml, 0.05-0.9 mg/ml, 0.05-0.8 mg/ml, 0.05-0.7 mg/ml, 0.05-0.6 mg/ml, 0.05-0.5 mg/ml, 0.05-0.4 mg/ml, 0.05-0.3 mg/ml, 0.05-0.2 mg/ml, 0.05-0.1 mg/ml, 0.1-1.0 mg/ml, 0.2-0.9 mg/ml, 0.3-0.8 mg/ml, 0.4-0.7 mg/ml, or 0.5-0.6 mg/ml. In some embodiments, a suitable mRNA solution may contain an mRNA at a concentration up to about 5.0 mg/ml, 4.0 mg/ml, 3.0 mg/ml, 2.0 mg/ml, 1.0 mg/ml, 0.9 mg/ml, 0.8 mg/ml, 0.7 mg/ml, 0.6 mg/ml, 0.5 mg/ml, 0.4 mg/ml, 0.3 mg/ml, 0.2 mg/ml, 0.1 mg/ml, 0.05 mg/ml, 0.04 mg/ml, 0.03 mg/ml, 0.02 mg/ml, 0.01 mg/ml, or 0.05 mg/ml. In some embodiments, a suitable gRNA solution may contain an gRNA at a concentration up to about 5.0 mg/ml, 4.0 mg/ml, 3.0 mg/ml, 2.0 mg/ml, 1.0 mg/ml, 0.9 mg/ml, 0.8 mg/ml, 0.7 mg/ml, 0.6 mg/ml, 0.5 mg/ml, 0.4 mg/ml, 0.3 mg/ml, 0.2 mg/ml, 0.1 mg/ml, 0.05 mg/ml, 0.04 mg/ml, 0.03 mg/ml, 0.02 mg/ml, 0.01 mg/ml, or 0.05 mg/ml.
In some embodiments, the LNP may have an average diameter of 20 nm to 200 nm, 20 to 180 nm, 20 nm to 170 nm, 20 nm to 150 nm, 20 nm to 120 nm, 20 nm to 100 nm, 20 nm to 90 nm, 30 nm to 200 nm, 30 to 180 nm, 30 nm to 170 nm, 30 nm to 150 nm, 30 nm to 120 nm, 30 nm to 100 nm, 30 nm to 90 nm, 40 nm to 200 nm, 40 to 180 nm, 40 nm to 170 nm, 40 nm to 150 nm, 40 nm to 120 nm, 40 nm to 100 nm, 40 nm to 90 nm, 40 nm to 80 nm, 40 nm to 70 nm, 50 nm to 200 nm, 50 to 180 nm, 50 nm to 170 nm, 50 nm to 150 nm, 50 nm to 120 nm, 50 nm to 100 nm, 50 nm to 90 nm, 60 nm to 200 nm, 60 to 180 nm, 60 nm to 170 nm, 60 nm to 150 nm, 60 nm to 120 nm, 60 nm to 100 nm, 60 nm to 90 nm, 70 nm to 200 nm, 70 to 180 nm, 70 nm to 170 nm, 70 nm to 150 nm, 70 nm to 120 nm, 70 nm to 100 nm, 70 nm to 90 nm, 80 nm to 200 nm, 80 to 180 nm, 80 nm to 170 nm, 80 nm to 150 nm, 80 nm to 120 nm, 80 nm to 100 nm, 80 nm to 90 nm, 90 nm to 200 nm, 90 to 180 nm, 90 nm to 170 nm, 90 nm to 150 nm, 90 nm to 120 nm, or 90 nm to 100 nm for easy introduction into liver tissue, hepatocytes and/or LSEC (liver sinusoidal endothelial cells). The LNP may be sized for easy introduction into organs or tissues, including but not limited to liver, lung, heart, spleen, as well as to tumors. When the size of the LNP is smaller than the above range, it can be difficult to maintain stability as the surface area of the LNP is excessively increased, and thus delivery to the target tissue and/or drug effect may be reduced. The LNP may specifically target liver tissue. Without wishing to be bound by theory, it is thought that one mechanism by which LNP may be used to deliver therapeutic agents is through the imitation of the metabolic behaviors of natural lipoproteins, and so LNP may be usefully delivered to a subject through the lipid metabolism processes carried out by the liver. During the delivery of therapeutic agents to hepatocytes or and/or LSEC (liver sinusoidal endothelial cells), the diameter of the fenestrae leading from the sinusoidal lumen to the hepatocytes and LSEC is about 140 nm in mammals and about 100 nm in humans, so the LNP composition for therapeutic agent delivery having LNPs with a diameter in the above ranges may have excellent delivery efficiency to hepatocytes and LSEC when compared to LNP having the diameter outside the above range.
According to one example, the LNPs of the LNP composition may comprise the ionizable cationic lipid:phospholipid:cholesterol:lipid-PEG conjugate in the range described above or at a molar ratio of 20 to 50:10 to 30:30 to 60:0.5 to 5, at a molar ratio of 25 to 45:10 to 25:40 to 50:0.5 to 3, at a molar ratio of 25 to 45:10 to 20:40 to 55:0.5 to 3, or at a molar ratio of 25 to 45:10 to 20:40 to 55:1.0 to 1.5. The LNP comprising components at a molar ratio in the above range may have excellent delivery efficiency of therapeutic agents specific to cells of target organs.
In certain aspects, the LNP exhibit a positive charge under the acidic pH condition by showing a pKa of 5 to 8, 5.5 to 7.5, 6 to 7, or 6.5 to 7, and may encapsulate a nucleic acid with high efficiency by easily forming a complex with a nucleic acid through electrostatic interaction with a therapeutic agent such as a nucleic acid showing a negative charge. In such cases, the LNP may be usefully used as a composition for intracellular or in vivo delivery of a therapeutic agent (for example, nucleic acid).
Herein, “encapsulate” or “encapsulation” refers to incorporation of a therapeutic agent efficiently inside a lipid envelope, i.e., by surrounding it by the particle surface and/or embedding it within the particle interior made of various lipids that self-assemble when the polarity of the solvent surrounding them is increased. The encapsulation efficiency means the content of the therapeutic agent encapsulated in the LNP relative the total therapeutic agent content measured per given volume of the LNP formulation measured post-disruption of the LNPs.
The encapsulation of the nucleic acids of the composition in the LNP may be 70% or more, 75% or more, 80% or more, 85% or more, 90% or more, 91% or more, 92% or more, 94% or more, or 95% or more of LNP in the composition encapsulate nucleic acids. In some embodiments, the encapsulation of the nucleic acids of the composition in the LNP is such that between 80% to 99%, between 80% to 97%, between 80% to 95%, between 85% to 95%, between 87% to 95%, between 90% to 95%, between 91% or more to 95% or less, 91% or more to 94% or less, over 91% to 95% or less, 92% to 99%, between 92% to 97%, or between 92% to 95% of the LNP in the composition encapsulate nucleic acids. In some embodiments, the mRNA encoding the repressor fusion protein and/or a gRNA of any of the embodiments of the disclosure are fully encapsulated in the LNP.
The target organs to which a nucleic acid is delivered by the LNP include, but are not limited to the liver, lung, heart, spleen, as well as to tumors. The LNP according to one example is liver tissue-specific and has excellent biocompatibility and can deliver the nucleic acids of a composition with high efficiency, and thus it can be usefully used in related technical fields such as lipid nanoparticle-mediated gene therapy. In a particular embodiment, the target cell to which the nucleic acids are delivered by the LNP according to one example may be a hepatocyte and/or LSEC in vivo. In other embodiments, the disclosure provides LNP formulated for delivery of the nucleic acids of the embodiments to cells ex vivo.
The disclosure provides a pharmaceutical composition comprising a plurality of LNPs comprising nucleic acids, such as mRNA encoding repressor fusion protein and/or a gRNA variant described herein, and a pharmaceutically acceptable carrier.
In certain embodiments, the LNP comprising the nucleic acid(s) has an electron dense core.
The disclosure provides LNP comprising one or more nucleic acids comprising: (a) an mRNA encoding the repressor fusion protein, and/or a gRNA variant described herein; (b) one or more cationic lipids or ionizable cationic lipids or salts thereof comprising from about 20 mol % to about 60 mol % of the total lipid present in the LNP; (c) one or more non-cationic lipids comprising from about 13 mol % to about 49.5 mol % of the total lipid present in the LNP; and (d) one or more conjugated lipids that inhibit aggregation of LNPs comprising from about 0.5 mol % to about 2 mol % of the total lipid present in the particle. In another embodiment, the disclosure provides LNP comprising one or more nucleic acids comprising: (a) an mRNA encoding the repressor fusion protein, and/or a gRNA variant described herein; (b) one or more cationic lipids or ionizable cationic lipids or salts thereof comprising from about 22 mol % to about 85 mol % of the total lipid present in the LNP; (c) one or more non-cationic/phospholipids comprising from about 10 mol % to about 70 mol % of the total lipid present in the LNP; (d) 15 mol % to about 50 mol % sterol, and (d) 1 mol % to about 5 mol % lipid-PEG or lipid-PEG-peptide in the particle. In certain embodiments the repressor fusion protein mRNA and gRNA may be present in the same nucleic acid-lipid particle, or they may be present in different nucleic acid-lipid particles.
The disclosure provides LNP comprising one or more nucleic acids comprising: (a) an mRNA encoding the repressor fusion proteins described herein; (b) a cationic lipid or a salt thereof comprising from about 52 mol % to about 62 mol % of the total lipid present in the LNP; (c) a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 36 mol % to about 47 mol % of the total lipid present in the LNP; and (d) a PEG-lipid conjugate comprising from about 1 mol % to about 2 mol % of the total lipid present in the LNP. In particular embodiments, the formulation is a four-component system comprising about 1.4 mol % PEG-lipid conjugate (e.g., PEG2000-C-DMA), about 57.1 mol % cationic lipid (e.g., DLin-K-C2-DMA) or a salt thereof, about 7.1 mol % DPPC (or DSPC), and about 34.3 mol % cholesterol (or derivative thereof).
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion proteins and/or a gRNA of any of the embodiments described herein; (b) a cationic lipid or a salt thereof comprising from about 46.5 mol % to about 66.5 mol % of the total lipid present in the LNP; (c) cholesterol or a derivative thereof comprising from about 31.5 mol % to about 42.5 mol % of the total lipid present in the LNP; and (d) a PEG-lipid conjugate comprising from about 1 mol % to about 2 mol % of the total lipid present in the LNP. In particular embodiments, the formulation is a three-component system which is phospholipid-free and comprises about 1.5 mol % PEG-lipid conjugate (e.g., PEG2000-C-DMA), about 61.5 mol % cationic lipid (e.g., DLin-K-C2-DMA) or a salt thereof, and about 36.9 mol % cholesterol (or derivative thereof).
Additional formulations are described in PCT Publication No. WO 09/127060 and US patent publication numbers US 2011/0071208 A1 and US 2011/0076335 A1, the disclosures of which are herein incorporated by reference in their entirety.
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion protein and a gRNA of any of the embodiments described herein; (b) one or more cationic lipid or ionizable cationic lipids or salts thereof comprising from about 2 mol % to about 50 mol % of the total lipid present in the LNP; (c) one or more non-cationic lipid or ionizable cationic lipids comprising from about 5 mol % to about 90 mol % of the total lipid present in the LNP; and (d) one or more conjugated lipids that inhibit aggregation of particles comprising from about 0.5 mol % to about 20 mol % of the total lipid present in the LNP.
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion protein and a gRNA of any of the embodiments described herein; (b) a cationic lipid or a salt thereof comprising from about 30 mol % to about 50 mol % of the total lipid present in the LNP; (c) a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 47 mol % to about 69 mol % of the total lipid present in the LNP; and (d) a PEG-lipid conjugate comprising from about 1 mol % to about 3 mol % of the total lipid present in the LNP. In particular embodiments, the formulation is a four-component system which comprises about 2 mol % PEG-lipid conjugate (e.g., PEG2000-C-DMA), about 40 mol % cationic lipid (e.g., DLin-K-C2-DMA) or a salt thereof, about 10 mol % DPPC (or DSPC), and about 48 mol % cholesterol (or derivative thereof).
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion protein and a gRNA of any of the embodiments described herein; (b) one or more cationic lipid or ionizable cationic lipids or salts thereof comprising from about 50 mol % to about 65 mol % of the total lipid present in the LNP; (c) one or more non-cationic lipid or ionizable cationic lipids comprising from about 25 mol % to about 45 mol % of the total lipid present in the LNP; and (d) one or more conjugated lipids that inhibit aggregation of particles comprising from about 5 mol % to about 10 mol % of the total lipid present in the LNP.
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion protein and a gRNA of any of the embodiments described herein; (b) a cationic lipid or a salt thereof comprising from about 50 mol % to about 60 mol % of the total lipid present in the LNP; (c) a mixture of a phospholipid and cholesterol or a derivative thereof comprising from about 35 mol % to about 45 mol % of the total lipid present in the LNP; and (d) a PEG-lipid conjugate comprising from about 5 mol % to about 10 mol % of the total lipid present in the LNP.
In certain embodiments, the non-cationic lipid mixture in the formulation comprises: (i) a phospholipid of from about 10 mol % to about 70 mol % of the total lipid present in the LNP; (ii) cholesterol or a derivative thereof of from about 15 mol % to about 50 mol % of the total lipid present in the LNP; and 1-5% lipid-PEG or lipid-PEG-peptide. In particular embodiments, the formulation is a four-component system which comprises about 7 mol % PEG-lipid conjugate (e.g., PEG750-C-DMA), about 54 mol % cationic lipid (e.g., DLin-K-C2-DMA) or a salt thereof, about 7 mol % DPPC (or DSPC), and about 32 mol % cholesterol (or derivative thereof).
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion protein and/or a gRNA of any of the embodiments described herein; (b) a cationic lipid or a salt thereof comprising from about 55 mol % to about 65 mol % of the total lipid present in the LNP; (c) cholesterol or a derivative thereof comprising from about 30 mol % to about 40 mol % of the total lipid present in the LNP; and (d) a PEG-lipid conjugate comprising from about 5 mol % to about 10 mol % of the total lipid present in the LNP. In particular embodiments, the formulation is a three-component system which is phospholipid-free and comprises about 7 mol % PEG-lipid conjugate (e.g., PEG750-C-DMA), about 58 mol % cationic lipid (e.g., DLin-K-C2-DMA) or a salt thereof, and about 35 mol % cholesterol (or derivative thereof).
In other embodiments, the LNP comprising one or more nucleic acids comprises: (a) an mRNA encoding the repressor fusion protein and/or a gRNA of any of the embodiments described herein; (b) a cationic lipid or a salt thereof comprising from about 48 mol % to about 62 mol % of the total lipid present in the LNP; (c) a mixture of a phospholipid and cholesterol or a derivative thereof, wherein the phospholipid comprises about 7 mol % to about 17 mol % of the total lipid present in the LNP, and wherein the cholesterol or derivative thereof comprises about 25 mol % to about 40 mol % of the total lipid present in the LNP; and (d) a PEG-lipid conjugate comprising from about 0.5 mol % to about 3.0 mol % of the total lipid present in the LNP.
VIII. Systems and Methods for Repression of PCSK9 Target Nucleic Acids
In another aspect, the present disclosure provides systems comprising a repressor fusion protein comprising a catalytically dead CRISPR protein, and one or more gRNAs (repressor fusion protein:gRNA system), for use in repressing a target nucleic acid of a PCSK9 gene in a population of cells. The systems provided herein are useful for various applications, including as therapeutics, diagnostics, and for research. To effect the methods of the disclosure, resulting in repression or silencing of the PCSK9 gene, provided herein are programmable repressor fusion protein:gRNA systems. The programmable nature of the systems provided herein allows for the precise targeting to achieve the desired effect at one or more regions of predetermined interest in the PCSK9 gene target nucleic acid. In some embodiments, it may be desirable to reduce or eliminate expression of the PCSK9 protein in a subject comprising mutations, for example dominant mutations leading to hypercholesterolemia or familial or autosomal dominant hypercholesterolemia. In some embodiments, it may be desirable to reduce or eliminate expression of the PCSK9 protein in a subject with elevated cholesterol levels that is not the result of mutations in the PCSK9 gene.
In some embodiments, the disclosure provides systems specifically designed for use in the methods to repress or silence transcription the target nucleic acid of a PCSK9 gene in eukaryotic cells; either in vitro, ex vivo, or in vivo in a subject. Generally, any portion of the gene can be targeted using the programmable systems and methods provided herein. In one embodiment, the disclosure provides for a method of repressing a target nucleic acid sequence of a PCSK9 gene in a population of cells, the method comprising introducing into each cell of the population: i) a repressor fusion protein:gRNA system comprising a repressor fusion protein and a gRNA of any of the embodiments described herein; ii) a nucleic acid encoding the repressor fusion protein and gRNA of any of the embodiments described herein; iii) a vector selected from the group consisting of a retroviral vector, a lentiviral vector, an adenoviral vector, an adeno-associated viral (AAV) vector, and a herpes simplex virus (HSV) vector, and comprising the nucleic acid of (iv), above; v) an LNP or a synthetic nanoparticle comprising a gRNA and a mRNA encoding the repressor fusion protein; or vi) combinations of two or more of (i) to (v), wherein transcription of the target nucleic acid sequence of the cells targeted by the gRNA is repressed by the repressor fusion protein. In some embodiments of the method, contacting cells with a repressor fusion protein:gRNA system of the embodiments results in repression of the PCSK9 target nucleic acid of at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, or at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60% or more of the cells of the population. In some embodiments of the method, the PCSK9 gene in the cells of the population is repressed or silenced such that expression of the PCSK9 protein is decreased by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% in comparison to a cell where the PCSK9 gene has not been targeted. In some embodiments, repression of transcription of the PCSK9 gene of the cells of the population is sustained for at least about 8 hours, at least about 1 day, at least about 7 days, at least 2 weeks, at least about 3 weeks, at least about 1 month, or at least about 2 months, when assayed in an in vitro assay. In some embodiments, repression of transcription of the PCSK9 gene of the cells of the population is heritable, wherein the repression of the PCKS9 gene persists for at least 1, 2, 3, 4, 5, or 6 or more cell divisions.
In some embodiments of the method, the repression of the cell occurs in vitro. In some embodiments of the method, the repression of the cell occurs ex vivo. In some embodiments, repression occurs in vitro inside of the cell prior to introducing the cell into a subject. In some embodiments, the cell is autologous or allogeneic with respect to the subject. In some embodiments of the method, the repression of the cell occurs in vivo in a subject administered a repressor fusion protein of any of the embodiments disclosed herein. In some embodiments of the method, the cell is a eukaryotic cell. In some embodiments of the method, the eukaryotic cell is selected from the group consisting of a rodent cell, a mouse cell, a rat cell, a primate cell, and a non-human primate cell. In some embodiments of the method, the eukaryotic cell is a human cell. In some embodiments of the method, the cell is an embryonic stem cell, an induced pluripotent stem cell, a germ cell, a fibroblast, an oligodendrocyte, a glial cell, a hematopoietic stem cell, a neuron progenitor cell, a neuron, an astrocyte, a muscle cell, a bone cell, a hepatocyte, a pancreatic cell, a retinal cell, a cancer cell, a T-cell, a B-cell, an NK cell, a fetal cardiomyocyte, a myofibroblast, a mesenchymal stem cell, an autotransplanted expanded cardiomyocyte, an adipocyte, a totipotent cell, a pluripotent cell, a blood stem cell, a myoblast, a bone marrow cell, a mesenchymal cell, a parenchymal cell, an epithelial cell, an endothelial cell, a mesothelial cell, fibroblasts, osteoblasts, chondrocytes, a hematopoietic stem cell, a bone-marrow derived progenitor cell, a myocardial cell, a skeletal cell, a fetal cell, an undifferentiated cell, a multi-potent progenitor cell, a unipotent progenitor cell, a monocyte, a cardiac myoblast, a skeletal myoblast, a macrophage, a capillary endothelial cell, a xenogeneic cell, an allogenic cell, or a post-natal stem cell.
In some embodiments, the disclosure provides a method for reversing the repression of the PCSK9 gene in a population of cells resulting from the repressor fusion protein:gRNA systems. In some embodiments, the repression is reversible by introducing into cells of the population an inhibitor of DNMT. In some embodiments of the method, the repression is reversible by use of a cytidine analog inhibitor of DNMT. In some embodiments, the repression is reversible by use of an inhibitor selected from the group consisting of azacytidine, decitabine, clofarabine, and zebularine. In some embodiments, the repression is reversible by use of an inhibitor at a concentration of 0.1 μM to 40 μM, or any intermediate concentration. In some embodiments, the method comprises administrations of a therapeutically effective dose of the inhibitor of DNMT to a subject treated with a system of the disclosure, thereby reversing the repression of PCSK9 by the system.
In some embodiments, the repressor fusion protein:gRNA systems comprise a repressor fusion protein comprising a sequence of SEQ ID NOS: 3131-3132 as set forth in Table 20, or a sequence at least 60% identical, at least 70% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, or at least 99.5% identical thereto, a gRNA scaffold comprising a sequence of SEQ ID NOS: 1744-1746 or 2947-2976, or a sequence at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical thereto, and the gRNA comprises a targeting sequence of SEQ ID NOS: 1824-2944 or a sequence at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical thereto and having between 15 and 20 amino acids. In some embodiments of the system, the gRNA comprises a targeting sequence of SEQ ID NOS: 1824-2944, as set forth in Table 7. In a particular embodiment, the repressor fusion protein of the system comprises a sequence selected from the group consisting of SEQ ID NOS: 3131-3132, the gRNA scaffold comprises a sequence selected from the group consisting of SEQ ID NOS: 1744-1746 and 2947-2976, and the targeting sequence of the gRNA of the repressor fusion protein:gRNA system is selected from the group consisting of the sequence of SEQ ID NOS: 1824-2545. In a particular embodiment, the repressor fusion protein comprises a sequence selected from the group consisting of the sequences of SEQ ID NOS: 3131-3132, the gRNA scaffold comprises a sequence selected from the group consisting of SEQ ID NOS: 1744-1746 and 2947-2976, and the targeting sequence of the gRNA is selected from the group consisting of the sequence of SEQ ID NOS: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714 as set forth in Table 8. In a particular embodiment, wherein the systems are formulated in LNP, the repressor fusion protein comprises a sequence selected from the group consisting of SEQ ID NOS: 3131-3132, and is encoded by an mRNA, the gRNA scaffold comprises a sequence of SEQ ID NO: 1746, and the targeting sequence of the gRNA is selected from the group consisting of SEQ ID NOS: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714.
In some embodiments, the systems comprise an mRNA comprising one or more sequences selected from the group consisting of SEQ ID NOS: 3105, 3109, and 3115-3128, or sequences at least 60% identical, at least 70% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, or at least 99.5% identical thereto. In some embodiments, the systems comprise an mRNA comprising one or more sequences selected from the group consisting of SEQ ID NOS: 3105, 3109, and 3115-3128. In a particular embodiment, the systems are formulated in LNP that encapsulate the mRNA sequence comprising one or more sequences selected from the group consisting of SEQ ID NOS: 3105, 3109, and 3115-3128, a gRNA selected from the group consisting of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976, and the targeting sequence of the gRNA is selected from the group consisting of the sequence of SEQ ID NOS: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714. In some embodiments, the mRNA comprises a sequence wherein at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 99%, or 100% of uridine nucleosides of the sequence are replaced with N1-methylpseudouridine. In some embodiments, the mRNA further comprises a 5′ untranslated region (UTR) and a 3′ untranslated region (UTR).
In one embodiment of the method, the system is introduced into the cells using LNP comprising mRNA encoding the repressor fusion protein and gRNA variant of any of the embodiments disclosed herein. In some embodiments, the LNP comprises an mRNA encoding the repressor fusion protein comprising one or more sequences selected from the group consisting of SEQ ID NOS: 3105, 3109, and 3115-3128, or a sequence having at least about 70%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or having at least about 99% sequence identity thereto. In some embodiments of the foregoing, the LNP comprises a gRNA variant of the disclosure having a targeting sequence complementary to the PCSK9 target nucleic acid. In some embodiments, the LNP comprises an mRNA encoding an repressor fusion protein, wherein the mRNA comprises a sequence selected from SEQ ID NOS: 3129-3130. In some embodiments, the LNP comprises gRNA variant scaffold 174 (SEQ ID NO: 1744). In some embodiments, the LNP comprises gRNA variant scaffold 235 (SEQ ID NO: 1745). In some embodiments, the LNP comprises gRNA variant scaffold 316 (SEQ ID NO: 1746). In some embodiments, the LNP comprises gRNA variant scaffold 316 with chemical modifications, including modifications set forth in the sequences of SEQ ID NOS: 2968-2976, or a sequence having at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto. In a particular embodiment, the LNP comprises an mRNA encoding a repressor fusion protein comprising the dCasX 491 (SEQ ID NO: 4) and gRNA variant 316 with chemical modifications selected from the group consisting of SEQ ID NOS: 2968-2976, or a sequence having at least about 70%, at least about 80%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% sequence identity thereto, with a linked targeting sequence selected from the group consisting of the sequences of SEQ ID NOS: 1824-2944 that are chemically modified. In a particular embodiment, the LNP comprises an mRNA encoding a repressor fusion protein comprising the dCasX 491 (SEQ ID NO: 4) and gRNA variant scaffold 316 with chemical modifications comprising the sequence of SEQ ID NO: 2968, with a linked targeting sequence selected from the group consisting of the sequences of SEQ ID NOS: 1824-2944 that are chemically modified. In some embodiments of the method, the cells to be modified are selected from the group consisting of rodent cells, mouse cells, rat cells, and non-human primate cells. In other embodiments of the method, the cells to be modified are human cells. In some embodiments of the method, the transcriptional repression of the population of cells occurs in vivo in a subject, wherein the subject is selected from the group consisting of a rodent, a mouse, a rat, a non-human primate, and a human. In some embodiments of the methods, the modified cell is a hepatocyte, or a cell of the intestine, the kidney, the central nervous system, a smooth muscle cell, macrophage or a cell of arterial walls such as the endothelium.
The LNP can be administered by a route of administration selected from the group consisting of intravenous, intraarterial, intraportal vein injection, intraperitoneal, intramuscular, intracerebroventricular, intracisternal, intrathecal, intracranial, intralumbar, intraocular, subcutaneous, and oral routes.
In some embodiments of the method of repression of a PCSK9 gene, the gene repressor systems of the present disclosure can be designed to target any region of, or proximal to, a PCSK9 gene or region of a PCSK9 gene for which repression of transcription is sought. When the entirety of the gene is to be repressed, designing a guide with a targeting sequence complementary to a sequence encompassing or proximal to the transcription start site (TSS) is contemplated by the disclosure. The TSS selection occurs at different positions within the promoter region, depending on promoter sequence and initiating-substrate concentration. The core promoter serves as a binding platform for the transcription machinery, which comprises Pol II and its associated general transcription factors (GTFs) (Haberle, V. et al. Eukaryotic core promoters and the functional basis of transcription initiation (Nat Rev Mol Cell Biol. 19(10):621 (2018)). Variability in TSS selection has been proposed to involve DNA ‘scrunching’ and ‘anti-scrunching,’ the hallmarks of which are: (i) forward and reverse movement of the RNA polymerase leading edge, but not trailing edge, relative to DNA, and (ii) expansion and contraction of the transcription bubble. In some embodiments, the target nucleic acid sequence bound by an RNP of the repressor fusion protein:gRNA system is within 1 kb of a transcription start site (TSS) of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 20 bp, 50 bp, 100 bp, 150 bp, 200 bp, 250 bp, 500 bps, or 1 kb upstream of a TSS of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 20 bp, 50 bp, 100 bp, 150 bp, 200 bp, 250 bp, 500 bps or 1 kb downstream of a TSS of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 500 bps upstream to 500 bps downstream, or 300 bps upstream to 300 bps downstream of a TSS of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by an RNP of the system is within 20 bp, 50 bp, 100 bp, 150 bp, 200 bp, 250 bp, 500 bps, or 1 kb of an enhancer of the PCSK9 gene. In some embodiments, the target nucleic acid sequence bound by a repressor fusion protein:gRNA RNP is within 1 kb 3′ to a 5′ untranslated region of the PCSK9 gene. In other embodiments, the target nucleic acid sequence bound by an RNP of the system is within the open reading frame of the PCSK9 gene, inclusive of introns (if any). In some embodiments, the targeting sequence of a gRNA of the system is designed to be specific for an exon of the PCSK9 gene. In a particular embodiment, the targeting sequence of a gRNA of the system is designed to be specific for exon 1 of the PCSK9 gene. In other embodiments, the targeting sequence of a gRNA of the system is designed to be specific for an intron of the PCSK9 gene. In other embodiments, the targeting sequence of the gRNA of the system is designed to be specific for an intron-exon junction of the PCSK9 gene. In other embodiments, the targeting sequence of the gRNA of the system is designed to be specific for a regulatory element of the PCSK9 gene. In other embodiments, the targeting sequence of the gRNA of the system is designed to be complementary to a sequence of an intergenic region of the PCSK9 gene. In other embodiments, the targeting sequence of a gRNA of the system is specific for a junction of the exon, an intron, and/or a regulatory element of the PCSK9 gene. In those cases where the targeting sequence is specific for a regulatory element, such regulatory elements include, but are not limited to promoter regions, enhancer regions, intergenic regions, 5′ untranslated regions (5′ UTR), 3′ untranslated regions (3′ UTR), conserved elements, and regions comprising cis-regulatory elements. In some embodiments, the targeting sequence of a gRNA of the system is complementary to the gene target nucleic acid sequence within 1 kb of an enhancer of the PCSK9 gene. In some embodiments, the targeting sequence of a gRNA of the system is complementary to the gene target nucleic acid sequence within the 3′ untranslated region of the PCSK9 gene. The promoter region is intended to encompass nucleotides within 5 kb of the initiation point of the encoding sequence or, in the case of gene enhancer elements or conserved elements, can be thousands of bp, hundreds of thousands of bp, or even millions of bp away from the encoding sequence of the PCSK9 gene. In the foregoing, the targets are those in which the encoding PCSK9 gene is intended to be repressed and/or epigenetically modified such that the PCSK9 gene product is not expressed or is expressed at a lower level in a cell. In some embodiments, upon binding of the RNP of the system to the binding location of the target nucleic acid, the system is capable of repressing transcription of the PCSK9 gene 5′ to the binding location of the RNP. In other embodiments, upon binding of the RNP of the system to the binding location of the target nucleic acid, the system is capable of repressing transcription of the PCSK9 gene 3′ to the binding location of the RNP.
The systems and methods described herein can be used in a variety of cells associated with disease, e.g., cells of the liver, the intestine, the kidney, the central nervous system, smooth muscle cells, macrophages or cells of arterial walls, in which the PCSK9 gene is to be repressed or silenced. This approach, therefore, could be used for applications in a subject with a PCSK9-related disorder such as, but not limited to autosomal dominant hypercholesterolemia (ADH), hypercholesterolemia, elevated total cholesterol levels, hyperlipidemia, elevated low-density lipoprotein (LDL) levels, elevated LDL-cholesterol levels, reduced high-density lipoprotein levels, liver steatosis, coronary heart disease, ischemia, stroke, peripheral vascular disease, thrombosis, type 2 diabetes, high elevated blood pressure, atherosclerosis, obesity, Alzheimer's disease, neurodegeneration, age-related macular degeneration (AMD), or a combination thereof.
IX. Therapeutic Methods
The present disclosure provides methods of treating a PCSK9-related disease or disorder in a subject in need thereof, including but not limited to autosomal dominant hypercholesterolemia (ADH), hypercholesterolemia, elevated total cholesterol levels, elevated low-density lipoprotein (LDL) levels, reduced high-density lipoprotein levels, liver steatosis, atherosclerotic cardiovascular disease, and coronary artery disease, ischemia, stroke, peripheral vascular disease, thrombosis, type 2 diabetes, high elevated blood pressure, obesity, Alzheimer's disease, neurodegeneration, age-related macular degeneration (AMD), or a combination thereof. In some embodiments, the methods of the disclosure can prevent, treat and/or ameliorate a PCSK9-related disease or disorder of a subject by the administering to the subject of a composition of the disclosure. In some embodiments, the PCSK9-related disease is autosomal dominant hypercholesterolemia (ADH), hypercholesterolemia, elevated total cholesterol levels, hyperlipidemia, elevated low-density lipoprotein (LDL) levels, elevated LDL-cholesterol levels, reduced high-density lipoprotein levels, liver steatosis, coronary heart disease, ischemia, stroke, peripheral vascular disease, thrombosis, type 2 diabetes, high elevated blood pressure, atherosclerosis, obesity, aortic stenosis, elevated PCSK9 levels, or a combination thereof. In some embodiments, the composition administered to the subject further comprises pharmaceutically acceptable carrier, diluent or excipient.
In some cases, the PCSK9 gene of the subject to be treated by the methods of the disclosure is wild-type, but the subject nevertheless has hypercholesterolemia, elevated total cholesterol levels, hyperlipidemia, elevated low-density lipoprotein (LDL) levels, elevated LDL-cholesterol levels, reduced high-density lipoprotein levels, liver steatosis, coronary heart disease, ischemia, stroke, peripheral vascular disease, thrombosis, type 2 diabetes, high elevated blood pressure, atherosclerosis, obesity, aortic stenosis, elevated PCSK9 levels, or a combination thereof. In such cases, the methods of the disclosure can prevent, treat and/or ameliorate a PCSK9-related disease or disorder of a subject by the administering to the subject of a composition of the disclosure.
In some cases, one or both alleles of the PCSK9 gene of the subject comprises a mutation. In some cases, the PCSK9-related disease or disorder mutation is a gain of function mutation, including, but not limited to mutations encoding amino acid substitutions selected from the group consisting of S127R, D129G, F216L, D374H, and D374Y relative to the sequence of SEQ ID NO: 1823. In other cases, the PCSK9-related disorder mutation is a loss of function mutation including, but not limited to mutations encoding amino acid substitutions selected from the group consisting of R46L, G106R, Y142X, N157K, R237W and C679X relative to the sequence of SEQ ID NO: 1823.
In some embodiments, the disclosure provides methods of treating a PCSK9 or related disease or disorder in a subject in need thereof comprising repressing or silencing a PCSK9 gene in a cell of the subject, the method comprising contacting said cells with a therapeutically effective dose of: i) a repressor fusion protein:gRNA system comprising a repressor fusion protein and a gRNA; ii) a nucleic acid encoding the repressor fusion protein and gRNA of any of the embodiments described herein; iii) an LNP or a synthetic nanoparticle comprising a gRNA and a mRNA encoding the repressor fusion protein of any one of the embodiments described herein; or iv) combinations of two or more of (i) to (iii), wherein the target nucleic acid sequence of the cells targeted by the gRNA is repressed or silenced by the repressor fusion protein. In some embodiments of the method, contacting cells with a repressor fusion protein:gRNA system results in repression of the PCSK9 target nucleic acid of at least about 1%, at least about 2%, at least about 3%, at least about 4%, at least about 5%, at least about 6%, at least about 7%, at least about 8%, at least about 9%, or at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60% or more of the cells of the targeted organ. In some embodiments of the method, the PCSK9 gene in the cells of the targeted organ are repressed such that expression of the PCSK9 protein is decreased by at least about 10%, at least about 20%, at least about 30%, at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90% in comparison to an untreated cell. In some embodiments of the method, contacting cells of the targeted organ with a repressor fusion protein:gRNA system results in heritable repression of the PCSK9 target nucleic acid in the cells. The cell of the treated subject can be a eukaryotic cell selected from the group consisting of a rodent cell, a mouse cell, a rat cell, a primate cell, and a non-human primate cell. In some embodiments, the eukaryotic cell of the treated subject is a human cell. In some embodiments, the cell is a cell involved in the production of LDL, including but not limited to a hepatocyte, or a cell of the intestine, the kidney, the central nervous system, a smooth muscle cell, macrophage, a retinal cell, or cell of arterial walls such as the endothelium. In some embodiments, the cell is an eye cell. In some embodiments of the methods of treating a PCSK9-related disorder in a subject, the subject is selected from the group consisting of mouse, rat, pig, non-human primate, and human.
A number of therapeutic strategies have been used to design the systems for use in the methods of treatment of a subject with a PCSK9-related disease or disorder. In some embodiments, the disclosure provides a method of treatment of a subject having a PCSK9-related disease or disorder, the method comprising administering to the subject a repressor fusion protein:gRNA composition according to a treatment regimen comprising one or more consecutive doses using a therapeutically effective dose. In some embodiments of the treatment regimen, the therapeutically effective dose of the composition is administered as a single dose. In other embodiments of the treatment regimen, the therapeutically effective dose is administered to the subject as two or more doses over a period of at least two weeks, or at least one month, or at least two months, or at least three months, or at least four months, or at least five months, or at least six months. In some embodiments of the treatment regiment, the effective doses are administered by a route selected from the group consisting of intravenous, intraportal vein injection, intraperitoneal, intramuscular, subcutaneous, intraocular, and oral routes.
In some embodiments, the disclosure provides systems of a repressor fusion protein and gRNA of any of the embodiments described herein for use in a method of treatment of a PCSK9-related disease or disorder, wherein a therapeutically effective dose of the composition is administered to a subject. In some embodiments, the composition comprises a repressor fusion protein of SEQ ID NOS: 3131-3132 as set forth in Table 20, or a sequence at least 60% identical, at least 70% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, or at least 99.5% identical thereto, the gRNA scaffold comprises a sequence selected from the group consisting of SEQ ID NOS: 1744-1746, as set forth in Table 9, and SEQ ID NOS: 2947-2976, or a sequence at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 81% identical, at least 82% identical, at least 83% identical, at least 84% identical, at least 85% identical, at least 86% identical, at least 86% identical, at least 87% identical, at least 88% identical, at least 89% identical, at least 89% identical, at least 90% identical, at least 91% identical, at least 92% identical, at least 93% identical, at least 94% identical, at least 95% identical, at least 96% identical, at least 97% identical, at least 98% identical, at least 99% identical, at least 99.5% identical thereto, and the gRNA comprises a targeting sequence a sequence selected from the group consisting of SEQ ID NOS: 1824-2944 or a sequence at least 65% identical, at least 70% identical, at least 75% identical, at least 80% identical, at least 85% identical, at least 90% identical, or at least 95% identical thereto and having between 15 and 20 amino acids. In some embodiments, the gRNA comprises a targeting sequence selected from the group consisting of SEQ ID NOS: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714, or a sequence having at least about 65%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, or at least about 95% identity thereto.
In some embodiments, the composition is administered in an LNP formulation. In some embodiments, the disclosure provides repressor fusion proteins and gRNA compositions for use in the manufacture of a medicament for use in the treatment of a PCSK9-related disease or disorder in a subject wherein repression of a PCSK9 leads to the amelioration of the disease or prevention of symptoms or clinical findings associated with the disease or disorder.
In some embodiments, the administering to a subject with a PCSK9-related disease or disorder of the therapeutically effective amount of the repressor fusion protein:gRNA modality, to repress or silence expression of PCSK9, leads to the prevention or amelioration of the underlying PCSK9-related disorder or disorder such that an improvement is observed in the subject, notwithstanding that the subject may still be afflicted with the underlying disorder. In some embodiments, the repressor fusion protein:gRNA modality comprises LNP comprising a gRNA and an mRNA encoding a repressor fusion protein and a guide ribonucleic acid disclosed herein. In some embodiments, the administration of the therapeutically effective amount of the repressor fusion protein:gRNA modality leads to an improvement in at least one clinically-relevant endpoint including, but not limited to percent change from baseline in LDL-cholesterol, decrease in plaque atheroma volume, reduction in in coronary plaque, reduction in atherosclerotic cardiovascular disease (ASCVD), cardiovascular death, nonfatal myocardial infarction, ischemic stroke, nonfatal stroke, coronary revascularization, unstable angina, or visual acuity. In some embodiments, the administration of the therapeutically effective amount of the repressor fusion protein:gRNA modality leads to an improvement in at least two clinically-relevant endpoints. In some embodiments, the subject is selected from mouse, rat, pig, dog, non-human primate, and human. In some embodiments, the subject is human.
In some embodiments, the methods of treatment further comprise administering a chemotherapeutic agent wherein the agent is effective in lowering LDL levels. Such agents include, but are not limited to, statins, niacin, fibrates, or anti-PCSK9 antibody drugs.
Methods of obtaining samples from treated subjects for analysis to determine the effectiveness of the treatment, such as body fluids or tissues, and methods of preparation of the samples to allow for analysis are well known to those skilled in the art. Methods for analysis of RNA and protein levels are discussed above and are well known to those skilled in the art. The effects of treatment can also be assessed by measuring biomarkers associated with the PCSK9 gene expression in the aforementioned fluids, tissues or organs, collected from an animal contacted with one or more compounds of the disclosure, by routine clinical methods known in the art. Biomarkers of PCSK9 disorders include, but are not limited to, PCSK9 levels, low-density lipoprotein (LDL-cholesterol), apolipoprotein B, non-HDL cholesterol, triglycerides and lipoprotein a, soluble CD40 ligand, osteopontin (OPN), osteoprotegerin (OPG), matrix metalloproteinases (MMP) and myeloperoxidase (MPOP), wherein the concentration of the marker is compared to concentrations known to be physiologically normal or in subjects not having a PCSK9 disorder.
Several mouse models expressing mutant forms of PCSK9 exist and are suitable for evaluating the methods of treatment. Transgenic mouse models of PCSK9-related disorders include knock-in mouse models having hPCSK9 (Carreras, A. In vivo genome and base editing of a human PCSK9 knock-in hypercholesterolemic mouse model. MC Biology 17:4 (2019); Herbert B., et al. Increased secretion of lipoproteins in transgenic mice expressing human D374Y PCSK9 under physiological genetic control. Arterioscler Thromb Vasc Biol. 30(7):1333 (2010)).
In some embodiments, the method of treating a PCSK9-related disease or disorder in a subject comprises pretreating the subject with a therapeutic agent that increases hepatic LDL receptor (LDLR) expression. In some embodiments, the therapeutic agent is a PCSK9 inhibitor, such as a monoclonal antibody, nucleic acid-based agent, or a small molecule. Exemplary therapeutic agents include, but are not limited to, evolocumab, inclisiran, alirocumab, and MK-0616. Without wishing to be bound by theory or mechanism, it is believed that the pretreatment with an inhibitor of PCSK9, may lead to an increase in hepatic LDL receptor (LDLR) expression that, in turn, may facilitate the uptake of the LNP comprising the CasX:gRNA composition that is subsequently administered to the subject. By increasing the hepatic cell uptake of the LNP, it is expected that editing of the PCSK9 gene will be enhanced such that an improvement in the PCSK9-related disorder would be attained.
X. Pharmaceutical Compositions, Kits, and Articles of Manufacture
In some embodiments, the disclosure provides pharmaceutical compositions comprising: i) a repressor fusion protein and a gRNA of the disclosure comprising a targeting sequence specific for a PCSK9 gene; ii) one or more nucleic acids encoding the repressor and the gRNA of (i); iii) an LNP or synthetic nanoparticle comprising a gRNA and an mRNA encoding a repressor fusion protein, together with one or more pharmaceutically suitable excipients. In some embodiments, the pharmaceutical composition is formulated for a route of administration selected from the group consisting of intravenous, intraportal vein injection, intraperitoneal, intramuscular, subcutaneous, intraocular, and oral routes. In one embodiment, the pharmaceutical composition is in a liquid form or a frozen form. In another embodiment, the pharmaceutical composition is in a pre-filled syringe for a single injection. In another embodiment, the pharmaceutical composition is in solid form, for example the pharmaceutical composition is lyophilized.
In other embodiments, provided herein are kits comprising a repressor fusion protein and one or a plurality of CasX gRNA of any of the embodiments of the disclosure comprising a targeting sequence specific for a PCSK9 gene and a suitable container (for example a tube, vial or plate).
In other embodiments, provided herein are kits comprising an LNP formulation encapsulating an mRNA encoding a repressor fusion protein and one or a plurality of CasX gRNA of any of the embodiments of the disclosure comprising a targeting sequence specific for a PCSK9 gene, and a suitable container (for example a tube, vial or plate). In exemplary embodiments, a kit of the disclosure comprises any one of the repressor fusion proteins disclosed herein and a gRNA scaffold of any one of SEQ ID NOS: 1744-1746 and 2947-2976.
In some embodiments, the kit comprises a gRNA or a vector encoding a gRNA, wherein the gRNA comprises a scaffold sequence selected from the group consisting of SEQ ID NOS: 1744-1746 and 2947-2976, and a targeting sequence selected from the group consisting of SEQ ID NOS: 1824-2944 as set forth in Table 7. In some embodiments, the gRNA scaffold comprises a sequence selected from the group consisting of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976, and a targeting sequence selected from the group consisting of SEQ ID NOS: 1824-2944 as set forth in Table 7. In some embodiments, the gRNA scaffold comprises a sequence selected from the group consisting of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976, and a targeting selected from the group consisting of the sequences of SEQ ID NOs: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714.
In certain embodiments, provided herein are kits comprising a repressor fusion protein and gRNA repressor pair comprising any one of the repressor fusion proteins disclosed herein, and a gRNA variant comprising a scaffold sequence selected from the group consisting of SEQ ID NOS: 1744-1746 as set forth in Table 9 and a targeting sequence selected from the group consisting of SEQ ID NOS: 1824-2944 as set forth in Table 7. In some embodiments, the gRNA of the gene repression pair comprises a scaffold sequence selected from the group consisting of SEQ ID NOS: 2947-2976 and a targeting sequence of any one of SEQ ID NOS: 1824-2944 as set forth in Table 7. In some embodiments, the gRNA of the gene repression pair comprises a scaffold sequence selected from the group consisting of SEQ ID NOS: 2948-2956, 2958-2966, and 2968-2976, and a targeting selected from the group consisting of the sequences of SEQ ID NOs: 1824-1890, 1910, 1925, 2672, 2675, 2694, and 2714.
In some embodiments, the kit further comprises a buffer, a nuclease inhibitor, a protease inhibitor, a liposome, a therapeutic agent, a label, a label visualization reagent, instructions for use, or any combination of the foregoing. In some embodiments, the kit further comprises a pharmaceutically acceptable carrier, diluent or excipient.
In some embodiments, the kit comprises appropriate control compositions for gene repression applications, and instructions for use.
In some embodiments, the kit comprises a vector comprising a sequence encoding a repressor fusion protein of the disclosure and a CasX gRNA of the disclosure. The following Examples are merely illustrative and are not meant to limit any aspects of the present disclosure in any way.
EXAMPLES
Example 1: Use of Repressor Fusion Proteins to Repress PCSK9 in Human Cells
Fusing chromatin remodelers and DNA methyltransferases to CasX to reduce expression of target genes is an alternative approach to conventional gene editing for reducing expression of proteins associated with certain diseases and disorders. Experiments were performed to transiently express long-term repressor proteins (LTRPs, also referred to interchangeably herein as repressor fusion proteins) in HepG2 cells to reduce PCSK9 levels without the use of permanent genome editing.
Materials and Methods
Spacer (also referred to as targeting sequence) design: Spacers 1 KB upstream of the PCSK9 promoter and through PCSK9 Exon 1 were chosen manually based on availability of TTC PAM sequences. Spacers in Intron 1, Exon 5, and Intron 5 were selected based on the availability of TTC PAMs in regions identified as hypomethylated in human livers.
Lentiviral plasmid constructs comprising sequences encoding an LTRP protein having the #1 configuration (as diagrammed in FIG. 1), guide scaffold variant 174, and the PCSK9-targeting spacers listed in Table 10 were generated using standard molecular cloning techniques. Cloned and sequence-validated constructs were midi-prepped and subjected to quality assessment prior to transfection into HepG2 cells. Plasmid constructs were transfected using Viafect transfection reagent according to the manufacturer's instructions.
HepG2s were grown in DMEM F/12 media supplemented with 10% FBS and 1% Pen/Strep and were kept in the growth phase.
mRNA was isolated using Zymo Quick-RNA™ kit and Reverse Transcription was performed using Thermo High-Capacity RNA-to-cDNA™ Kit according to the manufacturer instructions.
Secreted PCSK9 and human serum albumin levels were assessed via PerkinElmer/Cisbio cat #63ADK050PEH and HSA ELISA: Perkin Elmer®/Cisbio cat #6FHSAPEG respectively.







TABLE 10







Sequences of LTRP-specific spacers targeting the human PCSK9 locus.
















SEQ

SEQ



Spacer


ID

ID
Targeting


ID
PAM
Spacer DNA sequence
NO:
Spacer RNA sequence
NO:
region





6.1
TTC
GAGGAGGACGGCCTGGCCGA
2977
GAGGAGGACGGCCUGGCCGA
1834
Exon 1


 


6.4
TTC
GCCAGGCCGTCCTCCTCGGA
2978
GCCAGGCCGUCCUCCUCGGA
1836
Exon 1


 


6.5
TTC
GTGCTCGGGTGCTTCGGCCA
2979
GUGCUCGGGUGCUUCGGCCA
1837
Exon 1


 


6.112
TTC
CTTGGCAGTTGAGCACGCGC
2980
CUUGGCAGUUGAGCACGCGC
2223
Exon 5


 


6.117
TTC
ACTTTGTTTGCAAAGACCTC
2981
ACUUUGUUUGCAAAGACCUC
1838
Promoter


 


6.118
TTC
GAGTGAAATGGCCTGCTCTG
2982
GAGUGAAAUGGCCUGCUCUG
1839
Promoter


 


6.119
TTC
GAGCAGGCCATTTCACTCGG
2983
GAGCAGGCCAUUUCACUCGG
1840
Promoter


 


6.120
TTC
CTCGGAATCTGCTGTGCATC
2984
CUCGGAAUCUGCUGUGCAUC
1841
Promoter


 


6.121
TTC
GGAAGGGCTGTCGATACTGG
2985
GGAAGGGCUGUCGAUACUGG
1842
Promoter


 


6.122
TTC
CCTTTGTTTCTTCCCAGTAT
2986
CCUUUGUUUCUUCCCAGUAU
1883
Promoter


 


6.123
TTC
TCCCAGTATCGACAGCCCTT
2987
UCCCAGUAUCGACAGCCCUU
1843
Promoter


 


6.124
TTC
CAGTATCGACAGCCCTTCCA
2988
CAGUAUCGACAGCCCUUCCA
1844
Promoter


 


6.125
TTC
AGAAAGAGCAAGCCTCATGT
2989
AGAAAGAGCAAGCCUCAUGU
1845
Promoter


 


6.126
TTC
CCTTTTCATCCTCCTGCCTG
2990
CCUUUUCAUCCUCCUGCCUG
2672
Promoter


 


6.127
TTC
TCCTCCTGCCTGGTACACAA
2991
UCCUCCUGCCUGGUACACAA
1884
Promoter


 


6.128
TTC
AGAAATCAACTGGACAAGCA
2992
AGAAAUCAACUGGACAAGCA
1846
Promoter


 


6.129
TTC
TTTTACACACCATGTTCAAG
2993
UUUUACACACCAUGUUCAAG
2675
Promoter


 


6.130
TTC
ATTTGCAAAGATTCCTTTTA
2994
AUUUGCAAAGAUUCCUUUUA
2677
Promoter


 


6.131
TTC
TGAACATGGTGTGTAAAAGG
2995
UGAACAUGGUGUGUAAAAGG
1847
Promoter


 


6.132
TTC
AGAAGATTCAATTTGCAAAG
2996
AGAAGAUUCAAUUUGCAAAG
1848
Promoter


 


6.133
TTC
ATGGTAGGCACAAGCTCAGC
2997
AUGGUAGGCACAAGCUCAGC
1849
Promoter


 


6.134
TTC
GAATTCTATGGTAGGCACAA
2998
GAAUUCUAUGGUAGGCACAA
1850
Promoter


 


6.135
TTC
GGAAAGCTGAGCTTGTGCCT
2999
GGAAAGCUGAGCUUGUGCCU
1851
Promoter


 


6.136
TTC
GGTTTTAAGTTTGCAAAGAC
3000
GGUUUUAAGUUUGCAAAGAC
2683
Promoter


 


6.137
TTC
GAATGTACCTATATGACGTC
3001
GAAUGUACCUAUAUGACGUC
1885
Promoter


 


6.138
TTC
AGGGATTTATACTACAAAGA
3002
AGGGAUUUAUACUACAAAGA
1852
Promoter


 


6.139
TTC
AGGAGCAGCTAGTTGGTAAG
3003
AGGAGCAGCUAGUUGGUAAG
1853
Promoter


 


6.140
TTC
AAACTTAGCCTGGACCCCCT
3004
AAACUUAGCCUGGACCCCCU
1854
Promoter


 


6.141
TTC
ACTGGCCTTAACCTGGCAGC
3005
ACUGGCCUUAACCUGGCAGC
1855
Promoter


 


6.142
TTC
TTCCACTGGCCTTAACCTGG
3006
UUCCACUGGCCUUAACCUGG
1856
Promoter


 


6.143
TTC
GAATCAATCCTACTGTGGAC
3007
GAAUCAAUCCUACUGUGGAC
1857
Promoter


 


6.144
TTC
GTGGGCAGCGAGGAGTCCAC
3008
GUGGGCAGCGAGGAGUCCAC
1858
Promoter


 


6.145
TTC
TGGGTCCACCTTGTCTCCTG
3009
UGGGUCCACCUUGUCUCCUG
1859
Promoter


 


6.146
TTC
GAAGTCTCACTGGTCAGCAG
3010
GAAGUCUCACUGGUCAGCAG
1860
Promoter


 


6.147
TTC
GTGTTTCCTGGGTCCACCTT
3011
GUGUUUCCUGGGUCCACCUU
1861
Promoter


 


6.148
TTC
GCCGGGCCCACCTTTTCAGT
3012
GCCGGGCCCACCUUUUCAGU
2694
Promoter


 


6.149
TTC
AGCCCAGTTAGGATTTGGGA
3013
AGCCCAGUUAGGAUUUGGGA
1862
Promoter


 


6.150
TTC
TCCCTCTGCGCGTAATCTGA
3014
UCCCUCUGCGCGUAAUCUGA
1863
Promoter


 


6.151
TTC
CTCTGCGCGTAATCTGACGC
3015
CUCUGCGCGUAAUCUGACGC
1864
Promoter


 


6.152
TTC
GCCTCGCCCTCCCCAAACAG
3016
GCCUCGCCCUCCCCAAACAG
1865
Promoter


 


6.153
TTC
GTTAATGTTTAATCAGATAG
3017
GUUAAUGUUUAAUCAGAUAG
1866
Promoter


 


6.154
TTC
AGGGTGTGGGTGCTTGACGC
3018
AGGGUGUGGGUGCUUGACGC
1867
Promoter


 


6.155
TTC
GCAGCGACGTCGAGGCGCTC
3019
GCAGCGACGUCGAGGCGCUC
1868
Exon 1


 


6.156
TTC
GTTCAGGGTCTGAGCCTGGA
3020
GUUCAGGGUCUGAGCCUGGA
2702
Exon 1


 


6.157
TTC
GGGTCTGAGCCTGGAGGAGT
3021
GGGUCUGAGCCUGGAGGAGU
1869
Exon 1


 


6.158
TTC
GGAGCAGGGCGCGTGAAGGG
3022
GGAGCAGGGCGCGUGAAGGG
1870
Exon 1


 


6.159
TTC
GCGCGCCCCTTCACGCGCCC
3023
GCGCGCCCCUUCACGCGCCC
1871
Exon 1


 


6.160
TTC
CGCGCCCTGCTCCTGAACTT
3024
CGCGCCCUGCUCCUGAACUU
1872
Exon 1


 


6.161
TTC
GCTCCTGCACAGTCCTCCCC
3025
GCUCCUGCACAGUCCUCCCC
1873
Exon 1


 


6.167
TTC
CACTGAATAGCGCAGCCGCA
3026
CACUGAAUAGCGCAGCCGCA
1874
Intron 1


 


6.168
TTC
GTGGGAAGGTTCGCGGGGTT
3027
GUGGGAAGGUUCGCGGGGUU
1875
Intron 1


 


6.169
TTC
CGGGGTTGGGAGACCCGGAG
3028
CGGGGUUGGGAGACCCGGAG
1876
Intron 1


 


6.170
TTC
TCGGCCTCCGGGTCTCCCAA
3029
UCGGCCUCCGGGUCUCCCAA
1877
Intron 1


 


6.171
TTC
CAGTACGTTCCAGGCATTCA
3030
CAGUACGUUCCAGGCAUUCA
1878
Intron 1


 


6.172
TTC
GCTGAAACAGATGGAATACT
3031
GCUGAAACAGAUGGAAUACU
1879
Intron 1


 


6.173
TTC
ATCTGTTTCAGCCGAAGAAA
3032
AUCUGUUUCAGCCGAAGAAA
1922
Intron 1


 


6.174
TTC
TTTCTTCGGCTGAAACAGAT
3033
UUUCUUCGGCUGAAACAGAU
1923
Intron 1


 


6.175
TTC
GCCGAAGAAAAGAACCAGCT
3034
GCCGAAGAAAAGAACCAGCU
1924
Intron 1


 


6.176
TTC
CGAGGCCCATTGGCGTCCTT
3035
CGAGGCCCAUUGGCGUCCUU
1926
Intron 1


 


6.177
TTC
TCTCACTAGCTGTGGTGCTT
3036
UCUCACUAGCUGUGGUGCUU
1934
Intron 1


 


6.178
TTC
GTTGACCATGAGTGAACTTA
3037
GUUGACCAUGAGUGAACUUA
1938
Intron 1


 


6.179
TTC
CTGGCTCTGCGGCAGAGGCT
3038
CUGGCUCUGCGGCAGAGGCU
2225
Intron 5


 


6.180
TTC
TCTGCACTCGTGGCCACTGG
3039
UCUGCACUCGUGGCCACUGG
2226
Intron 5


 


6.181
TTC
TCATCTGCACTCGTGGCCAC
3040
UCAUCUGCACUCGUGGCCAC
2228
Intron 5


 


6.182
TTC
AGACTGTGACTACATTTAGT
3041
AGACUGUGACUACAUUUAGU
2235
Intron 5


 


6.183
TTC
TCAACTATTTAGCAGCTACG
3042
UCAACUAUUUAGCAGCUACG
2240
Intron 5


 


6.184
TTC
CAGCGAGTTCCCCAGCTTGA
3043
CAGCGAGUUCCCCAGCUUGA
2242
Intron 5


 


6.185
TTC
GCCCTGAGACTTTCCTACAG
3044
GCCCUGAGACUUUCCUACAG
2246
Intron 5


 


6.186
TTC
GCCCCATCAGGTGACCCCTT
3045
GCCCCAUCAGGUGACCCCUU
2248
Intron 5


 


6.187
TTC
GGAACTGACCTGACTGAGCC
3046
GGAACUGACCUGACUGAGCC
2249
Intron 5









Results
HepG2 cells were transiently transfected with LTRP fusion proteins in configuration #1 with the targeting spacers listed in Table 10 and were subsequently selected with puromycin. Puromycin-resistant cells were allowed to expand in culture. After 4 weeks of culture, the media was collected to measure secreted PCSK9 levels, and mRNA was analyzed. Secreted PCSK9 levels were normalized to secreted human serum albumin to control for differences in cell number in different wells, and the results are presented as dot plots in FIG. 3. Compared to the non-targeting (NT) control, ˜60% of the constructs demonstrated reduction of PCSK9 mRNA and protein levels, while ˜20% of constructs repressed PCSK9 by greater than 50%.
Example 2: Demonstration that Use of LTRP Fusion Proteins can Induce Silencing of the Endogenous PCSK9 Locus in Mouse Hepa 1-6 Cells
Experiments were performed to demonstrate the ability of LTRP fusion proteins to induce durable repression of the endogenous PCSK9 locus in mouse Hepa1-6 liver cells, when delivered as mRNA co-transfected with a targeting gRNA.
Materials and Methods
Experiment #1: DXR1 vs. LTRP #1 in Hepa1-6 Cells when Delivered as mRNA
Generation of dXR1 and LTRP #1 mRNA:
mRNA encoding dXR1, a dCasX fused to a ZIM3-KRAB domain, or LTRP #1 (configuration #1 in FIG. 1) containing the ZIM3-KRAB (hereafter known as dXR1 and LTRP1-ZIM3 respectively) domain was generated by in vitro transcription (IVT) either in-house or via a third-party. Briefly, constructs encoding for a 5′UTR region, dXR1 or LTRP1-ZIM3 harboring the ZIM3-KRAB domain with flanking SV40 NLSes, and a 3′UTR region were generated and cloned into a plasmid containing a T7 promoter and 80-nucleotide poly(A) tail. These constructs also contained a 2× FLAG sequence. Sequences encoding the dXR1 and LTRP1-ZIM3 molecules were codon-optimized using a codon utilization table, in addition to using a publicly available codon optimization tool and adjusting parameters such as GC content as needed. For in-house in vitro transcription (IVT), the resulting plasmid was linearized prior to use for IVT reactions, which were carried out with CleanCap® AG and N1-methyl-pseudouridine. IVT reactions were then subjected to DNase digestion and oligodT purification on-column. For experiment #1, the DNA sequences encoding the dXR1 and LTRP1-ZIM3 molecules are listed in Table 11. The corresponding mRNA sequences encoding the dXR1 and LTRP1-ZIM3 mRNAs are listed in Table 12. The protein sequences of the dXR1 and LTRP1-ZIM3 are shown in Table 13.







TABLE 11







Encoding sequences of the dXR1 and LTRP1-ZIM3 mRNA molecules


assessed in experiment #1 of this example*.









dXR or

DNA sequence


LTRP ID
Component
or SEQ ID NO:





dXR1 (codon-
5′UTR
3047


optimized)
START codon + NLS + linker
3048



dCasX491
3049



Linker + buffer sequence
3050



ZIM3-KRAB
3051



Buffer sequence + NLS
3052



Tag
3053



STOP codon + buffer sequence
3054



3′UTR
3055



Buffer sequence
TCTAG



Poly(A) tail
3057


LTRP #1 (codon-
5′UTR
3047


optimized)
START codon + NLS + buffer
3058



sequence + linker



START codon + DNMT3A catalytic
3059



domain



Linker
3060



DNMT3L interaction domain
3061



Linker
3062



dCasX491
3049



Linker
3050



ZIM3-KRAB
3051



Buffer sequence + NLS
3052



Tag
3053



STOP codons + buffer sequence
3054



3′UTR
3055



Buffer sequence
TCTAG



Poly(A) tail
3057





*Components are listed in a 5′ to 3′ order within the constructs













TABLE 12







Full-length RNA sequences of dXR1 and LTRP1-ZIM3 mRNA molecules assessed


in experiment #1 of this example. Modification ‘mψ’ = N1-methyl-pseudouridine.









dXR or
SEQ



LTRP
ID



ID
NO
RNA Sequence





dXR1
3063
AAAmψAAGAGAGAAAAGAAGAGmψAAGAAGAAAmψAmψAAGAGCCACCAmψGGCCCCm




ψAAGAAGAAGCGmψAAAGmψGAGCCGGGGCGGCAGCGGCGGCGGCAGCGCCCAGGAGA




mψmψAAACGGAmψCAACAAGAmψCAGAAGAAGACmψmψGmψGAAAGACAGCAACACCA




AGAAGGCCGGCAAGACAGGCCCCAmψGAAAACCCmψGCmψGGmψmψAGAGmψGAmψGA




CACCCGAmψCmψGAGAGAGCGGCmψGGAAAACCmψGAGAAAGAAGCCmψGAAAAmψAm




ψCCCCCAGCCCAmψCAGCAAmψACAmψCmψAGAGCCAACCmψGAAmψAAGCmψGCmψG




ACCGAmψmψACACCGAAAmψGAAGAAGGCGAmψCCmψGCAmψGmψGmψACmψGGGAAG




AGmψmψCCAGAAGGACCCmψGmψGGGCCmψGAmψGAGCCGGGmψGGCCCAGCCmψGCC




AGCAAGAAGAmψCGAmψCAGAACAAGCmψGAAACCmψGAGAmψGGACGAGAAGGGCAA




CCmψGACCACCGCCGGCmψmψmψGCCmψGcmψCmψCAGmψGmψGGCCAGCCCCmψGmψ




mψCGmψGmψACAAGCmψGGAGCAGGmψGmψCmψGAGAAGGGCAAGGCmψmψACACCAA




CmψACmψmψCGGACGGmψGCAAmψGmψGGCCGAGCACGAAAAGCmψGAmψCCmψGCmψ




GGCCCAGCmψGAAGCCCGAGAAGGAmψAGCGACGAAGCCGmψGACAmψAmψAGCCmψG




GGAAAGmψmψmψGGGCAGAGGGCCCmψGGAmψmψmψCmψACAGCAmψmψCAmψGmψGA




CCAAGGAGmψCCACCCACCCCGmψGAAGCCCCmψGGCCCAGAmψCGCCGGAAACAGAm




ψACGCCmψCCGGACCmψGmψGGGAAAGGCCCmψGAGCGACGCAmψGmψAmψGGGCACA




AmψCGCCmψCCmψmψCCmψGmψCmψAAGmψACCAGGACAmψCAmψCAmψCGAACACCA




GAAGGmψGGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGGGAGCmψGGCCG




GCAAGGAAAACCmψGGAAmψACCCmψAGCGmψGACCCmψGCCACCmψCAGCCmψCACA




CCAAGGAGGGCGmψmψGAmψGCCmψACAACGAAGmψGAmψCGCCCGGGmψGCGAAmψG




mψGGGmψGAACCmψGAACCmψGmψGGCAGAAGCmψGAAGCmψAAGCAGAGAmψGAmψG




CCAAGCCmψCmψGCmψGAGACmψGAAGGGAmψmψCCCmψmψCCmψmψmψCCmψCmψGG




mψCGAGAGACAGGCCAACGAAGmψGGACmψGGmψGGGACAmψGGmψGmψGmψAACGmψ




GAAGAAGCmψGAmψCAACGAGAAAAAGGAGGAmψGGCAAGGmψGmψmψmψmψGGCAGA




AmψCmψGGCmψGGCmψACAAGAGACAGGAAGCCCmψGAGACCAmψACCmψGAGCAGCG




AGGAAGAmψCGGAAGAAGGGAAAGAAAmψmψCGCmψCGGmψACCAGCmψGGGCGACCm




ψGCmψGCmψGCACCmψGGAAAAGAAGCACGGCGAGGACmψGGGGAAAGGmψGmψACGA




CGAGGCCmψGGGAGCGGAmψmψGACAAGAAAGmψGGAAGGCCmψGAGCAAGCACAmψC




AAGCmψGGAAGAGGAACGGAGAAGCGAGGACGCCCAGAGCAAGGCCGCCCmψGACCGA




CmψGGCmψGCGGGCmψAAGGCCAGCmψmψCGmψGAmψCGAGGGCCmψGAAGGAGGCCG




ACAAGGACGAGmψmψCmψGCAGAmψGCGAGCmψGAAGCmψGCAGAAGmψGGmψACGGG




GACCmψGCGGGGAAAGCCCmψmψCGCCAmψCGAAGCCGAGAACAGCAmψCCmψGGACA




mψCAGCGGCmψmψCAGCAAGCAGmψACAACmψGmψGCCmψmψCAmψCmψGGCAGAAGG




ACGGCGmψGAAGAAGCmψGAACCmψGmψACCmψGAmψCAmψCAACmψACmψmψCAAGG




GCGGCAAGCmψGCGGmψmψCAAGAAGAmψCAAACCmψGAAGCCmψmψCGAAGCCAACA




GamψmψCmψACACCGmψGAmψCAACAAAAAGAGCGGCGAGAmψCGmψGCCCAmψGGAG




GmψGAACmψmψCAACmψmψCGACGACCCCAACCmψGAmψCAmψCCmψGCCmψCmψGGC




CmψmψmψGGCAAGAGACAGGGCAGAGAAmψmψCAmψCmψGGAACGACCmψGCmψGmψC




CCmψGGAAACCGGCAGCCmψGAAGCmψGGCCAACGGAAGAGmψGAmψCGAGAAGACAC




mψGmψACAACAGAAGAACCCGGCAGGAmψGAGCCmψGCCCmψGmψmψCGmψGGCCCmψ




GACCmψmψCGAGCGGCGGGAGGmψCCmψGGACmψCCmψCCAAmψAmψCAAACCAAmψG




AACCmψGAmψCGGCGmψGGCAAGAGGCGAAAACAmψCCCCGCCGmψGAmψCGCCCmψG




ACCGACCCCGAGGGCmψGCCCACmψGAGCCGGmψmψmψAAGGAmψAGCCmψGGGAAAC




CCAACCCACAmψCCmψGAGAAmψCGGCGAGAGCmψAmψAAGGAGAAGCAGCGGACCAm




ψCCAGGCCAAGAAGGAGGmψGGAGCAGCGGAGAGCCGGCGGCmψACAGCCGGAAGmψA




CGCCAGCAAAGCCAAGAAmψCmψGGCAGACGAmψAmψGGmψGAGAAACACCGCmψAGA




GAmψCmψGCmψGmψACmψACGCCGmψGACCCAGGAmψGCCAmψGCmψGAmψCmψmψCG




CCAACCmψGAGCCGGGGCmψmψCGGCCGGCAGGGCAAGCGGACCmψmψCAmψGGCCGA




GAGACAGmψACACACGGAmψGGAGGACmψGGCmψGACCGCCAAGCmψGGCCmψACGAG




GGCCmψGAGCAAGACCmψACCmψGmψCCAAGACACmψGGCCCAGmψACACCmψCCAAG




ACAmψGCAGCAACmψGmψGGGmψmψmψACCAmψCACCAGCGCCGACmψACGACAGGGm




ψGCmψGGAGAAGCmψGAAGAAGACAGCAACAGGCmψGGAmψGACCACAAmψmψAACGG




CAAGGAGCmψGAAGGmψGGAGGGCCAGAmψmψACCmψACmψACAACAGAmψACAAGAG




ACAGAACGmψAGmψCAAGGACCmψGmψCCGmψCGAGCmψGGAmψAGACmψGAGCGAAG




AAmψCmψGmψGAACAACGACAmψCmψCCmψCCmψGGACAAAGGGCAGAAGCGGAGAAG




CmψCmψGAGCCmψCCmψGAAGAAAAGAmψmψCmψCCCAmψAGACCCGmψGCAGGAGAA




GmψmψCGmψGmψGCCmψGAACmψGCGGCmψmψCGAGACACACGCAGCCGAGCAAGCCG




CCCmψGAACAmψCGCCAGAmψCCmψGGCmψGmψmψCCmψGCGGAGCCAGGAGmψACAA




GAAAmψACCAGACAAACAAGACAACCGGCAACACCGAmψAAGAGAGCCmψmψCGmψCG




AGACCmψGGCAGmψCCmψmψmψmψACCGGAAGAAGCmψmψAAGGAGGmψGmψGGAAAC




CmψGCCGmψGCGGmψCmψGGCGGAmψCmψGGCGGAGGCmψCCACAAGCAmψGAACAAC




mψCCCAGGGCAGAGmψGACCmψmψCGAGGACGmψGACCGmψGAAmψmψmψmψACACAG




GGAGAGmψGGCAGAGACmψGAACCCCGAGCAGAGAAACCmψGmψACCGGGAmψGmψGA




mψGCmψGGAAAACmψACAGCAAmψCmψGGmψGmψCCGmψGGGCCAGGGCGAGACCACA




AAGCCmψGACGmψGAmψCCmψGCGmψCmψGGAGCAGGGCAAGGAACCCmψGGCmψGGA




GGAGGAGGAGGmψGCmψGGGAAGCGGACGGGCCGAGAAGAACGGCGACAmψCGGCGGA




CAGAmψCmψGGAAGCCmψAAGGACGmψGAAAGAAAGCCmψGACCAGCCCCAAGAAAAA




GAGAAAAGmψCGACmψACAAGGAmψGACGAmψGACAAGGACmψACAAGGAmψGACGAC




GACAAGmψAAmψAGAmψAAGCGGCCGCmψmψAAmψmψAAGCmψGCCmψmψCmψGCGGG




GCmψmψGCCmψmψCmψGGCCAmψGCCCmψmψCmψmψCmψCmψCCCmψmψGCACCmψGm




ψACCmψCmψmψGGmψCmψmψmψGAAmψAAAGCCmψGAGmψAGGAAGmψcmψagaaaaa




aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa




aaaaaaaaaaaaaaaaa


 


LTRP
3064
AAAmψAAGAGAGAAAAGAAGAGmψAAGAAGAAAmψAmψAAGAGCCACCAmψGGCCCCm


#1

ψAAGAAGAAGCGmψAAAGmψGAGCCGGGmψGAACGGCAGCGGCAGCGGCGGCGGCAmψ




GAACCACGACCAGGAGmψmψCGACCCCCCmψAAGGmψGmψACCCmψCCCGmψCCCCGC




CGAGAAGAGAAAGCCCAmψCCGGGmψCCmψGAGCCmψGmψmψCGAmψGGCAmψCGCCA




CCGGmψCmψGCmψGGmψGCmψGAAGGACCmψGGGCAmψCCAGGmψGGAmψAGGmψACA




mψmψGCCmψCCGAGGmψGmψGCGAGGACmψCCAmψCACCGmψGGGAAmψGGmψGCGmψ




CAmψCAGGGCAAGAmψCAmψGmψACGmψGGGCGACGmψGCGGAGCGmψGACACAGAAG




CAmψAmψCCAGGAGmψGGGGCCCmψmψmψCGACCmψGGmψGAmψCGGCGGCAGCCCmψ




mψGCAAmψGACCmψGAGCAmψCGmψGAACCCAGCCCGGAAGGGCCmψGmψACGAGGGA




ACCGGCAGACmψGmψmψCmψmψCGAGmψmψmψmψACAGACmψGCmψGCACGACGCCCG




GCCmψAAGGAAGGCGACGACCGGCCCmψmψCmψmψmψmψGGCmψGmψmψCGAGAAmψG




mψGGmψGGCCAmψGGGAGmψCAGCGACAAGCGGGAmψAmψmψAGCCGGmψmψCCmψGG




AGAGCAACCCCGmψGAmψGAmψCGAmψGCCAAGGAAGmψGAGCGCCGCCCACCGGGCC




AGAmψACmψmψCmψGGGGCAAmψCmψGCCmψGGCAmψGAACAGACCCCmψGGCCAGCA




CCGmψGAACGACAAGCmψGGAGCmψGCAGGAGmψGCCmψGGAGCACGGCCGGAmψCGC




CAAGmψmψCAGCAAGGmψGAGAACCAmψCACCACCCGAAGCAACAGCAmψCAAACAAG




GCAAGGACCAGCACmψmψmψCCmψGmψGmψmψCAmψGAACGAGAAGGAGGACAmψCCm




ψGmψGGmψGmψACCGAGAmψGGAGAGAGmψGmψmψCGGGmψmψCCCAGmψCCACmψAC




ACAGAmψGmψCAGCAACAmψGmψCmψAGACmψGGCCAGACAGAGACmψGCmψGGGAAG




AAGCmψGGmψCCGmψCCCmψGmψGAmψCAGACACCmψGmψmψCGCCCCmψCmψGAAGG




AGmψACmψmψCGCCmψGCGmψGAGCAGCGGCAACAGCAACGCCAACAGCCGGGGCCCC




AGCmψmψCmψCmψAGCGGCCmψGGmψGCCACmψGmψCCCmψGAGAGGGAGCCACAmψG




GGCCCCAmψGGAGAmψCmψACAAAACCGmψGAGCGCCmψGGAAGCGGCAGCCmψGmψG




CGCGmψGCmψGAGCCmψGmψmψmψCGGAAmψAmψCGAmψAAAGmψCCmψGAAAAGCCm




ψGGGAmψmψCCmψGGAGAGCGGCmψCmψGGCmψCCGGCGGmψGGCACCCmψGAAGmψA




CGmψGGAGGAmψGmψGACAAACGmψGGmψCAGACGGGAmψGmψGGAGAAGmψGGGGCC




CCmψmψCGAmψCmψGGmψGmψACGGCAGCACCCAACCCCmψGGGCAGCmψCmψmψGmψ




GACCGGmψGCCCmψGGCmψGGmψACAmψGmψmψmψCAGmψmψCCACCGGAmψCCmψGC




AGmψACGCCCmψGCCGAGACAGGAGmψCCCAGCGGCCAmψmψCmψmψmψmψGGAmψmψ




mψmψCAmψGGACAACmψmψGCmψGCmψGACCGAGGAmψGACCAGGAAACmψACCACmψ




CGGmψmψCCmψGCAGACCGAAGCCGmψGACCCmψGCAGGACGmψGAGAGGCCGGGACm




ψACCAGAACGCCAmψGCGGGmψGmψGGmψCCAACAmψCCCmψGGACmψGAAAAGCAAG




CACGCACCmψCmψGACCCCmψAAAGAAGAGGAGmψACCmψGCAGGCCCAGGmψGCGGA




GCAGAAGCAAGCmψGGACGCCCCmψAAGGmψGGAmψCmψGCmψGGmψGAAGAAmψmψG




CCmψCCmψGCCCCmψGAGAGAGmψACmψmψCAAGmψAmψmψmψCAGCCAGAAmψAGmψ




CmψGCCCCmψGGGCGGCCCAAGCAGCGGCGCCCCmψCCmψCCCAGCGGCGGCAGCCCA




GCCGGCmψCCCCAACCmψCmψACCGAGGAGGGCACCmψCmψGAGmψCCGCCACCCCCG




AGAGCGGCCCmψGGCACCmψCCACCGAGCCCAGCGAGGGCAGCGCACCCGGCAGCCCm




ψGCCGGCAGCCCCACCmψCCACAGAGGAGGGAACCAGCACCGAGCCCAGCGAAGGCAG




CGCCCCAGGCACCAGCACCGAGCCmψAGmψGAGGGCGGCmψCmψGGCGGCGGCAGCGC




CCAGGAGAmψmψAAACGGAmψCAACAAGAmψCAGAAGAAGACmψmψGmψGAAAGACAG




CAACACCAAGAAGGCCGGCAAGACAGGCCCCAmψGAAAACCCmψGCmψGGmψmψAGAG




mψGAmψGACACCCGAmψCmψGAGAGAGCGGCmψGGAAAACCmψGAGAAAGAAGCCmψG




AAAAmψAmψCCCCCAGCCCAmψCAGCAAmψACAmψCmψAGAGCCAACCmψGAAmψAAG




CmψGCmψGACCGAmψmψACACCGAAAmψGAAGAAGGCGAmψCCmψGCAmψGmψGmψAC




mψGGGAAGAGmψmψCCAGAAGGACCCmψGmψGGGCCmψGAmψGAGCCGGGmψGGCCCA




GCCmψGCCAGCAAGAAGAmψCGAmψCAGAACAAGCmψGAAACCmψGAGAmψGGACGAG




AAGGGCAACCmψGACCACCGCCGGCmψmψmψGCCmψGCmψCmψCAGmψGmψGGCCAGC




CCCmψGmψmψCGmψGmψACAAGCmψGGAGCAGGmψGmψCmψGAGAAGGGCAAGGCmψm




ψACACCAACmψACmψmψCGGACGGmψGCAAmψGmψGGCCGAGCACGAAAAGCmψGAmψ




CCmψGCmψGGCCCAGCmψGAAGCCCGAGAAGGAmψAGCGACGAAGCCGmψGACAmψAm




ψAGCCmψGGGAAAGmψmψmψGGGCAGAGGGCCCmψGGAmψmψmψCmψACAGCAmψmψC




AmψGmψGACCAAGGAGmψCCACCCACCCCGmψGAAGCCCCmψGGCCCAGAmψCGCCGG




AAACAGAmψACGCCmψCCGGACCmψGmψGGGAAAGGCCCmψGAGCGACGCAmψGmψAm




ψGGGCACAAmψCGCCmψCCmψmψCCmψGmψCmψAAGmψACCAGGACAmψCAmψCAmψC




GAACACCAGAAGGmψGGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGGGAG




CmψGGCCGGCAAGGAAAACCmψGGAAmψACCCmψAGCGmψGACCCmψGCCACCmψCAG




CCmψCACACCAAGGAGGGCGmψmψGAmψGCCmψACAACGAAGmψGAmψCGCCCGGGmψ




GCGAAmψGmψGGGmψGAACCmψGAACCmψGmψGGCAGAAGCmψGAAGCmψAAGCAGAG




AmψGAmψGCCAAGCCmψCmψGCmψGAGACmψGAAGGGAmψmψCCCmψmψCCmψmψmψC




CmψCmψGGmψCGAGAGACAGGCCAACGAAGmψGGACmψGGmψGGGACAmψGGmψGmψG




mψAACGmψGAAGAAGCmψGAmψCAACGAGAAAAAGGAGGAmψGGCAAGGmψGmψmψmψ




mψGGCAGAAmψCmψGGCmψGGCmψACAAGAGACAGGAAGCCCmψGAGACCAmψACCmψ




GAGCAGCGAGGAAGAmψCGGAAGAAGGGAAAGAAAmψmψCGCmψCGGmψACCAGCmψG




GGCGACCmψGCmψGCmψGCACCmψGGAAAAGAAGCACGGCGAGGACmψGGGGAAAGGm




ψGmψACGACGAGGCCmψGGGAGCGGAmψmψGACAAGAAAGmψGGAAGGCCmψGAGCAA




GCACAmψCAAGCmψGGAAGAGGAACGGAGAAGCGAGGACGCCCAGAGCAAGGCCGCCC




mψGACCGACmψGGCmψGCGGGCmψAAGGCCAGCmψmψCGmψGAmψCGAGGGCCmψGAA




GGAGGCCGACAAGGACGAGmψmψCmψGCAGAmψGCGAGCmψGAAGCmψGCAGAAGmψG




GmψACGGGGACCmψGCGGGGAAAGCCCmψmψCGCCAmψCGAAGCCGAGAACAGCAmψC




CmψGGACAmψCAGCGGCmψmψCAGCAAGCAGmψACAACmψGmψGCCmψmψCAmψCmψG




GCAGAAGGACGGCGmψGAAGAAGCmψGAACCmψGmψACCmψGAmψCAmψCAACmψACm




ψmψCAAGGGCGGCAAGCmψGCGGmψmψCAAGAAGAmψCAAACCmψGAAGCCmψmψCGA




AGCCAACAGAmψmψCmψACACCGmψGAmψCAACAAAAAGAGCGGCGAGAmψCGmψGCC




CAmψGGAGGmψGAACmψmψCAACmψmψCGACGACCCCAACCmψGAmψCAmψCCmψGCC




mψCmψGGCCmψmψmψGGCAAGAGACAGGGCAGAGAAmψmψCAmψCmψGGAACGACCmψ




GCmψGmψCCCmψGGAAACCGGCAGCCmψGAAGCmψGGCCAACGGAAGAGmψGAmψCGA




GAAGACACmψGmψACAACAGAAGAACCCGGCAGGAmψGAGCCmψGCCCmψGmψmψCGm




ψGGCCCmψGACCmψmψCGAGCGGCGGGAGGmψCCmψGGACmψCCmψCCAAmψAmψCAA




ACCAAmψGAACCmψGAmCGGCGmψGGCAAGAGGCGAAAACAmψCCCCGCCGmψGAmψC




GCCCmψGACCGACCCCGAGGGCmψGCCCACmψGAGCCGGmψmψmψAAGGAmψAGCCmψ




GGGAAACCCAACCCACAmψCCmψGAGAAmψCGGCGAGAGCmψAmψAAGGAGAAGCAGC




GGACCAmψCCAGGCCAAGAAGGAGGmψGGAGCAGCGGAGAGCCGGCGGCmψACAGCCG




GAAGmψACGCCAGCAAAGCCAAGAAmψCmψGGCAGACGAmψAmψGGmψGAGAAACACC




GCmψAGAGAmψCmψGCmψGmψACmψACGCCGmψGACCCAGGAmψGCCAmψGCmψGAmψ




ψGGCCGAGAGACAGmψACACACGGAmψGGAGGACmψGGCmψGACCGCCAAGCmψGGCC




mψACGAGGGCCmψGAGCAAGACCmψACCmψGmψCCAAGACACmψGGCCCAGmψACACC




mψCCAAGACAmψGCAGCAACmψGmψGGGmψmψmψACCAmψCACCAGCGCCGACmψACG




ACAGGGmψGCmψGGAGAAGCmψGAAGAAGACAGCAACAGGCmψGGAmψGACCACAAmψ




mψAACGGCAAGGAGCmψGAAGGmψGGAGGGCCAGAmψmψACCmψACmψACAACAGAmψ




ACAAGAGACAGAACGmψAGmψCAAGGACCmψGmψCCGmψCGAGCmψGGAmψAGACmψG




AGCGAAGAAmψCmψGmψGAACAACGACAmψCmψCCmψCCmψGGACAAAGGGCAGAAGC




GGAGAAGCmψCmψGAGCCmψCCmψGAAGAAAAGAmψmψCmψCCCAmψAGACCCGmψGC




AGGAGAAGmψmψCGmψGmψGCCmψGAACmψGCGGCmψmψCGAGACACACGCAGCCGAG




CAAGCCGCCCmψGAACAmψCGCCAGAmψCCmψGGCmψGmψmψCCmψGCGGAGCCAGGA




GmψACAAGAAAmψACCAGACAAACAAGACAACCGGCAACACCGAmψAAGAGAGCCmψm




ψCGmψCGAGACCmψGGCAGmψCCmψmψmψmψACCGGAAGAAGCmψmψAAGGAGGmψGm




ψGGAAACCmψGCCGmψGCGGmψCmψGGCGGAmψCmψGGCGGAGGCmψCCACAAGCAmψ




GAACAACmψCCCAGGGCAGAGmψGACCmψmψCGAGGACGmψGACCGmψGAAmψmψmψm




ψACACAGGGAGAGmψGGCAGAGACmψGAACCCCGAGCAGAGAAACCmψGmψACCGGGA




mψGmψGAmψGCmψGGAAAACmψACAGCAAmψCmψGGmψGmψCCGmψGGGCCAGGGCGA




GACCACAAAGCCmψGACGmψGAmψCCmψGCGmψCmψGGAGCAGGGCAAGGAACCCmψG




GCmψGGAGGAGGAGGAGGmψGCmψGGGAAGCGGACGGGCCGAGAAGAACGGCGACAmψ




CGGCGGACAGAmψCmψGGAAGCCmψAAGGACGmψGAAAGAAAGCCmψGACCAGCCCCA




AGAAAAAGAGAAAAGmψCGACmψACAAGGAmψGACGAmψGACAAGGACmψACAAGGAm




ψGACGACGACAAGmψAAmψAGAmψAAGCGGCCGCmψmψAAmψmψAAGCmψGCCmψmψC




mψGCGGGGCmψmψGCCmψmψCmψGGCCAmψGCCCmψmψCmψmψCmψCmψCCCmψmψGC




ACCmψGmψACCmψCmψmψGGmψCmψmψmψGAAmψAAAGCCmψGAGmψAGGAAGmψcmψ




agaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa




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TABLE 13







Full-length protein sequences of dXR1 and LTRP1-ZIM3


molecules assessed in experiment #1 of this example.











Amino acid sequence



dXR or LTRP ID
SEQ ID NO:







dXR1
3065



LTRP #1
3066










Synthesis of gRNAs:

In experiment #1, gRNAs targeting the PCSK9 locus were designed using gRNA scaffold 174 and chemically synthesized using the v1 modification profile (as described in Example 7, below). Spacers were designed in proximity to the PCSK9 promoter. The sequences of the PCSK9-targeting spacers and the resulting chemically-modified gRNAs are listed in Table 14.







TABLE 14







Sequences of spacers targeting the PCSK9 locus and chemically-modified gRNAs


used in this example. Chemical modifications: * = phosphorothioate bond; m = 2′OMe


modification.












gRNA ID







(scaffold-


SEQ

SEQ


variant

Targeting spacer
ID

ID


spacer)
Target
sequence (RNA)
NO:
Full gRNA sequence (RNA)
NO:





174-6.7
human
UCCUGGCUUCCUGGUGAAGA
2008
mA*mC*mU*GGCGCUUUUAUCUGAUU
3074



PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGUCCUGGCUU







CCUGGUGAmA*mG*mA



 


174-27.1
mouse
GCCUCGCCCUCCCCAGACAG
3067
mA*mC*mU*GGCGCUUUUAUCUGAUU
3075



PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGGCCUCGCCC







UCCCCAGAmC*mA*mG



 


174-
mouse
CGCUACCUGCCUAAACUUUG
3068
mA*mC*mU*GGCGCUUUUAUCUGAUU
3076


27.88
PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGCGCUACCUG







CCUAAACUMU*mU*mG



 


174-
mouse
CCCUCCAACAAUAUUAACUA
3069
mA*mC*mU*GGCGCUUUUAUCUGAUU
3077


27.92
PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGCCCUCCAAC







AAUAUUAAmC*mU*mA



 


174-
mouse
GGGGUCUCCCAGCCACCCCU
3070
mA*mC*mU*GGCGCUUUUAUCUGAUU
3078


27.93
PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGGGGGUCUCC







CAGCCACCmC*mC*mU



 


174-
mouse
CCCCUCUUAAUCCCCACUCC
3071
mA*mC*mU*GGCGCUUUUAUCUGAUU
3079


27.94
PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGCCCCUCUUA







AUCCCCACmU*mC*mC



 


174-
mouse
CUCUCUCUUUCUGAGGCUAG
3072
mA*mC*mU*GGCGCUUUUAUCUGAUU
3080


27.100
PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGCUCUCUCUU







UCUGAGGCmU*mA*mG



 


174-
mouse
UAAUCUCCAUCCUCGUCCUG
3073
mA*mC*mU*GGCGCUUUUAUCUGAUU
3081


27.103
PCSK9


ACUUUGAGAGCCAUCACCAGCGACUA







UGUCGUAGUGGGUAAAGCUCCCUCUU







CGGAGGGAGCAUCAAAGUAAUCUCCA







UCCUCGUCmC*mU*mG









Transfection of mRNA and gRNA into Hepa1-6 Cells and Intracellular PCSK9 Staining:

Seeded Hepa1-6 cells treated with the NATE™ inhibitor were lipofected with 300 ng of mRNA encoding dXR1 or LTRP1-ZIM3 (Table 12) and 150 ng of a PCSK9-targeting gRNA (Table 14). Seven different gRNAs spanning the promoter region of the mouse PCSK9 locus were tested, in addition to a non-targeting sequence complementary to the human PCSK9 gene (Table 14). Cells were harvested at 6, 13, and 25 days after transfection to measure intracellular levels of the PCSK9 protein using an intracellular flow cytometry staining protocol. Briefly, cells were fixed using 4% paraformaldehyde in PBS, permeabilized, and stained using a mouse anti-PCSK9 primary antibody (R&D Systems®), followed by a fluorescent goat anti-mouse IgG secondary antibody (Thermo Fisher®). Fluorescence levels were measured using the Attune™ NxT flow cytometer, and data were analyzed using the FlowJo™ software. Cell populations were gated using the non-targeting gRNA as a negative control.
Experiment #2: LTRP #1 vs. LTRP #5 in Hepa1-6 Cells when Delivered as mRNA
Generation of mRNA:
mRNA encoding LTRP #1 or LTRP #5 (configuration #5 in FIG. 1) containing the ZIM3-KRAB domain (hereafter known as LTRP1-ZIM3 or LTRP5-ZIM3 respectively; configurations are diagrammed in FIG. 1) was generated by IVT in-house using plasmid-based PCR templates. Briefly, PCR was performed on plasmids encoding LTRP #1 or LTRP #5 harboring the ZIM3-KRAB domain with flanking NLSes with a forward primer containing a T7 promoter and reverse primer encoding a 120-nucleotide poly(A) tail. These constructs also contained a 2× FLAG sequence. DNA sequences encoding these molecules are listed in Table 15. The resulting PCR templates were used for IVT reactions, which were carried out with CleanCap® AG and N1-methyl-pseudouridine. IVT reactions were then subjected to DNase digestion and on-column oligo dT purification. Full-length RNA sequences encoding the LTRP mRNAs are listed in Table 16.
As experimental controls, mRNA encoding catalytically-active CasX 491 was also similarly generated by IVT using a PCR template as described. Generation of mRNAs encoding LTRP1-ZIM3 and dCas9-ZNF10-DNMT3A/3L, a catalytically-dead Cas9 fused to both the ZNF10-KRAB domain and DNMT3A/L domains, by IVT by a third-party was performed as described above for experiment #1.







TABLE 15







Encoding sequences of the LTRP1-ZIM3 and LTRP5-ZIM3 mRNA


molecules assessed in experiment #2 of this example*.











DNA sequence


LTRP ID
Component
SEQ ID NO:





LTRP #1 -
5′UTR
3082


ZIM3-
START codon + NLS + linker
3083


KRAB
START codon + DNMT3A catalytic domain
3084



Linker
3085



DNMT3L interaction domain
3086



Linker
3087



Linker + buffer
3088



dCasX491
3089



Linker + buffer
3090



ZIM3-KRAB
3091



Buffer + NLS
3092



Tag
3093



Buffer
3094



Poly(A) tail
3095


LTRP #5 -
5′UTR
3082


ZIM3-
START codon + NLS + buffer
3096


KRAB
START codon + DNMT3A catalytic domain
3084



Linker
3085



DNMT3L interaction domain
3086



Linker
3097



ZIM3-KRAB
3091



Linker
3087



dCasX491
3089



Linker + buffer
3090



NLS
3098



Tag
3093



Buffer
3094



Poly(A) tail
3095





*Components are listed in a 5′ to 3′ order within the constructs













TABLE 16







Full-length RNA sequences of LTRP1-ZIM3 and LTRP5-ZIM3 mRNA molecules


assessed in experiment #2 of this example. Modification ‘mψ’ = N1-methyl-pseudouridine










SEQ



LTRP ID
ID NO
RNA Sequence





LTRP #1-
3099
GACCGGCCGCCACCAmψGGCCCCAAAGAAGAAGCGGAAGGmψCmψCmψAGAGmψmψA


ZIM3-

ACGGAmψCAGGCmψCmψGGAGGmψGGAAmψGAACCAmψGACCAGGAAmψmψmψGACC


KRAB

GmψGCmψGmψCmψCmψCmψmψmψGAmψGGGAmψmψGCmψACAGGGCmψCCmψGGmψG




CmψGAAGGACCmψGGGCAmψCCAAGmψGGACCGCmψACAmψCGCCmψCCGAGGmψGm




ψGmψGAGGACmψCCAmψCACGGmψGGGCAmψGGmψGCGGCACCAGGGAAAGAmψCAm




ψGmψACGmψCGGGGACGmψCCGCAGCGmψCACACAGAAGCAmψAmψCCAGGAGmψGG




GGCCCAmψmψCGACCmψGGmψGAmψmψGGAGGCAGmψCCCmψGCAACGACCmψCmψC




CAmψmψGmψCAACCCmψGCCCGCAAGGGACmψmψmψAmψGAGGGmψACmψGGCCGCC




GAGGGAGAmψGAmψCGCCCCmψmψCmψmψCmψGGCmψCmψmψmψGAGAAmψGmψGGm




ψGGCCAmψGGGCGmψmψAGmψGACAAGAGGGACAmψCmψCGCGAmψmψmψCmψmψGA




GGGCCCGmψmψACmψmψCmψGGGGmψAACCmψmψCCmψGGCAmψGAACAGGCCmψmψ




mψGGCAmψCCACmψGmψGAAmψGAmψAAGCmψGGAGCmψGCAAGAGmψGmψCmψGGA




GCACGGCAGAAmψAGCCAAgmψmψCAGCAAAGmψGAGGACCAmψmψACCACCAGGmψ




CAAACmψCmψAmψAAAGCAGGGCAAAGACCAGCAmψmψmψCCCCGmψCmψmψCAmψG




AACGAGAAGGAGGACAmψCCmψGmψGGmψGCACmψGAAmψGGAAAGGGmψGmψmψψm




ψGGCmψmψCCCCGmψCCACmψACACAGACGmψGmψCCAACAmψGAGCCGCmψmψGGC




GAGGCAGAGACmψGCmψGGGCCGGmψCGmψGGAGCGmψGCCGGmψCAmψCCGCCACC




mψCmψmψCGCmψCCGCmψGAAGGAAmψAmψmψmψmψGCmψmψGmψGmψGmψCmψAGC




GGCAAmψAGmψAACGCmψAACAGCCGCGGGCCGAGCmψmψCAGCAGCGGCCmψGGmψ




GCCGmψmψAAGCmψmψGCGCGGCAGCCAmψAmψGGGCCCmψAmψGGAGAmψAmψACA




AGACAGmψGmψCmψGCAmψGGAAGAGACAGCCAGmψGCGGGmψACmψGAGCCmψCmψ




mψCAGAAACAmψCGACAAGGmψACmψAAAGAGmψmψmψGGGCmψmψCmψmψGGAAAG




CGGmψmψCmψGGmψmψCmψGGGGGAGGAACGCmψGAAGmψACGmψGGAAGAmψGmψC




ACAAAmψGmψCGmψGAGGAGGGACGmψGGAGAAAmψGGGGCCCCmψmψmψGACCmψG




GmψGmψACGGCmψCGACGCAGCCCCmψAGGCAGCmψCmψmψGmψGAmψCGCmψGmψC




CCGGCmψGGmψACAmψGmψmψCCAGmψmψCCACCGGAmψCCmψGCAGmψAmψGCGCm




ψGCCmψCGCCAGGAGAGmψCAGCGGCCCmψmψCmψmψCmψGGAmψAmψmψCAmψGGA




CAAmψCmψGCmψGCmψGACmψGAGGAmψGACCAAGAGACAACmψACCCGCmψmvCCm




ψmψCAGACAGAGGCmψGψVGACCCmψCCAGGAmψGmψCCGmψGGCAGAGACmψACCA




GAAmψGCmψAmψGCGGGmψGmψGGAGCAACAmψmψCCAGGGCmψGAAGAGCAAGCAm




ψGCGCCCCmψGACCCCAAAGGAAGAAGAGmψAmψCmψGCAAGCCCAAGmψCAGAAGC




AGGAGCAAGCmψGGACGCCCCGAAAGmψmψGACCmψCCmψGGmψGAAGAACmψGCCm




ψmψCmψCCCGCmψGAGAGAGmψACmψmψCAAGmψAmψmψmψmψmψCmψCAAAACmψC




ACmψmψCCmψCmψmψGGAGGGCCGAGCmψCmψGGCGCACCCCCACCAAGmψGGAGGG




mψCmψCCmψGCCGGGmψCCCCAACAmψCmψACmψGAAGAAGGCACCAGCGAAmψCCG




CAACGCCCGAGmψCAGGCCCmψGGmψACCmψCCACAGAACCAmψCmψGAAGGmψAGm




ψGCGCCmψGGmψmψCCCCAGCmψGGAAGCCCmψACmψmψCCACCGAAGAAGGCACGm




ψCAACCGAACCAAGmψGAAGGAmψCmψGCCCCmψGGGACCAGCACmψGAACCAmψCm




ψGAGGGCGGmψmψCCGGCGGAGGAAGCGCmψCAAGAGAmψCAAGAGAAmψCAACAAG




AmψCAGAAGGAGACmψGGmψCAAGGACAGCAACACAAAGAAGGCCGGCAAGACAGGC




CCCAmψGAAAACCCmψGCmψCGmψCAGAGmψGAmψGACCCCmψGACCmψGAGAGAGC




GGCmψGGAAAACCmψGAGAAAGAAGCCCGAGAACAmψCCCmψCAGCCmψAmψCAGCA




ACACCAGCAGGGCCAACCmψGAACAAGCmψGCmψGACCGACmψACACCGAGAmψGAA




GAAAGCCAmψCCmψGCACGmψGmψACmψGGGAAGAGmψmψCCAGAAAGACCCCGmψG




GGCCmψGAmψGAGCAGAGmψmψGCmψCAGCCmψGCCAGCAAGAAGAmψCGACCAGAA




CAAGCmψGAAGCCCGAGAmψGGACGAGAAGGGCAAmψCmψGACCACAGCCGGCmψmψ




mψGCCmψGCmψCmψCAGmψGmψGGCCAGCCmψCmψGmψmψCGmψGmψACAAGCmψGG




AACAGGmψGmψCCGAGAAAGGCAAGGCCmψACACCAACmψACmψmψCGGCAGAmψGm




ψAACGmψGGCCGAGCACGAGAAGCmψGAmψmψCmψGCmψGGCCCAGCmψGAAACCmψ




GAGAAGGACmψCmψGAmψGAGGCCGmψGACCmψACAGCCmψGGGCAAGmψmψmψGGA




CAGAGAGCCCmψGGACmψmψCmψACAGCAmψCCACGmψGACCAAAGAAAGCACACAC




CCCGmψGAAGCCCCmψGGCmvCAGAmψCGCCGGCAAmψAGAmψACGCCmψCmψGGAC




CmψGmψGGGCAAAGCCCmψGmψCCGAmψGCCmψGCAmψGGGAACAAmψCGCCAGCmψ




mψCCmψGAGCAAGmψACCAGGACAmψCAmψCAmψCGAGCACCAGAAGGmψGGmψCAA




GGGCAACCAGAAGAGACmψGGAAAGCCmψGAGGGAGCmψGGCCGGCAAAGAGAACCm




ψGGAAmψACCCCAGCGmψGACCCmψGCCmψCCmψCAGCCmψCACACAAAAGAAGGCG




mψGGACGCCmψACAACGAAGmψGAmψCGCCAGAGmψGAGAAmψGmψGGGmψCAACCm




CmψGAGACmψGAAGGGCmψmψCCCmψAGCmψmψCCCmψCmψGGmψGGAAAGACAGGC




CAAmψGAAGmψGGAmψmψGGmψGGGACAmψGGmψCmψGCAACGmψGAAGAAGCmψGA




mψCAACGAGAAGAAAGAGGAmψGGCAAGGmψmψmψmψCmψGGCAGAACCmψGGCCGG




CmψACAAGAGACAAGAAGCCCmψGAGGCCmψmψACCmψGAGCAGCGAAGAGGACCGG




AAGAAGGGCAAGAAGmψmψCGCCAGAmψACCAGCmψGGGCGACCmψGCmψGCmψGCA




CCmψGGAAAAGAAGCACGGCGAGGACmψGGGGCAAAGmψGmψACGAmψGAGGCCmψG




GGAGAGAAmψCGACAAGAAGGmψGGAAGGCCmψGAGCAAGCACAmψmψAAGCmψGGA




AGAGGAAAGAAGGAGCGAGGACGCCCAAmψCmψAAAGCCGCmψCmψGACCGAmψmψG




GCmψGAGAGCCAAGGCCAGCmψmψmψGmψGAmψCGAGGGCCmψGAAAGAGGCCGACA




AGGACGAGmψmψCmψGCAGAmψGCGAGCmψGAAGCmψGCAGAAGmψGGmψACGGCGA




mψCmψGAGAGGCAAGCCCmψmψCGCCAmψmψGAGGCCGAGAACAGCAmψCCmψGGAC




AmψCAGCGGCmψmψCAGCAAGCAGmψACAACmψGCGCCmψmψCAmψmψmψGGCAGAA




AGACGGCGmψCAAGAAACmψGAACCmψGmψACCmψGAmψCAmψCAAmψmψACmψmψC




AAAGGCGGCAAGCmψGCGGmψmψCAAGAAGAmψCAAACCCGAGGCCmψmψCGAGGCm




ψAACAGAmψmψCmψACACCGmψGAmψCAACAAAAAGmψCCGGCGAGAmψCGmψGCCC




AmψGGAGmψGAACmψmψCAACmψmψCGACGACCCCAACCmψGAmψmψmAmψCCmψGC




CmψCmψGGCCmψmψCGGCAAGAGACAGGGCAGAGAGmψmψCAmψCmψGGAACGAmψC




mψGCmψGAGCCmψGGAAACCGGCmψCmψCmψGAAGCmψGGCCAAmψGGCAGAGmψGA




mψCGAGAAAACCCmψGmψACAACAGGAGAACCAGACAGGACGAGCCmψGCmψCmψGm




ψmψmψGmψGGCCCmψGACCmψmψCGAGAGAAGAGAGGmψGCmψGGACAGCAGCAACA




mψGmψGAmψCGCCCmψGACAGACCCmψGAAGGAmψGCCCACmψGAGCAGAmψmψCAA




GGACmψCCCmψGGGCAACCCmψACACACAmψCCmψGAGAAmψCGGCGAGAGCmψACA




AAGAGAAGCAGAGGACAAmψCCAGGCCAAGAAAGAGGmψGGAACAGAGAAGAGCCGG




CGGAmψACmψCmψAGGAAGmψACGCCAGCAAGGCCAAGAAmψCmψGGCCGACGACAm




ψGGmψCCGAAACACCGCCAGAGAmψCmψGCmψGmψACmψACGCCGmψGACACAGGAC




GCCAmψGCmψGAmψCmψmψCGCGAAmψCmψGAGCAGAGGCmψmψCGGCCGGCAGGGC




mψCACAGCmψAAACmψGGCCmψACGAGGGACmψGAGCAAGACCmψACCmψGmψCCAA




AACACmψGGCCCAGmψAmψACCmψCCAAGACCmψGCAGCAAmψmψGCGGCmψmψCAC




CAmψCACCAGCGCCGACmψACGACAGAGmψGCmψGGAAAAGCmψCAAGAAAACCGCC




ACCGGCmψGGAmψGACCACCAmψCAACGGCAAAGAGCmψGAAGGmψmψGAGGGCCAG




AmψCACCmψACmψACAACAGGmψACAAGAGGCAGAACGmψCGmψGAAGGAmψCmψGA




GCGmψGGAACmψGGACAGACmψGAGCGAAGAGAGCGmψGAACAACGACAmψCAGCAG




CmψGGACAAAGGGCAGAmψCAGGCGAGGCmψCmψGAGCCmψGCmψGAAGAAGAGGmψ




mψmψAGCCACAGACCmψGmψGCAAGAGAAGmψmψCGmψGmψGCCmψGAACmvGCGGC




mψmψCGAGACACACGCCGCmψGAACAGGCmψGCCCmψGAACAmψmψGCCAGAAGCmψ




GGCmψGmψmψCCmψGAGAAGCCAAGAGmψACAAGAAGmψACCAGACCAACAAGACCA




CCGGCAACACCGACAAGAGGGCCmψmψmψGmψGGAAACCmψGGCAGAGCmψmψCmψA




CAGAAAAAAGCmψGAAAGAAGmψCmψGGAAGCCCGCCGmψGCGAmψCGGGCGGmψmψ




CCGGCGGAGGmψmψCCACmψAGmψAmVGAACAAmψmψCCCAGGGAAGAGmψGACCmψ




mψCGAGGAmψGmψCACmψGmψGAACmψmψCACCCAGGGGGAGmψGGCAGCGGCmψGA




AmψCCCGAACAGAGAAACmψmψGmψACAGGGAmψGmψGAmψGCmψGGAGAAmψmψAC




AGCAACCmψmψGmψCmψCmψGmψGGGACAAGGGGAAACCACCAAACCCGAmψGmψGA




mψCmψmψGAGGmψmψGGAACAAGGAAAGGAGCCAmψGGmψmψGGAGGAAGAGGAAGm




ψGCmψGGGAAGmψGGCCGmψGCAGAAAAAAAmψGGGGACAmψmψGGAGGGCAGAmψm




ψmψGGAAGCCAAAGGAmψGmψGAAAGAGAGmψCmψCACmψAGmψCCAAAAAAGAAGA




GAAAGGmψAGAmψmψACAAAGAmψGACGAmψGACAAAGACmψACAAGGAmψGAmψGA




mψGAmψAAGGGAmψCCGGCmψGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAAAA


 


LTRP #5-
3100
GACCGGCCGCCACCAmψGGCCCCAAAGAAGAAGCGGAAGGmψCmψCmψAGAAmψGAA


ZIM3-

CCAmψGACCAGGAAmψmψmψGACCCCCCAAAGGmψmψmψACCCACCmψGmψGCCAGC


KRAB

mψGAGAAGAGGAAGCCCAmψCCGCGmψGCmψGmψCmψCmψCmψmψmψGAmψGGGAmψ




mψGCmψACAGGGCmψCCmψGGmψGCmψGAAGGACCmψGGGCAmψCCAAGmψGGACCG




CmψACAmψCGCCmψCCGAGGmψGmψGmψGAGGACmψCCAmψCACGGmψGGGCAmψGG




mψGCGGCACCAGGGAAAGAmψCAmψGmψACGmψCGGGGACGmψCCGCAGCGmψCACA




CAGAAGCAmψAmψCCAGGAGmψGGGGCCCAmψmψCGACCmψGGmψGAmψmψGGAGGC




AGmψCCCmψGCAACGACCmψCmψCCAmψmψGmψCAACCCmψGCCCGCAAGGGACmψm




ψmψAmψGAGGGmψACmψGGCCGCCmψCmψmψCmψmψmψGAGmψmψCmψACCGCCmψC




CmψGCAmψGAmψGCGCGGCCCAAGGAGGGAGAmψGAmψCGCCCCmψmψCmψmψCmψG




GCmψCmψmψmψGAGAAmψGmψGGmψGGCCAmψGGGCGmψmψAGmψGACAaGAGGGAC




AGAAGmψGmψCmψGCmψGCACACAGGGCCCGmψmψACmψmψCmψGGGGmψAACCmψm




ψccmψGGCAmψGAACAGGCCmψmvmψGGCAmψCCACmψGmψGAAmψGAmψAAGCmψG




GAGCmψGCAAGAGmψGmψCmψGGAGCACGGCAGAAmψAGCCAAGmψmψCAGCAAAGm




ψGAGGACCAmψmψACCACCAGGmψCAAACmψCmψAmψAAAGCAGGGCAAAGACCAGC




AmψmψmψCCCCGmψCmψmψCAmψGAACGAGAAGGAGGACAmψCCmψGmψGGmψGCAC




mψGAAAmψGGAAAGGGmψGmψmψmψGGCmψmψCCCCGmψCCACmψACACAGACGmψG




mψCCAACAmψGAGCCGCmψmψGGCGAGGCAGAGACmψGCmψGGGCCGGmψCGmψGGA




GCGmψGCCGGmψCAmψCCGCCACCmψCmψmψCGCmψCCGCmψGAAGGAAmψAmψmψm




ψmψGCmψmψGmψGmψGmψCmψAGCGGCAAmψAGmψAACGCmψAACAGCCGCGGGCCG




AGCmψmψCAGCAGCGGCCmψGGmψGCCGmψmψAAGCmψmψGCGCGGCAGCCAmψAmψ




GGGCCCmψAmψGGAGAmψAmψACAAGACAGmψGmψCmψGCAmψGGAAGAGACAGCCA




GmψGCGGGmψACmψGAGCCmψCmψmψCAGAAACAmψCGACAAGGmψACmψAAAGAGm




ψmψmψGGGCmψmψCmψmψGGAAAGCGGmψmψCmψGGmψmψCmψGGGGGAGGAACGCm




ψGAAGmψACGmψGGAAGAmψGmψCACAAAmψGmψCGmψGAGGAGGGACGmψGGAGAA




AmψGGGGCCCCmψmψmψGACCmψGGmψGmψACGGCmψCGACGCAGCCCCmψAGGCAG




CmψCmψmψGmψGAmψCGCmψGmψCCCGGCmψGGmψACAmψGmψmψCCAGmψmψCCAC




CGGAmψCCmψGCAGmψAmψGCGCmψGCCmψCGCCAGGAGAGmψCAGCGGCCCmψmψC




mψmψCmψGGAmψAmψmψCAmψGGACAAmψCmψGCmψGCmψGACmψGAGGAmψGACCA




AGAGACAACmψACCCGCmψmψCCmψmψCAGACAGAGGCmψGmψGACCCmψCCAGGAm




ψGmψCCGmψGGCAGAGACmψACCAGAAmψGCmψAmψGCGGGmψGmψGGaGCAACAmψ




mψCCAGGGCmψGAAGAGCAAGCAmψGCGCCCCmψGACCCCAAAGGAAGAAGAGmψAm




ψCmψGCAAGCCCAAGmψCAGAAGCAGGAGCAAGCmψGGACGCCCCGAAAGmψmψGAC




CmψCCmψGGmψGAAGAACmψGCCmψmψCmψCCCGCmψGAGAGAGmψACmψmψCAAGm




ψAmψmψmψmψmψCmψCAAAACmψCACmψmψCCmψCmψmψGGCGGmψmψCCGGCGGAG




GAAmψGAACAAmψmψCCCAGGGAAGAGmψGACCmψmψCGAGGAmψGmψCACmψGmψG




AACmψmψCACCCAGGGGGAGmψGGCAGCGGCmψGAAmψCCCGAACAGAGAAACmψmψ




GmψACAGGGAmψGmψGAmψGCmψGGAGAAmψmψACAGCAACCmψmψGmψCmψCmψGm




ψGGGACAAGGGGAAACCACCAAACCCGAmψGmψGAmψCmψmψGAGGmψmψGGAACAA




GGAAAGGAGCCAmψGGmψmψGGAGGAAGAGGAAGmψGCmψGGGAAGmψGGCCGmψGC




AGAAAAAAAmψGGGGACAmψmψGGAGGGCAGAmψmψmψGGAAGCCAAAGGAmψGmψG




AAAGAGAGmψCmψCGGAGGGCCGAGCmψCmψGGCGCACCCCCACCAAGmψGGAGGGm




ψCmψCCmψGCCGGGmψCCCCAACAmψCmψACmψGAAGAAGGCACCAGCGAAmψCCGC




AACGCCCGAGmψCAGGCCCmψGGmψACCmψCCACAGAACCAmψCmψGAAGGmψAGmψ




GCGCCmψGGmψmψCCCCAGCmψGGAAGCCCmψACmψmψCCACCGAAGAAGGCACGmψ




CAACCGAACCAAGmψGAAGGAmψCmψGCCCCmψGGGACCAGCACmψGAACCAmψCmψ




GAGCAAGAGAmψCAAGAGAAmψCAACAAGAmψCAGAAGGAGACmψGGmψCAAGGACA




GCAACACAAAGAAGGCCGGCAAGACAGGCCCCAmψGAAAACCCmψGCmψCGmψCAGA




GmψGAmψGACCCCmψGACCmψGAGAGAGCGGCmψGGAAAACCmψGAGAAAGAAGCCC




GAGAACAmψCCCmψCAGCCmψAmψCAGCAACACCAGCAGGGCCAACCmψGAACAAGC




mψGCmψGACCGACmψACACCGAGAmψGAAGAAAGCCAmψCCmψGCACGmψGmψACmψ




GGGAAGAGmψmψCCAGAAAGACCCCGmψGGGCCmψGAmvGAGCAGAGmvmψGCmψCA




GCCmψGCCAGCAAGAAGAmψCGACCAGAACAAGCmψGAAGCCCGAGAmψGGACGAGA




AGGGCAAmψCmψGACCACAGCCGGCmψmψmψGCCmψGCmψCmψCAGmψGmψGGCCAG




CCmψCmψGmψmψCGmψGmψACAAGCmψGGAACAGGmψGmψCCGAGAAAGGCAAGGCC




mψACACCAACmψACmψmψCGGCAGAmψGmψAACGmψGGCCGAGCACGAGAAGCmψGA




mψmψCmψGCmψGGCCCAGCmψGAAACCmψGAGAAGGACmψCmψGAmψGAGGCCGmψG




ACCmψACAGCCmψGGGCAAGmψmψmψGGACAGAGAGCCCmψGGACmψmψCmψACAGC




AmψCCACGmψGACCAAAGAAAGCACACACCCCGmψGAAGCCCCmψGGCmψCAGAmψC




GCCGGCAAmψAGAmψACGCCmψCmψGGACCmψGmψGGGCAAAGCCCmψGmψCCGAmψ




GCCmψGCAmψGGGAACAAmψCGCCAGCmψmψCCmψGAGCAAGmψACCAGGACAmψCA




mψCAmψCGAGCACCAGAAGGmψGGmψCAAGGGCAACCAGAAGAGACmψGGAAAGCCm




ψGAGGGAGCmψGGCCGGCAAAGAGAACCmψGGAAmψACCCCAGCGmψGACCCmψGCC




mψCCmψCAGCCmψCACACAAAAGAAGGCGmψGGACGCCmVACAACGAAGmψGAmψCG




CCAGAGmψGAGAAmψGmψGGGmψCAACCmψGAACCmψGmψGGCAGAAGCmψGAAACm




ψGmψCCAGGGACGACGCCAAGCCmψCmψGCmψGAGACmψGAAGGGCmψmψCCCmψAG




CmψmψCCCmψCmψGGmψGGAAAGACAGGCCAAmψGAAGmψGGAmψmψGGmψGGGACA




mψGGmψCmψGCAACGmψGAAGAAGCmψGAmψCAACGAGAAGAAAGAGGAmUGGCAAG




GmψmψmψmψCmψGGCAGAACCmψGGCCGGCmψACAAGAGACAAGAAGCCCmψGAGGC




CmψmψACCmψGAGCAGCGAAGAGGACCGGAAGAAGGGCAAGAAGmψmψCGCCAGAmψ




ACCAGCmψGGGCGACCmψGCmψGCmψGCACCmψGGAAAAGAAGCACGGCGAGGACmψ




GGGGCAAAGmψGmψACGAmψGAGGCCmψGGGAGAGAAmψCGACAAGAAGGmψGGAAG




GCCmψGAGCAAGCACAmψmψAAGCmψGGAAGAGGAAAGAAGGAGCGAGGACGCCCAA




mψCmψAAAGCCGCmψCmψGACCGAmψmψGGCmψGAGAGCCAAGGCCAGCmψmψmψGm




ψGAmψCGAGGGCCmψGAAAGAGGCCGACAAGGACGAGmψmψCmψGCAGAmψGCGAGC




mψGAAGCmψGCAGAAGmψGGmψACGGCGAmψCmψGAGAGGCAAGCCCmψmψCGCCAm




ψmψGAGGCCGAGAACAGCAmψCCmψGGACAmψCAGCGGCmψmψCAGCAAGCAGmψAC




ACAAAAAGmψCCGGCGAGAmψCGmVGCCCAmψGGAAGmψGAACmψmψCAACmψmψCG




mψACCmψGAmψCAmψCAAmψmψACmψmψCAAAGGCGGCAAGCmψGCGGmψmψCAAGA




AGAmψCAAACCCGAGGCCmψmψCGAGGCmψAACAGAmψmψCmψACACCGmψGAmψCA




ACAAAAAGmψCCGGCGAGAmψCGmψGCCCAmψGGAAGmψGAACmψmψCAACmψmψCG




ACGACCCCAACCmψGAmψmψAmψCCmψGCCmψCmψGGCCmψmψCGGCAAGAGACAGG




GCAGAGAGmψmψCAmψCmψGGAACGAmψCmψGCmψGAGCCmψGGAAACCGGCmψCmψ




CmψGAAGCmψGGCCAAmψGGCAGAGmψGAmψCGAGAAAACCCmψGmψACAACAGGAG




AACCAGACAGGACGAGCCmψGCmψCmψGmψmψmψGmψGGCCCmψGACCmψmψCGAGA




GAAGAGAGGmψGCmψGGACAGCAGCAACAmψCAAGCCCAmψGAACCmψGAmψCGGCG




mψGGCCCGGGGCGAGAAmψAmψCCCmψGCmψGmψGAmψCGCCCmψGACAGACCCmψG




AAGGAmψGCCCACmψGAGCAGAmψmψCAAGGACmψCCCmψGGGCAACCCmψACACAC




AmψCCmψGAGAAmψCGGCGAGAGCmψACAAAGAGAAGCAGAGGACAAmψCCAGGCCA




AGAAAGAGGmψGGAACAGAGAAGAGCCGGCGGAmψACmψCmψAGGAAGmψACGCCAG




CAAGGCCAAGAAmψCmψGGCCGACGACAmψGGmψCCGAAACACCGCCAGAGAmψCmψ




GCmψGmψACmψACGCCGmψGACACAGGACGCCAmψGCmψGAmψCmψmψCGCGAAmψC




mψGAGCAGAGGCmψmψCGGCCGGCAGGGCAAGAGAACCmψmψmψAmψGGCCGAGAGG




CAGmψACACCAGAAmψGGAAGAmψmψGGCmψCACAGCmψAAACmψGGCCmψACGAGG




GACmψGAGCAAGACCmψACCmψGmψCCAAAACACmψGGCCCAGmψAmψACCmψCCAA




GACCmψGCAGCAAmψmψGCGGCmψmψCACCAmψCACCAGCGCCGACmψACGACAGAG




mψGCmψGGAAAAGCmψCAAGAAAACCGCCACCGGCmψGGAmψGACCACCAmψCAACG




GCAAAGAGCmψGAAGGmψmψGAGGGCCAGAmψCACCmψACmψACAACAGGmψACAAG




AGGCAGAACGmψCGmψGAAGGAmψCmψGAGCGmψGGAACmψGGACAGACmψGAGCGA




AGAGAGCGmψGAACAACGACAmψCAGCAGCmψGGACAAAGGGCAGAmψCAGGCGAGG




CmψCmψGAGCCmψGCmψGAAGAAGAGGmψmψmψAGCCACAGACCmψGmψGCAAGAGA




AGmψmψCGmψGmψGCCmψGAACmψGCGGCmψmψCGAGACACACGCCGCmψGAACAGG




CmψGCCCmψGAACAmψmψGCCAGAAGCmψGGCmψGmψmψCCmψGAGAAGCCAAGAGm




ψACAAGAAGmψACCAGACCAACAAGACCACCGGCAACACCGACAAGAGGGCCmψmψm




ψGmψGGAAACCmψGGCAGAGCmψmψCmψACAGAAAAAAGCmψGAAAGAAGmψCmψGG




AAGCCCGCCGmψGCGAmψCGGGCGGmψmψCCGGCGGAGGmψmψCCACmψAGmψCCAA




AAAAGAAGAGAAAGGmψAGAmψmψACAAAGAmψGACGAmψGACAAAGACmψACAAGG




AmψGAmψGAmψGAmψAAGGGAmψCCGGCmψGAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA









For experiment #2, synthesis of PCSK9-targeting gRNAs was performed as described above for experiment #1, and the sequences of the targeting spacers are listed in Table 14. For pairing with dCas9-ZNF10-DNMT3A/3L, targeting spacers were as follows: 1) 7.148 (B2M, as non-targeting control; CGCGAGCACAGCUAAGGCCA; SEQ ID NO: 3101), 27.126 (PCSK9; CACGCCACCCCGAGCCCCAU; SEQ ID NO: 3102), and 27.128 (PCSK9; CAGCCUGCGCGUCCACGUGA; SEQ ID NO: 3103).
Transfection of mRNA and gRNA into Hepa1-6 Cells and Intracellular PCSK9 Staining:
Seeded Hepa1-6 cells treated with the NATE™ inhibitor were lipofected with 300 ng of mRNA encoding LTRP1-ZIM3, LTRP5-ZIM3, catalytically-active CasX 491, or dCas9-ZNF10-DNMT3A/3L, and 150 ng of PCSK9-targeting gRNA (Table 14). Intracellular levels of PCSK9 protein were measured at 7, 14, 21, 36, and 71 days post-transfection using an intracellular staining protocol as described earlier for experiment #1.
Results
In experiment #1, mRNAs encoding dXR1 or LTRP1-ZIM3 were co-transfected with a PCSK9-targeting gRNA into mouse Hepa1-6 cells to assess their ability to induce PCSK9 knockdown by silencing the mouse PCSK9 locus. The quantification of the resulting PCSK9 knockdown is shown in FIGS. 4-6. The data demonstrate that at day 6, use of six out of seven gRNAs targeting the mouse PCSK9 locus with LTRP1-ZIM3 mRNA resulted in >50% knockdown of intracellular PCSK9, with the leading spacer 27.94 achieving >80% repression level (FIG. 4). A similar trend was observed with use of dXR1 mRNA at day 6, although the degree of repression was less substantial when paired with certain spacers, such as spacer 27.92 and 27.100 (FIG. 4). The results also demonstrate that use of LTRP1-ZIM3 mRNA led to sustained repression of the PCSK9 locus through at least 25 days, with use of the top two spacers 27.94 and 27.88 showing the strongest permanence in silencing PCSK9 (FIG. 6). However, the PCSK9 repression mediated by dXR1 that was observed at day 6 reverted to similar levels of PCSK9 as detected with the non-targeting control (spacer 6.7) by day 13; such transient repression was noticeable for all gRNAs assayed that targeted the PCSK9 gene (FIG. 5).
In experiment #2, mRNAs encoding LTRP1-ZIM3 or LTRP5-ZIM3, dCas9-ZNF10-DNMT3A/3L, or catalytically active CasX 491 were co-transfected with a PCSK9-targeting gRNA into mouse Hepa1-6 cells to assess their ability to induce PCSK9 knockdown by silencing the mouse PCSK9 locus. The quantification of the resulting PCSK9 repression is shown in FIGS. 7-8. The data demonstrate that delivery of IVT-produced LTRP1-ZIM3 or LTRP5-ZIM3 mRNA resulted in comparable levels of sustained PCSK9 knockdown when paired with a targeting gRNA with the top spacer 27.94 (˜40% knockdown by day 71), while use of an alternative spacer 27.88 did not result in as effective of a sustained PCSK9 knockdown by day 71 (˜12%) (FIG. 7). Furthermore, third-party-produced mRNA encoding LTRP1-ZIM3 and dCas9-ZNF10-DNMT3A/3L led to similar levels of durable PCSK9 knockdown when paired with gRNAs containing various spacers, with use of spacer 27.94 still resulting in the highest level of PCSK9 repression (FIG. 8).
These experiments demonstrate that LTRP molecules, having different configurations, can induce heritable silencing of an endogenous locus in a mouse liver cell line. Meanwhile, as anticipated, use of dXR constructs result in efficient repression of the target locus at early timepoints, but their use does not lead to durable silencing. These findings also show that dXR and LTRP molecules (of different configurations) can be delivered as mRNA and co-transfected with a targeting gRNA to cells, indicating that the transient nature of the delivered payload is still sufficient to induce silencing.
Example 3: Assessment of Spacers in Achieving Repression of the PCSK9 Locus in Human Hepatocyte Cells when Paired with an LTRP5-ADD Molecule
Experiments were performed to demonstrate that multiple spacers with the TTC recognition motif, when paired with an LTRP molecule in configuration #5 (LTRP5; diagrammed in FIG. 2) containing the ADD domain, can induce durable repression of a therapeutically-relevant endogenous locus in human cells. Specifically, an initial proof-of-concept experiment was performed in human Huh7 cells to evaluate a subset of spacers that exhibit sequence conservation to the non-human primate (NHP) genome to identify leading spacers for testing in future in vivo NHP studies.
Materials and Methods
Computational Selection of PCSK9-Targeting Spacers for Experimental Testing with an LTRP5 Molecule Containing the ADD Domain:
To determine potential LTRP-specific spacers throughout the human PCSK9 locus, a target search region was defined as starting at 5 KB upstream of the transcription start site (TSS) through 5 KB downstream of the transcription stop site. Spacers were determined based on the availability of TTC PAMs; consequently, a total of 1,121 TTC spacers were identified throughout the target PCSK9 locus. These spacers were then functionally annotated by overlaying key genomic features based on their positioning, i.e., determining whether the putative spacer targeted an exon, an intron, or a candidate cis-regulatory element (cCRE), within the promoter region, and/or overlapped with a common site of genetic variation (e.g., SNPs). To narrow down and determine an initial group of spacers for experimental screening, the extracted spacers were subjected to a set of filtering criteria. Firstly, non-specific spacers were excluded by removing spacers with off-target sites that contain up to one base pair mismatch with the on-target site. Furthermore, spacers containing the following mononucleotide repeats were excluded: thymine nucleotide repeats greater than four base pairs (bp) in length or adenine, guanine, or cytosine nucleotide repeats greater than 5 bp in length. Next, from this filtered set, spacers with more than one off-target site containing mismatches in the last four nucleotides of the spacer were excluded. Lastly, spacers that targeted >2 KB upstream of the TSS and >2 KB downstream of the transcription stop site were excluded. This resulted in a filtered set of 722 TTC spacers (SEQ ID NO: 1824-2545). From this filtered set of 722 spacers, spacers that were TSS-proximal (within 1100 bp upstream and downstream of the TSS) were selected for experimental assessment, resulting in the identification of 67 TTC spacers. Two additional spacers, TG-06-354 and TG-06-352, positioned beyond the 1100 bp threshold window, were also selected for inclusion. The sequences of the resulting 69 TTC spacers are shown in Table 17.







TABLE 17







RNA sequences of the 69 TTC spacers targeting


the human PCSK9 locus. Bolded spacers were


spacers having sequence consensus between human


and non-human primate genomes and were assessed


in this example.









Spacer

SEQ


ID
Spacer RNA sequence
ID NO:





TG-06-342
AAUUACAGGCAACAGGAAGG
1824


 


TG-06-343
CCCCAUGUAAGAGAGGAAGU
1825


 


TG-06-344
CAGUUUCUGCCUCGCCGCGG
1826


 


TG-06-345
GCCUCGCCGCGGCACAGGUG
1827


 


TG-06-346
CCCACCUGUGCCGCGGCGAG
1828


 


TG-06-347
CUCCUUCACCCACCUGUGCC
1829


 


TG-06-348
AGGCAUUCACUCCUUCACCC
1830


 


TG-06-349
CUGUGCCUGGUGCAGUUCCC
1831


 


TG-06-350
GUGUCAUAAAGAAAUUGCCU
1832


 


TG-06-351
UUAUGACACAGAACUCAUGC
1833


 


TG-06-001
GAGGAGGACGGCCUGGCCGA
1834


 


TG-06-002
ACCGCUGCGCCAAGGUGCGG
1835


 


TG-06-004
GCCAGGCCGUCCUCCUCGGA
1836


 


TG-06-005
GUGCUCGGGUGCUUCGGCCA
1837


 


TG-06-117
ACUUUGUUUGCAAAGACCUC
1838


 


TG-06-118
GAGUGAAAUGGCCUGCUCUG
1839


 


TG-06-119
GAGCAGGCCAUUUCACUCGG
1840


 


TG-06-120
CUCGGAAUCUGCUGUGCAUC
1841


 


TG-06-121
GGAAGGGCUGUCGAUACUGG
1842


 


TG-06-123
UCCCAGUAUCGACAGCCCUU
1843


 


TG-06-124
CAGUAUCGACAGCCCUUCCA
1844


 


TG-06-125
AGAAAGAGCAAGCCUCAUGU
1845


 


TG-06-128
AGAAAUCAACUGGACAAGCA
1846


 


TG-06-131
UGAACAUGGUGUGUAAAAGG
1847


 


TG-06-132
AGAAGAUUCAAUUUGCAAAG
1848


 


TG-06-133
AUGGUAGGCACAAGCUCAGC
1849


 


TG-06-134
GAAUUCUAUGGUAGGCACAA
1850


 


TG-06-135
GGAAAGCUGAGCUUGUGCCU
1851


 


TG-06-138
AGGGAUUUAUACUACAAAGA
1852


 


TG-06-139
AGGAGCAGCUAGUUGGUAAG
1853


 


TG-06-140
AAACUUAGCCUGGACCCCCU
1854


 


TG-06-141
ACUGGCCUUAACCUGGCAGC
1855


 


TG-06-142
UUCCACUGGCCUUAACCUGG
1856


 


TG-06-143
GAAUCAAUCCUACUGUGGAC
1857


 


TG-06-144
GUGGGCAGCGAGGAGUCCAC
1858


 


TG-06-145
UGGGUCCACCUUGUCUCCUG
1859


 


TG-06-146
GAAGUCUCACUGGUCAGCAG
1860


 


TG-06-147
GUGUUUCCUGGGUCCACCUU
1861


 


TG-06-149
AGCCCAGUUAGGAUUUGGGA
1862


 


TG-06-150
UCCCUCUGCGCGUAAUCUGA
1863


 


TG-06-151
CUCUGCGCGUAAUCUGACGC
1864


 


TG-06-152
GCCUCGCCCUCCCCAAACAG
1865


 


TG-06-153
GUUAAUGUUUAAUCAGAUAG
1866


 


TG-06-154
AGGGUGUGGGUGCUUGACGC
1867


 


TG-06-155
GCAGCGACGUCGAGGCGCUC
1868


 


TG-06-157
GGGUCUGAGCCUGGAGGAGU
1869


 


TG-06-158
GGAGCAGGGCGCGUGAAGGG
1870


 


TG-06-159
GCGCGCCCCUUCACGCGCCC
1871


 


TG-06-160
CGCGCCCUGCUCCUGAACUU
1872


 


TG-06-161
GCUCCUGCACAGUCCUCCCC
1873


 


TG-06-167
CACUGAAUAGCGCAGCCGCA
1874


 


TG-06-168
GUGGGAAGGUUCGCGGGGUU
1875


 


TG-06-169
CGGGGUUGGGAGACCCGGAG
1876


 


TG-06-170
UCGGCCUCCGGGUCUCCCAA
1877


 


TG-06-171
CAGUACGUUCCAGGCAUUCA
1878


 


TG-06-172
GCUGAAACAGAUGGAAUACU
1879


 


TG-06-249
AAACCAAAUCGGAACCCACU
1880


 


HS-6-147
UGUUGCCUGUAAUUGGAAUU
1881


 


HS-6-149
CCUUCCUGUUGCCUGUAAUU
1882


 


TG-06-122
CCUUUGUUUCUUCCCAGUAU
1883


 


TG-06-127
UCCUCCUGCCUGGUACACAA
1884


 


TG-06-137
GAAUGUACCUAUAUGACGUC
1885


 


TG-06-188
CCCCGGCCUCCCAUCCCUAC
1886


 


TG-06-243
CUUGGCACGAUCUUGGGGAC
1887


 


TG-06-250
GAUUUGGUUUGGAAAACAUG
1888


 


TG-06-251
CUCCAGGCCCUCCACCCUCC
1889


 


HS-6-159
CACCCCGCCCCUGUCUCGGG
1890


 


TG-06-354
CCCCUGCCCCUUCAGCUGGU
1925


 


TG-06-352
UCCCUCACCAAUUACCCCUC
1910





Note,


for spacer nomenclature throughout these Examples, dashes and periods are used interchangeably. Thus, spacer “06-146” is the same as spacer “6.146.” Assessment of PCSK9 secretion levels for select PCSK9-targeting spacers having sequence conservation with the non-human primate genome:






Of the 69 TTC spacers identified, 15 spacers that exhibited sequence conservation between human and non-human primate genomes (bolded spacers in Table 17) were initially tested to assess their effect on PCSK9 secretion levels.
mRNA encoding the following molecules were generated by IVT following similar methods as described in Example 2: 1) a catalytically-active CasX 676 (as described in Example 5), 2) dXR1 (as described in Example 2), and 3) LTRP5-ADD-ZIM3 (as described in Example 4). The DNA and mRNA sequences for CasX 676 are shown in Tables 21 and 22; the DNA and mRNA sequences for dXR1 are shown in Tables 11 and 12; the DNA and mRNA sequences for LTRP5-ADD-ZIM3 are shown in Tables 18 and 19.
gRNAs containing NHP-conserved spacers targeting the PCSK9 locus (bolded spacers in Table 17) were designed using gRNA scaffold 316 and chemically synthesized. Furthermore, a B2M-targeting gRNA was used as a non-targeting control, while spacer TG-06-138 (also known as spacer 6.138; SEQ ID NO: 1852) was used to pair with dXR1, and spacer TG-06-001 (also known as spacer 6.1; SEQ ID NO: 1834) was used to pair with CasX 676. Spacer TG-06-157 (also known as spacer 6.157; SEQ ID NO: 1869), which is not an NHP-conserved spacer, was included as a positive control given its demonstrated efficacy in sustaining repression of the PCSK9 locus, which is shown in Example 5, below.
To assess PCSK9 secretion, seeded Huh7 cells were transfected with mRNA encoding a catalytically-active CasX 676, dXR1, or LTRP5-ADD-ZIM3 and a gRNA with scaffold 316 and spacer targeting either the B2M or PCSK9 locus. Media supernatant was harvested at 6, 18, 36, and 87 days post-transfection to assess level of PCSK9 secretion by ELISA. Levels of PCSK9 secretion were normalized to total cell count. As an additional control, PCSK9 secretion was also measured in the media supernatant harvested from wells containing untreated, naïve cells.
Results
Quantification of normalized PCSK9 secretion level for Huh7 cells transfected with mRNA encoding catalytically-active CasX 676, dXR1, or LTRP5-ADD-ZIM3 with an NHP-conserved gRNA targeting the PCSK9 locus at the four timepoints is shown FIG. 9. The data demonstrate that use of most NHP-conserved spacers with LTRP5-ADD-ZIM3 resulted in sustained repression through 36 days post-transfection when compared with control conditions, i.e., naïve, untreated cells, cells treated with dXR1, and cells treated with the non-targeting control (using spacer 7.37 targeting the B2M locus). Specifically, in comparison to the PCSK9 secretion level observed with use of spacer 6.1 paired with CasX 676, use of TSS-proximal spacers TG-06-147, TG-06-167, TG-06-133, TG-06-146, and TG-06-154 paired with LTRP5-ADD-ZIM3 resulted in similar or further reduced level of sustained repression through day 36 (FIG. 9). Interestingly, use of TG-06-352, which is positioned beyond the 1100 bp threshold window designated here as “TSS-proximal”, also resulted in effective repression through day 36 (FIG. 9). Similar to the findings observed in Example 5, treatment with LTRP5-ADD-ZIM3 with spacer 6.157 resulted in sustained repression of secreted PCSK9 levels, while treatment with dXR1 and spacer 6.138 resulted in transient repression. Furthermore, treatment with any of the three mRNA molecules with spacer 7.37 targeting the B2M locus did not affect PCSK9 secretion (FIG. 9). However, by 87 days post-transfection, only use of spacers TG-06-157, TG-06-154, TG-06-167, and TG-06-243 paired with LTRP5-ADD-ZIM3 resulted in similar or further reduced level of sustained repression when compared to use of spacer 6.1 paired with CasX 676 (FIG. 9).
These results demonstrate that delivery of mRNA encoding an LTRP molecule with the ADD domain with the appropriate PCSK9-targeting gRNA can result in sustained repression of an endogenous target locus in human cells. Furthermore, these experiments revealed that several human spacers having consensus sequence with the non-human primate species achieved strong phenotypic effects from targeting a therapeutically-relevant locus, supporting the potential use of these select spacers in preclinical efficacy studies utilizing non-human primate models.
Example 4: Demonstration that Inclusion of the ADD Domain into an LTRP Molecule Enhances Repression of an Endogenous Locus in Mouse Hepa1-6 Cells
Experiments were performed to demonstrate that incorporation of the ADD domain into an LTRP molecule enhances the ability of LTRPs to induce durable repression of an endogenous locus in mouse Hepa1-6 liver cells, when delivered as mRNA co-transfected with a targeting gRNA.
Materials and Methods
Generation of LTRP #5 mRNA:
mRNA encoding two variants of the LTRP #5 molecule were generated by in vitro transcription (IVT): 1) an LTRP #5 molecule containing the ZIM3-KRAB domain (hereafter known as LTRP5-ZIM3) and 2) a LTRP5-ZIM3 containing the DNMT3A-ADD domain (hereafter known as LTRP5-ADD-ZIM3). Briefly, constructs encoding for a 5′UTR region, LTRP5-ZIM3 or LTRP5-ADD-ZIM3 with flanking SV40 NLSes, and a 3′UTR region were generated and cloned into a plasmid containing a T7 promoter and 79-nucleotide poly(A) tail. Sequences encoding the LTRP5-ZIM3 or LTRP5-ADD-ZIM3 molecules were codon-optimized using a codon utilization table, in addition to using a publicly available codon optimization tool and adjusting parameters such as GC content as needed. The DNA sequences encoding the LTRP5-ZIM3 and LTRP5-ADD-ZIM3 mRNAs are listed in Table 18. The corresponding mRNA sequences and protein sequences are listed in Table 19 and Table 20 respectively.







TABLE 18







Encoding DNA and RNA sequences of the LTRP5-ZIM3 and LTRP5-


ADD-ZIM3 mRNA molecules assessed in this example*.










LTRP

DNA sequence
RNA sequence


molecule
Component
or SEQ ID NO
or SEQ ID NO





LTRP5-
5′UTR
3047
3115


ZIM3
START codon +
3104
3116



NLS + linker



START codon +
3059
3117



DNMT3A catalytic



domain



Linker
3060
3118



DNMT3L
3061
3119



interaction domain



Linker
3105
3105



ZIM3-KRAB
3051
3120



Linker
3106
3121



dCasX491
3049
3122



Buffer + linker
3107
3123



NLS + STOP codon +
3108
3124



buffer sequence



3′UTR
3055
3125



Buffer sequence
TCTAG
UCUAG



Poly(A) tail
3109
3109


LTRP5-ADD-
5′UTR
3047
3115


ZIM3
START codon +
3104
3116



NLS + linker



START codon +
3111
3127



DNMT3A ADD



domain



DNMT3A catalytic
3112
3128



domain



Linker
3060
3118



DNMT3L
3061
3119



interaction domain



Linker
3105
3105



ZIM3-KRAB
3051
3120



Linker
3106
3121



dCasX491
3049
3122



Buffer + linker
3107
3123



NLS + STOP codon +
3108
3124



buffer sequence



3′UTR
3055
3125



Buffer sequence
3056
3126



Poly(A) tail
3109
3109





*Components are listed in a 5′ to 3′ order within the constructs













TABLE 19







Full-length RNA sequences of LTRP5-ZIM3 and LTRP5-ADD-ZIM3 mRNA


molecules assessed in this example. Modification ‘mψ’ = N1-methyl-pseudouridine.









LTRP
SEQ



molecule
ID NO
RNA Sequence





LTRP5-
3129
AAAmψAAGAGAGAAAAGAAGAGmψAAGAAGAAAmψAmψAAGAGCCACCAmψGGC


ZIM3

CCCmψAAGAAGAAGCGmψAAAGmψGAGCCGGAmψGAACCACGACCAGGAGmψmψ




CGACCCCCCmψAAGGmψGmψACCCmψCCCGmψCCCCGCCGAGAAGAGAAAGCCC




AmψCCGGGmψCCmψGAGCCmψGmψmψCGAmψGGCAmψCGCCACCGGmψCmψGCm




ψGGmψGCmψGAAGGACCmψGGGCAmψCCAGGmψGGAmψAGGmψACAmψmψGCCm




ψCCGAGGmψGmψGCGAGGACmψCCAmψCACCGmψGGGAamψGGmψGCGmψCAmψ




CAGGGCAAGAmψCAmψGmψACGmψGGGCGACGmψGCGGAGCGmψGACACAGAAG




CAmψAmψCCAGGAGmψGGGGCCCmψmψmψCGACCmψGGmψGAmψCGGCGGCAGC




CCmψmψGCAAmψGACCmψGAGCAmψCGmψGAACCCAGCCCGGAAGGGCCmψGmψ




ACGAGGGAACCGGCAGACmψGmψmψCmψmψCGAGmψmψmψmψACAGACmψGCmψ




GCACGACGCCCGGCCmψAAGGAAGGCGACGACCGGCCCmψmψCmψmψmψmψGGC




mψGmψmψCGAGAAmψGmψGGmψGGCCAmψGGGAGmψCAGCGACAAGCGGGAmψA




mψmψAGCCGGmψmψCCmψGGAGAGCAACCCCGmψGAmψGAmψCGAmψGCCAAGG




AAGmψGAGCGCCGCCCACCGGGCCAGAmψACmψmψCmψGGGGCAAmψCmψGCCm




ψGGCAmψGAACAGACCCCmψGGCCAGCACCGmψGAACGACAAGCmψGGAGCmψG




CAGGAGmψGCCmψGGAGCACGGCCGGAmψCGCCAAGmψmψCAGCAAGGmψGAGA




ACCAmψCACCACCCGAAGCAACAGCAmψCAAACAAGGCAAGGACCAGCACmψmψ




mψCCmψGmψGmψmψCAmψGAACGAGAAGGAGGACAmψCCmψGmψGGmψGmψACC




GAGAmψGGAGAGAGmψGmψmψCGGGmψmψCCCAGmψCCACmψACACAGAmψGmψ




CAGCAACAmψGmψCmψAGACmψGGCCAGACAGAGACmψGCmψGGGAAGAAGCmψ




GGmψCCGmψCCCmψGmψGAmψCAGACACCmψGmψmψCGCCCCmψCmψGAAGGAG




mψACmψmψCGCCmψGCGmψGAGCAGCGGCAACAGCAACGCCAACAGCCGGGGCC




CCAGCmψmψCmψCmψAGCGGCCmψGGmψGCCACmψGmψCCCmψGAGAGGGAGCC




ACAmψGGGCCCCAmψGGAGAmψCmψACAAAACCGmψGAGCGCCmψGGAAGCGGC




AGCCmψGmψGCGCGmψGCmψGAGCCmψGmψmψmψCGGAAmψAmψCGAmψAAAGm




ψCCmψGAAAAGCCmψGGGAmψmψCCmψGGAGAGCGGCmψCmψGGCmψCCGGCGG




mψGGCACCCmψGAAGmψACGmψGGAGGAmψGmψGACAAACGmψGGmψCAGACGG




GAmψGmψGGAGAAGmψGGGGCCCCmψmψCGAmψCmψGGmψGmψACGGCAGCACC




CAACCCCmψGGGCAGCmψCmψCmψGmψGCCGGmψGCCCmψGGCmψGGmψACAmψ




GmψmψmψCAGmψmψCCACCGGAmψCCmψGCAGmψACGCCCmψGCCGAGACAGGA




GmψCCCAGCGGCCAmψmψCmψmψmψmψGGAmψmψmψmψCAmψGGACAACmψmψG




CmψGCmψGACCGAGGAmψGACCAGGAAACmψACCACmψCGGmψmψCCmψGCAGA




CCGAAGCCGmψGACCCmψGCAGGACGmψGAGAGGCCGGGACmψACCAGAACGCC




AmψGCGGGmψGmψGGmψCCAACAmψCCCmψGGACmψGAAAAGCAAGCACGCACC




mψCmψGACCCCmψAAAGAAGAGGAGmψACCmψGCAGGCCCAGGmψGCGGAGCAG




AAGCAAGCmψGGACGCCCCmψAAGGmψGGAmψCmψGCmψGGmψGAAGAAmψmψG




CCmψCCmψGCCCCmψGAGAGAGmψACmψmψCAAGmψAmψmψmψCAGCCAGAAmψ




AGmψCmψGCCCCmψGGGAGGCAGCGGCGGCGGCAmψGAACAACmψCCCAGGGCA




GAGmψGACCmψmψCGAGGACGmψGACCGmψGAAmψmψmψmψACACAGGGAGAGm




ψGGCAGAGACmψGAACCCCGAGCAGAGAAACCmψGmψACCGGGAmψGmψGAmψG




CmψGGAAAACmψACAGCAAmψCmψGGmψGmψCCGmψGGGCCAGGGCGAGACCAC




AAAGCCmψGACGmψGAmψCCmψGCGmψCmψGGAGCAGGGCAAGGAACCCmψGGC




mψGGAGGAGGAGGAGGmψGCmψGGGAAGCGGACGGGCCGAGAAGAACGGCGACA




mψCGGCGGACAGAmψCmψGGAAGCCmψAAGGACGmψGAAAGAAAGCCmψGGGCG




GCCCAAGCAGCGGCGCCCCmψCCmψCCCAGCGGCGGCAGCCCAGCCGGCmψCCC




CAACCmψCmψACCGAGGAGGGCACCmψCmψGAGmψCCGCCACCCCCGAGAGCGG




CCCmψGGCACCmψCCACCGAGCCCAGCGAGGGCAGCGCACCCGGCAGCCCmψGC




CGGCAGCCCCACCmψCCACAGAGGAGGGAACCAGCACCGAGCCCAGCGAAGGCA




GCGCCCCAGGCACCAGCACCGAGCCmψAGmψGAGCAGGAGAmψmψAAACGGAmψ




CAACAAGAmψCAGAAGAAGACmψmψGmψGAAAGACAGCAACACCAAGAAGGCCG




GCAAGACAGGCCCCAmψGAAAACCCmψGCmψGGmψmψAGAGmψGAmψGACACCC




GAmψCmψGAGAGAGCGGCmψGGAAAACCmψGAGAAAGAAGCCmψGAAAAmψAmψ




CCCCCAGCCCAmψCAGCAAmψACAmψCmψAGAGCCAACCmψGAAmψAAGCmψGC




mψGACCGAmψmψACACCGAAAmψGAAGAAGGCGAmψCCmψGCAmψGmψGmψACm




ψGGGAAGAGmψmψCCAGAAGGACCCmψGmψGGGCCmψGAmψGAGCCGGGmψGGC




CCAGCCmψGCCAGCAAGAAGAmψCGAmψCAGAACAAGCmψGAAACCmψGAGAmψ




GGACGAGAAGGGCAACCmψGACCACCGCCGGCmψmψmψGCCmψGCmψCmψCAGm




ψGmψGGCCAGCCCCmψGmψmψCGmψGmψACAAGCmψGGAGCAGGmψGmψCmψGA




GAGCACGAAAAGCmψGAmψCCmψGCmψGGCCCAGCmψGAAGCCCGAGAAGGAmψ




GAGCACGAAAAGCmψGAmψCCmψGCmψGGCCCAGCmψGAAGCCCGAGAAGGAmψ




AGCGACGAAGCCGmψGACAmψAmTAGCCmψGGGAAAGmψmψmψGGGCAGAGGGC




CCmψGGAmψmψmψCmψACAGCAmψmψCAmψGmψGACCAAGGAGmψCCACCCACC




CCGmψGAAGCCCCmψGGCCCAGAmψCGCCGGAAACAGAmψACGCCmψCCGGACC




mψGmψGGGAAAGGCCCmψGAGCGACGCAmψGmψAmψGGGCACAAmψCGCCmψCC




mψmψCCmψGmψCmψAAGmψACCAGGACAmψCAmψCAmψCGAACACCAGAAGGmψ




GGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGGGAGCmψGGCCGGCA




AGGAAAACCmψGGAAmψACCCmψAGCGmψGACCCmψGCCACCmψCAGCCmψCAC




ACCAAGGAGGGCGmψmψGAmψGCCmψACAACGAAGmψGAmψCGCCCGGGmψGCG




AAmψGmψGGGmψGAACCmψGAACCmψGmψGGCAGAAGCmψGAAGCmψAAGCAGA




GAmψGAmψGCCAAGCCmψCmψGCmψGAGACmψGAAGGGAmψmψCCCmψmψCCmψ




mψmψCCmψCmψGGmψCGAGAGACAGGCCAACGAAGmψGGACmψGGmψGGGACAm




ψGGmψGmψGmψAACGmψGAAGAAGCmψGAmψCAACGAGAAAAAGGAGGAmψGGC




AAGGmψGmψmψmψmψGGCAGAAmψCmψGGCmψGGCmψACAAGAGACAGGAAGCC




CmψGAGACCAmψACCmψGAGCAGCGAGGAAGAmψCGGAAGAAGGGAAAGAAAmψ




mψCGCmψCGGmψACCAGCmψGGGCGACCmψGCmψGCmψGCACCmψGGAAAAGAA




GCACGGCGAGGACmψGGGGAAAGGmψGmψACGACGAGGCCmψGGGAGCGGAmψm




ψGACAAGAAAGmψGGAAGGCCmψGAGCAAGCACAmψCAAGCmψGGAAGAGGAAC




GGAGAAGCGAGGACGCCCAGAGCAAGGCCGCCCmψGACCGACmψGGCmψGCGGG




CmψAAGGCCAGCmψmψCGmψGAmψCGAGGGCCmψGAAGGAGGCCGACAAGGACG




AGmψmψCmψGCAGAmψGCGAGCmψGAAGCmψGCAGAAGmψGGmψACGGGGACCm




ψGCGGGGAAAGCCCmψmψCGCCAmψCGAAGCCGAGAACAGCAmψCCmψGGACAm




ψCAGCGGCmψmψCAGCAAGCAGmψACAACmψGmψGCCmψmψCAmψCmψGGCAGA




AGGACGGCGmψGAAGAAGCmψGAACCmψGmψACCmψGAmψCAmψCAACmψACmψ




mψCAAGGGCGGCAAGCmψGCGGmψmψCAAGAAGAmψCAAACCmψGAAGCCmψmψ




CGAAGCCAACAGAmψmψCmψACACCGmψGAmψCAACAAAAAGAGCGGCGAGAmψ




CGmψGCCCAmψGGAGGmψGAACmψmψCAACmψmψCGACGACCCCAACCmψGAmψ




CAmψCCmψGCCmψCmψGGCCmψmψmψGGCAAGAGACAGGGCAGAGAAmψmψCAm




ψCmψGGAACGACCmψGCmψGmψCCCmψGGAAACCGGCAGCCmψGAAGCmψGGCC




AACGGAAGAGmψGAmψCGAGAAGACACmψGmψACAACAGAAGAACCCGGCAGGA




mψGAGCCmψGCCCmψGmψmψCGmψGGCCCmψGACCmψmψCGAGCGGCGGGAGGm




ψCCmψGGACmψCCmψCCAAmψAmψCAAACCAAmψGAACCmψGAmψCGGCGmψGG




CAAGAGGCGAAAACAmψCCCCGCCGmψGAmψCGCCCmψGACCGACCCCGAGGGC




mψGCCCACmψGAGCCGGmψmψmψAAGGAmTAGCCmψGGGAAACCCAACCCACAm




ψCCmψGAGAAmψCGGCGAGAGCmψAmψAAGGAGAAGCAGCGGACCAmψCCAGGC




CAAGAAGGAGGmψGGAGCAGCGGAGAGCCGGCGGCmψACAGCCGGAAGmψACGC




CAGCAAAGCCAAGAAmψCmψGGCAGACGAmψAmψGGmψGAGAAACACCGCmψAG




AGAmψCmψGCmψGmψACmψACGCCGmψGACCCAGGAmψGCCAmψGCmψGAmψCm




ψmψCGCCAACCmψGAGCCGGGGCmψmψCGGCCGGCAGGGCAAGCGGACCmψmψC




AmψGGCCGAGAGACAGmψACACACGGAmψGGAGGACmψGGCmψGACCGCCAAGC




mψGGCCmψACGAGGGCCmψGAGCAAGACCmψACCmψGmψCCAAGACACmψGGCC




CAGmψACACCmψCCAAGACAmψGCAGCAACmψGmψGGGmψmψmψACCAmψCACC




AGCGCCGACmψACGACAGGGmψGCmψGGAGAAGCmψGAAGAAGACAGCAACAGG




CmψGGAmψGACCACAAmψmψAACGGCAAGGAGCmψGAAGGmψGGAGGGCCAGAm




ψmψACCmψACmψACAACAGAmψACAAGAGACAGAACGmψAGmψCAAGGACCmψG




mψCCGmψCGAGCmψGGAmψAGACmψGAGCGAAGAAmψCmψGmψGAACAACGACA




mψCmψCCmψCCmψGGACAAAGGGCAGAAGCGGAGAAGCmψCmψGAGCCmψCCmψ




GAAGAAAAGAmψmψCmψCCCAmψAGACCCGmψGCAGGAGAAGmψmψCGmψGmψG




CCmψGAACmψGCGGCmψmψCGAGACACACGCAGCCGAGCAAGCCGCCCmψGAAC




AmψCGCCAGAmψCCmψGGCmψGmψmψCCmψGCGGAGCCAGGAGmψACAAGAAAm




ψACCAGACAAACAAGACAACCGGCAACACCGAmψAAGAGAGCCmψmψCGmψCGA




GACCmψGGCAGmψCCmψmψmψmψACCGGAAGAAGCmψmψAAGGAGGmψGmψGGA




AACCmψGCCGmψGCGGmψCmψGGCGGAmψCmψGGCGGAGGCmψCCACCAGCCCC




AAGAAAAAGAGAAAAGmψCmψAAmψAGAmψAAGCmψGCCmψmψCmψGCGGGGCm




ψmψGCCmψmψCmψGGCCAmψGCCCmψmψCmψmψCmψCmψCCCmψmψGCACCmψG




mψACCmψCmψmψGGmψCmψmψmψGAAmψAAAGCCmψGAGmψAGGAAGmψCmψAg




AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAA


 


LTRP5-
3130
AAAmψAAGAGAGAAAAGAAGAGmψAAGAAGAAAmψAmψAAGAGCCACCAmψGGC


ADD-

CCCmψAAGAAGAAGCGmψAAAGmψGAGCCGGAmψGGAACGCCmψCGmψCmψACG


ZIM3

AGGmψGCGGCAGAAGmψGCAGAAACAmψCGAGGACAmψCmψGCAmψCmψCCmψG




CGGAmψCmψCmψGAACGmψGACCCmψGGAGCACCCACmψGmψmψCAmψCGGCGG




CAmψGmψGCCAGAACmψGmψAAAAACmψGmψmψmψmψCmψGGAGmψGmψGCCmψ




AmψCAAmψACGACGAmψGACGGCmψACCAGAGCmψACmψGCACCAmψCmψGmψm




ψGCGGCGGAAGAGAGGmψGCmψGAmψGmψGmψGGAAAmψAACAACmψGCmψGCC




GGmψGCmψmψCmψGCGmψGGAAmψGCGmψGGACCmψGCmψGGmψGGGCCCCGGC




GCCGCCCAGGCCGCmψAmψmψAAGGAAGAmψCCmψmψGGAACmψGCmψACAmψG




mψGCGGCCACAAGGGCACAmψACGGCCmψGCmψGAGACGGAGAGAGGACmψGGC




CmψAGCAGACmψGCAGAmψGmψmψCmψmψCGCCAAmψAACCACGACCAGGAGmψ




mψCGACCCCCCmψAAGGmψGmψACCCmψCCCGmψCCCCGCCGAGAAGAGAAAGC




CCAmψCCGGGmψCCmψGAGCCmψGmψmψCGAmψGGCAmψCGCCACCGGmψCmψG




CmψGGmψGCmψGAAGGACCmψGGGCAmψCCAGGmψGGAmψAGGmψACAmψmψGC




CmψCCGAGGmψGmψGCGAGGACmψCCAmψCACCGmψGGGAAmψGGmψGCGmψCA




mψCAGGGCAAGAmψCAmψGmψACGmψGGGCGACGmψGCGGAGCGmψGACACAGA




AGCAmψAmψCCAGGAGmψGGGGCCCmψmψmψCGACCmψGGmψGAmψCGGCGGCA




GCCCmψmψGCAAmψGACCmψGAGCAmψCGmψGAACCCAGCCCGGAAGGGCCmψG




mψACGAGGGAACCGGCAGACmψGmψmψCmψmψCGAGmψmψmψmψACAGACmψGC




mψGCACGACGCCCGGCCmψAAGGAAGGCGACGACCGGCCCmψmψCmψmψmψmψG




GCmψGmψmψCGAGAAmψGmψGGmψGGCCAmψGGGAGmψCAGCGACAAGCGGGAm




ψAmψmψAGCCGGmψmψCCmψGGAGAGCAACCCCGmψGAmψGAmψCGAmψGCCAA




GGAAGmψGAGCGCCGCCCACCGGGCCAGAmψACmψmψCmψGGGGCAAmψCmψGC




CmψGGCAmψGAACAGACCCCmψGGCCAGCACCGmψGAACGACAAGCmψGGAGCm




ψGCAGGAGmψGCCmψGGAGCACGGCCGGAmψCGCCAAGmψmψCAGCAAGGmψGA




GAACCAmψCACCACCCGAAGCAACAGCAmψCAAACAAGGCAAGGACCAGCACmψ




mψmψCCmψGmψGmψmψCAmψGAACGAGAAGGAGGACAmψCCmψGmψGGmψGmψA




CCGAGAmψGGAGAGAGmψGmψmψCGGGmψmψCCCAGmψCCACmψACACAGAmψG




mψCAGCAACAmψGmψCmψAGACmψGGCCAGACAGAGACmψGCmψGGGAAGAAGC




mψGGmψCCGmψCCCmψGmψGAmψCAGACACCmψGmψmψCGCCCCmψCmψGAAGG




AGmψACmψmψCGCCmψGCGmψGAGCAGCGGCAACAGCAACGCCAACAGCCGGGG




CCCCAGCmψmψCmψCmψAGCGGCCmψGGmψGCCACmψGmψCCCmψGAGAGGGAG




CCACAmψGGGCCCCAmψGGAGAmψCmψACAAAACCGmψGAGCGCCmψGGAAGCG




GCAGCCmψGmψGCGCGmψGCmψGAGCCmψGmψmψmψCGGAAmψAmψCGAmψAAA




GmψCCmψGAAAAGCCmψGGGAmψmψCCmψGGAGAGCGGCmψCmψGGCmψCCGGC




GGmψGGCACCCmψGAAGmψACGmψGGAGGAmψGmψGACAAACGmψGGmψCAGAC




GGGAmGmψGGAGAAGmψGGGGCCCCmψmψCGAmψψCmψGGmψGmψACGGCAGCA




CCCAACCCCmψGGGCAGCmψCmψmψGmψGACCGGmψGCCCmψGGCmψGGmψACA




mψGmψmψmψCAGmψmψCCACCGGAmψCCmψGCAGmψACGCCCmψGCCGAGACAG




GAGmψCCCAGCGGCCAmψmψCmψmψmψmψGGAmψmψmψmψCAmψGGACAACmψm




ψGCmψGCmψGACCGAGGAmψGACCAGGAAACmψACCACmψCGGmψmψCCmψGCA




GACCGAAGCCGmψGACCCmψGCAGGACGmψGAGAGGCCGGGACmψACCAGAACG




CCAmψGCGGGmψGmψGGmψCCAACAmψCCCmψGGACmψGAAAAGCAAGCACGCA




CCmψCmψGACCCCmψAAAGAAGAGGAGmψACCmψGCAGGCCCAGGmψGCGGAGC




AGAAGCAAGCmψGGACGCCCCmψAAGGmψGGAmψCmψGCmψGGmψGAAGAAmψm




ψGCCmψCCmψGCCCCmψGAGAGAGmψACmψmψCAAGmψAmψmψmψCAGCCAGAA




mψAGmψCmψGCCCCmψGGGAGGCAGCGGCGGCGGCAmψGAACAACmψCCCAGGG




CAGAGmψGACCmψmψCGAGGACGmψGACCGmψGAAmψmψmψmψACACAGGGAGA




GmψGGCAGAGACmψGAACCCCGAGCAGAGAAACCmψGmψACCGGGAmψGmψGAm




ψGCmψGGAAAACmψACAGCAAmψCmψGGmψGmψCCGmψGGGCCAGGGCGAGACC




ACAAAGCCmψGACGmψGAmψCCmψGCGmψCmψGGAGCAGGGCAAGGAACCCmψG




GCmψGGAGGAGGAGGAGGmψGCmψGGGAAGCGGACGGGCCGAGAAGAACGGCGA




CAmψCGGCGGACAGAmψCmψGGAAGCCmψAAGGACGmψGAAAGAAAGCCmψGGG




CGGCCCAAGCAGCGGCGCCCCmψCCmψCCCAGCGGCGGCAGCCCAGCCGGCmψC




CCCAACCmψCmψACCGAGGAGGGCACCmψCmψGAGmψCCGCCACCCCCGAGAGC




GGCCCmψGGCACCmψCCACCGAGCCCAGCGAGGGCAGCGCACCCGGCAGCCCmψ




GCCGGCAGCCCCACCmψCCACAGAGGAGGGAACCAGCACCGAGCCCAGCGAAGG




CAGCGCCCCAGGCACCAGCACCGAGCCmψAGmψGAGCAGGAGAmψmψAAACGGA




mψCAACAAGAmψCAGAAGAAGACmψmψGmψGAAAGACAGCAACACCAAGAAGGC




CGGCAAGACAGGCCCCAmψGAAAACCCmψGCmψGGmψmψAGAGmψGAmψGACAC




CCGAmψCmψGAGAGAGCGGCmψGGAAAACCCmψGAGAAAGAAGCCmψGAAAmψA




mψCCCCCAGCCCAmψCAGCAAmψACAmψCmψAGAGCCAACCmψGAAmψAAGCmψ




GCmψGACCGAmψmψACACCGAAAmψGAAGAAGGCGAmψCCmψGCAmψGmψGmψA




CmψGGGAAGAGmψmψCCAGAAGGACCCmψGmψGGGCCmψGAmψGAGCCGGGmψG




GCCCAGCCmψGCCAGCAAGAAGAmψCGAmψCAGAACAAGCmψGAAACCmψGAGA




mψGGACGAGAAGGGCAACCmψGACCACCGCCGGCmψmψmψGCCmψGCmψCmψCA




GmψGmψGGCCAGCCCCmψGmψmψCGmψGmψACAAGCmψGGAGCAGGmψGmψCmψ




GAGAAGGGCAAGGCmψmψACACCAACmψACmψmψCGGACGGmψGCAAmψGmψGG




CCGAGCACGAAAAGCmψGAmψCCmψGCmψGGCCCAGCmψGAAGCCCGAGAAGGA




mψAGCGACGAAGCCGmψGACAmψAmTAGCCmψGGGAAAGmψmψmψGGGCAGAGG




GCCCmψGGAmψmψmψCmψACAGCAmψmψCAmψGmψGACCAAGGAGmψCCACCCA




CCCCGmψGAAGCCCCmψGGCCCAGAmψCGCCGGAAACAGAmψACGCCmψCCGGA




CCmψGmψGGGAAAGGCCCmψGAGCGACGCAmGmtψAmψGGGCACAAmψCGCCmψ




CCmψmψCCmψGmψCmψAAGmψACCAGGACAmψCAmψCAmψCGAACACCAGAAGG




mψGGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGGGAGCmψGGCCGG




CAAGGAAAACCmψGGAAmψACCCmψAGCGmψGACCCmψGCCACCmψCAGCCmψC




ACACCAAGGAGGGCGmψmψGAmψGCCmψACAACGAAGmψGAmψCGCCCGGGmψG




CGAAmψGmψGGGmψGAACCmψGAACCmψGmψGGCAGAAGCmψGAAGCmψAAGCA




GAGAmψGAmψGCCAAGCCmψCmψGCmψGAGACmψGAAGGGAmψmψCCCmψmψCC




mψmψmψCCmψCmψGGmψCGAGAGACAGGCCAACGAAGmψGGACmψGGmψGGGAC




AmψGGmψGmψGmψAACGmψGAAGAAGCmψGAmψCAACGAGAAAAAGGAGGAmψG




GCAAGGmψGmψmψmψmψGGCAGAAmψCmψGGCmψGGCmψACAAGAGACAGGAAG




CCCmψGAGACCAmψACCmψGAGCAGCGAGGAAGAmψCGGAAGAAGGGAAAGAAA




mψmψCGCmψCGGmψACCAGCmψGGGCGACCmψGCmψGCmψGCACCmψGGAAAAG




AAGCACGGCGAGGACmψGGGGAAAGGmψGmψACGACGAGGCCmψGGGAGCGGAm




ψmψGACAAGAAAGmψGGAAGGCCmψGAGCAAGCACAmψCAAGCmψGGAAGAGGA




ACGGAGAAGCGAGGACGCCCAGAGCAAGGCCGCCCmψGACCGACmψGGCmψGCG




GGCmψAAGGCCAGCmψmψCGmψGAmψCGAGGGCCmψGAAGGAGGCCGACAAGGA




CGAGmψmψCmψGCAGAmψGCGAGCmψGAAGCmψGCAGAAGmψGGmψACGGGGAC




CmψGCGGGGAAAGCCCmψmψCGCCAmψCGAAGCCGAGAACAGCAmψCCmψGGAC




AmψCAGCGGCmψmψCAGCAAGCAGmψACAACmψGmψGCCmψmψCAmψCmψGGCA




GAAGGACGGCGmψGAAGAAGCmψGAACCmψGmψACCmψGAmψCAmψCAACmψAC




mψmψCAAGGGCGGCAAGCmvGCGGmψmψCAAGAAGAmψCAAACCmvGAAGCCmψ




mψCGAAGCCAACAGAmψmψCmψACACCGmψGAmψCAACAAAAAGAGCGGCGAGA




mψCGmψGCCCAmψGGAGGmψGAACmψmψCAACmψmψCGACGACCCCAACCmψGA




mψCAmψCCmψGCCmψCmψGGCCmψmψmψGGCAAGAGACAGGGCAGAGAAmψmψC




AmψCmψGGAACGACCmψGCmψGmψCCCmψGGAAACCGGCAGCCmψGAAGCmψGG




CCAACGGAAGAGmψGAmψCGAGAAGACACmψGmψACAACAGAAGAACCCGGCAG




GAmψGAGCCmψGCCCmψGmψmψCGmψGGCCCmψGACCmψmψCGAGCGGCGGGAG




GmψCCmψGGACmψCCmψCCAAmψAmψCAAACCAAmψGAACCmψGAmψCGGCGmψ




GGCAAGAGGCGAAAACAmψCCCCGCCGmψGAmψCGCCCmψGACCGACCCCGAGG




GCmψGCCCACmψGAGCCGGmψmψmψAAGGAmTAGCCmψGGGAAACCCAACCCAC




AmψCCmψGAGAAmψCGGCGAGAGCmψAmψAAGGAGAAGCAGCGGACCAmψCCAG




GCCAAGAAGGAGGmψGGAGCAGCGGAGAGCCGGCGGCmψACAGCCGGAAGmψAC




AGAGAmψGmψGCmψGmψACmψACGCCGmψGACCCAGGAmψGCCAmψGCmψGAmψ




CmψmψCGCCAACCmψGAGCCGGGGCmψmψCGGCCGGCAGGGCAAGCGGACCmψm




ψCAmψGGCCGAGAGACAGmψACACACGGAmψGGAGGACmψGGCmψGACCGCCAA




GCmψGGCCmψACGAGGGCCmψGAGCAAGACCmψACCmψGmψCCAAGACACmψGG




CCCAGmψACACCmψCCAAGACAmψGCAGCAACmψGmψGGGmψmψmψACCAmψCA




CCAGCGCCGACmψACGACAGGGmψGCmψGGAGAAGCmψGAAGAAGACAGCAACA




GGCmψGGAmψGACCACAAmψmψAACGGCAAGGAGCmψGAAGGmψGGAGGGCCAG




AmψmψACCmψACmψACAACAGAmψACAAGAGACAGAACGmψAGmψCAAGGACCm




ψGmψCCGmψCGAGCmψGGAmψAGACmψGAGCGAAGAAmψCmψGmψGAACAACGA




CAmψCmψCCmψCCmψGGACAAAGGGCAGAAGCGGAGAAGCmψCmψGAGCCmψCC




mψGAAGAAAAGAmψmψCmψCCCAmψAGACCCGmψGCAGGAGAAGmψmψCGmψGm




ψGCCmψGAACmψGCGGCmψmψCGAGACACACGCAGCCGAGCAAGCCGCCCmψGA




ACAmψCGCCAGAmψCCmψGGCmψGmψmψCCmψGCGGAGCCAGGAGmψACAAGAA




AmψACCAGACAAACAAGACAACCGGCAACACCGAmψAAGAGAGCCmψmψCGmψC




GAGACCmψGGCAGmψCCmψmψmψmψACCGGAAGAAGCmψmψAAGGAGGmψGmψG




GAAACCmψGCCGmψGCGGmψCmψGGCGGAmψCmψGGCGGAGGCmψCCACCAGCC




CCAAGAAAAAGAGAAAAGmψCmψAAmψAGAmψAAGCmψGCCmψmψCmψGCGGGG




CmψmψGCCmψmψCmψGGCCAmψGCCCmψmψCmψmψCmψCmψCCCmψmψGCACCm




ψGmψACCmψCmψmψGGmψCmψmψmψGAAmψAAAGCCmψGAGmψAGGAAGmψCmψ




AGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAA
















TABLE 20







Full-length protein sequences of LTRP5-ZIM3 and LTRP5-


ADD-ZIM3 mRNA molecules assessed in this example










LTRP molecule
Amino acid sequence SEQ ID NO







LTRP5-ZIM3
3131



LTRP5-ADD-ZIM3
3132










Synthesis of gRNAs:

Two gRNAs targeting the mouse PCSK9 locus were designed using gRNA scaffold 316 and chemically synthesized. PCSK9-targeting spacers 27.88 and 27.94 (sequences listed in Table 14) were assessed in this example. As shown in Example 2, use of spacer 27.88 was less effective in achieving PCSK9 knockdown than use of spacer 27.94.
Transfection of mRNA and gRNA into Hepa1-6 cells and intracellular PCSK9 staining were performed as described in Example 2. Briefly, each well of seeded Hepa1-6 cells was transfected with 300 ng of mRNA encoding LTRP5-ZIM3 or LTRP5-ADD-ZIM3 and 150 ng of PCSK9-targeting gRNA with spacer 27.88 or 27.94. Intracellular levels of PCSK9 protein were measured at various timepoints, up to day 53 post-transfection using an intracellular staining protocol as described earlier in Example 2. A non-targeting gRNA was used as an experimental control.
Results
To determine the effects of incorporating the ADD domain into an LTRP molecule on activity, i.e., inducing more durable repression of an endogenous locus in vitro, mRNAs encoding LTRP5-ZIM3 or LTRP5-ADD-ZIM3 were co-transfected with a PCSK9-targeting gRNA into Hepa1-6 cells. The quantification of the resulting PCSK9 knockdown is shown in FIGS. 10A-10B. The data demonstrate a noticeable improvement in achieving PCSK9 knockdown when the cells were treated with LTRP5-ADD-ZIM3 than with LTRP5-ZIM3, and this improvement was more pronounced when using a PCSK9-targeting gRNA containing the weaker spacer 27.88. Further supporting the data discussed in Example 2, use of spacer 27.94 resulted in more durable repression than use of spacer 27.88 by day 53 when paired with either the LTRP5-ZIM3 or LTRP5-ADD-ZIM3 molecule (FIG. 10B). As expected, use of the non-targeting spacer did not result in PCSK9 knockdown.
These experiments demonstrate that use of LTRP constructs with the ADD domain can result in increased durable repression of an endogenous locus in cells compared to constructs without the ADD domain. Furthermore, these findings show that LTRP molecules with the ADD domain can be delivered as mRNA and co-transfected with a targeting gRNA to cells to induce effective silencing.
Example 5: Demonstration that mRNA Encoding for LTRPs Containing the ADD Domain can Induce Repression of an Endogenous Locus in Multiple Human Cell Lines
Experiments were performed to demonstrate that mRNA encoding for LTRPs containing the ADD domain can induce long-term repression of an endogenous target locus in various human cell lines, when delivered as mRNA co-transfected with a targeting gRNA.
Materials and Methods
Generation of mRNA:
mRNA encoding the following molecules were generated by IVT following similar methods as described in Example 2: 1) a catalytically-active CasX 676, 2) dXR1 (as described in Example 2), and 3) LTRP5-ADD-ZIM3 (as described in Example 4). Sequences encoding these molecules were codon-optimized using a codon utilization table, in addition to using a publicly available codon optimization tool and adjusting parameters such as GC content. The DNA and mRNA sequences encoding the catalytically-active CasX 676 are shown in Table 21 and Table 22 respectively. The DNA and mRNA sequences encoding for dXR1 are shown in Table 11 and Table 12 respectively. The DNA and mRNA sequences encoding for LTRP5-ADD-ZIM3 are shown in Table 18 and Table 19 respectively.







TABLE 21







Encoding sequences of the catalytically-active CasX


676 mRNA molecule assessed in this example*.













DNA sequence


CasX mRNA ID
Component (ID)
Description
or SEQ ID NO:





CasX 676 mRNA
5′UTR
TriLink
3047



START codon + c-

3133



MYC NLS



CasX 676

3134



c-MYC NLS +

3135



STOP codons



3′UTR
Mouse HBA
3055



Xbal restriction site

TCTAG



(partial)



Poly(A) tail

3057





*Components are listed in a 5′ to 3′ order within the constructs













TABLE 22







Full-length RNA sequences of catalytically-active CasX 676 mRNA molecule


assessed in this example. Modification ‘mψ’ = N1-methyl-pseudouridine.









CasX
SEQ



mRNA
ID NO
RNA Sequence





CasX 676
3136
AAAmψAAGAGAGAAAAGAAGAGmψAAGAAGAAAmψAmψAAGAGCCACCAmψGGCCCCmψGCmψG


mRNA

CCAAGAGAGmψGAAGCmψGGAmψAGCAGACAGGAGAmψCAAGCGGAmψmψAAmψAAAAmψmψCG




GAGAAGACmψGGmψGAAGGAmψmψCmψAACACAAAGAAGGCmψGGCAAGACACGGGGCCCmψAm




ψGAAGACACmψGCmψGGmψGAGAGmψGAmψGACACCCGACCmψGAGAGAAAGACmψGGAAAACC




mψGAGAAAGAAGCCmψGAGAAmψAmψCCCCCAGCCCAmψCAGCAACACAAGCCGGGCCAACCmψ




GAAmψAAGCmψGCmψGACCGACmψACACCGAAAmψGAAGAAGGCCAmψCCmψGCACGmψGmψAm




ψmψGGGAAGAGmψmψCCAGAAAGACCCAGmψCGGCCmψGAmψGAGCAGAGmψGGCmψCAGCCmψ




GCCAGCAAGAAGAmψCGAmψCAGAACAAGCmψGAAGCCCGAAAmψGGACGAGAAGGGGAACCmψ




GACAACCGCCGGCmψmψmψGCCmψGmψAGCCAGmψGCGGCCAGCCCCmψGmψmψmψGmψGmψAC




AAACmψGGAACAGGmψGAGCGAAAAGGGCAAGGCmψmψACACGAAmψmψACmψmψCGGCAGAmψ




GCAACGmψGGCCGAGCACGAGAAGCmψGAmψCAAGCmψGGCCCAGCmψGAAGCCmψGAGAAGGA




mψAGCGAmψGAGGCAGmψGACAmψAmψmψCCCmψGGGCAAGmψmψCGGACAGCGGGCCCmψGGA




mψmψmψmψmψAmψmψCCAmψmψCAmψGmψGACCAAGGAAmψCCACCCACCCCGmψCAAGCCmψC




mψmψGCCCAAAmψmψGCCGGCAACAGAmψACGCCmψCCAGCCCCGmψGGGCAAGGCCCmψGAGC




GACGCCmψGmψAmψGGGCACCAmψCGCCAGCmψmψCCmψGmψCmψAAGmψACCAGGACAmψmψA




mψCAmψCGAGCACCAGAAGGmψGGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGCGA




GCmψGGCCGGCAAGGAAAACCmψGGAGmψAmψCCmψAGCGmψGACCCmψGCCmψCCmψCAGCCm




ψGGGmψGAACCmψGAAmψCmψGmψGGCAGAAGCmψGAAGCmψGmψCmψAGAGACGACGCCAAGC




ψGGGmψGAACCmψGAAmψCmψGmψGGCAGAAGCmψGAAGCmψGmψCmψAGAGACGACGCCAAGC




CCCmψGCmψGAGACmψGAAGGGCmψmψCCCCAGCmψmψCCCmψCmψGGmψGGAGAGACAGGCAA




AmψGAAGmψGGACmψGGmψGGGACAmψGGmψGmψGmψAACGmψGAAGAAGCmψGAmψCAAmψGA




GAAGAAGGAGGACGGCAAAGmψGmψmψCmψGGCAGAAmψCmψGGCCGGCmψACAAGCGmψCAGG




AGGCCCmψGCGGCCCmψACCmψGAGCAGCGAGGAAGACAGAAAGAAGGGCAAGAAGmψmψCGCC




CGGmψAmψCAGCmψGGGGGACCmψGCmψGCmψGCACCmψCGAGAAGAAGCACGGCGAAGACmψG




GGGGAAGGmψGmψACGAmψGAGGCCmψGGGAGCGGAmψCGAmψAAGAAGGmψGGAGGGCCmψGA




GCAAGCACAmψCAAGCmψGGAGGAGGAACGGAGAmψCmψGAGGACGCCCAGAGCAAGGCCGCCC




mψGACCGACmψGGCmψGAGAGCCAAGGCCAGCmψmψCGmψCAmψCGAGGGGCmψGAAGGAGGCC




GACAAGGACGAGmψmψCmψGCCGGmψGCGAACmψGAAGCmψGCAGAAGmψGGmψACGGAGAmψC




mψGAGAGGCAAACCmψmψmψCGCCAmψCGAGGCCGAGAACAGCAmψCCmψGGACAmψCAGCGGC




mψmψCAGCAAGCAGmψACAACmψGCGCCmψmψmψAmψmψmψGGCAGAAGGACGGAGmψGAAGAA




GCmψGAACCmψGmψACCmψGAmψCAmψCAACmψAmψmψmψCAAGGGCGGCAAGCmψGAGAmψmψ




CAAGAAGAmψCAAGCCmψGAAGCCmψmψCGAGGCCAACAGAmψmψCmψACACCGmψGAmψmψAA




CAAGAAAAGCGGAGAGAmψCGmψGCCAAmψGGAAGmψGAACmψmψCAACmψmψCGACGACCCmψ




AACCmψGAmψCAmψCCmψGCCCCmψGGCAmψmψmψGGCAAGCGGCAGGGCAGAGAGmψmψCAmψ




CmψGGAACGACCmψGCmψGmψCmψCmψGGAGACCGGCAGCCmψGAAGCmψGGCCAACGGCAGAG




mψGAmψCGAGAAGACACmψGmψACAACAGACGAACCAGACAAGACGAGCCCGCCCmψGmψmψmψ




GmψGGCCCmψGACCmψmψCGAGAGAAGAGAGGmψGCmψGGACAGCAGCAAmψAmψCAAGCCmψA




mψGAACCmψGAmψCGGCGmψGGACCGGGGCGAGAACAmψCCCmψGCCGmψGAmψCGCCCmψmψA




CCGACCCCGAGGGAmψGCCCmψCmψGAGCCGGmψmψmψAAAGACAGCCmψGGGCAACCCmψACC




CACAmψCCmψGAGAAmψmψGGCGAGmψCCmψACAAGGAGAAGCAGAGAACCAmψCCAGGCCAAG




AAGGAGGmψGGAGCAGCGGCGGGCmψGGCGGCmψACmψCCCGGAAGmψACGCCAGCAAGGCCAA




GAACCmψGGCCGACGACAmψGGmψmψAGAAAmψACCGCCAGAGACCmψCCmψGmψACmψACGCm




ψGmψGACCCAGGACGCCAmψGCmψGAmψCmψmψCGAGAACCmψGAGCAGAGGCmψmψCGGCAGA




CAGGGCAAGAGAACCmψmψCAmψGGCCGAGAGACAGmψACACCCGGAmψGGAGGACmψGGCmψG




ACCGCCAAGCmψGGCCmψACGAGGGCCmψGCCCmψCmψAAGACCmψACCmψGmψCCAAGACCmψ




mψGGCACAGmψACACCAGCAAGACAmψGCmψCmψAACmψGCGGCmψmψCACAAmψCACGAGCGC




CGACmψACGACCGGGmψGCmψGGAGAAACmψGAAGAAGACCGCCACAGGCmψGGAmψGACCACC




AmψmψAACGGCAAGGAGCmψGAAGGmψGGAGGGCCAGAmψCACCmψACmψACAACAGGmψACAA




ACGGCAGAACGmψGGmψGAAGGACCmψGAGCGmψGGAACmψGGAmψAGACmψGAGCGAGGAAAG




CGmψAAACAAmψGACAmψCAGCAGCmψGGACCAAGGGCCGGAGCGGCGAGGCCCmψGAGCCmψG




CmψGAAGAAGAGAmψmψCmψCCCACAGACCAGmψGCAGGAGAAGmψmψCGmψGmψGmψCmψGAA




CmψGCGGCmψmψCGAGACCCACGCCGACGAGCAAGCCGCCCmψGAACAmψCGCCCGGmψCmψmψ




GGCmψmψmψmψCCmψGCGGAGCCAGGAGmψACAAGAAGmψACCAGACAAACAAGACCACAGGCA




ACACAGACAAGAGAGCCmψmψCGmψCGAGACCmψGGCAGAGCmψmψCmψACAGAAAGAAGCmψG




AAGGAGGmψGmψGGAAGCCmψGCCGmψGGGAAGCCCCGCmψGCCAAGAGAGmψGAAGCmψGGAC




mψAAmψAGAmψAAGCmψGCCmψmψCmψGCGGGGCmψmψGCCmψmψCmψGGCCAmψGCCCmψmψC




mψmψCmψCmψCCCmψmψGCACCmψGmψACCmψCmψmψGGmψCmψmψmψGAAmψAAAGCCmψGAG




mψAGGAAGmψCmψAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA









Synthesis of gRNAs:

gRNAs targeting the human PCSK9 locus were designed using gRNA scaffold 316 and chemically synthesized. Furthermore, a B2M-targeting gRNA was used as an experimental control. Sequences of targeting spacers as assessed in this example as listed in Table 23.







TABLE 23







Sequences of spacers assessed in this example.










Spacer ID
Target
Targeting spacer sequence (RNA)
SEQ ID NO





7.37
human B2M
GGCCGAGAUGUCUCGCUCCG
3137


 


6.1
human PCSK9
GAGGAGGACGGCCUGGCCGA
1834


 


6.125
human PCSK9
AGAAAGAGCAAGCCUCAUGU
1845


 


6.138
human PCSK9
AGGGAUUUAUACUACAAAGA
1852


 


6.153
human PCSK9
GUUAAUGUUUAAUCAGAUAG
1866


 


6.157
human PCSK9
GGGUCUGAGCCUGGAGGAGU
1869


 


6.172
human PCSK9
GCUGAAACAGAUGGAAUACU
1879


 


6.181
human PCSK9
UCAUCUGCACUCGUGGCCAC
2228









Transfection of mRNA and gRNA into HepG2 Cells, Hep3B Cells, and Huh7 Cells and ELISA to Assess PCSK9 Secretion:

The following three human hepatocyte cancer cell lines were used in this experiment: HepG2 cells, Hep3B cells, and Huh7 cells. ˜15,000 cells of each cell line were seeded per well; the next day, seeded cells were transfected with mRNA encoding a catalytically-active CasX 676, dXR1, or LTRP5-ADD-ZIM3 and a gRNA with scaffold 316 and spacer targeting either the B2M or PCSK9 locus (see Table 23 for specific spacers and sequences). Media supernatant was harvested at 4 days post-transfection to assess level of PCSK9 secretion by ELISA, and levels of PCSK9 secretion were normalized to total cell count and illustrated in FIGS. 11A-11C. Culturing of treated Huh7 cells continued, and media supernatant was harvested at 14 and 27 days post-transfection for measuring PCSK9 secretion by ELISA. As an additional experimental control, PCSK9 secretion was also measured in the media supernatant harvested from wells containing untreated, naïve cells.
Results
HepG2 cells, Hep3B cells, and Huh7 cells were transfected with mRNA encoding catalytically-active CasX 676, dXR1, or LTRP5-ADD-ZIM3 with a gRNA targeting either the B2M or the PCSK9 locus, and secreted PCSK9 levels were measured. Quantification of normalized PCSK9 secretion levels for each condition at 4 days post-transfection is depicted in FIGS. 11A-11C. The data demonstrate that the most efficient knockdown of PCSK9 secretion by CasX 676, dXR1, or LTRP5-ADD-ZIM3 was observed in Huh7 cells, while HepG2 cells did not exhibit as efficient of a knockdown of secreted PCSK9 levels (FIG. 11A-11C). Meanwhile, Hep3B cells demonstrated low PCSK9 secretion levels overall, illustrating that, of the cell lines used, the Hep3B cell line is the least amenable to treatment to induce and demonstrate PCSK9 repression (FIG. 11A-11C).
Culturing of treated Huh7 cells continued up to day 27 post-transfection, and PCSK9 secretion was measured at day 14 and day 27. The bar plot in FIG. 12 shows the quantification results of PCSK9 repression at day 4, day 14, and day 27 timepoints displayed as PCSK9 knockdown relative to the levels detected for the naïve control at the day 4 timepoint. The data demonstrate that treatment of Huh7 cells with LTRP5-ADD-ZIM3 with gRNAs having spacers 6.138 and 6.157 resulted in the most effective repression of PCSK9 secretion, and this repression was sustained through day 27 post-transfection (FIG. 12). Similarly, sustained knockdown was observed when Huh7 cells were treated with catalytically-active CasX 676 with spacer 6.1. While treatment with dXR1 and spacer 6.138 resulted in an initial strong repression at day 4, this repressive effect was transient as PCSK9 secretion levels returned to baseline levels at day 14 and day 27 post-transfection (FIG. 12). As anticipated, treatment with any of the three mRNA molecules with spacer 7.37 targeting the B2M locus did not affect PCSK9 secretion levels during this time course experiment.
These experiments demonstrate that use of LTRP molecules with the ADD domain with the appropriate targeting spacer can result in long-term silencing of an endogenous target locus in various human cell lines. These findings also show that LTRP molecules with the ADD domain can be co-delivered as mRNA with a targeting gRNA to cells to induce repression.
Example 6: Demonstration that Use of Certain PCSK9-Targeting Spacers can Result in Undesired Intracellular PCSK9 Retention
Secretory proteins that cannot properly fold are consequently retained in the endoplasmic reticulum (ER) to be ultimately targeted for proteasomal degradation. However, excessive protein accumulation in the ER could cause ER stress. PCSK9 is initially synthesized as a zymogen (known as pro-PCSK9) that undergoes autocatalytic cleavage during maturation in the ER into an inactive secretory protein (also known as mature or processed PCSK9). Furthermore, certain gain-of-function mutations in the PCSK9 gene resulting in hypercholesterolemia have been shown to be associated with intracellular PCSK9 retention in the ER (Benjannet S et al. NARC-1/PCSK9 and its natural mutants: zymogen cleavage and effects on the low density lipoprotein (LDL) receptor and LDL cholesterol. J. Biol. Chem. 279:48865-48875 (2004); Park S W et al., Post-transcriptional regulation of low density lipoprotein receptor protein by proprotein convertase subtilisin/kexin type 9a in mouse liver. J. Biol. Chem. 279:50630-50638 (2004); Uribe K B et al. A Systematic Approach to Assess the Activity and Classification of PCSK9 Variants. Int. J. Mol. Sci. 22:13602 (2021)), an indication that targeting certain regions of the PCSK9 locus may result in undesired intracellular retention. As a result, experiments were performed to demonstrate that use of certain PCSK9-targeting spacers can result in unwanted increase in intracellular PCSK9 levels that may possibly cause unexpected consequences such as abnormal ER stress.
Materials and Methods
In vitro transcription of CasX 676 mRNA #2 (sequence listed in Table 28, below) was performed as described in Example 7, below. Guide RNAs using scaffold 316 and a PCSK9-targeting spacer were synthesized with a v1 modification profile (as discussed in Example 7). Spacers 6.1, 6.8, 6.86, 6.114, 6.197, and 6.203 (sequences listed in Table 24) were assessed for intracellular PCSK9 retention.







TABLE 24







Sequences of human PCSK9-targeting spacers











Spacer ID
Spacer DNA sequence
SEQ ID NO:
Spacer RNA sequence
SEQ ID NO:





6.1
GAGGAGGACGGCCTGGCCGA
2977
GAGGAGGACGGCCUGGCCGA
1834


 


6.8
TGGCTTCCTGGTGAAGATGA
3139
UGGCUUCCUGGUGAAGAUGA
2009


 


6.86
TGGTGAAGATGAGTGGCGAC
3464
UGGUGAAGAUGAGUGGCGAC
3466


 


6.114
TCCCAGGCCTGGAGTTTATT
3141
UCCCAGGCCUGGAGUUUAUU
2291


 


6.197
AGGTCATCACAGTTGGGGCC
3465
AGGUCAUCACAGUUGGGGCC
3467


 


6.203
CCAGGAGTGGGAAGCGGCGG
3144
CCAGGAGUGGGAAGCGGCGG
2341









In Vitro Delivery of CasX mRNA and gRNA Via Transfection:

To determine whether use of certain PCSK9-targeting spacers would result in potential intracellular PCSK9 retention, ˜50,000 HepG2 cells were seeded per well in a 96-well plate. CasX 676 mRNA #2 was transfected into HepG2 cells with a PCSK9-targeting gRNA using Lipofectamine™. After a media change, the following were harvested two days post-transfection: 1) media supernatant to measure secreted PCSK9 protein levels by ELISA; and 2) transfected cells for western blotting analysis to evaluate intracellular PCSK9 levels. Harvested cells were subjected to whole cell lysate extraction for western blotting analysis. Briefly, extracted protein samples were resolved by SDS-PAGE followed by immunoblotting to analyze levels of pro-PCSK9 and processed PCSK9, which were quantified by densitometry. Secreted PCSK9 levels in the media supernatant were analyzed using the BioLegend® ELISA MAX™ kit following the manufacturer's instructions. Naïve, untreated cells and cells transfected with CasX 676 mRNA #2 only served as two experimental controls.
Results
Following transfection of HepG2 cells with CasX 676 mRNA #2 and a PCSK9-targeting gRNA, secreted PCSK9 levels in the media supernatant were quantified by ELISA, and the results are shown in FIG. 13. The data demonstrate that transfection of HepG2s cells with CasX 676 mRNA and the PCSK9-targeting gRNAs resulted in reduced secreted PCSK9 levels to varying degrees. Of the spacers tested, use of spacers 6.1, 6.8, 6.86, and 6.203 resulted in nearly 50% reduction in secreted levels compared to cells transfected with CasX 676 mRNA only (FIG. 13).
Intracellular levels of PCSK9 were also evaluated in the transfected HepG2 cells. FIG. 14 is a western blot analysis of PCSK9 protein levels, along with the total protein loading control, in the transfected HepG2 cells, and FIG. 15 is a bar plot illustrating the densitometry quantification for pro-PCSK9, processed PCSK9, and total PCSK9 protein levels normalized to total PCSK9 levels from the naïve condition. The data show that of the PCSK9-targeting spacers assessed, only use of spacer 6.1 did not result in substantially increased pro-PCSK9 levels, therefore indicating that use of spacer 6.1 did not increase intracellular protein levels (FIGS. 14-15). While use of spacer 6.203 also did not noticeably increase intracellular protein levels, its use resulted in increased processed PCSK9 levels (FIGS. 14-15), appearing to contradict findings of its effects to reduce secreted PCSK9 levels (FIG. 13) when compared to the either the naïve or CasX mRNA only control. This apparent contradictory effect observed by use of spacer 6.203 indicates that retention of processed PCSK9 may be involved in the mechanism by which use of spacer 6.203 decreases PCSK9 secretion.
The results demonstrate that although use of certain PCSK9-targeting spacers would result in decreased secreted PCSK9 levels, there is a possibility for some of these seemingly effective spacers to exhibit potentially undesired characteristics, such as increased intracellular protein retention. Therefore, the findings from these experiments indicate the use of assessing increased intracellular protein retention as a potential safety criterion to identify effective targeting spacers for therapeutic use.
Example 7: Design and Assessment of Modified gRNAs in Improving Editing when Delivered Together with CasX mRNA In Vitro and In Vivo
Experiments were performed to identify new gRNA variant sequences and demonstrate that chemical modifications of these gRNA variants enhance the editing efficiency of the CasX:gRNA system when delivered in vitro in conjunction with CasX mRNA.
Materials and Methods
Synthesis of gRNAs:
All gRNAs tested in this example were chemically-synthesized and were derived from gRNA scaffolds 174, 235, and 316. The sequences of gRNA scaffolds 174, 235, and 316 and their chemical modification profiles are listed in Table 25. The sequences of the resulting gRNAs, including spacers targeting PCSK9, B2M, or ROSA26, and their chemical modification profiles assayed in this example are listed in Table 26. A schematic of the structure of gRNA scaffold variants 174, 235, and 316 are shown in FIGS. 19A-19C, respectively, and the sites of chemical modifications of the gRNA variants are shown schematically in FIGS. 16A, 16B, 18, 24, and 25.







TABLE 25







Sequences of gRNA scaffolds with their different chemical modification profiles


(denoted by version number), where “NNNNNNNNNNNNNNNNNNNN” is a spacer


placeholder. Chemical modifications: * = phosphorothioate bond; m = 2′OMe modification









gRNA scaffold

SEQ ID


(version)
gRNA sequence
NO:





174 (v0)
ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUGUCGUAG
2947



UGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAGNNNNNNNNNNNNNNNNNNN




N



 


174 (v1)
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUG
2948



UCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAGNNNNNNNNNNNNN




NNNNmN*mN*mN



 


174 (v2)
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUG
2949



UCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAAGNNNNNNNNNNNNN




NNNNNNN*mU*mU*mU



 


174 (v3)
mA*mC*mU*mGmGmCmGmCmUmUmUmUmAmUmCmUmGmAmUUACUUUGmAmGmA
2950



mGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGUAGUGmGmGmUmAmAmA




mGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmCmAmUmCmAAAGNNN




NNNNNNNNNNNNNNmN*mN*mN



 


174 (v4)
mA*mC*mU*mGmGmCmGmCUUUUmAmUmCmUmGmAmUUACUUUGmAmGmAmGmC
2951



mCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGUAGUGmGmGmUmAmAmAmGmC




mUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmCmAmUCAAAGNNNNNNNNN




NNNNNNNNmN*mN*mN



 


174 (v5)
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGAmCmUA
2952



UmGmUmCmGUAGUGGGUAAAmGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmG




mAmGmCAUCAAAGNNNNNNNNNNNNNNNNNmN*mN*mN



 


174 (v6)
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGACUAUG
2953



UCGUAGUGGGUAAAmGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmC




AUCAAAGNNNNNNNNNNNNNNNNNmN*mN*mN



 


174 (v7)
mA*mC*mU*GGmCGmCmUUUUAmUmCUGAUUACUUUGmAmGAGCCmAmUmCmAm
2954



CCAGCmGmAmCmUAUmGmUmCmGUAGUGGmGmUAmAmAmGmCmUmCmCmCmUmC




mUmUmCmGmGmAmGmGmGmAmGmCmAmUCAAAGNNNNNNNNNNNNNNNNN*mN*




mN*mN



 


174 (v8)
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCmAmUmCmAmCCAGCmG
2955



mAmCmUAUmGmUmCmGUAGUGGmGmUmAmAAmGmCmUmCmCmCmUmCmUmUmCm




GmGmAmGmGmGmAmGmCmAmUCAAAGNNNNNNNNNNNNNNNNN*mN*mN*mN



 


174 (v9)
mA*mC*mU*GGmCmGCmUUUUAmUmCUGAUUACUUUGmAmGAGCCAUCACCAGC
2956



mGmAmCmUAUmGmUmCmGUAGUGGGUAAAmGmCmUmCmCmCmUmCmUmUmCmGm




GmAmGmGmGmAmGmCAUCAAAGNNNNNNNNNNNNNNNNN*mN*mN*mN



 


235 (v0)
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUGUCGUAG
2957



UGGGUAAAGCCGCUUACGGACUUCGGUCCGUAAGAGGCAUCAGAGNNNNNNNNN




NNNNNNNNNNN



 


235 (v1)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUG
2958



UCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUCCGUAAGAGGCAUCAGAGNNN




NNNNNNNNNNNNNNmN*mN*mN



 


235 (v2)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUG
2959



UCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUCCGUAAGAGGCAUCAGAGNNN




NNNNNNNNNNNNNNNNN*mU*mU*mU



 


235 (v3)
mA*mC*mU*mGmGmCmGmCmUmUmCmUmAmUmCmUmGmAmUUACUCUGmAmGmC
2960



mGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGUAGUGmGmGmUmAmAmA




mGmCmCmGmCmUmUmAmCmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmA




mGmGmCmAmUmCmAGAGNNNNNNNNNNNNNNNNNmN*mN*mN



 


235 (v4)
mA*mC*mU*mGmGmCmGmCUUCUmAmUmCmUmGmAmUUACUCUGmAmGmCmGmC
2961



mCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGUAGUGmGmGmUmAmAmAmGmC




mCmGmCmUmUmAmCmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmG




mCmAmUCAGAGNNNNNNNNNNNNNNNNNmN*mN*mN



 


235 (v5)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAmCmUA
2962



UmGmUmCmGUAGUGGGUmAmAmAmGmCmCmGmCmUmUmAmCmGmGmAmCmUmUm




CmGmGmUmCmCmGmUmAmAmGmAmGmGmCAUCAGAGNNNNNNNNNNNNNNNNNm




N*mN*mN



 


235 (v6)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUG
2963



UCGUAGUGGGUmAmAmAmGmCmCmGmCmUmUmAmCmGmGmAmCmUmUmCmGmGm




UmCmCmGmUmAmAmGmAmGmGmCAUCAGAGNNNNNNNNNNNNNNNNNmN*mN*m




N



 


235 (v7)
mA*mC*mU*GGmCGmCmUUCUAmUmCUGAUUACUCUGmAmGCGCCmAmUmCmAm
2964



CCAGCmGmAmCmUAUmGmUmCmGUAGUGGmGmUmAmAAmGmCmCmGmCmUmUmA




mCmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCmAmUCAGAGN




NNNNNNNNNNNNNNNN*mN*mN*mN



 


235 (v8)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCmAmUmCmAmCCAGCmG
2965



mAmCmUAUmGmUmCmGUAGUGGmGmUmAmAAmGmCmCmGmCmUmUmAmCmGmGm




AmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCmAmUCAGAGNNNNNNNN




NNNNNNNNN*mN*mN*mN



 


235 (v9)
mA*mC*mU*GGmCGmCmUUCUAmUmCUGAUUACUCUGmAmGCGCCAUCACCAGC
2966



mGmAmCmUAUmGmUmCmGUAGUGGGUAAAmGmCmCmGmCmUmUmAmCmGmGmAm




CmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCAUCAGAGNNNNNNNNNNNN




NNNNN*mN*mN*mN



 


316 (v0)
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUGUCGUAG
2967



UGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGAGNNNNNNNNNNNNNNNNNNN




N



 


316 (v1)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUG
2968



UCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGAGNNNNNNNNNNNNN




NNNN*mN*mN*mN



 


316 (v2)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUG
2969



UCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGAGNNNNNNNNNNNNN




NNNNNNN*mU*mU*mU



 


316 (v3)
mA*mC*mU*mGmGmCmGmCmUmUmCmUmAmUmCmUmGmAmUUACUCUGmAmGmC
2970



mGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGUAGUGmGmGmUmAmAmA




mGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmCmAmUmCmAGAGNNN




NNNNNNNNNNNNNN*mN*mN*mN



 


316 (v4)
mA*mC*mU*mGmGmCmGmCUUCUmAmUmCmUmGmAmUUACUCUGmAmGmCmGmC
2971



mCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGUAGUGmGmGmUmAmAmAmGmC




mUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmCmAmUCAGAGNNNNNNNNN




NNNNNNNN*mN*mN*mN



 


316 (v5)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAmCmUA
2972



UmGmUmCmGUAGUGGGUAAAmGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmG




mAmGmCAUCAGAGNNNNNNNNNNNNNNNNN*mN*mN*mN



 


316 (v6)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGACUAUG
2973



UCGUAGUGGGUAAAmGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmC




AUCAGAGNNNNNNNNNNNNNNNNN*mN*mN*mN



 


316 (v7)
mA*mC*mU*GGmCGmCmUUCUAmUmCUGAUUACUCUGmAmGCGCCmAmUmCmAm
2974



CCAGCmGmAmCmUAUmGmUmCmGUAGUGGmGmUmAmAAmGmCmUmCmCmCmUmC




mUmUmCmGmGmAmGmGmGmAmGmCmAmUCAGAGNNNNNNNNNNNNNNNNN*mN*




mN*mN



 


316 (v8)
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCmAmUmCmAmCCAGCmG
2975



mAmCmUAUmGmUmCmGUAGUGGmGmUmAmAAmGmCmUmCmCmCmUmCmUmUmCm




GmGmAmGmGmGmAmGmCmAmUCAGAGNNNNNNNNNNNNNNNNN*mN*mN*mN



 


316 (v9)
mA*mC*mU*GGmCGmCmUUCUAmUmCUGAUUACUCUGmAmGCGCCAUCACCAGC
2976



mGmAmCmUAUmGmUmCmGUAGUGGGUAAAmGmCmUmCmCmCmUmCmUmUmCmGm




GmAmGmGmGmAmGmCAUCAGAGNNNNNNNNNNNNNNNNN*mN*mN*mN
















TABLE 26







Sequences of gRNAs with their different chemical modification profiles (denoted by


version number) assayed in this example. Chemical modifications: * = phosphorothioate


bond; m = 2′Ome modification










gRNA ID





(scaffold


SEQ ID


variant-spacer)
Target
gRNA sequence
NO:





174-6.7
human
ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGAC
3145


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAA





GUCCUGGCUUCCUGGUGAAGA



 


174-6.7
human
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACC
3074


(v1)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAAAGUCCUGGCUUCCUGGUGAmA*mG*mA



 


174-6.8
human
ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGAC
3146


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAA





GUGGCUUCCUGGUGAAGAUGA



 


174-6.8
human
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACC
3147


(v1)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAAAGUGGCUUCCUGGUGAAGAmU*mG*mA



 


174-7.9
human
ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGAC
3148


(v0)
B2M
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAA





GGUGUAGUACAAGAGAUAGAA



 


174-7.9
human
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACC
3149


(v1)
B2M
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAAAGGUGUAGUACAAGAGAUAmG*mA*mA



 


316-6.7
human
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3150


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGA





GUCCUGGCUUCCUGGUGAAGA



 


316-6.7
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3151


(v1′)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAGAGUCCUGGCUUCCUGGUGAmA*mG*mA



 


316-6.8
human
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3152


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGA





GUGGCUUCCUGGUGAAGAUGA



 


316-6.8
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3153


(v1′)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAGAGUGGCUUCCUGGUGAAGAmU*mG*mA



 


316-7.9
human
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3154


(v0)
B2M
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGA





GGUGUAGUACAAGAGAUAGAA



 


316-7.9
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3155


(v1′)
B2M
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAGAGGUGUAGUACAAGAGAUAmG*mA*mA



 


174-7.37
human
ACUGGCGCUUUUAUCUgAUUACUUUGAGAGCCAUCACCAGCGAC
3156


(v0)
B2M
UAUGUCGUAgUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAA





GGGCCGAGAUGUCUCGCUC



 


174-7.37
human
mA*mC*mU*GGCGCUUUUAUCUgAUUACUUUGAGAGCCAUCACC
3157


(v1*)
B2M
AGCGACUAUGUCGUAgUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAAAGGGCCGAGAUGUCUCG*mC*mU*mC



 


235-6.7
human
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3158


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUCCGUAAG





AGGCAUCAGAGUCCUGGCUUCCUGGUGAAGA



 


235-6.7
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3159


(v1)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUC





CGUAAGAGGCAUCAGAGUCCUGGCUUCCUGGUGAmA*mG*mA



 


235-6.7
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3160


(v2)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUC





CGUAAGAGGCAUCAGAGUCCUGGCUUCCUGGUGAAGAU*mU*mU





*mU



 


235-6.7
human
mA*mC*mU*mGmGmCmGmCmUmUmCmUmAmUmCmUmGmAmUUAC
3161


(v3)
PCSK9
UCUGmAmGmCmGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUm





CmGUAGUGmGmGmUmAmAmAmGmCmCmGmCmUmUmAmCmGmGmA





mCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCmAmUmCmA





GAGUCCUGGCUUCCUGGUGAmA*mG*mA



 


235-6.7
human
mA*mC*mU*mGmGmCmGmCUUCUmAmUmCmUmGmAmUUACUCUG
3162


(v4)
PCSK9
mAmGmCmGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGU





AGUGmGmGmUmAmAmAmGmCmCmGmCmUmUmAmCmGmGmAmCmU





mUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCmAmUCAGAGUCC





UGGCUUCCUGGUGAmA*mG*mA



 


235-6.7
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3163


(v5)
PCSK9
AGCGAmCmUAUmGmUmCmGUAGUGGGUmAmAmAmGmCmCmGmCm





UmUmAmCmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAm





GmGmCAUCAGAGUCCUGGCUUCCUGGUGAmA*mG*mA



 


235-6.7
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3164


(v6)
PCSK9
AGCGACUAUGUCGUAGUGGGUmAmAmAmGmCmCmGmCmUmUmAm





CmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCA





UCAGAGUCCUGGCUUCCUGGUGAmA*mG*mA



 


235-6.8
human
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3165


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUCCGUAAG





AGGCAUCAGAGUGGCUUCCUGGUGAAGAUGA



 


235-6.8
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3166


(v1)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUC





CGUAAGAGGCAUCAGAGUGGCUUCCUGGUGAAGAmU*mG*mA



 


235-6.8
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3167


(v2)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCCGCUUACGGACUUCGGUC





CGUAAGAGGCAUCAGAGUGGCUUCCUGGUGAAGAUGA*mU*mU*





mU



 


235-6.8
human
mA*mC*mU*mGmGmCmGmCmUmUmCmUmAmUmCmUmGmAmUUAC
3168


(v3)
PCSK9
UCUGmAmGmCmGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUm





CmGUAGUGmGmGmUmAmAmAmGmCmCmGmCmUmUmAmCmGmGmA





mCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCmAmUmCmA





GAGUGGCUUCCUGGUGAAGAmU*mG*mA



 


235-6.8
human
mA*mC*mU*mGmGmCmGmCUUCUmAmUmCmUmGmAmUUACUCUG
3169


(v4)
PCSK9
mAmGmCmGmCmCmAmUmCmAmCmCAGCGAmCmUAUmGmUmCmGU





AGUGmGmGmUmAmAmAmGmCmCmGmCmUmUmAmCmGmGmAmCmU





mUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCmAmUCAGAGUGG





CUUCCUGGUGAAGAmU*mG*mA



 


235-6.8
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3170


(v5)
PCSK9
AGCGAmCmUAUmGmUmCmGUAGUGGGUmAmAmAmGmCmCmGmCm





UmUmAmCmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAm





GmGmCAUCAGAGUGGCUUCCUGGUGAAGAmU*mG*mA



 


235-6.8
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3171


(v6)
PCSK9
AGCGACUAUGUCGUAGUGGGUmAmAmAmGmCmCmGmCmUmUmAm





CmGmGmAmCmUmUmCmGmGmUmCmCmGmUmAmAmGmAmGmGmCA





UCAGAGUGGCUUCCUGGUGAAGAmU*mG*mA



 


316-27.107
mouse
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3172


(v0)
PCSK9
UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGA





GCUGGCUUCUUGGUGAAGAUG



 


316-27.107
mouse
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3173


(v1)
PCSK9
AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAGAGCUGGCUUCUUGGUGAAG*mA*mU*mG



 


316-27.107
mouse
mA*mC*mU*GGmCGmCmUUCUAmUmCUGAUUACUCUGmAmGCGC
3174


(v7)
PCSK9
CmAmUmCmAmCCAGCmGmAmCmUAUmGmUmCmGUAGUGGmGmUm





AmAAmGmCmUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmC





mAmUCAGAGCUGGCUUCUUGGUGAAG*mA*mU*mG



 


316-27.107
mouse
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCmAmUmC
3175


(v8)
PCSK9
mAmCCAGCmGmAmCmUAUmGmUmCmGUAGUGGmGmUmAmAAmGm





CmUmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmCmAmUCAG





AGCUGGCUUCUUGGUGAAG*mA*mU*mG



 


316-27.107
mouse
mA*mC*mU*GGmCGmCmUUCUAmUmCUGAUUACUCUGmAmGCGC
3176


(v9*)
PCSK9
CAUCACCAGCmGmAmCmUAUmGmUmCmGUAGUGGGUAAAmGmCm





UmCmCmCmUmCmUmUmCmGmGmAmGmGmGmAmGmCAUCAGAGCU





GGCUUCUUGGUGAA*mG*mA*mU*mG



 


174-35.2 (v0)
ROSA26
ACUGGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACCAGCGAC
3177




UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAAA





GAGAAGAUGGGCGGGAGUCUU



 


174-35.2 (v2)
ROSA26
mA*mC*mU*GGCGCUUUUAUCUGAUUACUUUGAGAGCCAUCACC
3178




AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAAAGAGAAGAUGGGCGGGAGUCUU*mU*mU*mU



 


316-35.2 (v0)
ROSA26
ACUGGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACCAGCGAC
3179




UAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGCAUCAGA





GAGAAGAUGGGCGGGAGUCUU



 


316-35.2 (v1)
ROSA26
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3180




AGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGAGGGAGC





AUCAGAGAGAAGAUGGGCGGGAGU*mC*mU*mU



 


316-35.2 (v5)
ROSA26
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUCACC
3181




AGCGAmCmUAUmGmUmCmGUAGUGGGUAAAmGmCmUmCmCmCmU





mCmUmUmCmGmGmAmGmGmGmAmGmCAUCAGAGAGAAGAUGGGC





GGGAGU*mC*mU*mU





Note that gRNAs annotated with a v1′ design contain one less phosphorothioate bond on the 3′ end of the gRNA. gRNAs annotated with v1* contain one extra phosphorothioate bond on the 3′end of the gRNA. gRNAs annotated with a v9* contain an extra phosphorothioate bond on the 3′ end of the gRNA.






Biochemical Characterization of gRNA Activity:

Target DNA oligonucleotides with fluorescent moieties on the 5′ ends were purchased commercially (sequences listed in Table 27). Double-stranded DNA (dsDNA) targets were formed by mixing the oligos in a 1:1 ratio in 1× cleavage buffer (20 mM Tris HCl pH 7.5, 150 mM NaCl, 1 mM TCEP, 5% glycerol, 10 mM MgCl2), following by heating to 95° C. for 10 minutes, and then allowing the solution to cool to room temperature. CasX ribonucleoproteins (RNPs) were reconstituted with CasX 491 and the indicated gRNAs at a final concentration of 1 μM with 1.2-fold excess of the indicated gRNA in 1× cleavage buffer. RNPs were allowed to form at 37° C. for 10 minutes.
The effects of various structural and chemical modifications to the gRNA scaffold on the cleavage rate of CasX 491 RNPs were determined. Cleavage reactions were prepared with final RNP concentrations of 200 nM and final target concentrations of 10 nM, and reactions were carried out at 16° C. and initiated by the addition of the labeled target DNA substrate (Table 27). Aliquots of reactions were taken at 0.25, 0.5, 1, 2, 5, and 10 minutes and quenched by adding an equal volume of 95% formamide with 20 mM EDTA. Samples were denatured at 95° C. for 10 minutes and resolved on a 10% urea-PAGE gel. Gels were imaged on a Typhoon™ laser-scanner platform and quantified using ImageQuant™ TL 8.2 image analysis software (Cytiva™). The apparent first-order rate constant of non-target strand cleavage (kcleave-) was determined for each CasX:gRNA combination.
To determine the competent fraction formed by each gRNA, cleavage reactions were prepared with final RNP concentrations of 100 nM and final target concentrations of 100 nM. Reactions were carried out at 37° C. and initiated by the addition of the labeled target substrate (Table 27). Aliquots were taken at 0.5, 1, 2, 5, 10, and 30 minutes and quenched by adding an equal volume of 95% formamide with 25 mM EDTA. Samples were denatured by heating at 95° C. for 10 minutes and resolved on a 10% urea-PAGE gel. Gels were imaged and quantified as above. CasX was assumed to act as a single-turnover enzyme under the assayed conditions, as indicated by the observation that sub-stoichiometric amounts of enzyme would fail to cleave a greater-than-stoichiometric amount of target substrate even under extended time-scales, and instead would approach a plateau that scaled with the amount of enzyme present. Thus, the fraction of target substrate cleaved over long time-scales by an equimolar amount of RNP would be indicative of the fraction of RNP that was properly formed and active for cleavage. The cleavage traces were fitted with a biphasic rate model, as the cleavage reaction clearly deviated from monophasic under this concentration regime. The plateau of each fit was determined and reported as the active fraction for each RNP in Table 30.







TABLE 27







Sequences of target DNA substrate oligonucleotides with fluorescent moieties on the


5′ ends used for biochemical characterization of gRNA activity. /700/ = IRDye700;


/800/ = IRDye800








DNA substrate
Sequence





6.7/6.8 target top
/700/catgtcttccatggccttcttcctggcttcctggtgaagatgagtggcgacctg


strand
ctggag


(SEQ ID NO: 3182)



 


6.7/6.8 target
/800/ctccagcaggtcgccactcatcttcaccaggaagccaggaagaaggccatggaa


bottom strand
gacatg


(SEQ ID NO: 3183)









In Vitro Transcription of CasX mRNA:

DNA templates encoding for CasX 491 (see Table 28 for encoding sequences) used for in vitro transcription were generated by PCR using forward primers containing a T7 promoter, followed by agarose gel extraction of the appropriately sized DNA. 25 ng/μL final concentration of template DNA was used in each in vitro transcription reaction that was carried out following the manufacturer's recommended protocol with slight modifications. Following in vitro transcription reaction incubation for 2-3 hours at 37° C., which were carried out with CleanCap® AG and N1-methyl-pseudouridine, DNAse digestion of template DNA and column-based purification using the Zymo RNA miniprep kit were performed. The poly(A) tail was added using E. coli PolyA Polymerase following the manufacturer's protocol, followed by column-based purification as stated above. Poly(A) tailed in vitro transcribed RNA was eluted in RNAse free water, analyzed on an Agilent® TapeStation for integrity, and flash frozen prior to storage at −80° C.







TABLE 28







Encoding sequences of the CasX mRNA


molecules assessed in this example*.









CasX 491

DNA sequence


mRNA ID
Component (ID)
or SEQ ID NO:





CasX 491
5′UTR
3082


mRNA #1
START codon + c-MYC NLS + linker
3184



CasX 491
3185



Linker + c-MYC NLS
3186



P2A mScarlet + STOP codon
3187


CasX 676
5′UTR
3047


mRNA #2
START codon + c-MYC NLS
3133



CasX 676
3134



c-MYC NLS + STOP codons
3135



3′UTR
3055



Xbal restriction site (partial)
TCTAG



Poly(A) tail
3057





*Components are listed in a 5′ to 3′ order within the constructs






In Vitro Delivery of gRNA and CasX mRNA Via Transfection:

Editing at the PCSK9 locus and consequential effects on secreted PCSK9 levels were assessed for conditions using CasX 491 mRNA co-delivered with a PCSK9-targeting gRNA with scaffold variant 174 compared to conditions where a PCSK9-targeting gRNA with scaffold variant 316 was used. 100 ng of in vitro transcribed mRNA coding for CasX 491 with a P2A and mScarlet fluorescent protein was transfected into HepG2 cells with version 1 (v1) of gRNAs 174-6.7, 174-6.8, 316-6.7, and 316-6.8 (see Table 26) using Lipofectamine™. After a media change, the following were harvested at 28 hours post-transfection: 1) transfected cells were harvested for editing assessment at the PCSK9 locus by NGS (next generation sequencing); and 2) media supernatant was harvested to measure secreted PCSK9 protein levels by ELISA. For editing analysis by NGS, amplicons were amplified from 200 ng of extracted gDNA with a set of primers targeting the PCSK9 locus and processed by NGS (described below). Secreted PCSK9 levels in the media supernatant were also analyzed using a fluorescence resonance energy transfer-based immunoassay from CISBio following the manufacturer's instructions. Here, a gRNA using scaffold 174 with spacer 7.37 (v0; see Table 26), which targeted the endogenous B2M (beta-2-microglobulin) locus, served as the non-targeting (NT) control. These results are shown in FIG. 20.
To compare the editing potency of version 0 (v0) and version 1 (v1) of B2M-targeting gRNAs, ˜6E4 HepG2 hepatocytes were seeded per well of a 96-well plate. 24 hours later, seeded cells were co-transfected using Lipofectamine™ with 100 ng of in vitro transcribed mRNA coding for CasX 491 and different doses (1, 5, or 50 ng) of either v0 or v1 of the B2M-targeting gRNA containing scaffold variant 174 and spacer 7.37 (see Table 26). Six days post-transfection, cells were harvested for B2M protein expression analysis via immunostaining of the B2M-dependent HLA protein, followed by flow cytometry using the Attune™ NxT flow cytometer. These results are shown in FIG. 17.
V1 through v6 variants of chemically-modified PCSK9-targeting gRNAs (Table 26) were assessed for their effects on editing potency and consequential effects on secreted PCSK9 levels in vitro. Briefly, 100 ng of in vitro transcribed mRNA coding for CasX variant 491 and a P2A and mScarlet fluorescent protein was transfected into HepG2 cells with 50 ng of the indicated chemically-modified gRNA using Lipofectamine™. After a media change, the following were harvested at 28 hours post-transfection: 1) transfected cells for editing assessment at the PCSK9 locus by NGS as described above; and 2) media supernatant to measure secreted PCSK9 protein levels by ELISA, as described above. Here, a B2M-targeting gRNA was used as a non-targeting control. These results are shown in Table 31.
NGS Processing and Analysis:
Genomic DNA (gDNA) from harvested cells were extracted using the Zymo Quick-DNA Miniprep Plus kit following the manufacturer's instructions. Target amplicons were formed by amplifying regions of interest from −50-200 ng of extracted gDNA with a set of primers targeting the human PCSK9 locus. These gene-specific primers contained an additional sequence at the 5′ ends to introduce Illumina reads 1 and 2 sequences. Further, they contained a 16-nucleotide random sequence that functioned as a unique molecular identifier (UMI). The quality and quantification of the amplicon was assessed using a Fragment Analyzer DNA analyzer kit (Agilent®, dsDNA 35-1500 bp). Amplicons were sequenced on the Illumina MiSeq™ according to the manufacturer's instructions. Raw fastq sequencing files were processed by trimming for quality and adapter sequences and merging read 1 and read 2 into a single insert sequence; insert sequences were then analyzed by the CRISPResso2 (v 2.0.29) program. The percentage of reads modified in a window around the 3′ end of the spacer was determined. The activity of the CasX molecule was quantified as the total percent of reads that contain insertions, substitutions, and/or deletions anywhere within this window for each.
Formulations of Lipid Nanoparticles (LNPs):
CasX mRNA and gRNA were encapsulated into LNPs using GenVoy-ILM™ lipids on the Precision NanoSystems Inc. (PNI) Ignite™ Benchtop System and following the manufacturer's guidelines. GenVoy-ILM™ lipids are manufactured by PNI, with a proprietary composition of ionizable lipid:DSPC:cholesterol:stabilizer at 50:10:37.5:2.5 mol %.
Briefly, to formulate LNPs, equal mass ratios of CasX mRNA and gRNA were diluted in PNI Formulation Buffer, pH 4.0. GenVoy-ILM™ was diluted 1:1 in anhydrous ethanol. mRNA/gRNA co-formulations were performed using a predetermined N/P ratio. The RNA and lipids were run through a PNI laminar flow cartridge at a predetermined flow rate ratio (RNA:Genvoy-ILM™) on the PNI Ignite™ Benchtop System. After formulation, the LNPs were diluted in PBS, pH 7.4, to decrease the ethanol concentration and increase the pH, which increases the stability of the particles. Buffer exchange of the mRNA/sgRNA-LNPs was achieved by overnight dialysis into PBS, pH 7.4, at 4° C. using 10k Slide-A-Lyzer™ Dialysis Cassettes (Thermo Scientific™). Following dialysis, the mRNA/gRNA-LNPs were concentrated to >0.5 mg/mL using 100 kDa Amicon®-Ultra Centrifugal Filters (Millipore) and then filter-sterilized. Formulated LNPs were analyzed on a Stunner® (Unchained Labs) to determine their diameter and polydispersity index (PDI). Encapsulation efficiency and RNA concentration was determined by RiboGreen™ assay using Invitrogen's Quant-iT™ Ribogreen™ RNA assay kit. LNPs were used in various experiments as described herein to deliver CasX mRNA and gRNA to target cells and tissue.
Delivery of LNPs Encapsulating CasX mRNA and Targeting gRNAs In Vitro:
˜50,000 HepG2 cells, cultured in DMEM/F-12 media containing 10% FBS and 1% PenStrep, were seeded per well in a 96-well plate. The next day, seeded cells were treated with varying concentrations of LNPs, which were prepared in six 2-fold serial dilutions starting at 250 ng. These LNPs were formulated to encapsulate CasX 491 mRNA and a B2M-targeting gRNA incorporating either scaffold variant 174 or 316 with spacer 7.9 (v1; see Table 26). Media was changed 24 hours after LNP treatment, and cells were cultured for six additional days prior to harvesting for gDNA extraction for editing assessment at the B2M locus by NGS and B2M protein expression analysis via HLA immunostaining, followed by flow cytometry using the Attune NxT flow cytometer. Briefly, for editing assessment, amplicons were amplified from 200 ng of extracted gDNA with primers targeting the human B2M locus and processed by NGS using similar methods as described in Example 7. The results of these assays are shown in FIGS. 21A and 21B.
˜20,000 mouse Hepa1-6 hepatocytes were seeded per well in a 96-well plate. The following day, seeded cells were treated with varying concentrations of LNPs, which were prepared in eight 2-fold serial dilutions starting at 1000 ng. These LNPs were formulated to encapsulate CasX 676 mRNA #2 (see Table 28) and a ROSA26-targeting gRNA incorporating scaffold variant 316 with spacer 35.2 (v1 or 5; see Table 26). Media was changed 24 hours post-treatment with LNPs, and cells were cultured for seven additional days prior to harvesting for gDNA extraction for editing assessment at the ROSA26 locus by NGS. Briefly, amplicons were amplified from extracted gDNA with primers targeting the mouse ROSA26 locus and processed by NGS using similar methods as described in Example 7. The results of this experiment are shown in FIG. 22A.
Delivery of LNPs Encapsulating CasX mRNA and Targeting gRNA In Vivo:
To assess the effects of using v1 and v5 of scaffold 316 in vivo, CasX 676 mRNA #2 (see Table 28) and a ROSA26-targeting gRNA using scaffold 316 with spacer 35.2 (v1 or v5; see Table 26) were encapsulated within the same LNP using a 1:1 mass ratio for mRNA:gRNA. Formulated LNPs were buffer-exchanged to PBS for in vivo injection. Briefly, LNPs were administered intravenously through the retro-orbit sinus into 4-week old C57BL/6 mice. Mice were observed for five minutes after injection to ensure recovery from anesthesia before being placed into their home cage. Naïve, uninjected animals served as experimental controls. Six days post-administration, mice were euthanized, and the liver tissue was harvested for gDNA extraction using the Zymo Research Quick DNA/RNA Miniprep™ kit following the manufacturer's instructions. Target amplicons were then amplified from the extracted gDNA with a set of primers targeting the mouse ROSA26 locus and processed using similar methods as described in Example 7 for editing assessment by NGS. The results of this experiment are shown in FIG. 22B.
To compare the effects of using v7, v8, and v9 of scaffold 316 on editing at the PCSK9 locus in vivo, CasX 676 mRNA #1 (see Table 29 for sequences) and a PCSK9-targeting gRNA using scaffold 316 with spacer 27.107 (v1, v7, v8, or v9; see Table 26), were encapsulated within the same LNP using a 1:1 mass ratio for mRNA:gRNA for each gRNA. LNPs were administered retro-orbitally into 6-week old C57BL/6 mice, as described above, and mice were euthanized seven days post-injection to harvest liver tissue for gDNA extraction for editing assessment by NGS at the PCSK9 locus. The results of this experiment are shown in FIG. 23.







TABLE 29







Encoding sequences of CasX 676 mRNA #1 molecule










CasX ID
Component (ID)
Description
SEQ ID NO:





CasX 676 mRNA #1
5′UTR
hHBA
3188



START codon + c-

3133



MYC NLS



CasX 676

3134



c-MYC NLS +

3135



STOP codons



3′UTR
hHBA
3189



Poly(A) tail

3057





Components are listed in a 5′ to 3′ order within the constructs






Results
Assessing the Effects of Various Chemical Modifications on gRNA Activity:
Several studies involving Cas9 have demonstrated that chemical modifications of the gRNA resulted in significantly improved editing activity when delivered with Cas9 mRNA. Following delivery of Cas9 mRNA and gRNA into target cells, unprotected gRNA is susceptible to degradation during the mRNA translation process. Addition of chemical modifications such as 2′O-methyl (2′Ome) groups and phosphorothioate bonds can reduce the susceptibility of the gRNA to cellular Rnases, but also have the potential to disrupt folding of the gRNA and its interactions with the CRISPR-Cas protein. Given the lack of structural similarity between CasX and Cas9, as well as their respective gRNAs, appropriate chemical modification profiles must be designed and validated de novo. Using published structures of wild-type CasX from Deltaproteobacteria (PDB codes 6NY1, 6NY2, and 6NY3) as reference, residues that appeared potentially amenable to modification were selected. However, the published structures were of a wild type CasX ortholog and gRNA distinct from the species used as the basis for the engineered variants presented here, and they also lacked the resolution to confidently determine interactions between protein side-chains and the RNA backbone. These limitations introduced a significant amount of ambiguity into determining which nucleotides might be safely modified. As a result, six profiles of chemical modifications (denoted as versions) were designed for initial testing, and these six profiles are illustrated in FIGS. 16A and 16B. The v1 profile was designed as a simple end-protected structure, where the first and last three nucleotides were modified with 2′Ome and phosphorothioate bonds. In the v2 profile, 3′UUU tail was added to mimic the termination sequence used in cellular transcription systems and to move the modified nucleotides outside of the region of the spacer involved in target recognition. The v3 profile included the end protection as in v1, as well as the addition of 2′Ome modifications at all nucleotides identified to be potentially modifiable based on structural analysis. The v4 profile was modeled based on v3, but with all the modifications in the triplex region removed, as this structure was predicted to be more sensitive to any perturbation of the RNA helical structure and backbone flexibility. The v5 profile maintained chemical modifications in the scaffold stem and extended stem regions, while the v6 profile harbored modifications only in the extended stem. The extended stem is a region that would become fully exposed to solvent in the RNP and is amenable to replacement by other hairpin structures, and therefore presumably relatively insensitive to chemical modifications.
The minimally modified v1 gRNA was initially assessed against an unmodified gRNA (v0) to determine the potential benefit of such chemical modifications on editing when the gRNA was co-delivered with CasX mRNA to target cells. Modified (v1) and unmodified (v0) B2M-targeting gRNAs with spacer 7.37 were co-transfected with CasX mRNA into HepG2 cells, and editing at the B2M locus was measured by loss of surface presentation of the B2M-dependent HLA complex, as detected by flow cytometry (FIG. 17). The data demonstrate that use of the v1 gRNA resulted in substantially greater loss of B2M expression compared to the levels seen with v0 gRNA across the various doses, thereby confirming that end modifications of the gRNA increased CasX-mediated editing activity upon delivery of the CasX mRNA and gRNA.
The broader set of gRNA chemical modification profiles were assessed using PCSK9-targeting gRNAs using scaffold variant 235 and spacers 6.7 and 6.8 to determine whether the additional chemical modifications would be able to support the formation of active RNPs. In vitro cleavage assays described above were performed to determine kcleave and fraction competence for these engineered gRNAs harboring the various chemical modification profiles. The results from these in vitro cleavage assays are shown in Table 30. The data demonstrate that gRNAs with the v3 profiles exhibited no activity, an indication that the addition of some chemical modifications significantly interfered with RNP formation or activity. Adding v4 chemical modifications resulted in a reasonable cleavage rate in the excess RNP condition, but exhibited very low fraction competence. The difference between v3 and v4 modifications confirmed that modifications in the triplex region prevented the formation of any active RNP, either due to the inability of the gRNA to fold properly or a disruption in the gRNA-protein interactions. The reduced fraction competence resulting from appending v4 modifications suggest that while the gRNA was able to successfully assemble with the CasX protein to form a cleavage-competent RNP, a large majority of the gRNA was misfolded, or that the appended chemical modifications reduced the affinity of the gRNA for the CasX protein and impeded the efficiency of RNP formation. Application of the v5 or v6 profiles resulted in competent fractions that were comparable to, but slightly lower than, those obtained for reactions using the v1 and v2 modifications. While the kcleave values were relatively consistent between v5 and v6 gRNAs, both v5 and v6 gRNAs achieved nearly half of the kcleave values for v1 and v2 gRNAs. The reduced kcleave value for v6 gRNA was particularly surprising, given the lack of expected interaction between the gRNA and CasX protein in the modified extended stem. However, for both v5 and v6 gRNAs, it is possible that the reduced flexibility of the gRNA, resulting from the 2′Ome modifications, inhibited structural changes in the RNP required for efficient cleavage, or that the modified initial base-pairs of the hairpin involved in CasX protein interaction had been negatively impacted by the inclusion of the 2′Ome groups.







TABLE 30







Parameters of cleavage activity assessed for CasX


RNPs with the various PCSK9-targeting gRNAs using


scaffold 235 and harboring the indicated chemical


modification profile, denoted by version number.











gRNA





(scaffold variant-
Kcleave
Fraction



spacer, version no.)
(min−1)
competence















235-6.7, v1
0.901
0.398



235-6.8, v1
1.36
0.398



235-6.7, v2
0.454
0.386



235-6.8, v2
2.03
0.361



235-6.7, v3
0
0



235-6.8, v3
0
0



235-6.7, v4
0.434
0.031



235-6.8, v4
0.257
0.005



235-6.7, v5
0.506
0.313



235-6.8, v5
0.680
0.388



235-6.7, v6
0.462
0.346



235-6.8, v6
0.715
0.325










The chemically-modified PCSK9-targeting gRNAs based on scaffold 235 were subsequently assessed for editing in a cell-based assay. CasX mRNA and chemically modified PCSK9-targeting gRNAs were co-transfected into HepG2 cells using Lipofectamine™. Editing levels were measured by indel rate at the PCSK9 locus by NGS and secreted PCSK9 levels by ELISA, and the data are displayed in Table 31. The data demonstrate that use of v3 and v4 gRNAs resulted in minimal editing activity at the PCSK9 locus, consistent with findings from the biochemical in vitro cleavage assays shown in Table 30. Meanwhile, use of v5 and v6 gRNAs resulted in editing levels, measured by indel rate and PCSK9 secretion, that were slightly lower than the levels attained with use of v1 and v2 gRNAs (Table 31). Specifically, the results show that use of v1 and v2 gRNAs, which harbored end modifications, resulted in ˜80-85% editing at the PCSK9 locus, indicating that adding chemical modifications to the gRNA ends was sufficient to achieve efficient editing with CasX. While the data demonstrate that use of v5 and v6 gRNAs resulted in efficient editing in vitro, near-saturating levels of editing were observed with use of the v1 gRNA in this experiment where a single dose of the gRNA was transfected. As a result, the use of a single dose rendered it challenging to assess clearly the effects of the chemical modifications on editing under guide-limiting conditions. Therefore, profiles v1 and v5 were chosen for further testing, as v1 contains the simplest modification profile, and v5 is the most heavily modified profile whose application demonstrated robust activity in vitro (Tables 30 and 31).







TABLE 31







Editing levels measured by indel rate at PCSK9 locus by NGS and


secreted PCSK9 levels by ELISA in HepG2 cells co-transfected


with CasX 491 mRNA and various chemically-modified PCSK9-targeting


gRNAs using scaffold 235 and either spacer 6.7 or 6.8.









Experimental
Indel rate (edit fraction)
Secreted PCSK9 (ng/mL)











condition
Mean
Stdev
Mean
Stdev














CasX mRNA
0.0021
0.003
52
14


only


235-6.7, v1
0.83
0.0058
18
5.7


235-6.7, v2
0.79
0.0071
21
4


235-6.7, v3
0.024
0.02
48
19


235-6.7, v4
0.12
0.006
34
5.5


235-6.7, v5
0.73
0.023
21
9


235-6.7, v6
0.75
0.0069
22
8.8


235-6.8, v1
0.85
0.017
16
4.4


235-6.8, v2
0.83
0.0028
20
1.5


235-6.8, v3
0.023
0.0027
39
2.7


235-6.8, v4
0.088
0.0086
42
10


235-6.8, v5
0.77
0.017
19
1.6


235-6.8, v6
0.78
0.014
24
6.9


Non-targeting
0.0019
0.0026
42
12


ctrl









The v1 and v5 profiles were further tested in another cell-based assay to assess their effects on editing efficiency. LNPs were formulated to co-encapsulate CasX 676 mRNA #2 and v1 and v5 chemically-modified ROSA26-targeting gRNAs using the newly-designed gRNA scaffold 316 (described further in the following sub-section). The “v5” profile was modified slightly for application to the 316 scaffold. Three 2′ Ome modifications in the non-base-paired region immediately 5′ of the extended stem were removed to restrict modifications to the two stemloop regions. Hepa1-6 hepatocytes were treated with the resulting LNPs at various doses and harvested eight days post-treatment to assess editing at the ROSA26 locus, measured as indel rate detected by NGS (FIG. 22A). The data demonstrate that treatment with LNPs delivering the v5 ROSA26-targeting gRNA resulted in markedly lower editing levels across the range of doses compared to the levels achieved with the v1 counterpart (FIG. 22A). There are several possible explanations for the differences in relative activity observed with use of v5 gRNA in FIG. 22A relative to that observed in Table 31. The first and most likely possible explanation is that the single dose used to achieve editing shown in Table 31 was too high to measure differences in activity accurately between use of v5 gRNA and v1 gRNA. It is also possible that the removal of the modifications outside the stemloop motifs in the 316 version of v5 negatively impacted guide activity. While it is possible that these modifications provide stability benefits that outweigh an activity cost imparted by the stemloop modifications, this seems unlikely given that increasing levels of modification have so far resulted in decreased activity. A final possible explanation is that the modifications in the v5 profile might negatively impact LNP formulation or behavior through differential interactions between the modified nucleotide backbone and the ionizable lipid of the LNP, potentially resulting in less efficient gRNA encapsulation or in less efficient gRNA release following internalization.
LNPs co-encapsulating the CasX mRNA #2 and v1 and v5 chemically-modified ROSA26-targeting gRNAs based on scaffold 316 were further tested in vivo. FIG. 22B shows the results of the editing assay as percent editing measured as indel rate at the ROSA26 locus. The data demonstrate that use of the v5 gRNA resulted in ˜5-fold lower editing compared to that achieved with use of the v1 gRNA, under more relevant testing conditions of in vivo LNP delivery. These findings support the reduced cleavage rate observed biochemically for the v5 gRNA in Table 30, an indication that the v5 modifications have interfered with some aspect of CasX activity. Given the consistent decrease in activity detected in v5 and v6 profiles (Table 30), the reduced editing may be attributed to modifications in the extended stem region. Although the extended stem of the gRNA has minimal interactions with the CasX protein, it is possible that addition of 2′Ome groups at the first base-pair disrupted either the CasX protein-gRNA interactions or the complex RNA fold where the extended stem meets the pseudoknot and triplex regions. More specifically, inclusion of the 2′Ome groups might have adversely affected the basal base-pairs of the gRNA extended stem and residues R49, K50, and K51 of the CasX protein. Finally, structural studies of CasX have suggested that flexibility of the gRNA is required for efficient DNA cleavage (Liu J, et al, CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature 566:218-223 (2019); Tsuchida C A, et al, Chimeric CRISPR-CasX enzymes and guide RNAs for improved genome editing activity. Mol Cell 82(6): 1199-1209 (2022)). Thus, the addition of the 2′Ome groups throughout the extended stem might have enforced a more rigid A-form helical structure and prevented the needed flexibility for the gRNA for efficient cleavage. Furthermore, it is possible that the additional modifications in the scaffold stem in the v5 and v6 profiles might be detrimental to activity, though this is currently unclear given the limited comparisons between the v5 and v6 profiles.
Additional modification profiles were designed with the goal of enhancing gRNA stability while mitigating the adverse effects on RNP cleavage activity. Using recently published structures of wild-type CasX from Planctomycetes (PDB codes 7WAY, 7WAZ, 7WB0, 7WB1), which has a higher homology to the engineered CasX variants being assessed, additional chemical modification profiles for gRNAs were designed and are illustrated in FIG. 18. These profiles illustrate the addition of 2′Ome groups and phosphorothioate bonds to a newly-designed gRNA scaffold variant, which is described in the ensuing sub-section. These new gRNA chemical modification profiles were designed based on the initial data demonstrating sufficient editing activity observed in Table 31 with use of the v5 gRNA that suggested that modifications to the extended stem and scaffold stem regions would not negatively impact activity. The v7 profile was designed to include 2′Ome at residues likely to be modifiable throughout the gRNA structure, which excluded the triplex region, given the dramatic negative effects of adding such modifications observed earlier with the v3 profile. More conservative profiles, v8 and v9, were also designed, as illustrated in FIG. 18. For the v8 construct, modifications were removed in the pseudoknot and triplex loop region, but were retained in the scaffold stem, extended stem, and their flanking single-stranded regions, in addition to the 5′ and 3′ termini. For the v9 profile, modifications were removed in the single-stranded regions flanking the stemloops, but were retained in the stemloops themselves, in addition to the pseudoknot, triplex loop, and 5′ and 3′ termini. The additional chemical modification profiles v7, v8, and v9 of the newly designed gRNA scaffold variant 316 (discussed further below) were assessed in vivo at the PCSK9 locus. The results of the editing assay in vivo quantified as percent editing at the PCSK9 locus measured as indel rate as detected NGS are illustrated in FIG. 23. Despite the fact that low editing efficiency was detected overall, the data demonstrate that use of v7, v8, and v9 gRNAs resulted in lower editing levels at the PCSK9 locus compared to the indel rate achieved with use of the v1 gRNA (FIG. 23). Given the findings in FIGS. 22A-22B showing inferior editing activity attained with the v5 gRNA, it is unsurprising that v7, v8, and v9 profiles similarly demonstrated comparatively lower editing activity. As illustrated in FIG. 18, the v7, v8, and v9 profiles include modifications throughout the extended stem region, which might have interfered with RNP activity.
Comparison of gRNA Scaffold Variant 174 and 316 Using an In Vitro Cleavage Assay:
Previous work had established gRNA scaffold variant 235 as a top-performing scaffold variant across multiple delivery conditions. However, the longer length of scaffold 235 (119 bp, when using a 20 bp spacer) relative to gRNAs including scaffold 174 (109 bp, when using a 20 bp spacer) increased the difficulty of solid-phase RNA synthesis, which would result in increased manufacturing costs, decreased purity and yield, and higher rates of synthesis failures. To address these issues but retain the improved activity of using scaffold variant 235, a chimeric gRNA scaffold was designed primarily on the basis of the scaffold 235 sequence, but the extended stemloop of scaffold 235 was replaced with the shorter extended stemloop of scaffold variant 174 (FIGS. 19A-19C). The resulting chimeric scaffold, named scaffold 316, was synthesized in parallel with scaffold 174 and PCSK9-targeting spacers 6.7 and 6.8, and B2M-targeting spacer 7.9 harboring the v1 chemical modification profile, with 2′OMe and phosphorothioate bonds on the first and last three nucleotides of all gRNAs (see Table 26). Scaffold variant 174 was chosen as the comparator rather than variant 235 because variant 174 was the best previously characterized scaffold with the same length as variant 316.
In vitro cleavage activity was assessed for gRNAs with scaffold 174 and 316 and spacers 6.7 and 6.8. Cleavage assays were carried out with 20-fold excess RNP over a matching dsDNA target. Cleavage rates were quantified for all four guides, and the results are shown in Table 32. The data demonstrate that in the context of spacer 6.7, use of either scaffold 174 or 316 resulted in similar cleavage rates, with scaffold 316 resulting in marginally faster cleavage than that achieved with scaffold 174. In the context of spacer 6.8, the difference in cleavage activity was more pronounced: CasX RNPs using scaffold 316 were able to cleave DNA nearly twice as quickly as CasX RNPs using scaffold 174 (Table 32).
Assays were also performed with equimolar amounts of RNP and DNA target over a longer time course to assess the fraction of expected RNP active for cleavage. As the CasX RNP is essentially single-turnover over the tested timescale, and the concentrations used are expected to be substantially higher than the KD of the DNA-binding reaction, the amount of cleaved DNA should approximate the amount of active RNP. For either spacer 6.7 or 6.8, the active fraction of CasX RNPs incorporating scaffold 316 was 25-30% higher than for CasX RNPs using scaffold 174 (Table 32). These data suggest that a higher fraction of gRNA using scaffold 316 was properly folded for association with the CasX protein, or that the gRNA using scaffold 316 was able to associate more strongly with the CasX protein. Compared to scaffold 174, scaffold 316 harbors mutations expected to stabilize the pseudoknot and triplex structures required for proper gRNA folding. The increased stability of these motifs in particular, which were more likely to misfold than the simple hairpins found elsewhere in the gRNA structure, might result in a slightly higher fraction of the gRNAs folding into an active conformation.







TABLE 32







Parameters of cleavage activity assessed for CasX RNPs


with gRNAs containing scaffold variant 174 or 316 with


the version 1 (v1) chemical modification profile.









gRNA




(scaffold variant-spacer)
Kcleave (min−1)
Fraction competence












174-6.7, v1
0.236
0.194


174-6.8, v1
0.142
0.165


316-6.7, v1
0.264
0.244


316-6.8, v1
0.272
0.213









Comparison of gRNA Scaffold Variant 174 and 316 in a Cell-Based Assay:

An editing assessment using gRNA scaffold variant 174 compared to variant 316 was performed in a cell-based assay. CasX 491 mRNA and the version 1 (v1) of PCSK9-targeting gRNAs using spacers 6.7 and 6.8 were lipofected into HepG2 cells. Treated cells were harvested 28 hours post-transfection for analysis of editing levels at the PCSK9 locus by NGS and secreted PCSK9 levels by ELISA, and the data are presented in FIG. 20. The data demonstrate that use of any of the PCSK9-targeting gRNA tested resulted in efficient editing at the PCSK9 locus and substantial reduction in PCSK9 secretion compared to the non-targeting control using the B2M-targeting gRNA. The results also show that use of scaffold 316 resulted in more effective editing at the PCSK9 locus than that observed with use of scaffold 174 (˜10 percentage point increase in editing rate achieved with scaffold 316 over scaffold 174). This finding is further supported by the ELISA results, such that use of scaffold 316 resulted in more effective reduction of PCSK9 secretion compared to that achieved with use of scaffold 174.
Scaffold variants 174 and 316 were also assessed in an editing assay where LNPs were formulated to co-encapsulate CasX 491 mRNA and B2M-targeting gRNA harboring either scaffold variant. HepG2 cells were treated with the resulting LNPs at various doses and harvested seven days post-treatment to assess editing at the B2M locus, measured as indel rate detected by NGS (FIG. 21A) and loss of surface presentation of the B2M-dependent HLA complex, as detected by flow cytometry (FIG. 21B). The results from both assays demonstrate that treatment with LNPs to deliver the B2M-targeting gRNA using scaffold 316 resulted in higher editing potency at the B2M locus compared to LNPs delivering the gRNA using scaffold 174 at each dose (FIGS. 21A and 21B). Specifically, at the highest dose of 250 ng, use of scaffold 316 resulted in an editing level that was nearly two-fold higher than the level attained with using scaffold 174. This substantial increase in editing efficacy when using scaffold 316 versus scaffold 174, compared to the comparatively modest difference in activity observed from the in vitro cleavage assays, might be attributed to the destabilization of gRNA structure and folding during LNP formulation. The low pH conditions and association of cationic lipids during LNP formulation could adversely affect parts of the gRNA structure and result in unfolding. Consequently, it would be necessary for the gRNA to refold quickly in the cytoplasm upon delivery, both to bind the CasX protein to form the RNP and to evade Rnase degradation. The stability-increasing mutations in scaffold 316 compared to scaffold 174 might provide a substantial benefit in supporting proper gRNA refolding in the cytoplasm after LNP delivery, while the deliberate folding protocol carried out for the gRNA prior to biochemical experiments likely reduced the impact of these mutations.
Example 8: Demonstration that Altering the UTR Sequences of the Engineered CasX mRNA can Affect CasX-Mediated Editing
5′ and 3′UTRs are essential and required for efficient translation of mRNA. Here, experiments were performed to demonstrate that altering the 5′ and 3′ UTR sequences of the engineered CasX mRNA affects CasX-mediated editing at a target locus when CasX mRNA and targeting gRNAs were delivered in vitro via transfection.
Materials and Methods
IVT of CasX mRNA:
CasX 676 mRNA was generated by IVT. Briefly, constructs encoding for a 5′UTR region, a codon-optimized CasX 676 with flanking c-MYC NLSes, and a 3′UTR region were cloned into a plasmid containing a T7 promoter and 80-nucleotide poly(A) tail. The resulting plasmid was linearized prior to use for IVT reactions, which were carried out with CleanCap® AG and N1-methyl-pseudouridine. For the 5′ cap, the CleanCap® AG contains a m7G(5′)ppp(5′)mAG structure, where “m7G” denotes N7-methylguanosine, “mA” denotes 2′O-methyladenosine, and (5′)ppp(5′) denotes a 5′ to 5′ triphosphate bridge. An extra guanine nucleotide was incorporated following the CleanCap® AG to enhance transcription initiation, resulting in the incorporation of m7G(5′)ppp(5′)mAGG as the full 5′ cap structure. As discussed below in Example 9, the substitution of the uridine ribonucleoside to N1-methyl-pseudouridine improves mRNA performance and reduces mRNA immunogenicity.
IVT reactions were subsequently subjected to Dnase digestion to remove template DNA and purification using an oligo-dT column. In this example, two configurations of CasX 676 mRNAs were generated for assessment in vitro. The encoding sequences of the two CasX mRNA configurations are detailed in Table 33. Full-length RNA sequences encoding the CasX mRNA with the chemical modifications are listed in Table 34.







TABLE 33







Encoding sequences of the two CasX mRNA


molecules assessed in this example *.













DNA sequence or


CasX mRNA ID
Component (ID)
Description
SEQ ID NO:













CasX 676
5′UTR
Human HBA
3188


mRNA #1
START codon +

3133



c-MYC NLS



CasX 676

3134



c-MYC NLS +

3135



STOP codons



3′UTR
Human HBA
3189



Poly(A) tail

3057


CasX 676
5′UTR
Synthetic
3047


mRNA #2

(TriLink)



START codon +

3133



c-MYC NLS



CasX 676

3134



c-MYC NLS +

3135



STOP codons



3′UTR
Mouse HBA
3055



XbaI restriction site

TCTAG



(partial)



Poly(A) tail

3057





*Components are listed in a 5′ to 3′ order within the constructs













TABLE 34







Full-length RNA sequences of CasX mRNA molecules assessed in this example. The


5′ cap (m7G(5′)ppp(5′)mAG), discussed in the example herein, is not shown in the table.


Modification ‘mψ’ = N1-methyl-pseudouridine









CasX
SEQ



mRNA
ID NO
RNA Sequence





CasX
3190
ACmψCmψmψCmψGGmψCCCCACAGACmψCAGAGAGAACCCGCCACCAmψGGCCCCmψGCm


676

ψGCCAAGAGAGmψGAAGCmψGGAmψAGCAGACAGGAGAmψCAAGCGGAmψmψAAmψAAAA


mRNA

mψmψCGGAGAAGACmψGGmψGAAGGAmψmψCmψAACACAAAGAAGGCmψGGCAAGACACG


#1

GGGCCCmψAmψGAAGACACmψGCmψGGmψGAGAGmψGAmψGACACCCGACCmψGAGAGAA




AGACmψGGAAAACCmψGAGAAAGAAGCCmψGAGAAmψAmψCCCCCAGCCCAmψCAGCAAC




ACAAGCCGGGCCAACCmψGAAmψAAGCmψGCmψGACCGACmψACACCGAAAmψGAAGAAG




GCCAmψCCmψGCACGmψGmψAmψmψGGGAAGAGmψmψCCAGAAAGACCCAGmψCGGCCmψ




GAmψGAGCAGAGmψGGCmψCAGCCmψGCCAGCAAGAAGAmψCGAmψCAGAACAAGCmψGA




AGCCCGAAAmψGGACGAGAAGGGGAACCmψGACAACCGCCGGCmψmψmψGCCmψGmψAGC




CAGmψGCGGCCAGCCCCmψGmψmψmψGmψGmψACAAACmψGGAACAGGmψGAGCGAAAAG




GGCAAGGCmψmψACACGAAmψmψACmψmψCGGCAGAmψGCAACGmψGGCCGAGCACGAGA




AGCmψGAmψCAAGCmψGGCCCAGCmψGAAGCCmψGAGAAGGAmψAGCGAmψGAGGCAGmψ




GACAmψAmψmψCCCmψGGGCAAGmψmψCGGACAGCGGGCCCmψGGAmψmψmψmψmψAmψm




ψCCAmψmψCAmψGmψGACCAAGGAAmψCCACCCACCCCGmψCAAGCCmψCmψmψGCCCAA




AmψmψGCCGGCAACAGAmψACGCCmψCCAGCCCCGmψGGGCAAGGCCCmψGAGCGACGCC




mψGmψAmψGGGCACCAmψCGCCAGCmψmψCCmψGmψCmψAAGmψACCAGGACAmψmψAmψ




CAmψCGAGCACCAGAAGGmψGGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGC




GAGCmψGGCCGGCAAGGAAAACCmψGGAGmψAmψCCmψAGCGmψGACCCmψGCCmψCCmψ




CAGCCmψCAmψACAAAGGAGGGCGmψGGAmψGCCmψACAACGAAGmψGAmψCGCCCGGGm




ψGCGGAmψGmψGGGmψGAACCmψGAAmψGmψGmψGGCAGAAGCmψGAAGCmψGmψCmψAG




AGACGACGCCAAGCCCCmψGCmψGAGACmψGAAGGGCmψmψCCCCAGCmψmψCCCmψCmψ




GGmψGGAGAGACAGGCAAAmψGAAGmψGGACmψGGmψGGGACAmψGGmψGmψGmψAACGm




ψGAAGAAGCmψGAmψCAAmψGAGAAGAAGGAGGACGGCAAAGmψGmψmψCmψGGCAGAAm




ψCmψGGCCGGCmψACAAGCGmψCAGGAGGCCCmψGCGGCCCmψACCmψGAGCAGCGAGGA




AGACAGAAAGAAGGGCAAGAAGmψmψCGCCCGGmψAmψCAGCmψGGGGGACCmψGCmψGC




mψGCACCmψCGAGAAGAAGCACGGCGAAGACmψGGGGGAAGGmψGmψACGAmψGAGGCCm




ψGGGAGCGGAmψCGAmψAAGAAGGmψGGAGGGCCmψGAGCAAGCACAmψCAAGCmψGGAG




GAGGAACGGAGAmψCmψGAGGACGCCCAGAGCAAGGCCGCCCmψGACCGACmψGGCmψGA




GAGCCAAGGCCAGCmψmψCGmψCAmψCGAGGGGCmψGAAGGAGGCCGACAAGGACGAGmψ




mψCmψGCCGGmψGCGAACmψGAAGCmψGCAGAAGmψGGmψACGGAGAmψCmψGAGAGGCA




AACCmψmψmψCGCCAmψCGAGGCCGAGAACAGCAmψCCmψGGACAmψCAGCGGCmψmψCA




GCAAGCAGmψACAACmψGCGCCmψmψmψAmψmψmψGGCAGAAGGACGGAGmψGAAGAAGC




mψGAACCmψGmψACCmψGAmψCAmψCAACmψAmψmψmψCAAGGGCGGCAAGCmψGAGAmψ




mψCAAGAAGAmψCAAGCCmψGAAGCCmψmψCGAGGCCAACAGAmψmψCmψACACCGmψGA




mψmψAACAAGAAAAGCGGAGAGAmψCGmψGCCAAmψGGAAGmψGAACmψmψCAACmψmψC




GACGACCCmψAACCmψGAmψCAmψCCmψGCCCCmψGGCAmψmψmψGGCAAGCGGCAGGGC




AGAGAGmψmψCAmψCmψGGAACGACCmψGCmψGmψCmψCmψGGAGACCGGCAGCCmψGAA




GCmψGGCCAACGGCAGAGmψGAmψCGAGAAGACACmψGmψACAACAGACGAACCAGACAA




GACGAGCCCGCCCmψGmψmψmψGmψGGCCCmψGACCmψmψCGAGAGAAGAGAGGmψGCmψ




GGACAGCAGCAAmψAmψCAAGCCmψAmψGAACCmψGAmψCGGCGmψGGACCGGGGCGAGA




ACAmψCCCmψGCCGmψGAmψCGCCCmψmψACCGACCCCGAGGGAmψGCCCmψCmψGAGCC




GGmψmψmψAAAGACAGCCmψGGGCAACCCmψACCCACAmψCCmψGAGAAmψmψGGCGAGm




ψCCmψACAAGGAGAAGCAGAGAACCAmψCCAGGCCAAGAAGGAGGmψGGAGCAGCGGCGG




GCmψGGCGGCmψACmψCCCGGAAGmψACGCCAGCAAGGCCAAGAACCmψGGCCGACGACA




mψGGmψmψAGAAAmψACCGCCAGAGACCmψCCmψGmψACmψACGCmψGmψGACCCAGGAC




GCCAmψGCmψGAmψCmψmψCGAGAACCmψGAGCAGAGGCmψmψCGGCAGACAGGGCAAGA




GAACCmψmψCAmψGGCCGAGAGACAGmψACACCCGGAmψGGAGGACmψGGCmψGACCGCC




AAGCmψGGCCmψACGAGGGCCmψGCCCmψCmψAAGACCmψACCmψGmψCCAAGACCmψmψ




GGCACAGmψACACCAGCAAGACAmψGCmψCmψAACmψGCGGCmψmψCACAAmψCACGAGC




GCCGACmψACGACCGGGmψGCmψGGAGAAACmψGAAGAAGACCGCCACAGGCmψGGAmψG




ACCACCAmψmψAACGGCAAGGAGCmψGAAGGmψGGAGGGCCAGAmψCACCmψACmψACAA




CAGGmψACAAACGGCAGAACGmψGGmψGAAGGACCmψGAGCGmψGGAACmψGGAmψAGAC




mψGAGCGAGGAAAGCGmψAAACAAmψGACAmψCAGCAGCmψGGACCAAGGGCCGGAGCGG




CGAGGCCCmψGAGCCmψGCmψGAAGAAGAGAmψmψCmψCCCACAGACCAGmψGCAGGAGA




AGmψmψCGmψGmψGmψCmψGAACmψGCGGCmψmψCGAGACCCACGCCGACGAGCAAGCCG




CCCmψGAACAmψCGCCCGGmψCmψmψGGCmψmψmψmψCCmψGCGGAGCCAGGAGmψACAA




GAAGmψACCAGACAAACAAGACCACAGGCAACACAGACAAGAGAGCCmψmψCGmψCGAGA




CCmψGGCAGAGCmψmψCmψACAGAAAGAAGCmψGAAGGAGGmψGmψGGAAGCCmψGCCGm




ψGGGAAGCCCCGCmψGCCAAGAGAGmψGAAGCmψGGACmψAAmψAGAmψAAGCmψGGAGC




CmψCGGmψGGCCAmψGCmψmψCmψmψGCCCCmψmψGGGCCmψCCCCCCAGCCCCmψCCmψ




CCCCmψmψCCmψGCACCCGmψACCCCCGmψGGmψCmψmψmψGAAmψAAAGmψCmψGAGmψ




GGGCGGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAA


 


CasX
3136
See Table 22 for sequence


676




mRNA




#2









Synthesis of gRNAs:

In this example, gRNAs targeting the mouse PCSK9 locus were designed using gRNA scaffold 174 with a v1 modification profile (see Example 7) and chemically synthesized. The sequences of the PCSK9-targeting spacers are listed in Table 35.







TABLE 35







Sequences of spacers targeting the mouse PCSK9 locus assayed in this example










Spacer ID
Target
RNA sequence
SEQ ID NO:





27.103
mouse PCSK9
UAAUCUCCAUCCUCGUCCUG
3073


 


27.105
mouse PCSK9
CCAAGAAGCCAGGGAAGAGG
3192


 


27.106
mouse PCSK9
ACAUAUCUUUUAUGACCUCU
3193


 


27.107
mouse PCSK9
CUGGCUUCUUGGUGAAGAUG
3194


 


27.108
mouse PCSK9
UGGUGAAGAUGAGCAGUGAC
3195


 


27.116
mouse PCSK9
GCCGUUGCUCCAAGGUAUGG
3196


 


27.117
mouse PCSK9
UUCUUGGGGAUCAGGAGGCC
3197









Transfection of CasX mRNA and gRNA into Mouse Hepa1-6 Cells In Vitro:

Editing at the mouse PCSK9 locus was assessed by delivering in vitro transcribed CasX mRNA (CasX mRNA #1 or CasX mRNA #2; see Table 33) and synthesized gRNAs targeting PCSK9 into Hepa1-6 cells via transfection. Briefly, each well of 20,000 Hepa1-6 cells were lipofected with in vitro transcribed mRNA coding for CasX 676 and a PCSK9-targeting gRNA. After a media change, transfected cells were harvested at 20 hours post-transfection for editing assessment at the PCSK9 locus by NGS as described previously in Example 4. As experimental controls, individual transfections of CasX mRNA #1 and CasX mRNA #2 without gRNAs were performed.
Results
CasX-mediated editing at the mouse PCSK9 locus was used to evaluate the effects of incorporating different 5′ and 3′ UTRs into the engineered CasX mRNA. The plot in FIG. 26 shows the quantification of percent editing measured as indel rate at the PCSK9 locus in mouse Hepa1-6 cells transfected with CasX 676 mRNA #1 or CasX 676 mRNA #2 with the indicated PCSK9-targeting gRNAs. The data demonstrate that for all targeting spacers tested in this experiment, CasX mRNA #2 consistently exhibited higher editing levels at the mouse PCSK9 locus compared to editing levels achieved by CasX mRNA #1. Specifically, the highest level of editing rate achieved was with spacer 27.116, where use of CasX mRNA #2 resulted in ˜35% editing efficiency compared to ˜20% editing level by CasX mRNA #1 (FIG. 26).
The results demonstrate that altering the 5′UTR and 3′UTR sequences of the CasX mRNA can affect the editing activity of CasX at a target locus in a cell-based assay.
Example 9: Design and Assessment of Codon-Optimized CasX mRNA on Editing Efficiency when Delivered Together with Targeting gRNAs In Vitro
mRNA sequence and associated modifications can have a significant impact on the efficacy of mRNA-based delivery. Modified nucleotides, including those that encode the 5′ cap structure, are important determinants of mRNA stability, translatability, and immunogenicity. Here, for all designed and tested CasX mRNAs, a “Cap 1” structure was used, which included a 5′ m7G in a 5′-5′ triphosphate linkage to an initiating nucleotide with a 2′Ome modification. This structure, similar to the “Cap 0” structure lacking the 2′Ome modification, promotes efficient translation, and has reduced immunogenicity compared to the “Cap 0” structure. Furthermore, the use of modified nucleobases can reduce immunogenicity of the mRNA. Here, the N1-methyl-pseudouridine was used to substitute the uridine ribonucleoside for all in vitro transcription reactions, since published studies have demonstrated that the N1-methyl-pseudouridine substantially enhances mRNA performance and reduces mRNA immunogenicity. The modifications are expected to result in reduced immunogenicity and higher translation rates in vivo, potentially by avoiding activation of RIG-I, a primary cytosolic sensor for double-stranded RNA, which is a common contaminant of in vitro transcribed mRNA.
Optimization of the poly(A) tail will also be explored. The poly(A) tail is required for translation and mRNA stability, with longer tails being associated with a longer mRNA half-life. Polyadenylation can be carried out post-transcriptionally with a poly(A) polymerase, but this results in variable tail lengths and adds a step to the mRNA production process. mRNA productions were conducted using plasmids containing a template 80A-tail, terminating with a Type IIS restriction site to allow for run-off transcription, as constructs with plasmids containing a template 120A-tail were unstable during propagation in E. coli, often resulting in clones with significant reductions in tail length. Alternate plasmids were also cloned with a SphI restriction site between two-60A stretches, since published studies have demonstrated that similar constructs were more stable during subcloning and amplification in E. coli and produced mRNA with equivalent activity in mammalian cells. These alternate versions will be compared for activity using an in vitro editing assay across a range of CasX mRNA and gRNA doses to determine the consequential effects on editing activity. The sequences of the poly(A) tails described herein are listed in Table 36.
The sequences encoding the 5′ and 3′ UTRs, as well as the codons used for the CasX protein-coding sequences, are also critical for effective translation. UTRs were selected from annotated human gene transcripts based on genes (e.g., those encoding the a-globin, P-globin proteins) previously characterized to have high mRNA stability, as well as genes expected or previously demonstrated to be particularly well-expressed in the liver (i.e., genes encoding for the following proteins: albumin, complement 3, and cytochrome P450 2E1). The sequences of the 5′ and 3′ UTRs from these various genes are listed in Table 36. For the 3′ UTR, concatenations of individual 3′ UTRs were also tested. These constructs were cloned into plasmids containing a T7 promoter, CasX variant 515 or 676, and a poly(A) tail. To isolate the effects of individual 5′ and 3′ UTRs, each UTR was cloned into a construct that contained either the 3′ or 5′ a-globin UTR, respectively. IVTs will be performed and purified by binding to poly(dT) beads to capture full-length transcripts. The resulting mRNAs will initially be assessed by co-transfection with a B2M-targeting gRNA into HepG2 cells using a range of doses. Editing efficiency will be determined by HLA-immunostaining and flow cytometry as described in Example 7. The best-performing individual UTRs will be combined into various configurations, formulated into LNP, and tested in primary human hepatocytes and in mice.
Alternate codon optimizations are also being explored. In addition to the CasX codon optimization used for other delivery modalities, new versions were designed by building a codon usage table based on ribosomal protein codon usage and rebalancing CasX codon usage to match. In addition to potential improvements to the translation rate, this also effectively results in depletion of uracil bases, which may reduce immunogenicity. This codon optimization was also used for production of mRNAs. Additional codon usages have been designed using a variety of available codon optimization tools, adjusting settings as needed to achieve a range of GC content levels. These codon optimizations will be tested under a similar experimental design used for testing UTRs as described above, and the leading codon-optimized CasX candidates will be combined with leading UTR candidates to generate new CasX leads for further validation.







TABLE 36







List of encoding DNA sequences for the indicated elements used for the generation


and optimization of CasX mRNA.











SEQ ID


Description
Encoding Sequence
NO:










Poly(A) tails









A80
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3057



AAAAAAAAAAAAAAAAAAAAAAA



 


A120
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3198



AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAA



 


A60SphIA60
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
3199



AAAGCATGCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAA



 







5′ UTRs









α-globin
ACTCTTCTGGTCCCCACAGACTCAGAGAGAACCC
3200


 


ß-globin
ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACA
3201


 


Albumin
CTAGCTTTTCTCTTCTGTCAACCCCACACGCCTTT
3202


 


Cytochrome
CTCCCGGGCTGGCAGCAGGGCCCCAGC
3203


P450 2E1




(CYP2E1)




 


Complement
ACTCCTCCCCATCCTCTCCCTCTGTCCCTCTGTCCCTCTGACCCTGCACTGTCCC
3204


3 (C3)




 







3′ UTRs









α-globin
GCTGGAGCCTCGGTGGCCATGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTC
3189



CCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCA



 


Albumin
CATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGAT
3205



CAAAAGCTTATTCATCTGTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCTA




AAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAAA




AAATGGAAAGAATCTAATAGAGTGGTACAGCACTGTTATTTTTCAAAGATGTGTTGC




TATCCTGAAAATTCTGTAGGTTCTGTGGAAGTTCCAGTGTTCTCTCTTATTCCACTT




CGGTAGAGGATTTCTAGTTTCTTGTGGGCTAATTAAATAAATCATTAATACTCTTCT




AAGTTATGGATTATAAACATTCAAAATAATATTTTGACATTATGATAATTCTGAATA




AAAGAACAAAAACCA



 


Albumin
GCATCACATTTAAAAGCATCTCAGCCTACCATGAGAATAAGAGAAAGAAAATGAAGA
3206


(truncated)
TCAATAGCTTATTCATCTCTTTTTCTTTTTCGTTGGTGTAAAGCCAACACCCTGTCT




AAAAAACATAAATTTCTTTAATCATTTTGCCTCTTTTCTCTGTGCTTCAATTAATAA




AAAATGGAAAGAACCTAGATCT



 


ß-globin
GCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAAC
3207



TACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAA




AACATTTATTTTCATTGCAA



 


a-globin +
GCTGGAGCCTCGGTGGCCATGCTTCTTGCCCCTTGGGCCTCCCCCCAGCCCCTCCTC
3208


ß-globin
CCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAAAGTCTGAGTGGGCGGCAGCT




CGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTAC




TAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAAC




ATTTATTTTCATTGCAA



 


ß-globin + 
GCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAAC
3209


α-globin
TACTAAACTGGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAA




AACATTTATTTTCATTGCAAGCTGGAGCCTCGGTGGCCATGCTTCTTGCCCCTTGGG




CCTCCCCCCAGCCCCTCCTCCCCTTCCTGCACCCGTACCCCCGTGGTCTTTGAATAA




AGTCTGAGTGGGCGGCA









Example 10: Proof-of-Concept Experiment Demonstrating Delivery of LTRP mRNA and Targeting gRNA Via LNPs to Achieve Repression of Target Locus In Vitro
Experiments were performed to assess whether delivery of lipid nanoparticles (LNPs) encapsulating LTRP mRNA and a PCSK9-targeting gRNA could induce durable repression of the target PCSK9 locus in a cell-based assay. LNPs encapsulating an mRNA encoding for catalytically-active CasX 515 were formulated and included for comparison.
Materials and Methods
Generation of mRNAs:
mRNA encoding the following molecules were generated by IVT following similar methods as described in Example 2: 1) a catalytically-active CasX 515 and 2) LTRP5-ADD-ZIM3 (as described in Example 4). Briefly, for the generation of CasX 515, constructs encoding for a synthetic 5′UTR, a codon-optimized CasX 515 with flanking c-MYC NLSes, and a 3′UTR derived from the mouse hemoglobin alpha (mHBA) were cloned into a plasmid containing a T7 promoter and 79-nucleotide poly(A) tail. The resulting plasmid was linearized prior to use for IVT reactions, which were performed as similarly described in Example 2. The DNA and mRNA sequences encoding the catalytically-active CasX 515 are shown in Table 37 and Table 38 respectively. The DNA and mRNA sequences encoding for LTRP5-ADD-ZIM3 are shown in Table 18 and Table 19 respectively.







TABLE 37







Encoding sequences of the catalytically-active CasX


515 mRNA molecule assessed in this example*.













DNA sequence or


CasX mRNA ID
Component (ID)
Description
SEQ ID NO:













CasX 515
5′UTR
Synthetic
3274


mRNA

(TriLink)



START codon +

3275



c-MYC NLS



CasX 515

3276



c-MYC NLS +

3277



STOP codon



3′UTR
Mouse HBA
3278



XbaI restriction site

TCTAG



(partial)



Poly(A) tail

3279





*Components are listed in a 5′ to 3′ order within the constructs













TABLE 38







Full-length RNA sequences of catalytically-active CasX 515 mRNA molecule


assessed in this example. Modification ‘mψ’ = N1-methyl-pseudouridine.










SEQ



CasX
ID



mRNA
NO
RNA Sequence





CasX
3280
AAAmψAAGAGAGAAAAGAAGAGmψAAGAAGAAAmψAmψAAGAGCCACCAmψGGCCCCmψGCmψGCCAA


515

GAGAGmψGAAGCmψGGAmψTAGCAGACAGGAGAmψCAAGCGGAmmψAAmψAAAAmψmψCGGAGAAGAC


mRNA

mψGGmψGAAGGAmψmψCmψAACACAAAGAAGGCmψGGCAAGACAGGCCCmψAmψGAAGACACmψGCmψ




GGmψGAGAGmψGAmψGACACCCGACCmψGAGAGAAAGACmψGGAAAACCmψGAGAAAGAAGCCmψGAG




AAmψAmψCCCCCAGCCCAmψCAGCAACACAAGCCGGGCCAACCmψGAAmψAAGCmψGCmψGACCGACm




ψACACCGAAAmψGAAGAAGGCCAmψCCmwGCACGmψGmψAmψmψGGGAAGAGmψmψCCAGAAAGACCC




AGmψCGGCCmψGAmψGAGCAGAGmψGGCmψCAGCCmψGCCAGCAAGAAGAmψCGAmψCAGAACAAGCm




ψGAAGCCCGAAAmψGGACGAGAAGGGGAACCmψGACAACCGCCGGCmψmψmψGCCmψGmψAGCCAGmψ




GCGGCCAGCCCCmψGmψmψmψGmψGmψACAAACmψGGAACAGGmψGAGCGAAAAGGGCAAGGCmψmψA




CACGAAmψmψACmψmψCGGCAGAmψGCAACGmψGGCCGAGCACGAGAAGCmψGAmψCCmψGCmψGGCC




CAGCmψGAAGCCmψGAGAAGGAmψAGCGAmψGAGGCAGmψGACAmψAmψmψCCCmψGGGCAAGmψmψC




GGACAGCGGGCCCmψGGAmψmψmψmψmψAmψmψCCAmψmψCamψGmψGACCAAGGAAmψCCACCCACC




CCGmψCAAGCCmψCmψmψGCCCAAAmψmψGCCGGCAACAGAmψACGCCAGCGGCCCCGmψGGGCAAGG




CCCmψGAGCGACGCCmψGmψAmψGGGCACCAmψCGCCAGCmψmψCCmψGmψCmψAAGmψACCAGGACA




mψmψAmψCAmψCGAGCACCAGAAGGmψGGmψGAAGGGCAACCAGAAGAGACmψGGAGAGCCmψGCGCG




AGCmψGGCCGGCAAGGAAAACCmψGGAGmψAmψCCmψAGCGmψGACCCmψGCCmψCCmψCAGCCmψCA




mψACAAAGGAGGGCGmψGGAmψGCCmψACAACGAAGmψGAmψCGCCCGGGmψGCGGAmψGmψGGGmψG




AACCmψGAAmψCmwGmψGGCAGAAGCmwGAAGCmψGmψCmψAGAGACGACGCCAAGCCCCmψGCmψGA




GACmψGAAGGGCmψmψCCCCAGCmψmψCCCmψCmψGGmψGGAGAGACAGGCAAAmψGAAGmψGGACmψ




GGmψGGGACAmψGGmψGmψGmψAACGmψGAAGAAGCmψGAmψCAAmψGAGAAGAAGGAGGACGGCAAA




GmψGmψmψCmψGGCAGAAmψCmψGGCCGGCmψACAAGCGmψCAGGAGGCCCmψGCGGCCCmψACCmψG




AGCAGCGAGGAAGACAGAAAGAAGGGCAAGAAGmψmψCGCCCGGmψAmψCAGCmψGGGGGACCmψGCm




ψGCmψGCACCmψCGAGAAGAAGCACGGCGAAGACmψGGGGGAAGGmψGmψACGAmψGAGGCCmψGGGA




GCGGAmψCGAmψAAGAAGGmψGGAGGGCCmψGAGCAAGCACAmψCAAGCmψGGAGGAGGAACGGAGAm




ψCmψGAGGACGCCCAGAGCAAGGCCGCCCmψGACCGACmψGGCmψGAGAGCCAAGGCCAGCmψmψCGm




ψCAmψCGAGGGGCmψGAAGGAGGCCGACAAGGACGAGmψmψCmψGCCGGmψGCGAACmψGAAGCmψGC




AGAAGmψGGmψACGGAGAmψCmψGAGAGGCAAACCmψmψmyCGCCAmψCGAGGCCGAGAACAGCAmψC




CmψGGACAmψCAGCGGCmψmψCAGCAAGCAGmψACAACmψGCGCCmψmψmψAmψmψmψGGCAGAAGGA




CGGAGmψGAAGAAGCmψGAACCmψGmψACCmψGAmψCAmψCAACmψAmψmψmψCAAGGGCGGCAAGCm




ψGAGAmψmψCAAGAAGAmψCAAGCCmψGAAGCCmψmψCGAGGCCAACAGAmψmψCmψACACCGmψGAm




ψmψAACAAGAAAAGCGGAGAGAmψCGmψGCCAAmψGGAAGmψGAACmψmψCAACmψmψCGACGACCCm




ψAACCmψGAmψCAmψCCmψGCCCCmψGGCAmψmψmψGGCAAGCGGCAGGGCAGAGAGmψmψCAmψCmψ




GGAACGACCmψGCmψGmψCmψCmψGGAGACCGGCAGCCmψGAAGCmψGGCCAACGGCAGAGmψGAmψC




GAGAAGACACmψGmψACAACAGACGAACCAGACAAGACGAGCCCGCCCmψGmψmψmψGmψGGCCCmψG




ACCmψmψCGAGAGAAGAGAGGmψGCmψGGACAGCAGCAAmψAmyCAAGCCmψAmψGAACCmψGAmψCG




GCGmψGGACCGGGGCGAGAACAmψCCCmψGCCGmψGAmψCGCCCmψmψACCGACCCCGAGGGAmψGCC




CmψCmψGAGCCGGmψmψmψAAAGACAGCCmψGGGCAACCCmψACCCACAmψCCmψGAGAAmψmψGGCG




AGmψCCmψACAAGGAGAAGCAGAGAACCAmψCCAGGCCAAGAAGGAGGmψGGAGCAGCGGCGGGCmψG




GCGGCmψACmψCCCGGAAGmψACGCCAGCAAGGCCAAGAACCmψGGCCGACGACAmψGGmψmψAGAAA




mψACCGCCAGAGACCmψCCmψGmψACmψACGCmψGmψGACCCAGGACGCCAmψGCmψGAmψCmψmψCG




AGAACCmψGAGCAGAGGCmψmψCGGCAGACAGGGCAAGAGAACCmψmψCAmψGGCCGAGAGACAGmψA




CACCCGGAmψGGAGGACmψGGCmψGACCGCCAAGCmψGGCCmψACGAGGGCCmψGCCCmψCmψAAGAC




CmψACCmψGmψCCAAGACCmψmψGGCACAGmψACACCAGCAAGACAmψGCmψCmψAACmψGCGGCmψm




ψCACAAmψCACGAGCGCCGACmψACGACCGGGmψGCmψGGAGAAACmψGAAGAAGACCGCCACAGGCm




ψGGAmψGACCACCAmψmψAACGGCAAGGAGCmψGAAGGmψGGAGGGCCAGAmψCACCmψACmψACAAC




AGGmψACAAACGGCAGAACGmψGGmψGAAGGACCmψGAGCGmψGGAACmψGGAmψAGACmψGAGCGAG




GAAAGCGmψAAACAAmψGACAmψCAGCAGCmψGGACCAAGGGCCGGAGCGGCGAGGCCCmψGAGCCmψ




GCmψGAAGAAGAGAmψmψCmψCCCACAGACCAGmψGCAGGAGAAGmψmψCGmψGmψGmψCmψGAACmψ




GCGGCmψmψCGAGACCCACGCCGACGAGCAAGCCGCCCmψGAACAmψCGCCCGGmψCmψmψGGCmψmψ




mψmψCCmψGCGGAGCCAGGAGmψACAAGAAGmψACCAGACAAACAAGACCACAGGCAACACAGACAAG




AGAGCCmψmψCGmψCGAGACCmψGGCAGAGCmψmψCmψACAGAAAGAAGCmψGAAGGAGGmψGmψGGA




AGCCmψGCCGmψGGGAAGCCCCGCmψGCCAAGAGAGmψGAAGCmψGGACmψAAGCmψGCCmψmψCmψG




CGGGGCmψmψGCCmψmψCmψGGCCAmψGCCCmψmψCmψmψCmψCmψCCCmψmψGCACCmψGmψACCmψ




CmψmψGGmψCmψmψmψGAAmψAAAGCCmψGAGmψAGGAAGmψCmψAGAAAAAAAAAAAAAAAAAAAAA




AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA









Synthesis of gRNAs:

PCSK9-targeting gRNAs were designed using gRNA scaffold 316 and spacer 6.1 (sequence listed in Table 24) and chemically synthesized. The sequence of the PCSK9-targeting gRNA with the v1 modification profile (as described in Example 7 above) is listed in Table 39. A schematic of the sites of chemical modifications for a ‘v1’ profile of the gRNA scaffold variant 316 is shown in FIG. 24.







TABLE 39







Sequences of chemically modified the gRNA targeting the human PCSK9 locus


assayed in this example.










gRNA ID





(scaffold variant-


SEQ ID


spacer)
Target
gRNA sequence
NO





316-6.1 (v1)
human
mA*mC*mU*GGCGCUUCUAUCUGAUUACUCUGAGCGCCAUC
3447



PCSK9
ACCAGCGACUAUGUCGUAGUGGGUAAAGCUCCCUCUUCGGA





GGGAGCAUCAGAGGAGGAGGACGGCCUGGC*mC*mG*mA









LNP formulations were generated with the LNP lipids as listed in Table 40, using methods described in Example 11, below.
Delivery of LNPs Encapsulating LTRP or CasX mRNA and Targeting gRNA into Primary Cynomolgus Macaque (CM) Hepatocytes:
Two lots (termed BJE and VDU) of primary CM hepatocytes derived from two different donors (product number: M003055-P; BioIVT®), were used to assess LTRP-mediated repression or CasX-mediated editing at the PCSK9 locus when delivered by LNPs. For each lot, ˜50,000 cells, cultured in Williams' E complete media, were seeded per well in a 96-well plate. The next day, seeded cells were treated with varying concentrations of LNPs, which were prepared in six 3-fold serial dilutions starting at 1,200 ng/100 μL. These LNPs were formulated to co-encapsulate CasX 515 or LTRP5-ADD-ZIM3 mRNA and a PCSK9-targeting gRNA incorporating scaffold variant 316 with spacer 6.1 (v1; see Table 39). The LNP formulations tested in this example are shown in Table 40. Media was changed one day after LNP treatment, and cells were cultured for additional days prior to harvesting the media supernatant to measure PCSK9 secretion levels at the day 4 and day 11 timepoints. Briefly, PCSK9 secretion levels were measured by ELISA using the BioLegend® ELISA MAX™ kit following the manufacturer's instructions. To ensure accuracy in quantifying PCSK9 secretion levels, a standard curve was constructed using recombinant CM PCSK9 protein as a reference (Cynomolgus PCSK9 protein, from Acro Biosystems®). Baseline PCSK9 secretion levels (ng/mL) were also quantified for untreated primary CM hepatocytes (for each lot) at day 4.







TABLE 40







LNP formulations tested in this example.









LNP lipid
Encapsulated mRNA
Encapsulated gRNA





Gen Voy-ILMTM
CasX 515
gRNA scaffold 316 with


MC3

spacer 6.1 (v1)


MC3
LTRP5-ADD-ZIM3


ALC-0315


SM-102









Results
Two lots of primary CM hepatocytes were treated with five different LNPs, which co-encapsulated either CasX 515 or LTRP5-ADD-ZIM3 and a PCSK9-targeting gRNA using spacer 6.1, at various doses. The media supernatant was harvested 4 and 11 days post-treatment to assess effects on PCSK9 secretion (FIGS. 61-64). The results in FIGS. 61-64 demonstrate that either LTRP5-ADD-ZIM3 or CasX mRNA and the targeting gRNA could be co-encapsulated within the various LNPs, and were delivered to target cells where they reduced secreted PCSK9 levels. Dose-dependent reduction in secreted PCSK9 levels was observed for all formulated LNPs in both lots of primary CM hepatocytes at 4 days post-treatment (FIGS. 61-62). By 11 days post-treatment, dose-dependent reduction in secreted PCSK9 levels was observed for all formulated LNPs in both lots, with the exception of MC3-encapsulating LTRP5-ADD-ZIM3 and the targeting gRNA (FIGS. 63-64). Secreted PCSK9 levels will be examined at longer timepoints to determine further the effects of each LNP formulation on decreasing PCSK9 secretion.
The results from this experiment show that LTRP mRNA, as well as CasX mRNA, and targeting gRNA can be co-encapsulated within LNPs to be delivered to target cells to induce silencing of a target endogenous locus.
Example 11: Formulation of Lipid Nanoparticles (LNPs) to Deliver dXR or LTRP mRNA and gRNA Payloads to Target Cells and Tissue
As described in Example 10, experiments were performed to encapsulate dXR or LTRP mRNA and gRNA into LNPs for delivery to target cells and tissues. The following example provides the methods used for formulating LNPs with various LNP lipids.
For Experiments that Used GenVoy-ILM™-Based LNPs:
dXR or LTRP mRNA and gRNA were encapsulated into LNPs using GenVoy-ILM™ lipids using the Precision NanoSystems Inc. (PNI) Ignite™ Benchtop System, following the manufacturer's guidelines. GenVoy-ILM™ lipids are a composition of ionizable lipid:DSPC:cholesterol:stabilizer at 50:10:37.5:2.5 mol %. Briefly, to formulate LNPs, equal mass ratios of dXR or LTRP mRNA and gRNA were diluted in PNI Formulation Buffer, pH 4.0. GenVoy-ILM™ lipids were diluted 1:1 in anhydrous ethanol. mRNA/gRNA co-formulations were generated using a predetermined N/P ratio. The RNA and lipids were run through a PNI laminar flow cartridge at a predetermined flow rate ratio on the PNI Ignite™ Benchtop System. After formulation, the LNPs were diluted in PBS, pH 7.4, to decrease the ethanol concentration and increase the pH, which would increase the stability of the particles. Buffer exchange of the mRNA/sgRNA-LNPs was achieved by overnight dialysis into PBS, pH 7.4, at 4° C. using 10k Slide-A-Lyzer™ Dialysis Cassettes (Thermo Scientific™). Following dialysis, the mRNA/gRNA-LNPs was concentrated to >0.5 mg/mL using 100 kDa Amicon®-Ultra Centrifugal Filters (Millipore) and then filter-sterilized. Formulated LNPs were analyzed on a Stunner® (Unchained Labs) to determine their diameter and polydispersity index (PDI). Encapsulation efficiency and RNA concentration was determined by RiboGreen™ assay using Invitrogen's Quant-iT™ RiboGreen™ RNA assay kit.
For experiments that used ALC-0315 (6-((2-hexyldecanoyl)oxy)-N-(6-((2-hexyldecanoyl)oxy)hexyl)-N-(4-hydroxybutyl)hexan-1-aminium), SM-102 (8-[(2-hydroxyethyl)[6-oxo-6-(undecyloxy)hexyl]amino]-octanoic acid, 1-octylnonyl ester), and MC3 (DLin-MC3-DMA)-based LNPs:
dXR or LTRP mRNA and gRNA were encapsulated into LNPs using ALC-0315, SM-102, or MC3-based lipid mix using a custom-made T-mixer micro mixing device, at a flow rate of 20 mL/min and 3:1 mixing ratio of aqueous to organic phase. For all three lipid mixes, the composition was the following: ionizable lipid:DSPC:cholesterol:DMG-PEG2000 at 50:10:38.5:1.5 mol %. Briefly, to formulate LNPs, equal mass ratios of dXR or LTRP mRNA and gRNA were diluted in 25 mM sodium acetate, pH 4.0. The lipid mix was made at a 10 mM concentration in anhydrous ethanol. mRNA/gRNA co-formulations were generated using a predetermined N/P ratio. The RNA and lipids are run through a custom-made T-mixer device at a predetermined flow rate ratio using syringe pump infusers. After formulation, the LNPs were dialyzed into PBS, pH 7.4, to decrease the ethanol concentration and increase the pH, which increases the stability of the particles. Buffer exchange of the mRNA/sgRNA-LNPs was achieved by overnight dialysis into PBS, pH 7.4, at 4° C. using 10k Slide-A-Lyzer™ Dialysis or Cassettes (Thermo Scientific™) or 12-14 kDa dialysis tubing (Repligen). Following dialysis, the mRNA/gRNA-LNPs was concentrated to >0.2 mg/mL using 30-100 kDa Amicon®-Ultra Centrifugal Filters (Millipore) and then sterile-filtered using Acrodisc PES membrane filters. Formulated LNPs were analyzed on a Malvern Zetasizer to determine their diameter and polydispersity index (PDI). Encapsulation efficiency and RNA concentration was determined by RiboGreen™ assay using Invitrogen's Quant-iT™ RiboGreen™ RNA assay kit.
The GenVoy-ILM™, ALC-0315, SM-102, and MC3 LNPs described above were used in various experiments to deliver XR or LTRP mRNA and gRNA to target cells, and can further be used for delivery to target tissues.
Example 12: CpG-Depletion of DNA Encoding the Guide RNA Scaffold Improves CasX-Mediated Editing In Vitro
Pathogen-associated molecular patterns (PAMPs), such as unmethylated CpG motifs, are small molecular motifs conserved within a class of microbes. They are recognized by toll-like receptors (TLRs) and other pattern recognition receptors in eukaryotes and often induce a non-specific immune activation. In the context of gene therapy, therapeutics containing PAMPs are often not as well-tolerated and are rapidly cleared from the patient given the strong immune response triggered, which ultimately leads to reduced therapeutic efficacy. CpG motifs are short single-stranded DNA sequences containing the dinucleotide CG. When these CpG motifs are unmethylated, they act as PAMPs and therefore stimulate the immune response. In this example, experiments were performed to deplete CpG motifs in the guide scaffold coding sequence in the context of an AAV construct encoding CasX variant 491, guide scaffold variant 235, and spacer 7.37 targeting the endogenous B2M (beta-2-microglobulin) locus, and test the effect of CpG-depletion in the guide scaffold on editing of the B2M locus in vitro.
Materials and Methods
Design of CpG-Depleted Guide Scaffolds:
Nucleotide substitutions were rationally-designed to replace native CpG motifs within the base gRNA scaffold variant (gRNA scaffold 235) with the intent to preserve editing activity while reducing scaffold immunogenicity. It was believed that as many CpG-motifs as possible should be removed from the scaffold coding sequence in order to sufficiently reduce immunogenicity. Scaffold 235 contains a total of eight CpG elements; six of which are predicted to basepair and form complementary strands of a double-stranded secondary structure (see FIG. 27A). Therefore, the six basepairing CpGs forming three pairs were mutated in concert to maintain important secondary structures. This reduced the number of independent CpG-containing regions to five (three pairs and two single CpGs) to be considered independently for CpG-removal. Specifically, mutations were designed in (1) the pseudoknot stem, (2) the scaffold stem, (3) the extended stem bubble, (4) the extended step, and (5) the extended stem loop, as diagrammed in FIG. 27B and described in detail below.
In the pseudoknot stem (region 1), the CpG pair was flipped to a GpC to minimize the alteration of the base composition and sequence. Based on previous experiments involving replacing individual base pairs, it was anticipated that this mutation was not likely to be detrimental to the structure and function of the guide RNA scaffold.
Similarly, in the scaffold stem (region 2) the CpG pair was flipped to a GpC to minimize the alteration of the base composition and sequence. It was anticipated that this mutation was likely to be detrimental to the structure and function of the guide RNA scaffold because strong sequence conservation was seen in this region in previous experiments mutating individual bases or base pairs. This strong sequence conservation is likely due to the scaffold stem loop being important in interacting with the CasX protein as well as in the formation of a triplex structural element with the pseudoknot region.
In the extended stem bubble (region 3) the single CpG was removed by one of three strategies. First, the bubble was deleted by mutating CG→C. Second, the bubble was resolved to restore ideal basepairing by mutating CG→CT. Third, the entire extended stem loop was replaced with the extended stem loop of scaffold 174. Note that, by itself, the replacement of the extended stem loop with that of scaffold 174 recapitulates scaffold 316, which has previously been shown to edit efficiently. There are no CpG motifs in the extended stem loop of scaffold 174. Therefore, replacing the extended stem loop with that of scaffold 174 also removes the CpG motif in the extended stem (region 4). Based on previous experiments showing the relative robustness of the extended stem to small changes, it was anticipated that mutating the extended stem bubble was moderately likely to be detrimental to the structure and function of the guide RNA scaffold.
In the extended stem (region 4), the CpG pair could not be flipped to GpC without generating additional CpG motifs. Therefore, the CpGs were changed to a GG and a complementary CC motif. Similar to region 3, based on the relative robustness of the extended stem to small changes, it was anticipated that this mutation was not likely to be detrimental to the structure and function of the guide RNA scaffold.
Finally, the extended stem loop (region 5) was mutated in one of three ways that were designed based on previous experiments examining the stability of the stem loop. In particular, several variations of the stem loop had previously been shown to have similar stability levels, and some of these variations of the stem loop do not contain CpGs. Based on these findings, first, the loop was replaced with a new loop with a CUUG sequence. Second, the loop was replaced with a new loop with a GAAA sequence. Since the GAAA loop replacement would generate a novel CpG adjacent to the loop, it was combined with a C→G base swap and the corresponding G→C base swap on the complementary strand, ultimately resulting in a CUUCGG→GGAAAC exchange. Third, the loop was mutated by the insertion of an A to interrupt the CpG motif and thereby increase the size of the loop from 4 to 5 bases. It was anticipated that randomly mutating the extended stem loop would likely have detrimental effects on secondary structure stability and hence on editing. However, relying on previously confirmed sequences was believed to have a lower risk associated with a replacement.
To generate guide RNA scaffolds encoded by DNA with reduced CpG levels, the mutations described above were combined in various configurations. Table 41, below, summarizes combinations of the mutations that were used. In Table 41, a 0 indicates that no mutation was introduced to a given region, a 1, 2, or 3 indicates that a mutation was introduced in that region, as diagrammed in FIG. 27B, and n/a indicates not applicable. Specifically, for region 1, the pseudoknot stem, a 1 indicates that a CG→GC mutation was introduced. For region 2, the scaffold stem, a 1 indicates that a CG→GC mutation was introduced. For region 3, the extended stem bubble, a 1 indicates that the bubble was removed by the deletion of the G and A bases that form the bubble, a 2 indicates that the bubble was resolved by a CG→CU mutation that allows for basepairing between the A and U bases, and a 3 indicates that the extended stem loop was replaced with the extended step loop from guide scaffold 174. For region 4, the extended stem, a 1 indicates that a CG→GC mutation was introduced. For region 5, the extended stem loop, a 1 indicates that the loop was replaced from UUCG→CUUG, a 2 indicates that the loop was replaced along with a basepair adjacent to the loop, from CUUCGG→GGAAAC, and a 3 indicates that an A was inserted between the C and the G.







TABLE 41







Summary of mutations for CpG-reduction


and depletion in guide scaffold 235















Region 3

Region 5



Region 1
Region 2
(Extended
Region 4
(Extended


Scaffold
(Pseudoknot
(Scaffold
stem
(Extended
stem


ID
stem)
stem)
bubble)
stem)
loop)















320
1
0
0
1
0


321
1
0
1
1
0


322
1
0
2
1
0


323
1
0
3
n/a
0


324
1
0
1
1
1


325
1
0
2
1
1


326
1
0
3
n/a
1


327
1
0
1
1
2


328
1
0
2
1
2


329
1
0
3
n/a
2


330
1
0
1
1
3


331
1
0
2
1
3


332
1
0
3
n/a
3


334
1
1
2
1
1


335
1
1
3
n/a
1


336
1
1
1
1
2


337
1
1
2
1
2


338
1
1
3
n/a
2


339
1
1
1
1
3


340
1
1
2
1
3


341
1
1
3
n/a
3


235
0
0
0
0
0









Table 42, below, lists the DNA sequences encoding the designed CpG-reduced or depleted guide scaffolds.







TABLE 42







DNA sequences encoding CpG-reduced


or depleted guide RNA scaffolds










Scaffold ID
SEQ ID NO














320
3210



321
3211



322
3212



323
3213



324
3214



325
3215



326
3216



327
3217



328
3218



329
3219



330
3220



331
3221



332
3222



333
3223



334
3224



335
3225



336
3226



337
3227



338
3228



339
3229



340
3230



341
3231










Generation of CpG-Depleted AAV Plasmids:

The CpG-reduced or depleted gRNA scaffolds were tested in the context of AAV vectors that were otherwise CpG-depleted, with the exception of the AAV2 ITRs. Specifically, nucleotide substitutions to replace native CpG motifs in AAV components were designed in silico based on homologous nucleotide sequences from related species for the following elements: the murine Ula snRNA (small nuclear RNA) gene promoter, the bGHpA (bovine growth hormone polyadenylation) sequence, and the human U6 promoter. The coding sequence for CasX 491 was codon-optimized for CpG depletion. All resulting sequences (Tables 42 and 43) were ordered as gene fragments with the appropriate overhangs for cloning and isothermal assembly to replace individually the corresponding elements of the existing base AAV plasmid (construct ID 183). Spacer 7.37 (GGCCGAGAUGUCUCGCUCCG; SEQ ID NO: 3137), which targets the endogenous B2M gene, was used for the experiments discussed in this example. The first time that the experiment was performed (“N=1”), a sample with the non-targeting spacer 0.0 was also included as a control (CGAGACGUAAUUACGUCUCG, SEQ ID NO: 3232; see FIG. 28).
The resulting AAV constructs were generated using standard molecular cloning techniques. Cloned and sequence-validated plasmid constructs were midi-prepped for subsequent nucleofection and AAV vector production. The sequences of the additional components of AAV constructs, with the exception of sequences encoding the gRNAs (Table 41), are listed in Table 43.







TABLE 43







Sequences of AAV elements (5′-3′ in AAV construct)











DNA sequence



Element
SEQ ID NO:














AAV2 5′ ITR
3233



CpG-depleted Ula promoter
3234



CpG-depleted cMycNLS-CasX491-
3235



cMycNLS



CpG-depleted bGH-polyA sequence
3236



CpG-depleted U6 promoter
3237







See sgRNA sequences in Table 42, above.










AAV2 3′ ITR
3238










AAV Production:

Suspension-adapted HEK293T cells, maintained in FreeStyle™ 293 media, were seeded in 20-30 mL of media at 1.5E6 cells/mL on the day of transfection. Endotoxin-free pAAV plasmids with the transgene flanked by ITR repeats were co-transfected with plasmids supplying the adenoviral helper genes for replication and AAV rep/cap genome using PEI Max® (Polysciences®) in serum-free Opti-MEM™ media. Three days later, cultures were centrifuged to separate the supernatant from the cell pellet, and the AAV particles were collected, concentrated, and filtered following standard procedures.
To determine the viral genome (vg) titer, 1 μL from crude lysate viruses was digested with DNase and ProtK, followed by quantitative PCR. 5 μL of digested virus was used in a 25 μL qPCR reaction composed of IDT primetime master mix and a set of primer and 6′FAM/Zen/IBFQ probe (IDT) designed to amplify a 62 bp-fragment located in the AAV2-ITR. An AAV ITR plasmid was used as reference standards to calculate the titer (vg/mL) of viral samples.
AAV Transduction of Induced Neurons In Vitro:
24 hours prior to transduction, 50,000 induced neurons per well were seeded on Matrigel-coated 96-well plates. AAVs expressing the CasX:gRNA system with various versions of the guide scaffold were then diluted in neuronal plating media and added to cells. The first time that the experiment was performed (“N=1”), cells were transduced at a multiplicity of infection (MOI) of 4e3 viral genomes (vg)/cell (see FIG. 28). Seven days post-plating, induced neurons were transduced with virus diluted in fresh feeding media. Eight days post-transduction, cells were lifted using lysis buffer, 4-well replicates were pooled per experimental condition, and genomic DNA (gDNA) was harvested and prepared for editing analysis at the B2M locus using next generation sequencing (NGS). The second time that the experiment was performed (“N=2”), cells were transduced at an MOI of 3e3 vg/cell, 1e3 vg/cell, or 3e2 vg/cell (see FIG. 29, FIG. 30, and FIG. 31). Seven days post-plating, induced neurons were transduced with virus diluted in fresh feeding media. Seven days post-transduction, cells were lifted using lysis buffer, 2-well replicates were pooled per experimental condition, and gDNA was harvested and prepared for editing analysis at the B2M locus using NGS. Samples that were not transduced with AAV were included as controls.
NGS Processing and Analysis:
Genomic DNA (gDNA) from harvested cells were extracted using the Zymo Quick-DNA Miniprep Plus kit following the manufacturer's instructions. Target amplicons were formed by amplifying regions of interest from 200 ng of extracted gDNA with a set of primers specific to the human B2M gene. These gene-specific primers contained an additional sequence at the 5′ end to introduce an Illumina adapter and a 16-nucleotide unique molecule identifier. Amplified DNA products were purified with the Ampure XP DNA cleanup kit. Quality and quantification of the amplicon were assessed using a Fragment Analyzer DNA Analysis kit (Agilent®, dsDNA 35-1500 bp). Amplicons were sequenced on the Illumina Miseq according to the manufacturer's instructions. Raw fastq files from sequencing were quality-controlled and processed using cutadapt v2.1, flash2 v2.2.00, and CRISPResso2 v2.0.29. Each sequence was quantified for containing an insertion or deletion (indel) relative to the reference sequence, in a window around the 3′ end of the spacer (30 bp window centered at −3 bp from 3′ end of spacer). CasX activity was quantified as the total percent of reads that contain insertions, substitutions, and/or deletions anywhere within this window for each sample.
Results
Mutations were introduced into the guide scaffold 235 in order to reduce the CpG content of the DNA sequence coding the guide scaffold. Surprisingly, compared to scaffold 235, all of the CpG-reduced and CpG-depleted scaffold variants produced higher levels of editing in induced neurons. This was the case with two independent repeats of the experiment (with the results from the first repeat of the experiment shown in FIG. 28, and the results of the second repeat of the experiment shown in FIGS. 29-31), and across multiple MOIs (see FIGS. 30-31). The enhanced level of editing was surprising because the goal of reducing CpG content was to simply preserve editing activity while reducing immunogenicity. Instead, the mutations enhanced editing activity, rather than merely preserving it.
Notably, scaffold 320 showed a significant increase in potency over scaffold 235. Scaffold 320 includes mutations to only two regions of the scaffold; in the pseudoknot stem and the extended stem (regions 1 and 4). Further, some combinations of mutations produced worse editing than scaffold 320. However, even the CpG-reduced scaffolds that performed worse than scaffold 320, such as scaffolds 331 and 334, performed similar to or better than scaffold 235.
Based on these results, without wishing to be bound by theory, it is believed that the boost in potency seen in many of the CpG-reduced and CpG-depleted scaffolds is likely caused by one of the mutations present in all CpG-reduced scaffolds (i.e., region 1 and/or 4). Since the mutation to region 4 is not present in the scaffolds with the extended stem loop replacement (i.e., the third mutation to region 3) and these scaffolds show a similar improvement in potency over 235 as 320 did, it is believed that the beneficial effect is likely caused by the mutation in region 1 (pseudoknot stem), which is present in all of the tested scaffolds. Further experiments will be performed to test the effect of the individual mutations in the pseudoknot stem (region 1) and the extended stem (region 4) separately.
Further, the N=1 data as presented in FIG. 28 indicate that all the new scaffolds carrying the mutation in region 2 (scaffold stem) edited at a slightly lower level than their respective counterparts without this mutation. This suggests that mutating this position in the scaffold stem may have a small deleterious effect on editing potency. This will be examined in additional experiments.
The results described here demonstrate that introducing mutations that reduced the CpG content of the DNA encoding the guide RNA scaffold resulted in improvements in gene editing relative to guide scaffold 235.
Example 13: Use of a Catalytically-Dead CasX Repressor System Fused with Additional Domains from DNMT3A and DNMT3L to Induce Durable Silencing of the B2M Locus
Experiments were performed to determine whether rationally-designed LTRP constructs, with three repressor domains composed of a transcriptional repressor domain, the catalytic domain from DNMT3A and the interaction domain from DNMT3L fused to catalytically-dead CasX (dCasX) 491, would induce durable long-term repression of the endogenous B2M locus in vitro. In addition, multiple configurations of the LTRP molecules, which contain varying placements of the epigenetic domains relative to dCasX, were designed to assess how their arrangement would affect the duration of silencing of the B2M locus, as well as the specificity of their on-target methylation activity.
Materials and Methods
Generation of LTRP Constructs and Lentiviral Plasmid Cloning:
Lentiviral plasmid constructs coding for an LTRP molecule were built using standard molecular cloning techniques. These constructs comprised of sequences coding for catalytically-dead CasX protein 491 (dCasX491), a KRAB domain from ZNF10 or ZIM3, and the catalytic domain and interaction domain from DNMT3A (D3A) and DNMT3L (D3L) respectively. Briefly, constructs were ordered as oligonucleotides and assembled by overlap extension PCR followed by isothermal assembly. Amino acid sequences of these key LTRP elements are provided in Table 44. The resulting plasmids contained constructs positioned in varying configurations to generate an LTRP molecule. The protein sequences for the LTRP molecules are listed in Table 45, and the LTRP configurations are illustrated in FIG. 1. Sequences encoding the LTRP molecules also contained a 2× FLAG tag. Plasmids also harbored sequences encoding gRNA scaffold variant 174 having either a spacer targeting the endogenous B2M locus or a non-targeting control (spacer sequences listed in Table 46). These constructs were all cloned upstream of a P2A-puromycin element on the lentiviral plasmid. Cloned and sequence-validated constructs were midi-prepped and subjected to quality assessment prior to transfection in HEK293T cells.







TABLE 44







Sequences of LTRP components (e.g., additional domains fused to


CasX) to generate LTRP variant plasmids (illustrated in FIG. 1)










Component
SEQ ID NO














ZNF10 KRAB domain
3239



ZIM3 KRAB domain
3240



DNMT3A catalytic domain
3241



DNMT3L interaction domain
127



dCasX491
4



Linker 1
123



Linker 2
122



Linker 3A
120



Linker 3B



Linker 4
121



NLS A
30

















TABLE 45







Protein sequences of LTRP molecules










LTRP ID
SEQ ID NO














1.A
3242



1.B
3243



2.A
3244



2.B
3245



3.A
3246



3.B
3247



4.A
3248



4.B
3249



5.A
3250



5.B
3251

















TABLE 46







Sequences of spacers used in constructs











Spacer



SEQ ID


ID
Target gene
PAM
Sequence
NO





7.37
B2M
TTC
GGCCGAGAUGUCUCGCUCCG
3137


 


7.148
B2M
NGG
CGCGAGCACAGCUAAGGCCA
3101


 


0.0
Non-target
N/A
CGAGACGUAAUUACGUCUCG
3232









HEK293T cells were seeded at a density of 30,000 cells in each well of a 96-well plate. The next day, each well was transiently transfected using Lipofectamine™ with 100 ng of LTRP variant plasmids, each containing a construct encoding for a differently configured LTRP protein (FIG. 1), with the gRNA having either non-targeting spacer 0.0 or targeting spacer 7.37 to the B2M locus. Specifically, for one experiment, HEK293T cells were transfected with plasmids encoding LTRP proteins #1-3, and in a second experiment, cells were lipofected with plasmids encoding LTRP protein #1, 4, and 5. In both experiments, LTRP molecules harbored a KRAB domain either from ZNF10 or ZIM3. Experimental controls included dCasX491 (with or without the ZNF10 repressor domain), catalytically-active CasX 491, and a catalytically-dead Cas9 fused to both the ZNF10-KRAB domain and DNMT3A/L domains, each with the same B2M-targeting or non-targeting gRNA. Each construct was tested in triplicate. 24 hours post-transfection, cells were selected with 1 g/mL puromycin for two days. Starting six days after transfection, cells were harvested for repression analysis every 2-3 days by analyzing B2M protein expression via HLA immunostaining followed by flow cytometry. B2M expression was determined by using an antibody that would detect the B2M-dependent HLA protein expressed on the cell surface. HLA+ cells were measured using the Attune™ NxT flow cytometer. In addition, in a separate experiment, HEK293T cells transiently transfected with LTRP variant plasmids and the B2M-targeting gRNA or non-targeting gRNA were harvested at five days post-lipofection for genomic DNA (gDNA) extraction for bisulfite sequencing.
Bisulfite Sequencing to Assess LTRP Specificity Measured by Off-Target Methylation Levels at Target Locus:
To determine off-target methylation levels at the B2M locus, gDNA from harvested cells was extracted using the Zymo Quick-DNA Miniprep Plus kit following the manufacturer's instructions. The extracted gDNA was then subjected to bisulfite conversion using the EZ DNA Methylation™ Kit (Zymo) following the manufacturer's protocol, converting any non-methylated cytosine into uracil. The resulting bisulfite-treated DNA was subsequently sequenced using next-generation sequencing (NGS) to determine the levels of off-target methylation at the B2M and VEGFA loci.
NGS Processing and Analysis:
Target amplicons were amplified from 100 ng bisulfite-treated DNA via PCR with a set of primers specific to the bisulfite-converted target locations of interest (human B2M and VEGFA loci). These gene-specific primers contained an additional sequence at the 5′ end to introduce an Illumina™ adapter. Amplified DNA products were purified with the Cytiva® Sera-Mag Select™ DNA cleanup kit. Quality and quantification of the amplicon were assessed using a Fragment Analyzer DNA Analysis kit (Agilent®, dsDNA 35-1500 bp). Amplicons were sequenced on the Illumina™ Miseq™ according to the manufacturer's instructions. Raw fastq files from sequencing were processed using Bismark Bisulfite Read Mapper and Methylation caller. PCR amplification of the bisulfite-treated DNA would convert all uracil nucleotides into thymine, and sequencing of the PCR product would determine the rate of cytosine-to-thymine conversion as a readout of the level of potential off-target methylation at the B2M and VEGFA loci mediated by each LTRP molecule.
Results
LTRP variant plasmids encoding for differently configured LTRP proteins (FIG. 1) were transiently transfected into HEK293T cells to determine whether the rationally-designed LTRP molecules could heritably silence gene expression of the target B2M locus in vitro. FIGS. 32A and 32B depict the results of a time-course experiment assessing B2M protein repression mediated by LTRP proteins #1-3, each of which harbored a KRAB domain from ZNF10 (FIG. 32A) or ZIM3 (FIG. 32B). Table 47 shows the average percentage of cells characterized as HLA-negative (indicative of depleted B2M expression) for each condition at 50 days post-transfection. The results illustrate that all LTRP molecules with a gRNA targeting the B2M locus were able to demonstrate sustained B2M repression for 50 days in vitro, although the potency of repression varied by the choice of KRAB domain and LTRP configuration. For instance, harboring a ZIM3-KRAB domain rendered the LTRP protein a more efficacious repressor than harboring a ZNF10-KRAB, and this effect was most prominently observed for LTRP #2 (compare FIG. 32A to FIG. 32B). Furthermore, positioning the DNMT3A/L domains at the N-terminus of dCasX491 (LTRP #1) resulted in more stable silencing of B2M expression compared to effects mediated by LTRPs with DNMT3A/L domains at the C-terminus of dCasX491 (LTRP #2 and #3; FIGS. 32A and 32B). These results also revealed that the relative positioning of the two types of repressor domains (i.e., dCasX491-KRAB-DNMT3A/L for LTRP #2 vs. dCasX491-DNMT3A/L-KRAB for LTRP #3) could also influence the overall potency of the LTRP molecule, despite both configurations being C-terminal fusions of dCasX491 (LTRP #2 and #3; FIGS. 32A and 32B).
In a second time-course experiment, durable B2M repression was assessed for LTRP proteins #1, #4, and #5, where both the DNMT3A/L and KRAB domains were positioned at the N-terminus of dCasX491 for LTRP #4 and #5 (FIG. 1). Table 48 shows the average percentage of HLA-negative cells for each condition at 73 days post-lipofection. As similarly seen in the first time-course, all LTRP conditions with a B2M-targeting gRNA maintained durable silencing of the B2M locus (FIGS. 33A and 33B; Table 48). In fact, the results in this experiment demonstrate that LTRP #5 was able to achieve and sustain the highest level of B2M repression compared to that achieved by LTRP #1 or LTRP #4 for 73 days in vitro (FIGS. 33A and 33B). Furthermore, LTRP #4 containing the ZIM3-KRAB also appeared to outperform its LTRP #1 counterpart (FIG. 33B). For both time-course experiments discussed above, CasX 491-mediated editing resulted in durable silencing of the B2M expression, while an XR construct fusing only the KRAB domain to dCasX491 (dCasX491-ZNF10) only resulted in transient B2M knockdown.







TABLE 47







Levels of B2M repression mediated by CasX and Cas9 molecules and


LTRP constructs #1-3 quantified at 50 days post-transfection












% HLA-
Standard


Molecule
Spacer
negative cells (mean)
deviation













CasX 491
0.0
0.29
0.09


dCasX491
0.0
N/A
N/A


dCasX491-ZNF10
0.0
0.40
0.18


dCas9-ZNF10-
0.0
1.05
0.63


D3A/L


LTRP1-ZNF10
0.0
0.99
0.35


LTRP2-ZNF10
0.0
0.61
0.11


LTRP3-ZNF10
0.0
0.79
0.29


LTRP1-ZIM3
0.0
0.99
0.22


LTRP2-ZIM3
0.0
0.78
0.27


LTRP3-ZIM3
0.0
0.71
0.53


CasX 491
7.37
76.57
11.03


dCasX491
7.37
0.49
0.10


dCasX491-ZNF10
7.148
0.89
0.19


dCas9-ZNF10-
7.148
57.30
17.36


D3A/L


LTRP1-ZNF10
7.37
69.97
7.89


(LTRP #1.B)


LTRP2-ZNF10
7.37
36.87
8.31


(LTRP #2.B)


LTRP3-ZNF10
7.37
17.07
3.50


(LTRP #3.B)


LTRP1-ZIM3
7.37
73.70
9.28


(LTRP #1.A)


LTRP2-ZIM3
7.37
58.83
0.87


(LTRP #2.A)


LTRP3-ZIM3
7.37
17.50
4.30


(LTRP #3.A)
















TABLE 48







Levels of B2M repression mediated by CasX and Cas9 molecules


and LTRP constructs #1, #4, and #5 quantified


at 73 days post-transfection














% HLA-






negative cells
Standard



Molecule
Spacer
(mean)
deviation
















CasX 491
0.0
0.71
0.05



dCasX491
0.0
N/A
N/A



dCasX491-ZNF10
0.0
0.76
0.12



dCas9-ZNF10-
0.0
0.83
0.08



D3A/L



LTRP1-ZNF10
0.0
1.04
0.44



LTRP4-ZNF10
0.0
1.17
0.52



LTRP5-ZNF10
0.0
1.94
1.27



LTRP1-ZIM3
0.0
1.83
0.76



LTRP4-ZIM3
0.0
N/A
N/A



LTRP5-ZIM3
0.0
1.15
0.26



CasX 491
7.37
73.30
8.43



dCasX491
7.37
0.83
0.16



dCasX491-ZNF10
7.148
1.37
0.37



dCas9-ZNF10-
7.148
68.97
5.21



D3A/L



LTRP1-ZNF10
7.37
48.27
3.66



(LTRP #1.B)



LTRP4-ZNF10
7.37
55.17
4.83



(LTRP #4.B)



LTRP5-ZNF10
7.37
60.77
8.12



(LTRP #5.B)



LTRP1-ZIM3
7.37
58.90
2.69



(LTRP #1.A)



LTRP4-ZIM3
7.37
69.00
6.58



(LTRP #4.A)



LTRP5-ZIM3
7.37
74.90
10.61



(LTRP #5.A)










To evaluate the degree of off-target CpG methylation at the B2M locus mediated by the DNMT3A/L domains within the LTRP molecules, bisulfite sequencing was performed using genomic DNA extracted from HEK293T cells treated with LTRP proteins #1-3 containing the ZIM3-KRAB domain and harvested at five days post-lipofection. FIG. 34 illustrates the findings from bisulfite sequencing, specifically showing the distribution of the number of CpG sites around the transcription start site of the B2M locus that harbored a certain level of CpG methylation for each experimental condition. The results revealed that while LTRP #1 demonstrated the strongest on-target CpG-methylating activity (LTRP1-ZIM3 7.37), it induced the highest level of off-target CpG methylation (LTRP1-ZIM3 NT). LTRP #2 and LTRP #3 displayed weaker on-target CpG-methylating activity but relatively lower off-target methylation (FIG. 34). FIG. 35 is a scatterplot mapping the activity-specificity profiles for LTRP proteins #1-3 benchmarked against CasX 491 and dCas9-ZNF10-DNMT3A/L, where activity was measured as the average percentage of HLA-negative cells at day 21, and specificity was represented by the percentage of off-target CpG methylation at the B2M locus quantified at day 5.
The degree of off-target CpG methylation mediated by the DNMT3A/L domain was further evaluated by assessing the level of CpG methylation at a different locus, i.e., VEGFA, by performing bisulfite sequencing using the same extracted gDNA as was used previously for FIG. 34. The violin plot in FIG. 36 illustrates the bisulfite sequencing results showing the distribution of CpG sites with CpG methylation at the VEGFA locus in cells treated with LTRP proteins #1-3 containing the ZIM3-KRAB domain and a B2M-targeting gRNA. The findings further demonstrate that use of LTRP #1 resulted in the highest level of off-target CpG methylation, supporting the data shown earlier in FIG. 34. In comparison, use of either LTRP #2 or LTRP #3 resulted in substantially lower off-target methylation at the −3 locus (FIG. 36).
The extent of off-target CpG methylation at the VEGFA locus for LTRP molecules #1, #4, and #5 was also analyzed. The plots in FIG. 37A-37B illustrate bisulfite sequencing results showing the distribution of CpG-methylated sites at the VEGFA locus in cells treated with LTRP #1, 4, and 5 containing a ZNF10 or ZIM3-KRAB domain and either a non-targeting gRNA (FIG. 37B) or a B2M-targeting gRNA (FIG. 37A). The data in FIG. 37B show that use of LTRP4-ZNF10, LTRP5-ZFN10, or LTRP5-ZIM3 resulted in markedly lower off-target CpG methylation at the VEGFA locus in comparison to use of LTRP1-ZNF10 or LTRP1-ZIM3. Similarly, the data in FIG. 37A show that use of LTRP #4 or LTRP #5 with either KRAB domain resulted in substantially lower levels of off-target CpG methylated sites compared to use with LTRP1-ZNF10. As exhibited in both FIGS. 37A and 37B, the level of non-specific CpG methylation demonstrated by LTRP #1 is comparable to that achieved by the dCas9-ZNF10-DNMT3A/L benchmark.
FIG. 38 is a scatterplot mapping the activity-specificity profiles for LTRP molecules #1-5, containing either ZNF10- or ZIM3-KRAB domain, benchmarked against CasX 491 and dCas9-ZNF10-DNMT3A/L, where activity was measured as the average percentage of HLA-negative cells at day 21, and specificity was represented by the median percentage of off-target CpG methylation at the VEGFA locus detected at day 5. The data show that of the five LTRP molecules assessed, use of LTRP #5 resulted in the highest level of repressive activity, while use of LTRP #4 resulted in the strongest level of specificity.
The experiments demonstrate that the rationally-engineered LTRP molecules were able to transcriptionally and heritably repress the endogenous B2M locus, resulting in sustained depletion of the target protein. The findings also show that the choice of KRAB domain and position and relative configuration of the DNMT3A/L domains could affect the overall potency and specificity of the LTRP molecule in durably silencing the target locus.
Example 14: Demonstration that Inclusion of the ADD Domain from DNMT3A Enhances Activity and Specificity of LTRP Molecules
In addition to its C-terminal methyltransferase domain, DNMT3A contains two N-terminal domains that regulate its function and recruitment to chromatin: the ADD domain and the PWWP domain. The PWWP domain reportedly interacts with methylated histone tails, including H3K36me3. The ADD domain is known to have two key functions: 1) it allosterically regulates the catalytic activity of DNMT3A by serving as a methyltransferase auto-inhibitory domain, and 2) it recognizes unmethylated H3K4 (H3K4me0). The interaction of the ADD domain with the H3K4me0 mark unveils the catalytic site of DNMT3A, thereby recruiting an active DNMT3A to chromatin to implement de novo methylation at these sites.
Given these functions of the ADD domain, experiments were performed to assess whether the incorporation of the ADD domain into the LTRP #5 construct, described previously in Example 13, would result in improved long-term repression of the target locus and reduced off-target methylation. The effect of incorporating the PWWP domain along with the ADD domain on LTRP activity and specificity was also assessed.
Materials and Methods
Generation of LTRP Constructs and Plasmid Cloning:
Plasmid constructs encoding for variants of the LTRP #5 construct with the ZIM3-KRAB domain (LTRP #5.A; see FIG. 1 for LTRP #5 configuration) were built using standard molecular cloning techniques. The resulting constructs comprised of sequences encoding for one of the following four alternative variations of LTRP5-ZIM3, where the additional DNMT3A domains were incorporated: 1) LTRP5-ZIM3+ADD; 2) LTRP5-ZIM3+ADD+PWWP; 3) LTRP5-ZIM3+ADD without the DNMT3A catalytic domain; and 4) LTRP5-ZIM3+ADD+PWWP without the DNMT3A catalytic domain. The sequences of key elements within the LTRP5-ZIM3 molecule and its variants are listed in Table 49, with the full-length protein sequence for each LTRP5-ZIM3 and its variants listed in Table 50. FIG. 45 is a schematic that illustrates the various LTRP #5 architectures assayed in this example. Sequences encoding the LTRP molecules also contained a 2× FLAG tag. Plasmids also harbored constructs encoding for the gRNA scaffold variant 174 having either a spacer targeting the endogenous B2M locus or a non-targeting control (spacer sequences listed in Table 51).







TABLE 49







Sequences of LTRP components (e.g., additional domains fused to


dCasX) to generate LTRP5 variant plasmids illustrated in FIG. 45









Amino acid sequence


Component
SEQ ID NO











ZIM3 KRAB domain
3240


DNMT3A catalytic domain (CD)
126


DNMT3L interaction domain
127


dCasX491
4


Linker 1
123


Linker 2
122


Linker 3A′
124


Linker 3B
120


Linker 4
121


NLS A
30


NLS B


DNMT3A ADD domain
125


DNMT3A PWWP domain
3252


Endogenous sequence between DNMT3A
3253


PWWP and ADD domains (endo)
















TABLE 50







Protein sequences of LTRP5 variants assayed in this example











Amino acid sequence



LTRP ID
SEQ ID NO














LTRP5-ZIM3
3131



LTRP5-ZIM3 + ADD
3132



LTRP5-ZIM3 + ADD + PWWP
3254



LTRP5-ZIM3 + ADD − CD
3255



LTRP5-ZIM3 + ADD + PWWP − CD
3256

















TABLE 51







Sequences of spacers used in constructs










Spacer





ID
Target gene
Sequence
SEQ ID NO





0.0
Non-target
CGAGACGUAAUUACGUCUCG
3232


 


7.37
B2M
GGCCGAGAUGUCUCGCUCCG
3137


 


7.160
B2M
UAAACAUCACGAGACUCUAA
3113


 


7.165
B2M
UCCCUAUGUCCUUGCUGUUU
3114









Transfection of HEK293T Cells:

Seeded HEK293T cells were transiently transfected with 100 ng of LTRP5 variant plasmids, each containing an LTRP:gRNA construct encoding for LTRP5-ZIM3 or one of its alternative variations (FIG. 45; Table 50 for sequences), with the gRNA having either non-targeting spacer 0.0 or a B2M-targeting spacer (Table 51 for spacer sequences). Spacers 7.160 and 7.165 have been shown to be repress the B2M locus when used with LTRPs, but not when used with dXRs made up of a dCasX fused to the ZIM3 KRAB domain (data not shown). Each construct was tested in triplicate. 24 hours post-transfection, cells were selected with 1 g/mL puromycin for three days. Cells were harvested for repression analysis at day 5, day 12, day 21, and day 51 post-transfection. Briefly, repression analysis was conducted by analyzing B2M protein expression via HLA immunostaining followed by flow cytometry, as described in Example 13. In addition, HEK293T cells transiently transfected with LTRP5 variant plasmids and a B2M-targeting gRNA or non-targeting gRNA were harvested at seven days post-transfection for gDNA extraction for bisulfite sequencing to assess off-target methylation at the VEGFA locus, which was performed as described in Example 13.
Results
The effects of incorporating the ADD domain with or without the PWWP domain into the LTRP5 molecule on increasing long-term repression of the target B2M locus and reducing off-target methylation were assessed. Variations of the LTRP5-ZIM3 molecule were evaluated with either a B2M-targeting gRNA (with spacer 7.37 and LTRP-specific spacers 7.160 and 7.165) or a non-targeting gRNA, and the results are depicted in the plots in FIGS. 39-42. FIG. 39 shows that use of spacer 7.37 resulted in saturating levels of repression activity when paired with LTRP5-ZIM3, LTRP5-ZIM3+ADD, and LTRP5-ZIM3+ADD+PWWP, rendering it more challenging to assess activity differences among the LTRP5 variants. However, the differences in repression activity among the LTRP5 variants were more pronounced when using spacers 7.160 and 7.165 (FIGS. 40 and 41). The data demonstrate that incorporation of the ADD domain resulted in a significant increase in long-term repression when paired with the two LTRP-specific spacers compared to the repression levels achieved with the other LTRP5-ZIM3 molecules. Meanwhile, incorporation of both ADD and PWWP domains did not result in improved repression of the B2M locus, especially compared to the baseline LTRP5-ZIM3 molecule. As anticipated, the two LTRP5 variants without the DNMT3A catalytic domain exhibited poor long-term repression. Furthermore, the results depicted in FIG. 42 indicate that addition of the ADD domain appeared to result in increased specificity, given the lower percentage of HLA-negative cells observed, relative to the baseline LTRP5-ZIM3 molecule.
Off-target CpG methylation at the VEGFA locus potentially mediated by the LTRP5 variants was assessed using bisulfite sequencing. FIG. 43 depicts the results from bisulfite sequencing, specifically showing the percentage of CpG methylation around the VEGFA locus. The results demonstrate that for all the B2M-targeting gRNAs, as well as the non-targeting gRNA, incorporation of the ADD domain into the LTRP5-ZIM3 molecule dramatically reduced the level of off-target methylation at the VEGFA locus (FIG. 43). FIG. 44 is a scatterplot mapping the activity-specificity profiles for the LTRP5-ZIM3 variants investigated in this example, where activity was measured as the average percentage of HLA-negative cells at day 21 when paired with spacer 7.160, and specificity was represented by the percentage of off-target CpG methylation at the VEGFA locus quantified at day 7 when paired with spacer 7.160. The scatterplot clearly shows that addition of the ADD domain significantly increased the activity of the LTRP5 molecule relative to the baseline ELX5 molecule without the ADD domain (FIG. 44).
The experiments demonstrate that inclusion of the DNMT3A ADD domain, but not inclusion of both the ADD and PWWP domains, improved repression activity and specificity of LTRP molecules. This enhancement of activity and specificity was observed with multiple gRNAs, demonstrating the significance of the incorporation of the ADD domain into LTRPs.
Example 15: Demonstration that Inclusion of the ADD Domain from DNMT3A into LTRPs Enhances On-Target Activity and Decreases Off-Target Methylation
Experiments were performed to assess the effects of incorporating the ADD domain into LTRP molecules having configurations #1, #4, and #5, described previously in Example 13, on long-term repression of the target locus and off-target methylation.
Materials and Methods
Generation of LTRP Constructs and Plasmid Cloning:
Plasmid constructs encoding for LTRP molecules having configurations #1, #4, and #5 with the ZNF10-KRAB or ZIM3-KRAB domain and the DNMT3A ADD domain were built using standard molecular cloning techniques. Sequences of the resulting LTRP molecules are listed in Table 52, which also shows the abbreviated construct names for a particular LTRP molecule (e.g., LTRP #1.A, #1.B). FIG. 46 is a schematic that illustrates the general architectures of LTRP molecules with the ADD domain incorporated for LTRP configuration #1, #4, and #5. Sequences encoding the LTRP molecules also contained a 2× FLAG tag. Plasmids also harbored sequences encoding gRNA scaffold 174 having either a spacer targeting the endogenous B2M locus or a non-targeting control (spacer sequences listed in Table 51).







TABLE 52







Protein sequences of the various LTRP #1, #4, and #5 variants assayed in this example











Amino acid sequence


LTRP #
Domains
SEQ ID NO












LTRP #1
ZNF10-KRAB, DNMT3A ADD, DNMT3A CD,
3257



DNMT3L Interaction



(LTRP #1.D)



ZIM3-KRAB, DNMT3A ADD, DNMT3A CD, DNMT3L
3258



Interaction



(LTRP #1.C)



ZNF10-KRAB, DNMT3A CD, DNMT3L Interaction
3259



(LTRP #1.B)



ZIM3-KRAB, DNMT3A CD, DNMT3L Interaction
3066



(LTRP #1.A)


LTRP #4
ZNF10-KRAB, DNMT3A ADD, DNMT3A CD,
3260



DNMT3L Interaction



(LTRP #4.D)



ZIM3-KRAB, DNMT3A ADD, DNMT3A CD, DNMT3L
3261



Interaction



(LTRP #4.C)



ZNF10-KRAB, DNMT3A CD, DNMT3L Interaction
3262



(LTRP #4.B)



ZIM3-KRAB, DNMT3A CD, DNMT3L Interaction
3263



(LTRP #4.A)


LTRP #5
ZNF10-KRAB, DNMT3A ADD, DNMT3A CD,
3264



DNMT3L Interaction



(LTRP #5.D)



ZIM3-KRAB, DNMT3A ADD, DNMT3A CD, DNMT3L
3132



Interaction



(LTRP #5.C)



ZNF10-KRAB, DNMT3A CD, DNMT3L Interaction
3265



(LTRP #5.B)



ZIM3-KRAB, DNMT3A CD, DNMT3L Interaction
3131



(LTRP #5.A)









Transfection of HEK293T Cells:

Seeded HEK293T cells were transiently transfected with 100 ng of LTRP variant plasmids, each containing an LTRP:gRNA construct encoding for an LTRP molecule (Table 52; FIG. 46), with the gRNA having either non-targeting spacer 0.0 or a B2M-targeting spacer (Table 51). Each construct was tested in triplicate. 24 hours post-transfection, cells were selected with 1l g/mL puromycin for 3 days. Cells were harvested for repression analysis at day 8, day 13, day 20, and day 27 post-transfection. Briefly, repression analysis was conducted by analyzing B2M protein expression via HLA immunostaining followed by flow cytometry, as described in Example 13. In addition, cells were also harvested on day 5 post-transfection for gDNA extraction for bisulfite sequencing to assess off-target methylation at the non-targeted VEGFA locus, which was performed using similar methods as described in Example 13.
Results
The effects of incorporating the ADD domain into the LTRP molecules having configurations #1, #4, or #5 (see FIG. 2), with either a ZNF10 or ZIM-KRAB, on long-term repression of the B2M locus and off-target methylation were evaluated. LTRP molecules were tested with either a B2M-targeting gRNA or a non-targeting gRNA, and the results are depicted in the plots in FIGS. 47A-50B. The data demonstrate that incorporation of the ADD domain into the LTRP molecules clearly resulted in a substantial increase in B2M repression across all the time points for all LTRP configurations containing the ZIM3-KRAB when using spacer 7.160 (FIG. 47A), and similar findings were observed when using spacers 7.165 and 7.37 (data not shown). FIG. 47B shows the resulting B2M repression upon use of LTRP #5 containing either the ZNF10 or ZIM3-KRAB when paired with a gRNA with spacer 7.160; the data demonstrate that including the ADD domain increased durable B2M repression overall, with LTRP5-ZIM3+ADD having a higher activity compared with that of LTRP5-ZNF10+ADD. Similar time course findings were observed for LTRP #1 and LTRP #4 and the other two spacers (data not shown). FIG. 47C shows the resulting B2M repression upon use of LTRP #5 containing the ZIM3-KRAB when paired with any of the three B2M-targeting gRNAs, and the data demonstrate that inclusion of the ADD domain resulted in higher B2M repression overall. Similar time course findings were also observed for LTRP #1 and LTRP #4 (data not shown).
FIGS. 48A-48C shows the resulting B2M repression at the day 27 time point for all the LTRP configurations and gRNAs tested. The results show that the increase in B2M repression was more prominent with use of the sub-optimal spacers 7.160 and 7.165 compared to use of spacer 7.37. Furthermore, use of LTRP #1 and LTRP #5, which contained the DNMT3A and DNMT3L domains on the N-terminus of the molecule, resulted in the highest increase in B2M repression upon addition of the DNMT3A ADD domain (FIGS. 48A-48C). Use of LTRP #4, which harbored the DNMT3A/3L domains 3′ to the KRAB domain and 5′ to the dCasX, resulted in lower activity gains, which may be attributable to a decreased ability of the ADD domain to interact with chromatin properly.
The specificity of LTRP molecules was determined by profiling the level of CpG methylation at the VEGFA gene, an off-target locus, using bisulfite sequencing, and the data are illustrated in FIGS. 49A-52B. The data demonstrate that inclusion of the DNMT3A ADD domain resulted in a substantial decrease in off-target methylation of the VEGFA locus across all conditions tested (FIGS. 49A-49C). Notably, the increased specificity mediated by the inclusion of the ADD domain was most prominent with the LTRP #1 and LTRP #5 configurations, both of which harbored the DNMT3A/3L domains on the N-terminal end of the molecule. Interestingly, LTRP molecules containing the ZIM3-KRAB domain led to stronger off-target methylation of the VEGFA locus. Furthermore, use of LTRP #4 and #5 configurations, even in the absence of an ADD domain, resulted in higher specificity compared to use of the LTRP #1 configuration. Compared to LTRP1-ZIM3 and LTRP4-ZIM3 configurations, inclusion of the ADD domain into LTRP5-ZIM3 resulted in the lowest off-target methylation.
FIGS. 50A-52B are a series of scatterplots mapping the activity-specificity profiles for the various LTRP molecules, where activity was measured as the average percentage of HLA-negative cells at day 27, and specificity was determined by the percentage of off-target CpG methylation at the VEGFA locus at day 5. The data demonstrate that across all three B2M-targeting spacers tested, inclusion of the ADD domain resulted in increased on-target B2M repression and decreased off-target methylation at the VEGFA locus. LTRP molecules having #1 and #5 configurations exhibited the greatest increases in activity and specificity at each spacer tested.
The results of the experiments discussed in this example support the findings in Example 14, in that the data demonstrate that inclusion of the DNMT3A ADD domain enhances both the strength of repression at early timepoints and the heritability of silencing across cell divisions, as well as decreases the off-target methylation incurred by the DNMT3A catalytic domain in the LTRP molecules. The data also confirm that different LTRP configurations have intrinsic differences in specificity, which can be exacerbated by use of a more potent KRAB domain. This decrease in specificity can be mitigated by inclusion of the DNMT3A ADD domain, which also can lead to greater on-target repression overall. The gains in repression activity are believed to be mediated by the function of the DNMT3A ADD domain to recognize H3K4me0 and subsequent recruitment to chromatin. The gains in specificity are believed to be mediated via the function of the DNMT3A ADD domain to induce allosteric inhibition of the catalytic domain of DNMT3A in the absence of binding to H3K4me0. The results also highlight that positioning of the ADD domain in the different configurations tested is important to achieve the strongest gains in both specificity and activity of LTRP molecules.
Example 16: Demonstration of dXR Effectiveness on HBEGF for High-Throughput Screening
Experiments were performed to determine the feasibility of using dXR constructs for high-throughput screening of molecules in mammalian cells.
Materials and Methods
HEK293T cells were seeded in a 6-well plate at 300,000 cells/well and lipofected with 1 μg of plasmid encoding either a CasX molecule (491), a catalytically-dead CasX 491 with the ZNF10-KRAB repressor domain (dXR) and a guide scaffold 174 (SEQ ID NO: 1744) with a spacer targeting the HBEGF gene or a non-targeting spacer. Five combinations of CasX-based molecules and gRNAs with the indicated spacers (Table 53) were transfected into five separate wells. HBEGF is the receptor that mediates entry of diphtheria toxin that, when added to the cells, inhibits translation and leads to cell death. Targeting of the HBEGF gene with a CasX or dXR molecule and targeting gRNA should prevent toxin entry and allow survival of the cells, whereas cells treated with CasX and dXR molecules and a non-targeting gRNA should not survive. One day post-transfection, cells in each transfected well were split into 12 different wells in a 96-well plate and selected with puromycin. Over three days, cells were treated with six different concentrations of diphtheria toxin (0, 0.2, 2, 20, 200, and 2000 ng/mL), and biological duplicates were performed. After another two days, cells were split into fresh media, and total cell counts were measured on an ImageXpress® Pico Automated Cell Imaging System.







TABLE 53







Sequences of spacers tested










Spacer ID
RNA sequence
SEQ ID NO
Molecule





34.19
ACUGGGAGGCUCAGCCCAUG
3266
CasX


 


34.21
UGUUCUGUCUUGAACUAGCU
3267
CasX


 


34.28
UGAGUGUCUUGUCUUGCUCA
3268
dXR


 


 0.0
CGAGACGUAAUUACGUCUCG
3232
CasX & dXR









Results
The results of the diphtheria toxin assay are illustrated in the plot in FIG. 53. dXR-mediated repression of the HBEGF gene resulted in survival of cells, but only at low doses of toxin (0.2-20 ng/mL). However, those same doses led to complete cell death in the control cells treated with non-targeting constructs. High doses (>20 ng/mL) of toxin led to cell death in both the dXR and control samples, suggesting that the basal level of transcription permitted by dXR allows sufficient toxin to enter and trigger cell death. The results show that CasX-edited cells remained protected as editing of the locus leads to complete loss of functional protein. The non-targeting controls died at all doses, demonstrating the efficacy of the toxin when HBEGF is not repressed or edited.
The results show that dXR protects at low doses of toxin, demonstrating that this construct can be screened in a range of 0.2-20 ng/mL diphtheria toxin, with highest fold-enrichment between dXR and control observed at 0.2 ng/mL. Note that while CasX protects at all doses, repression by dXR still induced low basal expression of the target that led to toxicity of the cells at high doses of the toxin.
Example 17: Development of a Selection Scheme to Identify Improved Repressor Domains for Inclusion in Repressor Fusion Proteins
To develop better LTRP fusion protein constructs, a library of transcriptional effector domains from many non-human species was tested in a selection assay. As KRAB domains are one of the largest and most rapidly-evolved domains in vertebrates, repressor domains from species not previously evaluated were anticipated to provide improved strength and permanence of repression.
Materials and Methods
Identification of Candidate Repressor Domains:
Homologs of KRAB domains were identified by downloading all sequences annotated with Prosite accession ps50805 (the accession number for KRAB domains). All domains were extended by 100 amino acids (with the annotation centered in the middle) to include potential unannotated functional sequences. In addition, HMMER, a tool to identify domains, was run on a set of high-quality primate annotations from recently completed alignments of long-read primate genome assemblies described (Warren, W C, et al. Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility. Science 370, Issue 6523, eabc6617 in (2020); Fiddes, I T, et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 28(7):1029 (2018); Mao, Y, et al. A high-quality bonobo genome refines the analysis of hominid evolution. Nature 594:77 (2021)), to identify domains in these assemblies, most of which were not present in UniProt. The search resulted in 32,120 unique sequences from 159 different organisms for testing for their potency in transcriptional repression. Additionally, 580 random amino acid sequence 80 residues in length were included in the library as negative controls, and 304 human KRAB domains were included based on work by Tycko, J. et al. (Cell. 2020 Dec. 23; 183(7):2020-2035).
Screening Methods:
The domains described above were synthesized as DNA oligos, amplified, and cloned into a dCasX491 C-terminal GS linker lentiviral construct along with guide scaffold 174 (SEQ ID NO: 1744) with Spacer 34.28, to repress HBEGF and confer survival in a diphtheria toxin selection as described in Example 16, above. For each domain, the C-terminal GS linker was synonymously substituted to produce unique DNA barcodes that could be differentiated by NGS allowing internal technical replicates to be assessed in each pooled experiment. These plasmids were used to generate the lentiviral constructs of the library.
HEK293T cells were transduced, treated with 1 μg/mL puromycin to remove untransduced cells, and selection was carried out at 2 ng/mL diphtheria toxin for 48 hours. gDNA was extracted, amplified, and sequenced as described above. gDNA samples were also extracted, amplified, and sequenced from the cells before selection with diphtheria toxin, as a control. Two independent replicates were performed for the diphtheria toxin selection.
Assessment of B2M Repression:
Representative domains were cloned into a dCasX491 C-terminal GS linker lentiviral construct along with guide scaffold 316 (SEQ ID NO: 1746) with spacer 7.15 (GGAAUGCCCGCCAGCGCGAC; SEQ ID NO: 3110), targeting the B2M locus. Separately, representative domains were cloned into a dCasX491 C-terminal GS linker lentiviral construct along with guide scaffold 174 (SEQ ID NO: 1744) with spacer 7.37 (GGCCGAGAUGUCUCGCUCCG; SEQ ID NO: 3137), targeting the B2M locus. The lentiviral plasmid constructs encoding dXRs with various domains were generated using standard molecular cloning techniques. These constructs included sequences encoding dCasX491, and a KRAB domain from ZNF10, ZIM3, or one of the domains tested in the library. Cloned and sequence-validated constructs were midi-prepped and subjected to quality assessment prior to transfection in HEK293T cells.
HEK293T cells were seeded at a density of 30,000 cells in each well of a 96-well plate. The next day, each well was transiently transfected using Lipofectamine™ with 100 ng of dXR plasmids, each containing a dXR construct with a different domain and a gRNA having a targeting spacer to the B2M locus. Experimental controls included dXR constructs with KRAB domains from ZNF10 or ZIM3, domains that were in the library but not among the top 95 or 1597 most effective repressors, or dCas9-ZNF10, each with a corresponding B2M-targeting gRNA. Each construct was tested in triplicate. 24 hours post-transfection, cells were selected with 1 g/mL puromycin for two days. Seven or ten days after transfection, cells were harvested for editing repression analysis by analyzing B2M protein expression via HLA immunostaining followed by flow cytometry. B2M expression was determined by using an antibody that would detect the B2M-dependent HLA protein expressed on the cell surface. HLA+ cells were measured using the Attune™ NxT flow cytometer.
Data Analysis:
To understand the diversity of protein sequences in the tested library, an evolutionary scale modeling (ESM) transformer (ESM-1b) was applied to the initial library of 32,120 domain amino acid sequences to generate a high dimensional representation of the sequences (Rives, A. et al. Proc Natl Acad Sci USA. 2021 Apr. 13; 118(15)). Next, Uniform Manifold Approximation and Projection (UMAP) was applied to reduce the data set to a two-dimensional representation of the sequence diversity (McInnes, L., Healy, J., ArXiv e-prints 1802.03426, 2018). Using this technique, 75 clusters of domain sequences were identified.
Protein sequence motifs were generated using the STREME algorithm (Bailey, T., Bioinformatics. 2021 Mar. 24; 37(18):2834-2840) to identify motifs enriched in strong repressors.
Results
Selections were performed to identify the domains out of a library of 32,120 unique sequences that were the most potent transcriptional repressors. The fold change in the abundance of each domain in the library before and after selection was calculated for each barcode-domain pair such that together the two independent replicates of the experiment represent 12 measurements of each domain's fitness.
FIG. 54 shows the range of log 2(fold change) values for the entire library, the randomized sequences that served as negative controls, a positive control set of KRAB domains that were shown to have a log 2(fold change) greater than 1 on day 5 of the HT-recruit experiment performed by Tycko et al. (Cell. 2020 Dec. 23; 183(7):2020-2035). As shown in FIG. 54, the diphtheria toxin selection successfully enriched for domains that were more potent transcriptional repressors. The negative control sequences were de-enriched from the library following selection.
To identify the domains that were reproducibly enriched in the post-selection library, a p-value threshold of less than 0.01 and a log 2(fold change) threshold of greater than 2 was set. 1597 domains met these criteria. P-values were calculated via the MAGeCK algorithm which uses a permutation test and false discovery rate adjustment for multiple testing (Wei, L. et al. Genome Biol. 2014; 15(12):554). The log 2(fold change) values of these top 1597 repressor domains are shown in FIG. 54, and the amino acid sequences, p-values, and log 2(fold change) values are provided in Table 54, below. In contrast, ZIM3 had a log 2(fold change) of 1.7787, standard ZNF10 had a log 2(fold change) of 1.3637, and an alternate ZNF10 corresponding to the ZNF10 KRAB domain used in Tycko, J. et al. (Cell. 2020 Dec. 23; 183(7):2020-2035) had a log 2(fold change) of 1.6182. Therefore, the 1597 top repressor domains were substantially superior transcriptional repressors to ZNF10 and ZIM3. Many of these top repressor domains contained amino acids with residues that are predicted to stabilize interactions with the Trim28 protein when compared to ZIM3 and ZNF10 (Stoll, G. A. et al., bioRxiv 2022.03.17.484746).
To further narrow down the list of repressor domains while maintaining a breadth of amino acid sequence diversity, a set of 95 repressor domains was chosen from within the 1597 by selecting the most effective repressor from each cluster, as well as the top 25 best repressors of the 1597, as shown in Table 54.







TABLE 54







List of 1,597 repressor domain candidates identified from the high-throughput


screen assessing dXR repression of the HBEGF gene and subsequent application of


the following criteria: p-value <0.01 and log2(fold change) >2













SEQ ID
Log2 (fold



Domain ID
Species
NO
change)
P-value










Top 95 most effective repressor domains











DOMAIN_7694
Columba livia
130
3.7111
1.13E−04


DOMAIN_10123
Rattus norvegicus
131
3.6356
8.11E−06


DOMAIN_15507
Cebus imitator
132
3.8531
1.53E−07


DOMAIN_17905
Chimp
133
2.5038
5.60E−04


DOMAIN_20505
Chlorocebus sabaeus
134
3.4989
2.91E−06


DOMAIN_26749
Ophiophagus hannah
135
5.4323
1.53E−07


DOMAIN_27604
Ailuropoda melanoleuca
136
2.8198
6.05E−05


DOMAIN_29304
Peromyscus maniculatus bairdii
137
4.0496
1.53E−07


DOMAIN_30173
Phyllostomus discolor
138
2.2538
5.41E−04


DOMAIN_737
Bonobo
139
4.544
1.53E−07


DOMAIN_10331
Colobus angolensis palliatus
140
3.6796
1.53E−07


DOMAIN_10948
Colobus angolensis palliatus
141
3.2959
2.30E−06


DOMAIN_11029
Mandrillus leucophaeus
142
3.5748
1.53E−07


DOMAIN_17358
Bos indicus × Bos taurus
143
4.9878
1.53E−07


DOMAIN_17759
Felis catus
144
3.3159
1.38E−06


DOMAIN_18258
Physeter macrocephalus
145
3.75
3.42E−04


DOMAIN_19804
Callorhinus ursinus
146
3.8217
1.53E−07


DOMAIN_221
Bonobo
147
3.5533
3.06E−06


DOMAIN_881
Bonobo
148
4.3546
4.59E−07


DOMAIN_2380
Orangutan
149
3.2024
1.74E−04


DOMAIN_2942
Gibbon
150
3.3658
1.38E−06


DOMAIN_4687
Marmoset
151
5.2288
3.22E−06


DOMAIN_4806
Marmoset
152
3.3896
1.58E−04


DOMAIN_4968
Marmoset
153
3.0315
0.0022262


DOMAIN_5066
Marmoset
154
2.9062
0.0067409


DOMAIN_5290
Owl Monkey
155
3.0993
5.16E−05


DOMAIN_5463
Owl Monkey
156
3.2102
0.0022788


DOMAIN_6248
Saimiri boliviensis boliviensis
157
2.4415
0.0056883


DOMAIN_6445
Alligator sinensis
158
3.1151
4.51E−04


DOMAIN_6802
Pantherophis guttatus
159
3.0403
5.18E−04


DOMAIN_6807
Xenopus laevis
160
3.1615
5.16E−05


DOMAIN_7255
Microcaecilia unicolor
161
4.5265
1.38E−06


DOMAIN_8503
Mus caroli
162
2.8193
0.003503


DOMAIN_8790
Marmota monax
163
2.7436
2.06E−04


DOMAIN_8853
Mesocricetus auratus
164
4.6199
1.53E−07


DOMAIN_9114
Peromyscus maniculatus bairdii
165
2.2058
0.0048423


DOMAIN_9331
Peromyscus maniculatus bairdii
166
4.1063
4.59E−07


DOMAIN_9538
Mus musculus
167
3.5443
1.20E−04


DOMAIN_9960
Octodon degus
168
3.4751
1.07E−06


DOMAIN_10277
Dipodomys ordii
169
2.8257
4.16E−04


DOMAIN_10577
Colobus angolensis palliatus
170
4.1248
1.53E−07


DOMAIN_11348
Chlorocebus sabaeus
171
3.3651
2.95E−05


DOMAIN_11386
Capra hircus
172
3.7637
4.75E−06


DOMAIN_11486
Bos mutus
173
4.8326
1.53E−07


DOMAIN_11683
Nomascus leucogenys
174
2.9249
0.0015672


DOMAIN_12292
Sus scrofa
175
4.3194
1.53E−07


DOMAIN_12452
Neophocaena asiaeorientalis
176
3.8774
5.05E−06



asiaeorientalis


DOMAIN_12631
Macaca fascicularis
177
3.6926
1.53E−07


DOMAIN_13331
Macaca fascicularis
178
3.5154
2.15E−04


DOMAIN_13468
Phascolarctos cinereus
179
4.1548
1.38E−06


DOMAIN_13539
Gorilla
180
3.4924
1.79E−05


DOMAIN_14659
Acinonyx jubatus
181
4.0495
1.06E−05


DOMAIN_14755
Cebus imitator
182
3.1667
1.88E−04


DOMAIN_15126
Callithrix jacchus
183
2.9781
4.08E−04


DOMAIN_16444
Acinonyx jubatus
184
3.2246
2.30E−06


DOMAIN_16688
Lipotes vexillifer
185
3.5601
4.26E−05


DOMAIN_16806
Sapajus apella
186
3.9386
1.53E−07


DOMAIN_17317
Otolemur garnettii
187
3.4551
1.81E−04


DOMAIN_17432
Otolemur garnettii
188
3.11
1.36E−05


DOMAIN_18137
Monodelphis domestica
189
3.292
3.51E−05


DOMAIN_18216
Physeter macrocephalus
190
3.0602
9.40E−04


DOMAIN_18563
Owl Monkey
191
3.0406
0.0034849


DOMAIN_19229
Enhydra lutris kenyoni
192
4.0294
5.01E−05


DOMAIN_19460
Monodelphis domestica
193
3.995
1.97E−05


DOMAIN_19476
Owl Monkey
194
4.1343
1.53E−07


DOMAIN_19821
Rhinopithecus roxellana
195
3.583
1.53E−07


DOMAIN_19892
Ursus maritimus
196
3.1396
5.21E−04


DOMAIN_19896
Ovis aries
197
2.2228
1.58E−04


DOMAIN_19949
Callorhinus ursinus
198
3.2903
2.62E−04


DOMAIN_21247
Neovison vison
199
2.741
0.0043129


DOMAIN_21317
Pteropus vampyrus
200
4.0893
1.18E−05


DOMAIN_21336
Equus caballus
201
2.738
0.005135


DOMAIN_21603
Lipotes vexillifer
202
2.8535
4.35E−04


DOMAIN_21755
Equus caballus
203
3.1889
0.0028238


DOMAIN_22153
Zalophus californianus
204
3.6967
3.52E−06


DOMAIN_22270
Bonobo
205
2.3813
0.0030391


DOMAIN_23394
Vicugna pacos
206
4.0769
3.06E−07


DOMAIN_23723
Carlito syrichta
207
3.5301
8.71E−05


DOMAIN_24125
Saimiri boliviensis boliviensis
208
3.9692
1.53E−07


DOMAIN_24458
Lynx pardinus
209
3.4012
9.66E−05


DOMAIN_24663
Myotis brandtii
210
2.9806
1.49E−04


DOMAIN_25289
Ursus maritimus
211
3.4113
7.70E−05


DOMAIN_25379
Sapajus apella
212
3.5892
1.53E−07


DOMAIN_25405
Desmodus rotundus
213
3.8846
3.20E−05


DOMAIN_26070
Geotrypetes seraphini
214
3.7958
1.53E−07


DOMAIN_26322
Geotrypetes seraphini
215
2.9265
7.13E−04


DOMAIN_26732
Meleagris gallopavo
216
2.7548
0.0057183


DOMAIN_27060
Gopherus agassizii
217
2.7943
0.0029172


DOMAIN_27385
Octodon degus
218
4.1339
2.77E−05


DOMAIN_27506
Bos mutus
219
3.8121
4.29E−06


DOMAIN_27811
Callithrix jacchus
220
2.9728
8.34E−05


DOMAIN_28640
Colinus virginianus
221
3.624
4.13E−06


DOMAIN_28803
Monodelphis domestica
222
3.0697
2.07E−05


DOMAIN_30661
Physeter macrocephalus
223
2.15
4.76E−05


DOMAIN_31643
Micrurus lemniscatus
224
3.8782
3.57E−04



lemniscatus







Remaining repressor domains in the top 1597 most effective repressor domains











DOMAIN_10870
Vicugna pacos
225
2.5964
0.004315


DOMAIN_10918
Odobenus rosmarus divergens
226
3.2079
9.21E−04


DOMAIN_92
Bonobo
227
2.1475
0.0021413


DOMAIN_98
Bonobo
228
2.7848
0.0055875


DOMAIN_134
Bonobo
229
2.9322
0.004676


DOMAIN_143
Bonobo
230
3.63
3.17E−05


DOMAIN_145
Bonobo
231
3.1497
4.09E−05


DOMAIN_214
Bonobo
232
2.1073
0.00941


DOMAIN_225
Bonobo
233
2.259
0.0013991


DOMAIN_226
Bonobo
234
3.0188
2.76E−04


DOMAIN_235
Bonobo
235
2.9615
0.0016622


DOMAIN_302
Bonobo
236
2.5092
0.0033327


DOMAIN_313
Bonobo
237
2.4558
0.0049862


DOMAIN_344
Bonobo
238
2.4948
0.0087725


DOMAIN_362
Bonobo
239
3.6736
2.38E−04


DOMAIN_382
Bonobo
240
3.1625
0.0019781


DOMAIN_389
Bonobo
241
3.011
3.42E−04


DOMAIN_407
Bonobo
242
3.8312
1.59E−04


DOMAIN_418
Bonobo
243
3.2429
1.37E−04


DOMAIN_419
Bonobo
244
3.5913
5.13E−05


DOMAIN_421
Bonobo
245
3.2969
1.06E−05


DOMAIN_451
Bonobo
246
3.0774
0.0018269


DOMAIN_504
Bonobo
247
3.2187
4.17E−04


DOMAIN_516
Bonobo
248
2.0448
0.0018554


DOMAIN_621
Bonobo
249
2.1025
0.0034678


DOMAIN_623
Bonobo
250
3.3299
6.50E−04


DOMAIN_624
Bonobo
251
2.8281
0.0031625


DOMAIN_629
Bonobo
252
3.6318
1.09E−05


DOMAIN_668
Bonobo
253
2.9256
6.60E−04


DOMAIN_718
Bonobo
254
3.9
8.73E−06


DOMAIN_731
Bonobo
255
2.1318
0.0058273


DOMAIN_749
Bonobo
256
3.1162
0.0060655


DOMAIN_759
Bonobo
257
3.3019
0.0046077


DOMAIN_761
Bonobo
258
3.181
9.64E−04


DOMAIN_784
Bonobo
259
2.4886
0.0083818


DOMAIN_801
Bonobo
260
2.4863
0.0040602


DOMAIN_802
Bonobo
261
2.6563
5.66E−04


DOMAIN_811
Bonobo
262
2.4706
0.0035997


DOMAIN_812
Bonobo
263
2.8201
0.0013526


DOMAIN_888
Bonobo
264
2.8951
0.0033756


DOMAIN_893
Bonobo
265
2.7511
5.41E−04


DOMAIN_938
Bonobo
266
2.2926
0.0040367


DOMAIN_966
Chimp
267
3.3535
5.49E−04


DOMAIN_972
Chimp
268
3.7627
5.59E−05


DOMAIN_980
Chimp
269
2.9297
0.0011707


DOMAIN_987
Chimp
270
2.6881
5.48E−04


DOMAIN_999
Chimp
271
2.7361
0.0038248


DOMAIN_1006
Chimp
272
3.2119
1.28E−04


DOMAIN_1079
Chimp
273
3.7915
3.90E−05


DOMAIN_1137
Chimp
274
3.1719
4.58E−04


DOMAIN_1153
Chimp
275
3.7928
5.16E−04


DOMAIN_1184
Chimp
276
3.2772
5.47E−04


DOMAIN_1237
Chimp
277
2.1795
0.0059151


DOMAIN_1242
Chimp
278
2.7144
0.0037672


DOMAIN_1247
Chimp
279
2.9622
4.18E−04


DOMAIN_1378
Gorilla
280
3.2279
0.0022191


DOMAIN_1381
Gorilla
281
4.1424
3.35E−05


DOMAIN_1382
Gorilla
282
3.0579
1.91E−04


DOMAIN_1457
Gorilla
283
2.6896
0.0026956


DOMAIN_1523
Gorilla
284
2.8607
0.0042127


DOMAIN_1539
Gorilla
285
2.9337
0.0028055


DOMAIN_1561
Gorilla
286
2.8783
0.0011557


DOMAIN_1565
Gorilla
287
2.771
3.04E−04


DOMAIN_1578
Gorilla
288
3.4875
5.97E−04


DOMAIN_1621
Gorilla
289
3.3004
1.20E−04


DOMAIN_1790
Gorilla
290
3.0669
0.0038707


DOMAIN_1816
Gorilla
291
3.108
0.0011178


DOMAIN_1818
Gorilla
292
3.2866
6.15E−04


DOMAIN_1822
Gorilla
293
2.4697
1.04E−04


DOMAIN_1870
Gorilla
294
2.215
0.0044522


DOMAIN_1875
Gorilla
295
2.5576
0.0043383


DOMAIN_1893
Gorilla
296
2.3898
0.0043422


DOMAIN_1946
Orangutan
297
3.1449
9.41E−04


DOMAIN_1952
Orangutan
298
3.0762
5.53E−04


DOMAIN_1964
Orangutan
299
2.3009
0.0099771


DOMAIN_1978
Orangutan
300
3.2215
0.0029968


DOMAIN_2014
Orangutan
301
2.7323
3.95E−04


DOMAIN_2034
Orangutan
302
3.7415
1.38E−06


DOMAIN_2119
Orangutan
303
2.2117
0.0054271


DOMAIN_2208
Orangutan
304
2.3044
0.009903


DOMAIN_2223
Orangutan
305
2.6106
0.0087315


DOMAIN_2229
Orangutan
306
2.9337
0.0032308


DOMAIN_2245
Orangutan
307
3.2712
0.0012727


DOMAIN_2255
Orangutan
308
3.1952
0.002815


DOMAIN_2295
Orangutan
309
3.2816
6.61E−04


DOMAIN_2299
Orangutan
310
2.5125
0.0042678


DOMAIN_2376
Orangutan
311
2.1539
9.52E−04


DOMAIN_2391
Orangutan
312
2.4608
0.0045936


DOMAIN_2398
Orangutan
313
3.3125
3.44E−04


DOMAIN_2470
Orangutan
314
2.3815
0.0031273


DOMAIN_2499
Orangutan
315
3.114
0.0050479


DOMAIN_2563
Orangutan
316
2.8105
0.003781


DOMAIN_2576
Orangutan
317
3.1733
2.56E−04


DOMAIN_2590
Orangutan
318
2.8348
0.0091663


DOMAIN_2629
Orangutan
319
3.092
0.0015715


DOMAIN_2652
Orangutan
320
4.3981
4.59E−07


DOMAIN_2744
Gibbon
321
2.863
0.003897


DOMAIN_2754
Gibbon
322
3.7601
1.17E−04


DOMAIN_2786
Gibbon
323
2.5449
0.0037666


DOMAIN_2806
Gibbon
324
3.1649
0.0083733


DOMAIN_2808
Gibbon
325
2.6227
0.0079231


DOMAIN_2813
Gibbon
326
2.9522
4.12E−04


DOMAIN_2851
Gibbon
327
3.3945
3.80E−04


DOMAIN_2867
Gibbon
328
3.0591
4.79E−04


DOMAIN_2888
Gibbon
329
2.4267
0.0043214


DOMAIN_2891
Gibbon
330
2.7489
0.0082897


DOMAIN_2896
Gibbon
331
2.7253
0.0094587


DOMAIN_2904
Gibbon
332
2.8035
0.0019408


DOMAIN_2908
Gibbon
333
2.6452
0.0062379


DOMAIN_2943
Gibbon
334
2.9574
9.75E−04


DOMAIN_2962
Gibbon
335
2.1784
6.34E−04


DOMAIN_2992
Gibbon
336
2.6341
0.0045667


DOMAIN_2994
Gibbon
337
3.1921
0.0022412


DOMAIN_2997
Gibbon
338
2.9911
0.0016588


DOMAIN_3000
Gibbon
339
2.9522
5.36E−04


DOMAIN_3062
Gibbon
340
2.6076
0.0035414


DOMAIN_3087
Gibbon
341
2.7999
5.44E−04


DOMAIN_3092
Gibbon
342
3.1954
2.80E−05


DOMAIN_3094
Gibbon
343
3.7195
2.83E−05


DOMAIN_3096
Gibbon
344
3.3962
2.16E−04


DOMAIN_3123
Gibbon
345
3.1293
1.88E−05


DOMAIN_3137
Gibbon
346
2.8303
0.0038836


DOMAIN_3300
Gibbon
347
3.0127
2.76E−04


DOMAIN_3328
Gibbon
348
2.3718
0.0015893


DOMAIN_3332
Gibbon
349
2.8786
0.0036582


DOMAIN_3335
Gibbon
350
4.0001
4.75E−06


DOMAIN_3336
Gibbon
351
3.5946
4.75E−06


DOMAIN_3337
Gibbon
352
2.9398
0.0053162


DOMAIN_3344
Gibbon
353
3.2218
4.60E−04


DOMAIN_3373
Gibbon
354
3.0768
0.0030033


DOMAIN_3434
Gibbon
355
2.4767
0.0035835


DOMAIN_3463
Gibbon
356
3.5462
5.96E−04


DOMAIN_3557
Rhesus
357
2.4416
0.0024889


DOMAIN_3575
Rhesus
358
3.7842
1.53E−07


DOMAIN_3585
Rhesus
359
2.4981
0.0036466


DOMAIN_3586
Rhesus
360
2.365
0.0033728


DOMAIN_3602
Rhesus
361
2.0444
0.0061662


DOMAIN_3661
Rhesus
362
2.4083
0.0088114


DOMAIN_3691
Rhesus
363
2.8393
0.0018244


DOMAIN_3759
Rhesus
364
2.5324
0.004454


DOMAIN_3760
Rhesus
365
2.7025
0.0017399


DOMAIN_3781
Rhesus
366
2.9317
0.0024892


DOMAIN_3782
Rhesus
367
2.3058
0.0048669


DOMAIN_3803
Rhesus
368
3.0165
0.0083941


DOMAIN_3832
Rhesus
369
2.7334
0.0026058


DOMAIN_4030
Rhesus
370
2.5274
0.0038526


DOMAIN_4036
Rhesus
371
2.7725
0.001577


DOMAIN_4046
Rhesus
372
2.7847
0.0088564


DOMAIN_4120
Rhesus
373
3.3237
4.55E−05


DOMAIN_4121
Rhesus
374
3.3195
1.53E−07


DOMAIN_4126
Rhesus
375
3.529
1.65E−04


DOMAIN_4129
Rhesus
376
3.7382
9.33E−04


DOMAIN_4184
Rhesus
377
3.2397
9.40E−04


DOMAIN_4185
Rhesus
378
2.9116
0.0032623


DOMAIN_4199
Rhesus
379
2.6844
0.0058444


DOMAIN_4239
Rhesus
380
4.4187
9.19E−07


DOMAIN_4394
Marmoset
381
3.8103
4.09E−05


DOMAIN_4425
Marmoset
382
2.9741
0.0087646


DOMAIN_4461
Marmoset
383
3.0094
0.0076595


DOMAIN_4463
Marmoset
384
2.9717
0.008252


DOMAIN_4515
Marmoset
385
4.2166
1.21E−05


DOMAIN_4516
Marmoset
386
2.7603
0.0027577


DOMAIN_4534
Marmoset
387
2.6242
0.0034292


DOMAIN_4574
Marmoset
388
2.7135
9.16E−04


DOMAIN_4580
Marmoset
389
2.9618
3.22E−06


DOMAIN_4589
Marmoset
390
2.507
0.0070104


DOMAIN_4665
Marmoset
391
3.2985
0.0011116


DOMAIN_4705
Marmoset
392
3.5232
5.02E−04


DOMAIN_4722
Marmoset
393
4.8639
1.53E−07


DOMAIN_4748
Marmoset
394
3.0477
5.73E−04


DOMAIN_4749
Marmoset
395
3.5545
2.83E−05


DOMAIN_4751
Marmoset
396
3.238
4.91E−05


DOMAIN_4774
Marmoset
397
2.8894
0.0029528


DOMAIN_4823
Marmoset
398
2.7527
0.0083334


DOMAIN_4913
Marmoset
399
2.8878
0.0028098


DOMAIN_4921
Marmoset
400
3.5291
4.44E−06


DOMAIN_4922
Marmoset
401
4.0258
1.82E−05


DOMAIN_4978
Marmoset
402
2.7787
0.0025526


DOMAIN_5005
Marmoset
403
2.8406
0.00183


DOMAIN_5006
Marmoset
404
3.8614
1.38E−06


DOMAIN_5029
Marmoset
405
2.2642
0.0022609


DOMAIN_5031
Marmoset
406
2.8605
0.0025559


DOMAIN_5060
Marmoset
407
2.6043
8.74E−04


DOMAIN_5096
Marmoset
408
2.456
0.008963


DOMAIN_5099
Marmoset
409
3.1407
0.0021138


DOMAIN_5102
Marmoset
410
2.7241
0.0024099


DOMAIN_5103
Marmoset
411
2.1016
0.0093552


DOMAIN_5125
Marmoset
412
2.911
0.0015369


DOMAIN_5188
OwlMonkey
413
2.1842
0.0046295


DOMAIN_5201
OwlMonkey
414
3.3658
1.53E−07


DOMAIN_5217
OwlMonkey
415
2.4689
0.0031316


DOMAIN_5235
OwlMonkey
416
3.437
4.62E−04


DOMAIN_5246
OwlMonkey
417
2.7473
0.0042075


DOMAIN_5248
OwlMonkey
418
4.1052
1.53E−07


DOMAIN_5267
OwlMonkey
419
3.1247
0.0016383


DOMAIN_5273
OwlMonkey
420
2.4023
0.0069063


DOMAIN_5299
OwlMonkey
421
2.7399
0.0093892


DOMAIN_5337
OwlMonkey
422
3.7616
4.52E−05


DOMAIN_5370
OwlMonkey
423
3.0452
0.0088803


DOMAIN_5440
OwlMonkey
424
2.7871
0.0048658


DOMAIN_5485
OwlMonkey
425
2.7826
0.0080202


DOMAIN_5489
OwlMonkey
426
2.6774
0.0021808


DOMAIN_5518
OwlMonkey
427
2.8542
0.0030235


DOMAIN_5527
OwlMonkey
428
3.1092
0.0016793


DOMAIN_5603
OwlMonkey
429
3.2806
0.0015418


DOMAIN_5716
OwlMonkey
430
3.0606
5.36E−04


DOMAIN_5742
Homo sapiens
431
2.8617
0.0029913


DOMAIN_5765
Rattus norvegicus
432
4.2973
1.53E−07


DOMAIN_5774
Homo sapiens
433
2.9608
3.75E−05


DOMAIN_5782
Homo sapiens
434
2.9086
4.56E−04


DOMAIN_5791
Homo sapiens
435
2.6823
0.0051494


DOMAIN_5792
Homo sapiens
436
3.0218
8.56E−04


DOMAIN_5806
Homo sapiens
437
2.866
0.0037801


DOMAIN_5822
Homo sapiens
438
2.9335
0.0074467


DOMAIN_5843
Homo sapiens
439
3.1821
2.83E−05


DOMAIN_5866
Homo sapiens
440
2.6362
0.0080677


DOMAIN_5883
Homo sapiens
441
3.0097
5.52E−04


DOMAIN_5896
Bos taurus
442
2.9429
0.0023166


DOMAIN_5901
Homo sapiens
443
3.2935
0.0012981


DOMAIN_5914
Homo sapiens
444
2.5527
0.0029099


DOMAIN_5921
Homo sapiens
445
2.4715
0.00101


DOMAIN_5943
Mus musculus
446
2.501
0.0027917


DOMAIN_5946
Homo sapiens
447
3.2998
1.38E−06


DOMAIN_5968
Bos taurus
448
3.2856
3.86E−04


DOMAIN_5984
Homo sapiens
449
2.9852
2.37E−04


DOMAIN_5989
Mus musculus
450
3.6632
9.30E−04


DOMAIN_5994
Orangutan
451
2.9214
5.04E−04


DOMAIN_6038
Homo sapiens
452
3.3315
2.59E−04


DOMAIN_6053
Orangutan
453
3.2566
1.21E−04


DOMAIN_6063
Homo sapiens
454
3.5653
0.0019059


DOMAIN_6078
Homo sapiens
455
2.6246
0.0075453


DOMAIN_6134
Homo sapiens
456
2.7081
0.0034203


DOMAIN_6169
Homo sapiens
457
3.3909
1.68E−06


DOMAIN_6172
Homo sapiens
458
3.883
1.07E−06


DOMAIN_6249
Saimiri boliviensis boliviensis
459
3.5469
4.44E−06


DOMAIN_6293
Rattus norvegicus
460
2.6707
0.0034812


DOMAIN_6354
Terrapene carolina triunguis
461
2.4812
0.0095055


DOMAIN_6356
Terrapene carolina triunguis
462
2.9197
0.0031965


DOMAIN_6382
Gopherus agassizii
463
3.2875
1.66E−04


DOMAIN_6398
Gopherus agassizii
464
2.8238
0.0059966


DOMAIN_6410
Podarcis muralis
465
2.7633
0.0034243


DOMAIN_6433
Podarcis muralis
466
3.0313
1.16E−04


DOMAIN_6458
Gopherus agassizii
467
2.8973
0.0048435


DOMAIN_6472
Alligator sinensis
468
2.9259
0.0052565


DOMAIN_6482
Paroedura picta
469
3.3106
0.0019705


DOMAIN_6501
Paroedura picta
470
3.4172
0.0010204


DOMAIN_6539
Paroedura picta
471
3.2371
0.0025654


DOMAIN_6555
Paroedura picta
472
3.534
4.92E−04


DOMAIN_6577
Terrapene carolina triunguis
473
3.3168
3.95E−04


DOMAIN_6595
Terrapene carolina triunguis
474
2.2407
0.0027133


DOMAIN_6599
Terrapene carolina triunguis
475
3.3653
4.49E−05


DOMAIN_6697
Podarcis muralis
476
2.6712
7.35E−04


DOMAIN_6737
Microcaecilia unicolor
477
2.4861
0.0065704


DOMAIN_6738
Microcaecilia unicolor
478
2.9275
7.79E−04


DOMAIN_6741
Microcaecilia unicolor
479
3.5726
2.50E−04


DOMAIN_6866
Alligator mississippiensis
480
3.5825
1.02E−04


DOMAIN_6936
Callipepla squamata
481
3.5294
9.07E−04


DOMAIN_6938
Alligator mississippiensis
482
2.6093
0.0020584


DOMAIN_6952
Alligator mississippiensis
483
2.3403
0.0084774


DOMAIN_6970
Phasianus colchicus
484
3.343
3.02E−04


DOMAIN_7000
Phasianus colchicus
485
2.8279
0.0039843


DOMAIN_7098
Microcaecilia unicolor
486
2.7074
0.0030553


DOMAIN_7109
Microcaecilia unicolor
487
2.9932
0.0077318


DOMAIN_7123
Microcaecilia unicolor
488
2.9074
0.0043723


DOMAIN_7166
Microcaecilia unicolor
489
3.1419
5.72E−04


DOMAIN_7183
Microcaecilia unicolor
490
2.4918
1.27E−04


DOMAIN_7184
Microcaecilia unicolor
491
2.2019
0.0099168


DOMAIN_7328
Terrapene carolina triunguis
492
3.1808
5.04E−05


DOMAIN_7353
Microcaecilia unicolor
493
2.6649
0.0042219


DOMAIN_7365
Microcaecilia unicolor
494
2.597
0.0042403


DOMAIN_7480
Gopherus agassizii
495
3.1707
5.44E−04


DOMAIN_7510
Gopherus agassizii
496
3.0452
6.73E−04


DOMAIN_7534
Gopherus agassizii
497
3.4086
2.50E−04


DOMAIN_7553
Gopherus agassizii
498
2.9036
0.0088341


DOMAIN_7605
Alligator sinensis
499
2.8444
0.0018789


DOMAIN_7607
Alligator sinensis
500
2.7102
0.0018612


DOMAIN_7641
Gallus gallus
501
3.6727
4.51E−04


DOMAIN_7653
Gallus gallus
502
3.3772
0.0028364


DOMAIN_7678
Chelonia mydas
503
2.7348
0.0039197


DOMAIN_7711
Columba livia
504
3.7965
1.67E−05


DOMAIN_7716
Pogona vitticeps
505
3.1171
0.0011931


DOMAIN_7745
Meleagris gallopavo
506
3.4946
0.0016126


DOMAIN_7750
Columba livia
507
2.8111
0.0012249


DOMAIN_7774
Pogona vitticeps
508
3.427
8.09E−04


DOMAIN_7796
Chelonia mydas
509
2.9513
1.04E−04


DOMAIN_7813
Columba livia
510
3.4645
7.95E−04


DOMAIN_7824
Columba livia
511
2.9383
5.45E−04


DOMAIN_7850
Terrapene carolina triunguis
512
3.124
5.15E−04


DOMAIN_7895
Patagioenas fasciata monilis
513
3.2254
0.0013863


DOMAIN_7925
Gallus gallus
514
3.3919
0.0025195


DOMAIN_8012
Callipepla squamata
515
3.2046
0.0023734


DOMAIN_8013
Callipepla squamata
516
3.9783
2.13E−05


DOMAIN_8014
Callipepla squamata
517
3.7425
6.23E−05


DOMAIN_8036
Alligator mississippiensis
518
2.3504
0.0094483


DOMAIN_8041
Dipodomys ordii
519
3.6568
3.47E−04


DOMAIN_8054
Cavia porcellus
520
3.5889
4.15E−05


DOMAIN_8148
Cricetulus griseus
521
3.6904
4.82E−05


DOMAIN_8151
Cricetulus griseus
522
3.1527
0.0034782


DOMAIN_8154
Cricetulus griseus
523
2.8774
0.0027807


DOMAIN_8167
Mus musculus
524
3.9362
1.04E−04


DOMAIN_8179
Mesocricetus auratus
525
3.0623
0.0026242


DOMAIN_8182
Mus caroli
526
2.2411
0.0018051


DOMAIN_8216
Cricetulus griseus
527
3.1747
9.05E−05


DOMAIN_8226
Rattus norvegicus
528
2.4602
0.0090772


DOMAIN_8235
Mus caroli
529
2.8965
0.0012522


DOMAIN_8282
Peromyscus maniculatus bairdii
530
3.9882
1.07E−06


DOMAIN_8289
Peromyscus maniculatus bairdii
531
3.3026
2.94E−04


DOMAIN_8301
Mesocricetus auratus
532
3.1084
0.0017647


DOMAIN_8303
Ictidomys tridecemlineatus
533
3.6843
1.34E−04


DOMAIN_8305
Ictidomys tridecemlineatus
534
2.5554
0.0084633


DOMAIN_8308
Marmota monax
535
2.6564
3.69E−04


DOMAIN_8317
Mus caroli
536
3.3091
2.40E−05


DOMAIN_8340
Peromyscus maniculatus bairdii
537
2.2764
0.0086378


DOMAIN_8353
Peromyscus maniculatus bairdii
538
2.7989
4.14E−04


DOMAIN_8370
Cavia porcellus
539
3.5737
2.58E−04


DOMAIN_8412
Mus musculus
540
2.4486
0.0077639


DOMAIN_8418
Cricetulus griseus
541
2.4014
0.001307


DOMAIN_8424
Peromyscus maniculatus bairdii
542
2.7945
0.0019818


DOMAIN_8425
Peromyscus maniculatus bairdii
543
2.8391
0.004804


DOMAIN_8460
Peromyscus maniculatus bairdii
544
3.1352
6.66E−05


DOMAIN_8467
Mesocricetus auratus
545
3.8156
7.15E−05


DOMAIN_8489
Mus caroli
546
2.8336
0.0042299


DOMAIN_8492
Mus musculus
547
3.3107
0.0032374


DOMAIN_8502
Cricetulus griseus
548
2.1429
4.22E−04


DOMAIN_8545
Rattus norvegicus
549
3.1044
0.0011282


DOMAIN_8546
Mus musculus
550
2.9439
0.0033958


DOMAIN_8547
Mus caroli
551
3.3997
0.0022286


DOMAIN_8549
Mus caroli
552
2.8508
0.0052033


DOMAIN_8555
Cricetulus griseus
553
3.2852
5.62E−05


DOMAIN_8618
Mesocricetus auratus
554
2.6363
0.008293


DOMAIN_8688
Mus musculus
555
2.4409
2.00E−04


DOMAIN_8689
Mus musculus
556
2.8548
6.62E−04


DOMAIN_8712
Mesocricetus auratus
557
2.7776
0.0028768


DOMAIN_8742
Peromyscus maniculatus bairdii
558
2.3354
0.002149


DOMAIN_8746
Mesocricetus auratus
559
3.317
1.64E−04


DOMAIN_8789
Marmota monax
560
3.1756
0.0021937


DOMAIN_8793
Mus caroli
561
2.6774
9.60E−05


DOMAIN_8816
Peromyscus maniculatus bairdii
562
2.4156
2.32E−04


DOMAIN_8830
Cavia porcellus
563
3.0644
0.0025588


DOMAIN_8839
Peromyscus maniculatus bairdii
564
3.0637
0.0036542


DOMAIN_8844
Peromyscus maniculatus bairdii
565
4.1629
7.81E−06


DOMAIN_8850
Peromyscus maniculatus bairdii
566
2.695
0.0040575


DOMAIN_8862
Marmota monax
567
2.3521
0.0061537


DOMAIN_8881
Cricetulus griseus
568
3.743
1.49E−05


DOMAIN_8886
Cricetulus griseus
569
3.5727
1.94E−05


DOMAIN_8899
Mesocricetus auratus
570
3.2182
9.45E−05


DOMAIN_8931
Cricetulus griseus
571
2.9497
8.73E−04


DOMAIN_8936
Cricetulus griseus
572
4.3486
1.07E−06


DOMAIN_8953
Mus caroli
573
2.5941
0.0032969


DOMAIN_8982
Mesocricetus auratus
574
3.1585
3.54E−05


DOMAIN_8989
Marmota monax
575
2.2309
0.0094553


DOMAIN_9012
Mus musculus
576
2.3905
0.0070058


DOMAIN_9042
Mus caroli
577
2.5894
0.0033885


DOMAIN_9060
Cricetulus griseus
578
2.5974
0.0027286


DOMAIN_9119
Mesocricetus auratus
579
2.2985
0.0052412


DOMAIN_9141
Mus caroli
580
3.035
2.62E−05


DOMAIN_9159
Dipodomys ordii
581
3.0141
0.0023052


DOMAIN_9174
Peromyscus maniculatus bairdii
582
2.5194
0.0035749


DOMAIN_9175
Peromyscus maniculatus bairdii
583
2.4231
0.0042293


DOMAIN_9189
Heterocephalus glaber
584
3.3801
1.76E−04


DOMAIN_9192
Mus caroli
585
2.7981
0.008526


DOMAIN_9217
Mesocricetus auratus
586
3.8919
5.43E−05


DOMAIN_9235
Mus musculus
587
2.7307
0.0035899


DOMAIN_9250
Marmota monax
588
3.466
0.0012007


DOMAIN_9265
Mus musculus
589
2.1221
0.0021172


DOMAIN_9290
Peromyscus maniculatus bairdii
590
4.256
1.07E−06


DOMAIN_9303
Marmota monax
591
2.5344
0.0051732


DOMAIN_9313
Mus musculus
592
2.7692
0.0061916


DOMAIN_9324
Peromyscus maniculatus bairdii
593
3.1782
0.0020198


DOMAIN_9329
Peromyscus maniculatus bairdii
594
4.263
7.81E−06


DOMAIN_9332
Peromyscus maniculatus bairdii
595
3.9002
1.38E−06


DOMAIN_9356
Ictidomys tridecemlineatus
596
2.9297
0.0037302


DOMAIN_9389
Marmota monax
597
3.1785
2.65E−05


DOMAIN_9424
Dipodomys ordii
598
3.771
1.53E−07


DOMAIN_9435
Fukomys damarensis
599
3.1672
3.01E−04


DOMAIN_9446
Marmota monax
600
2.8722
3.80E−04


DOMAIN_9489
Dipodomys ordii
601
3.0215
0.0074336


DOMAIN_9503
Ictidomys tridecemlineatus
602
2.9864
0.0021536


DOMAIN_9526
Mesocricetus auratus
603
2.9435
0.0042492


DOMAIN_9530
Mesocricetus auratus
604
2.7003
0.0026178


DOMAIN_9541
Dipodomys ordii
605
2.8442
0.0028404


DOMAIN_9542
Octodon degus
606
2.6734
0.0036809


DOMAIN_9544
Octodon degus
607
2.9143
0.0054966


DOMAIN_9559
Mus caroli
608
3.327
0.001653


DOMAIN_9563
Mus musculus
609
3.7261
3.81E−05


DOMAIN_9576
Octodon degus
610
2.1952
0.0094564


DOMAIN_9617
Mesocricetus auratus
611
2.4034
0.0040152


DOMAIN_9643
Dipodomys ordii
612
3.4306
0.0023603


DOMAIN_9697
Octodon degus
613
2.7566
0.0063579


DOMAIN_9704
Dipodomys ordii
614
3.1674
0.0013462


DOMAIN_9706
Octodon degus
615
2.821
0.0041809


DOMAIN_9713
Cricetulus griseus
616
3.0323
0.002243


DOMAIN_9716
Mus caroli
617
2.9009
0.0040762


DOMAIN_9723
Mus caroli
618
2.1903
0.0058971


DOMAIN_9725
Mus caroli
619
2.9654
0.0028095


DOMAIN_9776
Marmota monax
620
2.6258
0.0084697


DOMAIN_9787
Mus caroli
621
3.2962
8.37E−05


DOMAIN_9789
Mus musculus
622
2.5801
0.0012534


DOMAIN_9822
Ictidomys tridecemlineatus
623
2.9382
0.0065879


DOMAIN_9824
Heterocephalus glaber
624
3.1306
8.34E−05


DOMAIN_9827
Mus caroli
625
2.1904
0.0077554


DOMAIN_9843
Mus musculus
626
2.3385
0.0035982


DOMAIN_9846
Cricetulus griseus
627
2.7865
0.0025033


DOMAIN_9857
Mesocricetus auratus
628
3.3666
8.92E−04


DOMAIN_9858
Mesocricetus auratus
629
3.0047
1.33E−04


DOMAIN_9878
Marmota monax
630
3.7349
2.61E−04


DOMAIN_9891
Mus caroli
631
2.8116
3.13E−04


DOMAIN_9915
Mus caroli
632
3.4011
3.45E−04


DOMAIN_9962
Rattus norvegicus
633
2.7249
0.004063


DOMAIN_9993
Rattus norvegicus
634
2.7601
0.0035973


DOMAIN_10018
Octodon degus
635
3.3372
4.27E−04


DOMAIN_10041
Mus caroli
636
2.8662
0.0062437


DOMAIN_10044
Mus musculus
637
2.826
0.0043095


DOMAIN_10050
Octodon degus
638
3.3147
0.0020066


DOMAIN_10057
Mus musculus
639
2.2961
0.0026799


DOMAIN_10091
Fukomys damarensis
640
2.1679
4.36E−04


DOMAIN_10127
Peromyscus maniculatus bairdii
641
3.6912
3.83E−06


DOMAIN_10160
Ictidomys tridecemlineatus
642
2.9333
4.23E−04


DOMAIN_10184
Mus caroli
643
4.2854
1.53E−07


DOMAIN_10241
Octodon degus
644
3.5766
8.19E−05


DOMAIN_10257
Octodon degus
645
3.1757
5.20E−04


DOMAIN_10294
Mus musculus
646
2.689
0.0067073


DOMAIN_10334
Mustela putorius furo
647
3.3529
5.07E−05


DOMAIN_10351
Delphinapterus leucas
648
3.3309
3.78E−04


DOMAIN_10359
Delphinapterus leucas
649
2.9199
0.0036842


DOMAIN_10381
Vicugna pacos
650
2.215
0.0057838


DOMAIN_10386
Odobenus rosmarus divergens
651
2.8337
0.0028753


DOMAIN_10403
Vicugna pacos
652
3.3993
0.0016441


DOMAIN_10420
Odobenus rosmarus divergens
653
3.7185
1.01E−04


DOMAIN_10425
Delphinapterus leucas
654
2.8616
0.0041775


DOMAIN_10427
Carlito syrichta
655
2.3719
0.0078328


DOMAIN_10491
Vicugna pacos
656
3.7199
0.0012761


DOMAIN_10495
Delphinapterus leucas
657
3.4705
5.27E−04


DOMAIN_10526
Delphinapterus leucas
658
2.4499
0.0033355


DOMAIN_10573
Cervus elaphus hippelaphus
659
2.4077
5.02E−04


DOMAIN_10612
Vicugna pacos
660
2.4997
0.0035134


DOMAIN_10613
Odobenus rosmarus divergens
661
2.9148
5.62E−05


DOMAIN_10623
Carlito syrichta
662
3.2233
0.0018333


DOMAIN_10646
Delphinapterus leucas
663
2.9354
0.0036496


DOMAIN_10647
Delphinapterus leucas
664
2.9514
7.60E−04


DOMAIN_10675
Ornithorhynchus anatinus
665
3.2777
5.13E−05


DOMAIN_10684
Odobenus rosmarus divergens
666
4.531
1.64E−05


DOMAIN_10704
Colobus angolensis palliatus
667
3.1582
0.004292


DOMAIN_10705
Colobus angolensis palliatus
668
3.6392
4.09E−05


DOMAIN_10733
Odobenus rosmarus divergens
669
3.315
0.0028523


DOMAIN_10762
Erinaceus europaeus
670
3.9254
4.55E−05


DOMAIN_10763
Mustela putorius furo
671
2.5924
0.0073193


DOMAIN_10765
Mustela putorius furo
672
2.5661
0.0076445


DOMAIN_10807
Erinaceus europaeus
673
3.5237
1.54E−04


DOMAIN_10882
Vicugna pacos
674
3.6289
2.93E−04


DOMAIN_10902
Vicugna pacos
675
3.1052
0.0096752


DOMAIN_10917
Odobenus rosmarus divergens
676
3.7871
1.53E−07


DOMAIN_10943
Cervus elaphus hippelaphus
677
2.5554
0.0037715


DOMAIN_10974
Chelonia mydas
678
2.6444
0.0091318


DOMAIN_11006
Loxodonta africana
679
2.6669
6.71E−04


DOMAIN_11024
Suricata suricatta
680
3.2397
2.77E−04


DOMAIN_11031
Mandrillus leucophaeus
681
2.5516
0.005857


DOMAIN_11034
Mandrillus leucophaeus
682
2.2541
0.0042161


DOMAIN_11040
Sus scrofa
683
3.5161
3.39E−04


DOMAIN_11049
Neophocaena asiaeorientalis
684
2.7072
0.0015299



asiaeorientalis


DOMAIN_11053
Nomascus leucogenys
685
3.677
4.44E−06


DOMAIN_11069
Capra hircus
686
3.2745
0.0036948


DOMAIN_11071
Chrysochloris asiatica
687
3.1268
0.0012421


DOMAIN_11097
Mandrillus leucophaeus
688
3.239
0.0011508


DOMAIN_11110
Sus scrofa
689
3.6632
4.76E−04


DOMAIN_11129
Nomascus leucogenys
690
2.3864
1.88E−04


DOMAIN_11130
Nomascus leucogenys
691
2.3487
6.64E−04


DOMAIN_11132
Bos indicus
692
3.5671
3.08E−05


DOMAIN_11157
Suricata suricatta
693
3.6671
8.22E−05


DOMAIN_11158
Chrysochloris asiatica
694
2.6889
0.0035388


DOMAIN_11162
Mandrillus leucophaeus
695
3.2804
2.65E−04


DOMAIN_11178
Sus scrofa
696
2.4845
0.0043413


DOMAIN_11192
Neophocaena asiaeorientalis
697
2.8798
2.10E−04



asiaeorientalis


DOMAIN_11202
Nomascus leucogenys
698
3.5851
4.18E−05


DOMAIN_11204
Nomascus leucogenys
699
3.5793
5.22E−05


DOMAIN_11225
Capra hircus
700
3.606
0.0011566


DOMAIN_11227
Capra hircus
701
2.7556
0.0032733


DOMAIN_11264
Sus scrofa
702
3.5019
5.64E−04


DOMAIN_11265
Sus scrofa
703
4.2521
1.53E−07


DOMAIN_11282
Suricata suricatta
704
3.536
1.53E−07


DOMAIN_11289
Suricata suricatta
705
2.69
2.48E−04


DOMAIN_11291
Suricata suricatta
706
4.0373
4.59E−07


DOMAIN_11307
Mandrillus leucophaeus
707
3.6383
1.07E−06


DOMAIN_11312
Sus scrofa
708
3.8532
9.26E−05


DOMAIN_11314
Sus scrofa
709
2.9575
0.0015357


DOMAIN_11321
Nomascus leucogenys
710
2.9718
0.0086853


DOMAIN_11331
Capra hircus
711
3.0611
4.37E−04


DOMAIN_11332
Capra hircus
712
3.0468
2.19E−04


DOMAIN_11356
Sus scrofa
713
2.6549
0.0027629


DOMAIN_11359
Sus scrofa
714
3.1036
0.0092232


DOMAIN_11381
Nomascus leucogenys
715
3.1705
4.83E−04


DOMAIN_11393
Suricata suricatta
716
3.4256
1.65E−04


DOMAIN_11401
Suricata suricatta
717
2.6345
0.0077459


DOMAIN_11403
Suricata suricatta
718
3.4222
2.27E−04


DOMAIN_11413
Sus scrofa
719
2.1814
0.0084919


DOMAIN_11433
Neophocaena asiaeorientalis
720
3.3986
1.91E−05



asiaeorientalis


DOMAIN_11446
Nomascus leucogenys
721
2.6971
3.26E−04


DOMAIN_11461
Equus caballus
722
2.508
0.0090515


DOMAIN_11466
Suricata suricatta
723
3.4716
0.0027896


DOMAIN_11470
Mandrillus leucophaeus
724
3.1038
0.0012895


DOMAIN_11502
Trichechus manatus latirostris
725
3.601
4.21E−05


DOMAIN_11505
Trichechus manatus latirostris
726
3.0969
9.19E−07


DOMAIN_11534
Sus scrofa
727
3.8118
1.91E−05


DOMAIN_11554
Nomascus leucogenys
728
3.0498
4.11E−04


DOMAIN_11567
Zalophus californianus
729
3.4239
0.0010611


DOMAIN_11581
Equus caballus
730
3.1882
4.10E−04


DOMAIN_11612
Loxodonta africana
731
3.3006
0.0040119


DOMAIN_11621
Chrysochloris asiatica
732
3.2074
5.42E−04


DOMAIN_11643
Nomascus leucogenys
733
2.3544
0.0020207


DOMAIN_11662
Capra hircus
734
3.7889
2.36E−04


DOMAIN_11672
Suricata suricatta
735
3.318
0.0022931


DOMAIN_11701
Capra hircus
736
2.5282
0.0084694


DOMAIN_11726
Sus scrofa
737
3.4183
1.09E−05


DOMAIN_11749
Chlorocebus sabaeus
738
3.2721
0.0023817


DOMAIN_11753
Mandrillus leucophaeus
739
2.6119
0.0062269


DOMAIN_11760
Neophocaena asiaeorientalis
740
2.8102
0.0039794



asiaeorientalis


DOMAIN_11796
Sus scrofa
741
2.2811
0.0010219


DOMAIN_11813
Canis lupus familiaris
742
3.5195
7.62E−04


DOMAIN_11825
Mandrillus leucophaeus
743
3.9893
1.53E−07


DOMAIN_11851
Nomascus leucogenys
744
3.0241
1.32E−04


DOMAIN_11858
Canis lupus familiaris
745
3.6419
1.53E−07


DOMAIN_11862
Canis lupus familiaris
746
2.8817
0.0032412


DOMAIN_11865
Muntiacus muntjak
747
3.0474
0.0026931


DOMAIN_11868
Mandrillus leucophaeus
748
3.5158
4.44E−06


DOMAIN_11908
Canis lupus familiaris
749
2.894
0.0035529


DOMAIN_11923
Sus scrofa
750
3.2271
0.0018734


DOMAIN_11925
Mandrillus leucophaeus
751
3.5582
3.04E−04


DOMAIN_11928
Neophocaena asiaeorientalis
752
3.751
7.59E−04



asiaeorientalis


DOMAIN_11933
Neophocaena asiaeorientalis
753
4.1135
1.52E−05



asiaeorientalis


DOMAIN_11944
Bos indicus
754
3.2762
0.0022727


DOMAIN_11950
Canis lupus familiaris
755
4.3869
2.91E−06


DOMAIN_11988
Muntiacus muntjak
756
3.5916
3.83E−06


DOMAIN_11996
Canis lupus familiaris
757
3.0831
0.0015161


DOMAIN_11999
Canis lupus familiaris
758
3.7891
5.04E−05


DOMAIN_12001
Mandrillus leucophaeus
759
2.4384
0.0057376


DOMAIN_12021
Canis lupus familiaris
760
2.4637
0.0018489


DOMAIN_12051
Muntiacus muntjak
761
2.7925
0.0039375


DOMAIN_12057
Muntiacus muntjak
762
2.0631
0.0086017


DOMAIN_12079
Muntiacus muntjak
763
2.4029
0.0095567


DOMAIN_12092
Bos mutus
764
3.1752
1.82E−05


DOMAIN_12114
Neophocaena asiaeorientalis
765
3.3227
6.62E−04



asiaeorientalis


DOMAIN_12133
Canis lupus familiaris
766
3.0204
0.0034751


DOMAIN_12139
Canis lupus familiaris
767
2.8097
0.0066678


DOMAIN_12147
Neophocaena asiaeorientalis
768
2.6974
9.14E−04



asiaeorientalis


DOMAIN_12158
Nomascus leucogenys
769
3.0332
0.006631


DOMAIN_12187
Canis lupus familiaris
770
3.6477
5.13E−05


DOMAIN_12191
Muntiacus muntjak
771
3.6138
8.18E−04


DOMAIN_12195
Canis lupus familiaris
772
2.9023
1.11E−04


DOMAIN_12206
Bos mutus
773
2.9101
5.13E−04


DOMAIN_12210
Bos indicus
774
3.6136
0.0018284


DOMAIN_12214
Muntiacus muntjak
775
2.613
9.76E−04


DOMAIN_12231
Nomascus leucogenys
776
2.6703
0.00421


DOMAIN_12261
Neophocaena asiaeorientalis
777
2.7989
0.0029785



asiaeorientalis


DOMAIN_12285
Gorilla
778
2.2573
0.0091023


DOMAIN_12313
Bos indicus
779
2.6903
0.0012684


DOMAIN_12320
Muntiacus muntjak
780
2.5075
0.0023021


DOMAIN_12365
Nomascus leucogenys
781
3.5626
7.78E−04


DOMAIN_12395
Ailuropoda melanoleuca
782
3.1504
3.56E−04


DOMAIN_12459
Bos indicus
783
4.0425
3.06E−06


DOMAIN_12463
Ailuropoda melanoleuca
784
3.2567
0.009339


DOMAIN_12467
Gorilla
785
2.9575
4.85E−04


DOMAIN_12498
Muntiacus muntjak
786
2.8947
0.0075569


DOMAIN_12499
Muntiacus muntjak
787
2.2932
0.0064341


DOMAIN_12508
Gorilla
788
3.0173
0.0024497


DOMAIN_12511
Gorilla
789
3.0694
0.0023557


DOMAIN_12517
Lynx canadensis
790
2.6983
0.0017522


DOMAIN_12544
Gorilla
791
3.306
4.83E−04


DOMAIN_12550
Ailuropoda melanoleuca
792
3.0229
2.37E−04


DOMAIN_12576
Gorilla
793
3.04
0.0044151


DOMAIN_12590
Bos indicus
794
2.5531
0.0020023


DOMAIN_12591
Bos indicus
795
3.4169
0.0011553


DOMAIN_12598
Muntiacus muntjak
796
3.3709
4.18E−05


DOMAIN_12599
Muntiacus muntjak
797
2.2098
0.007064


DOMAIN_12630
Macaca fascicularis
798
3.6424
4.03E−05


DOMAIN_12646
Myotis lucifugus
799
3.487
0.0014708


DOMAIN_12686
Phascolarctos cinereus
800
2.76
0.0032103


DOMAIN_12698
Phascolarctos cinereus
801
2.8029
0.0066675


DOMAIN_12704
Myotis lucifugus
802
2.9127
0.0034078


DOMAIN_12712
Puma concolor
803
2.1195
0.008023


DOMAIN_12728
Lynx canadensis
804
3.1999
9.49E−04


DOMAIN_12734
Phyllostomus discolor
805
3.5207
1.38E−06


DOMAIN_12755
Oryctolagus cuniculus
806
2.8082
0.0061475


DOMAIN_12764
Desmodus rotundus
807
3.9505
1.53E−07


DOMAIN_12769
Macaca fascicularis
808
2.0555
0.0080928


DOMAIN_12777
Phascolarctos cinereus
809
2.1778
0.0057731


DOMAIN_12780
Phascolarctos cinereus
810
3.2671
1.01E−04


DOMAIN_12801
Sapajus apella
811
2.0238
0.006988


DOMAIN_12811
Macaca fascicularis
812
2.4278
0.0068959


DOMAIN_12815
Macaca fascicularis
813
2.7296
0.0029445


DOMAIN_12818
Macaca fascicularis
814
3.6211
9.69E−05


DOMAIN_12829
Phascolarctos cinereus
815
3.3994
3.20E−04


DOMAIN_12831
Phascolarctos cinereus
816
2.9845
0.0029084


DOMAIN_12839
Oryctolagus cuniculus
817
3.4039
3.03E−04


DOMAIN_12849
Muntiacus muntjak
818
4.1042
1.53E−07


DOMAIN_12896
Macaca fascicularis
819
2.0413
0.0010397


DOMAIN_12901
Macaca fascicularis
820
3.5686
4.75E−06


DOMAIN_12902
Macaca fascicularis
821
3.3489
0.0016432


DOMAIN_12912
Puma concolor
822
2.7422
4.78E−04


DOMAIN_12941
Phyllostomus discolor
823
2.4012
0.0062382


DOMAIN_12985
Phascolarctos cinereus
824
3.7331
3.05E−05


DOMAIN_13004
Macaca fascicularis
825
3.2216
1.37E−04


DOMAIN_13022
Phascolarctos cinereus
826
3.0468
0.003082


DOMAIN_13029
Myotis lucifugus
827
3.1708
3.58E−04


DOMAIN_13062
Ursus maritimus
828
2.9752
2.10E−04


DOMAIN_13068
Ailuropoda melanoleuca
829
3.6132
2.43E−05


DOMAIN_13089
Sapajus apella
830
2.8761
0.0065934


DOMAIN_13111
Ailuropoda melanoleuca
831
2.6151
0.0090675


DOMAIN_13121
Macaca fascicularis
832
3.353
3.98E−04


DOMAIN_13125
Macaca fascicularis
833
3.2101
3.31E−04


DOMAIN_13171
Phascolarctos cinereus
834
3.0052
0.0061932


DOMAIN_13193
Sapajus apella
835
3.8948
1.53E−07


DOMAIN_13227
Oryctolagus cuniculus
836
2.3234
0.0034855


DOMAIN_13269
Desmodus rotundus
837
2.7236
0.0010081


DOMAIN_13277
Macaca fascicularis
838
2.9151
4.66E−04


DOMAIN_13282
Phascolarctos cinereus
839
3.5504
8.75E−04


DOMAIN_13284
Phascolarctos cinereus
840
3.0903
0.0057642


DOMAIN_13293
Myotis lucifugus
841
2.5884
6.56E−04


DOMAIN_13325
Macaca fascicularis
842
2.4051
0.0085787


DOMAIN_13332
Phascolarctos cinereus
843
2.685
0.0052498


DOMAIN_13333
Phascolarctos cinereus
844
2.9787
0.0079948


DOMAIN_13339
Puma concolor
845
3.2731
5.64E−04


DOMAIN_13346
Oryctolagus cuniculus
846
2.9551
0.0031649


DOMAIN_13363
Phyllostomus discolor
847
2.2178
0.0041619


DOMAIN_13364
Macaca fascicularis
848
3.5606
2.40E−05


DOMAIN_13379
Phascolarctos cinereus
849
3.2967
0.0018734


DOMAIN_13380
Myotis lucifugus
850
3.6615
1.09E−05


DOMAIN_13387
Sapajus apella
851
2.8731
0.001777


DOMAIN_13417
Ailuropoda melanoleuca
852
3.7056
1.17E−04


DOMAIN_13439
Sapajus apella
853
2.5091
0.0050786


DOMAIN_13470
Phascolarctos cinereus
854
3.7598
2.40E−05


DOMAIN_13486
Puma concolor
855
3.4895
7.93E−04


DOMAIN_13501
Macaca fascicularis
856
2.8162
0.0083892


DOMAIN_13509
Phascolarctos cinereus
857
2.8053
0.00351


DOMAIN_13516
Phascolarctos cinereus
858
2.4421
0.0034809


DOMAIN_13536
Gorilla
859
3.3269
0.0064418


DOMAIN_13537
Ailuropoda melanoleuca
860
3.3265
8.83E−05


DOMAIN_13562
Phascolarctos cinereus
861
3.7608
4.71E−04


DOMAIN_13565
Phascolarctos cinereus
862
2.994
0.0032926


DOMAIN_13574
Puma concolor
863
3.1114
6.89E−04


DOMAIN_13591
Lynx canadensis
864
3.215
5.12E−04


DOMAIN_13601
Macaca fascicularis
865
2.4865
0.0065955


DOMAIN_13609
Phascolarctos cinereus
866
3.1787
0.002393


DOMAIN_13610
Phascolarctos cinereus
867
3.1925
0.0018707


DOMAIN_13644
Phascolarctos cinereus
868
3.2677
0.001927


DOMAIN_13648
Oryctolagus cuniculus
869
3.1393
0.0014022


DOMAIN_13650
Ailuropoda melanoleuca
870
3.8556
4.44E−06


DOMAIN_13664
Macaca fascicularis
871
2.7443
0.002582


DOMAIN_13670
Phascolarctos cinereus
872
3.154
4.21E−04


DOMAIN_13690
Sapajus apella
873
3.2587
0.0017001


DOMAIN_13691
Sapajus apella
874
2.6205
0.0033052


DOMAIN_13703
Lynx canadensis
875
3.7947
2.43E−05


DOMAIN_13705
Phyllostomus discolor
876
2.496
0.009207


DOMAIN_13722
Phascolarctos cinereus
877
2.4814
0.0058557


DOMAIN_13723
Phascolarctos cinereus
878
2.9677
0.0026349


DOMAIN_13733
Sapajus apella
879
3.3285
1.82E−04


DOMAIN_13783
Macaca fascicularis
880
2.5821
0.0093056


DOMAIN_13805
Lynx canadensis
881
3.1769
0.0088613


DOMAIN_13823
Macaca fascicularis
882
4.219
1.53E−07


DOMAIN_13830
Phascolarctos cinereus
883
2.6435
0.0033465


DOMAIN_13832
Phascolarctos cinereus
884
2.9705
0.0077505


DOMAIN_13843
Phascolarctos cinereus
885
3.6119
1.81E−04


DOMAIN_13851
Canis lupus familiaris
886
2.6472
0.0033845


DOMAIN_13859
Macaca fascicularis
887
2.2006
0.0086366


DOMAIN_13878
Ailuropoda melanoleuca
888
4.3232
4.75E−06


DOMAIN_13880
Lynx canadensis
889
3.0991
0.0013743


DOMAIN_13907
Phascolarctos cinereus
890
2.4263
0.0084749


DOMAIN_13910
Bos mutus
891
2.9556
0.0048664


DOMAIN_13915
Muntiacus muntjak
892
2.8554
0.0080147


DOMAIN_13958
Phascolarctos cinereus
893
3.2926
9.78E−05


DOMAIN_13970
Lynx canadensis
894
2.89
0.0058701


DOMAIN_13979
Macaca fascicularis
895
2.6188
0.0016793


DOMAIN_13981
Phascolarctos cinereus
896
2.8041
0.0024451


DOMAIN_13984
Phascolarctos cinereus
897
2.8513
0.0029797


DOMAIN_13987
Myotis lucifugus
898
3.0633
4.59E−04


DOMAIN_13997
Puma concolor
899
2.984
2.51E−04


DOMAIN_14009
Ailuropoda melanoleuca
900
2.9207
5.05E−05


DOMAIN_14013
Ailuropoda melanoleuca
901
2.4619
0.0082352


DOMAIN_14031
Phyllostomus discolor
902
3.0963
0.0045422


DOMAIN_14040
Phascolarctos cinereus
903
3.0933
0.0065673


DOMAIN_14041
Phascolarctos cinereus
904
2.9069
0.0077333


DOMAIN_14049
Phascolarctos cinereus
905
2.7761
0.0052936


DOMAIN_14069
Lynx canadensis
906
2.9182
0.0020008


DOMAIN_14082
Phyllostomus discolor
907
3.2495
2.19E−04


DOMAIN_14083
Phyllostomus discolor
908
2.7465
0.0042213


DOMAIN_14108
Canis lupus familiaris
909
3.0621
0.004127


DOMAIN_14129
Lynx canadensis
910
2.8195
0.0026925


DOMAIN_14135
Bos mutus
911
2.426
0.0033513


DOMAIN_14147
Canis lupus familiaris
912
3.3683
2.59E−04


DOMAIN_14153
Muntiacus muntjak
913
2.883
0.0011637


DOMAIN_14197
Muntiacus muntjak
914
2.9589
0.0041555


DOMAIN_14219
Ailuropoda melanoleuca
915
2.6653
0.0035657


DOMAIN_14226
Lynx canadensis
916
3.1176
0.0020645


DOMAIN_14228
Lynx canadensis
917
3.3445
7.54E−04


DOMAIN_14256
Lynx canadensis
918
2.4946
0.0066852


DOMAIN_14287
Bos indicus
919
3.6232
1.66E−04


DOMAIN_14295
Muntiacus muntjak
920
3.4018
7.22E−04


DOMAIN_14322
Desmodus rotundus
921
3.3716
1.94E−04


DOMAIN_14337
Muntiacus muntjak
922
3.2753
2.86E−05


DOMAIN_14338
Ailuropoda melanoleuca
923
3.1071
0.0022421


DOMAIN_14358
Lynx canadensis
924
2.7094
8.85E−04


DOMAIN_14365
Desmodus rotundus
925
3.0706
1.39E−04


DOMAIN_14373
Macaca fascicularis
926
2.5861
0.0069375


DOMAIN_14382
Phascolarctos cinereus
927
4.0523
7.52E−05


DOMAIN_14444
Phyllostomus discolor
928
2.4641
0.0037357


DOMAIN_14487
Ailuropoda melanoleuca
929
2.7981
0.0050538


DOMAIN_14526
Ailuropoda melanoleuca
930
3.2232
0.003818


DOMAIN_14532
Lynx canadensis
931
3.2071
2.43E−04


DOMAIN_14534
Lynx canadensis
932
2.8122
0.0039834


DOMAIN_14546
Muntiacus muntjak
933
3.5039
5.01E−05


DOMAIN_14551
Ailuropoda melanoleuca
934
3.6894
2.30E−06


DOMAIN_14557
Lynx canadensis
935
2.9876
2.85E−04


DOMAIN_14574
Gorilla
936
3.3356
7.83E−04


DOMAIN_14576
Ailuropoda melanoleuca
937
3.2158
0.0028459


DOMAIN_14602
Gorilla
938
3.2145
0.0037718


DOMAIN_14627
Acinonyx jubatus
939
2.9501
0.0033732


DOMAIN_14639
Rhesus
940
2.7046
0.0033915


DOMAIN_14714
Odocoileus virginianus texanus
941
3.2752
2.48E−04


DOMAIN_14746
Odocoileus virginianus texanus
942
2.605
0.0084645


DOMAIN_14773
Sapajus apella
943
3.5997
1.45E−05


DOMAIN_14794
Acinonyx jubatus
944
3.4295
4.09E−04


DOMAIN_14795
Rhinopithecus roxellana
945
2.8119
0.0024062


DOMAIN_14800
Rhinopithecus roxellana
946
2.274
0.0012494


DOMAIN_14815
Cebus imitator
947
3.3826
0.0075808


DOMAIN_14820
Callithrix jacchus
948
2.8836
0.0021743


DOMAIN_14829
Rhinopithecus roxellana
949
2.7188
4.08E−04


DOMAIN_14845
Cebus imitator
950
2.7224
0.0041993


DOMAIN_14849
Cebus imitator
951
2.3659
0.0093133


DOMAIN_14862
Callithrix jacchus
952
2.8116
0.0079314


DOMAIN_14864
Rhesus
953
3.3492
2.46E−04


DOMAIN_14885
Cebus imitator
954
3.5373
4.09E−05


DOMAIN_14901
Bos taurus
955
2.9774
0.0085175


DOMAIN_14905
Rhinopithecus roxellana
956
3.372
0.0034794


DOMAIN_14928
Callithrix jacchus
957
3.1547
2.58E−04


DOMAIN_14939
Callorhinus ursinus
958
2.3884
0.0071338


DOMAIN_14946
Acinonyx jubatus
959
3.2842
7.46E−04


DOMAIN_14948
Acinonyx jubatus
960
3.3727
1.73E−04


DOMAIN_14974
Sapajus apella
961
2.9963
0.0091608


DOMAIN_14977
Sapajus apella
962
3.0085
5.11E−04


DOMAIN_14978
Acinonyx jubatus
963
3.0358
0.0017363


DOMAIN_14983
Rhinopithecus roxellana
964
3.704
1.53E−07


DOMAIN_14994
Bison bison bison
965
2.4997
0.0054874


DOMAIN_14995
Cebus imitator
966
3.5057
4.13E−06


DOMAIN_15042
Ovis aries
967
3.0774
0.0045881


DOMAIN_15070
Callithrix jacchus
968
4.0108
2.60E−04


DOMAIN_15083
Ovis aries
969
2.7541
7.89E−04


DOMAIN_15086
Ovis aries
970
3.5994
2.56E−04


DOMAIN_15089
Vulpes vulpes
971
2.3585
0.0076298


DOMAIN_15102
Acinonyx jubatus
972
3.0929
0.0033921


DOMAIN_15103
Bison bison bison
973
2.652
0.0021839


DOMAIN_15119
Callithrix jacchus
974
3.3838
2.60E−06


DOMAIN_15137
Ovis aries
975
2.7071
0.0022528


DOMAIN_15138
Vulpes vulpes
976
3.1771
6.85E−04


DOMAIN_15159
Ovis aries
977
3.2135
0.0012084


DOMAIN_15171
Vulpes vulpes
978
3.2837
2.40E−05


DOMAIN_15174
Vulpes vulpes
979
3.1387
0.0033116


DOMAIN_15184
Acinonyx jubatus
980
3.0092
0.0021588


DOMAIN_15197
Acinonyx jubatus
981
3.0957
0.0012736


DOMAIN_15227
Rhinopithecus roxellana
982
3.5532
4.75E−06


DOMAIN_15233
Rhinopithecus roxellana
983
2.788
0.0046622


DOMAIN_15234
Acinonyx jubatus
984
3.546
0.0019916


DOMAIN_15241
Odocoileus virginianus texanus
985
3.3955
3.85E−04


DOMAIN_15251
Callithrix jacchus
986
2.2209
9.47E−04


DOMAIN_15254
Callithrix jacchus
987
3.5159
2.32E−04


DOMAIN_15267
Ovis aries
988
2.8528
0.0020149


DOMAIN_15269
Ovis aries
989
2.0839
0.0057336


DOMAIN_15278
Callithrix jacchus
990
3.2523
0.0089241


DOMAIN_15279
Callithrix jacchus
991
3.8574
6.87E−05


DOMAIN_15352
Cebus imitator
992
3.0832
0.0079363


DOMAIN_15354
Tursiops truncatus
993
3.5099
5.16E−05


DOMAIN_15356
Acinonyx jubatus
994
3.5466
0.0019099


DOMAIN_15360
Neophocaena asiaeorientalis
995
3.2575
3.95E−04



asiaeorientalis


DOMAIN_15363
Orangutan
996
4.3121
1.53E−07


DOMAIN_15391
Leptonychotes weddellii
997
3.9053
1.53E−07


DOMAIN_15406
Chimp
998
3.4616
1.53E−07


DOMAIN_15419
Rhinopithecus roxellana
999
2.6943
0.0012439


DOMAIN_15426
Odocoileus virginianus texanus
1000
2.9673
0.0024959


DOMAIN_15447
Rhinopithecus roxellana
1001
3.1112
0.0031907


DOMAIN_15451
Bison bison bison
1002
3.2905
0.0024601


DOMAIN_15527
Balaenoptera acutorostrata
1003
3.0354
0.0023685



scammoni


DOMAIN_15536
Cebus imitator
1004
2.4515
0.0048713


DOMAIN_15540
Callithrix jacchus
1005
3.124
0.0020464


DOMAIN_15575
Callithrix jacchus
1006
2.594
0.0095671


DOMAIN_15577
Callithrix jacchus
1007
2.4456
0.0010642


DOMAIN_15581
Callorhinus ursinus
1008
3.2465
0.0031873


DOMAIN_15586
Callorhinus ursinus
1009
2.6157
0.002815


DOMAIN_15603
Cebus imitator
1010
3.5111
0.0027084


DOMAIN_15605
Cebus imitator
1011
3.8196
2.50E−04


DOMAIN_15634
Delphinapterus leucas
1012
3.3574
0.0025587


DOMAIN_15636
Chimp
1013
2.2086
0.0062339


DOMAIN_15638
Sapajus apella
1014
3.4277
1.53E−07


DOMAIN_15669
Callorhinus ursinus
1015
2.8865
0.0027889


DOMAIN_15687
Cebus imitator
1016
2.5362
0.0063187


DOMAIN_15688
Cebus imitator
1017
3.2098
6.98E−04


DOMAIN_15693
Rhesus
1018
3.8571
9.95E−06


DOMAIN_15699
Bos taurus
1019
3.5255
7.09E−04


DOMAIN_15753
Ovis aries
1020
3.1699
0.0035272


DOMAIN_15759
Ovis aries
1021
3.1884
0.0011061


DOMAIN_15764
Otolemur garnettii
1022
3.107
3.97E−04


DOMAIN_15800
Otolemur garnettii
1023
3.4462
1.80E−04


DOMAIN_15814
Rhesus
1024
3.9503
3.26E−05


DOMAIN_15823
Ovis aries
1025
2.8458
0.0034405


DOMAIN_15834
Otolemur garnettii
1026
3.7629
1.30E−05


DOMAIN_15839
Callithrix jacchus
1027
2.3399
0.0090833


DOMAIN_15863
Vulpes vulpes
1028
2.7434
0.0042734


DOMAIN_15931
Ovis aries
1029
3.0861
0.0028731


DOMAIN_15940
Enhydra lutris kenyoni
1030
2.8684
0.007571


DOMAIN_15956
Bos taurus
1031
3.2271
4.36E−04


DOMAIN_15972
Enhydra lutris kenyoni
1032
2.3299
1.05E−04


DOMAIN_16009
Zalophus californianus
1033
3.2738
0.0020718


DOMAIN_16011
Delphinapterus leucas
1034
4.3363
1.53E−07


DOMAIN_16017
Ovis aries
1035
2.6715
0.0041604


DOMAIN_16023
Rhinopithecus bieti
1036
2.2831
0.0064672


DOMAIN_16050
Ovis aries
1037
2.7105
0.0086883


DOMAIN_16063
Rhesus
1038
2.1603
0.0054023


DOMAIN_16084
Enhydra lutris kenyoni
1039
3.0131
0.0022672


DOMAIN_16115
Bos taurus
1040
2.9023
0.0027605


DOMAIN_16123
Ovis aries
1041
2.3799
0.0079176


DOMAIN_16147
Orangutan
1042
2.5699
4.83E−04


DOMAIN_16184
Ovis aries
1043
3.7743
4.44E−06


DOMAIN_16188
Otolemur garnettii
1044
2.5145
0.0014414


DOMAIN_16238
Orangutan
1045
3.8734
2.87E−04


DOMAIN_16246
Rhesus
1046
2.3971
3.89E−04


DOMAIN_16253
Ovis aries
1047
4.488
1.53E−07


DOMAIN_16266
Otolemur garnettii
1048
3.075
0.0019834


DOMAIN_16274
Otolemur garnettii
1049
2.7655
0.0014904


DOMAIN_16312
Vicugna pacos
1050
2.4302
0.0024702


DOMAIN_16323
Trichechus manatus latirostris
1051
4.0053
2.15E−04


DOMAIN_16340
Ovis aries
1052
2.778
0.0034068


DOMAIN_16372
Odocoileus virginianus texanus
1053
4.2664
1.53E−07


DOMAIN_16378
Callithrix jacchus
1054
2.9868
0.0037718


DOMAIN_16399
Rhinopithecus roxellana
1055
4.0639
1.53E−07


DOMAIN_16408
Cebus imitator
1056
2.0194
0.009233


DOMAIN_16461
Cebus imitator
1057
3.1155
0.0020676


DOMAIN_16471
Acinonyx jubatus
1058
3.3465
0.0021006


DOMAIN_16478
Rhinopithecus roxellana
1059
2.8285
0.0023275


DOMAIN_16516
Rhesus
1060
3.8473
1.94E−05


DOMAIN_16517
Callithrix jacchus
1061
3.3189
2.60E−06


DOMAIN_16534
Acinonyx jubatus
1062
2.7531
0.0057425


DOMAIN_16556
Rhinopithecus roxellana
1063
2.4217
0.0084734


DOMAIN_16566
Odocoileus virginianus texanus
1064
3.3903
7.82E−04


DOMAIN_16576
Chimp
1065
2.6949
0.0021998


DOMAIN_16597
Cebus imitator
1066
2.9869
0.0023416


DOMAIN_16611
Papio anubis
1067
3.4786
1.53E−07


DOMAIN_16618
Ursus maritimus
1068
3.1184
0.0015351


DOMAIN_16629
Cebus imitator
1069
3.7569
1.57E−04


DOMAIN_16630
Cebus imitator
1070
3.2435
1.36E−04


DOMAIN_16638
Macaca nemestrina
1071
3.3871
0.0011337


DOMAIN_16648
Physeter macrocephalus
1072
3.629
1.88E−05


DOMAIN_16651
Delphinapterus leucas
1073
2.0926
0.0074143


DOMAIN_16659
Leptonychotes weddellii
1074
3.8913
2.37E−05


DOMAIN_16664
Leptonychotes weddellii
1075
3.4502
1.76E−05


DOMAIN_16673
Phascolarctos cinereus
1076
3.0938
0.0039727


DOMAIN_16677
Orangutan
1077
3.1577
0.0023254


DOMAIN_16694
Callorhinus ursinus
1078
2.0979
0.0094743


DOMAIN_16695
Callorhinus ursinus
1079
3.965
3.06E−07


DOMAIN_16696
Tursiops truncatus
1080
3.0806
0.002705


DOMAIN_16703
Phascolarctos cinereus
1081
3.3969
2.19E−04


DOMAIN_16731
Ursus arctos horribilis
1082
2.849
1.30E−05


DOMAIN_16734
Leptonychotes weddellii
1083
3.4791
2.57E−04


DOMAIN_16738
Chimp
1084
3.5957
8.11E−06


DOMAIN_16744
Enhydra lutris kenyoni
1085
3.637
6.38E−05


DOMAIN_16763
Monodelphis domestica
1086
2.9244
0.0053031


DOMAIN_16771
Saimiri boliviensis boliviensis
1087
3.3025
0.0027295


DOMAIN_16773
Balaenoptera acutorostrata
1088
4.5309
1.38E−06



scammoni


DOMAIN_16776
Callorhinus ursinus
1089
3.0877
0.0024757


DOMAIN_16809
Delphinapterus leucas
1090
2.4357
0.0068567


DOMAIN_16811
Balaenoptera acutorostrata
1091
3.5141
3.08E−04



scammoni


DOMAIN_16856
Ursus maritimus
1092
2.7613
0.0040844


DOMAIN_16865
Papio anubis
1093
3.9619
1.53E−07


DOMAIN_16876
Callorhinus ursinus
1094
3.2183
4.66E−04


DOMAIN_16877
Rhinolophus ferrumequinum
1095
3.3745
3.78E−05


DOMAIN_16936
Rhinopithecus roxellana
1096
2.9808
0.0044295


DOMAIN_16953
Callorhinus ursinus
1097
3.3286
1.62E−04


DOMAIN_16973
Delphinapterus leucas
1098
3.0187
0.0041062


DOMAIN_16994
Odocoileus virginianus texanus
1099
3.0575
0.0025431


DOMAIN_17001
Rhinolophus ferrumequinum
1100
3.045
0.003661


DOMAIN_17023
Sapajus apella
1101
2.5472
0.0041588


DOMAIN_17027
Balaenoptera acutorostrata
1102
3.131
0.0028042



scammoni


DOMAIN_17041
Rhinopithecus roxellana
1103
2.7589
0.0074146


DOMAIN_17062
Rhinopithecus roxellana
1104
3.2594
7.33E−05


DOMAIN_17105
Rhesus
1105
2.637
0.0054256


DOMAIN_17108
Phyllostomus discolor
1106
2.4499
0.0018315


DOMAIN_17134
Panthera pardus
1107
3.2502
0.0016926


DOMAIN_17139
Ursus arctos horribilis
1108
4.0326
2.13E−05


DOMAIN_17153
Ursus arctos horribilis
1109
2.1759
0.0043459


DOMAIN_17167
Ursus maritimus
1110
4.1644
1.52E−05


DOMAIN_17177
Physeter macrocephalus
1111
3.2446
0.002928


DOMAIN_17180
Zalophus californianus
1112
2.945
0.0082198


DOMAIN_17195
Ursus maritimus
1113
3.0566
0.0037464


DOMAIN_17202
Ursus arctos horribilis
1114
2.6589
0.0072284


DOMAIN_17206
Pteropus vampyrus
1115
3.7092
5.05E−06


DOMAIN_17234
Delphinapterus leucas
1116
2.0152
0.0059669


DOMAIN_17236
Rhinolophus ferrumequinum
1117
2.7166
0.0039056


DOMAIN_17241
Muntiacus muntjak
1118
2.2217
0.003544


DOMAIN_17264
Vicugna pacos
1119
3.0866
0.0021294


DOMAIN_17278
Tursiops truncatus
1120
3.4898
4.12E−05


DOMAIN_17279
Bison bison bison
1121
3.591
8.11E−06


DOMAIN_17333
Camelus dromedarius
1122
2.8765
0.003642


DOMAIN_17340
Leptonychotes weddellii
1123
3.1536
5.34E−05


DOMAIN_17382
Leptonychotes weddellii
1124
3.075
0.0035284


DOMAIN_17383
Leptonychotes weddellii
1125
2.953
0.0032519


DOMAIN_17412
Ovis aries
1126
4.9319
1.53E−07


DOMAIN_17421
Vulpes vulpes
1127
3.3129
2.83E−05


DOMAIN_17474
Monodelphis domestica
1128
2.683
0.0036059


DOMAIN_17483
Cercocebus atys
1129
3.5742
3.44E−05


DOMAIN_17495
Neomonachus schauinslandi
1130
3.1828
5.59E−05


DOMAIN_17497
Monodelphis domestica
1131
2.8088
5.07E−05


DOMAIN_17509
Physeter macrocephalus
1132
3.438
8.07E−04


DOMAIN_17516
Monodelphis domestica
1133
3.1523
4.18E−04


DOMAIN_17525
Myotis davidii
1134
3.4986
7.28E−04


DOMAIN_17534
Cercocebus atys
1135
2.9374
0.0033612


DOMAIN_17547
Neomonachus schauinslandi
1136
3.2455
5.64E−04


DOMAIN_17548
Neomonachus schauinslandi
1137
2.8002
5.08E−04


DOMAIN_17574
Cercocebus atys
1138
3.4893
2.80E−05


DOMAIN_17632
Monodelphis domestica
1139
3.3689
2.06E−04


DOMAIN_17658
Monodelphis domestica
1140
3.8781
1.99E−06


DOMAIN_17662
Monodelphis domestica
1141
2.7612
0.0040459


DOMAIN_17666
Monodelphis domestica
1142
2.6895
0.002059


DOMAIN_17671
Monodelphis domestica
1143
3.0937
0.008519


DOMAIN_17689
Cercocebus atys
1144
3.6469
1.53E−07


DOMAIN_17704
Neomonachus schauinslandi
1145
3.1047
0.0028404


DOMAIN_17714
Monodelphis domestica
1146
2.2724
0.0043612


DOMAIN_17717
Physeter macrocephalus
1147
2.9442
7.54E−04


DOMAIN_17748
Leptonychotes weddellii
1148
3.0918
2.44E−04


DOMAIN_17752
Leptonychotes weddellii
1149
3.2541
4.59E−04


DOMAIN_17775
Camelus dromedarius
1150
2.6595
0.0033885


DOMAIN_17798
Orangutan
1151
3.3458
5.16E−05


DOMAIN_17801
Orangutan
1152
2.9733
0.0022819


DOMAIN_17871
Leptonychotes weddellii
1153
3.1894
1.49E−05


DOMAIN_17873
Leptonychotes weddellii
1154
3.4076
3.00E−04


DOMAIN_17890
Cercocebus atys
1155
4.2356
2.80E−05


DOMAIN_17898
Enhydra lutris kenyoni
1156
3.2117
0.0034476


DOMAIN_17903
Orangutan
1157
2.4683
0.0030976


DOMAIN_17925
Otolemur garnettii
1158
2.7982
0.0042639


DOMAIN_18048
OwlMonkey
1159
2.5186
0.0087422


DOMAIN_18083
Papio anubis
1160
2.9283
4.79E−04


DOMAIN_18100
Neomonachus schauinslandi
1161
2.3606
0.0061598


DOMAIN_18103
Monodelphis domestica
1162
2.7334
0.0056181


DOMAIN_18136
Monodelphis domestica
1163
2.7288
6.75E−04


DOMAIN_18155
Sarcophilus harrisii
1164
2.7528
0.0052222


DOMAIN_18161
Cercocebus atys
1165
2.6663
0.0060803


DOMAIN_18181
Physeter macrocephalus
1166
4.696
4.59E−07


DOMAIN_18203
Monodelphis domestica
1167
3.7912
4.81E−04


DOMAIN_18206
Monodelphis domestica
1168
2.3929
0.0046062


DOMAIN_18214
Physeter macrocephalus
1169
2.6389
0.0094737


DOMAIN_18227
OwlMonkey
1170
3.5267
5.66E−06


DOMAIN_18241
Leptonychotes weddellii
1171
3.8187
9.60E−05


DOMAIN_18243
Felis catus
1172
3.5331
6.96E−04


DOMAIN_18244
Leptonychotes weddellii
1173
3.1726
0.0050817


DOMAIN_18272
Neomonachus schauinslandi
1174
2.9141
0.0085916


DOMAIN_18303
Monodelphis domestica
1175
2.9174
0.0018489


DOMAIN_18312
Monodelphis domestica
1176
2.8473
8.20E−04


DOMAIN_18323
Monodelphis domestica
1177
2.3956
0.0040336


DOMAIN_18325
Monodelphis domestica
1178
2.7636
0.0038297


DOMAIN_18332
Monodelphis domestica
1179
3.4328
4.68E−04


DOMAIN_18345
Monodelphis domestica
1180
3.349
4.43E−04


DOMAIN_18356
Monodelphis domestica
1181
3.1967
4.67E−04


DOMAIN_18385
Neomonachus schauinslandi
1182
2.1472
0.0044932


DOMAIN_18415
Neomonachus schauinslandi
1183
2.9768
4.55E−04


DOMAIN_18424
Physeter macrocephalus
1184
3.7744
3.31E−04


DOMAIN_18426
Physeter macrocephalus
1185
2.8011
0.0079672


DOMAIN_18428
Physeter macrocephalus
1186
2.5903
0.0095383


DOMAIN_18433
OwlMonkey
1187
3.4614
0.0022427


DOMAIN_18441
Felis catus
1188
3.7534
1.77E−04


DOMAIN_18458
Monodelphis domestica
1189
3.1061
0.0018603


DOMAIN_18459
Monodelphis domestica
1190
3.1352
2.38E−04


DOMAIN_18483
Monodelphis domestica
1191
2.8259
5.19E−04


DOMAIN_18485
Monodelphis domestica
1192
2.8817
0.0011922


DOMAIN_18498
OwlMonkey
1193
2.7354
0.0021141


DOMAIN_18502
Myotis davidii
1194
3.4127
1.93E−04


DOMAIN_18504
Cercocebus atys
1195
3.2213
5.38E−04


DOMAIN_18536
Camelus dromedarius
1196
3.2028
0.0011217


DOMAIN_18580
Cercocebus atys
1197
4.4477
3.22E−06


DOMAIN_18589
Neomonachus schauinslandi
1198
3.039
0.0025063


DOMAIN_18594
Monodelphis domestica
1199
3.2119
0.0036607


DOMAIN_18618
Physeter macrocephalus
1200
2.6489
0.0072165


DOMAIN_18646
Monodelphis domestica
1201
2.4678
0.007646


DOMAIN_18670
Neomonachus schauinslandi
1202
3.1792
3.80E−04


DOMAIN_18677
Monodelphis domestica
1203
2.2686
0.0068996


DOMAIN_18693
Camelus dromedarius
1204
3.0179
0.0013759


DOMAIN_18698
Felis catus
1205
3.3067
0.0093304


DOMAIN_18711
Vulpes vulpes
1206
2.2749
0.0063986


DOMAIN_18724
Chimp
1207
3.2062
5.16E−04


DOMAIN_18726
Myotis davidii
1208
2.9362
0.0025771


DOMAIN_18734
Monodelphis domestica
1209
2.8813
0.0092612


DOMAIN_18752
Monodelphis domestica
1210
3.5544
4.85E−05


DOMAIN_18753
Monodelphis domestica
1211
2.6101
3.54E−04


DOMAIN_18760
Chimp
1212
3.1806
7.49E−05


DOMAIN_18785
Leptonychotes weddellii
1213
2.9139
0.0019203


DOMAIN_18817
Monodelphis domestica
1214
2.2496
0.0091589


DOMAIN_18830
Monodelphis domestica
1215
3.2719
0.0032764


DOMAIN_18835
Camelus dromedarius
1216
2.4878
8.56E−05


DOMAIN_18873
Camelus dromedarius
1217
3.262
0.0049846


DOMAIN_18891
Orangutan
1218
3.6429
1.38E−06


DOMAIN_18923
Callithrix jacchus
1219
2.2053
0.0054504


DOMAIN_18935
Ovis aries
1220
3.4507
3.14E−05


DOMAIN_18947
Enhydra lutris kenyoni
1221
3.3167
7.58E−04


DOMAIN_18971
Enhydra lutris kenyoni
1222
3.3941
5.05E−06


DOMAIN_18977
Orangutan
1223
3.6262
9.03E−06


DOMAIN_18979
Orangutan
1224
2.0034
0.0071822


DOMAIN_19005
Enhydra lutris kenyoni
1225
3.4092
4.57E−04


DOMAIN_19028
Orangutan
1226
2.3618
0.0022277


DOMAIN_19056
Bos indicus × Bos taurus
1227
3.0542
0.001874


DOMAIN_19072
Vulpes vulpes
1228
2.8133
0.0016331


DOMAIN_19079
Otolemur garnettii
1229
4.0159
4.88E−05


DOMAIN_19125
Otolemur garnettii
1230
2.9892
8.36E−04


DOMAIN_19207
Enhydra lutris kenyoni
1231
2.655
0.0091617


DOMAIN_19220
Camelus dromedarius
1232
3.1947
0.0088687


DOMAIN_19221
Camelus dromedarius
1233
3.1733
4.21E−04


DOMAIN_19299
Myotis davidii
1234
2.8882
0.0043533


DOMAIN_19351
Orangutan
1235
3.1988
2.17E−04


DOMAIN_19385
Monodelphis domestica
1236
2.9198
0.008105


DOMAIN_19387
Monodelphis domestica
1237
3.4706
1.85E−04


DOMAIN_19388
Physeter macrocephalus
1238
3.2831
7.71E−04


DOMAIN_19404
Monodelphis domestica
1239
2.0125
0.0031965


DOMAIN_19423
Monodelphis domestica
1240
3.49
0.002544


DOMAIN_19424
Monodelphis domestica
1241
2.5838
0.0041846


DOMAIN_19437
OwlMonkey
1242
2.826
0.001773


DOMAIN_19445
Monodelphis domestica
1243
2.1105
0.0078325


DOMAIN_19447
Monodelphis domestica
1244
3.4492
1.40E−04


DOMAIN_19487
Monodelphis domestica
1245
3.4312
6.00E−04


DOMAIN_19497
Monodelphis domestica
1246
3.466
2.80E−05


DOMAIN_19517
Monodelphis domestica
1247
3.3361
1.04E−04


DOMAIN_19533
Papio anubis
1248
2.5831
4.67E−04


DOMAIN_19563
Papio anubis
1249
2.5522
0.0089134


DOMAIN_19580
Monodelphis domestica
1250
3.5716
3.29E−05


DOMAIN_19585
Monodelphis domestica
1251
3.0031
0.0032403


DOMAIN_19596
Monodelphis domestica
1252
3.8583
8.18E−05


DOMAIN_19597
Monodelphis domestica
1253
3.5081
4.46E−04


DOMAIN_19600
Monodelphis domestica
1254
2.5854
0.0042185


DOMAIN_19602
Physeter macrocephalus
1255
2.7219
0.0058524


DOMAIN_19611
Lipotes vexillifer
1256
3.3901
4.24E−04


DOMAIN_19629
Monodelphis domestica
1257
3.0535
0.0017954


DOMAIN_19699
Otolemur garnettii
1258
2.8474
3.15E−04


DOMAIN_19708
Bos indicus × Bos taurus
1259
3.6339
8.02E−04


DOMAIN_19713
Chimp
1260
3.845
2.95E−05


DOMAIN_19721
Otolemur garnettii
1261
2.6913
0.0089069


DOMAIN_19776
Enhydra lutris kenyoni
1262
2.617
0.0093497


DOMAIN_19777
Orangutan
1263
3.2427
0.0075444


DOMAIN_19780
Orangutan
1264
3.0867
1.72E−04


DOMAIN_19786
Chimp
1265
2.9155
5.94E−04


DOMAIN_19788
Enhydra lutris kenyoni
1266
3.3393
4.71E−04


DOMAIN_19800
Zalophus californianus
1267
2.368
0.009162


DOMAIN_19805
Rhinolophus ferrumequinum
1268
2.6527
0.0030997


DOMAIN_19818
Rhinopithecus roxellana
1269
2.3477
0.0022161


DOMAIN_19883
Zalophus californianus
1270
3.5504
3.42E−04


DOMAIN_19886
Panthera pardus
1271
2.8642
4.04E−05


DOMAIN_19889
Vicugna pacos
1272
3.1963
4.15E−05


DOMAIN_19891
Zalophus californianus
1273
3.2135
0.0010023


DOMAIN_19921
Callorhinus ursinus
1274
2.0083
0.0055679


DOMAIN_19944
Zalophus californianus
1275
3.8559
8.71E−05


DOMAIN_19947
Bonobo
1276
2.2608
0.00818


DOMAIN_19967
Tursiops truncatus
1277
2.9548
0.0027997


DOMAIN_19968
Tursiops truncatus
1278
2.8089
0.004093


DOMAIN_19990
Panthera pardus
1279
3.5329
0.0018768


DOMAIN_19993
Tursiops truncatus
1280
3.4227
0.0047476


DOMAIN_20012
Leptonychotes weddellii
1281
3.8253
3.41E−05


DOMAIN_20023
Physeter macrocephalus
1282
3.6893
5.78E−04


DOMAIN_20025
Carlito syrichta
1283
2.2451
0.002157


DOMAIN_20030
Tursiops truncatus
1284
4.1273
3.22E−06


DOMAIN_20089
Panthera pardus
1285
4.2275
8.99E−05


DOMAIN_20095
Phascolarctos cinereus
1286
3.7141
1.55E−05


DOMAIN_20115
Physeter macrocephalus
1287
3.1154
0.0030089


DOMAIN_20134
Acinonyx jubatus
1288
3.2457
3.20E−04


DOMAIN_20136
Sus scrofa
1289
3.3856
2.94E−04


DOMAIN_20147
Odocoileus virginianus texanus
1290
3.7467
1.53E−07


DOMAIN_20171
Trichechus manatus latirostris
1291
3.951
1.03E−05


DOMAIN_20208
Pteropus vampyrus
1292
2.4805
0.0041634


DOMAIN_20249
Vicugna pacos
1293
2.7041
0.0043741


DOMAIN_20250
Phascolarctos cinereus
1294
3.5525
1.37E−04


DOMAIN_20287
Cercocebus atys
1295
3.4486
5.29E−04


DOMAIN_20318
Callithrix jacchus
1296
3.5311
3.52E−06


DOMAIN_20332
Callithrix jacchus
1297
3.2855
0.0011689


DOMAIN_20336
Panthera pardus
1298
2.3293
0.0076785


DOMAIN_20345
Cebus imitator
1299
3.8132
1.53E−07


DOMAIN_20352
Vicugna pacos
1300
2.9839
9.79E−04


DOMAIN_20359
Pteropus vampyrus
1301
3.9594
4.06E−05


DOMAIN_20371
Ursus arctos horribilis
1302
2.8418
0.0061393


DOMAIN_20381
Saimiri boliviensis boliviensis
1303
2.0412
0.0013486


DOMAIN_20398
Physeter macrocephalus
1304
3.1266
0.0039215


DOMAIN_20436
Sus scrofa
1305
2.724
0.0058616


DOMAIN_20455
Nomascus leucogenys
1306
3.112
2.94E−04


DOMAIN_20462
Trichechus manatus latirostris
1307
5.4429
1.53E−07


DOMAIN_20469
Equus caballus
1308
2.7506
0.0077201


DOMAIN_20487
Mandrillus leucophaeus
1309
2.8325
0.0020982


DOMAIN_20524
Nomascus leucogenys
1310
3.2893
0.0024993


DOMAIN_20537
Chlorocebus sabaeus
1311
3.2762
0.0027249


DOMAIN_20540
Mandrillus leucophaeus
1312
2.8477
0.0021931


DOMAIN_20545
Sus scrofa
1313
2.711
0.0086718


DOMAIN_20561
Chrysochloris asiatica
1314
3.8309
3.52E−05


DOMAIN_20565
Suricata suricatta
1315
3.148
2.90E−04


DOMAIN_20601
Sus scrofa
1316
2.9097
0.0037911


DOMAIN_20652
Neophocaena asiaeorientalis
1317
2.7283
0.0038931



asiaeorientalis


DOMAIN_20667
Suricata suricatta
1318
3.7485
1.38E−06


DOMAIN_20674
Mandrillus leucophaeus
1319
3.3115
1.53E−07


DOMAIN_20716
Suricata suricatta
1320
3.6174
3.02E−05


DOMAIN_20729
Mandrillus leucophaeus
1321
2.5535
0.0090894


DOMAIN_20746
Chrysochloris asiatica
1322
3.4727
4.79E−04


DOMAIN_20767
Sus scrofa
1323
3.1224
3.16E−04


DOMAIN_20835
Suricata suricatta
1324
3.0025
0.0031432


DOMAIN_20915
Mandrillus leucophaeus
1325
2.4373
0.0054586


DOMAIN_20998
Bonobo
1326
2.6659
0.0044767


DOMAIN_21010
Equus caballus
1327
2.2253
0.0040982


DOMAIN_21023
Sarcophilus harrisii
1328
3.1196
0.0023342


DOMAIN_21067
Zalophus californianus
1329
3.0246
0.0010917


DOMAIN_21082
Loxodonta africana
1330
3.2032
0.0040056


DOMAIN_21086
Pteropus vampyrus
1331
2.1339
0.0079029


DOMAIN_21095
Trichechus manatus latirostris
1332
2.5003
0.0091721


DOMAIN_21110
Neovison vison
1333
2.499
0.0065113


DOMAIN_21123
Callorhinus ursinus
1334
3.237
4.13E−04


DOMAIN_21133
Suricata suricatta
1335
3.1021
4.18E−04


DOMAIN_21161
Sarcophilus harrisii
1336
3.2208
5.87E−04


DOMAIN_21162
Sarcophilus harrisii
1337
2.885
6.85E−04


DOMAIN_21175
Callorhinus ursinus
1338
3.3334
2.29E−04


DOMAIN_21197
Tursiops truncatus
1339
2.214
0.0073288


DOMAIN_21226
Sarcophilus harrisii
1340
2.6942
0.0033484


DOMAIN_21260
Pteropus vampyrus
1341
3.1806
0.0039855


DOMAIN_21276
Mandrillus leucophaeus
1342
3.0178
0.0029699


DOMAIN_21277
OwlMonkey
1343
2.7115
0.0075352


DOMAIN_21312
Lipotes vexillifer
1344
3.5287
4.75E−06


DOMAIN_21333
Zalophus californianus
1345
3.5801
3.57E−05


DOMAIN_21334
Equus caballus
1346
2.9508
8.67E−04


DOMAIN_21335
Equus caballus
1347
2.518
0.0034809


DOMAIN_21367
Equus caballus
1348
2.9921
0.0091001


DOMAIN_21369
Equus caballus
1349
2.7947
0.0011824


DOMAIN_21371
Physeter macrocephalus
1350
3.8804
4.44E−06


DOMAIN_21421
Pteropus vampyrus
1351
2.7713
7.52E−05


DOMAIN_21481
Bonobo
1352
2.7056
0.0012415


DOMAIN_21494
Tursiops truncatus
1353
3.783
1.36E−04


DOMAIN_21583
Sarcophilus harrisii
1354
3.1529
0.0026931


DOMAIN_21588
Callorhinus ursinus
1355
3.4914
5.39E−04


DOMAIN_21612
OwlMonkey
1356
3.2931
4.09E−05


DOMAIN_21626
Monodelphis domestica
1357
3.5419
1.57E−04


DOMAIN_21632
Monodelphis domestica
1358
2.6551
0.0071923


DOMAIN_21658
Monodelphis domestica
1359
3.1325
2.50E−04


DOMAIN_21786
Trichechus manatus latirostris
1360
3.2249
2.76E−04


DOMAIN_21822
Equus caballus
1361
3.5647
3.22E−06


DOMAIN_21823
Equus caballus
1362
3.2474
0.0072446


DOMAIN_21844
OwlMonkey
1363
3.467
4.44E−06


DOMAIN_21862
Chlorocebus sabaeus
1364
2.3797
0.0032299


DOMAIN_21889
Equus caballus
1365
3.6563
4.18E−04


DOMAIN_21896
Lipotes vexillifer
1366
2.8718
0.0093653


DOMAIN_21900
Equus caballus
1367
2.7606
0.0041711


DOMAIN_21909
Suricata suricatta
1368
3.2301
3.40E−04


DOMAIN_21928
Callorhinus ursinus
1369
3.758
1.67E−05


DOMAIN_21947
Trichechus manatus latirostris
1370
3.1204
0.003623


DOMAIN_21951
Equus caballus
1371
2.8972
3.24E−04


DOMAIN_21985
Suricata suricatta
1372
3.6273
1.99E−06


DOMAIN_21988
Sarcophilus harrisii
1373
3.3393
0.0011817


DOMAIN_21993
Lipotes vexillifer
1374
2.5494
0.0039206


DOMAIN_22022
Tursiops truncatus
1375
3.9558
4.44E−06


DOMAIN_22079
Trichechus manatus latirostris
1376
3.4511
6.43E−04


DOMAIN_22117
Sarcophilus harrisii
1377
2.5969
0.0040801


DOMAIN_22143
Pteropus vampyrus
1378
2.6595
9.36E−04


DOMAIN_22151
Trichechus manatus latirostris
1379
3.1615
5.26E−04


DOMAIN_22158
Lipotes vexillifer
1380
2.0562
0.0010562


DOMAIN_22166
Trichechus manatus latirostris
1381
4.2024
2.53E−05


DOMAIN_22192
Trichechus manatus latirostris
1382
2.8134
0.0083622


DOMAIN_22220
Bonobo
1383
2.8922
0.0013379


DOMAIN_22268
Lipotes vexillifer
1384
2.6534
0.0053876


DOMAIN_22278
Pteropus vampyrus
1385
3.3575
0.0037798


DOMAIN_22280
Pteropus vampyrus
1386
3.1521
0.0017347


DOMAIN_22285
Trichechus manatus latirostris
1387
3.0261
6.83E−04


DOMAIN_22297
Sarcophilus harrisii
1388
2.4261
0.0066953


DOMAIN_22311
Monodelphis domestica
1389
2.9903
0.0017115


DOMAIN_22322
Tursiops truncatus
1390
3.4452
3.85E−04


DOMAIN_22366
OwlMonkey
1391
4.848
3.06E−07


DOMAIN_22375
Tursiops truncatus
1392
2.5484
0.0090894


DOMAIN_22381
Tursiops truncatus
1393
3.8641
2.63E−04


DOMAIN_22383
Pteropus vampyrus
1394
3.4752
2.48E−04


DOMAIN_22407
OwlMonkey
1395
2.5308
0.0081831


DOMAIN_22425
OwlMonkey
1396
3.0333
0.0032208


DOMAIN_22430
Callorhinus ursinus
1397
2.982
0.0064761


DOMAIN_22454
Monodelphis domestica
1398
2.6042
0.0022491


DOMAIN_22458
Monodelphis domestica
1399
3.0003
0.0025373


DOMAIN_22459
Monodelphis domestica
1400
2.9261
0.0013171


DOMAIN_22462
Monodelphis domestica
1401
3.5597
2.34E−05


DOMAIN_22471
Papio anubis
1402
3.6293
1.68E−06


DOMAIN_22479
OwlMonkey
1403
3.9668
4.18E−05


DOMAIN_22483
OwlMonkey
1404
2.1702
0.0013107


DOMAIN_22495
Callorhinus ursinus
1405
2.2623
0.0043918


DOMAIN_22512
OwlMonkey
1406
2.93
0.003255


DOMAIN_22518
Lipotes vexillifer
1407
2.8869
0.0024472


DOMAIN_22520
Callorhinus ursinus
1408
3.3586
2.83E−05


DOMAIN_22527
Tursiops truncatus
1409
2.989
9.71E−04


DOMAIN_22566
Papio anubis
1410
3.5278
6.63E−05


DOMAIN_22586
Nomascus leucogenys
1411
2.1811
0.0021723


DOMAIN_22615
Homo sapiens
1412
3.0957
4.43E−04


DOMAIN_22654
Ursus arctos horribilis
1413
3.248
5.59E−05


DOMAIN_22667
Saimiri boliviensis boliviensis
1414
3.4947
0.0037256


DOMAIN_22669
Balaenoptera acutorostrata
1415
3.583
4.34E−04



scammoni


DOMAIN_22692
Propithecus coquereli
1416
3.2791
3.52E−04


DOMAIN_22710
Propithecus coquereli
1417
3.4387
0.0032081


DOMAIN_22740
Panthera pardus
1418
2.692
0.0027611


DOMAIN_22742
Panthera pardus
1419
2.9133
0.0027938


DOMAIN_22768
Ursus maritimus
1420
4.0609
7.81E−06


DOMAIN_22771
Ursus americanus
1421
3.3498
2.83E−05


DOMAIN_22776
Propithecus coquereli
1422
2.7757
2.88E−04


DOMAIN_22778
Saimiri boliviensis boliviensis
1423
3.1251
4.93E−04


DOMAIN_22782
Vombatus ursinus
1424
3.1663
4.24E−04


DOMAIN_22917
Cervus elaphus hippelaphus
1425
3.8061
2.77E−05


DOMAIN_22919
Colobus angolensis palliatus
1426
2.8609
0.003796


DOMAIN_22928
Tupaia chinensis
1427
3.0141
0.0015348


DOMAIN_22937
Ursus arctos horribilis
1428
3.0779
0.0032951


DOMAIN_22939
Muntiacus reevesi
1429
3.6187
1.78E−04


DOMAIN_22944
Muntiacus reevesi
1430
3.3908
5.28E−04


DOMAIN_23007
Lynx pardinus
1431
3.7329
1.09E−04


DOMAIN_23009
Saimiri boliviensis boliviensis
1432
3.1269
0.0062706


DOMAIN_23011
Cervus elaphus hippelaphus
1433
3.6236
3.51E−05


DOMAIN_23012
Cervus elaphus hippelaphus
1434
3.6131
2.50E−04


DOMAIN_23013
Cervus elaphus hippelaphus
1435
3.4615
4.85E−04


DOMAIN_23018
Colobus angolensis palliatus
1436
3.4177
2.30E−04


DOMAIN_23039
Saimiri boliviensis boliviensis
1437
2.8829
5.70E−04


DOMAIN_23040
Saimiri boliviensis boliviensis
1438
2.5742
0.0056531


DOMAIN_23041
Vombatus ursinus
1439
3.6194
1.92E−04


DOMAIN_23050
Balaenoptera acutorostrata
1440
2.9754
0.003318



scammoni


DOMAIN_23082
Mustela putorius furo
1441
3.9481
5.17E−05


DOMAIN_23093
Propithecus coquereli
1442
3.2165
5.48E−04


DOMAIN_23109
Mustela putorius furo
1443
2.9639
0.0019589


DOMAIN_23113
Camelus ferus
1444
3.4612
3.52E−04


DOMAIN_23136
Vicugna pacos
1445
3.285
2.16E−04


DOMAIN_23181
Colobus angolensis palliatus
1446
2.7665
0.0021609


DOMAIN_23196
Odobenus rosmarus divergens
1447
4.3363
3.22E−06


DOMAIN_23200
Ursus americanus
1448
3.755
1.84E−06


DOMAIN_23215
Vombatus ursinus
1449
3.0212
0.0035725


DOMAIN_23217
Vombatus ursinus
1450
4.1674
2.76E−06


DOMAIN_23239
Vicugna pacos
1451
3.0945
0.0090937


DOMAIN_23250
Delphinapterus leucas
1452
2.71
3.14E−04


DOMAIN_23260
Tupaia chinensis
1453
2.7567
0.0029622


DOMAIN_23281
Colobus angolensis palliatus
1454
2.5048
0.0036625


DOMAIN_23286
Mustela putorius furo
1455
3.3651
1.66E−04


DOMAIN_23301
Gulo gulo
1456
2.6839
0.0035226


DOMAIN_23323
Erinaceus europaeus
1457
3.2619
0.0031362


DOMAIN_23331
Carlito syrichta
1458
2.8995
5.23E−04


DOMAIN_23336
Carlito syrichta
1459
2.239
0.0065533


DOMAIN_23341
Carlito syrichta
1460
2.656
0.0058992


DOMAIN_23375
Vicugna pacos
1461
3.266
7.64E−04


DOMAIN_23378
Odobenus rosmarus divergens
1462
3.0623
0.0016508


DOMAIN_23419
Gulo gulo
1463
3.5213
7.41E−04


DOMAIN_23453
Carlito syrichta
1464
2.2331
0.006161


DOMAIN_23454
Carlito syrichta
1465
3.0632
7.96E−04


DOMAIN_23458
Vicugna pacos
1466
2.4232
0.0045857


DOMAIN_23480
Odobenus rosmarus divergens
1467
3.4432
3.38E−04


DOMAIN_23494
Mustela putorius furo
1468
3.847
5.05E−06


DOMAIN_23508
Mustela putorius furo
1469
2.3582
0.0047712


DOMAIN_23513
Tupaia chinensis
1470
3.2927
5.31E−05


DOMAIN_23514
Odobenus rosmarus divergens
1471
3.0166
4.77E−04


DOMAIN_23561
Colobus angolensis palliatus
1472
3.2392
0.0021906


DOMAIN_23574
Gulo gulo
1473
2.939
0.0083249


DOMAIN_23575
Erinaceus europaeus
1474
3.4624
0.001589


DOMAIN_23576
Erinaceus europaeus
1475
3.8014
2.89E−05


DOMAIN_23590
Odobenus rosmarus divergens
1476
2.8653
0.0052881


DOMAIN_23604
Vicugna pacos
1477
2.6984
0.0046123


DOMAIN_23641
Carlito syrichta
1478
2.6942
0.0081075


DOMAIN_23642
Delphinapterus leucas
1479
3.8829
2.28E−04


DOMAIN_23654
Carlito syrichta
1480
2.337
0.0083622


DOMAIN_23679
Tupaia chinensis
148
3.7951
5.10E−05


DOMAIN_23680
Vicugna pacos
1482
2.712
0.0034785


DOMAIN_23709
Carlito syrichta
1483
4.545
1.53E−07


DOMAIN_23711
Gulo gulo
1484
2.658
0.0016432


DOMAIN_23721
Carlito syrichta
1485
2.972
0.0022972


DOMAIN_23731
Colobus angolensis palliatus
1486
3.1609
2.35E−04


DOMAIN_23745
Myotis brandtii
1487
3.4544
3.54E−04


DOMAIN_23793
Odobenus rosmarus divergens
1488
2.7573
0.0081197


DOMAIN_23804
Colobus angolensis palliatus
1489
2.3403
0.0086366


DOMAIN_23827
Odobenus rosmarus divergens
1490
2.3013
0.009767


DOMAIN_23854
Gulo gulo
1491
3.838
7.18E−05


DOMAIN_23856
Erinaceus europaeus
1492
3.1072
0.0035694


DOMAIN_23863
Mustela putorius furo
1493
2.8758
0.0085493


DOMAIN_23885
Colobus angolensis palliatus
1494
3.033
0.0034316


DOMAIN_23895
Mustela putorius furo
1495
2.6148
0.003318


DOMAIN_23898
Mustela putorius furo
1496
2.7383
0.0035921


DOMAIN_23916
Odobenus rosmarus divergens
1497
3.3232
1.63E−04


DOMAIN_23931
Gulo gulo
1498
3.8077
1.49E−05


DOMAIN_23940
Homo sapiens
1499
2.5087
0.0010424


DOMAIN_23953
Muntiacus reevesi
1500
2.4156
0.0075055


DOMAIN_23979
Balaenoptera acutorostrata
1501
4.0461
5.77E−05



scammoni


DOMAIN_24020
Rhinolophus ferrumequinum
1502
3.1125
1.66E−04


DOMAIN_24028
Ursus arctos horribilis
1503
3.8797
1.53E−07


DOMAIN_24035
Propithecus coquereli
1504
3.2225
0.0017975


DOMAIN_24042
Propithecus coquereli
1505
3.3038
4.75E−06


DOMAIN_24083
Myotis brandtii
1506
3.9804
2.77E−05


DOMAIN_24113
Propithecus coquereli
1507
3.3264
2.89E−04


DOMAIN_24152
Vombatus ursinus
1508
3.3664
0.0022672


DOMAIN_24204
Propithecus coquereli
1509
3.0779
4.60E−04


DOMAIN_24212
Pteropus alecto
1510
2.498
0.0034998


DOMAIN_24230
Muntiacus reevesi
1511
3.1832
1.53E−07


DOMAIN_24256
Ursus arctos horribilis
1512
2.7933
0.0018808


DOMAIN_24282
Muntiacus reevesi
1513
2.694
0.0052575


DOMAIN_24306
Propithecus coquereli
1514
3.2084
0.0023952


DOMAIN_24317
Myotis brandtii
1515
3.9767
3.17E−05


DOMAIN_24379
Macaca nemestrina
1516
2.4643
0.0086804


DOMAIN_24393
Propithecus coquereli
1517
3.8008
2.45E−06


DOMAIN_24446
Propithecus coquereli
1518
3.6312
7.27E−05


DOMAIN_24463
Balaenoptera acutorostrata
1519
2.5362
0.007147



scammoni


DOMAIN_24496
Ursus americanus
1520
3.6403
4.24E−04


DOMAIN_24515
Balaenoptera acutorostrata
1521
3.7358
5.28E−05



scammoni


DOMAIN_24518
Balaenoptera acutorostrata
1522
3.4135
3.05E−05



scammoni


DOMAIN_24546
Ursus americanus
1523
3.4262
8.42E−06


DOMAIN_24570
Saimiri boliviensis boliviensis
1524
3.6773
1.45E−05


DOMAIN_24571
Balaenoptera acutorostrata
1525
2.6912
0.0038376



scammoni


DOMAIN_24600
Ursus americanus
1526
3.156
0.0012483


DOMAIN_24614
Cervus elaphus hippelaphus
1527
2.6295
0.0046463


DOMAIN_24615
Colobus angolensis palliatus
1528
2.4075
0.0069247


DOMAIN_24653
Cervus elaphus hippelaphus
1529
2.9883
0.0083016


DOMAIN_24677
Lynx pardinus
1530
2.3115
0.0094713


DOMAIN_24719
Muntiacus reevesi
1531
2.7499
0.005142


DOMAIN_24725
Ursus arctos horribilis
1532
3.4496
4.09E−05


DOMAIN_24771
Myotis brandtii
1533
3.3701
0.0025351


DOMAIN_24786
Vombatus ursinus
1534
2.9237
0.0078001


DOMAIN_24788
Vombatus ursinus
1535
2.7694
0.0021557


DOMAIN_24838
Pteropus alecto
1536
2.3323
0.0042954


DOMAIN_24867
Nomascus leucogenys
1537
3.469
2.97E−04


DOMAIN_24903
Ailuropoda melanoleuca
1538
3.0377
0.0030054


DOMAIN_24939
Phascolarctos cinereus
1539
3.3066
6.08E−04


DOMAIN_24947
Ursus maritimus
1540
2.9491
0.0055208


DOMAIN_24975
Muntiacus muntjak
1541
3.2737
0.0069767


DOMAIN_24993
Oryctolagus cuniculus
1542
3.3817
5.00E−04


DOMAIN_25016
Oryctolagus cuniculus
1543
2.9822
0.0034776


DOMAIN_25052
Pteropus alecto
1544
2.3634
0.0072024


DOMAIN_25060
Ailuropoda melanoleuca
1545
3.6002
4.82E−04


DOMAIN_25063
Phascolarctos cinereus
1546
2.9436
0.0042752


DOMAIN_25070
Sapajus apella
1547
2.9649
0.0043634


DOMAIN_25091
Phascolarctos cinereus
1548
2.9006
0.0039332


DOMAIN_25094
Phascolarctos cinereus
1549
3.0413
0.0026876


DOMAIN_25106
Canis lupus familiaris
1550
2.8622
0.0075508


DOMAIN_25126
Puma concolor
1551
2.1478
0.005514


DOMAIN_25128
Sapajus apella
1552
2.588
0.0029475


DOMAIN_25131
Sapajus apella
1553
2.592
0.0051895


DOMAIN_25146
Macaca nemestrina
1554
3.629
1.68E−06


DOMAIN_25150
Muntiacus reevesi
1555
3.147
0.0018391


DOMAIN_25157
Myotis brandtii
1556
3.0902
0.0012442


DOMAIN_25194
Macaca nemestrina
1557
2.4613
0.003597


DOMAIN_25204
Panthera pardus
1558
2.7595
0.0027917


DOMAIN_25234
Saimiri boliviensis boliviensis
1559
2.743
0.0042296


DOMAIN_25235
Oryctolagus cuniculus
1560
3.6965
1.76E−05


DOMAIN_25334
Phascolarctos cinereus
1561
2.7501
0.0096299


DOMAIN_25384
Rhinolophus ferrumequinum
1562
3.5139
8.10E−05


DOMAIN_25389
Ursus maritimus
1563
3.0814
6.54E−04


DOMAIN_25400
Lynx canadensis
1564
2.2285
3.10E−04


DOMAIN_25410
Puma concolor
1565
2.8699
0.0022843


DOMAIN_25443
Muntiacus reevesi
1566
3.2531
0.0016615


DOMAIN_25534
Ursus maritimus
1567
2.2698
0.0054246


DOMAIN_25554
Panthera pardus
1568
3.0101
0.003898


DOMAIN_25564
Muntiacus reevesi
1569
3.4378
6.04E−04


DOMAIN_25565
Muntiacus reevesi
1570
2.6133
0.0011572


DOMAIN_25623
Ursus maritimus
1571
3.4886
2.91E−06


DOMAIN_25628
Rhinopithecus bieti
1572
2.8332
0.0022213


DOMAIN_25649
Ursus arctos horribilis
1573
3.6884
5.62E−05


DOMAIN_25654
Pteropus alecto
1574
2.2996
0.0031144


DOMAIN_25671
Muntiacus reevesi
1575
3.5244
1.53E−07


DOMAIN_25682
Rhinopithecus bieti
1576
2.5621
0.002108


DOMAIN_25686
Panthera pardus
1577
2.8635
0.0031882


DOMAIN_25726
Pteropus alecto
1578
2.8203
0.0039506


DOMAIN_25741
Sapajus apella
1579
3.7244
1.32E−04


DOMAIN_25780
Rhinopithecus bieti
1580
2.8383
0.0018385


DOMAIN_25807
Puma concolor
1581
3.6511
0.0018679


DOMAIN_25842
Rhinolophus ferrumequinum
1582
3.0942
2.44E−04


DOMAIN_25844
Ursus maritimus
1583
2.5635
0.0037997


DOMAIN_25857
Balaenoptera acutorostrata
1584
2.898
0.0026959



scammoni


DOMAIN_25865
Vombatus ursinus
1585
3.1027
0.0066133


DOMAIN_25869
Vombatus ursinus
1586
2.3538
0.006932


DOMAIN_25972
Geotrypetes seraphini
1587
3.2178
0.0036689


DOMAIN_25973
Geotrypetes seraphini
1588
2.7804
0.001766


DOMAIN_25996
Geotrypetes seraphini
1589
3.984
1.24E−05


DOMAIN_26010
Geotrypetes seraphini
1590
2.1911
0.008383


DOMAIN_26012
Geotrypetes seraphini
1591
2.3532
9.70E−04


DOMAIN_26044
Geotrypetes seraphini
1592
2.8874
0.0068616


DOMAIN_26103
Geotrypetes seraphini
1593
2.5308
0.0033422


DOMAIN_26127
Geotrypetes seraphini
1594
2.5183
0.00586


DOMAIN_26131
Geotrypetes seraphini
1595
2.4087
0.0068533


DOMAIN_26134
Geotrypetes seraphini
1596
2.4433
0.0072939


DOMAIN_26163
Geotrypetes seraphini
1597
2.4527
0.0041806


DOMAIN_26177
Geotrypetes seraphini
1598
3.4467
1.27E−05


DOMAIN_26180
Geotrypetes seraphini
1599
3.4522
1.35E−04


DOMAIN_26194
Geotrypetes seraphini
1600
2.8857
0.0031518


DOMAIN_26211
Pelodiscus sinensis
1601
2.6058
0.0064871


DOMAIN_26233
Colinus virginianus
1602
3.6739
1.77E−04


DOMAIN_26236
Pelodiscus sinensis
1603
2.7094
0.003991


DOMAIN_26265
Geotrypetes seraphini
1604
2.5922
3.31E−04


DOMAIN_26268
Geotrypetes seraphini
1605
2.1404
0.0020397


DOMAIN_26292
Geotrypetes seraphini
1606
2.4722
0.0074388


DOMAIN_26299
Geotrypetes seraphini
1607
2.3704
0.0058481


DOMAIN_26305
Geotrypetes seraphini
1608
3.0107
0.0084216


DOMAIN_26306
Geotrypetes seraphini
1609
2.6178
0.0051922


DOMAIN_26335
Colinus virginianus
1610
4.0965
3.41E−04


DOMAIN_26340
Pelodiscus sinensis
1611
3.1704
0.003352


DOMAIN_26353
Pelodiscus sinensis
1612
3.5785
1.16E−04


DOMAIN_26373
Pseudonaja textilis
1613
3.3204
5.13E−04


DOMAIN_26407
Colinus virginianus
1614
2.9778
0.0049206


DOMAIN_26414
Pelodiscus sinensis
1615
2.9544
0.0089308


DOMAIN_26415
Pelodiscus sinensis
1616
2.5032
0.0035489


DOMAIN_26416
Pelodiscus sinensis
1617
3.6321
4.36E−05


DOMAIN_26417
Pelodiscus sinensis
1618
4.1057
4.46E−05


DOMAIN_26423
Pelodiscus sinensis
1619
3.0169
0.0025697


DOMAIN_26430
Pelodiscus sinensis
1620
2.6946
0.0051824


DOMAIN_26439
Pelodiscus sinensis
1621
3.2468
0.0010568


DOMAIN_26463
Pelodiscus sinensis
1622
2.8812
0.003427


DOMAIN_26469
Pelodiscus sinensis
1623
3.021
5.08E−04


DOMAIN_26496
Geotrypetes seraphini
1624
2.7991
0.0040994


DOMAIN_26501
Geotrypetes seraphini
1625
2.6513
0.0041882


DOMAIN_26518
Geotrypetes seraphini
1626
2.397
0.0087878


DOMAIN_26577
Geotrypetes seraphini
1627
2.4722
0.0035247


DOMAIN_26634
Gopherus agassizii
1628
2.8182
0.0079972


DOMAIN_26636
Gopherus agassizii
1629
2.6934
0.0090052


DOMAIN_26660
Phasianus colchicus
1630
3.201
4.90E−04


DOMAIN_26679
Paroedura picta
1631
2.6033
0.001326


DOMAIN_26780
Meleagris gallopavo
1632
3.1696
0.0031591


DOMAIN_26783
Meleagris gallopavo
1633
3.2848
0.0020241


DOMAIN_26795
Meleagris gallopavo
1634
3.3538
0.001228


DOMAIN_26800
Meleagris gallopavo
1635
3.8197
1.62E−04


DOMAIN_26803
Aquila chrysaetos chrysaetos
1636
3.4265
0.001246


DOMAIN_26852
Mus musculus
1637
2.8783
0.0025253


DOMAIN_26853
Mus musculus
1638
3.6235
7.59E−04


DOMAIN_26886
Homo sapiens
1639
3.3209
0.0016312


DOMAIN_26925
Alligator sinensis
1640
3.2248
0.0036928


DOMAIN_26999
Xenopus laevis
1641
3.4317
4.75E−06


DOMAIN_27032
Alligator mississippiensis
1642
3.4805
0.0019423


DOMAIN_27285
Peromyscus maniculatus bairdii
1643
3.092
5.16E−04


DOMAIN_27498
Sus scrofa
1644
2.9278
0.0029754


DOMAIN_27521
Suricata suricatta
1645
2.7447
0.0010703


DOMAIN_27563
Muntiacus muntjak
1646
3.6292
6.63E−05


DOMAIN_27566
Muntiacus muntjak
1647
2.7825
0.0020795


DOMAIN_27579
Muntiacus muntjak
1648
3.8878
7.50E−06


DOMAIN_27581
Canis lupus familiaris
1649
2.4582
0.0090172


DOMAIN_27639
Macaca fascicularis
1650
2.452
0.0032574


DOMAIN_27642
Puma concolor
1651
2.8615
0.0015287


DOMAIN_27690
Myotis lucifugus
1652
3.1465
0.0012118


DOMAIN_27705
Phascolarctos cinereus
1653
2.5921
0.0030483


DOMAIN_27759
Bos taurus
1654
2.2124
0.0070756


DOMAIN_27767
Callithrix jacchus
1655
2.2153
0.0023952


DOMAIN_27777
Odocoileus virginianus texanus
1656
2.6766
0.0067364


DOMAIN_27784
Ovis aries
1657
2.1631
0.0040915


DOMAIN_27809
Cebus imitator
1658
2.8715
0.0025161


DOMAIN_27827
Vulpes vulpes
1659
3.1318
2.13E−05


DOMAIN_27833
Callithrix jacchus
1660
3.0164
4.27E−04


DOMAIN_27866
Orangutan
1661
2.9226
0.0029981


DOMAIN_27886
Bison bison bison
1662
2.735
0.0036356


DOMAIN_27902
Vulpes vulpes
1663
2.9068
0.0039341


DOMAIN_27988
Camelus dromedarius
1664
2.5381
0.0015476


DOMAIN_28051
Neomonachus schauinslandi
1665
2.4353
0.0018581


DOMAIN_28071
Enhydra lutris kenyoni
1666
3.2938
2.61E−04


DOMAIN_28085
Enhydra lutris kenyoni
1667
2.2962
0.0029074


DOMAIN_28103
Physeter macrocephalus
1668
2.4116
0.009594


DOMAIN_28118
OwlMonkey
1669
3.1049
0.0027807


DOMAIN_28158
Odocoileus virginianus texanus
1670
3.0762
0.0016156


DOMAIN_28164
Callithrix jacchus
1671
2.7356
0.0064115


DOMAIN_28299
Capra hircus
1672
3.5584
6.41E−05


DOMAIN_28309
Pteropus vampyrus
1673
3.5338
3.28E−04


DOMAIN_28335
Bonobo
1674
3.3013
2.50E−04


DOMAIN_28341
Homo sapiens
1675
2.7008
5.14E−04


DOMAIN_28417
Gulo gulo
1676
2.5366
5.02E−04


DOMAIN_28421
Erinaceus europaeus
1677
3.0763
0.0038713


DOMAIN_28507
Muntiacus reevesi
1678
3.2874
8.76E−04


DOMAIN_28513
Propithecus coquereli
1679
2.3747
0.0050076


DOMAIN_28533
Propithecus coquereli
1680
2.7575
0.0031303


DOMAIN_28588
Rhinolophus ferrumequinum
1681
2.6131
0.0030648


DOMAIN_28619
Rhinolophus ferrumequinum
1682
2.6504
0.0027237


DOMAIN_28823
Microcaecilia unicolor
1683
2.331
0.0078575


DOMAIN_28845
Camelus ferus
1684
3.0175
0.0017733


DOMAIN_28929
Mus musculus
1685
3.1025
6.70E−04


DOMAIN_29066
Xenopus tropicalis
1686
2.6393
3.67E−04


DOMAIN_29164
Chelonia mydas
1687
2.1345
0.0029635


DOMAIN_29260
Peromyscus maniculatus bairdii
1688
2.5127
0.0074146


DOMAIN_29339
Mesocricetus auratus
1689
2.9581
0.0028165


DOMAIN_29377
Mesocricetus auratus
1690
2.672
0.0070692


DOMAIN_29426
Mus caroli
1691
2.0491
6.64E−04


DOMAIN_29434
Mus caroli
1692
2.2707
0.005184


DOMAIN_29467
Mus caroli
1693
3.4689
5.79E−05


DOMAIN_29471
Cricetulus griseus
1694
3.1911
4.18E−05


DOMAIN_29511
Peromyscus maniculatus bairdii
1695
3.4739
7.00E−05


DOMAIN_29614
Peromyscus maniculatus bairdii
1696
3.4528
1.82E−04


DOMAIN_29616
Mesocricetus auratus
1697
2.2807
0.0035376


DOMAIN_29765
Erinaceus europaeus
1698
3.3088
9.79E−04


DOMAIN_29900
Nomascus leucogenys
1699
2.1583
0.0098463


DOMAIN_30185
Rhinopithecus roxellana
1700
3.0766
5.83E−05


DOMAIN_30211
Bison bison bison
1701
2.3322
0.0023122


DOMAIN_30236
Callithrix jacchus
1702
2.7293
0.0021744


DOMAIN_30329
Rhesus
1703
2.1216
0.0099018


DOMAIN_30783
Chimp
1704
2.952
0.001698


DOMAIN_31235
Vicugna pacos
1705
2.2828
0.0067045


DOMAIN_31340
Homo sapiens
1706
2.8261
0.0021028


DOMAIN_31383
Propithecus coquereli
1707
2.1919
0.0087058


DOMAIN_31638
Balaenoptera acutorostrata
1708
2.0254
0.0036297



scammoni


DOMAIN_31798
Notechis scutatus
1709
4.8007
7.82E−04


DOMAIN_31935
Rhinolophus ferrumequinum
1710
3.5544
0.0084786


DOMAIN_32127
Human
1711
3.7547
2.62E−05


DOMAIN_32145
Human
1712
3.1866
1.67E−05


DOMAIN_32146
Human
1713
2.7628
0.0016129


DOMAIN_32159
Human
1714
2.7874
0.0021753


DOMAIN_32215
Human
1715
3.2653
0.001461


DOMAIN_32223
Human
1716
2.8836
0.0068873


DOMAIN_32255
Human
1717
3.8237
1.39E−05


DOMAIN_32279
Human
1718
2.4917
0.0060199


DOMAIN_32286
Human
1719
2.8921
0.0070992


DOMAIN_32312
Human
1720
2.9151
0.0030308


DOMAIN_32321
Human
1721
3.0441
0.0040854


DOMAIN_32327
Human
1722
3.1024
0.0044212


DOMAIN_32334
Human
1723
2.8117
0.0015241


DOMAIN_32351
Human
1724
2.0727
0.0036362


DOMAIN_32386
Human
1725
3.5521
3.87E−04


DOMAIN_32390
Human
1726
3.757
4.30E−05









The repressor domain with the highest log 2 (fold change) was derived from the king cobra, Ophiophagus hannah (DOMAIN_26749; SEQ ID NO: 135). Surprisingly, this sequence was highly divergent from human KRAB domains (with only 41% sequence identity) and was grouped in a sequence cluster of poor repressor domains.
To verify that the domains identified in the selection supported transcriptional repression in an independent assay, representative members of the top 95 and 1597 repressor domains were used to generate dXR constructs, and their ability to repress transcription of the B2M locus was tested. As shown in FIG. 55, seven days after transduction, dXRs with all but one of the representative top 95 or 1597 repressor domains tested repressed B2M to a greater extent than did the dXR with the ZNF10 KRAB domain. As shown in FIG. 56, ten days after transduction, the majority of the dXRs with representative top 95 or 1597 repressor domains tested repressed B2M to a greater extent than did ZNF10 or ZIM3. dXR repression of a target locus tends to deteriorate over time, and ten days following transduction is believed to be a relatively late timepoint for measuring dXR repression. Therefore, it is particularly notable that many of the dXR constructs with repressor domains in the top 95 and 1597 were able to repress B2M to a greater extent than dXR with KRAB domains derived from ZNF10 or ZIM3 as late as ten days following transduction.
To further understand the basis of the superior ability of the identified repressor domains to repress transcription, protein sequence motifs were identified from the top 1597 repressor domains using the STREME algorithm. Specifically, five motifs (motifs 1-5) were generated by comparing the amino acid sequences of the top 1597 repressor domains to a negative training set of 1506 repressor domains with p-values less than 0.01, and log 2 (fold change) values less than 0. Logos of motifs 1-5 are provided in FIGS. 57A, 57B, 57C, 57D, and 57E. In addition, four motifs (motifs 6-9) were generated by comparing the top 1597 repressor domains to shuffled sequences derived from the 1597 repressor domain sequences. Logos of motifs 6-9 are provided in FIGS. 57F, 57G, 57H, and 57I.
Table 55, below, provides the p-value, E-value (a measure of statistical significance), and number and percentage of sequences matching the motif in the top 1597 repressor domains for each of the nine motifs, as calculated by STREME. Table 56 provides the sequences of each motif, showing the amino acid residues present at each position within the motifs (from N- to C-terminus).







TABLE 55







Characteristics of protein sequence


motifs of top 1597 repressor domains










Motif


Number and percentage of sites matching


ID
P-value
E-value
motif in top 1597 repressor domains










Motifs generated compared to a negative training set











1
3.7e−014
7.1e−013
1158
(72.5%)


2
3.4e−012
6.4e−011
978
(61.2%)


3
7.5e−010
1.4e−008
1017
(63.7%)


4
7.0e−008
1.3e−006
987
(61.8%)


5
1.7e−007
3.3e−006
678
(42.5%)







Motifs generated compared to shuffled sequences











6
1.2e−048
1.5e−047
1597
(100.0%)


7
1.2e−048
1.5e−047
1597
(100.0%)


8
1.3e−042
1.6e−041
1377
(86.2%)


9
2.1e−040
2.7e−039
1483
(92.9%)
















TABLE 56







Sequences of protein sequence motifs


of top 1597 repressor domains













Amino acid residues





with >5%



Motif
Position
representation in



ID
in motif
motif











Motifs generated compared to a negative


training set











1
1
P




2
A, D, E, N




3
L, V




4
I, V




5
S, T, F




6
H, K, L, Q, R, W




7
L, M




8
E




9
G, K, Q, R



2
1
L, V




2
A, G, L, T, V




3
A, F, S




4
L, V




5
G




6
C, F, H, I, L, Y




7
A, C, P, Q, S




8
A, F, G, I, S, V




9
A, P, S, T




10
K, R



3
1
Q




2
K, R




3
A, D, E, G, N, S, T




4
L




5
Y




6
R




7
D, E, S




8
V




9
M




10
L, R



4
1
A, L, P, S




2
L, V




3
S, T




4
F




5
A, E, G, K, R




6
D




7
V




8
A, T




9
I, V




10
D, E, N, Y




11
F




12
S, T




13
E, P, Q, R, W




14
E, N




15
E, Q



5
1
E, G, R




2
E, K




3
A, D, E




4
P




5
C, W




6
I, K, L, M, T, V




7
I, L, P, V




8
D, E, K, V




9
E, G, K, P, R




10
A, D, R, G, K, Q, V




11
D, E, G, I, L, R, S, V







Motifs generated compared to shuffled


sequences











6
1
L




2
Y




3
K, R




4
D, E




5
V




6
M




7
L, Q, R




8
E




9
N, T




10
F, Y




11
A, E, G, Q, R, S




12
H, L, N




13
L, V




14
A, G, I, L, T, V




15
A, F, S



7
1
F




2
A, E, G, K, R




3
D




4
V




5
A, S, T




6
I, V




7
D, E, N, Y




8
F




9
S, T




10
E, L, P, Q, R, W




11
D, E




12
E




13
W




14
A, E, G, Q, R



8
1
K, R




2
P




3
A, D, E, N




4
I, L, M, V




5
I, V




6
F, S, T




7
H, K, L, Q, R, W




8
L




9
E




10
K, Q, R




11
E, G, R




12
D, E, K




13
A, D, E




14
L, P




15
C, W



9
1
C, H, L, Q, W




2
L




3
D, G, N, R, S




4
L, P, S, T




5
A, S, T




6
Q




7
K, R




8
A, D, E, K, N, S, T










Notably, motifs 6 and 7 were present in 100% of the top 1597 repressor domains. Many of the highly conserved positions in motif 6 (e.g., amino acid residues L1, Y2, V5, M6, and E8) are known to form an interface with Trim28 (also known as Kap1), which is responsible for recruiting transcriptional repressive machinery to a locus. Similarly, residues in motif 7 (D3, V4, E11, E12) all contribute to Trim28 recruitment. It is believed that many of the amino acid residues identified as enriched in the top repressor domains strengthen Trim28 recruitment. Notably, some of these residues are absent in commonly used KRAB domains. Specifically, in the site in ZNF10 that matches motif 6, the residue at the first position is a valine instead of a leucine. In the site in ZIM3 that matches motif 7, the residue at position 11 is a glycine instead of a glutamic acid. Many of the other motifs described above that are not present in all KRAB domains may represent additional and novel mechanisms of repression that are specific to sequence clusters of repressor domains with homology to KRAB domains.
Taken together, the experiments described herein have identified a suite of non-human transcriptional repressor domains that are effective for promoting transcriptional repression in the context of a dXR molecule. These domains repressed transcription to a greater extent than ZNF10 and ZIM3. Finally, protein sequence motifs were identified that are associated with the domains that were the strongest transcriptional repressors.
Example 18: Members of the Top 95 Repressor Domains Increase LTRP5 Activity
As described in Example 17, non-human repressor domains were identified that resulted in enhanced repression in the context of dXR constructs. Here, experiments were performed to test whether the enhanced repressor domains identified in Example 17 were also superior transcriptional repressors in the context of LTRP5.
Materials and Methods
Representative repressor domains identified in Example 17 and determined to be members of the top 95 performing repressors (Table 65) were cloned into an LTRP5 construct without the DNMT3A ADD domain (FIG. 1). The LTRP5 constructs were constructed as described in Example 13 (Table 45), except that an SV40 NLS was present downstream of the repressor domains. An LTRP5 molecule with a ZIM3 KRAB domain was used as a control. A separate plasmid was used to encode guide scaffold 316 (SEQ ID NO: 1746) with spacer 7.165 (UCCCUAUGUCCUUGCUGUUU; SEQ ID NO: 3114) targeting the B2M locus. Additional controls included a dXR molecule with a ZIM3 KRAB domain with a gRNA having scaffold 316 and spacer 7.165, and LTRP5 and dXR molecules with the ZIM3 KRAB and a non-targeting gRNA. Spacer 7.165 was chosen because it is known to be a relatively inefficient spacer, which would therefore increase the dynamic range of the assay for discerning differences between the various LTRP molecules tested.
HEK293T cells were transfected as described in Example 14, except that the cells were transfected with 50 ng each of a plasmid encoding the LTRP construct and a plasmid encoding the gRNA. Repression analysis was conducted by analyzing B2M protein expression via HLA immunostaining followed by flow cytometry as described in Example 13. 72 of the 95 top repressor domains were assessed together in one experiment where B2M expression was measured at 7, 14, 19, and 26 days after transfection, and the data shown in Tables 57-60. For the remaining 24 repressor domains assessed in a second experiment, B2M expression was measured at 6, 13, 20, and 27 days after transfection, and the data are shown in Tables 61-64. A construct encoding catalytically-active CasX 491, paired with the B2M-targeting spacer 7.37 (SEQ ID NO: 3137) was also included as a control.
Results
The results of the B2M assay are provided in Tables 57-64, below.







TABLE 57







Levels of B2M repression mediated by dXR and LTRP constructs with


various repressor domains quantified at 7 days post-transfection.















Mean %







HLA-


Repressor
Repressor

negative
Standard
Sample


construct
domain
Spacer
cells
deviation
size















dXR
ZIM3
NT
7.347
1.955
15


LTRP5
ZIM3
NT
5.619
2.520
15


dXR
ZIM3
7.165
6.334
1.335
14


LTRP5
DOMAIN_11029
7.165
33.467
1.290
3


LTRP5
DOMAIN_4968
7.165
30.133
2.804
3


LTRP5
DOMAIN_27811
7.165
22.633
0.643
3


LTRP5
DOMAIN_5066
7.165
37.833
1.026
3


LTRP5
DOMAIN_15126
7.165
30.333
0.306
3


LTRP5
DOMAIN_17358
7.165
27.767
3.062
3


LTRP5
DOMAIN_8503
7.165
29.700
0.889
3


LTRP5
DOMAIN_11486
7.165
36.667
1.320
3


LTRP5
DOMAIN_28803
7.165
30.367
0.902
3


LTRP5
DOMAIN_17317
7.165
25.933
0.586
3


LTRP5
DOMAIN_24125
7.165
32.667
1.290
3


LTRP5
DOMAIN_8853
7.165
48.100
4.458
3


LTRP5
DOMAIN_19949
7.165
31.967
2.511
3


LTRP5
DOMAIN_737
7.165
41.467
3.258
3


LTRP5
DOMAIN_16444
7.165
36.367
1.704
3


LTRP5
DOMAIN_11386
7.165
35.633
1.677
3


LTRP5
DOMAIN_27506
7.165
39.467
1.504
3


LTRP5
DOMAIN_10331
7.165
38.300
1.308
3


LTRP5
DOMAIN_13539
7.165
40.800
2.307
3


LTRP5
DOMAIN_2380
7.165
41.100
1.277
3


LTRP5
DOMAIN_18258
7.165
29.133
0.777
3


LTRP5
DOMAIN_23723
7.165
33.400
2.170
3


LTRP5
DOMAIN_16806
7.165
35.667
1.450
3


LTRP5
DOMAIN_18216
7.165
41.400
0.819
3


LTRP5
DOMAIN_17432
7.165
43.967
0.907
3


LTRP5
DOMAIN_4806
7.165
36.767
1.747
3


LTRP5
DOMAIN_25379
7.165
46.467
3.868
3


LTRP5
DOMAIN_16643
7.165
41.133
1.206
3


LTRP5
DOMAIN_21603
7.165
34.367
0.404
3


LTRP5
DOMAIN_21247
7.165
37.867
2.219
3


LTRP5
DOMAIN_28640
7.165
39.900
1.277
3


LTRP5
ZIM3
7.165
31.940
1.637
15


LTRP5
DOMAIN_14659
7.165
37.933
1.767
3


LTRP5
DOMAIN_6248
7.165
36.000
2.352
3


LTRP5
DOMAIN_11348
7.165
38.433
1.286
3


LTRP5
DOMAIN_19229
7.165
33.967
0.321
3


LTRP5
DOMAIN_17759
7.165
43.233
0.924
3


LTRP5
DOMAIN_24663
7.165
39.433
6.048
3


LTRP5
DOMAIN_18137
7.165
44.033
0.404
3


LTRP5
DOMAIN_13331
7.165
38.700
2.163
3


LTRP5
DOMAIN_6807
7.165
39.500
0.436
3


LTRP5
DOMAIN_16688
7.165
41.800
0.265
3


LTRP5
DOMAIN_26322
7.165
42.767
4.661
3


LTRP5
DOMAIN_6802
7.165
45.767
1.888
3


LTRP5
DOMAIN_22270
7.165
32.500
1.100
3


LTRP5
DOMAIN_7255
7.165
43.567
0.451
3


LTRP5
DOMAIN_5463
7.165
32.533
0.404
3


LTRP5
DOMAIN_12631
7.165
40.300
0.624
3


LTRP5
DOMAIN_9960
7.165
43.967
2.363
3


LTRP5
DOMAIN_6445
7.165
45.667
2.730
3


LTRP5
DOMAIN_23394
7.165
40.733
2.285
3


LTRP5
DOMAIN_10948
7.165
42.733
0.924
3


LTRP5
DOMAIN_19804
7.165
42.067
1.914
3


LTRP5
DOMAIN_5290
7.165
43.400
1.136
3


LTRP5
DOMAIN_24458
7.165
43.567
1.332
3


LTRP5
DOMAIN_19896
7.165
43.600
0.624
3


LTRP5
DOMAIN_21755
7.165
38.667
1.498
3


LTRP5
DOMAIN_8790
7.165
34.900
0.608
3


LTRP5
DOMAIN_881
7.165
43.533
1.858
3


LTRP5
DOMAIN_14755
7.165
37.350
0.071
2


LTRP5
DOMAIN_20505
7.165
45.367
0.569
3


LTRP5
DOMAIN_9114
7.165
43.267
1.501
3


LTRP5
DOMAIN_13468
7.165
43.700
1.572
3


LTRP5
DOMAIN_11683
7.165
40.267
0.153
3


LTRP5
DOMAIN_22153
7.165
46.833
0.643
3


LTRP5
DOMAIN_25289
7.165
38.533
0.945
3


LTRP5
DOMAIN_17905
7.165
36.933
1.447
3


LTRP5
DOMAIN_221
7.165
43.433
0.751
3


LTRP5
DOMAIN_7694
7.165
52.400
0.436
3


LTRP5
DOMAIN_15507
7.165
44.067
0.907
3


LTRP5
DOMAIN_29304
7.165
51.700
1.400
3


LTRP5
DOMAIN_10123
7.165
47.833
0.666
3


LTRP5
DOMAIN_30173
7.165
53.900
0.100
3
















TABLE 58







Levels of B2M repression mediated by dXR and


LTRP constructs with various repressor domains


quantified at 14 days post-transfection.















Mean %







HLA-


Repressor
Repressor

negative
Standard
Sample


construct
domain
Spacer
cells
deviation
size















dXR
ZIM3
NT
1.768
0.862
15


LTRP5
ZIM3
NT
2.902
0.966
15


dXR
ZIM3
7.165
3.397
3.091
15


LTRP5
DOMAIN_11029
7.165
14.667
1.620
3


LTRP5
DOMAIN_4968
7.165
18.933
1.557
3


LTRP5
DOMAIN_27811
7.165
15.100
0.854
3


LTRP5
DOMAIN_5066
7.165
21.133
1.286
3


LTRP5
DOMAIN_15126
7.165
18.767
2.060
3


LTRP5
DOMAIN_17358
7.165
16.667
1.815
3


LTRP5
DOMAIN_8503
7.165
17.367
1.582
3


LTRP5
DOMAIN_11486
7.165
21.567
2.401
3


LTRP5
DOMAIN_28803
7.165
20.533
0.666
3


LTRP5
DOMAIN_17317
7.165
18.833
1.358
3


LTRP5
DOMAIN_24125
7.165
23.767
0.321
3


LTRP5
DOMAIN_8853
7.165
25.250
0.212
2


LTRP5
DOMAIN_19949
7.165
23.633
1.767
3


LTRP5
DOMAIN_737
7.165
26.767
2.589
3


LTRP5
DOMAIN_16444
7.165
25.267
0.862
3


LTRP5
DOMAIN_11386
7.165
26.800
1.868
3


LTRP5
DOMAIN_27506
7.165
26.267
1.501
3


LTRP5
DOMAIN_10331
7.165
25.733
1.286
3


LTRP5
DOMAIN_13539
7.165
28.700
2.152
3


LTRP5
DOMAIN_2380
7.165
27.533
1.858
3


LTRP5
DOMAIN_18258
7.165
21.967
0.777
3


LTRP5
DOMAIN_23723
7.165
23.333
1.501
3


LTRP5
DOMAIN_16806
7.165
26.367
2.060
3


LTRP5
DOMAIN_18216
7.165
27.667
1.358
3


LTRP5
DOMAIN_17432
7.165
29.433
0.462
3


LTRP5
DOMAIN_4806
7.165
25.500
2.272
3


LTRP5
DOMAIN_25379
7.165
29.450
2.051
2


LTRP5
DOMAIN_16643
7.165
26.333
1.890
3


LTRP5
DOMAIN_21603
7.165
31.367
4.219
3


LTRP5
DOMAIN_21247
7.165
29.467
0.651
3


LTRP5
DOMAIN_28640
7.165
28.133
1.350
3


LTRP5
ZIM3
7.165
25.287
1.914
15


LTRP5
DOMAIN_14659
7.165
28.167
2.676
3


LTRP5
DOMAIN_6248
7.165
25.433
0.115
3


LTRP5
DOMAIN_11348
7.165
29.433
2.501
3


LTRP5
DOMAIN_19229
7.165
25.367
1.656
3


LTRP5
DOMAIN_17759
7.165
29.867
1.250
3


LTRP5
DOMAIN_24663
7.165
30.500
1.323
3


LTRP5
DOMAIN_18137
7.165
28.967
0.839
3


LTRP5
DOMAIN_13331
7.165
29.333
1.701
3


LTRP5
DOMAIN_6807
7.165
28.133
0.208
3


LTRP5
DOMAIN_16688
7.165
29.667
0.153
3


LTRP5
DOMAIN_26322
7.165
30.033
8.565
3


LTRP5
DOMAIN_6802
7.165
30.900
1.670
3


LTRP5
DOMAIN_22270
7.165
26.967
2.967
3


LTRP5
DOMAIN_7255
7.165
31.500
2.536
3


LTRP5
DOMAIN_5463
7.165
24.167
1.358
3


LTRP5
DOMAIN_12631
7.165
31.967
2.108
3


LTRP5
DOMAIN_9960
7.165
31.900
1.493
3


LTRP5
DOMAIN_6445
7.165
34.533
1.484
3


LTRP5
DOMAIN_23394
7.165
25.767
0.666
3


LTRP5
DOMAIN_10948
7.165
34.267
1.750
3


LTRP5
DOMAIN_19804
7.165
32.567
2.212
3


LTRP5
DOMAIN_5290
7.165
34.967
2.810
3


LTRP5
DOMAIN_24458
7.165
30.433
1.762
3


LTRP5
DOMAIN_19896
7.165
32.200
0.954
3


LTRP5
DOMAIN_21755
7.165
27.867
3.630
3


LTRP5
DOMAIN_8790
7.165
25.033
0.058
3


LTRP5
DOMAIN_881
7.165
27.533
0.987
3


LTRP5
DOMAIN_14755
7.165
29.867
0.404
3


LTRP5
DOMAIN_20505
7.165
35.733
1.150
3


LTRP5
DOMAIN_9114
7.165
34.467
0.981
3


LTRP5
DOMAIN_13468
7.165
28.633
1.721
3


LTRP5
DOMAIN_11683
7.165
32.333
0.757
3


LTRP5
DOMAIN_22153
7.165
34.533
3.592
3


LTRP5
DOMAIN_25289
7.165
30.467
2.495
3


LTRP5
DOMAIN_17905
7.165
32.800
0.529
3


LTRP5
DOMAIN_221
7.165
33.233
1.012
3


LTRP5
DOMAIN_7694
7.165
42.367
1.531
3


LTRP5
DOMAIN_15507
7.165
34.600
2.600
3


LTRP5
DOMAIN_29304
7.165
42.067
2.948
3


LTRP5
DOMAIN_10123
7.165
39.667
2.984
3


LTRP5
DOMAIN_30173
7.165
49.167
1.266
3
















TABLE 59







Levels of B2M repression mediated by dXR and


LTRP constructs with various repressor domains


quantified at 19 days post-transfection.















Mean %







HLA-


Repressor
Repressor

negative
Standard
Sample


construct
domain
Spacer
cells
deviation
size















dXR
ZIM3
NT
7.326
4.796
15


LTRP5
ZIM3
NT
6.060
4.855
15


dXR
ZIM3
7.165
10.038
10.782
15


LTRP5
DOMAIN_11029
7.165
10.257
1.970
3


LTRP5
DOMAIN_4968
7.165
14.333
2.579
3


LTRP5
DOMAIN_27811
7.165
13.200
1.212
3


LTRP5
DOMAIN_5066
7.165
15.800
0.781
3


LTRP5
DOMAIN_15126
7.165
17.133
1.097
3


LTRP5
DOMAIN_17358
7.165
22.700
2.364
3


LTRP5
DOMAIN_8503
7.165
12.267
2.285
3


LTRP5
DOMAIN_11486
7.165
16.600
2.138
3


LTRP5
DOMAIN_28803
7.165
15.200
0.300
3


LTRP5
DOMAIN_17317
7.165
17.267
1.026
3


LTRP5
DOMAIN_24125
7.165
19.700
1.652
3


LTRP5
DOMAIN_8853
7.165
21.333
3.842
3


LTRP5
DOMAIN_19949
7.165
16.600
1.082
3


LTRP5
DOMAIN_737
7.165
19.367
1.168
3


LTRP5
DOMAIN_16444
7.165
20.433
2.026
3


LTRP5
DOMAIN_11386
7.165
19.333
0.924
3


LTRP5
DOMAIN_27506
7.165
23.300
1.970
3


LTRP5
DOMAIN_10331
7.165
22.800
2.007
3


LTRP5
DOMAIN_13539
7.165
24.267
2.150
3


LTRP5
DOMAIN_2380
7.165
25.067
3.668
3


LTRP5
DOMAIN_18258
7.165
21.467
2.344
3


LTRP5
DOMAIN_23723
7.165
20.367
3.329
3


LTRP5
DOMAIN_16806
7.165
22.267
1.656
3


LTRP5
DOMAIN_18216
7.165
22.200
2.193
3


LTRP5
DOMAIN_17432
7.165
25.967
0.404
3


LTRP5
DOMAIN_4806
7.165
20.133
2.593
3


LTRP5
DOMAIN_25379
7.165
26.400
4.583
3


LTRP5
DOMAIN_16643
7.165
24.733
2.205
3


LTRP5
DOMAIN_21603
7.165
24.500
5.186
3


LTRP5
DOMAIN_21247
7.165
23.667
1.002
3


LTRP5
DOMAIN_28640
7.165
26.767
3.880
3


LTRP5
ZIM3
7.165
22.520
3.682
15


LTRP5
DOMAIN_14659
7.165
26.067
3.386
3


LTRP5
DOMAIN_6248
7.165
26.833
4.140
3


LTRP5
DOMAIN_11348
7.165
24.400
2.476
3


LTRP5
DOMAIN_19229
7.165
23.133
1.858
3


LTRP5
DOMAIN_17759
7.165
27.667
0.902
3


LTRP5
DOMAIN_24663
7.165
26.667
5.493
3


LTRP5
DOMAIN_18137
7.165
23.967
1.206
3


LTRP5
DOMAIN_13331
7.165
23.367
1.626
3


LTRP5
DOMAIN_6807
7.165
23.700
0.265
3


LTRP5
DOMAIN_16688
7.165
26.367
1.930
3


LTRP5
DOMAIN_26322
7.165
25.367
8.700
3


LTRP5
DOMAIN_6802
7.165
45.967
33.520
3


LTRP5
DOMAIN_22270
7.165
21.133
0.709
3


LTRP5
DOMAIN_7255
7.165
30.267
2.103
3


LTRP5
DOMAIN_5463
7.165
18.033
1.893
3


LTRP5
DOMAIN_12631
7.165
29.100
2.516
3


LTRP5
DOMAIN_9960
7.165
29.067
3.134
3


LTRP5
DOMAIN_6445
7.165
31.267
2.040
3


LTRP5
DOMAIN_23394
7.165
25.267
2.957
3


LTRP5
DOMAIN_10948
7.165
29.400
1.473
3


LTRP5
DOMAIN_19804
7.165
26.400
1.442
3


LTRP5
DOMAIN_5290
7.165
29.133
1.021
3


LTRP5
DOMAIN_24458
7.165
25.600
2.500
3


LTRP5
DOMAIN_19896
7.165
28.600
1.997
3


LTRP5
DOMAIN_21755
7.165
30.233
1.185
3


LTRP5
DOMAIN_8790
7.165
20.733
0.723
3


LTRP5
DOMAIN_881
7.165
34.400
3.378
3


LTRP5
DOMAIN_14755
7.165
25.000
1.700
3


LTRP5
DOMAIN_20505
7.165
33.800
2.095
3


LTRP5
DOMAIN_9114
7.165
28.533
0.961
3


LTRP5
DOMAIN_13468
7.165
31.333
3.580
3


LTRP5
DOMAIN_11683
7.165
29.533
2.219
3


LTRP5
DOMAIN_22153
7.165
32.167
3.383
3


LTRP5
DOMAIN_25289
7.165
31.233
1.890
3


LTRP5
DOMAIN_17905
7.165
40.933
5.052
3


LTRP5
DOMAIN_221
7.165
33.933
1.662
3


LTRP5
DOMAIN_7694
7.165
38.067
2.003
3


LTRP5
DOMAIN_15507
7.165
31.633
3.609
3


LTRP5
DOMAIN_29304
7.165
36.900
4.424
3


LTRP5
DOMAIN_10123
7.165
45.250
0.212
2


LTRP5
DOMAIN_30173
7.165
42.200
1.414
2
















TABLE 60







Levels of B2M repression mediated by dXR and LTRP constructs with


various repressor domains quantified at 26 days post-transfection.












Repressor
Repressor

Mean % HLA-
Standard
Sample


construct
domain
Spacer
negative cells
deviation
size















dXR
ZIM3
NT
3.113
3.228
15


LTRP5
ZIM3
NT
4.327
3.294
15


dXR
ZIM3
7.165
6.341
4.981
15


LTRP5
DOMAIN_11029
7.165
8.727
0.401
3


LTRP5
DOMAIN_4968
7.165
9.963
0.616
3


LTRP5
DOMAIN_27811
7.165
10.480
1.753
3


LTRP5
DOMAIN_5066
7.165
11.633
1.790
3


LTRP5
DOMAIN_15126
7.165
11.897
2.133
3


LTRP5
DOMAIN_17358
7.165
12.700
2.022
3


LTRP5
DOMAIN_8503
7.165
13.000
1.480
3


LTRP5
DOMAIN_11486
7.165
13.300
2.762
3


LTRP5
DOMAIN_28803
7.165
13.433
1.626
3


LTRP5
DOMAIN_17317
7.165
14.333
2.346
3


LTRP5
DOMAIN_24125
7.165
14.967
0.961
3


LTRP5
DOMAIN_8853
7.165
15.333
1.531
3


LTRP5
DOMAIN_19949
7.165
15.600
1.082
3


LTRP5
DOMAIN_737
7.165
16.600
1.127
3


LTRP5
DOMAIN_16444
7.165
17.067
0.833
3


LTRP5
DOMAIN_11386
7.165
17.633
1.270
3


LTRP5
DOMAIN_27506
7.165
17.667
1.450
3


LTRP5
DOMAIN_10331
7.165
18.033
2.055
3


LTRP5
DOMAIN_13539
7.165
18.100
2.390
3


LTRP5
DOMAIN_2380
7.165
18.133
0.723
3


LTRP5
DOMAIN_18258
7.165
18.200
1.852
3


LTRP5
DOMAIN_23723
7.165
18.667
1.290
3


LTRP5
DOMAIN_16806
7.165
18.800
2.718
3


LTRP5
DOMAIN_18216
7.165
19.333
2.802
3


LTRP5
DOMAIN_17432
7.165
19.367
1.626
3


LTRP5
DOMAIN_4806
7.165
19.400
2.022
3


LTRP5
DOMAIN_25379
7.165
19.667
5.994
3


LTRP5
DOMAIN_16643
7.165
19.833
1.550
3


LTRP5
DOMAIN_21603
7.165
20.033
3.482
3


LTRP5
DOMAIN_21247
7.165
20.067
0.473
3


LTRP5
DOMAIN_28640
7.165
20.500
2.587
3


LTRP5
ZIM3
7.165
20.607
4.413
15


LTRP5
DOMAIN_14659
7.165
20.633
2.371
3


LTRP5
DOMAIN_6248
7.165
20.867
1.193
3


LTRP5
DOMAIN_11348
7.165
21.367
3.811
3


LTRP5
DOMAIN_19229
7.165
21.533
1.266
3


LTRP5
DOMAIN_17759
7.165
21.567
0.833
3


LTRP5
DOMAIN_24663
7.165
21.633
1.701
3


LTRP5
DOMAIN_18137
7.165
21.833
1.097
3


LTRP5
DOMAIN_13331
7.165
21.900
1.153
3


LTRP5
DOMAIN_6807
7.165
21.900
1.735
3


LTRP5
DOMAIN_16688
7.165
22.200
2.265
3


LTRP5
DOMAIN_26322
7.165
22.233
11.832
3


LTRP5
DOMAIN_6802
7.165
22.433
1.150
3


LTRP5
DOMAIN_22270
7.165
22.533
2.084
3


LTRP5
DOMAIN_7255
7.165
22.867
4.271
3


LTRP5
DOMAIN_5463
7.165
22.900
2.516
3


LTRP5
DOMAIN_12631
7.165
23.433
2.641
3


LTRP5
DOMAIN_9960
7.165
23.500
3.996
3


LTRP5
DOMAIN_6445
7.165
23.633
3.308
3


LTRP5
DOMAIN_23394
7.165
23.900
1.127
3


LTRP5
DOMAIN_10948
7.165
23.900
2.166
3


LTRP5
DOMAIN_19804
7.165
24.133
1.966
3


LTRP5
DOMAIN_5290
7.165
24.233
2.139
3


LTRP5
DOMAIN_24458
7.165
24.367
1.531
3


LTRP5
DOMAIN_19896
7.165
24.633
1.361
3


LTRP5
DOMAIN_21755
7.165
25.333
1.097
3


LTRP5
DOMAIN_8790
7.165
25.567
1.320
3


LTRP5
DOMAIN_881
7.165
26.367
0.208
3


LTRP5
DOMAIN_14755
7.165
26.867
1.563
3


LTRP5
DOMAIN_20505
7.165
27.467
3.101
3


LTRP5
DOMAIN_9114
7.165
28.100
0.872
3


LTRP5
DOMAIN_13468
7.165
28.100
2.663
3


LTRP5
DOMAIN_11683
7.165
28.300
1.300
3


LTRP5
DOMAIN_22153
7.165
28.500
3.716
3


LTRP5
DOMAIN_25289
7.165
28.600
3.579
3


LTRP5
DOMAIN_17905
7.165
30.367
0.839
3


LTRP5
DOMAIN_221
7.165
31.433
3.707
3


LTRP5
DOMAIN_7694
7.165
32.833
2.517
3


LTRP5
DOMAIN_15507
7.165
32.933
3.011
3


LTRP5
DOMAIN_29304
7.165
32.933
4.409
3


LTRP5
DOMAIN_10123
7.165
35.500
4.814
3


LTRP5
DOMAIN_30173
7.165
41.967
2.318
3
















TABLE 61







Levels of B2M repression mediated by dXR and LTRP constructs with


various repressor domains quantified at 6 days post-transfection.













Repressor

Mean % HLA-
Standard
Sample


Construct
domain
Spacer
negative cells
deviation
size















dXR
ZIM3
7.165
7.165
2.389
6


dXR
ZIM3
NT
3.625
0.408
6


LTRP5
ZIM3
NT
5.888
0.976
6


LTRP5
DOMAIN_31643
7.165
15.633
0.551
3


LTRP5
DOMAIN_19460
7.165
17.133
0.231
3


LTRP5
DOMAIN_26732
7.165
21.333
0.751
3


LTRP5
DOMAIN_18563
7.165
21.700
1.100
3


LTRP5
DOMAIN_19892
7.165
21.967
0.569
3


LTRP5
DOMAIN_21317
7.165
25.633
0.416
3


LTRP5
DOMAIN_9114
7.165
23.233
0.907
3


LTRP5
DOMAIN_10277
7.165
22.900
0.361
3


LTRP5
DOMAIN_27060
7.165
26.533
0.666
3


LTRP5
DOMAIN_12452
7.165
26.900
1.510
3


LTRP5
DOMAIN_21336
7.165
23.533
0.961
3


LTRP5
DOMAIN_30661
7.165
24.867
1.801
3


LTRP5
DOMAIN_12292
7.165
30.700
0.436
3


LTRP5
DOMAIN_8853
7.165
31.167
0.987
3


LTRP5
DOMAIN_9538
7.165
29.800
1.952
3


LTRP5
DOMAIN_19821
7.165
26.200
1.652
3


LTRP5
ZIM3
7.165
23.083
3.178
6


LTRP5
DOMAIN_26070
7.165
29.433
2.272
3


LTRP5
DOMAIN_19476
7.165
27.867
0.808
3


LTRP5
DOMAIN_4687
7.165
30.133
0.808
3


LTRP5
DOMAIN_25405
7.165
33.467
1.097
3


LTRP5
DOMAIN_10577
7.165
28.933
0.473
3


LTRP5
DOMAIN_2942
7.165
30.633
1.429
3


LTRP5
DOMAIN_27604
7.165
28.700
1.300
3


LTRP5
DOMAIN_7694
7.165
36.633
0.666
3


LTRP5
DOMAIN_29304
7.165
34.933
0.289
3


LTRP5
DOMAIN_9331
7.165
37.733
0.321
3


LTRP5
DOMAIN_30173
7.165
33.900
0.794
3


LTRP5
DOMAIN_26749
7.165
40.467
0.945
3


LTRP5
DOMAIN_27385
7.165
35.933
0.473
3


CasX 491
N/A
7.37
76.167
0.808
3
















TABLE 62







Levels of B2M repression mediated by dXR and LTRP constructs with


various repressor domains quantified at 13 days post-transfection.













Repressor

Mean % HLA-
Standard
Sample


Construct
domain
Spacer
negative cells
deviation
size















dXR
ZIM3
7.165
7.258
14.130
6


dXR
ZIM3
NT
1.218
0.144
6


LTRP5
ZIM3
NT
1.712
0.328
6


LTRP5
DOMAIN_31643
7.165
6.800
0.786
3


LTRP5
DOMAIN_19460
7.165
9.690
0.147
3


LTRP5
DOMAIN_26732
7.165
10.800
0.173
3


LTRP5
DOMAIN_18563
7.165
12.100
1.587
3


LTRP5
DOMAIN_19892
7.165
12.900
0.458
3


LTRP5
DOMAIN_21317
7.165
13.967
0.513
3


LTRP5
DOMAIN_9114
7.165
13.767
1.504
3


LTRP5
DOMAIN_10277
7.165
15.333
1.150
3


LTRP5
DOMAIN_27060
7.165
13.867
1.457
3


LTRP5
DOMAIN_12452
7.165
15.700
1.562
3


LTRP5
DOMAIN_21336
7.165
14.267
0.651
3


LTRP5
DOMAIN_30661
7.165
14.933
1.537
3


LTRP5
DOMAIN_12292
7.165
17.967
0.666
3


LTRP5
DOMAIN_8853
7.165
18.600
0.361
3


LTRP5
DOMAIN_9538
7.165
18.733
1.102
3


LTRP5
DOMAIN_19821
7.165
15.867
2.237
3


LTRP5
ZIM3
7.165
18.267
3.578
6


LTRP5
DOMAIN_26070
7.165
18.233
1.960
3


LTRP5
DOMAIN_19476
7.165
20.100
1.323
3


LTRP5
DOMAIN_4687
7.165
19.767
0.961
3


LTRP5
DOMAIN_25405
7.165
22.100
1.609
3


LTRP5
DOMAIN_10577
7.165
21.133
1.266
3


LTRP5
DOMAIN_2942
7.165
21.633
2.101
3


LTRP5
DOMAIN_27604
7.165
24.700
2.364
3


LTRP5
DOMAIN_7694
7.165
26.900
0.436
3


LTRP5
DOMAIN_29304
7.165
25.367
0.462
3


LTRP5
DOMAIN_9331
7.165
27.133
0.681
3


LTRP5
DOMAIN_30173
7.165
25.400
0.656
3


LTRP5
DOMAIN_26749
7.165
27.700
0.608
3


LTRP5
DOMAIN_27385
7.165
27.733
0.808
3


CasX 491
N/A
7.37
81.167
0.945
3
















TABLE 63







Levels of B2M repression mediated by dXR and LTRP constructs with


various repressor domains quantified at 20 days post-transfection.













Repressor

Mean % HLA-
Standard
Sample


Construct
domain
Spacer
negative cells
deviation
size















dXR
ZIM3
7.165
1.120
0.345
6


dXR
ZIM3
NT
1.425
1.093
6


LTRP5
ZIM3
NT
2.412
2.055
6


LTRP5
DOMAIN_31643
7.165
6.147
1.909
3


LTRP5
DOMAIN_19460
7.165
8.290
0.460
3


LTRP5
DOMAIN_26732
7.165
7.950
1.171
3


LTRP5
DOMAIN_18563
7.165
10.163
1.163
3


LTRP5
DOMAIN_19892
7.165
11.800
1.249
3


LTRP5
DOMAIN_21317
7.165
12.833
2.581
3


LTRP5
DOMAIN_9114
7.165
12.467
0.681
3


LTRP5
DOMAIN_10277
7.165
13.633
0.635
3


LTRP5
DOMAIN_27060
7.165
12.400
1.375
3


LTRP5
DOMAIN_12452
7.165
13.233
0.451
3


LTRP5
DOMAIN_21336
7.165
12.733
0.503
3


LTRP5
DOMAIN_30661
7.165
13.633
0.379
3


LTRP5
DOMAIN_12292
7.165
14.300
0.100
3


LTRP5
DOMAIN_8853
7.165
16.200
2.524
3


LTRP5
DOMAIN_9538
7.165
16.200
1.100
3


LTRP5
DOMAIN_19821
7.165
14.233
1.790
3


LTRP5
ZIM3
7.165
17.033
4.457
6


LTRP5
DOMAIN_26070
7.165
16.467
1.401
3


LTRP5
DOMAIN_19476
7.165
17.133
0.569
3


LTRP5
DOMAIN_4687
7.165
16.700
0.755
3


LTRP5
DOMAIN_25405
7.165
19.300
1.114
3


LTRP5
DOMAIN_10577
7.165
18.167
0.551
3


LTRP5
DOMAIN_2942
7.165
18.567
2.001
3


LTRP5
DOMAIN_27604
7.165
21.533
1.850
3


LTRP5
DOMAIN_7694
7.165
22.467
0.709
3


LTRP5
DOMAIN_29304
7.165
22.033
1.365
3


LTRP5
DOMAIN_9331
7.165
22.800
1.510
3


LTRP5
DOMAIN_30173
7.165
24.800
3.936
3


LTRP5
DOMAIN_26749
7.165
24.633
1.290
3


LTRP5
DOMAIN_27385
7.165
23.633
1.935
3


CasX 491
N/A
7.37
83.633
3.443
3
















TABLE 64







Levels of B2M repression mediated by dXR and LTRP constructs with


various repressor domains quantified at 27 days post-transfection.













Repressor

Mean % HL A-
Standard
Sample


Construct
domain
Spacer
negative cells
deviation
size















dXR
ZIM3
7.165
1.845
1.522
6


dXR
ZIM3
NT
2.463
2.385
6


LTRP5
ZIM3
NT
3.022
2.959
6


LTRP5
DOMAIN_31643
7.165
3.687
0.562
3


LTRP5
DOMAIN_19460
7.165
5.853
0.416
3


LTRP5
DOMAIN_26732
7.165
6.647
0.985
3


LTRP5
DOMAIN_18563
7.165
7.660
0.939
3


LTRP5
DOMAIN_19892
7.165
8.920
0.596
3


LTRP5
DOMAIN_21317
7.165
9.640
0.487
3


LTRP5
DOMAIN_9114
7.165
10.167
2.191
3


LTRP5
DOMAIN_10277
7.165
10.237
0.446
3


LTRP5
DOMAIN_27060
7.165
10.377
1.046
3


LTRP5
DOMAIN_12452
7.165
10.473
0.654
3


LTRP5
DOMAIN_21336
7.165
10.767
0.404
3


LTRP5
DOMAIN_30661
7.165
11.133
1.790
3


LTRP5
DOMAIN_12292
7.165
11.833
0.252
3


LTRP5
DOMAIN_8853
7.165
11.967
1.401
3


LTRP5
DOMAIN_9538
7.165
12.100
1.000
3


LTRP5
DOMAIN_19821
7.165
12.200
1.868
3


LTRP5
ZIM3
7.165
12.483
2.585
6


LTRP5
DOMAIN_26070
7.165
13.533
2.401
3


LTRP5
DOMAIN_19476
7.165
13.900
1.153
3


LTRP5
DOMAIN_4687
7.165
13.900
1.970
3


LTRP5
DOMAIN_25405
7.165
14.467
1.387
3


LTRP5
DOMAIN_10577
7.165
15.233
1.301
3


LTRP5
DOMAIN_2942
7.165
15.433
2.255
3


LTRP5
DOMAIN_27604
7.165
18.600
2.307
3


LTRP5
DOMAIN_7694
7.165
19.067
1.021
3


LTRP5
DOMAIN_29304
7.165
19.167
1.935
3


LTRP5
DOMAIN_9331
7.165
19.333
0.808
3


LTRP5
DOMAIN_30173
7.165
20.133
0.764
3


LTRP5
DOMAIN_26749
7.165
20.467
0.493
3


LTRP5
DOMAIN_27385
7.165
21.000
1.411
3


CasX 491
N/A
7.37
80.933
0.451
3









As shown in Tables 57-64, treatment with most LTRP5 constructs containing an enhanced repressor domain, paired with a gRNA containing spacer 7.165, resulted in higher levels of B2M repression in comparison to the level of repression achieved with use of an LTRP5-ZIM3 construct. The data from these experiments were used to identify the top 9 candidate repressor domains using the following criteria. First, demonstration of at least a 20% increase in mean repressive activity as measured by B2M knockdown over the mean repressive activity exhibited by the LTRP5-ZIM3 control at all four timepoints in the experiments above, which resulted in the selection of three repressor domains. To identify more candidate repressor domains, domains that exhibited at least a 20% increase in mean activity over that exhibited by the LTRP5-ZIM3 control in at least two timepoints, prioritizing later timepoints; and, third, selecting the best performing domains from each of the 75 clusters (discussed in Example 17) to maintain diversity of amino acid sequences or eliminating domains with >90% sequence identity to previously identified human repressor domains (Tycko, J. et al., High-Throughput Discovery and Characterization of Human Transcriptional Effectors Cell. 183(7):2020-2035 (2020)). The nine most effective repressor domains identified were DOMAIN7694e DOMAIN_10123, DOMAIN_15507, DOMAIN_17905, DOMAIN_20505, DOMAIN_26749, DOMAIN_27604, DOMAIN_29304, and DOMAIN_30173, and their sequences are listed in Table 65.







TABLE 65







List of top 9 and top 95 most effective repressor domains.











SEQ ID


Domain ID
Description
NO










Top 9 repressor domains









DOMAIN_7694
Columba livia repressor domain
130


DOMAIN_10123
Rattus norvegicus repressor domain
131


DOMAIN_15507
Cebus imitator repressor domain
132


DOMAIN_17905
Chimp repressor domain
133


DOMAIN_20505
Chlorocebus sabaeus repressor domain
134


DOMAIN_26749
Ophiophagus hannah repressor domain
135


DOMAIN_27604
Ailuropoda melanoleuca repressor domain
136


DOMAIN_29304
Peromyscus maniculatus bairdii repressor domain
137


DOMAIN_30173
Phyllostomus discolor repressor domain
138







Remaining repressor domains in the top 95 repressor domains









DOMAIN_737
Bonobo repressor domain
139


DOMAIN_10331
Colobus angolensis palliatus repressor domain
140


DOMAIN_10948
Colobus angolensis palliatus repressor domain
141


DOMAIN_11029
Mandrillus leucophaeus repressor domain
142


DOMAIN_17358
Bos indicus × Bos taurus repressor domain
143


DOMAIN_17759
Felis catus repressor domain
144


DOMAIN_18258
Physeter macrocephalus repressor domain
145


DOMAIN_19804
Callorhinus ursinus repressor domain
146


DOMAIN_221
Bonobo repressor domain
147


DOMAIN_881
Bonobo repressor domain
148


DOMAIN_2380
Orangutan repressor domain
149


DOMAIN_2942
Gibbon repressor domain
150


DOMAIN_4687
Marmoset repressor domain
151


DOMAIN_4806
Marmoset repressor domain
152


DOMAIN_4968
Marmoset repressor domain
153


DOMAIN_5066
Marmoset repressor domain
154


DOMAIN_5290
Owl Monkey repressor domain
155


DOMAIN_5463
Owl Monkey repressor domain
156


DOMAIN_6248
Saimiri boliviensis boliviensis repressor domain
157


DOMAIN_6445
Alligator sinensis repressor domain
158


DOMAIN_6802
Pantherophis guttatus repressor domain
159


DOMAIN_6807
Xenopus laevis repressor domain
160


DOMAIN_7255
Microcaecilia unicolor repressor domain
161


DOMAIN_8503
Mus caroli repressor domain
162


DOMAIN_8790
Marmota monax repressor domain
163


DOMAIN_8853
Mesocricetus auratus repressor domain
164


DOMAIN_9114
Peromyscus maniculatus bairdii repressor domain
165


DOMAIN_9331
Peromyscus maniculatus bairdii repressor domain
166


DOMAIN_9538
Mus musculus repressor domain
167


DOMAIN_9960
Octodon degus repressor domain
168


DOMAIN_10277
Dipodomys ordii repressor domain
169


DOMAIN_10577
Colobus angolensis palliatus repressor domain
170


DOMAIN_11348
Chlorocebus sabaeus repressor domain
171


DOMAIN_11386
Capra hircus repressor domain
172


DOMAIN_11486
Bos mutus repressor domain
173


DOMAIN_11683
Nomascus leucogenys repressor domain
174


DOMAIN_12292
Sus scrofa repressor domain
175


DOMAIN_12452
Neophocaena asiaeorientalis asiaeorientalis repressor domain
176


DOMAIN_12631
Macaca fascicularis repressor domain
177


DOMAIN_13331
Macaca fascicularis repressor domain
178


DOMAIN_13468
Phascolarctos cinereus repressor domain
179


DOMAIN_13539
Gorilla repressor domain
180


DOMAIN_14659
Acinonyx jubatus repressor domain
181


DOMAIN_14755
Cebus imitator repressor domain
182


DOMAIN_15126
Callithrix jacchus repressor domain
183


DOMAIN_16444
Acinonyx jubatus repressor domain
184


DOMAIN_16688
Lipotes vexillifer repressor domain
185


DOMAIN_16806
Sapajus apella repressor domain
186


DOMAIN_17317
Otolemur garnettii repressor domain
187


DOMAIN_17432
Otolemur garnettii repressor domain
188


DOMAIN_18137
Monodelphis domestica repressor domain
189


DOMAIN_18216
Physeter macrocephalus repressor domain
190


DOMAIN_18563
OwlMonkey repressor domain
191


DOMAIN_19229
Enhydra lutris kenyoni repressor domain
192


DOMAIN_19460
Monodelphis domestica repressor domain
193


DOMAIN_19476
OwlMonkey repressor domain
194


DOMAIN_19821
Rhinopithecus roxellana repressor domain
195


DOMAIN_19892
Ursus maritimus repressor domain
196


DOMAIN_19896
Ovis aries repressor domain
197


DOMAIN_19949
Callorhinus ursinus repressor domain
198


DOMAIN_21247
Neovison vison repressor domain
199


DOMAIN_21317
Pteropus vampyrus repressor domain
200


DOMAIN_21336
Equus caballus repressor domain
201


DOMAIN_21603
Lipotes vexillifer repressor domain
202


DOMAIN_21755
Equus caballus repressor domain
203


DOMAIN_22153
Zalophus californianus repressor domain
204


DOMAIN_22270
Bonobo repressor domain
205


DOMAIN_23394
Vicugna pacos repressor domain
206


DOMAIN_23723
Carlito syrichta repressor domain
207


DOMAIN_24125
Saimiri boliviensis boliviensis repressor domain
208


DOMAIN_24458
Lynx pardinus repressor domain
209


DOMAIN_24663
Myotis brandtii repressor domain
210


DOMAIN_25289
Ursus maritimus repressor domain
211


DOMAIN_25379
Sapajus apella repressor domain
212


DOMAIN_25405
Desmodus rotundus repressor domain
213


DOMAIN_26070
Geotrypetes seraphini repressor domain
214


DOMAIN_26322
Geotrypetes seraphini repressor domain
215


DOMAIN_26732
Meleagris gallopavo repressor domain
216


DOMAIN_27060
Gopherus agassizii repressor domain
217


DOMAIN_27385
Octodon degus repressor domain
218


DOMAIN_27506
Bos mutus repressor domain
219


DOMAIN_27811
Callithrix jacchus repressor domain
220


DOMAIN_28640
Colinus virginianus repressor domain
221


DOMAIN_28803
Monodelphis domestica repressor domain
222


DOMAIN_30661
Physeter macrocephalus repressor domain
223


DOMAIN_31643
Micrurus lemniscatus lemniscatus repressor domain
224









Accordingly, the experiments described herein demonstrate that the use of the enhanced repressor domains identified in Example 17 resulted in improved levels of transcriptional repression in the context of an LTRP construct.
Example 19: Identification of Alternative Consensus Protein Sequence Motifs of Enhanced Repressor Domains
In the previous Example 17, nine protein sequence motifs (FIGS. 57A-57I) were generated for the top 1597 enhanced repressor domains using the following methods: 1) comparing the amino acid sequences of the top 1597 repressor domains to a negative training set of 1506 repressor domains with p-values less than 0.01 and log 2(fold change) values less than 0, and 2), and comparing the amino acid sequences of the top 1597 domains to shuffled sequences derived from the 1597 sequences. In this example, five more alternative consensus protein sequence motifs were generated by comparing the amino acid sequences of the top 1597 repressors domains to a negative training set containing the amino acid sequences of human ZIM3 (SEQ ID NO: 128) and ZNF10 KRAB domains (SEQ ID NO: 129). Logos of these resulting five motifs are provided in FIGS. 58A-58E. Table 66, below, provides the unadjusted p-value and number and percentage of sequences matching the motif in the top 1597 novel repressor domains for each of the five alternative motifs, as calculated by STREME. Table 67 provides the sequences of each motif, showing the amino acid residues present at each position within the motifs (from N- to C-terminus).







TABLE 66







Characteristics of alternative consensus protein sequence motifs


of top 1597 enhanced repressor domains generated when compared


to a negative training set containing ZIM3 and ZNF10.









Alternative
Unadjusted
Number and percentage of sites matching


Motif ID
P-value
motif in 1597 enhanced domains





1
1.7E−001
1432 (89.7%)


2
2.1E−001
1236 (77.4%)


3
2.7E−001
1058 (66.2%)


4
4.2E−001
1554 (97.3%)


5
4.3E−001
 679 (42.5%)
















TABLE 67







Characteristics of alternative consensus protein sequence


motifs of 1597 enhanced repressor domains.












Position
Amino acid residues with >5%



Motif ID
in motif
representation in motif















1
1
D




2
V




3
A




4
V




5
Y




6
F




7
S




8
P




9
E




10
E




11
W




12
G




13
C




14
L



2
1
A, D, G, N, R, S




2
P, S, T




3
A, S, T




4
Q




5
K, R




6
A, D, K, N, S, T




7
L




8
Y



3
1
A, P, S




2
K




3
P




4
A, D, E




5
L, M, V




6
I, V




7
F, S, T




8
H, KL, Q, R, W



4
1
L




2
E




3
E, K, Q, R




4
E, G, R




5
A, D, E, K




6
A, D, E




7
L, P




8
C, W



5
1
D, E




2
V




3
M




4
L




5
E




6
N, T




7
Y




8
A, E, G, Q, R, S




9
H, N




10
L, M, V




11
A, L, V




12
S




13
L, V




14
A, G, V




15
C, F, L










The methods used as described in this example resulted in the generation of alternative motifs associated with the 1597 repressor domains that were identified as the strongest transcriptional repressors in Example 17. Notably, alternative motifs 1, 2, 3, and 5 were not found in either ZIM3 or ZNF10, and instead were uniquely found in the majority of the 1597 top repressor domains. Furthermore, every amino acid position of alternative motif 1 appeared to be highly conserved and was found in nearly 90% of the 1597 domains; this sequence is believed to be important in mediating the recruitment of Trim28 and downstream factors involved in transcriptional and epigenetic repression. As for the other alternative consensus motifs identified, these motifs may represent additional and novel mechanisms of repression that are specific to certain clusters of repressor domains.
Example 20: Demonstration that Silencing of a Target Locus Mediated by LTRP Molecules is Reversible Using a DNMT1 Inhibitor
Experiments were performed to demonstrate that durable repression of a target locus mediated by LTRP molecules is reversible, such that treatment with a DNMT1 inhibitor would remove methyl marks to reactivate expression of the target gene.
Materials and Methods
LTRP #5 containing the ZIM3-KRAB domain, which was generated as described in Example 13, and CasX variant 491 were used in this experiment. A B2M-targeting gRNA with scaffold 174 containing spacer 7.37 (SEQ ID NO: 3137) or a non-targeting gRNA containing spacer 0.0 (SEQ ID NO: 3232) were used in this experiment.
Transfection of HEK293T Cells:
HEK293T cells were transfected with 100 ng of a plasmid containing a construct encoding for either CasX 491 or LTRP #5 containing the ZIM3-KRAB domain with a B2M-targeting gRNA or non-targeting gRNA and cultured for 58 days. These transfected HEK293T cells were subsequently re-seeded at ˜30,000 cells well of a 96-well plate and were treated with 5-aza-2′-deoxycytidine (5-azadC), a DNMT1 inhibitor, at concentrations ranging from 0 μM to 20 μM. Six days post-treatment with 5-azadC, cells were harvested for B2M silencing analysis at day 5, day 12, and day 21 post-transfection. Briefly, repression analysis was conducted by analyzing B2M protein expression via HLA immunostaining followed by flow cytometry, as described in Example 13. Treatments for each dose of 5-azadC for each experimental condition were performed in triplicates.
Results
The plot in FIG. 59 shows the percentage of transfected HEK293T cells treated with the indicated concentrations of 5-azadC that expressed the B2M protein. The data demonstrate that 5-azadC treatment of cells transfected with a plasmid encoding LTRP5-ZIM3 with the B2M-targeting gRNA resulted in a reactivation of the B2M gene (FIG. 59). Specifically, ˜75% of treated cells exhibited B2M expression with 20 μM 5-azadC, compared to the 25% of cells with B2M expression at 0 μM concentration (FIG. 59). Furthermore, 5-azadC treatment of cells transfected with a plasmid encoding CasX 491 with the B2M-targeting gRNA did not exhibit reactivation of the B2M gene. FIG. 60 is a plot that juxtaposes B2M repression activity with gene reactivation upon 5-azadC treatment. The data show B2M repression post-transfection with either CasX 491 or LTRP5-ZIM3 with the B2M-targeting gRNA, resulting in ˜75% repression of B2M expression by day 58; however, B2M expression is increased upon 5-azadC treatment (FIG. 60). As anticipated, 5-azadC treatment of cells transfected with either CasX 491 or LTRP5-ZIM3 with the non-targeting gRNA did not demonstrate repression or reactivation (FIGS. 59-60).
The experiments demonstrate reversibility of LTRP-mediated repression of a target locus. By using a DNMT1 inhibitor to remove methyl marks implemented by LTRP molecules, the silenced target gene was reactivated to induce expression of the target protein.
Example 21: Exemplary Sequences of LTRP Fusion Proteins
Table 68 provides exemplary full-length LTRP fusion proteins in configurations 1, 4, or 5 with the ADD domain (FIG. 2), with human ZIM3 or ZNF10 KRAB domains or one of the top nine most effective repressor domains: DOMAIN-7694 DOMAIN_10123, DOMAIN_15507, DOMAIN_17905, DOMAIN_20505, DOMAIN_26749, DOMAIN_27604, DOMAIN-29304, and DOMAIN_30173. In Table 68, the components are listed in order from N- to C-terminus.







TABLE 68







Exemplary protein sequences of LTRP fusion proteins













Amino acid





sequence


LTRP #
Components
Domains
SEQ ID NO













LTRP1 with
START codon + NLS +

3269


ADD domain
buffer sequence



START codon + DNMT3A

3270



ADD domain



DNMT3A catalytic domain

126



Linker (L2)

122



DNMT3L interaction domain

127



Linker (L1)

123



Linker (L3A) + buffer

3271



dCasX491

4



Buffer + linker (L3B)

3272



Repressor domain 1
Human ZIM3
3240




Human ZNF10
3239




Columba livia repressor
130




domain (DOMAIN_7694)




Rattus norvegicus repressor
131




domain (DOMAIN_10123)




Cebus imitator repressor
132




domain (DOMAIN_15507)




Chimpanzee repressor
133




domain (DOMAIN_17905)




Chlorocebus sabaeus
134




repressor domain




(DOMAIN_20505)




Ophiophagus hannah
135




repressor domain




(DOMAIN_26749)




Ailuropoda melanoleuca
136




repressor domain




(DOMAIN_27604)




Peromyscus maniculatus
137




bairdii repressor domain




(DOMAIN_29304)




Phyllostomus discolor
138




repressor domain




(DOMAIN_30173)



Buffer + NLS

3273


LTRP4 with
START codon + NLS +

3269


ADD domain
buffer sequence



Repressor domain 1
Human ZIM3
3240




Human ZNF10
3239




Columba livia repressor
130




domain (DOMAIN_7694)




Rattus norvegicus repressor
131




domain (DOMAIN_10123)




Cebus imitator repressor
132




domain (DOMAIN_15507)




Chimpanzee repressor
133




domain (DOMAIN_17905)




Chlorocebus sabaeus
134




repressor domain




(DOMAIN_20505)




Ophiophagus hannah
135




repressor domain




(DOMAIN_26749)




Ailuropoda melanoleuca
136




repressor domain




(DOMAIN_27604)




Peromyscus maniculatus
137




bairdii repressor domain




(DOMAIN_29304)




Phyllostomus discolor
138




repressor domain




(DOMAIN_30173)



Linker (L3A) + buffer

3271



START codon + DNMT3A

3270



ADD domain



DNMT3A catalytic domain

126



Linker (L2)

122



DNMT3L interaction domain

127



Linker (L1)

123



dCasX491

4



Buffer + linker (L3B)

3272



NLS

30


LTRP5 with
START codon + NLS +

3269


ADD domain
buffer sequence



START codon + DNMT3A

3270



ADD domain



DNMT3A catalytic domain

126



Linker (L2)

122



DNMT3L interaction domain

127



Linker (L3A)

124



Repressor domain 1
Human ZIM3
3240




Human ZNF10
3239




Columba livia repressor
130




domain (DOMAIN_7694)




Rattus norvegicus repressor
131




domain (DOMAIN_10123)




Cebus imitator repressor
132




domain (DOMAIN_15507)




Chimpanzee repressor
133




domain (DOMAIN_17905)




Chlorocebus sabaeus
134




repressor domain




(DOMAIN_20505)




Ophiophagus hannah
135




repressor domain




(DOMAIN_26749)




Ailuropoda melanoleuca
136




repressor domain




(DOMAIN_27604)




Peromyscus maniculatus
137




bairdii repressor domain




(DOMAIN_29304)




Phyllostomus discolor
138




repressor domain




(DOMAIN_30173)



Linker (L1)

123



dCasX491

4



Buffer + linker (L3B)

3272



NLS

30









Table 69 provides exemplary amino acid sequences of components of LTRP constructs. In Table 69, the protein domains are shown without starting methionines.







TABLE 69







Exemplary protein sequences of components of LTRP constructs.











Amino acid sequence



Component
SEQ ID NO














DNMT3A catalytic domain (CD)
126



DNMT3L interaction domain
127



dCasX491
4



Linker 1 (L1)
123



Linker 2 (L2)
122



Linker 3A (L3A)
124



Linker 3B (L3B)
120



NLS
30



DNMT3A ADD domain
125










Example 22: a Preliminary Evaluation of Genome-Wide Transcriptomic Effects of Using an LTRP Molecule and a PCSK9-Targeting gRNA to Repress the PCSK9 Locus to Decrease PCSK9 Secretion In Vitro
Experiments were performed to determine the effects of using an LTRP molecule with a targeting gRNA to repress the PCSK9 locus and reduce PCSK9 secretion levels in human cells. Specifically, genome-wide transcriptomic effects were evaluated to determine the extent of off-target effects of treating the cells with LTRP5-ADD-ZIM3 and select PCSK9-targeting spacers.
Materials and Methods
Transfection of Human Huh7 Cells:
mRNA encoding the following molecules were generated by IVT using similar methods as described in Example 2: 1) a catalytically-active CasX 676 (as described in Example 5), 2) dXR1 (as described in Example 2), and 3) LTRP5-ADD-ZIM3 (as described in Example 2). The DNA and mRNA sequences for CasX 676 are shown in Tables 21 and 22; the DNA and mRNA sequences for dXR1 are shown in Tables 11 and 12; the DNA and mRNA sequences for LTRP5-ADD-ZIM3 are shown in Tables 18 and 19.
gRNAs containing select NHP-conserved spacers targeting the PCSK9 locus were designed using gRNA scaffold 316 and chemically synthesized with the v1 modification profile (as described in Example 7). These NHP-conserved spacers, which were selected given their efficacy in sustaining PCSK9 repression through at least day 36 as demonstrated in Example 3, were TG-06-154, TG-06-167, TG-06-133, TG-06-146, and TG-06-352, TG-06-138 (see Table 17 for SEQ ID NOS) was used to pair with dXR1 as well as LTRP5-ADD-ZIM3, and spacer TG-06-001 (also known as spacer 6.1; SEQ ID NO: 1834) was used to pair with CasX 676. A non-targeting spacer was used as an experimental control.
Seeded Huh7 cells were transfected with mRNA encoding a catalytically-active CasX 676, dXR1, or LTRP5-ADD-ZIM3 and a gRNA with scaffold 316 and a spacer targeting the PCSK9 locus. Cells were harvested at 6 and 26 days post-transfection and subsequently lysed and stored in DNA/RNA Shield (Zymo Research). As an additional control, untreated, naïve cells were also harvested. The collected samples were subjected to gDNA/RNA extraction using the Quick-DNA/RNA Miniprep Plus kit (Zymo Research). RNA samples were used for total RNA sequencing (RNA-seq), which was performed by a third-party. Raw FASTQ files were received and processed with FASTQC, and adapters were trimmed using Trim Galore. Transcript expression was then quantified against the hg38 genome using Salmon to generate normalized counts for each gene (transcripts per million, or TPM). Differential expression analysis was performed using DESeq2. Genes with fewer than 10 counts in all samples were omitted from analysis, and all pairwise comparisons (e.g., differential gene expression analyses between untreated and treated conditions at the two individual timepoints) were done with significance thresholds of |log 2FC|>2 and adjusted p-value<0.001.
Results
Huh7 cells were transfected with mRNA encoding CasX 676, dXR1 or LTRP5-ADD-ZIM3 with a PCSK9-targeting gRNA and harvested at the 6 and 26 days post-transfection for RNA-seq analysis. Quantification of normalized PCSK9 read counts was determined for each experimental condition, and log 2 fold changes in normalized PCSK9 transcript counts comparing each experimental condition and the untreated, naïve condition were calculated (Table 70). RNA-seq analyses revealed that use of spacers TG-06-154, TG-06-167, and TG-06-133, when paired with LTRP5-ADD-ZIM3, durably repress PCSK9 expression through day 26 (Table 70). Furthermore, while use of the non-targeting spacer with LTRP5-ADD-ZIM3 appeared to reduce PCSK9 expression, this level of repression was not as high compared to the repression levels achieved with spacers TG-06-154, TG-06-167, and TG-06-133. As anticipated, use of spacer TG-06-138 with dXR1 resulted in transient silencing of the PCSK9 locus, although unexpectedly, PCSK9 downregulation was attenuated by day 26 when using spacer 6.1 paired with CasX 676 (Table 70).







TABLE 70







Log2FC of normalized PCSK9 read counts for each indicated experimental


condition compared to untreated, naive condition.












Log2FC of PCSK9 read
Log2FC of PCSK9 read


Molecule
Spacer
counts - Day 6
counts - Day 26













CasX 676
NT
0.022
−0.001


CasX 676
6.1
−1.826
−0.818


dXR1
NT
0.016
0.068


dXR1
TG-06-138
−4.291
−0.266


LTRP5-ADD-ZIM3
NT
−0.700
−1.094


LTRP5-ADD-ZIM3
TG-06-138
−4.254
−1.861


LTRP5-ADD-ZIM3
TG-06-154
−5.202
−4.283


LTRP5-ADD-ZIM3
TG-06-167
−3.404
−2.856


LTRP5-ADD-ZIM3
TG-06-133
−3.342
−2.773


LTRP5-ADD-ZIM3
TG-06-146
−3.709
−1.755


LTRP5-ADD-ZIM3
TG-06-352
−3.330
−1.981









Differential gene expression analyses were performed by comparing each experimental condition to the untreated, naïve control to determine the number of upregulated and downregulated genes detected at 6 days and 26 days after treatment. Quantification of differentially expressed genes is shown in Table 71. Representative volcano plots illustrating the differential gene expression analyses for LTRP5-ADD-ZIM3 with the non-targeting spacer, LTRP5-ADD-ZIM3 with spacer TG-06-154, and LTRP5-ADD-ZIM3 with spacer TG-06-133 are shown in FIGS. 65A-65B, 66A-66B, and 67A-67B respectively. TG-06-154, TG-06-133, and TG-06-167 were selected based on their ability to repress PCSK9 expression through day 26. The data demonstrate that of these three PCSK9-targeting spacers, when assessed with LTRP5-ADD-ZIM3, use of spacer TG-06-133 resulted in the lowest number of differentially regulated off-target genes. Meanwhile, use of spacer TG-06-154 or TG-06-167 resulted in a higher number of differentially regulated off-target genes, especially at the later timepoint of 26 days post-transfection (Table 71). Furthermore, transient repression using dXR1 and spacer TG-06-138 resulted in minimal transcriptomic changes by day 26.







TABLE 71







Number of differentially regulated off-target genes for each treatment condition


compared to untreated, naive control at the two indicated timepoints. Statistical


significance thresholds applied were |log2FC| > 2 and adjusted p-value <0.001.










# of differentially expressed
# of differentially expressed



genes (off-target) - Day 6
genes (off-target) - Day 26












Molecule
Spacer
Downregulated
Upregulated
Downregulated
Upregulated















CasX 676
NT
0
0
0
0


CasX 676
6.1
0
0
0
0


dXR1
NT
0
0
0
0


dXR1
TG-06-138
3
14
0
1


LTRP5-ADD-
NT
0
0
9
35


ZIM3


LTRP5-ADD-
TG-06-138
2
0
0
0


ZIM3


LTRP5-ADD-
TG-06-154
2
0
6
10


ZIM3


LTRP5-ADD-
TG-06-167
2
0
18
21


ZIM3


LTRP5-ADD-
TG-06-133
2
0
0
0


ZIM3


LTRP5-ADD-
TG-06-146
1
7
0
0


ZIM3


LTRP5-ADD-
TG-06-352
2
1
0
0


ZIM3









These experiments show a preliminary analysis of the genome-wide transcriptomic effects of using an LTRP molecule and a PCSK9-targeting gRNA to repress the PCSK9 locus in human cells. The data from these experiments show that analyzing these genome-wide transcriptomic effects would help with the identification of candidate spacers for targeting the PCSK9 locus.
Example 23: Assessment of PCSK9 Spacers in Achieving in Human Hepatocyte Cells when Paired with an LTRP5-ADD Molecule
Experiments were performed to carry out a comprehensive evaluation of PCSK9-targeting spacers, with the TTC recognition motif, when paired with an LTRP molecule in configuration #5 containing the ADD domain (LTRP5; diagrammed in FIG. 2). Briefly, in vitro experiments were conducted to assess spacers that induce durable repression of the human PCSK9 locus, resulting in substantial reduction in PCSK9 secretion.
Materials and Methods
A computational screen was performed as described in Example 3 that resulted in the identification of 69 TTC spacers for subsequent experimental assessment. Of these 69 TTC spacers, 61 spacers were subjected to further in vitro screening using a cell-based assay as described in the ensuing methods. In addition to the 61 spacers, four more spacers were identified in an independent computational screen using methods similar to those described in Example 3, with the addition of one criterion: i.e., TTC spacers that overlapped with a SNP having a minor allele frequency (MAF) of >0.05 were excluded. Therefore, a total of 65 spacers were subjected to an in vitro experiment using a cell-based assay described in the methods that follow. The 61 out of 65 PCSK9-targeting spacers tested in this experiment are listed in Table 72, with the corresponding SEQ ID NOS listed in Table 17. The four additional spacers that were independently identified are shown in Table 73.







TABLE 72







List of 61 out of 65 PCSK9-targeting


spacers assessed in this example.









Spacer ID
Spacer ID
Spacer ID





TG-06-342
TG-06-142
TG-06-002


TG-06-117
TG-06-144
TG-06-343


TG-06-118
TG-06-143
TG-06-167


TG-06-119
TG-06-146
TG-06-168


TG-06-120
TG-06-145
TG-06-169


TG-06-122
TG-06-147
TG-06-170


TG-06-123
TG-06-149
TG-06-344


TG-06-121
TG-06-150
TG-06-345


TG-06-124
TG-06-151
TG-06-346


TG-06-125
TG-06-152
TG-06-347


TG-06-127
TG-06-153
TG-06-348


TG-06-128
TG-06-154
TG-06-171


TG-06-131
TG-06-155
TG-06-349


TG-06-132
TG-06-157
TG-06-249


TG-06-135
TG-06-159
TG-06-250


TG-06-133
TG-06-158
TG-06-251


TG-06-134
TG-06-160
TG-06-350


TG-06-138
TG-06-161
TG-06-351


TG-06-139
TG-06-004
TG-06-172


TG-06-140
TG-06-001


TG-06-141
TG-06-005
















TABLE 73







RNA sequences of the four additional TTC spacers


targeting the human PCSK9 locus.









Spacer ID
Spacer RNA sequence
SEQ ID NO:





TG-06-126
CCUUUUCAUCCUCCUGCCUG
2672


 


TG-06-129
UUUUACACACCAUGUUCAAG
2675


 


TG-06-148
GCCGGGCCCACCUUUUCAGU
2694


 


TG-06-1046
UCUCUUACAUGGGGGGAAAC
2714









Assessment of PCSK9 Secretion Levels for the 65 PCSK9-Targeting Spacers:

mRNA encoding the LTRP5-ADD-ZIM3 molecule was generated by IVT using methods similar to those described in Example 2. The DNA and mRNA sequences for LTRP5-ADD-ZIM3 are shown in Tables 18 and 19.
gRNAs containing each of the 65 PCSK9-targeting spacers (Tables 72-73) were designed using gRNA scaffold 316 and chemically synthesized with the v1modification profile (as described in Example 7). Furthermore, a non-targeting gRNA was used as non-targeting control.
To assess PCSK9 secretion, seeded Huh7 cells were co-transfected with mRNA encoding for LTRP5-ADD-ZIM3 and a gRNA with scaffold 316 and spacer targeting the PCSK9 locus using Lipofectamine™ 3000. Two doses of total RNA input at a 2:1 mass ratio of mRNA to gRNA were used for screening: 50 ng mRNA:25 ng gRNA and 25 ng mRNA:12.5 ng gRNA. Media supernatant was harvested at 6 days post-transfection to assess level of PCSK9 secretion by ELISA (Table 74). Levels of PCSK9 secretion were normalized to total cell count. As an additional control, PCSK9 secretion was also measured in the media supernatant harvested from cells transfected with mRNA encoding for mScarlet.
Media supernatant is further sampled at 13, 20, and 27 days post-transfection, and levels of PCSK9 secretion are measured by ELISA as described above.
Results
PCSK9 secretion levels for Huh7 cells transfected with mRNA encoding LTRP5-ADD-ZIM3 with a PCSK9-targeting gRNA at the 6-day timepoint are shown in Table 74. Specifically, Table 74 provides the level of secreted PCSK9 (ng/mL) in cells transfected with gRNAs with each of the spacers, the percent reduction in PCSK9 secretion relative to the control transfected with a non-targeting gRNA, and the distance in basepairs of each targeting sequence to the PCSK9 transcription start site (TSS). The average percent reduction in PCSK9 secretion with each dose for each spacer is also provided, and spacers in constructs that resulted in greater than 50% reduction in PCSK9 secretion averaged from the two doses are bolded in the table.







TABLE 74







Results of ELISA assay evaluating the functional effects of 65 PCSK9-targeting


spacers on PCSK9 secretion levels when paired with LTRP5-ADD-ZIM3*











50 ng mRNA:25 ng gRNA
25 ng mRNA:12.5 ng gRNA
Average
















Percent

Percent
percent



Distance
Secreted
reduction
Secreted
reduction
reduction



to TSS
PCSK9
in PCSK9
PCSK9
in PCSK9
in PCSK9


Spacer ID
(bp)
(ng/mL)
secretion
(ng/mL)
secretion
secretion
















TG-06-342
−1086
51.55
37.34
75.23
5.6
15.87


TG-06-117
−917
68.98
16.16
98.05
37.62
10.73


TG-06-118
−860
35.5
56.86
54.78
23.11
39.99


TG-06-119
−858
70.37
14.47
84.54
18.66
2.1


TG-06-120
−843
21.43
73.95
47.97
32.67
53.31


TG-06-122
−800
79.36
3.54
86.06
20.79
8.63


TG-06-123
−789
30.49
62.95
51.32
27.97
45.46


TG-06-121
−787
28.33
65.57
37.13
47.89
56.73


TG-06-124
−786
16.54
79.9
30.59
57.06
68.48


TG-06-125
−767
24.93
69.7
46.11
35.28
52.49


TG-06-126
−707
23.48
71.46
44.82
37.09
54.27


TG-06-127
−699
22.57
72.56
49.1
31.08
51.82


TG-06-128
−664
42.21
48.7
62.29
12.57
30.63


TG-06-129
−646
59.93
27.16
90.82
27.47
0.16


TG-06-131
−644
28.4
65.48
57.89
18.74
42.11


TG-06-132
−621
56.68
31.11
75.01
5.29
12.91


TG-06-135
−601
25.66
68.82
44.59
37.42
53.12


TG-06-133
−596
29.45
64.21
42.13
40.86
52.53


TG-06-134
−589
43.79
46.77
57.45
19.37
33.07


TG-06-138
−527
18.99
76.92
30.87
56.67
66.79


TG-06-139
−463
15.03
81.73
25.45
64.28
73.01


TG-06-140
−408
61.68
25.04
59.94
15.87
20.45


TG-06-141
−383
13.86
83.16
12.58
82.34
82.75


TG-06-142
−379
30.87
62.48
27.27
61.73
62.1


TG-06-144
−351
23.42
71.53
29
59.29
65.41


TG-06-143
−337
38.69
52.97
22.33
68.66
60.81


TG-06-146
−316
40.84
50.36
20.34
71.45
60.9


TG-06-145
−299
15.8
80.8
18.54
73.98
77.39


TG-06-147
−291
53.6
34.85
37.43
47.46
41.15


TG-06-148
−273
71.46
13.15
44.77
37.16
25.15


TG-06-149
−177
21.18
74.26
38.33
46.21
60.23


TG-06-150
−148
18.33
77.73
39.59
44.42
61.08


TG-06-151
−145
53.44
35.05
66.42
6.77
20.91


TG-06-152
−126
36.95
55.09
57.43
19.39
37.24


TG-06-153
−76
73.23
10.99
86.58
21.52
5.27


TG-06-154
−13
6.87
91.65
24.48
65.64
78.64


TG-06-155
18
29.45
64.21
56.36
20.89
42.55


TG-06-157
70
12.32
85.03
32.4
54.53
69.78


TG-06-159
169
53.15
35.4
80.84
13.47
10.97


TG-06-158
175
9.39
88.59
31.72
55.48
72.03


TG-06-160
182
20.63
74.93
48.67
31.69
53.31


TG-06-161
204
29.55
64.08
53.16
25.38
44.73


TG-06-004
448
54.83
33.35
73.05
2.54
15.41


TG-06-001
451
18.21
77.86
32.86
53.88
65.87


TG-06-005
464
67.08
18.47
76.37
7.19
5.64


TG-06-002
503
81.95
0.4
83.15
16.71
8.16


TG-06-1046
592
78.9
4.1
76.27
7.05
1.48


TG-06-343
598
62.8
23.67
75.55
6.04
8.82


TG-06-167
751
39.55
51.93
66.61
6.51
29.22


TG-06-168
768
19.1
76.78
50.96
28.47
52.62


TG-06-169
781
66.39
19.3
62.55
12.2
15.75


TG-06-170
786
64.19
21.98
72.96
2.41
9.79


TG-06-344
851
82.29
0.01
76.43
7.28
3.64


TG-06-345
859
81.22
1.28
85.68
20.26
9.49


TG-06-346
861
77.02
6.39
81.63
14.58
4.09


TG-06-347
869
26.55
67.73
51.83
27.24
47.49


TG-06-348
878
23.14
71.88
35.55
50.1
60.99


TG-06-171
889
52.41
36.3
55.95
21.46
28.88


TG-06-349
908
91.34
11.02
87.55
22.89
16.95


TG-06-249
949
87.36
6.18
82.36
15.61
10.89


TG-06-250
959
86.92
5.64
80.42
12.87
9.26


TG-06-251
985
36.8
55.28
44.62
37.37
46.32


TG-06-350
1063
71.25
13.4
67.87
4.74
9.07


TG-06-351
1074
56.34
31.52
62.93
11.67
21.6


TG-06-172
1097
44.44
45.99
59.31
16.75
31.37


Non-
—
82.28
0
71.24
0
0


targeting


mScarlet
—
84.85
3.12
—
—
—


mRNA





*Data are shown rounded to the nearest hundredth.






The data presented in Table 74 demonstrate that constructs with most of the tested spacers produced decreased levels of secreted PCSK9 at 6 days post-transfection. The spacers were complementary to the PCSK9 locus in a region ranging from 1086 basepairs upstream to 1097 basepairs downstream of the TSS, and effective spacers were found throughout the tested region, with many of the most effective spacers clustering between the TSS and approximately 500 basepairs upstream of the TSS.
The construct with the TG-06-141 spacer was the most effective overall at the 6-day timepoint, with an 82.75% average reduction in secreted PCSK9 levels. Constructs with spacers TG-06-154, TG-06-145, TG-06-139, TG-06-158, TG-06-157, TG-06-124, TG-06-138, TG-06-001 and TG-06-144 were also highly effective, with each producing greater than a 65% average reduction in secreted PCSK9 levels.
13, 20, and 27 days post-transfection timepoints are further assessed in order to identify spacers that support PCSK9 repression and a reduction of secreted PCSK9 levels over longer time periods.
These results demonstrate that delivery of mRNA encoding an LTRP molecule with the ADD domain with the appropriate targeting gRNA can result in repression of the PCSK9 locus to reduce PCSK9 secretion in a cell-based assay.
Example 24: Additional Assessment of the Effects of Using CpG-Reduced or Depleted gRNA Scaffolds on CasX-Mediated Editing Activity
As discussed in Example 12, above, unmethylated CpG motifs act as PAMPs that potently trigger undesired immune activation. Therefore, nucleotide substitutions to replace native CpG motifs in the AAV constructs, including constructs encoding for guide scaffold variants 235 and 316, were designed and generated. Here, experiments were performed to evaluate further the effects of using these resulting CpG-reduced or depleted gRNA scaffolds on CasX-mediated editing activity.
Materials and Methods
The CpG-reduced or depleted scaffolds 320-341 were evaluated in three in vitro experiments described below; the sequences of scaffolds 320-341 are listed in Table 42. In addition, two newly engineered gRNA scaffolds, scaffold 382 and 392 (sequences listed in Table 75), were also assessed. As benchmark comparisons, scaffolds 174, 235, and 316 (sequences listed in Table 9 and Table 75) were also included for evaluation.







TABLE 75







Sequences of additional gRNA scaffolds tested in this example













DNA

RNA


Scaffold

SEQ ID

SEQ ID


ID
DNA sequence
NO:
RNA sequence
NO:





Scaffold
ACTGGCGCTTCTATCTGATTACTCT
3448
ACUGGCGCUUCUAUCUGAUUACUCU
3451


382
GAGCCGCCATCACCAGCGACTATGT

GAGCCGCCAUCACCAGCGACUAUGU




CGTAGTGGGTAAAGCTCCCTCTTCG

CGUAGUGGGUAAAGCUCCCUCUUCG




GAGGGAGCATCAGAG

GAGGGAGCAUCAGAG



 


Scaffold
ACTGGGCCTTCTATCTGATTACTCT
3449
ACUGGGCCUUCUAUCUGAUUACUCU
3452


392
GAGGCCCATCACCAGCGACTATGTC

GAGGCCCAUCACCAGCGACUAUGUC




GTAGTGGGTAAAGCCGCTTACGGAC

GUAGUGGGUAAAGCCGCUUACGGAC




TTCGGTCCGTAAGAGGCATCAGAG

UUCGGUCCGUAAGAGGCAUCAGAG



 


Scaffold
ACTGGCGCTTTTATCTGATTACTTT
3450
ACUGGCGCUUUUAUCUGAUUACUUU
1744


174
GAGAGCCATCACCAGCGACTATGTC

GAGAGCCAUCACCAGCGACUAUGUC




GTAGTGGGTAAAGCTCCCTCTTCGG

GUAGUGGGUAAAGCUCCCUCUUCGG




AGGGAGCATCAAAG

AGGGAGCAUCAAAG









AAV constructs were designed and generated as previously described in Example 12. The CpG-reduced or depleted gRNA scaffolds were tested in two different AAV backbones. Specifically, for the experiment involving lipofection of HEK293 cells as described below, scaffolds 235 and 320-341 were tested in AAV vectors that were CpG-depleted, with the exception of AAV2 ITRs, as previously described in Example 12. Briefly, the CpG-depleted AAV backbone construct encoded for CpG-depleted versions of the following elements: U1A promoter, CasX 491, bGH poly(A) signal sequence, and U6 promoter. For the experiment involving AAV transduction of human induced neurons (iNs) and HEK293 cells as described below, scaffolds 174, 235, 316, 320-341, 382, and 392 (see Tables 9, 42 and 75 for sequences) were tested in an AAV backbone that was not CpG-depleted (see Table 76 for sequences). Furthermore, spacer 7.37 targeting the B2M locus was used in two experiments described below involving HEK293 cells: lipofection and AAV transduction. Spacer 31.63 targeting the AAVS1 locus was used in an experiment described below involving human iNs. Table 77 below lists the AAV constructs that were tested in the context of a non-CpG-depleted AAV vector and the experimental conditions in which these constructs were assessed.







TABLE 76







Sequences encoding for a base AAV plasmid into which gRNA scaffolds in Table 75


were cloned









Component Name
DNA sequence
SEQ ID NO





5′ ITR
CCTGCAGGCAGCTGCGCGCTCGCTCGCTCACTGAGGCCGCCCG
3233



GGCGTCGGGCGACCTTTGGTCGCCCGGCCTCAGTGAGCGAGCG




AGCGCGCAGAGAGGGAGTGGCCAACTCCATCACTAGGGGTTCC




T



 


buffer sequence
GCGGCCTCTAGACTCGAGGCGTT
3453


 


U1A promoter
AATGGAGGCGGTACTATGTAGATGAGAATTCAGGAGCAAACTG
3454



GGAAAAGCAACTGCTTCCAAATATTTGTGATTTTTACAGTGTA




GTTTTGGAAAAACTCTTAGCCTACCAATTCTTCTAAGTGTTTT




AAAATGTGGGAGCCAGTACACATGAAGTTATAGAGTGTTTTAA




TGAGGCTTAAATATTTACCGTAACTATGAAATGCTACGCATAT




CATGCTGTTCAGGCTCCGTGGCCACGCAACTCATACT



 


buffer sequence
CTCTGGCTAACTACCGGT
3455


 


Kozak
GCCACC
N.D.


 


start codon + c-
ATGGCCCCAGCGGCCAAACGGGTGAAGCTGGAC
3456


MYC NLS




 


linker
TCTAGA
N.D.


 


CasX 515
CAAGAGATCAAGAGAATCAACAAGATCAGAAGGAGACTGGTCA
3457



AGGACAGCAACACAAAGAAGGCCGGCAAGACAGGCCCCATGAA




AACCCTGCTCGTCAGAGTGATGACCCCTGACCTGAGAGAGCGG




CTGGAAAACCTGAGAAAGAAGCCCGAGAACATCCCTCAGCCTA




TCAGCAACACCAGCAGGGCCAACCTGAACAAGCTGCTGACCGA




CTACACCGAGATGAAGAAAGCCATCCTGCACGTGTACTGGGAA




GAGTTCCAGAAAGACCCCGTGGGCCTGATGAGCAGAGTTGCTC




AGCCTGCCAGCAAGAAGATCGACCAGAACAAGCTGAAGCCCGA




GATGGACGAGAAGGGCAATCTGACCACAGCCGGCTTTGCCTGC




TCTCAGTGTGGCCAGCCTCTGTTCGTGTACAAGCTGGAACAGG




TGTCCGAGAAAGGCAAGGCCTACACCAACTACTTCGGCAGATG




TAACGTGGCCGAGCACGAGAAGCTGATTCTGCTGGCCCAGCTG




AAACCTGAGAAGGACTCTGATGAGGCCGTGACCTACAGCCTGG




GCAAGTTTGGACAGAGAGCCCTGGACTTCTACAGCATCCACGT




GACCAAAGAAAGCACACACCCCGTGAAGCCCCTGGCTCAGATC




GCCGGCAATAGATACGCCTCTGGACCTGTGGGCAAAGCCCTGT




CCGATGCCTGCATGGGAACAATCGCCAGCTTCCTGAGCAAGTA




CCAGGACATCATCATCGAGCACCAGAAGGTGGTCAAGGGCAAC




CAGAAGAGACTGGAAAGCCTGAGGGAGCTGGCCGGCAAAGAGA




ACCTGGAATACCCCAGCGTGACCCTGCCTCCTCAGCCTCACAC




AAAAGAAGGCGTGGACGCCTACAACGAAGTGATCGCCAGAGTG




AGAATGTGGGTCAACCTGAACCTGTGGCAGAAGCTGAAACTGT




CCAGGGACGACGCCAAGCCTCTGCTGAGACTGAAGGGCTTCCC




TAGCTTCCCTCTGGTGGAAAGACAGGCCAATGAAGTGGATTGG




TGGGACATGGTCTGCAACGTGAAGAAGCTGATCAACGAGAAGA




AAGAGGATGGCAAGGTTTTCTGGCAGAACCTGGCCGGCTACAA




GAGACAAGAAGCCCTGAGGCCTTACCTGAGCAGCGAAGAGGAC




CGGAAGAAGGGCAAGAAGTTCGCCAGATACCAGCTGGGCGACC




TGCTGCTGCACCTGGAAAAGAAGCACGGCGAGGACTGGGGCAA




AGTGTACGATGAGGCCTGGGAGAGAATCGACAAGAAGGTGGAA




GGCCTGAGCAAGCACATTAAGCTGGAAGAGGAAAGAAGGAGCG




AGGACGCCCAATCTAAAGCCGCTCTGACCGATTGGCTGAGAGC




CAAGGCCAGCTTTGTGATCGAGGGCCTGAAAGAGGCCGACAAG




GACGAGTTCTGCAGATGCGAGCTGAAGCTGCAGAAGTGGTACG




GCGATCTGAGAGGCAAGCCCTTCGCCATTGAGGCCGAGAACAG




CATCCTGGACATCAGCGGCTTCAGCAAGCAGTACAACTGCGCC




TTCATTTGGCAGAAAGACGGCGTCAAGAAACTGAACCTGTACC




TGATCATCAATTACTTCAAAGGCGGCAAGCTGCGGTTCAAGAA




GATCAAACCCGAGGCCTTCGAGGCTAACAGATTCTACACCGTG




ATCAACAAAAAGTCCGGCGAGATCGTGCCCATGGAAGTGAACT




TCAACTTCGACGACCCCAACCTGATTATCCTGCCTCTGGCCTT




CGGCAAGAGACAGGGCAGAGAGTTCATCTGGAACGATCTGCTG




AGCCTGGAAACCGGCTCTCTGAAGCTGGCCAATGGCAGAGTGA




TCGAGAAAACCCTGTACAACAGGAGAACCAGACAGGACGAGCC




TGCTCTGTTTGTGGCCCTGACCTTCGAGAGAAGAGAGGTGCTG




GACAGCAGCAACATCAAGCCCATGAACCTGATCGGCGTGGACC




GGGGCGAGAATATCCCTGCTGTGATCGCCCTGACAGACCCTGA




AGGATGCCCACTGAGCAGATTCAAGGACTCCCTGGGCAACCCT




ACACACATCCTGAGAATCGGCGAGAGCTACAAAGAGAAGCAGA




GGACAATCCAGGCCAAGAAAGAGGTGGAACAGAGAAGAGCCGG




CGGATACTCTAGGAAGTACGCCAGCAAGGCCAAGAATCTGGCC




GACGACATGGTCCGAAACACCGCCAGAGATCTGCTGTACTACG




CCGTGACACAGGACGCCATGCTGATCTTCGAGAATCTGAGCAG




AGGCTTCGGCCGGCAGGGCAAGAGAACCTTTATGGCCGAGAGG




CAGTACACCAGAATGGAAGATTGGCTCACAGCTAAACTGGCCT




ACGAGGGACTGCCCAGCAAGACCTACCTGTCCAAAACACTGGC




CCAGTATACCTCCAAGACCTGCAGCAATTGCGGCTTCACCATC




ACCAGCGCCGACTACGACAGAGTGCTGGAAAAGCTCAAGAAAA




CCGCCACCGGCTGGATGACCACCATCAACGGCAAAGAGCTGAA




GGTTGAGGGCCAGATCACCTACTACAACAGGTACAAGAGGCAG




AACGTCGTGAAGGATCTGAGCGTGGAACTGGACAGACTGAGCG




AAGAGAGCGTGAACAACGACATCAGCAGCTGGACAAAGGGCAG




ATCAGGCGAGGCTCTGAGCCTGCTGAAGAAGAGGTTTAGCCAC




AGACCTGTGCAAGAGAAGTTCGTGTGCCTGAACTGCGGCTTCG




AGACACACGCCGATGAACAGGCTGCCCTGAACATTGCCAGAAG




CTGGCTGTTCCTGAGAAGCCAAGAGTACAAGAAGTACCAGACC




AACAAGACCACCGGCAACACCGACAAGAGGGCCTTTGTGGAAA




CCTGGCAGAGCTTCTACAGAAAAAAGCTGAAAGAAGTCTGGAA




GCCCGCCGTG



 


linker
GGATCC
N.D.


 


c-MYC NLS
CCAGCCGCGAAGCGAGTGAAACTGGAC
3458


 


stop codon
TAA
N.D.


 


buffer sequence
GAATTCCTAGAGCTCGCTGATCAGCCTCGA
3459


 


bGH poly(A) signal
CTGTGCCTTCTAGTTGCCAGCCATCTGTTGTTTGCCCCTCCCC
3460


sequence
CGTGCCTTCCTTGACCCTGGAAGGTGCCACTCCCACTGTCCTT




TCCTAATAAAATGAGGAAATTGCATCGCATTGTCTGAGTAGGT




GTCATTCTATTCTGGGGGGTGGGGTGGGGCAGGACAGCAAGGG




GGAGGATTGGGAAGAGAATAGCAGGCATGCTGGGGA



 


buffer sequence
GGTACCGT
N.D.


 


U6 promoter
GAGGGCCTATTTCCCATGATTCCTTCATATTTGCATATACGAT
3461



ACAAGGCTGTTAGAGAGATAATTGGAATTAATTTGACTGTAAA




CACAAAGATATTAGTACAAAATACGTGACGTAGAAAGTAATAA




TTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTTAAAATGG




ACTATCATATGCTTACCGTAACTTGAAAGTATTTCGATTTCTT




GGCTTTATATATCTTGTGGAAAGGAC



 


buffer sequence
GAAACACC
N.D.


 


Scaffold variants
See sequences listed in Tables 9, 42, and 75
See sequences




listed in Tables 9,




42, and 75


 


B2M spacer (spacer
GGCCGAGATGTCTCGCTCCG
3137


7.37)




 


AAVSI spacer
CAAGAGGAGAAGCAGTTTGG
3462


(spacer 31.63)




 


Non-targeting
CGAGACGTAATTACGTCTCG
3232


spacer (spacer 0.0)




 


buffer sequence
TTTTTTTTGGCGGCCGC
3463


 


3′ ITR
AGGAACCCCTAGTGATGGAGTTGGCCACTCCCTCTCTGCGCGC
3238



TCGCTCGCTCACTGAGGCCGGGCGACCAAAGGTCGCCCGACGC




CCGGGCTTTGCCCGGGCGGCCTCAGTGAGCGAGCGAGCGCGCA




GCTGCCTGCAGG
















TABLE 77







List of AAV constructs and scaffold variants tested in a non-


CpG-depleted AAV vector (see Table 76 for sequences) and the


experimental conditions in which these constructs were assessed











Scaffold

Experimental


AAV construct ID
variant
Spacer
conditions













262
235
31.63
AAV transduction in iNs


263
328
31.63
AAV transduction in iNs


264
329
31.63
AAV transduction in iNs


265
382
31.63
AAV transduction in iNs


266
174
31.63
AAV transduction in iNs


267
335
31.63
AAV transduction in iNs


268
325
31.63
AAV transduction in iNs


269
330
31.63
AAV transduction in iNs


270
327
31.63
AAV transduction in iNs


271
334
31.63
AAV transduction in iNs


272
339
31.63
AAV transduction in iNs


273
337
31.63
AAV transduction in iNs


274
235
Non-targeting
AAV transduction in iNs


275
331
7.37
AAV transduction in HEK293s


276
335
7.37
AAV transduction in HEK293s


277
316
7.37
AAV transduction in HEK293s


278
392
7.37
AAV transduction in HEK293s


279
325
7.37
AAV transduction in HEK293s


280
334
7.37
AAV transduction in HEK293s


281
324
7.37
AAV transduction in HEK293s


282
336
7.37
AAV transduction in HEK293s


283
330
7.37
AAV transduction in HEK293s


284
320
7.37
AAV transduction in HEK293s


285
332
7.37
AAV transduction in HEK293s


286
321
7.37
AAV transduction in HEK293s


287
339
7.37
AAV transduction in HEK293s


288
235
7.37
AAV transduction in HEK293s


289
235
Non-targeting
AAV transduction in HEK293s









AAV production was performed using methods described in Example 12. For the experiment involving lipofection of HEK293 cells as described below, AAV titering was performed following methods described in Example 12. For the two experiments involving AAV transduction of human iNs or HEK293 cells as described below, AAV titering was performed by ddPCR. Cell-based assays evaluating the effects of using CpG-depleted or reduced gRNA scaffolds on editing activity:
In one experiment, ˜20,000 HEK293 cells per well were seeded in 96-well plates 24 hours prior to transfection. Seeded cells were then transfected with CpG-depleted AAV plasmids containing various versions of the guide scaffold (scaffolds 320-341). 5 days post transfection, cells were harvested for B2M protein expression analysis via HLA immunostaining following by flow cytometry. A CpG-depleted AAV plasmid with scaffold variant 235 served as an experimental control. An AAV plasmid with a CMV promoter driving mCherry expression was used as a transfection control, and a ˜41% transfection rate was observed. The results from this experiment are shown in FIG. 68.
In a second experiment, ˜20,000 induced neuron (iN) cells per well were seeded on Matrigel-coated 96-well plates 7 days prior to transduction. AAVs expressing the CasX:gRNA system, containing various versions of the guide scaffold (AAV construct ID #262-274; see Table 77), were diluted in neuronal plating media and added to cells 7 days post-plating. Cells were transduced at three MOIs (3E4, 1E4 or 3E3 vg/cell). 7 days post-transduction, cells were gDNA extraction for editing analysis at the AAVS1 locus using NGS. The results from this experiment are shown in FIGS. 69A-69C.
In a third experiment, ˜10,000 HEK293 cells per well were seeded in 96-well plates 24 hours prior to transfection. Seeded cells were then transduced with AAVs expressing the CasX:gRNA system, containing various versions of the guide scaffold (AAV construct ID #275-289; see Table 77). Cells were transduced at three MOIs (1E4, 3E3, or 1E3 vg/cell). 5 days post-transduction, cells were harvested for B2M protein expression analysis via HLA immunostaining following by flow cytometry. The results from this experiment are shown in FIGS. 70A-70C.
Results
Experiments were performed to evaluate further the effects of using CpG-reduced or depleted gRNA scaffolds on CasX-mediated editing activity. In the first experiment (N=1), HEK293 cells were lipofected with CpG-depleted AAV plasmids containing various versions of the gRNA scaffold (scaffolds 320-341, see Table 42 for sequences). B2M protein expression was subsequently analyzed, and the results of the assay are shown in FIG. 68. The data demonstrate that use of scaffolds 320-341 did not improve editing activity at the target B2M locus, since use of these scaffolds produced a lower percentage of cells with B2M− relative to the level achieved when using an AAV construct containing scaffold 235. These results do not recapitulate the results described in Example 12 (see FIGS. 28-31).
In the second experiment (N=1), human iNs were transduced with AAV particles expressing the CasX:gRNA system, containing various versions of the guide scaffold (AAV construct ID #262-274). Editing at the AAVS1 locus was analyzed, and the results of the assay are shown in FIGS. 69A-69C. The data demonstrate that of the scaffold variants tested, use of scaffold variant 329 and 382 appeared to improve editing at the AAVS1 locus when compared to use of scaffold 235, especially at MOI of 1E4 and 3E3 vg/cell. Furthermore, the effects on editing activity were observed in a dose-dependent manner.
In the third experiment (N=1), HEK293 cells were transduced with AAV particles expressing the CasX:gRNA system, containing various versions of the guide scaffold (AAV construct ID #275-289). B2M protein expression was subsequently analyzed, and the results of the assay are shown in FIGS. 70A-70C. The data demonstrate that of the scaffold variants tested, use of scaffolds 316, 392 and 332 appeared to improve editing at the B2M locus when compared to use of scaffold 235 overall. Specifically, at the higher MOI of 1E4 and 3E3 vg/cell, slightly improved editing was observed with use of scaffolds 316, 392, and 332 (FIGS. 70A-70B), while a stronger editing improvement was observed at the lower MOI of 1E3 vg/cell (FIG. 70C). Notably, scaffold 332 and 392 both include CG>GC mutations in the pseudoknot stem (region 1; FIGS. 27A-27B), effectively reducing the overall number of CpGs when compared to scaffold 235, thereby potentially contributing to the increase in editing activity. Furthermore, scaffolds 316 and 332 both have a truncated extended stem when compared to scaffold 235, removing the bubble and the CG dinucleotide (region 3; FIGS. 27A-27B), thereby also potentially contributing to the observed increase in editing activity. Further experiments are performed, especially at lower MOIs, to unravel the intricacies of the effects of individual CpG mutations on editing potency.
The results from the experiments described here demonstrate that use of guide scaffolds with different levels of CpG depletion can result in varying levels of editing mediated by the CasX:gRNA system, and that the resulting editing levels can vary by method of delivery (e.g., plasmid transfection vs. AAV transduction).