CRISPR-associated (Cas) proteins with reduced immunogenicity
11566052 · 2023-01-31
Assignee
Inventors
Cpc classification
C12N2310/20
CHEMISTRY; METALLURGY
C12N9/22
CHEMISTRY; METALLURGY
C12N2710/10045
CHEMISTRY; METALLURGY
International classification
C07K14/00
CHEMISTRY; METALLURGY
C12N9/22
CHEMISTRY; METALLURGY
C12N15/86
CHEMISTRY; METALLURGY
C12N15/90
CHEMISTRY; METALLURGY
Abstract
The invention relates to methods of reducing the immunogenicity of CRISPR-associated (Cas) proteins and the modified Cas proteins produced therefrom. In addition, the invention relates to methods for cell and gene therapy, including any and all genetic modifications and alterations of gene expression (and/or genetic elements) made in-vivo or ex-vivo using Cas proteins with reduced immunogenicity.
Claims
1. A method for reducing the immunogenicity of a CRISPR-associated 9 (Cas9) protein, the method comprising introducing one or more amino acid substitutions into one or more residues corresponding to one or more major histocompatibility (MHC) Class I and/or Class II binding sites of the Cas9 protein to form a recombinant Cas9 protein; wherein the amino acid sequence of the Cas9 protein is at least 95% identical to full-length SEQ ID NO:5; and wherein the one or more amino acid substitutions are one or more of: L106D, K263D, L696G, L847D, or I1281D.
2. The method of claim 1, wherein there are two or more amino acid substitutions selected from two of: L106D, K263D, L696G, L847D, or I1281D.
3. The method of claim 1, wherein there are three or more amino acid substitutions selected from three of: L106D, K263D, L696G, L847D, or I1281D.
4. The method of claim 1, wherein there are four or more amino acid substitutions selected from four of: L106D, K263D, L696G, L847D, or I1281D.
5. The method of claim 1, wherein there are five amino acid substitutions: L106D, K263D, L696G, L847D, and I1281D.
6. A recombinant CRISPR-associated 9 (Cas9) protein made by a method comprising introducing one or more amino acid substitutions into one or more residues corresponding to one or more major histocompatibility (MHC) Class I and/or Class II binding sites of the Cas9 protein to form the recombinant Cas9 protein; wherein the amino acid sequence of the Cas9 protein is at least 95% identical to full-length SEQ ID NO:5; and wherein the one or more amino acid substitutions are one or more of: L106D, K263D, L696G, L847D, or I1281D.
7. An isolated cell comprising the recombinant Cas9 protein of claim 6.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
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DETAILED DESCRIPTION OF THE INVENTION
(16) The invention provided herein uses components of the CRISPR-Cas system, which can be utilized to accomplish genomic engineering, including gene editing and altering expression of a gene and/or genetic element. Such genomic engineering can be used in various therapeutic strategies, including the treatment of genetic diseases. In addition, described herein are methods for creating Cas proteins with reduced immunogenicity that can be used in conjunction with other CRISPR components. In certain embodiments, described herein are recombinant Cas proteins with reduced immunogenicity, isolated nucleic acids that encode such recombinant Cas proteins, vectors comprising these nucleic acids, and cells comprising the nucleic acids and/or vectors. The creation of Cas proteins with reduced immunogenicity may allow for more stable, efficient, and efficacious use of the CRISPR-Cas system in a host organism, including humans.
Definitions
(17) The use of the word “a” or “an” when used in conjunction with the term “comprising” in the claims and/or the specification may mean “one,” but it is also consistent with the meaning of “one or more,” “at least one,” and “one or more than one.”
(18) Throughout this application, the term “about” is used to indicate that a value includes the inherent variation of error for the method/device being employed to determine the value, or the variation that exists among the study subjects. Typically the term is meant to encompass approximately or less than 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15%, 16%, 17%, 18%, 19% or 20% variability depending on the situation.
(19) The use of the term “or” in the claims is used to mean “and/or” unless explicitly indicated to refer only to alternatives or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and “and/or.”
(20) As used in this specification and claim(s), the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), “including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited, elements or method steps. It is contemplated that any embodiment discussed in this specification can be implemented with respect to any method, system, host cells, expression vectors, and/or composition of the invention. Furthermore, compositions, systems, host cells, and/or vectors of the invention can be used to achieve methods and proteins of the invention.
(21) The use of the term “for example” and its corresponding abbreviation “e.g.” (whether italicized or not) means that the specific terms recited are representative examples and embodiments of the invention that are not intended to be limited to the specific examples referenced or cited unless explicitly stated otherwise.
(22) A “nucleic acid,” “nucleic acid molecule,” “oligonucleotide” or “polynucleotide” means a polymeric compound comprising covalently linked nucleotides. The term “nucleic acid” includes polyribonucleic acid (RNA) and polydeoxyribonucleic acid (DNA), both of which may be single- or double-stranded. DNA includes, but is not limited to, complimentary DNA (cDNA), genomic DNA, plasmid or vector DNA, and synthetic DNA. In some embodiments, the invention is directed to a polynucleotide encoding any one of the polypeptides disclosed herein, e.g., is directed to a polynucleotide encoding a Cas protein or variant thereof. In some embodiments, the invention is directed to a polynucleotide encoding Cas3, Cas9, Cas10 or variants thereof.
(23) A “gene” refers to an assembly of nucleotides that encode a polypeptide, and includes cDNA and genomic DNA nucleic acid molecules. “Gene” also refers to a nucleic acid fragment that can act as a regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding sequences) the coding sequence.
(24) The terms “peptide,” “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.
(25) An “amino acid” as used herein refers to a compound containing both a carboxyl (—COOH) and amino (—NH.sub.2) group. “Amino acid” refers to both natural and unnatural, i.e., synthetic, amino acids. Natural amino acids, with their three-letter and single letter abbreviations, include Alanine (Ala; A); Arginine (Arg, R); Asparagine (Asn; N); Aspartic acid (Asp; D); Cysteine (Cys; C); Glutamine (Gln; Q); Glutamic acid (Glu; E); Glycine (Gly; G); Histidine (His; H); Isoleucine (Ile; I); Leucine (Leu; L); Lysine (Lys; K); Methionine (Met; M); Phenylalanine (Phe; F); Proline (Pro; P); Serine (Ser; S); Threonine (Thr; T); Tryptophan (Trp; W); Tyrosine (Tyr; Y); and Valine (Val; V).
(26) An “amino acid substitution” refers to a polypeptide or protein comprising one or more substitutions of a wild-type or naturally occurring amino acid with a different amino acid relative to the wild-type or naturally occurring amino acid at that amino acid residue. The substituted amino acid of the invention may be a synthetic or naturally occurring amino acid. In certain embodiments, the substituted amino acid is a naturally occurring amino acid selected from the group consisting of: A, R, N, D, C, Q, E, G, H, I, L, K, M, F, P, S, T, W, Y, and V. Substitution mutants may be described using an abbreviated system. For example, a substitution mutation in which the fifth (5.sup.th) amino acid residue is substituted may be abbreviated as “X5Y,” wherein “X” is the wild-type or naturally occurring amino acid to be replaced, “5” is the amino acid residue within the protein or polypeptide, and “Y” is the substituted, or non-wild-type or non-naturally occurring, amino acid.
(27) The term “recombinant” when used in reference to a nucleic acid molecule, peptide, polypeptide, or protein means of, or resulting from, a new combination of genetic material that is not known to exist in nature. A recombinant molecule can be produced by any of the well-known techniques available in the field of recombinant technology, including, but not limited to, polymerase chain reaction (PCR), gene splicing (e.g., using restriction endonucleases), and solid state synthesis of nucleic acid molecules, peptides, or proteins.
(28) An “isolated” polypeptide, protein, peptide, or nucleic acid is a molecule that has been removed from its natural environment. It is also to be understood that “isolated” polypeptides, proteins, peptides, or nucleic acids may be formulated with excipients such as diluents or adjuvants and still be considered isolated.
(29) The terms “sequence identity” or “% identity” in the context of nucleic acid sequences or amino acid sequences refers to the percentage of residues in the compared sequences that are the same when the sequences are aligned over a specified comparison window. A comparison window can be a segment of at least 10 to over 1000 residues in which the sequences can be aligned and compared. Methods of alignment for determination of sequence identity are well-known can be performed using publically available databases such as BLAST (blast.ncbi.nlm.nih.gov/Blast.cgi.). “Percent identity” or “% identity” when referring to amino acid sequences can be determined by methods known in the art. For example, in some embodiments, “percent identity” of two amino acid sequences is determined using the algorithm of Karlin and Altschul, Proc. Natl. Acad. Sci. USA 87:2264-68, 1990, modified as in Karlin and Altschul Proc. Natl. Acad. Sci. USA 90:5873-77, 1993. Such an algorithm is incorporated into the NBLAST and XBLAST programs (version 2.0) of Altschul, et al., J. Mol. Biol. 215:403-10 (1990). BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3 to obtain amino acid sequences homologous to the protein molecules of the invention. Where gaps exist between two sequences, Gapped BLAST can be utilized as described in Altschul et al., Nucleic Acids Res. 25(17):3389-3402, 1997. When utilizing BLAST and Gapped BLAST programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used.
(30) In certain embodiments of the invention, polypeptides or nucleic acid molecules have 70%, at least 70%, 75%, at least 75%, 80%, at least 80%, 85%, at least 85%, 90%, at least 90%, 95%, at least 95%, 97%, at least 97%, 98%, at least 98%, 99%, or at least 99% or 100% sequence identity with a reference polypeptide or nucleic acid molecule, respectively (or a fragment of the reference polypeptide or nucleic acid molecule). In some embodiments, polypeptides or nucleic acid molecules have about 70%, at least about 70%, about 75%, at least about 75%, about 80%, at least about 80%, about 85%, at least about 85%, about 90%, at least about 90%, about 95%, at least about 95%, about 97%, at least about 97%, about 98%, at least about 98%, about 99%, at least about 99% or about 100% sequence identity with a reference polypeptide or nucleic acid molecule, respectively (or a fragment of the reference polypeptide or nucleic acid molecule).
(31) The RNA molecule that binds to CRISPR-Cas components and targets them to a specific location within the target DNA is referred to herein as “guide RNA,” “gRNA,” or “small guide RNA” and may also be referred to herein as a “DNA-targeting RNA.” A guide RNA comprises at least two nucleotide segments: at least one “DNA-binding segment” and at least one “polypeptide-binding segment.” By “segment” is meant a part, section, or region of a molecule, e.g., a contiguous stretch of nucleotides of an RNA molecule. The definition of “segment,” unless otherwise specifically defined, is not limited to a specific number of total base pairs.
(32) The guide RNA can be introduced into the target cell as an isolated RNA molecule, or is introduced into the cell using an expression vector containing DNA encoding the guide RNA.
(33) The “DNA-binding segment” (or “DNA-targeting sequence”) of the guide RNA comprises a nucleotide sequence that is complementary to a specific sequence within a target DNA.
(34) The guide RNA of the current disclosure can include one or more polypeptide-binding sequences/segments. The polypeptide-binding segment (or “protein-binding sequence”) of the guide RNA interacts with the RNA-binding domain of a Cas protein of the current disclosure. Such polypeptide-binding segments or sequences are known to those of skill in the art, e.g., those disclosed in U.S. patent application publications 2014/0068797, 2014/0273037, 2014/0273226, 2014/0295556, 2014/0295557, 2014/0349405, 2015/0045546, 2015/0071898, 2015/0071899, and 2015/0071906, the disclosures of which are incorporated herein in their entireties.
(35) “T cell” or “T-cell” are used interchangeably and refer to a type of lymphocytic cell that plays a central role in cell-mediated immunity and expresses a T-cell receptor (TCR) on its surface. T-cells include CD4+ and CD8+ T-cells but are distinguished from other lymphocytes, such as B cells and natural killer cells (NK cells).
(36) A “major histocompatibility complex” or “MHC” protein as used herein refers to a set of cell surface molecules encoded by a large gene family that play a significant role in the immune system of vertebrates. A key function of these proteins is to bind peptide fragments derived from endogenous or exogenous (foreign) proteins and display them on the cell surface for recognition by the appropriate T-cells of the host organism. The MHC gene family is divided into three subgroups: Class I, Class II, and Class III. The human MHC Class I and Class II genes are also referred to as human leukocyte antigen (HLA)—HLA Class I and HLA Class II, respectively. Some of the most studied HLA genes in humans are the nine MHC genes: HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB1, HLA-DQA1, HLA-DQB1, HLA-DRA, HLA-DRB1 and HLA-DRB345.
(37) “Binding” or “interaction” as used herein refers to a non-covalent interaction between macromolecules (e.g., between DNA and RNA, or between a polypeptide and a polynucleotide). “Binding” may also be referred to as “associated with” or “interacting.” “Binding” as used herein means that the binding partners are capable of binding to each other (e.g., will not necessarily bind to each other). Some portions of a binding interaction may be sequence-specific, but not all components of a binding interaction need be sequence-specific (e.g., contacts with phosphate residues in a DNA backbone). Binding interactions are generally characterized by a dissociation constant (Kd), e.g., less than 1 mM, less than 100 uM, less than 10 uM, less than 1 uM, less than 100 nM, less than 10 nM. “Affinity” refers to the strength of binding, increased binding affinity being correlated with a lower Kd.
(38) As used herein, “promoter,” “promoter sequence,” or “promoter region” refers to a DNA regulatory region/sequence capable of binding RNA polymerase and involved in initiating transcription of a downstream coding or non-coding sequence. In some examples of the present disclosure, the promoter sequence includes the transcription initiation site and extends upstream to include the minimum number of bases or elements necessary to initiate transcription at levels detectable above background. In some embodiments, the promoter sequence includes a transcription initiation site, as well as protein binding domains responsible for the binding of RNA polymerase. Eukaryotic promoters will often, but not always, contain “TATA” boxes and “CAT” boxes. Various promoters, including inducible promoters, may be used to drive the various vectors of the present invention.
(39) A “vector” or “expression vector” is a replicon, such as a plasmid, phage, virus, or cosmid, to which another DNA segment may be attached to bring about the replication and/or expression of the attached DNA segment in a cell. “Vector” includes episomal (e.g., plasmids) and non episomal vectors. In some embodiments of the present disclosure the vector is an episomal vector, which is removed/lost from a population of cells after a number of cellular generations, e.g., by asymmetric partitioning. The term “vector” includes both viral and nonviral means for introducing a nucleic acid molecule into a cell in vitro, in vivo, or ex vivo. Vectors may be introduced into the desired host cells by well-known methods, including, but not limited to, transfection, transduction, cell fusion, and lipofection. Vectors can comprise various regulatory elements including promoters. In some embodiments, vector designs can be based on constructs designed by Mali et al. “Cas9 as a versatile tool for engineering biology,” Nature Methods 10:957-63 (2013). In some embodiments, the invention is directed to an expression vector comprising any of the polynucleotides described herein, e.g., an expression vector comprising polynucleotides encoding a Cas protein or variant thereof. In some embodiments, the invention is directed to an expression vector comprising polynucleotides encoding a Cas3, Cas9, or Cas10 protein or variant thereof.
(40) “Transfection” as used herein means the introduction of an exogenous nucleic acid molecule, including a vector, into a cell. A “transfected” cell comprises an exogenous nucleic acid molecule inside the cell and a “transformed” cell is one in which the exogenous nucleic acid molecule within the cell induces a phenotypic change in the cell. The transfected nucleic acid molecule can be integrated into the host cell's genomic DNA and/or can be maintained by the cell, temporarily or for a prolonged period of time, extra-chromosomally. Host cells or organisms that express exogenous nucleic acid molecules or fragments are referred to as “recombinant,” “transformed,” or “transgenic” organisms. In some embodiments, the invention is directed to a host cell comprising any of the expression vectors described herein, e.g., an expression vector comprising a polynucleotide encoding a Cas protein or variant thereof. In some embodiments, the invention is directed to a host cell comprising an expression vector comprising a polynucleotide encoding a Cas3, Cas 9 or Cas10 protein or variant thereof.
(41) The term “in silico” as used herein refers to a process or analysis preformed on a computer, including computer modeling and computer simulation. In some embodiments, the term “in silico” refers to the EPIBASE® epitope prediction method.
Recombinant CRISPR-Associated (Cas) Proteins
(42) As described above, Cas proteins are a critical component in the CRISPR-Cas system, which can be used for, inter alia, genome editing, gene regulation, genetic circuit construction, and functional genomics. While the Cas1 and Cas2 proteins appear to be universal to all the presently identified CRISPR systems, the Cas3, Cas9, and Cas10 proteins are thought to be specific to the Type I, Type II, and Type III CRISPR systems, respectively. In certain embodiments of the present invention, the recombinant Cas protein with reduced immunogenicity, including methods of deriving such proteins, is derived from a Cas3, Cas9, or Cas10 protein. In some embodiments, the recombinant Cas protein with reduced immunogenicity, including methods of deriving such a protein, is derived from a Cas9 protein.
(43) Following initial publications around the CRISPR-Cas9 system (Type II system), Cas9 variants have been identified in a range of bacterial species and a number have been functionally characterized. See, e.g., Chylinski, et al., “Classification and evolution of type II CRISPR-Cas systems,” Nucleic Acids Research 42(10):6091-105 (2014), Ran, et al., “In vivo genome editing using Staphylococcus aureus Cas9,” Nature 520(7546):186-91 (2015) and Esvelt, et al., “Orthogonal Cas9 proteins for RNA-guided gene regulation and editing,” Nature Methods 10(11):1116-21 (2013), each of which is incorporated by reference herein in its entirety.
(44) Cas9 variants from Streptococcus pyogenes, Streptococcus thermophilus, Staphylococcus aureus, and Neisseria meningitidis, in particular, have been well-characterized. In some embodiments, the recombinant Cas protein with reduced immunogenicity, including methods of deriving such a protein, is derived from a Cas9 protein from a bacterium of the genera, Streptococcus, Staphylococcus, or Neisseria. In certain embodiments, the recombinant Cas9 protein is derived from a Cas9 protein from Streptococcus pyogenes, Streptococcus thermophilus, Staphylococcus aureus, or Neisseria meningitidis. In some embodiments, the recombinant Cas9 protein is derived from a Streptococcus pyogenes Cas9 protein. In other embodiments, the recombinant Cas9 protein is derived from a Staphylococcus aureus Cas9 protein.
(45) Following is an exemplary nucleotide sequence (SEQ ID NO: 1) that encodes the Streptococcus pyogenes Cas9 protein:
(46) TABLE-US-00002 ATGGACAAGAAGTACTCCATTGGGCTCGATATCGGCACAAACAGCGTC GGCTGGGCCGTCATTACGGACGAGTACAAGGTGCCGAGCAAAAAATT CAAAGTTCTGGGCAATACCGATCGCCACAGCATAAAGAAGAACCTCA TTGGCGCCCTCCTGTTCGACTCCGGGGAGACGGCCGAAGCCACGCGGC TCAAAAGAACAGCACGGCGCAGATATACCCGCAGAAAGAATCGGATC TGCTACCTGCAGGAGATCTTTAGTAATGAGATGGCTAAGGTGGATGAC TCTTTCTTCCATAGGCTGGAGGAGTCCTTTTTGGTGGAGGAGGATAAA AAGCACGAGCGCCACCCAATCTTTGGCAATATCGTGGACGAGGTGGC GTACCATGAAAAGTACCCAACCATATATCATCTGAGGAAGAAGCTTGT AGACAGTACTGATAAGGCTGACTTGCGGTTGATCTATCTCGCGCTGGC GCATATGATCAAATTTCGGGGACACTTCCTCATCGAGGGGGACCTGAA CCCAGACAACAGCGATGTCGACAAACTCTTTATCCAACTGGTTCAGAC TTACAATCAGCTTTTCGAAGAGAACCCGATCAACGCATCCGGAGTTGA CGCCAAAGCAATCCTGAGCGCTAGGCTGTCCAAATCCCGGCGGCTCGA AAACCTCATCGCACAGCTCCCTGGGGAGAAGAAGAACGGCCTGTTTG GTAATCTTATCGCCCTGTCACTCGGGCTGACCCCCAACTTTAAATCTAA CTTCGACCTGGCCGAAGATGCCAAGCTTCAACTGAGCAAAGACACCTA CGATGATGATCTCGACAATCTGCTGGCCCAGATCGGCGACCAGTACGC AGACCTTTTTTTGGCGGCAAAGAACCTGTCAGACGCCATTCTGCTGAG TGATATTCTGCGAGTGAACACGGAGATCACCAAAGCTCCGCTGAGCGC TAGTATGATCAAGCGCTATGATGAGCACCACCAAGACTTGACTTTGCT GAAGGCCCTTGTCAGACAGCAACTGCCTGAGAAGTACAAGGAAATTTT CTTCGATCAGTCTAAAAATGGCTACGCCGGATACATTGACGGCGGAGC AAGCCAGGAGGAATTTTACAAATTTATTAAGCCCATCTTGGAAAAAAT GGACGGCACCGAGGAGCTGCTGGTAAAGCTTAACAGAGAAGATCTGT TGCGCAAACAGCGCACTTTCGACAATGGAAGCATCCCCCACCAGATTC ACCTGGGCGAACTGCACGCTATCCTCAGGCGGCAAGAGGATTTCTACC CCTTTTTGAAAGATAACAGGGAAAAGATTGAGAAAATCCTCACATTTC GGATACCCTACTATGTAGGCCCCCTCGCCCGGGGAAATTCCAGATTCG CGTGGATGACTCGCAAATCAGAAGAGACCATCACTCCCTGGAACTTCG AGGAAGTCGTGGATAAGGGGGCCTCTGCCCAGTCCTTCATCGAAAGG ATGACTAACTTTGATAAAAATCTGCCTAACGAAAAGGTGCTTCCTAAA CACTCTCTGCTGTACGAGTACTTCACAGTTTATAACGAGCTCACCAAG GTCAAATACGTCACAGAAGGGATGAGAAAGCCAGCATTCCTGTCTGG AGAGCAGAAGAAAGCTATCGTGGACCTCCTCTTCAAGACGAACCGGA AAGTTACCGTGAAACAGCTCAAAGAAGACTATTTCAAAAAGATTGAA TGTTTCGACTCTGTTGAAATCAGCGGAGTGGAGGATCGCTTCAACGCA TCCCTGGGAACGTATCACGATCTCCTGAAAATCATTAAAGACAAGGAC TTCCTGGACAATGAGGAGAACGAGGACATTCTTGAGGACATTGTCCTC ACCCTTACGTTGTTTGAAGATAGGGAGATGATTGAAGAACGCTTGAAA ACTTACGCTCATCTCTTCGACGACAAAGTCATGAAACAGCTCAAGAGG CGCCGATATACAGGATGGGGGCGGCTGTCAAGAAAACTGATCAATGG GATCCGAGACAAGCAGAGTGGAAAGACAATCCTGGATTTTCTTAAGTC CGATGGATTTGCCAACCGGAACTTCATGCAGTTGATCCATGATGACTC TCTCACCTTTAAGGAGGACATCCAGAAAGCACAAGTTTCTGGCCAGGG GGACAGTCTTCACGAGCACATCGCTAATCTTGCAGGTAGCCCAGCTAT CAAAAAGGGAATACTGCAGACCGTTAAGGTCGTGGATGAACTCGTCA AAGTAATGGGAAGGCATAAGCCCGAGAATATCGTTATCGAGATGGCC CGAGAGAACCAAACTACCCAGAAGGGACAGAAGAACAGTAGGGAAA GGATGAAGAGGATTGAAGAGGGTATAAAAGAACTGGGGTCCCAAATC CTTAAGGAACACCCAGTTGAAAACACCCAGCTTCAGAATGAGAAGCT CTACCTGTACTACCTGCAGAACGGCAGGGACATGTACGTGGATCAGGA ACTGGACATCAATCGGCTCTCCGACTACGACGTGGATCATATCGTGCC CCAGTCTTTTCTCAAAGATGATTCTATTGATAATAAAGTGTTGACAAG ATCCGATAAAAATAGAGGGAAGAGTGATAACGTCCCCTCAGAAGAAG TTGTCAAGAAAATGAAAAATTATTGGCGGCAGCTGCTGAACGCCAAA CTGATCACACAACGGAAGTTCGATAATCTGACTAAGGCTGAACGAGGT GGCCTGTCTGAGTTGGATAAAGCCGGCTTCATCAAAAGGCAGCTTGTT GAGACACGCCAGATCACCAAGCACGTGGCCCAAATTCTCGATTCACGC ATGAACACCAAGTACGATGAAAATGACAAACTGATTCGAGAGGTGAA AGTTATTACTCTGAAGTCTAAGCTGGTCTCAGATTTCAGAAAGGACTT TCAGTTTTATAAGGTGAGAGAGATCAACAATTACCACCATGCGCATGA TGCCTACCTGAATGCAGTGGTAGGCACTGCACTTATCAAAAAATATCC CAAGCTTGAATCTGAATTTGTTTACGGAGACTATAAAGTGTACGATGT TAGGAAAATGATCGCAAAGTCTGAGCAGGAAATAGGCAAGGCCACCG CTAAGTACTTCTTTTACAGCAATATTATGAATTTTTTCAAGACCGAGAT TACACTGGCCAATGGAGAGATTCGGAAGCGACCACTTATCGAAACAA ACGGAGAAACAGGAGAAATCGTGTGGGACAAGGGTAGGGATTTCGCG ACAGTCCGGAAGGTCCTGTCCATGCCGCAGGTGAACATCGTTAAAAAG ACCGAAGTACAGACCGGAGGCTTCTCCAAGGAAAGTATCCTCCCGAA AAGGAACAGCGACAAGCTGATCGCACGCAAAAAAGATTGGGACCCCA AGAAATACGGCGGATTCGATTCTCCTACAGTCGCTTACAGTGTACTGG TTGTGGCCAAAGTGGAGAAAGGGAAGTCTAAAAAACTCAAAAGCGTC AAGGAACTGCTGGGCATCACAATCATGGAGCGATCAAGCTTCGAAAA AAACCCCATCGACTTTCTCGAGGCGAAAGGATATAAAGAGGTCAAAA AAGACCTCATCATTAAGCTTCCCAAGTACTCTCTCTTTGAGCTTGAAAA CGGCCGGAAACGAATGCTCGCTAGTGCGGGCGAGCTGCAGAAAGGTA ACGAGCTGGCACTGCCCTCTAAATACGTTAATTTCTTGTATCTGGCCAG CCACTATGAAAAGCTCAAAGGGTCTCCCGAAGATAATGAGCAGAAGC AGCTGTTCGTGGAACAACACAAACACTACCTTGATGAGATCATCGAGC AAATAAGCGAATTCTCCAAAAGAGTGATCCTCGCCGACGCTAACCTCG ATAAGGTGCTTTCTGCTTACAATAAGCACAGGGATAAGCCCATCAGGG AGCAGGCAGAAAACATTATCCACTTGTTTACTCTGACCAACTTGGGCG CGCCTGCAGCCTTCAAGTACTTCGACACCACCATAGACAGAAAGCGGT ACACCTCTACAAAGGAGGTCCTGGACGCCACACTGATTCATCAGTCAA TTACGGGGCTCTATGAAACAAGAATCGACCTCTCTCAGCTCGGTGGAG ACTGA
(47) Following is an exemplary nucleotide sequence (SEQ ID NO: 2) that encodes the Streptococcus thermophilus Cas9 protein:
(48) TABLE-US-00003 ATGAGCGACCTGGTGCTGGGCCTGGACATCGGCATCGGCAGCGTGGG CGTGGGCATCCTGAACAAGGTGACCGGCGAGATCATCCACAAGAACA GTCGCATCTTCCCTGCTGCTCAGGCTGAGAACAACCTGGTGCGCCGCA CCAACCGCCAGGGTCGCCGGCTTGCTCGCCGCAAGAAGCACCGGCGC GTGCGCCTGAACCGCCTGTTCGAGGAGAGCGGCCTGATCACCGACTTC ACCAAGATCAGCATCAACCTGAACCCCTACCAGCTGCGCGTGAAGGG CCTGACCGACGAGCTGAGCAACGAGGAGCTGTTCATCGCCCTGAAGA ACATGGTGAAGCACCGCGGCATCAGCTACCTGGACGACGCCAGCGAC GACGGCAACAGCAGCGTGGGCGACTACGCCCAGATCGTGAAGGAGAA CAGCAAGCAGCTGGAGACCAAGACCCCCGGCCAGATCCAGCTGGAGC GCTACCAGACCTACGGCCAGCTGCGCGGCGACTTCACCGTGGAGAAG GACGGCAAGAAGCACCGCCTGATCAACGTGTTCCCCACCAGCGCCTAC CGCAGCGAGGCCCTGCGCATCCTGCAGACCCAGCAGGAGTTCAACCC CCAGATCACCGACGAGTTCATCAACCGCTACCTGGAGATCCTGACCGG CAAGCGCAAGTACTACCACGGCCCCGGCAACGAGAAGAGCCGCACCG ACTACGGCCGCTACCGCACCAGCGGCGAGACCCTGGACAACATCTTCG GCATCCTGATCGGCAAGTGCACCTTCTACCCCGACGAGTTCCGCGCCG CCAAGGCCAGCTACACCGCCCAGGAGTTCAACCTGCTGAACGACCTG AACAACCTGACCGTGCCCACCGAGACCAAGAAGCTGAGCAAGGAGCA GAAGAACCAGATCATCAACTACGTGAAGAACGAGAAGGCCATGGGCC CCGCCAAGCTGTTCAAGTACATCGCCAAGCTGCTGAGCTGCGACGTGG CCGACATCAAGGGCTACCGCATCGACAAGAGCGGCAAGGCCGAGATC CACACCTTCGAGGCCTACCGCAAGATGAAGACCCTGGAGACCCTGGA CATCGAGCAGATGGACCGCGAGACCCTGGACAAGCTGGCCTACGTGC TGACCCTGAACACCGAGCGCGAGGGCATCCAGGAGGCCCTGGAGCAC GAGTTCGCCGACGGCAGCTTCAGCCAGAAGCAGGTGGACGAGCTGGT GCAGTTCCGCAAGGCCAACAGCAGCATCTTCGGCAAGGGCTGGCACA ACTTCAGCGTGAAGCTGATGATGGAGCTGATCCCCGAGCTGTACGAGA CCAGCGAGGAGCAGATGACCATCCTGACCCGCCTGGGCAAGCAGAAG ACCACCAGCAGCAGCAACAAGACCAAGTACATCGACGAGAAGCTGCT GACCGAGGAGATCTACAACCCCGTGGTGGCCAAGAGCGTGCGCCAGG CCATCAAGATCGTGAACGCCGCCATCAAGGAGTACGGCGACTTCGAC AACATCGTGATCGAGATGGCCCGCGAGACCAACGAGGACGACGAGAA GAAGGCCATCCAGAAGATCCAGAAGGCCAACAAGGACGAGAAGGAC GCCGCCATGCTGAAGGCCGCCAACCAGTACAACGGCAAGGCCGAGCT GCCCCACAGCGTGTTCCACGGCCACAAGCAGCTGGCCACCAAGATCC GCCTGTGGCACCAGCAGGGCGAGCGCTGCCTGTACACCGGCAAGACC ATCAGCATCCACGACCTGATCAACAACAGCAACCAGTTCGAGGTGGA CCACATCCTGCCCCTGAGCATCACCTTCGACGACAGCCTGGCCAACAA GGTGCTGGTGTACGCCACCGCCAACCAGGAGAAGGGCCAGCGCACCC CCTACCAGGCCCTGGACAGCATGGACGACGCCTGGAGCTTCCGCGAG CTGAAGGCCTTCGTGCGCGAGAGCAAGACCCTGAGCAACAAGAAGAA GGAGTACCTGCTGACCGAGGAGGACATCAGCAAGTTCGACGTGCGCA AGAAGTTCATCGAGCGCAACCTGGTGGACACCCGCTACGCCAGCCGC GTGGTGCTGAACGCCCTGCAGGAGCACTTCCGCGCCCACAAGATCGAC ACCAAGGTGAGCGTGGTGCGCGGCCAGTTCACCAGCCAGCTGCGCCG CCACTGGGGCATCGAGAAGACCCGCGACACCTACCACCACCACGCCG TGGACGCCCTGATCATTGCGGCTTCTAGCCAGCTGAACCTGTGGAAGA AGCAGAAGAACACCCTGGTGAGCTACAGCGAGGACCAGCTGCTGGAC ATCGAGACCGGCGAGCTGATCAGCGACGACGAGTACAAGGAGAGCGT GTTCAAGGCCCCCTACCAGCACTTCGTGGACACCCTGAAGAGCAAGG AGTTCGAGGACAGCATCCTGTTCAGCTACCAGGTGGACAGCAAGTTCA ACCGCAAGATCAGCGACGCCACCATCTACGCCACCCGCCAGGCCAAG GTGGGCAAGGACAAGGCCGACGAGACCTACGTGCTGGGCAAGATCAA GGACATCTACACCCAGGACGGCTACGACGCCTTCATGAAGATCTACAA GAAGGACAAGAGCAAGTTCCTGATGTACCGCCACGACCCCCAGACCT TCGAGAAGGTGATCGAGCCCATCCTGGAGAACTACCCCAACAAGCAG ATCAACGATAAAGGCAAGGAGGTGCCCTGCAACCCCTTCCTGAAGTA CAAGGAGGAGCACGGCTACATCCGCAAGTACAGCAAGAAGGGCAACG GCCCCGAGATCAAGAGCCTGAAGTACTACGACAGCAAGCTGGGCAAC CACATCGACATCACCCCCAAGGACAGCAACAACAAGGTGGTGCTGCA GAGCGTGAGCCCCTGGCGCGCCGACGTGTACTTCAACAAGACCACCG GCAAGTACGAGATCCTGGGCCTGAAGTACGCCGACCTGCAGTTTGATA AGGGCACCGGCACCTACAAGATCAGCCAGGAGAAGTACAACGACATC AAGAAGAAGGAGGGCGTGGACAGCGACAGCGAGTTCAAGTTCACCCT GTACAAGAACGACCTTCTGCTGGTGAAGGACACCGAGACCAAGGAGC AACAGCTGTTCCGCTTCCTGAGCCGCACCATGCCCAAGCAGAAGCACT ACGTGGAGCTGAAGCCCTACGACAAGCAGAAGTTCGAGGGCGGCGAG GCCCTGATCAAGGTGCTGGGCAACGTGGCCAACAGCGGCCAGTGCAA GAAGGGCCTGGGCAAGAGCAACATCAGCATCTACAAGGTGCGCACCG ACGTGCTGGGCAACCAGCACATCATCAAGAACGAGGGCGACAAGCCC AAGCTGGACTTCTGA
(49) Following is an exemplary nucleotide sequence (SEQ ID NO: 3) that encodes the Staphylococcus aureus Cas9 protein:
(50) TABLE-US-00004 ATGAAGCGGAACTACATCCTGGGCCTGGACATCGGCATCACCAGCGT GGGCTACGGCATCATCGACTACGAGACACGGGACGTGATCGATGCCG GCGTGCGGCTGTTCAAAGAGGCCAACGTGGAAAACAACGAGGGCAGG CGGAGCAAGAGAGGCGCCAGAAGGCTGAAGCGGCGGAGGCGGCATA GAATCCAGAGAGTGAAGAAGCTGCTGTTCGACTACAACCTGCTGACCG ACCACAGCGAGCTGAGCGGCATCAACCCCTACGAGGCCAGAGTGAAG GGCCTGAGCCAGAAGCTGAGCGAGGAAGAGTTCTCTGCCGCCCTGCT GCACCTGGCCAAGAGAAGAGGCGTGCACAACGTGAACGAGGTGGAAG AGGACACCGGCAACGAGCTGTCCACCAAAGAGCAGATCAGCCGGAAC AGCAAGGCCCTGGAAGAGAAATACGTGGCCGAACTGCAGCTGGAACG GCTGAAGAAAGACGGCGAAGTGCGGGGCAGCATCAACAGATTCAAGA CCAGCGACTACGTGAAAGAAGCCAAACAGCTGCTGAAGGTGCAGAAG GCCTACCACCAGCTGGACCAGAGCTTCATCGACACCTACATCGACCTG CTGGAAACCCGGCGGACCTACTATGAGGGACCTGGCGAGGGCAGCCC CTTCGGCTGGAAGGACATCAAAGAATGGTACGAGATGCTGATGGGCC ACTGCACCTACTTCCCCGAGGAACTGCGGAGCGTGAAGTACGCCTACA ACGCCGACCTGTACAACGCCCTGAACGACCTGAACAATCTCGTGATCA CCAGGGACGAGAACGAGAAGCTGGAATATTACGAGAAGTTCCAGATC ATCGAGAACGTGTTCAAGCAGAAGAAGAAGCCCACCCTGAAGCAGAT CGCCAAAGAAATCCTCGTGAACGAAGAGGATATTAAGGGCTACAGAG TGACCAGCACCGGCAAGCCCGAGTTCACCAACCTGAAGGTGTACCAC GACATCAAGGACATTACCGCCCGGAAAGAGATTATTGAGAACGCCGA GCTGCTGGATCAGATTGCCAAGATCCTGACCATCTACCAGAGCAGCGA GGACATCCAGGAAGAACTGACCAATCTGAACTCCGAGCTGACCCAGG AAGAGATCGAGCAGATCTCTAATCTGAAGGGCTATACCGGCACCCAC AACCTGAGCCTGAAGGCCATCAACCTGATCCTGGACGAGCTGTGGCAC ACCAACGACAACCAGATCGCTATCTTCAACCGGCTGAAGCTGGTGCCC AAGAAGGTGGACCTGTCCCAGCAGAAAGAGATCCCCACCACCCTGGT GGACGACTTCATCCTGAGCCCCGTCGTGAAGAGAAGCTTCATCCAGAG CATCAAAGTGATCAACGCCATCATCAAGAAGTACGGCCTGCCCAACG ACATCATTATCGAGCTGGCCCGCGAGAAGAACTCCAAGGACGCCCAG AAAATGATCAACGAGATGCAGAAGCGGAACCGGCAGACCAACGAGC GGATCGAGGAAATCATCCGGACCACCGGCAAAGAGAACGCCAAGTAC CTGATCGAGAAGATCAAGCTGCACGACATGCAGGAAGGCAAGTGCCT GTACAGCCTGGAAGCCATCCCTCTGGAAGATCTGCTGAACAACCCCTT CAACTATGAGGTGGACCACATCATCCCCAGAAGCGTGTCCTTCGACAA CAGCTTCAACAACAAGGTGCTCGTGAAGCAGGAAGAAAACAGCAAGA AGGGCAACCGGACCCCATTCCAGTACCTGAGCAGCAGCGACAGCAAG ATCAGCTACGAAACCTTCAAGAAGCACATCCTGAATCTGGCCAAGGG CAAGGGCAGAATCAGCAAGACCAAGAAAGAGTATCTGCTGGAAGAAC GGGACATCAACAGGTTCTCCGTGCAGAAAGACTTCATCAACCGGAAC CTGGTGGATACCAGATACGCCACCAGAGGCCTGATGAACCTGCTGCG GAGCTACTTCAGAGTGAACAACCTGGACGTGAAAGTGAAGTCCATCA ATGGCGGCTTCACCAGCTTTCTGCGGCGGAAGTGGAAGTTTAAGAAAG AGCGGAACAAGGGGTACAAGCACCACGCCGAGGACGCCCTGATCATT GCCAACGCCGATTTCATCTTCAAAGAGTGGAAGAAACTGGACAAGGC CAAAAAAGTGATGGAAAACCAGATGTTCGAGGAAAAGCAGGCCGAGA GCATGCCCGAGATCGAAACCGAGCAGGAGTACAAAGAGATCTTCATC ACCCCCCACCAGATCAAGCACATTAAGGACTTCAAGGACTACAAGTA CAGCCACCGGGTGGACAAGAAGCCTAATAGAGAGCTGATTAACGACA CCCTGTACTCCACCCGGAAGGACGACAAGGGCAACACCCTGATCGTG AACAATCTGAACGGCCTGTACGACAAGGACAATGACAAGCTGAAAAA GCTGATCAACAAGAGCCCCGAAAAGCTGCTGATGTACCACCACGACC CCCAGACCTACCAGAAACTGAAGCTGATTATGGAACAGTACGGCGAC GAGAAGAATCCCCTGTACAAGTACTACGAGGAAACCGGGAACTACCT GACCAAGTACTCCAAAAAGGACAACGGCCCCGTGATCAAGAAGATTA AGTATTACGGCAACAAACTGAACGCCCATCTGGACATCACCGACGACT ACCCCAACAGCAGAAACAAGGTCGTGAAGCTGTCCCTGAAGCCCTAC AGATTCGACGTGTACCTGGACAATGGCGTGTACAAGTTCGTGACCGTG AAGAATCTGGATGTGATCAAAAAAGAAAACTACTACGAAGTGAATAG CAAGTGCTATGAGGAAGCTAAGAAGCTGAAGAAGATCAGCAACCAGG CCGAGTTTATCGCCTCCTTCTACAACAACGATCTGATCAAGATCAACG GCGAGCTGTATAGAGTGATCGGCGTGAACAACGACCTGCTGAACCGG ATCGAAGTGAACATGATCGACATCACCTACCGCGAGTACCTGGAAAA CATGAACGACAAGAGGCCCCCCAGGATCATTAAGACAATCGCCTCCA AGACCCAGAGCATTAAGAAGTACAGCACAGACATTCTGGGCAACCTG TATGAAGTGAAATCTAAGAAGCACCCTCAGATCATCAAAAAGGGCTA A
(51) Following is an exemplary nucleotide sequence (SEQ ID NO: 4) that encodes the Neisseria meningitidis Cas9 protein:
(52) TABLE-US-00005 ATGGCCGCCTTCAAGCCCAACCCCATCAACTACATCCTGGGCCTGGAC ATCGGCATCGCCAGCGTGGGCTGGGCCATGGTGGAGATCGACGAGGA CGAGAACCCCATCTGCCTGATCGACCTGGGTGTGCGCGTGTTCGAGCG CGCTGAGGTGCCCAAGACTGGTGACAGTCTGGCTATGGCTCGCCGGCT TGCTCGCTCTGTTCGGCGCCTTACTCGCCGGCGCGCTCACCGCCTTCTG CGCGCTCGCCGCCTGCTGAAGCGCGAGGGTGTGCTGCAGGCTGCCGAC TTCGACGAGAACGGCCTGATCAAGAGCCTGCCCAACACTCCTTGGCAG CTGCGCGCTGCCGCTCTGGACCGCAAGCTGACTCCTCTGGAGTGGAGC GCCGTGCTGCTGCACCTGATCAAGCACCGCGGCTACCTGAGCCAGCGC AAGAACGAGGGCGAGACCGCCGACAAGGAGCTGGGTGCTCTGCTGAA GGGCGTGGCCGACAACGCCCACGCCCTGCAGACTGGTGACTTCCGCAC TCCTGCTGAGCTGGCCCTGAACAAGTTCGAGAAGGAGAGCGGCCACA TCCGCAACCAGCGCGGCGACTACAGCCACACCTTCAGCCGCAAGGAC CTGCAGGCCGAGCTGATCCTGCTGTTCGAGAAGCAGAAGGAGTTCGGC AACCCCCACGTGAGCGGCGGCCTGAAGGAGGGCATCGAGACCCTGCT GATGACCCAGCGCCCCGCCCTGAGCGGCGACGCCGTGCAGAAGATGC TGGGCCACTGCACCTTCGAGCCAGCCGAGCCCAAGGCCGCCAAGAAC ACCTACACCGCCGAGCGCTTCATCTGGCTGACCAAGCTGAACAACCTG CGCATCCTGGAGCAGGGCAGCGAGCGCCCCCTGACCGACACCGAGCG CGCCACCCTGATGGACGAGCCCTACCGCAAGAGCAAGCTGACCTACG CCCAGGCCCGCAAGCTGCTGGGTCTGGAGGACACCGCCTTCTTCAAGG GCCTGCGCTACGGCAAGGACAACGCCGAGGCCAGCACCCTGATGGAG ATGAAGGCCTACCACGCCATCAGCCGCGCCCTGGAGAAGGAGGGCCT GAAGGACAAGAAGAGTCCTCTGAACCTGAGCCCCGAGCTGCAGGACG AGATCGGCACCGCCTTCAGCCTGTTCAAGACCGACGAGGACATCACCG GCCGCCTGAAGGACCGCATCCAGCCCGAGATCCTGGAGGCCCTGCTG AAGCACATCAGCTTCGACAAGTTCGTGCAGATCAGCCTGAAGGCCCTG CGCCGCATCGTGCCCCTGATGGAGCAGGGCAAGCGCTACGACGAGGC CTGCGCCGAGATCTACGGCGACCACTACGGCAAGAAGAACACCGAGG AGAAGATCTACCTGCCTCCTATCCCCGCCGACGAGATCCGCAACCCCG TGGTGCTGCGCGCCCTGAGCCAGGCCCGCAAGGTGATCAACGGCGTG GTGCGCCGCTACGGCAGCCCCGCCCGCATCCACATCGAGACCGCCCGC GAGGTGGGCAAGAGCTTCAAGGACCGCAAGGAGATCGAGAAGCGCCA GGAGGAGAACCGCAAGGACCGCGAGAAGGCCGCCGCCAAGTTCCGCG AGTACTTCCCCAACTTCGTGGGCGAGCCCAAGAGCAAGGACATCCTGA AGCTGCGCCTGTACGAGCAGCAGCACGGCAAGTGCCTGTACAGCGGC AAGGAGATCAACCTGGGCCGCCTGAACGAGAAGGGCTACGTGGAGAT CGACCACGCCCTGCCCTTCAGCCGCACCTGGGACGACAGCTTCAACAA CAAGGTGCTGGTGCTGGGCAGCGAGAACCAGAACAAGGGCAACCAGA CCCCCTACGAGTACTTCAACGGCAAGGACAACAGCCGCGAGTGGCAG GAGTTCAAGGCCCGCGTGGAGACCAGCCGCTTCCCCCGCAGCAAGAA GCAGCGCATCCTGCTGCAGAAGTTCGACGAGGACGGCTTCAAGGAGC GCAACCTGAACGACACCCGCTACGTGAACCGCTTCCTGTGCCAGTTCG TGGCCGACCGCATGCGCCTGACCGGCAAGGGCAAGAAGCGCGTGTTC GCCAGCAACGGCCAGATCACCAACCTGCTGCGCGGCTTCTGGGGCCTG CGCAAGGTGCGCGCCGAGAACGACCGCCACCACGCCCTGGACGCCGT GGTGGTGGCCTGCAGCACCGTGGCCATGCAGCAGAAGATCACCCGCTT CGTGCGCTACAAGGAGATGAACGCCTTCGACGGTAAAACCATCGACA AGGAGACCGGCGAGGTGCTGCACCAGAAGACCCACTTCCCCCAGCCC TGGGAGTTCTTCGCCCAGGAGGTGATGATCCGCGTGTTCGGCAAGCCC GACGGCAAGCCCGAGTTCGAGGAGGCCGACACCCCCGAGAAGCTGCG CACCCTGCTGGCCGAGAAGCTGAGCAGCCGCCCTGAGGCCGTGCACG AGTACGTGACTCCTCTGTTCGTGAGCCGCGCCCCCAACCGCAAGATGA GCGGTCAGGGTCACATGGAGACCGTGAAGAGCGCCAAGCGCCTGGAC GAGGGCGTGAGCGTGCTGCGCGTGCCCCTGACCCAGCTGAAGCTGAA GGACCTGGAGAAGATGGTGAACCGCGAGCGCGAGCCCAAGCTGTACG AGGCCCTGAAGGCCCGCCTGGAGGCCCACAAGGACGACCCCGCCAAG GCCTTCGCCGAGCCCTTCTACAAGTACGACAAGGCCGGCAACCGCACC CAGCAGGTGAAGGCCGTGCGCGTGGAGCAGGTGCAGAAGACCGGCGT GTGGGTGCGCAACCACAACGGCATCGCCGACAACGCCACCATGGTGC GCGTGGACGTGTTCGAGAAGGGCGACAAGTACTACCTGGTGCCCATCT ACAGCTGGCAGGTGGCCAAGGGCATCCTGCCCGACCGCGCCGTGGTG CAGGGCAAGGACGAGGAGGACTGGCAGCTGATCGACGACAGCTTCAA CTTCAAGTTCAGCCTGCACCCCAACGACCTGGTGGAGGTGATCACCAA GAAGGCCCGCATGTTCGGCTACTTCGCCAGCTGCCACCGCGGCACCGG CAACATCAACATCCGCATCCACGACCTGGACCACAAGATCGGCAAGA ACGGCATCCTGGAGGGCATCGGCGTGAAGACCGCCCTGAGCTTCCAG AAGTACCAGATCGACGAGCTGGGCAAGGAGATCCGCCCCTGCCGCCT GAAGAAGCGCCCTCCTGTGCGCTGA
(53) In some embodiments of the present invention, the recombinant Cas protein is derived from a Cas protein encoded by a nucleic acid molecule comprising a nucleotide sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the nucleotide sequence of SEQ ID NO: 1.
(54) In certain embodiments, the recombinant Cas protein is derived from a Cas protein encoded by a nucleic acid molecule comprising a nucleotide sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the nucleotide sequence of SEQ ID NO: 2.
(55) In some embodiments, the recombinant Cas protein is derived from a Cas protein encoded by a nucleic acid molecule comprising a nucleotide sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the nucleotide sequence of SEQ ID NO: 3.
(56) In certain embodiments, the recombinant Cas protein is derived from a Cas protein encoded by a nucleic acid molecule comprising a nucleotide sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the nucleotide sequence of SEQ ID NO: 4.
(57) Following is the amino acid sequence of the Streptococcus pyogenes Cas9 protein (SEQ ID NO: 5) (see Esvelt, et al., “Orthogonal Cas9 proteins for RNA-guided gene regulation and editing,” Nature Methods 10(11):1116-21 (2013), which is incorporated by reference herein in its entirety):
(58) TABLE-US-00006 MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLI GALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDS FFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVD STDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTY NQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGN LIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYAD LFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLK ALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMD GTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPF LKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEE VVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVK YVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFD SVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLT LFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRD KQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQ TTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYL QNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNR GKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELD KAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKS KLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEF VYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGE IRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGG FSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKG KSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPK YSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGS PEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNK HRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLD ATLIHQSITGLYETRIDLSQLGGD
(59) Following is the amino acid sequence of the Streptococcus thermophilus LMD-9 Cas9 protein (SEQ ID NO: 6) (see Esvelt, et al., “Orthogonal Cas9 proteins for RNA-guided gene regulation and editing,” Nature Methods 10(11):1116-21 (2013), which is incorporated by reference herein in its entirety):
(60) TABLE-US-00007 MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRT NRQGRRLARRKKHRRVRLNRLFEESGLITDFTKISINLNPYQLRVKGL TDELSNEELFIALKNMVKHRGISYLDDASDDGNSSVGDYAQIVKENSK QLETKTPGQIQLERYQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSE ALRILQTQQEFNPQITDEFINRYLEILTGKRKYYHGPGNEKSRTDYGR YRTSGETLDNIFGILIGKCTFYPDEFRAAKASYTAQEFNLLNDLNNLT VPTETKKLSKEQKNQIINYVKNEKAMGPAKLFKYIAKLLSCDVADIKG YRIDKSGKAEIHTFEAYRKMKTLETLDIEQMDRETLDKLAYVLTLNTE REGIQEALEHEFADGSFSQKQVDELVQFRKANSSIFGKGWHNFSVKLM MELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIYNP VVAKSVRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQK ANKDEKDAAMLKAANQYNGKAELPHSVFHGHKQLATKIRLWHQQGERC LYTGKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATANQE KGQRTPYQALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISK FDVRKKFIERNLVDTRYASRVVLNALQEHFRAHKIDTKVSVVRGQFTS QLRRHWGIEKTRDTYHHHAVDALIIAASSQLNLWKKQKNTLVSYSEDQ LLDIETGELISDDEYKESVFKAPYQHFVDTLKSKEFEDSILFSYQVDS KFNRKISDATIYATRQAKVGKDKADETYVLGKIKDIYTQDGYDAFMKI YKKDKSKFLMYRHDPQTFEKVIEPILENYPNKQINDKGKEVPCNPFLK YKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDITPKDSNNKVVLQ SVSPWRADVYFNKTTGKYEILGLKYADLQFDKGTGTYKISQEKYNDIK KKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTMPKQKHYV ELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLGKSNISIYKVRTDVL GNQHIIKNEGDKPKLDF
(61) Following is the amino acid sequence of the Staphylococcus aureus subsp. aureus Cas9 protein (SEQ ID NO: 7) (see Ran, et al., “In vivo genome editing using Staphylococcus aureus Cas9,” Nature 520(7546):186-91 (2015), which is incorporated by reference herein in its entirety):
(62) TABLE-US-00008 MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRR SKRGARRLKRRRRHRIQRVKKLLFDYNLLTDHSELSGINPYEARVKGL SQKLSEEEFSAALLHLAKRRGVHNVNEVEEDTGNELSTKEQISRNSKA LEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQ LDQSFIDTYIDLLETRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYF PEELRSVKYAYNADLYNALNDLNNLVITRDENEKLEYYEKFQIIENVF KQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDIT ARKEIIENAELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQIS NLKGYTGTHNLSLKAINLILDELWHTNDNQIAIFNRLKLVPKKVDLSQ QKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAR EKNSKDAQKMINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHD MQEGKCLYSLEAIPLEDLLNNPFNYEVDHIIPRSVSFDNSENNKVLVK QEENSKKGNRTPFQYLSSSDSKISYETFKKHILNLAKGKGRISKTKKE YLLEERDINRFSVQKDFINRNLVDTRYATRGLMNLLRSYFRVNNLDVK VKSINGGFTSFLRRKWKFKKERNKGYKHHAEDALIIANADFIFKEWKK LDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFKD YKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKL KKLINKSPEKLLMYHHDPQTYQKLKLIMEQYGDEKNPLYKYYEETGNY LTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSRNKVVKLSLKPY RFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQA EFIASFYNNDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENM NDKRPPRIIKTIASKTQSIKKYSTDILGNLYEVKSKKHPQIIKKG
(63) Following is the amino acid sequence of the Neisseria meningitidis Cas9 protein (SEQ ID NO: 8) (see Esvelt, et al., “Orthogonal Cas9 proteins for RNA-guided gene regulation and editing,” Nature Methods 10(11):1116-21 (2013), which is incorporated by reference herein in its entirety):
(64) TABLE-US-00009 MAAFKPNPINYILGLDIGIASVGWAMVEIDEDENPICLIDLGVRVFER AEVPKTGDSLAMARRLARSVRRLTRRRAHRLLRARRLLKREGVLQAAD FDENGLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHRGYLSQR KNEGETADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHI RNQRGDYSHTFSRKDLQAELILLFEKQKEFGNPHVSGGLKEGIETLLM TQRPALSGDAVQKMLGHCTFEPAEPKAAKNTYTAERFIWLTKLNNLRI LEQGSERPLTDTERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLR YGKDNAEASTLMEMKAYHAISRALEKEGLKDKKSPLNLSPELQDEIGT AFSLFKTDEDITGRLKDRIQPEILEALLKHISFDKFVQISLKALRRIV PLMEQGKRYDEACAEIYGDHYGKKNTEEKIYLPPIPADEIRNPVVLRA LSQARKVINGVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENRK DREKAAAKFREYFPNFVGEPKSKDILKLRLYEQQHGKCLYSGKEINLG RLNEKGYVEIDHALPFSRTWDDSFNNKVLVLGSENQNKGNQTPYEYFN GKDNSREWQEFKARVETSRFPRSKKQRILLQKFDEDGFKERNLNDTRY VNRFLCQFVADRMRLTGKGKKRVFASNGQITNLLRGFWGLRKVRAEND RHHALDAVVVACSTVAMQQKITRFVRYKEMNAFDGKTIDKETGEVLHQ KTHFPQPWEFFAQEVMIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSS RPEAVHEYVTPLFVSRAPNRKMSGQGHMETVKSAKRLDEGVSVLRVPL TQLKLKDLEKMVNREREPKLYEALKARLEAHKDDPAKAFAEPFYKYDK AGNRTQQVKAVRVEQVQKTGVWVRNHNGIADNATMVRVDVFEKGDKYY LVPIYSWQVAKGILPDRAVVQGKDEEDWQLIDDSFNFKFSLHPNDLVE VITKKARMFGYFASCHRGTGNINIRIHDLDHKIGKNGILEGIGVKTAL SFQKYQIDELGKEIRPCRLKKRPPVR
(65) In some embodiments of the present invention, the recombinant Cas protein is derived from a Cas protein comprising an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the amino acid sequence of SEQ ID NO: 5.
(66) In certain embodiments, the recombinant Cas protein is derived from a Cas protein comprising an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the amino acid sequence of SEQ ID NO: 6.
(67) In some embodiments, the recombinant Cas protein is derived from a Cas protein comprising an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the amino acid sequence of SEQ ID NO: 7.
(68) In certain embodiments, the recombinant Cas protein is derived from a Cas protein comprising an amino acid sequence having at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% identity with the amino acid sequence of SEQ ID NO: 8.
(69) The present invention is also directed to recombinant Cas proteins comprising one or more amino acid substitutions in one or more residues corresponding to one or more MHC Class I and/or MHC Class II binding sites in a wild-type Cas protein. In certain embodiments, the recombinant Cas protein is derived from the wild-type protein containing the corresponding MHC Class I and/or Class II binding sites. In some embodiments, the recombinant Cas protein has reduced immunogenicity compared to the wild-type Cas protein from which it is derived. In some embodiments, the recombinant Cas protein is isolated and in other embodiments it is located within a cell.
(70) In some embodiments, the recombinant Cas protein is derived from a Cas9-like protein, such as Cpf1, disclosed in Zetsche et al., “Cpf1 is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System,” Cell 163:759-771 (2015), incorporated herein by reference in its entirety.
(71) In some embodiments, the disclosure is directed to a recombinant CRISPR-associated (Cas) protein, wherein said protein comprises one or more amino acid variation compared to a while-type Cas protein, wherein the one or more amino acid variation is at one or more positions corresponding to amino acid residues in the polypeptide of SEQ ID NO: 5, wherein the variation is at a position selected from the group consisting of (i) residues 100 to 120, (ii) residues 250 to 280, (iii) residues 690 to 710, (iv) residues 840 to 860, and (v) residues 1270 to 1295. In some embodiments, the variation is at a position selected from the group consisting of (i) residues 102 to 120, (ii) residues 253 to 277, (iii) residues 692 to 709, (iv) residues 692 to 709, and (v) residues 1276 to 1292.
(72) In some embodiments, the variation is at a position selected from residues 102 to 120. In some embodiments, the variation is at a position selected from residues 253 to 277. In some embodiments, the variation is at a position selected from residues 692 to 709. In some embodiments, the variation is at a position selected from residues 692 to 709. In some embodiments, the variation is at a position selected from residues 1276 to 1292.
(73) In some embodiments, the recombinant Cas protein comprises two or more amino acid variations. In some embodiments, the recombinant Cas protein comprises three or more amino acid variations. In some embodiments, the amino acid variation is determined using in silico epitope mapping.
(74) The term “variation,” when referring to a variation at a given polypeptide residue position, refers to any modifications at those residues. For example, the term variation can refer to substituting (i.e., replacing) an amino acid (i.e., residue) at a given position with a different amino acid. In some embodiments, the amino acid can be substituted with a different amino acid having a different property. Various predictive algorithms for determining the immunogenic properties of a polypeptide are known in the art, and can include (1) the ratio between the frequencies of aspargine, glutamine, leucine, lysine, methionine, serine, threonine, and valine residues in the stretch and the remaining antigen sequence; (2) Grantham polarity scale (Grantham et al., Science. 185: 862-864 (1974)); (3) Karplus and Schulz flexibility scale (Karplus et al., Naturwissenschaften 72: 212-213 (1985)); (4) Kolaskar and Tongaonkar antigenicity scale (Kolaskar et al., FEBS Lett. 276: 172-174 (1990)); (5) Parker hydrophilicity scale (Parker et al., Biochemistry 25: 5425-5432 (1986)); (6) Ponnuswamy polarity scale (Ponnuswamy et al., Biochim. Biophys. Acta. 623: 301-326 (1980)); and, (7) Atchley et al. factor1 scale (Atchley et al., Proc. Natl. Acad. Sci. U.S.A. 102: 6395-6400 (2005)). In some embodiments, EPIBASE® can be used to determine what amino acid can be used to reduce immunogenicity of the polypeptide.
(75) For example, in some embodiments, one or more of aspargine, glutamine, leucine, lysine, methionine, serine, threonine, and valine residues can be replaced with a different amino acid. In some embodiments, the amino acid variation comprises replacing a polar amino acid with a nonpolar amino acid. In some embodiments, the amino acid variation comprises replacing a hydrophilic amino acid with a hydrophobic amino acid. In some embodiments, and amino acid with a large side chain can be replaced with an amino acid with a smaller side chain.
(76) In some embodiments, the term variation can refer to deleting one or more amino acids residues into the Cas protein. For example, in some embodiments, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18 or 20 amino acids can be deleted in one epitope. In some embodiments, one or more amino acids can be deleted from two or more epitopes on the same protein. In some embodiments, the deletions are not contiguous on the polypeptide, e.g., one deletion can occur on one region of the polypeptide, and a separate deletion can occur on a separate part of the polypeptide.
(77) In some embodiments, the term variation can refer to inserting one or more amino acid residues into the Cas protein. For example, in some embodiments, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 16, 18 or 20 amino acids can be inserted in one epitope. In some embodiments, one or more amino acids can be inserted into two or more epitopes on the same protein. In some embodiments, the insertions are not contiguous on the polypeptide, e.g., one insertion can occur on one region of the polypeptide, and a separate insertion can occur on a separate part of the polypeptide.
(78) In some embodiments, the Cas protein can have various types of variations. For example, in some embodiments, the Cas protein can have one or more amino acid substitutions, one or more amino acid deletions, and one or more amino acid insertions.
(79) In some embodiments, the wild-type Cas protein has a sequence 90% identical to SEQ ID NO: 5. In some embodiments, the wild-type Cas protein has a sequence 90% identical to SEQ ID NO: 6. In some embodiments, the wild-type Cas protein has a sequence 90% identical to SEQ ID NO: 7. In some embodiments, the wild-type Cas protein has a sequence 90% identical to SEQ ID NO: 8. In some embodiments, the wild-type Cas protein has a sequence 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 5. In some embodiments, the wild-type Cas protein has a sequence 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 6. In some embodiments, the wild-type Cas protein has a sequence 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 7. In some embodiments, the wild-type Cas protein has a sequence 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98% or 99% identical to SEQ ID NO: 8.
(80) In some embodiments, the wild-type Cas protein is derived from a prokaryote. In some embodiments, the prokaryote is a bacterium. In some embodiments, the bacterium is from the genera Streptococcus, Staphylococcus, or Neisseria. In some embodiments, the bacterium is Streptococcus pyogenes, Streptococcus thermophilus, Staphylococcus aureus, or Neisseria meningitidis.
(81) In some embodiments, the recombinant Cas protein is derived from Cas3, Cas9, or Cas10. In some embodiments, the recombinant Cas protein is derived from Cas9.
Polynucleotides, Expression Vectors, and Host Cells
(82) In some embodiments, the polynucleotides or expression vectors encoding Cas proteins (or variants thereof) are placed in a host cell, e.g, a prokaryote or eukaryote cell. The devices, facilities and methods described herein are suitable for culturing any desired cell line including prokaryotic and/or eukaryotic cell lines. Further, in some embodiments, the devices, facilities and methods are suitable for culturing suspension cells or anchorage-dependent (adherent) cells and are suitable for production operations configured for production of pharmaceutical and biopharmaceutical products—such as polypeptide products, nucleic acid products (for example DNA or RNA).
(83) In embodiments, the host cells express or produce a product, such as a Cas protein or variant thereof, or expression vectors encoding the Cas protein or variant thereof.
(84) In some embodiments, devices, facilities and methods allow for the production of host eukaryotic cells comprising the described expression vectors, e.g., mammalian cells or lower eukaryotic cells such as for example yeast cells or filamentous fungi cells, or prokaryotic cells such as Gram-positive or Gram-negative cells, synthesised by the host cells in a large-scale manner. Unless stated otherwise herein, the devices, facilities, and methods can include any desired volume or production capacity including but not limited to bench-scale, pilot-scale, and full production scale capacities.
(85) Moreover and unless stated otherwise herein, the host cells can be generated using devices, facilities, and methods including any suitable reactor(s) including but not limited to stirred tank, airlift, fiber, microfiber, hollow fiber, ceramic matrix, fluidized bed, fixed bed, and/or spouted bed bioreactors. As used herein, “reactor” can include a fermentor or fermentation unit, or any other reaction vessel and the term “reactor” is used interchangeably with “fermentor.” For example, in some aspects, an example bioreactor unit can perform one or more, or all, of the following: feeding of nutrients and/or carbon sources, injection of suitable gas (e.g., oxygen), inlet and outlet flow of fermentation or cell culture medium, separation of gas and liquid phases, maintenance of temperature, maintenance of oxygen and CO2 levels, maintenance of pH level, agitation (e.g., stirring), and/or cleaning/sterilizing. Example reactor units, such as a fermentation unit, may contain multiple reactors within the unit, for example the unit can have 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, or 100, or more bioreactors in each unit and/or a facility may contain multiple units having a single or multiple reactors within the facility. In various embodiments, the bioreactor can be suitable for batch, semi fed-batch, fed-batch, perfusion, and/or a continuous fermentation processes. Any suitable reactor diameter can be used. In embodiments, the bioreactor can have a volume between about 100 mL and about 50,000 L. Non-limiting examples include a volume of 100 mL, 250 mL, 500 mL, 750 mL, 1 liter, 2 liters, 3 liters, 4 liters, 5 liters, 6 liters, 7 liters, 8 liters, 9 liters, 10 liters, 15 liters, 20 liters, 25 liters, 30 liters, 40 liters, 50 liters, 60 liters, 70 liters, 80 liters, 90 liters, 100 liters, 150 liters, 200 liters, 250 liters, 300 liters, 350 liters, 400 liters, 450 liters, 500 liters, 550 liters, 600 liters, 650 liters, 700 liters, 750 liters, 800 liters, 850 liters, 900 liters, 950 liters, 1000 liters, 1500 liters, 2000 liters, 2500 liters, 3000 liters, 3500 liters, 4000 liters, 4500 liters, 5000 liters, 6000 liters, 7000 liters, 8000 liters, 9000 liters, 10,000 liters, 15,000 liters, 20,000 liters, and/or 50,000 liters. Additionally, suitable reactors can be multi-use, single-use, disposable, or non-disposable and can be formed of any suitable material including metal alloys such as stainless steel (e.g., 316 L or any other suitable stainless steel) and Inconel, plastics, and/or glass.
(86) In some embodiments and unless stated otherwise herein, the methods described herein can also include any suitable unit operation and/or equipment not otherwise mentioned, such as operations and/or equipment for separation, purification, and isolation of Cas proteins or variants thereof, or expression vectors expressing the Cas proteins or variants thereof. Any suitable facility and environment can be used, such as traditional stick-built facilities, modular, mobile and temporary facilities, or any other suitable construction, facility, and/or layout. For example, in some embodiments modular clean-rooms can be used. Additionally and unless otherwise stated, the devices, systems, and methods described herein can be housed and/or performed in a single location or facility or alternatively be housed and/or performed at separate or multiple locations and/or facilities.
(87) By way of non-limiting examples and without limitation, U.S. Publication Nos. 2013/0280797; 2012/0077429; 2011/0280797; 2009/0305626; and U.S. Pat. Nos. 8,298,054; 7,629,167; and 5,656,491, which are hereby incorporated by reference in their entirety, describe example facilities, equipment, and/or systems that may be suitable.
(88) In some embodiments, the host cells are eukaryotic cells, e.g., mammalian cells. The mammalian cells can be for example human or rodent or bovine cell lines or cell strains. Examples of such cells, cell lines or cell strains are e.g. mouse myeloma (NSO)-cell lines, Chinese hamster ovary (CHO)-cell lines, HT1080, H9, HepG2, MCF7, MDBK Jurkat, NIH3T3, PC12, BHK (baby hamster kidney cell), VERO, SP2/0, YB2/0, Y0, C127, L cell, COS, e.g., COS1 and COS7, QC1-3,HEK-293, VERO, PER.C6, HeLA, EB1, EB2, EB3, oncolytic or hybridoma-cell lines. Preferably the mammalian cells are CHO-cell lines. In one embodiment, the cell is a CHO cell. In one embodiment, the cell is a CHO-K1 cell, a CHO-K1 SV cell, a DG44 CHO cell, a DUXB11 CHO cell, a CHOS, a CHO GS knock-out cell, a CHO FUT8 GS knock-out cell, a CHOZN, or a CHO-derived cell. The CHO GS knock-out cell (e.g., GSKO cell) is, for example, a CHO-K1 SV GS knockout cell. The CHO FUT8 knockout cell is, for example, the Potelligent® CHOK1 SV (Lonza Biologics, Inc.). Eukaryotic cells can also be avian cells, cell lines or cell strains, such as for example, EBx® cells, EB14, EB24, EB26, EB66, or EBvl3.
(89) In some embodiments, the host cells are stem cells. The stem cells can be, for example, pluripotent stem cells, including embryonic stem cells (ESCs), adult stem cells, induced pluripotent stem cells (iPSCs), tissue specific stem cells (e.g., hematopoietic stem cells) and mesenchymal stem cells (MSCs).
(90) In some embodiments, the host cell is a differentiated form of any of the cells described herein. In one embodiment, the host cell is a cell derived from any primary cell in culture.
(91) In some embodiments, the host cell is a hepatocyte such as a human hepatocyte, animal hepatocyte, or a non-parenchymal cell. For example, the host cell can be a plateable metabolism qualified human hepatocyte, a plateable induction qualified human hepatocyte, plateable Qualyst Transporter Certified™ human hepatocyte, suspension qualified human hepatocyte (including 10-donor and 20-donor pooled hepatocytes), human hepatic kupffer cells, human hepatic stellate cells, dog hepatocytes (including single and pooled Beagle hepatocytes), mouse hepatocytes (including CD-1 and C57BI/6 hepatocytes), rat hepatocytes (including Sprague-Dawley, Wistar Han, and Wistar hepatocytes), monkey hepatocytes (including Cynomolgus or Rhesus monkey hepatocytes), cat hepatocytes (including Domestic Shorthair hepatocytes), and rabbit hepatocytes (including New Zealand White hepatocytes). Example hepatocytes are commercially available from Triangle Research Labs, LLC, 6 Davis Drive Research Triangle Park, N.C., USA 27709.
(92) In one embodiment, the host cell is a lower eukaryotic cell such as e.g. a yeast cell (e.g., Pichia genus (e.g. Pichia pastoris, Pichia methanolica, Pichia kluyveri, and Pichia angusta), Komagataella genus (e.g. Komagataella pastoris, Komagataella pseudopastoris or Komagataella phaffii), Saccharomyces genus (e.g. Saccharomyces cerevisae, cerevisiae, Saccharomyces kluyveri, Saccharomyces uvarum), Kluyveromyces genus (e.g. Kluyveromyces lactis, Kluyveromyces marxianus), the Candida genus (e.g. Candida utilis, Candida cacaoi, Candida boidinii,), the Geotrichum genus (e.g. Geotrichum fermentans), Hansenula polymorpha, Yarrowia lipolytica, or Schizosaccharomyces pombe. Preferred is the species Pichia pastoris. Examples for Pichia pastoris strains are X33, GS115, KM71, KM71H; and CBS7435.
(93) In some embodiments, the host cell is a fungal cell (e.g. Aspergillus (such as A. niger, A. fumigatus, A. orzyae, A. nidula), Acremonium (such as A. thermophilum), Chaetomium (such as C. thermophilum), Chrysosporium (such as C. thermophile), Cordyceps (such as C. militaris), Corynascus, Ctenomyces, Fusarium (such as F. oxysporum), Glomerella (such as G. graminicola), Hypocrea (such as H. jecorina), Magnaporthe (such as M. orzyae), Myceliophthora (such as M. thermophile), Nectria (such as N. heamatococca), Neurospora (such as N. crassa), Penicillium, Sporotrichum (such as S. thermophile), Thielavia (such as T. terrestris, T. heterothallica), Trichoderma (such as T. reesei), or Verticillium (such as V. dahlia)).
(94) In some embodiments, the host cell is an insect cell (e.g., Sf9, Mimic™ Sf9, Sf21, High Five™ (BT1-TN-5B1-4), or BT1-Ea88 cells), an algae cell (e.g., of the genus Amphora, Bacillariophyceae, Dunaliella, Chlorella, Chlamydomonas, Cyanophyta (cyanobacteria), Nannochloropsis, Spirulina, or Ochromonas), or a plant cell (e.g., cells from monocotyledonous plants (e.g., maize, rice, wheat, or Setaria), or from a dicotyledonous plants (e.g., cassava, potato, soybean, tomato, tobacco, alfalfa, Physcomitrella patens or Arabidopsis).
(95) In some embodiments, the host cell is a bacterial or prokaryotic cell.
(96) In some embodiments, the host cell is a Gram-positive cells such as Bacillus, Streptomyces Streptococcus, Staphylococcus or Lactobacillus. Bacillus that can be used is, e.g. the B. subtilis, B. amyloliquefaciens, B. licheniformis, B. natto, or B. megaterium. In embodiments, the cell is B. subtilis, such as B. subtilis 3NA and B. subtilis 168. Bacillus is obtainable from, e.g., the Bacillus Genetic Stock Center, Biological Sciences 556, 484 West 12.sup.th Avenue, Columbus Ohio 43210-1214.
(97) In some embodiments, the host cell is a Gram-negative cell, such as Salmonella spp. or Escherichia coli, such as e.g., TG1, TG2, W3110, DH1, DHB4, DH5a, HMS174, HMS174 (DE3), NM533, C600, HB101, JM109, MC4100, XL1-Blue and Origami, as well as those derived from E. coli B-strains, such as for example BL-21 or BL21 (DE3), all of which are commercially available.
(98) Suitable host cells are commercially available, for example, from culture collections such as the DSMZ (Deutsche Sammlung von Mikroorganismen and Zellkulturen GmbH, Braunschweig, Germany) or the American Type Culture Collection (ATCC).
Immunogenicity and T-cell Responses in Humans
(99) In humans, a cytotoxic T lymphocyte (CTL) response is initiated when a T-cell's unique T-cell receptor (TCR) recognizes a peptide bound to the HLA Class I molecules, displayed on the surface of most nucleated cells. Only those peptides with sufficient affinity for the HLA Class I receptor can be presented on the cell's surface, and potentially trigger a CTL response. Knowing which peptides within a protein have a strong affinity for HLA Class I receptors is therefore an important step towards determining the immunogenic regions of the protein.
(100) The HLA Class I molecule is made of up two polypeptide chains: the α chain and β-2 microglobulin, each of which is derived from a different gene. Individuals express multiple genes encoding the α-chain: A, B, C, E, F, G, K and L. The dominant α-chain genes, A-C, are highly polymorphic. Different HLA Class I molecules are described as HLA allotypes.
(101) For a complete analysis of the immunogenicity of a protein or peptide, one should therefore test the affinity/immunogenicity of each peptide for each possible HLA Class I allotype. Fortunately, however, some allotypes have a higher prevalence in a given population than others. As a result, the analysis for any population can be done in most cases by focusing on a limited number of allotypes. In general, an individual's T-cell population has been selected not to contain cells that recognize “self-peptides” (peptides derived from endogenous proteins) presented on HLA Class I receptors. Therefore, peptides from an exogenous protein that correspond to (known) self-peptides will normally not induce a CTL response, even if they have a high affinity for HLA Class I receptors. It is not always clear which endogenous proteins are presented and as such give rise to self-peptides.
(102) A T.sub.h (T-helper) response is sparked when a T.sub.h Cell's unique T-Cell receptor (TCR) recognizes a peptide bound to the HLA Class II molecules displayed on antigen presenting cells (APCs). These peptides are generated from proteins internalized by an antigen presenting cell, and then cleaved through its endosomal cleavage pathway. Only those peptides with sufficient affinity for the HLA Class II receptor can be presented on the cells surface and potentially trigger a T.sub.h response. Knowing which peptides within a protein have a strong affinity for HLA Class II receptors is therefore an important step towards determining the protein's immunogenic regions.
(103) The picture, however, can be complicated by the fact that there are several HLA Class II genes, almost all of which are highly polymorphic. Each HLA Class II molecule consists of an α and β chain, each derived from a different gene, which further increases the number of possible HLA Class II molecules. Specifically, every human individual expresses the following genes: DRA/DRB, DQA/DQB and DPA/DPB. Of these, only DRA is non-polymorphic. In addition, a “second” DRB gene (DRB3, DRB4 or DRB5) may also be present, whose product also associates with the DRA chain.
(104) For a complete analysis of the immunogenicity of a protein or peptide, one should therefore test the affinity/immunogenicity of each peptide for each possible HLA Class II allotype. Fortunately however, some allotypes have a higher prevalence in a given population than others. As a result, the analysis for any population can be performed in most cases by focusing on a limited number of allotypes.
(105) Furthermore, the expression levels of receptors of the DQ and DP gene families are known to be significantly lower than those of DRB, making the latter the primary focus of immunogenicity profiling. See Laupeze et al., “Differential expression of major histocompatibility complex class Ia, Ib, and II molecules on monocytes-derived dendritic and macrophagic cells,” Hum. Immunol. 60(7):591-7 (1999); Gansbacher and Zier, “Regulation of HLA-DR, DP, and DQ expression in activated T cells,” Cell Immunol. 117(1):22-34 (1988); Berdoz, et al., “Constitutive and induced expression of the individual HLA-DR beta and alpha chain loci in different cell types,” J. Immunol. 139(4):1336-41 (1987); and Stunz, et al., “HLA-DRB1 and -DRB4 genes are differentially regulated at the transcriptional level,” J. Immunol. 143(9):3081-6 (1989), each of which is incorporated by reference herein in its entirety.
(106) Differences of expression exist between presenting cells, e.g., dendritic cells vs. macrophages. See Laupeze, et al. Also, differences in HLA expression levels have been correlated with the magnitude of the T-cell response. Vader, et al., “The HLA-DQ2 gene dose effect in celiac disease is directly related to the magnitude and breadth of gluten-specific T cell responses,” PNAS 100(21):12390-5 (2003), which is incorporated by reference herein in its entirety. Cases of DQ- and DP-restricted T-cell response have been documented (see e.g., Castelli, et al., “HLA-DP4, the most frequent HLA II molecule, defines new supertype of peptide-binding specificity,” J. Immunol. 169(12):6928-34 (2002), which is incorporated by reference herein in its entirety), thus it is recommended that strong DQ and DP binders are not ignored when analyzing the immunogenicity of a protein.
(107) In general, an individual's T-cell population has been selected not to contain cells that recognize “self-peptides” presented on HLA Class II receptors. These are peptides derived from endogenous proteins after internalization by an antigen presenting cell. Therefore, peptides from an exogenous protein which correspond to (known) self-peptides will normally not induce a T.sub.h response, even if they have a high affinity for HLA Class II receptors. It is not clear which endogenous proteins are internalized and as such give rise to self-peptides. See Kirschmann, et al., “Naturally processed peptides from rheumatoid arthritis associated and non-associated HLA-DR alleles,” J. Immunol. 155(12):5655-62 (1995) and Verreck, et al., “Natural peptides isolated from Gly86/Val86-containing variants of HLA-DR1, -DR11, -DR13, and -DR52,” Immunogenetics 43(6):392-7 (1996), each of which is incorporated by reference herein in its entirety.
(108) In addition to epitopes bound to HLA molecules, as described above, it is also important to consider presence of epitopes bound by surface IgG molecules (B cell receptors) found on B cells. B cell receptors are responsible for selective uptake of antigens and presentation on B cells via HLA Class II, for subsequent interaction with T cell receptors found on T helper cells. In contrast to peptides bound by HLA molecules which have been processed such that they are considered only in linear terms, B cell epitopes can also be conformational, as they are found in the native context of the protein.
(109) The conformational aspect of B cell epitopes makes in silico prediction problematic relative to T cell epitopes (HLA binding). In vitro assays, however, can be used to identify B cell activation in response to either full length proteins (conformational and linear epitopes) or derived peptides (linear epitopes) covering the relevant regions.
Methods for Reducing Immunogenicity
(110) Certain embodiments of the present invention are directed to methods for making a recombinant Cas protein having reduced immunogenicity, i.e., with a reduced ability to elicit a CTL or T.sub.h response in a host, such as a human. In some embodiments, the method comprises introducing one or more amino acid residues corresponding to one or more histocompatibility (MHC) Class I and/or Class II binding sites of the Cas protein to form a recombinant Cas protein, wherein the recombinant Cas protein has reduced immunogenicity compared to the Cas protein from which it was derived. In some embodiments of the invention, the position of the amino acid substitution(s) is determined through epitope mapping. In certain embodiments, the position of the amino acid substitution(s) is determined using in silico epitope mapping and in some embodiments the position of the amino acid substitution(s) is determined using cell-based epitope mapping.
Methods for Epitope Mapping
(111) In certain embodiments of the invention, the position of one or more amino acid substitutions for reducing the immunogenicity of a Cas protein is selected through in silico epitope mapping. Methods for in silico prediction of immunogenicity that can be used in the present invention are available from academic and commercial sources. Examples include those provided by Lonza (EPIBASE®; see, e.g., U.S. Pat. No. 7,702,465 and EP1516275, each of which is incorporated by reference herein in its entirety) and the Centre of Biological Sequence Analysis at the Technical University of Denmark (NetMHC; cbs.dtu.dk/services/NetMHC/). Such tools, on occasion, can be over-predictive of immunogenic epitopes and are therefore frequently combined with in vitro or ex vivo assays, such as those provided herein, in order to further refine results. A description of such in silico methodologies in combination with cell-based assays, as well as its utilization to reduce the impact of immunogenicity risks in therapeutics, has been reviewed elsewhere (see e.g., Zurdo 2013 and Zurdo et al. 2015, each of which is incorporated by reference herein in its entirety).
(112) In some embodiments of the present invention, epitope mapping of Cas proteins is performed using cell-based methods. For example, in certain embodiments, antigen presenting cells (APCs) are incubated in the presence of Cas proteins. Subsequently, MHC Class I and Class II proteins (e.g., HLA Class I and Class II proteins) are isolated from the APCs and the Cas9-derived peptides bound the MHC Class I and/or Class II proteins are identified. In certain embodiments, the MHC Class I and Class II proteins are isolated by immunoprecipitation. In some embodiments, the Cas9 derived peptides bound the MHC Class I and Class II proteins are identified by mass spectrometry (MS).
(113) In other embodiments of the invention, short synthetic peptides representing putative T-cell epitopes from the Cas proteins are incubated with cells (e.g., dendritic cells (DCs)). The cells are co-cultured with CD4+ and/or CD8+ T-cells and T-cell activation is determined. The amount of T-cell activation is indicative of the immunogenicity of the putative epitope where higher T-cell activation indicates a more immunogenic peptide or epitope. In certain embodiments, T-cell activation is measured by flow cytometry or FluoroSpot.
Assaying Immunogenicity of Cas-Derived Proteins
(114) In certain embodiments of the invention, the immunogenicity of recombinant Cas proteins made by the methods described herein is determined by measuring the level of T-cell activation induced by such recombinant proteins. In some embodiments, the T-cells comprise CD4+ and/or CD8+ T-cells. In certain embodiments, the level of activation of T-cells is measured using methods well-known in the art, including, but not limited to, flow cytometry and/or FluoroSpot. In some embodiments, the level of T-cell activation induced by the recombinant Cas protein is compared to the level of T-cell activation induced by the wild-type Cas protein from which the recombinant Cas protein was derived. If the level of T-cell activation induced by the recombinant Cas protein is lower than that induced by the wild-type Cas protein from which the recombinant Cas protein was derived, then the recombinant Cas protein is considered to have reduced immunogenicity.
MHC-Associated Peptide Proteomics (MAPPs) Assay
(115) In some embodiments, MHC-associated Peptide Proteomics (MAPPs) assays are used to identify prominent epitopes from the Cas protein. MAPPs technology is a high-throughput approach yielding hundreds of peptide sequences from a small amount of starting material, allowing sequence analysis of self-peptide repertoires from low abundance cell types. See, e.g., Rohn, et al., Nature Immunol. 5:909-918 (2004), and Penna et al., J. Immunol. 167:1862-1866 (2001). The MHC-associated Peptide Proteomics (MAPPs) assay involves in vitro identification of HLA class II or class I associated peptides, which are processed by professional antigen presenting cells (APCs) such as dendritic cells, and used to identify specific peptides that are bound to either Class II or Class I antigens. Antigen uptake, processing and presentation processes are taken into account. The naturally processed HLA class II-associated peptides or class I-associated peptides are identified by liquid chromatography-mass spectrometry (Kropshofer and Spindeldreher (2005) in Antigen Presenting Cells: From Mechanisms to Drug Development, eds. Kropshofer and Vogt, Wiley-VCH, Weinheim, 159-98).
Recombinant Cas Proteins Made by the Methods Described Herein
(116) The present invention is also directed to recombinant Cas proteins made by the methods described above. For example, in certain embodiments, the invention is directed to a recombinant Cas protein made by a process comprising introducing one or more amino acid substitutions into one or more residues corresponding to one or more MHC Class I and/or Class II binding sites of a wild-type Cas protein to form the recombinant protein. In some embodiments, the recombinant Cas protein made by the methods disclosed herein has reduced immunogenicity compared to a wild-type Cas protein.
Vectors of the Invention
(117) Viral transduction with adeno-associated virus (AAV) and lentiviral vectors (where administration can be local, targeted or systemic) have been used as delivery methods for in-vivo gene therapy. In certain embodiments of the present invention, the Cas protein can be expressed intracellularly by transduced cells Immunogenicity responses to the Cas would thus be largely mediated by MHC Class I receptors (e.g., HLA Class I receptors), which are present in all nucleated cells, thereby activating CD8+ T cells.
(118) For many therapeutic strategies, included those envisaged by the present invention, Cas protein expression may only be required transiently. As a result, in certain embodiments of the invention, delivery of the Cas protein into cells can be achieved using non-integrative viral vectors. In addition, there are certain embodiments where the expression of CRISPR-Cas system components is required for extended periods—for example, when used in gene circuits which are permanently integrated into the genome of target cells. Such applications have been discussed by Agustín-Pavón, et al., “Synthetic biology and therapeutic strategies for the degenerating brain,” Bioessays 36(10):979-990 (2014), which is incorporated by reference herein in its entirety. In some embodiments of the present invention, immunogenicity can have elevated relevance in relation to potential selective clearance of cells stably expressing Cas protein by the immune system.
(119) In certain embodiments, the Cas proteins and methods of the present invention can be used in ex vivo gene editing, such as CAR-T type therapies. These embodiments may involve modification of cells from human donors. In these instances, viral vectors can be also used; however, there is the additional option to directly transfect the Cas protein (along with in-vitro transcribed guide RNA and donor DNA) into cultured cells. In this case both MHC Class I and Class II (e.g., HLA Class 1 and HLA Class 2) receptors may be involved. Furthermore, a phenomenon known as “cross-presentation” can result in presentation of peptides derived from extracellular proteins by HLA Class I receptors, adding additional weight to considering immunogenicity of Cas proteins in relation to both Class I and Class II HLA presentation.
Cell-Types of the Invention
(120) The present invention is also directed to a cell comprising the recombinant Cas protein of the invention, a nucleic acid expressing the recombinant protein of the invention, and/or a vector comprising a nucleic acid of the invention. In certain embodiments, the cell is a prokaryotic cell, for example an E. coli cell. In some embodiments, the cell is a mammalian cell. In some embodiments, the cell is a eukaryotic cell, for example, a lymphocytic cell, a myeloid cell, an induced pluripotent stem cell (iPSC), or a T cell, although all mammalian cell types are envisage as being used in the invention.
Library for Identifying Cas Proteins with Reduced Immunogenicity
(121) The present invention also encompasses a library comprising at least one recombinant Cas protein comprising one or more amino acid substitutions in one or more residues corresponding to one or more MHC Class I and/or MHC Class II binding sites of a wild-type Cas protein. In certain embodiments, the library can be used to screen for functional recombinant Cas proteins, including recombinant Cas proteins with reduced immunogenicity. This is important as it is highly likely that many amino acid substitutions that reduce immunogenicity may also reduce Cas functionality that is essential to its application. The immunogenicity of functional recombinant Cas proteins in the library can be assessed using well-known techniques, including those described herein.
Methods for Altering Gene Expression Using the Recombinant Cas Proteins
(122) The invention is also directed to methods for altering the DNA sequence at defined genomic locations containing a target sequence comprising introducing into a cell containing the target genetic element a guide RNA that hybridizes to the target sequence and a recombinant Cas protein of the invention.
EXAMPLES
(123) Described below are experimental procedures for reducing the immunogenicity of Cas proteins, in particular Cas9 variants from S. pyogenes and S. aureus. S. pyogenes Cas9 has been more extensively characterized for in vitro gene-editing studies, whereas S. aureus Cas9 has also been utilized for in vivo gene editing, in part due to its smaller size facilitating delivery via adeno-associated virus (AAV) vectors.
Example 1: In-Silico Prediction of Cas9 Immunogenic Epitopes for Cas9 Variants and Cell Based Immunogenicity Assays for Wildtype Cas9 (S. Pyogenes)
Example 1.1: In Silico Prediction of HLA Class I and Class II Binding for Cas9 Proteins
(124) This process involves creating a profile sequence for HLA Class I & Class II T-cell epitopes using in silico methods such as those described above, for Cas9 sequences from Streptococcus pyogenes, Streptococcus thermophilus, Staphylococcus aureus, and Neisseria meningitidis
(125) A randomizer algorithm was applied to assess effects of amino acid substitutions on immunogenicity of all 9 and 10mer (containing 9 or 10 amino acid residues, respectively) sequences within the Cas9 proteins. This indicates whether potential substitutions can increase or decrease the immunogenicity of the associated 9mer or 10mer.
HLA Class I Mapping
(126) HLA Class I epitopes were mapped for the four Cas9 variant sequences provided above (SEQ ID NOs: 1-4), but are exemplified for Streptococcus pyogenes Cas9 (SEQ ID NO: 5) below. In short, the platform analyzes the HLA binding specificities of all 9 and 10-mer peptides derived from a target sequence (for more details refer to paragraphs below). Profiling is performed at the allotype level for a total of 28 HLA Class I receptors.
(127) EPIBASE® calculates binding affinity of a peptide for each of the 28 HLA Class I receptors. Based on this, peptides are classified as strong (S), medium (M), or non (N) binders.
(128) The allotypes predicted were selected based on frequencies in a variety of populations (Caucasian, Indo-European, Oriental, North Oriental, West African, East African, Mestizo and Austronesian).
(129) Compiled data are presented in Table 1, indicating the number of Streptococcus pyogenes Cas9 epitopes specific to each HLA allotype. Peptides in the two binding classes (S and M) are counted separately.
(130) TABLE-US-00010 TABLE 1 Strong and medium binding Streptococcus pyogenes Cas9 epitopes for HLA-A and HLA-B. Total numbers of epitopes in each category for 9-mer and 10-mer sequences are presented (values for different allotypes are represented separately, with allotype references restricted to two digits). HLA 9-mer 10-mer Allotype Strong Medium Strong Medium A*01 8 60 6 43 A*02 30 110 37 99 A*02 39 110 43 99 A*02 51 127 53 112 A*02 22 64 18 69 A*03 34 88 29 106 A*11 43 89 41 84 A*23 32 93 114 233 A*24 18 57 51 135 A*26 15 66 22 78 A*29 45 119 61 142 A*30 24 104 58 190 A*31 60 159 50 169 A*33 24 113 74 226 A*68 59 143 234 300 A*68 48 128 107 218 B*07 14 47 6 62 B*08 26 105 15 80 B*15 16 64 23 73 B*18 21 84 46 121 B*27 7 100 13 105 B*35 24 110 21 73 B*40 19 49 11 57 B*44 0 25 1 28 B*51 0 7 0 11 B*53 14 77 35 132 B*57 0 15 0 25 B*58 15 94 11 119
(131) HLA Class I epitope maps for two regions of Streptococcus pyogenes Cas9 (positions 1-125 and 1026-1150) are shown in
(132) Information regarding allotype frequencies can be helpful to further assess the global immunogenic response of the protein of interest. It is remarked that allotype frequencies cannot just be added up to estimate total population response: epitope processing, clustering of binders into short sequence fragments, immunodominance, T-cell receptor properties, presence of B-cell epitopes (antigenicity) and Mendelian genetics are all factors that complicate global immunogenicity assessment. As a result, the population response can be different from the sum of allotype frequencies.
HLA Class II Mapping
(133) HLA Class II epitopes have been mapped for the four Cas9 variants sequences provided above (SEQ ID NOs: 1-4), but are exemplified for Streptococcus pyogenes Cas9 (SEQ ID NO: 5), below. In short, the platform analyzes the HLA binding specificities of all 10-mer peptides derived from a target sequence (for more details refer to the paragraphs below). Profiling is performed at the allotype level for a number of HLA Class II receptors. Table 2 indicates the number of Streptococcus pyogenes Cas9 epitopes specific to each receptor.
(134) EPIBASE® calculates the binding affinity of a peptide for each of the available HLA Class II receptors. Based on this, peptides are classified as strong (S), medium (M), or non-binders (N). We refer to Kapoerchan et al., for the successful usage of EPIBASE® in predicting binders against selected HLA Class II receptors.
(135) TABLE-US-00011 TABLE 2 Strong and medium binding Streptococcus pyogenes Cas9 epitopes for different HLA Class II allotypes. Total numbers of epitopes in each category for 10-mer sequences are presented (values for different allotypes are represented separately, with allotype references restricted to two digits). 10-mer Allotype Strong Medium DRB1*01 16 65 DRB1*01 21 81 DRB1*03 7 46 DRB1*03 6 33 DRB1*03 7 46 DRB1*04 8 26 DRB1*04 10 35 DRB1*04 10 35 DRB1*04 16 45 DRB1*04 16 46 DRB1*04 9 32 DRB1*04 19 68 DRB1*04 19 68 DRB1*07 8 39 DRB1*08 4 64 DRB1*08 5 67 DRB1*08 4 64 DRB1*08 7 70 DRB1*09 6 30 DRB1*10 15 67 DRB1*11 21 70 DRB1*11 6 24 DRB1*11 27 86 DRB1*11 27 86 DRB1*11 21 70 DRB1*12 12 92 DRB1*12 12 92 DRB1*13 8 28 DRB1*13 5 29 DRB1*13 26 59 DRB1*13 1 31 DRB1*13 26 59 DRB1*14 27 73 DRB1*14 32 77 DRB1*14 27 73 DRB1*14 27 86 DRB1*14 33 87 DRB1*15 16 6 DRB1*15 13 52 DRB1*15 16 67 DRB1*15 16 67 DRB1*16 16 78 DRB1*16 16 78 DRB3*01 4 44 DRB3*02 0 48 DRB3*02 1 40 DRB3*03 7 67 DRB4*01 9 37 DRB5*01 28 82 DRB5*01 2 40 DRB5*02 5 45 DQA1*01 2 43 DQA1*01 2 43 DQA1*01 3 33 DQA1*01 2 33 DQA1*01|DQB1*05 2 33 DQA1*01|DQB1*06 4 36 DQA1*01|DQB1*06 4 36 DQA1*01|DQB1*06 3 49 DQA1*01|DQB1*06 3 49 DQA1*01|DQB1*06 3 49 DQA1*02|DQB1*02 0 42 DQA1*03|DQB1*03 5 36 DQA1*03|DQB1*03 3 39 DQA1*03|DQB1*03 0 34 DQA1*03|DQB1*04 3 54 DQA1*03|DQB1*04 3 54 DQA1*04|DQB1*03 7 37 DQA1*04|DQB1*04 1 36 DQA1*05|DQB1*02 0 42 DQA1*05|DQB1*03 9 36 DQA1*06|DQB1*03 7 37 DPA1*01|DPB1*02 3 76 DPA1*01|DPB1*03/05 4 79 DPA1*01|DPB1*04 11 44 DPA1*01|DPB1*04/06 11 84 DPA1*02|DPB1*01 7 82 DPA1*02|DPB1*05 7 49 DPA1*02|DPB1*09 3 77 DPA1*02|DPB1*09/13 8 99 DPA1*02|DPB1*17 3 65 DPA1*02|DPB1*01 7 82 DPA1*02|DPB1*05 7 49 DPA1*03|DPB1*04/06 6 80
(136) HLA Class II epitope maps for two regions of Streptococcus pyogenes Cas9 (positions 1-125 and 1026-1150) are shown in
(137) In the humoral response raised against an antigen, the observed T.sub.h Cell activation/proliferation is generally interpreted in terms of the DRB1 specificity. However, it can also be important to take into account the possible contribution of the DRB3/4/5, DQ and DP genes.
(138) Given the lower expression levels of the DQ and DP receptors compared to the DRB receptors, the class of medium epitopes for DQ and DP was ignored. Those epitopes that are strong binders (or better) to any allotype or are medium binders for DRB1 or DRB3/4/5 are operationally defined as “critical epitopes.”
(139) Information regarding allotype frequencies can be beneficial for further assessment of the global immunogenicity risk of therapeutic proteins. Allotype frequencies cannot simply be added together to estimate the total population response: epitope processing, clustering of binders into short sequence fragments, immunodominance, T-cell receptor properties, presence of B-cell epitopes (antigenicity) and Mendelian genetics are all factors which contribute to a global immunogenicity assessment. As a result, the population response can be different from the sum of allotype frequencies.
Randomization of Cas9 Sequences for Reduced Immunogenicity
(140) Randomization was carried out in relation to HLA Class I and Class II for all four Cas9 sequences (Streptococcus pyogenes, Streptococcus thermophilus, Staphylococcus aureus, and Neisseria meningitides). Data is presented on a single identified immunogenic region from Streptococcus pyogenes Cas9. This can be found between amino acids 1035 and 1038 of the Cas9 sequence (originally identified from the HLA Class I epitope profile). The epitope maps for amino acids 1026-1150 (i.e., including this region) are shown for HLA Class I and HLA Class II in
(141) The randomization data and plots are shown in for 9-mers and 10-mers in
(142)
(143) The amino acid substitution deimmunisation scores for 9-mers and 10-mers for Streptococcus pyogenes Cas9 are presented in
(144) Amino acid substitution deimmunisation scores (and their corresponding amino acid positions) were subsequently filtered based on those which gave scores lower than a cut-off threshold of −20. These are exemplified for Streptococcus pyogenes Cas9 in
Example 1.2: Assessment of Cas9 Structural and Functional Regions
(145) A three-dimensional model was generated using the coordinates of a publically available Cas9 complex crystal structure in the protein data-bank (PDB) (see Nishimasu, et al., “Crystal structure of Cas9 in complex with guide RNA and target DNA,” Cell 156(5):935-49 (2014), which is incorporated by reference herein in its entirety). This structural model can be used to assess structural criteria for each amino acid residue. This information can be combined with immunogenicity data from Example 1.1 to prioritize sequence modifications of the Cas9 protein which are likely to maintain functionality while reducing immunogenicity.
(146) Further to the data generated in the preceding paragraph, the proximity of prioritized/relevant HLA Class I and HLA Class II epitopes to key structural or functional motifs of the Cas9 sequence were performed. The Cas9 proteins from S. pyogenes and S. aureus were used for illustrative purposes.
(147) While the macro-homology across Cas9 variants is limited—see
(148) Those epitopes that were chosen for further characterization were aligned to corresponding domains of other species. Based, at least in part, on these alignments, three-dimensional molecular models of the target epitopes were generated. Functionally relevant positions/regions in the Cas9 proteins were identified and mapped into the three-dimensional structure of the proteins.
Example 1.3: Prioritisation of Cas9 Amino Acid Substitutions Based on Examples 1.1 and 1.2
(149) The data compiled from Examples 1.1 and 1.2 were used to identify which epitopes could be targeted to both minimize immunogenicity risks while also retaining as much biological activity as possible in the recombinant, i.e., engineered, protein. Such domains have been described by Nishimasu et al. (2014). For example, one criterion utilized was to avoid changing amino acids present within 5 angstroms of the known nuclease domains of Cas9. For those epitopes selected to effectuate reduced immunogenicity, amino acid substitutions were selected to preserve structural features of the Cas9 protein (e.g., alpha helices/beta-sheets) as much as possible.
(150) A global list of positions/regions that can be randomized/changed for potential reduced immunogenicity can be generated. Assessment of the effect of amino acid substitution of the identified regions can be carried out in multiple ways.
(151) Limitations exist in the number of Cas9 variants that can be practically screened for immunogenicity in Example 2, below. It therefore highly likely that the final Cas9 variants assessed will contain multiple substitutions. However, there is considerable flexibility in how the Cas9 functionality screens can be carried out. A step-wise approach can be utilized to minimize the potential impact of the deimmunising substitutions in Cas9 function. In this method more variants can be screened (e.g., using a library approach), exhibiting larger numbers of substitutions, individually and in combination, and also to utilize multiple subsequent rounds of screening-selection, where results from primary screens are used to inform library design for subsequent rounds.
Example 1.4: In-Vitro Immunogenicity Assays on Purified Cas9 Protein
(152) Assays were carried out, using purified, non-deimmunised (“wildtype”), Cas9 proteins, i.e., SEQ ID NOs: 5-8, in order to assess the starting level of immunogenicity relative to proteins of known immunogenicity (shown in
(153) Assays were performed using peripheral blood mononuclear cells (PBMCs) from healthy human donors corresponding to different HLA allotypes. Typically PBMCs from at least 10 or 20 different donors were utilized. There was prior evidence that HLA Class I presentation can occur even in cases where cells are exposed “externally” to whole antigens (a phenomenon known as “cross-presentation”). This was used to explore how antigen presentation can influence the activation of CD4+ (helper T-cells) or CD8+ (cytotoxic T-cells) lymphocytes.
(154) PBMCs were incubated with recombinant Cas9 protein (Cas9 protein with incorporated amino acid substitutions determined from the analysis in Examples 1.1-1.3 above). The recombinant Cas9 protein was purified to eliminate LPS (lipopolysaccharide) contamination (endotoxin can induce T cell activation and hence give false positive results). CD4+ or CD8+ T-cell activation was assessed by measuring the proliferation of the T-cells by flow cytometry or FluoroSpot. Activation of CD4+ T-cells indicated the presence of HLA Class II T-cell epitopes, whereas the activation of CD8+ T-cells indicated that HLA Class I epitopes were present in the Cas9 protein sequence.
Example 1.5: HLA Class I and HLA Class II MAPPS (MHC-Associated Peptide Proteomics) Assay
(155) Further to use of the EPIBASE® platform for in silico prediction of immunogenic epitopes, an in vitro approach was applied to experimentally identify which epitopes are presented by HLA Class I and Class II molecules. Use of EPIBASE® can be helpful due to the high number of immunogenic epitopes identified in silico.
(156) This assay involved immunoprecipitation of HLA Class I (HLA-A, B and C) or HLA Class II (HLA-DR, DP and DQ) proteins from antigen presenting cells (APCs) previously incubated in the presence of antigen, i.e., Cas9 protein. Cas9-derived peptides bound to the HLA molecules were acid-eluted and identified by Mass Spectrometry (MS). Identification of Cas9-derived HLA-binding peptides provides data on which peptides are processed and presented preferentially by these APCs. Analysis of this data helped to further define which of the in silico predicted epitopes are actually more relevant in potentially triggering an immune response (an example is shown in
(157) Analysis of HLA Class I bound peptides may additionally be carried out using cells expressing and/or transfected with Cas9.
Example 1.6: Activation of CD4+ and CD8+ T-cells by Short Peptides from Cas9
(158) These assays evaluate the relative immunogenicity of different Cas9-derived peptides by incubating dendritic cells (DC) with short synthetic peptides representing the potential T-cell epitopes from Cas9 and co-culturing them with autologous T-cells (CD4+ or CD8+) to evaluate the impact of each peptide on T-cell activation. These assays can be utilized to rank the relative importance of different in silico-predicted epitopes and prioritize those to be removed to achieve reduced immunogenicity. These assays could also help inform the engineering process coming out of Example 1.3.
Example 1.7: Identification of B-cell Epitopes
(159) In addition to epitopes bound to HLA molecules, as described above, it is also important to consider presence of epitopes bound by surface IgG molecules (B cell receptors) found on B cells. B cell receptors are responsible for selective uptake of antigens and presentation on B cells via HLA Class II, for subsequent interaction with T cell receptors found on T helper cells. In contrast to peptides bound by HLA molecules, which have been processed such that they are considered only in linear terms, B cell epitopes can also be conformational, as they are found in the native context of the protein.
(160) The conformational aspect of B cell epitopes makes in silico prediction problematic relative to T cell epitopes (HLA binding). In vitro assays, however, can be used to identify B cell activation in response to either full length proteins (conformational and linear epitopes) or derived peptides (linear epitopes) covering the relevant regions.
Example 2: Functional Testing of Cas9 Variants in Mammalian Cell Lines
Example 2.1: Generation and Preparation of Mammalian Expression Vectors for Cas9 Variants and gRNAs
(161) Based on the data from Example 1 above, transient vectors for mammalian expression of recombinant Cas9 can be generated for a number of Cas9 variants.
(162) Vector designs can be based on constructs designed by Mali et al. “Cas9 as a versatile tool for engineering biology,” Nature Methods 10:957-63 (2013)—see Supplementary Figure S1, which is incorporated by reference herein in its entirety. Coding sequences for different Cas9 variants (either from different bacterial species, or containing modified immunogenic epitopes) can be inserted in place of the S. pyogenes sequence as appropriate. Guide RNA and Cas9 regions can be synthesized by a gene synthesis company (e.g., GeneART/DNA2.0) and cloned into a standard E. coli cloning vector. Guide RNA sequences can be appropriate to the Cas9 variant in question, i.e., as described by Esvelt (2013) and Ran et al. (2015). Large preparations of these vectors can be made using standard plasmid preparation procedures (e.g., Qiagen Maxi-prep) in order to produce DNA suitable for transfection.
(163) Cas9 and guide RNA plasmids can be co-precipitated (standard sodium acetate/ethanol precipitation) and re-suspended in TE ready for transfection. Final DNA concentrations are assessed by spectrophotometry (Nanodrop instrument, or equivalent) before being adjusted to compensate for variable precipitation efficiency.
Example 2.2: Testing of In-Vitro_Functionality in CHO Cells (vs. WT Control) Using Model Cell Line Expressing eGFP
(164) A Chinese hamster ovary cell line derived from CHOK1SV and containing stably integrated copies of eGFP can be used to test functionality of the different Cas9 variants identified above as having potential reduced immunogenicity. In this cell line, expression of eGFP is constitutive and is directed by the cytomegalovirus (CMV) promoter.
(165) A gRNA vector can be designed to target a region early in the eGFP coding sequence. Co-transfection of the gRNA and Cas9 vector will result in introduction of double-strand breaks (DSB) in the eGFP coding sequence. DSBs are repaired by the cell's endogenous DNA repair machinery but this is largely error prone, resulting in introduction of small insertions and deletions (indels). In the majority of cases, indels result in frame shift mutations to the coding sequence, which would prevent production of functional (fluorescent) eGFP.
(166) Functionality of Cas9 variants can be assessed by knock-down of eGFP flurourescence 2-4 days after transfection and/or by analysis of genomic DNA-derived PCR products flanking the target site. In all cases, results from Cas9 variants can be compared to the unmodified sequences in order to assess relative functionality.
(167) PCR products can be treated with an enzyme that cleaves heteroduplex DNA (e.g., T7EI) and analyzed qualitatively by gel electrophoresis. In this case, the percentage of the PCR product that is cleaved by the T7EI enzyme is indicative of the efficiency, i.e., functionality, of the Cas9 enzyme. Alternatively, the PCR products can be sequenced using next generation sequencing techniques, where the high level repeat sequencing of the PCR product gives a quantitative measure of the different modified or unmodified sequences present (again indicating Cas9 functionality).
Alternatives to Examples 2.1 and 2.2
(168) Multiple different approaches can be employed to generate rationally designed libraries of Cas9 variants, which can be screened to identify those variants that are functional. One approach would be to utilize a cell line with an integrated, substrate dependent suicide gene. Viral transduction of the cell line with DNA encoding the Cas9 library plus a guide RNA targeting the suicide gene would result in introduction of a double strand break (DSB) early in the suicide gene coding sequence where the Cas9 is functional. Addition of the suicide gene substrate would kill cells where Cas9 had failed to cleave the suicide gene sequence. Cas9 sequences could be recovered from surviving cells and analyzed by next-generation sequencing. Limitations imposed by library construction methods and transduction efficiency, for example, would inform the number of variants that could be screened using the selected method. Results from Example 2, in which ever from, will need to be ranked/prioritized in order to provide a practical number of variants for input to the process of Example 3 below.
Example 3: Generation of Purified Cas9 Proteins for Immunogenicity Assays Using E. Coli Expression System
Example 3.1: Expression of S. Pyogenes Cas9 Protein in E. Coli
(169) Cas9 from S. pyogenes can be expressed in E. coli using methods and expression constructs described by Gagnon et al. (2014), or equivalent. See Gagnon, et al. “Efficient mutagenesis by Cas9 protein-mediated oligonucleotide insertion and large-scale assessment of single-guide RNAs,” PLOS One 9(8):e106396 (2014), which is incorporated by reference herein in its entirety. All variants will contain a 6×His-tag to aid purification.
(170) Selected variants will feature SV40 (or alternative) nuclear localization sequences to test additional impact on immunogenicity. It is currently unclear whether such sequences would be required for the therapeutic use of Cas9.
Example 3.2: Purification of E. Coli-Derived Cas9 Protein
(171) Cas9 purification methods can be tested and endotoxin load assessed (aim 5-10 mg, <1 EU/mg). A commercial nickel column can be used for protein purification (such as the Ni-NTA system from Life Technologies) according to the manufacturer's instructions. This can be followed by a Capto Q (GE Life Sciences) purification step to reduce endotoxin load. Endotoxin levels can be assessed by a commercial assay (such as the Endosafe-PTS system from Charles River), according to the manufacturer's instructions. Proteins can be quantified during purification procedure and in the final eluted product by Bradford assay or A280 reading on suitable spectrophotometer (Nanodrop or equivalent).
Example 3.3: Expression and Purification of Cas9 Variants for Immunogenicity Testing
(172) Based on data from Examples 1 and 2 above, a range of different recombinant Cas9 variants can be produced and purified. E. coli expression vectors tested in Example 3.1 can be modified to encode for the preferred recombinant Cas9 variant sequences using standard molecular cloning techniques. Proteins can be expressed and purified as described in Example 3.2 above.
Example 4: Evaluation of Immunogenicity of Cas9 Variants
(173) Cas9 variants produced and purified in Example 3 above can be assessed again in PBMC samples obtained from the same donors assessed in Example 1. PBMCs can be incubated with different endotoxin-free Cas9 variants (up to 10-12). CD4+ or CD8+ T-cell activation can be assessed by measuring the proliferation of the T-cells by flow cytometry or ELISpot.
(174) CD4+ or CD8+ T-cell activation can be assessed for each one of the new variants and compared to that of the parental (wild-type) molecule. Analysis of the response will determine whether additional cycles of re-engineering would be required to reduce even further the immunogenicity of the protein.
Example 5: Additional Iterations of the Above Examples
(175) Optionally, additional re-design processes outlined in the above Examples can be implemented in order to refine the final designs.
(176) Additional iterations of the procedures in the above Examples can be performed at various stages throughout the entire process above. For example, in silico mapping, or in silico re-engineering, can be performed by repeating the process of Examples 1.1-1.3 and incorporating the information obtained from Examples 1.5, 1.6, 2 and 4.
(177) For example, deimmunising substitutions were determined for Cas9 from Streptococcus pyogenes. Several naturally presented HLA Class II binding peptides from Cas9 protein were identified using MAPPs HLA Class II assay (one donor only). These peptides form five different clusters (see Table 3 and
(178) TABLE-US-00012 TABLE 3 Naturally presented HLA binding regions from Cas9. cluster # residues 1 103-120 2 254-277 3 693-709 4 842-858 5 1277-1292
(179) EPIBASE® in silico platform was used to identify residue substitutions in these clusters which are predicted to remove HLA binders from these regions. Table 4 contains a list of residues and possible amino acid substitutions (the list is not exclusive) which reduce/remove HLA binding in the identified clusters. In addition, Table 4 contains a predicted reduction in DRB1 score of the protein if one of the suggested substitutions is made.
(180) The immunogenic risk of a protein or peptide can be represented by an approximate score, the DRB1 score, calculated taking into account a number of factors including the numbers of critical HLA binders and the population frequencies of the affected HLA allotypes.
(181) TABLE-US-00013 TABLE 4 List of residues and possible amino acid substitutions removing/reducing HLA binding. Reduction in DRB1 Original score due to Cluster Position residue Possible substitutions substitution cluster 1 105 F D, E −34 cluster 1 106 L D, E, G, K, P, Q, R between −22 and −58 cluster 1 107 V D, E, G between −28 and −40 cluster 2 258 L D, E, G, K, P −24 cluster 2 263 K A, D, E, G, N, P, S, T between −36 and −49 cluster 2 264 L A, D, E, G, H, K, N, P, Q, R, S, T, V between −31 and −61 cluster 2 265 Q D, E, G, N, P, T between −28 and −50 cluster 2 266 L A, D, E, G, N, P, Q, S, T, V between −24 and −50 cluster 2 267 S A, D, E, G, H, P, T between −34 and −50 cluster 3 696 L E, G, P between −26 and −30 cluster 4 846 F E, W between −31 and −33 cluster 4 847 L D, E, F, G, H, K, N, P, Q, S, T, W between −33 and −58 cluster 4 852 I D, E, F, G, Y −20 cluster 4 855 K D, E, G, P, S between −23 and −25 cluster 5 1278 K A, D, E, F, G, N, P, Q, S, T, V, W between −22 and −92 cluster 5 1279 R D, E, H, K, Q between −23 and −116 cluster 5 1280 V A, D, E, G, K, N, P, Q, S, T between −31 and −92 cluster 5 1281 I A, D, E, F, G, H, K, N, P, Q, R, S, T, W between −47 and −116 cluster 5 1282 L A, D, E, G, H, N, P, S, T between −34 and −102
(182) Substitutions listed in Table 4 were selected with the objective of removing/reducing HLA binding. Aspects of structural integrity and functionality of Cas9 were not considered at this point. In addition, deimmunising substitutions were selected only in five clusters identified based on data from one donor.
(183) The following example demonstrates a reduction in predicted immunogenic risk if five substitutions (one in each cluster) are made. Calculations were determined using the following substitutions in the amino acid sequence of Cas9: L106D, K263D, L696G, L847D, I1281D. The deimmunised version of Cas9 protein has a reduced DRB1 score, as shown in Table 5, with overall reduction by 295. Looking at the DRB1 score restricted to the combined five clusters, the original Cas9 has a DRB1 score of 177.6 and the deimmunised Cas9 protein has a DRB1 score of 23.3, achieving an 87% reduction. Furthermore, the five substitutions completely removed DRB1 epitopes restricted by the HLA allotypes of the donor (DRB1*03 and DRB1*13).
(184) TABLE-US-00014 TABLE 5 DRB1 scores of the Cas9 protein and deimmunised Cas9 protein with five substitutions. DRB1 DRB1 score Number of critical score for due to epitopes in five whole protein five clusters * cluster regions * Cas9 12693.6 177.6 16 Deimmunised Cas9 12398.6 23.3 9 with 5 substitutions * Only epitopes/binders fully contained in the five clusters are included.