WO2020041791A1 - Fasl immunomodulatory gene therapy compositions and methods for use - Google Patents

Fasl immunomodulatory gene therapy compositions and methods for use Download PDF

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Publication number
WO2020041791A1
WO2020041791A1 PCT/US2019/048148 US2019048148W WO2020041791A1 WO 2020041791 A1 WO2020041791 A1 WO 2020041791A1 US 2019048148 W US2019048148 W US 2019048148W WO 2020041791 A1 WO2020041791 A1 WO 2020041791A1
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Prior art keywords
sequence
rna
disclosure
promoter
composition
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PCT/US2019/048148
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French (fr)
Inventor
David A. Nelles
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Locana, Inc.
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Priority to JP2021509984A priority Critical patent/JP2021533803A/en
Priority to EP19852324.3A priority patent/EP3841116A4/en
Priority to CA3110282A priority patent/CA3110282A1/en
Priority to US17/271,123 priority patent/US20220175960A1/en
Priority to AU2019326617A priority patent/AU2019326617A1/en
Publication of WO2020041791A1 publication Critical patent/WO2020041791A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70575—NGF/TNF-superfamily, e.g. CD70, CD95L, CD153, CD154
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/001—Preparations to induce tolerance to non-self, e.g. prior to transplantation
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N7/00—Viruses; Bacteriophages; Compositions thereof; Preparation or purification thereof
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases RNAses, DNAses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14122—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • the disclosure is directed to molecular biology, gene therapy, and/or modifying expression and activity of RNA molecules, and more, specifically, to compositions and methods for attenuating the immune response to cells subjected to RNA modification and/or gene therapies via elimination of immune effector cells.
  • compositions and methods for promoting the elimination of immune effector cells specific to cells treated or modified by gene therapy techniques are provided.
  • FasL Fas Ligand
  • Activated T-cells upregulate Fas and become sensitive to FasL-mediated apoptosis in the process of activation-induced cell death and tolerance to self- antigens.
  • Deficiencies in Fas or FasL often cause autoimmune pathologies or aberrant lymphoproliferation demonstrating the apparent lack of compensatory mechanisms in the pathway. While local presentation of mutated FasL has been shown to prevent rejection of transplanted cells in mice, ectopic expression of FASL in certain transplantation settings has had mixed results in achieving graft survival.
  • gene therapies delivering a non-self therapeutic transgene, such as a CRISPR/Cas complex, to a patient in need of such treatment can trigger an undesirable immune response to the therapeutic transgene and/or to the vector delivering the transgene.
  • a non-self therapeutic transgene such as a CRISPR/Cas complex
  • the disclosure provides a composition comprising: a sequence encoding a non-self polypeptide of interest (POI), and a sequence encoding a non-cleavable FasL, wherein expression of the non-cleavable FasL eliminates MHC-mediated immunogenic peptides and helper T cells specific to the expression of the POI.
  • the POI is a CRISPR-Cas protein.
  • the POI is a viral capsid polypeptide such as an AAV viral capsid.
  • the POI is a heterologous non-self (foreign) protein antigen, fragment or variant thereof.
  • non-self proteins or POIs are selected from the group consisting of bacterial proteins, archaeal proteins, viral proteins, parasitic proteins, tumor proteins, mycoplasma proteins, yeast proteins or allergen proteins.
  • a non-self POI is a bacterially-derived CRISPR/Cas protein or an archaeal-derived CRISPR/Cas protein.
  • gRNA guide RNA
  • the target sequence comprises at least one repeated sequence.
  • compositions of the disclosure are within the same vector.
  • the vector is a viral vector.
  • the viral vector is an AAV vector, an adenoviral vector, or a retroviral vector such as a lentiviral vector.
  • the vector is an AAV vector and the vector comprises sequences encoding the AAV capsid.
  • the sequences comprise an IRES (Internal Ribosomal Entry Site) or a 2A ribosomal site
  • the mutated non- cleavable FasL comprises at least one mutation or deletion in its metalloproteinase cleavage site.
  • the mutated non-cleavable FasL comprises at least one mutation or deletion in its protease recognition region.
  • the protease recognition region is at least amino acid residues 119 to 154 of wild-type human FasL.
  • the metalloproteinase cleavage site comprises the amino acid sequence ELAELR.
  • the mutation comprises one or more of a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition of the amino acid sequence ELAELR.
  • the non-cleavable FASL comprises the amino acid sequence of:
  • the non-cleavable FASL comprises the amino acid sequence of:
  • expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the non-self polypeptide, and wherein expression of FASL is in the presence of IL-6 or TNF- alpha.
  • the non-cleavable FASL comprises an intron, wherein the intron blocks FASL splicing in the absence of IL-6 or TNF-alpha.
  • the non-cleavable FASL comprises an intron, wherein the intron blocks FASL splicing in the absence of IL-6 or TNF-alpha.
  • the composition comprises synthetic mRNA target sites which are expressed in the presence of IL-6 or TNF-alpha.
  • compositions comprise 1) a synthetic notch system, 2) microRNA target sites, or a 3) split intein and engineered IL-6 or TNF-alpha receptors for regulating expression of FASL in the presence of IL-6 or TNF-alpha.
  • the RNA-binding polypeptide or RNA-binding portion thereof is selected from the group consisting of Cas9, Cas13d, PUF, PUMBY, and PPR.
  • the sequences comprise a promoter or promoters.
  • the promoter driving expression of FASL is regulated by the presence of IL-6 receptor or TNF-alpha receptor.
  • a promoter capable of driving FASL expression in the presence of IL-6 receptor or TNF-alpha receptor is a promoter listed in Table 1 or Table 2.
  • the non-self POI is a nucleoprotein complex encoded by (i) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule, and (ii) a sequence encoding an RNA-binding polypeptide.
  • gRNA guide RNA
  • the sequence comprising the gRNA further comprises a sequence encoding a promoter capable of expressing the gRNA in a eukaryotic cell.
  • the eukaryotic cell is an animal cell.
  • the animal cell is a mammalian cell.
  • the animal cell is a human cell.
  • the promoter is a constitutively active promoter.
  • the promoter comprises a sequence isolated or derived from a promoter capable of diving expression of an RNA polymerase.
  • the promoter sequence comprises a sequence isolated or derived from a U6 promoter.
  • the promoter sequence comprises a sequence isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA)
  • the promoter sequence comprises a sequence isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan
  • Figure 1A-B are schematic diagrams relevant to the compositions of the disclosure.
  • A Depicts typical therapeutic non-self transgene delivery via AAV which result in presentation of non-self polypeptides that can activate T helper cells and potentiate a cytotoxic effect against treated tissue or cells.
  • compositions of the disclosure by including sequences encoding mutated (metalloproteinase non-cleavable) versions of FasL in vector constructs comprising therapeutic transgenes (Tx genes), such as transgene components encoding a CRISPR/Cas9 complex, thereby resulting in the promotion of programmed death of T-cells that interrogate treated tissue or cells and preventing cytotoxic activity against the treated tissue or cells.
  • Tx genes therapeutic transgenes
  • FIGS. 2A-B are schematic diagrams relevant to the compositions of the disclosure.
  • A Depicts repeated AAV administration in humans which results in formation of adaptive immunity against the AAV capsid in the form of both humoral and cellular responses.
  • B Depicts compositions of the disclosure by including sequences encoding both mutated non- cleavable FasL and polypeptides from the AAV vector capsid in the vector constructs additionally comprising a therapeutic transgene (self or non-self). This results in elimination of T-cells specific to the viral capsid and prevention of the formation of adaptive immunity against the viral capsid which allows for efficient and safe redosing with the AAV vector.
  • FIGS. 3A-F are schematic diagrams relevant to embodiments of the compositions disclosed herein that are capable of detecting the activity of T cells
  • A Depicts a construct configuration embodiment comprising FASL driven by a promoter that is regulated by IL-6 receptor or TNF-alpha receptor.
  • B Depicts a construct configuration embodiment comprising a Cas13d RNA-targeting system and FASL.
  • the FASL comprises an intron whose splicing is negatively regulated by Cas13d.
  • Cas13d is titrated away from the FASL construct so that splicing of FASL is allowed and FASL protein is produced.
  • (C) Depicts a construct configuration embodiment similar to the construct configuration in (B) but with the addition of another component: engineered mRNA that is regulated by TNF-alpha receptor or IL-6 receptor that contains concatenated sites which titrate Cas13d away from the FASL pre-mRNA.
  • (D) Depicts a construct configuration embodiment comprising an engineered receptor such as Syn-notch that detects IL-6 or TNF-alpha and subsequently releases a transcription factor such as GAL4 thereby promoting expression of a GAL4-regulated FASL gene.
  • (E) Depicts a construct configuration embodiment comprising an engineered mRNA that codes for FASL and also contains concatenated target sites in the 3’UTR for a microRNA (miRNA) that is downregulated upon stimulation by TNF-alpha or IL-6.
  • (F) Depicts a construct configuration embodiment comprising an engineered version of IL-6 receptor or TNF-alpha receptor that carries an intein on the intracellular domain along with a Cas13d-intein fusion present in the nucleus.
  • This construct embodiment is similar to the embodiment of (B) in that the Cas13d regulates splicing of FASL but the release of the intein from the cell membrane and translocation to the nucleus upon IL-6 or TNF-alpha detection results in intein activity on Cas13d thereby releasing the splicing block on FASL.
  • the disclosure provides compositions and methods for combined therapeutic and immune masking activity.
  • the immune masking activity eliminates MHC-mediated immunogenic peptides and helper T-cells specific to the expression of a non-self therapeutic activity, i.e., a non-self therapeutic protein such as a CRISPR/Cas ribonucleoprotein complex.
  • the compositions comprise nucleic acid sequences which encode at least two functional components– a non-self protein of interest (POI) and a non-cleavable mutated FasL.
  • POI non-self protein of interest
  • the compositions comprise nucleic acid sequences comprising a gRNA that specifically binds a target sequence within an RNA molecule, a sequence encoding an RNA-binding polypeptide or RNA-binding portion thereof and a sequence encoding a non-cleavable FasL
  • the compositions comprise vector constructs.
  • the sequences comprise a promoter driving the functional components or separate promoters driving expression of each or certain of the functional components. Additional elements often used in the expression of multiple coding sequences such as 2A ribosomal skipping sites, or IRESs can be incorporated in the compositions comprising the vector constructs.
  • compositions and methods of the disclosure are controlling the timing and levels associated with FASL expression. Constitutive expression of FASL is associated with toxicity but by expressing FASL when cells are challenged by activated T cells, selective T cell elimination is achieved while avoiding these toxicity issues.
  • temporal control of FASL expression is achieved by utilizing delivery modes that promote short-term expression of the FASL system.
  • nonviral delivery modes such as lipid nanoparticles carrying DNA or RNA encoding the FASL system promotes transient expression of the system in the target tissue.
  • AAV vectors or other viral delivery or nonviral delivery modes comprise built-in temporal controls.
  • One such approach involves promoters that cycle with circadian rhythms such as the clock gene.
  • GAL galactose
  • AOX alcohol oxidase
  • cellobiohydrolase or glucoamylase.
  • integrated sensors promote FASL expression only under controlled conditions.
  • a genetic circuit that recognizes expression of specific genes is used to identify the activity of cytotoxic T cells and subsequently promote FASL expression only in the presence of these activated T cells.
  • the disclosure provides compositions and methods for regulating and/or controlling expression of mutant (mFASL).
  • the composition produces mFASL only in the presence of activated T cells via detection of the cytokines, IL-6 or TNFalpha.
  • This mFASL protein protects the therapeutic-treated cells via specific killing of the activated T cell.
  • the cells downregulate FASL which avoids safety issues associated with broad, constitutive expression of FASL.
  • the production of mFASL is only in the presence of activated T cells via use of a construct configuration, such as Fig 3A, comprising a promoter which is specifically activated by one or both of IL-6 and/or TNF-alpha.
  • a construct configuration such as Fig 3A
  • Exemplary promoters which are specifically activated by one or both IL-6 and/or TNF-alpha include, without limitation, promoters listed in Table 1 and/or Table 2 [038] Table 1: Genes with promoters regulated by TNF-alpha
  • mFASL expression is regulated by a construct
  • RNA-targeting system e.g., Cas13d
  • the FASL comprises an intron whose splicing is negatively regulated by the RNA-binding protein (e.g., Cas13d).
  • the RNA-targeting system Upon TNFalpha or IL-6 signaling, the RNA-targeting system is drawn to a stronger binding site in an RNA that is expressed upon TNFalpha or IL-6 signaling, that is, Cas13d is titrated away from the FASL construct. This releases the splicing block on mFASL (and splicing of FASL is permitted) and promotes production of the protein.
  • the Cas13d guide RNA is antisense to the mRNA of the regulated FASL construct configuration (such as in Fig 3A).
  • Spacer sequences for gRNAs targeting the IL6 or TNF-alpha-regulated mRNAs are listed in Table 3. [041] Table 3. Spacer sequences for gRNAs targeting the IL6 or TNF-alpha-regulated mRNAs
  • a construct configuration such as Fig.3C, comprises an engineered RNA comprising concatenated sites that titrate Cas13d away from the FASL pre- mRNA and which is regulated by TNFalpha or IL-6 via use of an appropriate promoter (such as, without limitation, a promoter in Table 1 or Table 2).
  • the engineered RNA contains multiple target sites for the RNA-targeting system. As such, expression of the engineered RNA releases the splicing block on the mFASL mRNA.
  • a construct configuration such as Fig.3D, comprises an engineered receptor such as synthetic notch detects IL-6 or TNFalpha and regulates expression of a promoter that drives mFASL. In this manner, mFASL is only produced in the presence of TNFalpha or IL-6 signaling.
  • such an engineered Syn-notch receptor would detect IL-6 or TNF- alpha and subsequently release a transcription factor such as GAL4 which promotes expression of a GAL4-regulated FASL gene.
  • the engineered receptor comprises three modules (from N- to C-terminus):
  • an IL-6 or TNF-alpha binding section such as, without limitation, an IL-6 scFV having an amino acid sequence as follows:
  • a synthetic notch such as, without limitation, having an amino acid sequence as follows:
  • a transcription factor such as, without limitation, GAL4 having the amino acid sequence as follows:
  • mFASL is regulated via placement of microRNA (miRNA) binding sites of interest in the mRNA 3’UTR.
  • the engineered mRNA comprises concatenated target sites (for an miRNA or miRNAs of interest) and are selected so that these microRNAs are expressed in cells that are not subjected to TNFalpha or IL-6.
  • Cells that experience TNF-alpha or IL-6 reduce expression of the microRNA (i.e., the miRNA is downregulated upon stimulation by TNF- alpha or IL-6), resulting in mFASL expression only in the presence of cytokine signaling.
  • the engineered mRNA comprises target sites for miRNA, without limitation, selected from the group consisting of hsa-miR-934, hsa-miR-1269a, hsa-miR-671- 5p, hsa-miR-663a, hsa-miR-1292, hsa-miR-615-5p, hsa-miR-2276, hsa-miR-1307-3p, hsa- miR-3654, hsa-miR-4741, hsa-miR-100-5p, hsa-miR-3189-3p, hsa-miR-548t-5p, hsa-miR- 769-3p, hsa-miR-1307-5p, hsa-miR-3687, hsa-miR-324-5p, hsa-miR-449c-5p, hs
  • a construct configuration such as Fig.3F, comprises an engineered receptor that detects IL-6 or TNFalpha and comprises a split intein (e.g., an intein on the intracellular domain along with a Cas13d-intein fusion that is present in the nucleus).
  • the RNA-targeting system (such as Cas13d) regulates the splicing of an mRNA encoding mFASL and releases the intein from the cell membrane. Accordingly, upon activation of the synthetic receptor, the fused split intein translocates to the nucleus where it interacts with the split intein fused to the RNA-targeting system. The result is the destruction of a functional RNA-targeting system, correct mFASL mRNA splicing, and the production of mFASL protein.
  • the disclosure provides vectors, compositions and cells comprising the therapeutic and FasL immune masking nucleic acid sequences.
  • the disclosure provides methods of using the vectors, compositions and cells of the disclosure to treat a disease or disorder and at the same time eliminate the MHC-mediated immunogenic response specific to the vectors and/or compositions and treated cells. Preventing adaptive immune response to a non-self therapeutic transgene
  • An AAV vector carrying a therapeutic, non-self transgene is packaged with mutant FALS (mFASL) so that both genes are expressed.
  • treated cells After administration of the AAV vector, treated cells begin to express both the transgene and mFASL.
  • Peptides derived from the transgene are displayed by MHC as part of the typical and typical process of antigen presentation conducted by many cell types. The formation of regulatory and effector T cells that target the non-self peptides occurs.
  • These transgene-specific T cells interrogate infected (treated) cells that display the non-self peptides and simultaneously encounter mFASL. The presence of this non-self peptide display and mFASL results in apoptosis of the transgene- specific T cells. This eliminates this facet of adaptive immune response against the therapeutic transgene and the cells that harbor it.
  • compositions of the disclosure are used for the treatment of myotonic dystrophy type I (DM1) wherein an RNA-targeting CRISPR system composed of a therapeutic transgene (Cas9) and single guide RNA targeting the CUG repeats that cause DM1 are delivered to patient muscle or the central nervous system.
  • DM1 myotonic dystrophy type I
  • mFASL single guide RNA targeting the CUG repeats that cause DM1 are delivered to patient muscle or the central nervous system.
  • mFASL causes the elimination of T cells that are specific to Cas9 and potentially cytotoxic against treated cells.
  • compositions of the disclosure are used for the treatment of hemophilia.
  • a secreted transgene such as Factor IX is used for the treatment of hemophilia.
  • a vector carrying an expression cassette for factor IX along with mFASL reduces, eliminates, or prevents an adaptive immune response to Factor IX-expressing cells Preventing adaptive immune response to a non-self therapeutic transgene while simultaneously preventing immune response to repeated AAV administrations
  • compositions of the disclosure may comprise an AAV vector containing an expressed polypeptide composed of all or part of AAV viral capsid protein.
  • the AAV capsid polypeptide is identical to the serotype used to deliver the system. Co-expression of this AAV capsid polypeptide causes the elimination of T cells that are specific to the AAV capsid in a manner described above. This causes depletion of T cells that can regulate both cellular and humoral immunity to the AAV capsid. This allows repeated dosing of the same AAV serotype.
  • an individual AAV serotype could not be used in more than once in a patient due to the formation of adaptive immune response against the viral capsid.
  • compositions of the disclosure may be useful in situations wherein incomplete therapeutic transfer occurs during the first administration of a gene therapy or wherein a second dose is desired.
  • the second dose of the gene therapy does not require the presence of the mFASL and AAV capsid polypeptide unless subsequent doses beyond the second dose are desired.
  • One situation could be during the treatment of large organs such as skeletal muscle where the volume of virus required to transduce muscle in a single dose is prohibitively high.
  • Another situation could be during treatment involving complicated administration methods in the brain or spine where initial treatments do not provide satisfactory infection of targeted cells.
  • Non-cleavable FasL Non-cleavable FasL
  • TCR T cell receptor
  • Apoptosis This phenomenon has been termed Antigen Induced Cell Death (AICD).
  • AICD Antigen Induced Cell Death
  • Fas/FasL interaction contributes to immune privilege is also well established.
  • a number of studies demonstrate engineered immune privilege via the induction of FasL expression in transplantation settings Bellgrau et al Nature 377:630- 632 (1995); Griffith et al., Science 270:1189-1192 (1995), Lau et al., Science 273:109-112 (1996).
  • FasL is proteolytically cleaved by matrix metalloproteases and bound to the cell membrane. Because soluble FasL is released into and circulated widely throughout the circulatory system, it is known to cause non-specific and widespread cell death. Ogasawara et al., Nature 364:806-809 (1993), published erratum, Nature 365:568 (1993), Tanaka et al., Nature Med.2:317-322 (1996), Rodriguez et al., J. Exp. Med.183:1031-1036 (1996).
  • FasL protease recognition region As such, selective modulation of Fas/FasL and the subsequent selective induction of apoptosis to specific target tissues and cells has been achieved by the mutation of the FasL protease recognition region. This is because it has been found that making at least one mutation or deletion in the wild-type FasL protease recognition region inhibits proteolytic cleavage of the FasL polypeptide from the cell membrane and minimizes the production of and the deleterious non-selective effects of soluble FasL.
  • the sequence of the wild-type, full-length human FasL is known in the art.
  • the extracellular domain of the wild-type, full-length human FasL is defined by amino acid residues 103 to 281, and the protease recognition region of wild-type human FasL comprises at least amino acid residues 119 to 154. Residues are numbered by reference to the known amino acid sequence of wild-type human FasL. See Takahashi et al., Int'l Immunol.6:1567-1574 (1994). Moreover, non-cleavable mutated FasL polypeptides and methods of generating the same can be found, e.g., in WO 1999/036079, which is incorporated herein by reference in its entirety.
  • an exemplary mutated non-cleavable FasL (mus musculus) (MMP cleavage site in bold) can be generated by making one or more mutations or deletions in the following amino acid sequence:
  • an exemplary mutated non-cleavable FasL (homo sapiens) (MMP cleavage site in bold) can be generated by making one or more mutations or deletions in the following amino acid sequence: [066] MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPP LPPPPPPPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKEL AELRESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGI VLLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLV MMEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGL YKL (SEQ ID NO: 210).
  • a nucleic acid sequence of the composition encodes a non-self protein of interest (POI).
  • a non-self POI is a heterologous non-self (or foreign) protein antigen, fragment or variant thereof.
  • Exemplary non-self proteins or POIs include, without limitation, bacterial proteins, archaeal proteins, viral proteins (e.g., viral capsids), parasitic proteins, tumor proteins, mycoplasma proteins, yeast proteins or allergen proteins.
  • a non-self POI is a bacterially-derived CRISPR/Cas protein or an archaeal- derived CRISPR/Cas protein.
  • a non-self POI is a viral capsid specific to the viral vector carrying a therapeutic transgene (self or non-self transgene).
  • the expression of the viral capsid polypeptide causes infected cells to display peptides specific to the viral capsid via MHC which will promote interaction among capsid-specific T cells (with TCRs for the viral capsid peptides) and infected cells.
  • the co-expression of FASL on the infected cells will promote killing of these capsid-specific T-cells.
  • T-cells are required for mounting of both cellular and humoral immunity against the capsid, subsequent treatments with the same AAV serotype will not be attenuated by the adaptive immune system.
  • AAV capsids for use in the compositions disclosed herein are derived from AAV serotypes which include, without limitation, AAV1, AAV2, AAV4, AAV5, AAV6 (a hybrid of AAV1 and AAV2), AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, and synthetic AAV serotypes, such as, without limitation, Anc80 AAV (an ancestor of AAV 1, 2, 6, 8 and 9).
  • the AAV capsid is derived from the AAV9 VP1 amino acid sequence which is:
  • the predicted surface residues of AAV9 capsid (subset of VP1) is:
  • the AAV capsid is derived from the AAV12 VP1 amino acid sequence which is:
  • the AAV capsid is derived from the AAV2 VP1 amino acid sequence which is:
  • the AAV capsid is derived from the AAV8 VP1 amino acid sequence which is:
  • RNA-binding protein, polypeptide, or domain of the disclosure includes, without limitation, an RNA-binding portion or portions of the RNA-binding protein or polypeptide or domain.
  • the sequence encoding an RNA-binding protein or RNA-binding portion thereof comprises a sequence isolated or derived from a CRISPR Cas protein.
  • the CRISPR Cas protein comprises a Type II CRISPR Cas protein.
  • the Type II CRISPR Cas protein comprises a Cas9 protein.
  • Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
  • Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Streptococcus pyogenes, Haloferax mediteranii, Mycobacterium tuberculosis, Francisella tularensis subsp. novicida, Pasteurella multocida, Neisseria meningitidis, Campylobacter jejune, Streptococcus thermophilus, Campylobacter lari CF89- 12, Mycoplasma gallisepticum str. F, Nitratifractor salsuginis str. DSM 16511,
  • Parvibaculum lavamentivorans Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, a
  • Gluconacetobacter diazotrophicus an Azospirillum B510, a Sphaerochaeta globus str.
  • Mycoplasma mobile Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Treponema denticola, Legionella pneumophila str. Paris, Sutterella wadsworthensis, Corynebacter diphtherias, Streptococcus aureus, and Francisella novicida.
  • Exemplary wild type S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Nuclease inactivated S. pyogenes Cas9 proteins may comprise a substitution of an Alanine (A) for an Aspartic Acid (D) at position 10 and an alanine (A) for a Histidine (H) at position 840.
  • Exemplary nuclease inactivated S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence (D10A and H840A bolded and
  • Nuclease inactivated S. pyogenes Cas9 proteins may comprise deletion of a RuvC nuclease domain or a portion thereof, an HNH domain, a DNAse active site, a bba-metal fold or a portion thereof comprising a DNAse active site or any combination thereof.
  • exemplary Cas9 proteins or portions thereof may comprise or consist of the following amino acid sequences.
  • the Cas9 protein can be S. pyogenes Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. aureus Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. thermophiles CRISPR1 Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be N. meningitidis Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Parvibaculum.
  • lavamentivorans Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Corynebacter diphtheria Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Streptococcus pasteurianus Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Neisseria cinerea Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Campylobacter lari Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be T. denticola Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. mutans Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be S. thermophilus CRISPR 3 Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be C. jejuni Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be P. multocida Cas9 and may comprise or consist of the amino acid sequence: MQTTNLSYILGLDLGIASVGWAVVEINENEDPIGLIDVGVRIFERAEVPKTGESLALSRRLARSTRRLIRR RAHRLLLAKRFLKREGILSTIDLEKGLPNQAWELRVAGLERRLSAIEWGAVLLHLIKHRGYLSKRKNES QTNNKELGALLSGVAQNHQLLQSDDYRTPAELALKKFAKEEGHIRNQRGAYTHTFNRLDLLAELNLLF AQQHQFGNPHCKEHIQQYMTELLMWQKPALSGEAILKMLGKCTHEKNEFKAAKHTYSAERFVWLTK LNNLRILEDGAERALNEEERQLLINHPYEKSKLTYAQVRKLLGLSEQAIFKHLRYSKENAESATFMELK AWHAIRKALENQGLKDTWQDLAKKPDLLDEIGTAFSLYKTDEDIQQYLTNK
  • the Cas9 protein can be F. novicida Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Lactobacillus buchneri Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be Listeria innocua Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be L. pneumophilia Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be N. lactamica Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be N. meningitides Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be B. longum Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be A. muciniphila Cas9 and may comprise or consist of the amino acid sequence:
  • the Cas9 protein can be O. laneus Cas9 and may comprise or consist of the amino acid sequence:
  • the sequence encoding the fRNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein.
  • the CRISPR Cas protein comprises a Type V CRISPR Cas protein.
  • the Type V CRISPR Cas protein comprises a Cpf1 protein.
  • Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
  • Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Francisella tularensis subsp. novicida, Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium sp. ND2006.
  • Exemplary Cpf1 proteins of the disclosure may be nuclease inactivated.
  • Novicida Cpf1 (FnCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary wild type Lachnospiraceae bacterium sp. ND2006 Cpf1 (LbCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary wild type Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • the sequence encoding the RNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein or RNA-binding portion thereof.
  • the CRISPR Cas protein comprises a Type VI CRISPR Cas protein.
  • the Type VI CRISPR Cas protein comprises a Cas13 protein.
  • Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
  • Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Leptotrichia wadei, Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954), Lachnospiraceae bacterium, Clostridium aminophilum DSM 10710, Carnobacterium gallinarum DSM 4847, Paludibacter propionicigenes WB4, Listeria weihenstephanensis FSL R9-0317, Listeria
  • Exemplary Cas13 proteins of the disclosure may be DNA nuclease inactivated.
  • Exemplary Cas13 proteins of the disclosure include, but are not limited to, Cas13a, Cas13b, Cas13c, Cas13d and orthologs thereof.
  • Exemplary Cas13b proteins of the disclosure include, but are not limited to, subtypes 1 and 2 referred to herein as Csx27 and Csx28, respectively.
  • Exemplary Cas13a proteins include, but are not limited to:
  • Exemplary wild type Cas13a proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Exemplary wild type Bergeyella zoohelcum ATCC 43767 Cas13b (BzCas13b) proteins of the disclosure may comprise or consist of the amino acid sequence:
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a
  • CasRX/Cas13d protein is an effector of the type VI-D CRISPR-Cas systems.
  • the CasRX/Cas13d protein is an RNA-guided RNA endonuclease enzyme that can cut or bind RNA.
  • the CasRX/Cas13d protein can include one or more higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains.
  • HEPN prokaryotes nucleotide-binding
  • the CasRX/Cas13d protein can include either a wild-type or mutated HEPN domain.
  • the CasRX/Cas13d protein includes a mutated HEPN domain that cannot cut RNA but can process guide RNA. In some embodiments, the CasRX/Cas13d protein does not require a protospacer flanking sequence. Also see WO Publication No. WO2019/040664 & US2019/0062724, which is incorporated herein by reference in its entirety, for further examples and sequences of CasRX/Cas13d protein, without limitation, specific reference is made to
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig546000275:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4114000374:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig721000619:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2002000411:
  • EKQNKAKYQA IISLYLMVMY QIVKNMIYVN SRYVIAFHCL
  • ERDSNQLLGR FNSRDASMYN 60 KLTQKFITDK YLNDGAQGCS KKVGNYLSHN
  • ITCCSDELRK EYRNQVDHFA
  • VVRMIGKYAA 120 DIGKFSTWFE LYHYVMQRII FDKRNPLSET ERTYKQLIAK HHTYCKDLVK ALNTPFGYNL 180 ARYKNLSIGE LFDRNNYNAK TKET 204 (SEQ ID NO: 69).
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig13552000311:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig10037000527:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig238000329:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2643000492:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig874000057:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4781000489:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig12144000352:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig5590000448:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig525000349:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7229000302:
  • KKISSLTKFC LGESDEKKLK ALAKKSLEEL KTTNSKLYEN YIKYSDERKA EEAKRQINRE 60 RAKTAMNAHL RNTKWNDIMY GQLKDLADSK SRICSEFRNK AAHLEVARYA HMYINDISEV 120 KSYFRLYHYI MQRRIIDVIE NNPKAKYEGK VKVYFEDVKK NKKYNKNLLK LMCVPFGYCI 180 PRFKNLSIEQ MFDMNETDNS DKKKEK 206 (SEQ ID NO: 90).
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig3227000343:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7030000469:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d gut_metagenome_P17E0k2120140920, c87000043:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • KILAKHITNI IYTVNSFDRN YNQSGNDTIG FGLNYRVPYS EYGGGKDSNG EPKNQSKWEK 240
  • GVSDDTKVLE NTYNKYFDSK EKTDKQSQKV STFLMNNVIN NNRFKYVIKY INPADINGLA 660
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg
  • An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OGZC01000639.1 (human gut metagenome assembly):
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): from contig emb
  • KRVLPVLNEK NDNAGILLDF RKTIAHLNVV HKMVDYVDEI KGITSYYAFF CYVLQRMLVG 960
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OIZX01000427.1:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OCTW011587266.1: MKQNDRENNN KIKKSAAKAV GVKSLARLSD GSTVVSSFGK GAAAELESLI TGGEIRKLSD 60
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb
  • NIDFLKEIMY GSNYTDRGSD SLECSYFNFA ILKQNKNMGF SITSIRECLL DLYELNFESM 360 QNLRPRANSF CDFLIYDYYC KNESERANLV DCLRSAASEE EKKNIYFQTA ERVKEKFRNA 420 FNRISRFDAS YIKNSREKNL SGGSSLPKYS FIEGFTKRSK KINDNDEKNA DLFCNMLYYL 480
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736:
  • An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736 (SEQ ID NO: 107) comprises or consists of the nucleic acid sequence: CasRX/Cas13d Direct repeat 1: gtgagaagtc tccttatggg gagatgctac
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129306_1000735:
  • TYCDPAALNE REREKVTVSK QHFDAFMQNP RLAYYGNAFF RKLSKAERLA RGREIFDKES 240 PERRQEILGS RGKNKSVDDE IRALAPEWVK REERDVYSEL VLMSELRQSC FHGQQKNSAR 300 IFRLDNDLGP GVDGARELLD RLYAEKINDL RSFDKTSASS NFRLLFNAYH ADNEKKKELA 360 QEFYRFSVLK VSKNTGFSIR TLREKIIEDH AAQYRDKIYD SMRKKLFSTF DFFLWRFYEE 420 REDEAEELRA CLRAARSDEE KEQIYAEAAA SCWPSVKPFV ESVAATLCDV VKGRTKLNKL 480 KLSADESTLV RNAIDGVRIS PRASYFTKLI YLMTLFLDGK EINDLLTTLI HAFENIDSFL 540 SVLGSERLER TFDANYRIFA DSGVIAQELR AVNSFARMTT EP
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129317_1008067:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0224415_10048792:
  • APENT 965 (SEQ ID NO: 111).
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence CasRX/Cas13d 160582958 _gene49834:
  • An exemplary direct repeat sequence of CasRX/Cas13d proteins may comprise or consist of the sequence
  • CasRX/Cas13d 160582958 _gene49834 (SEQ ID NO: 112) comprises or consists of the nucleic acid sequence: CasRX/Cas13d DR:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d 250twins_35838_GL0110300:
  • Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence:
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence: [0163] Cas13d (Ruminococcus flavefaciens XPD3002) sequence:
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • An exemplary direct repeat sequence of Cas13d (contig e ⁇ k87_11092736) (SEQ ID NO: 46) comprises or consists of the nucleic acid sequence:Cas13d (contig e ⁇ k87_11092736) Direct Repeat Sequence): GTGAGAAGTCTCCTTATGGGGAGATGCTAC (SEQ ID NO: 47).
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • An exemplary direct repeat sequence of Cas13d (160582958_gene49834) (SEQ ID NO: 48) comprises or consists of the nucleic acid sequence:
  • Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
  • Cas13d (contig tpg
  • An exemplary direct repeat sequence of Cas13d (contig tpg
  • the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • the spacer sequence has 100% complementarity to the target RNA sequence.
  • the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides.
  • the spacer sequence comprises or consists of the sequence UGGAGCGAGCAUCCCCCAAA (SEQ ID NO: 1), GUUUGGGGGAUGCUCGCUCCA (SEQ ID NO: 2), CCCUCACUGCUGGGGAGUCC (SEQ ID NO: 3), GGACUCCCCAGCAGUGAGGG (SEQ ID NO: 4),
  • GCAACUGGAUCAAUUUGCUG SEQ ID NO: 5
  • GCAGCAAAUUGAUCCAGUUGC SEQ ID NO: 6
  • GCAUUCUUAUCUGGUCAGUGC SEQ ID NO: 7
  • GCACUGACCAGAUAAGAAUG SEQ ID NO: 8
  • GAGCAGCAGCAGCAGCAGCAG SEQ ID NO: 9
  • GCAGGCAGGCAGGCAGGCAGGCAGG SEQ ID NO: 10
  • GCCCCGGCCCCGGCCCCGGCCCCGGC (SEQ ID NO: 11)
  • GCTGCTGCTGCTGCTGCTGC (SEQ ID NO: 12)
  • GGGGCCGGGGCCGGGGCCGG (SEQ ID NO: 74)
  • the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of the sequence GUGAUAAGUGGAAUGCCAUG (SEQ ID NO: 14),
  • the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • the spacer sequence has 100% complementarity to the target RNA sequence.
  • the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides.
  • the spacer sequence comprises or consists of a sequence comprising at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
  • the sequence comprising the gRNA further comprises a scaffold sequence that specifically binds to the first RNA binding protein.
  • the scaffold sequence comprises a stem- loop structure.
  • the scaffold sequence comprises or consists of 90 nucleotides.
  • the scaffold sequence comprises or consists of 93 nucleotides.
  • the scaffold sequence comprises or consists of the sequence
  • the scaffold sequence comprises or consists of the sequence
  • the scaffold sequence comprises or consists of the sequence
  • the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule.
  • an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • the sequence encoding the RNA-binding protein encodes a CRISPR-Cas protein or RNA-binding portion thereof.
  • the RNA-binding protein is a fusion protein.
  • the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • the RNA- binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein In some embodiments the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • the RNA binding protein comprises a CRISPR-Cas protein or RNA-binding portion thereof.
  • the CRISPR-Cas protein is a Type V CRISPR-Cas protein.
  • the first RNA binding protein comprises a Cpf1 polypeptide or an RNA- binding portion thereof.
  • the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • the RNA binding protein comprises a CRISPR-Cas protein or RNA-binding portion thereof.
  • the CRISPR-Cas protein is a Type VI CRISPR-Cas protein.
  • the RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
  • the RNA binding protein comprises a Cas13d polypeptide or an RNA-binding portion thereof.
  • the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • the mutation occurs in an amino acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition.
  • the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • a target RNA-binding fusion protein is not an RNA-guided target RNA-binding fusion protein and as such comprises at least one RNA-binding polypeptide which is capable of binding a target RNA without a corresponding gRNA sequence.
  • Such non-guided RNA-binding polypeptides include, without limitation, at least one RNA-binding protein or RNA-binding portion thereof which is a PUF (Pumilio and FBF homology family). This type RNA-binding polypeptide can be used in place of a gRNA- guided RNA binding protein such as CRISPR/Cas.
  • compositions of the disclosure is a PUF (Pumilio and FBF homology family).
  • PUF Panmilio and FBF homology family
  • the unique RNA recognition mode of PUF proteins (named for Drosophila Pumilio and C. elegans fem-3 binding factor) that are involved in mediating mRNA stability and translation are well known in the art.
  • the PUF domain of human Pumilio1 also known in the art, binds tightly to cognate RNA sequences and its specificity can be modified. It contains eight PUF repeats that recognize eight consecutive RNA bases with each repeat recognizing a single base.
  • a PUF domain can be designed to specifically bind most 8-nt RNA. Wang et al., Nat Methods.2009; 6(11): 825-830. See also WO2012/068627 which is incorporated by reference herein in its entirety.
  • the RNA-binding protein or RNA-binding portion thereof is a PUMBY (Pumilio-based assembly) protein.
  • RNA-binding protein PumHD Pano homology domain, a member of the PUF family
  • These modules can be concatenated in chains of varying composition and length to bind desired target RNAs
  • the specificity of such Pumby–RNA interactions is high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence.
  • the first RNA binding protein comprises a Pumilio and FBF (PUF) protein. In some embodiments, the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein. In some embodiments,
  • a PUF1 protein of the disclosure comprises or consists of the amino acid sequence of
  • a PUF3 protein of the disclosure comprises or consists of the amino acid sequence of
  • a PUF5 protein of the disclosure comprises or consists of the amino acid sequence of
  • the RNA-binding protein or RNA-binding portion thereof is a PPR protein.
  • PPR proteins proteins with pentatricopeptide repeat (PPR) motifs derived from plants
  • PPR proteins are nuclear-encoded and exclusively controlled at the RNA level organelles (chloroplasts and mitochondria), cutting, translation, splicing, RNA editing, genes specifically acting on RNA stability.
  • PPR proteins are typically a motif of 35 amino acids and have a structure in which a PPR motif is about 10 contiguous amino acids.
  • the combination of PPR motifs can be used for sequence-selective binding to RNA.
  • PPR proteins are often comprised of PPR motifs of about 10 repeat domains.
  • PPR domains or RNA-binding domains may be configured to be catalytically inactive. WO 2013/058404 incorporated herein by reference in its entirety.
  • a fusion protein comprises the RNA-binding polypeptide.
  • the fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity.
  • the first RNA binding protein comprises a CRISPR-Cas protein.
  • the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • the CRISPR- Cas protein is a Type V CRISPR-Cas protein.
  • the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein is a Type VI CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cas13 polypeptide or an RNA- binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity.
  • the native RNA nuclease activity is reduced or inhibited.
  • the native RNA nuclease activity is increased or induced.
  • the CRISPR-Cas protein comprises a native DNA nuclease activity and wherein the native DNA nuclease activity is inhibited.
  • the CRISPR-Cas protein comprises a mutation.
  • a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein.
  • the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a
  • the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • the first RNA binding protein comprises a Pumilio and FBF (PUF) protein.
  • the first RNA binding protein comprises a Pumilio- based assembly (PUMBY) protein.
  • the first RNA binding protein comprises a PPR (pentatricopeptide repeat) protein.
  • compositions of the disclosure including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide
  • the first RNA binding protein does not require multimerization for RNA-binding activity.
  • the first RNA binding protein is not a monomer of a multimer complex.
  • a multimer protein complex does not comprise the first RNA binding protein [0193]
  • the first RNA binding protein selectively binds to a target sequence within the RNA molecule.
  • the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule.
  • the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • compositions of the disclosure including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • compositions of the disclosure including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide
  • the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • compositions of the disclosure including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide
  • the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS).
  • the sequence encoding a nuclear localization signal (NLS) is positioned 3’ to the sequence encoding the first RNA binding protein.
  • the first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. In some embodiments, the sequence encoding the first NLS or the second NLS is positioned 3’ to the sequence encoding the first RNA binding protein. In some embodiments, the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein.
  • the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the second RNA binding protein binds RNA in a manner in which it associates with RNA. In some embodiments, the second RNA binding protein associates with RNA in a manner in which it cleaves RNA [0198] In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an RNAse.
  • the second RNA binding protein comprises or consists of a nuclease domain.
  • the sequence encoding the second RNA binding protein comprises or consists of an RNAse.
  • the second RNA binding protein comprises or consists of an RNAse1.
  • the sequence encoding the RNAse1 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse4.
  • the sequence encoding the RNAse4 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse6.
  • the sequence encoding the RNAse6 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse7.
  • the sequence encoding the RNAse7 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse8.
  • the sequence encoding the RNAse8 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse2.
  • the sequence encoding the RNAse2 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse6PL.
  • the sequence encoding the RNAse6PL comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAseL.
  • the sequence encoding the RNAseL comprises or consists of:
  • RNAseT2 the sequence encoding the RNAseT2 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAse11.
  • the sequence encoding the RNAse11 comprises or consists of:
  • the second RNA binding protein comprises or consists of an RNAseT2-like.
  • the sequence encoding the RNAseT2-like comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated RNAse.
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide.
  • Rnase1(K41R) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide.
  • the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide.
  • Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1.
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide.
  • the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
  • Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide that comprises or consists of: KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCRPVNTFVHEPLVDVQ NVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEG SPYVPVNFEASVEDST (SEQ ID NO: 208).
  • Rnase1 R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E
  • the sequence encoding the second RNA binding protein comprises or consists of a NOB1 polypeptide.
  • the sequence encoding the second RNA binding protein comprises or consists of an endonuclease. In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an endonuclease V (ENDOV). In some embodiments, the sequence encoding the ENDOV comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of an endonuclease G (ENDOG).
  • ENDOG endonuclease G
  • the sequence encoding the ENDOG comprises or consists of:
  • sequence encoding the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1).
  • sequence encoding the ENDOD1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1). In some embodiments, the sequence encoding the hFEN1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide.
  • hSLFN14 human Schlafen 14
  • sequence encoding the hSLFN14 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide.
  • the sequence encoding the hLACTB2 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide.
  • APEX2 comprises or consists of:
  • the sequence encoding the APEX2 comprises or consists of: MLRVVSWNINGIRRPLQGVANQEPSNCAAVAVGRILDELDADIVCLQETKVTRDAL TEPLAIVEGYNSYFSFSRNRSGYSGVATFCKDNATPVAAEEGLSGLFATQNGDVGCY GNMDEFTQEELRALDSEGRALLTQHKIRTWEGKEKTLTLINVYCPHADPGRPERLVF KMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECFEEDPGRKWMD SLLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGD RTLVIDTFQASFLLPEVMGSDHCPVGAVLSVSSVPAKQCPPLCTRFLPEFAGTQLKIL RFLVPLEQSP (SEQ ID NO: 39).
  • the sequence encoding the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide.
  • ANG angiogenin
  • the sequence encoding the ANG comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide.
  • HRSP12 heat responsive protein 12
  • the sequence encoding the HRSP12 comprises or consists of: SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGVAEEAKQALK NMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAALP KGSRIEIEAVAIQGPLTTASL (SEQ ID NO: 41).
  • the sequence encoding the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide.
  • the sequence encoding the ZC3H12A comprises or consists of:
  • the sequence encoding the ZC3H12A comprises or consists of:
  • sequence encoding the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide.
  • RIDA Reactive Intermediate Imine Deaminase A
  • the sequence encoding the RIDA comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide.
  • PDL6 Phospholipase D Family Member 6
  • the sequence encoding the PDL6 comprises or consists of: EALFFPSQVTCTEALLRAPGAELAELPEGCPCGLPHGESALSRLLRALLAARASLDLC LFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRHDQDPG YMHHKFAIVDKRVLITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIWEQFNP TKYTFFPPKKSHGSCAPPVSRAGGRLLSWHRTCGTSSESQT (SEQ ID NO: 126).
  • the sequence encoding the second RNA binding protein comprises or consists of a Endonuclease III-like protein 1 (NTHL) polypeptide.
  • the sequence encoding the NTHL comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a Mitochondrial ribonuclease P catalytic subunit(KIAA0391) polypeptide.
  • the sequence encoding the KIAA0391 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide.
  • the sequence encoding the APEX1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide.
  • the sequence encoding the AGO2 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide.
  • EXOG mitochondrial nuclease EXOG
  • the sequence encoding the EXOG comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D)
  • sequence encoding the ZC3H12D comprises or consists of:
  • RQQQPQVVEKQQETPLAPADFAHISQDAQSLHSGASRRSQKRLQSPSKQAQPLDDPE AEQLTVVGKISFNPKDVLGRGAGGTFVFRGQFEGRAVAVKRLLRECFGLVRREVQL LQESDRHPNVLRYFCTERGPQFHYIALELCRASLQEYVENPDLDRGGLEPEVVLQQL MSGLAHLHSLHIVHRDLKPGNILITGPDSQGLGRVVLSDFGLCKKLPAGRCSFSLHSG IPGTEGWMAPELLQLLPPDSPTSAVDIFSAGCVFYYVLSGGSHPFGDSLYRQANILTG APCLAHLEEEVHDKVVARDLVGAMLSPLPQPRPSAPQVLAHPFFWSRAKQLQFFQD VSDWLEKESEQEPLVRALEAGGCAVVRDNWHEHISMPLQTDLRKFRSYKGTSVRDL LRAVRNKKHHYRELPVEVRQALGQVPDGFVQY
  • the sequence encoding the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide.
  • the sequence encoding the PELO comprises or consists of:
  • sequence encoding the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide.
  • sequence encoding the YBEY comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide.
  • CPSF4L polyadenylation specific factor 4 like
  • the sequence encoding the CPSF4L comprises or consists of:
  • sequence encoding the second RNA binding protein comprises or consists of an hCG_2002731polypeptide.
  • sequence encoding the hCG_2002731 comprises or consists of:
  • sequence encoding the hCG_2002731 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide.
  • the sequence encoding the ERCC1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide.
  • the sequence encoding the RAC1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide.
  • RAA1 Ribonuclease A A1
  • the sequence encoding the RAA1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide.
  • RAB1 Ras Related Protein
  • the sequence encoding the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide.
  • the sequence encoding the DNA2 comprises or consists of:
  • sequence encoding the second RNA binding protein comprises or consists of a FLJ35220 polypeptide
  • sequence encoding the FLJ35220 comprises or consists of:
  • sequence encoding the second RNA binding protein comprises or consists of a FLJ13173 polypeptide.
  • sequence encoding the FLJ13173 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide.
  • ERCC4 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide.
  • the sequence encoding the TENM1 comprises or consists of:
  • the sequence encoding the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide.
  • the sequence encoding the TENM2 comprises or consists of:
  • the second RNA binding protein comprises or consists of a transcription activator-like effector nuclease (TALEN) polypeptide or a nuclease domain thereof.
  • TALEN transcription activator-like effector nuclease
  • the sequence encoding the TALEN polypeptide comprises or consists of:
  • sequence encoding the TALEN polypeptide comprises or consists of:
  • the second RNA binding protein comprises or consists of a zinc finger nuclease polypeptide or a nuclease domain thereof.
  • the sequence encoding the zinc finger nuclease polypeptide comprises or consists of:
  • gRNA guide RNA
  • sgRNA single guide RNA
  • Guide RNAs (gRNAs) of the disclosure may comprise of a spacer sequence and a scaffolding sequence.
  • a guide RNA is a single guide RNA (sgRNA) comprising a contiguous spacer sequence and scaffolding sequence.
  • the spacer sequence and the scaffolding sequence are not contiguous.
  • a sequence encoding a guide RNA or single guide RNA of the disclosure comprises or consists of a spacer sequence and a scaffolding sequence, that are separated by a linker sequence.
  • the linker sequence may comprise or consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between.
  • the linker sequence may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between.
  • Guide RNAs (gRNAs) of the disclosure may comprise non-naturally occurring nucleotides.
  • a guide RNA of the disclosure or a sequence encoding the guide RNA comprises or consists of modified or synthetic RNA nucleotides.
  • Exemplary modified RNA nucleotides include, but are not limited to, pseudouridine (Y), dihydrouridine (D), inosine (I), and 7-methylguanosine (m7G), hypoxanthine, xanthine, xanthosine, 7- methylguanine, 5, 6-Dihydrouracil, 5-methylcytosine, 5-methylcytidine, 5- hydropxymethylcytosine, isoguanine, and isocytosine.
  • Guide RNAs (gRNAs) of the disclosure may bind modified RNA within a target sequence.
  • guide RNAs (gRNAs) of the disclosure may bind modified RNA.
  • Exemplary epigenetically or post-transcriptionally modified RNA include, but are not limited to, 2’-O-Methylation (2’-OMe) (2’-O-methylation occurs on the oxygen of the free 2’-OH of the ribose moiety), N6-methyladenosine (m6A), and 5-methylcytosine (m5C).
  • a guide RNA of the disclosure comprises at least one sequence encoding a non-coding C/D box small nucleolar RNA (snoRNA) sequence.
  • the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the target sequence of the RNA molecule comprises at least one 2’-OMe.
  • the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the at least one sequence that is complementary to the target RNA comprises a box C motif (RUGAUGA) and a box D motif (CUGA).
  • Spacer sequences of the disclosure bind to the target sequence of an RNA molecule.
  • Spacer sequences of the disclosure may comprise a CRISPR RNA (crRNA).
  • Spacer sequences of the disclosure comprise or consist of a sequence having sufficient
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence.
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence.
  • Scaffolding sequences of the disclosure bind the first RNA-binding polypeptide of the disclosure.
  • Scaffolding sequences of the disclosure may comprise a trans acting RNA (tracrRNA).
  • Scaffolding sequences of the disclosure comprise or consist of a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence.
  • the scaffolding sequence may guide a fusion protein to the RNA molecule.
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence.
  • a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence.
  • scaffolding sequences of the disclosure comprise or consist of a sequence that binds to a first RNA binding protein or a second RNA binding protein of a fusion protein of the disclosure.
  • scaffolding sequences of the disclosure comprise a secondary structure or a tertiary structure.
  • Exemplary secondary structures include, but are not limited to, a helix, a stem loop, a bulge, a tetraloop and a pseudoknot.
  • Exemplary tertiary structures include, but are not limited to, an A-form of a helix, a B-form of a helix, and a Z-form of a helix.
  • Exemplary tertiary structures include but are not limited to a twisted or helicized stem loop. Exemplary tertiary structures include, but are not limited to, a twisted or helicized pseudoknot.
  • scaffolding sequences of the disclosure comprise at least one secondary structure or at least one tertiary structure. In some embodiments, scaffolding sequences of the disclosure comprise one or more secondary structure(s) or one or more tertiary structure(s).
  • a guide RNA or a portion thereof selectively binds to a tetraloop motif in an RNA molecule of the disclosure.
  • a target sequence of an RNA molecule comprises a tetraloop motif.
  • the tetraloop motif is a“GRNA” motif comprising or consisting of one or more of the sequences of GAAA, GUGA, GCAA or GAGA.
  • a guide RNA or a portion thereof that binds to a target sequence of an RNA molecule hybridizes to the target sequence of the RNA molecule.
  • a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein covalently binds to the first RNA binding protein or to the second RNA binding protein.
  • a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein non-covalently binds to the first RNA binding protein or to the second RNA binding protein.
  • a guide RNA or a portion thereof comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints.
  • a spacer sequence of the disclosure comprises or consists of between 10 and 30 nucleotides, inclusive of the endpoints.
  • a spacer sequence of the disclosure comprises or consists of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides.
  • the spacer sequence of the disclosure comprises or consists of 20 nucleotides.
  • the spacer sequence of the disclosure comprises or consists of 21 nucleotides.
  • a scaffold sequence of the disclosure comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints.
  • a spacer sequence of the disclosure comprises or consists of 30, 35, 40, 45, 50, 55, 60, 65, 70, 76, 80, 87, 90, 95, 100 or any number of nucleotides in between.
  • the scaffold sequence of the disclosure comprises or consists of between 85 and 95 nucleotides, inclusive of the endpoints.
  • the scaffold sequence of the disclosure comprises or consists of 85 nucleotides
  • the scaffold sequence of the disclosure comprises or consists of 90 nucleotides.
  • the scaffold sequence of the disclosure comprises or consists of 93 nucleotides.
  • a guide RNA or a portion thereof does not comprise a nuclear localization sequence (NLS).
  • NLS nuclear localization sequence
  • a guide RNA or a portion thereof does not comprise a sequence complementary to a protospacer adjacent motif (PAM).
  • PAM protospacer adjacent motif
  • Therapeutic or pharmaceutical compositions of the disclosure do not comprise a PAMmer oligonucleotide.
  • non-therapeutic or non- pharmaceutical compositions may comprise a PAMmer oligonucleotide.
  • a guide RNA or a portion thereof comprises a sequence complementary to a protospacer flanking sequence (PFS).
  • PFS protospacer flanking sequence
  • the first RNA binding protein may comprise a sequence isolated or derived from a Cas13 protein.
  • the first RNA binding protein may comprise a sequence encoding a Cas13 protein or an RNA- binding portion thereof.
  • the guide RNA or a portion thereof does not comprise a sequence complementary to a PFS.
  • a sequence encoding a guide RNA of the disclosure further comprises a sequence encoding a promoter to drive expression of the guide RNA.
  • a vector comprising a sequence encoding a guide RNA of the disclosure further comprises a sequence encoding a promoter to drive expression of the guide RNA.
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a constitutive promoter.
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding an inducible promoter.
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a hybrid or a recombinant promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a promoter capable of expressing the guide RNA in a mammalian cell.
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a promoter capable of expressing the guide RNA in a human cell
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a promoter capable of expressing the guide RNA and restricting the guide RNA to the nucleus of the cell.
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a human RNA polymerase promoter or a sequence isolated or derived from a sequence encoding a human RNA polymerase promoter.
  • a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a U6 promoter or a sequence isolated or derived from a sequence encoding a U6 promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a human tRNA promoter or a sequence isolated or derived from a sequence encoding a human tRNA promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a human valine tRNA promoter or a sequence isolated or derived from a sequence encoding a human valine tRNA promoter.
  • a sequence encoding a promoter to drive expression of the guide RNA further comprises a regulatory element.
  • a vector comprising a sequence encoding a promoter to drive expression of the guide RNA further comprises a regulatory element.
  • a regulatory element enhances expression of the guide RNA.
  • Exemplary regulatory elements include, but are not limited to, an enhancer element, an intron, an exon, or a combination thereof.
  • a vector of the disclosure comprises one or more of a sequence encoding a guide RNA, a sequence encoding a promoter to drive expression of the guide RNA and a sequence encoding a regulatory element.
  • the vector further comprises a sequence encoding a fusion protein of the disclosure.
  • Fusion proteins in the context of the compositions of the disclosure may comprise a first RNA binding protein and a second RNA binding protein.
  • the sequence encoding the first RNA binding protein is positioned 5’ of the sequence encoding the second RNA binding protein.
  • the sequence encoding the first RNA binding protein is positioned 3’ of the sequence encoding the second RNA binding protein.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of selectively binding an RNA molecule and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule and inducing a break in the RNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and neither binding nor inducing a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein with no DNA nuclease activity.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity is inactivated and wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity to a level at which the DNA nuclease activity does not induce a break in a DNA molecule a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
  • the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity and the mutation comprises one or more of a substitution, inversion, transposition, insertion, deletion, or any combination thereof to a nucleic acid sequence or amino acid sequence encoding the first RNA binding protein or a nuclease domain thereof.
  • the fusion protein disclosed herein comprises a linker between the at least two RNA-binding polypeptides.
  • the linker is a peptide linker.
  • the peptide linker comprises one or more repeats of the tri-peptide GGS. In other embodiments, the linker is a non-peptide linker.
  • the non-peptide linker comprises polyethylene glycol (PEG), polypropylene glycol (PPG), co-poly(ethylene/propylene) glycol, polyoxyethylene (POE), polyurethane, polyphosphazene, polysaccharides, dextran, polyvinyl alcohol, polyvinylpyrrolidones, polyvinyl ethyl ether, polyacryl amide, polyacrylate, polycyanoacrylates, lipid polymers, chitins, hyaluronic acid, heparin, or an alkyl linker.
  • PEG polyethylene glycol
  • PPG polypropylene glycol
  • POE polyoxyethylene
  • polyurethane polyphosphazene
  • polysaccharides dextran
  • polyvinyl alcohol polyvinylpyrrolidones
  • polyvinyl ethyl ether polyacryl amide
  • polyacrylate polycyanoacrylates
  • lipid polymers chitins, hyaluronic
  • the at least one RNA-binding protein does not require multimerization for RNA-binding activity.
  • the at least one RNA- binding protein is not a monomer of a multimer complex.
  • a multimer protein complex does not comprise the RNA binding protein.
  • the at least one of RNA-binding protein selectively binds to a target sequence within the RNA molecule.
  • the at least one RNA-binding protein does not comprise an affinity for a second sequence within the RNA molecule.
  • the at least one RNA-binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • the at least one RNA-binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
  • the at least one RNA-binding protein of the fusion proteins disclosed herein further comprises a sequence encoding a nuclear localization signal (NLS).
  • a nuclear localization signal (NLS) is positioned 3’ to the RNA binding protein.
  • the at least one RNA-binding protein comprises an NLS at a C-terminus of the protein.
  • the at least one RNA-binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS.
  • the first NLS or the second NLS is positioned 3’ to the RNA-binding protein
  • the at least one RNA- binding protein comprises the first NLS or the second NLS at a C-terminus of the protein.
  • the at least one RNA-binding protein further comprises an NES (nuclear export signal) or other peptide tag or secretory signal.
  • a fusion protein disclosed herein comprises the at least one RNA-binding protein as a first RNA-binding protein together with a second RNA-binding protein comprising or consisting of a nuclease domain.
  • the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the C-terminus of the first RNA-binding polypeptide. In some embodiments, the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the N-terminus of the first RNA-binding polypeptide.
  • one such exemplary fusion protein is E99 which is configured so that
  • RNAse1 (R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the N-terminus of SpyCas9 whereas another exemplary fusion protein, E100, is configured so that
  • RNAse1 (R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the C-terminus of SpyCas9.
  • a target sequence of an RNA molecule comprises a sequence motif corresponding to the RNA binding protein and/or the RNA binding proteins and/or fusion protein thereof.
  • the sequence motif is a signature of a disease or disorder.
  • a sequence motif of the disclosure may be isolated or derived from a sequence of foreign or exogenous sequence found in a genomic sequence, and therefore translated into an mRNA molecule of the disclosure or a sequence of foreign or exogenous sequence found in an RNA sequence of the disclosure.
  • a sequence motif of the disclosure may comprise or consist of a mutation in an endogenous sequence that causes a disease or disorder.
  • the mutation may comprise or consist of a sequence substitution, inversion, deletion, insertion, transposition, or any combination thereof.
  • a sequence motif of the disclosure may comprise or consist of a repeated sequence.
  • the repeated sequence may be associated with a microsatellite instability (MSI).
  • MSI microsatellite instability
  • a hypervariable sequence of DNA may be transcribed into an mRNA of the disclosure comprising a target sequence comprising or consisting of the hypervariable sequence.
  • a sequence motif of the disclosure may comprise or consist of a biomarker.
  • the biomarker may indicate a risk of developing a disease or disorder.
  • the biomarker may indicate a healthy gene (low or no determinable risk of developing a disease or disorder.
  • the biomarker may indicate an edited gene.
  • Exemplary biomarkers include, but are not limited to, single nucleotide polymorphisms (SNPs), sequence variations or mutations, epigenetic marks, splice acceptor sites, exogenous sequences, heterologous sequences, and any combination thereof.
  • a sequence motif of the disclosure may comprise or consist of a secondary, tertiary or quaternary structure.
  • the secondary, tertiary or quaternary structure may be endogenous or naturally occurring.
  • the secondary, tertiary or quaternary structure may be induced or non- naturally occurring.
  • the secondary, tertiary or quaternary structure may be encoded by an endogenous, exogenous, or heterologous sequence.
  • a target sequence of an RNA molecule comprises or consists of between 2 and 100 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 50 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 20 nucleotides or nucleic acid bases, inclusive of the endpoints.
  • a target sequence of an RNA molecule is continuous.
  • the target sequence of an RNA molecule is discontinuous.
  • the target sequence of an RNA molecule may comprise or consist of one or more nucleotides or nucleic acid bases that are not contiguous because one or more intermittent nucleotides are positioned in between the nucleotides of the target sequence.
  • a target sequence of an RNA molecule is naturally occurring.
  • the target sequence of an RNA molecule is non-naturally occurring.
  • Exemplary non-naturally occurring target sequences may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
  • a target sequence of an RNA molecule binds to a guide RNA of the disclosure.
  • a target sequence of an RNA molecule binds to a first RNA binding protein of the disclosure.
  • RNA Molecules binds to a second RNA binding protein of the disclosure.
  • an RNA molecule of the disclosure comprises a target sequence. In some embodiments, the RNA molecule of the disclosure comprises at least one target sequence. In some embodiments, the RNA molecule of the disclosure comprises one or more target sequence(s). In some embodiments, the RNA molecule of the disclosure comprises two or more target sequences.
  • an RNA molecule of the disclosure is a naturally occurring RNA molecule.
  • the RNA molecule of the disclosure is a non-naturally occurring molecule.
  • Exemplary non- naturally occurring RNA molecules may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a virus.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a prokaryotic organism. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species or strain of archaea or a species or strain of bacteria.
  • the RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a eukaryotic organism.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species of protozoa parasite protist algae, fungi, yeast, amoeba, worm, microorganism, invertebrate, vertebrate, insect, rodent, mouse, rat, mammal, or a primate.
  • an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a human.
  • the RNA molecule of the disclosure comprises or consists of a sequence derived from a coding sequence from a genome of an organism or a virus.
  • the RNA molecule of the disclosure comprises or consists of a primary RNA transcript, a precursor messenger RNA (pre-mRNA) or messenger RNA (mRNA).
  • pre-mRNA precursor messenger RNA
  • mRNA messenger RNA
  • the RNA molecule of the disclosure comprises or consists of a gene product that has not been processed (e.g. a transcript).
  • the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to post-transcriptional processing (e.g.
  • the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to alternative splicing (e.g. a splice variant). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to removal of non-coding and/or intronic sequences (e.g. a messenger RNA (mRNA)).
  • mRNA messenger RNA
  • the RNA molecule of the disclosure comprises or consists of a sequence derived from a non-coding sequence (e.g. a non-coding RNA (ncRNA)).
  • a non-coding RNA e.g. a non-coding RNA (ncRNA)
  • the RNA molecule of the disclosure comprises or consists of a ribosomal RNA.
  • the RNA molecule of the disclosure comprises or consists of a small ncRNA molecule.
  • Exemplary small RNA molecules of the disclosure include, but are not limited to, microRNAs
  • miRNAs small interfering (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), extracellular or exosomal RNAs
  • RNA molecules of the disclosure comprises or consists of a long ncRNA molecule.
  • exemplary long RNA molecules of the disclosure include, but are not limited to, X-inactive specific transcript (Xist) and HOX transcript antisense RNA (HOTAIR).
  • the RNA molecule of the disclosure contacted by a composition of the disclosure in an intracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a
  • composition of the disclosure in a cytosolic space In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a nucleus In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a vesicle, membrane-bound compartment of a cell, or an organelle.
  • the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an exosome. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a liposome, a polymersome, a micelle or a nanoparticle. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular matrix. In some
  • the RNA molecule of the disclosure contacted by a composition of the disclosure in a droplet. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a microfluidic droplet.
  • a RNA molecule of the disclosure comprises or consists of a single-stranded sequence.
  • the RNA molecule of the disclosure comprises or consists of a double-stranded sequence.
  • the double-stranded sequence comprises two RNA molecules.
  • the double-stranded sequence comprises one RNA molecule and one DNA molecule.
  • compositions of the disclosure selectively bind and, optionally, selectively cut the RNA molecule.
  • a vector comprises a guide RNA of the disclosure.
  • the vector comprises at least one guide RNA of the disclosure.
  • the vector comprises one or more guide RNA(s) of the disclosure.
  • the vector comprises two or more guide RNAs of the disclosure.
  • the vector further comprises a fusion protein of the disclosure.
  • the fusion protein comprises a first RNA binding protein and a second RNA binding protein.
  • a first vector comprises a guide RNA of the disclosure and a second vector comprises a fusion protein of the disclosure.
  • the first vector comprises at least one guide RNA of the disclosure.
  • the first vector comprises one or more guide RNA(s) of the disclosure.
  • the first vector comprises two or more guide RNA(s) of the disclosure.
  • the fusion protein comprises a first RNA binding protein and a second RNA binding protein.
  • the first vector and the second vector are identical. In some embodiments, the first vector and the second vector are not identical.
  • the vector is or comprises a component of a“2-component RNA targeting system” comprising (a) nucleic acid sequence encoding a RNA-targeted fusion protein of the disclosure; and (b) a single guide RNA (sgRNA) sequence comprising: on its 5’ end, an RNA sequence (or spacer sequence) that hybridizes to or binds to a target RNA sequence; and on its 3’ end, an RNA sequence (or scaffold sequence) capable of binding to or associating with the CRISPR/Cas protein of the fusion protein; and wherein the 2-component RNA targeting system recognizes and alters the target RNA in a cell in the absence of a PAMmer.
  • sgRNA single guide RNA
  • sequences of the 2-component system are in a single vector.
  • the spacer sequence of the 2-component system targets a repeat sequence selected from the group consisting of CUG, CCUG, CAG, and GGGGCC.
  • a vector of the disclosure is a viral vector.
  • the viral vector comprises a sequence isolated or derived from a retrovirus.
  • the viral vector comprises a sequence isolated or derived from a lentivirus.
  • the viral vector comprises a sequence isolated or derived from an adenovirus.
  • the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV).
  • AAV adeno-associated virus
  • the viral vector is replication incompetent.
  • the viral vector is isolated or recombinant.
  • the viral vector is self- complementary.
  • the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV).
  • AAV adeno-associated virus
  • the viral vector comprises an inverted terminal repeat sequence or a capsid sequence that is isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12, or the vector and/or components are derived from a synthetic AAV serotype, such as, without limitation, Anc80 AAV (an ancestor of AAV 1, 2, 6, 8 and 9).
  • the viral vector is replication incompetent.
  • the viral vector is isolated or recombinant (rAAV).
  • the viral vector is self-complementary (scAAV).
  • a vector of the disclosure is a non-viral vector.
  • the vector comprises or consists of a nanoparticle, a micelle, a liposome or lipoplex, a polymersome, a polyplex or a dendrimer.
  • the vector is an expression vector or recombinant expression system.
  • the term“recombinant expression system” refers to a genetic construct for the expression of certain genetic material formed by recombination.
  • an expression vector, viral vector or non-viral vector provided herein includes without limitation, an expression control element.
  • An“expression control element” as used herein refers to any sequence that regulates the expression of a coding sequence, such as a gene.
  • Exemplary expression control elements include but are not limited to promoters, enhancers, microRNAs, post-transcriptional regulatory elements, polyadenylation signal sequences, and introns. Expression control elements may be constitutive, inducible, repressible, or tissue- specific, for example.
  • A“promoter” is a control sequence that is a region of a polynucleotide sequence at which initiation and rate of transcription are controlled.
  • Non-limiting exemplary promoters include CMV, CBA, CAG, Cbh, EF-1a, PGK, UBC, GUSB, UCOE, hAAT, TBG, Desmin, MCK, C5-12, NSE, Synapsin, PDGF, MecP2, CaMKII, mGluR2, NFL, NFH, nb2, PPE, ENK, EAAT2, GFAP, MBP, and U6 promoters.
  • An“enhancer” is a region of DNA that can be bound by activating proteins to increase the likelihood or frequency of transcription.
  • posttranscriptional regulatory elements include the CMV enhancer and WPRE.
  • an expression vector, viral vector or non-viral vector includes without limitation, vector elements such as an IRES or 2A peptide sites for configuration of “multicistronic” or“polycistronic” or“bicistronic” or tricistronic” constructs, i.e., having double or triple or multiple coding areas or exons, and as such will have the capability to express from mRNA two or more proteins from a single construct.
  • Multicistronic vectors simultaneously express two or more separate proteins from the same mRNA.
  • the two strategies most widely used for constructing multicistronic configurations are through the use of an IRES or a 2A self-cleaving site.
  • an“IRES” refers to an internal ribosome entry site or portion thereof of viral, prokaryotic, or eukaryotic origin which are used within polycistronic vector constructs.
  • an IRES is an RNA element that allows for translation initiation in a cap-independent manner.
  • self-cleaving peptides or“sequences encoding self-cleaving peptides” or“2A self-cleaving site” refer to linking sequences which are used within vector constructs to incorporate sites to promote ribosomal skipping and thus to generate two polypeptides from a single promoter, such self- cleaving peptides include without limitation, T2A, and P2A peptides or sequences encoding the self-cleaving peptides.
  • the vector is a viral vector.
  • the vector is an adenoviral vector, an adeno-associated viral (AAV) vector, or a lentiviral vector.
  • the vector is a retroviral vector, an adenoviral/retroviral chimera vector, a herpes simplex viral I or II vector, a parvoviral vector, a reticuloendotheliosis viral vector, a polioviral vector, a papillomaviral vector, a vaccinia viral vector, or any hybrid or chimeric vector incorporating favorable aspects of two or more viral vectors.
  • the vector further comprises one or more expression control elements operably linked to the polynucleotide. In some embodiments, the vector further comprises one or more selectable markers. In some embodiments, the AAV vector has low toxicity. In some embodiments, the AAV vector does not incorporate into the host genome, thereby having a low probability of causing insertional mutagenesis. In some embodiments, the AAV vector can encode a range of total polynucleotides from 4.5 kb to 4.75 kb.
  • exemplary AAV vectors that may be used in any of the herein described compositions, systems, methods, and kits can include an AAV1 vector, a modified AAV1 vector, an AAV2 vector, a modified AAV2 vector, an AAV3 vector, a modified AAV3 vector, an AAV4 vector, a modified AAV4 vector, an AAV5 vector, a modified AAV5 vector, an AAV6 vector, a modified AAV6 vector, an AAV7 vector, a modified AAV7 vector, an AAV8 vector, an AAV9 vector, an AAV.rh10 vector, a modified AAV.rh10 vector, an AAV.rh32/33 vector, a modified AAV.rh32/33 vector, an AAV.rh43 vector, a modified AAV.rh43 vector, an AAV.rh64R1 vector, and a modified AAV.rh64R1 vector and any combinations or equivalents thereof.
  • the lentiviral vector is an integrase-competent lentiviral vector (ICLV).
  • the lentiviral vector can refer to the transgene plasmid vector as well as the transgene plasmid vector in conjunction with related plasmids (e g a packaging plasmid a rev expressing plasmid an envelope plasmid) as well as a lentiviral-based particle capable of introducing exogenous nucleic acid into a cell through a viral or viral-like entry mechanism.
  • related plasmids e.g a packaging plasmid a rev expressing plasmid an envelope plasmid
  • Lentiviral vectors are well-known in the art (see, e.g., Trono D. (2002) Lentiviral vectors, New York: Spring-Verlag Berlin Heidelberg and Durand et al. (2011) Viruses 3(2):132-159 doi: 10.3390/v3020132).
  • exemplary lentiviral vectors that may be used in any of the herein described compositions, systems, methods, and kits can include a human immunodeficiency virus (HIV) 1 vector, a modified human immunodeficiency virus (HIV) 1 vector, a human immunodeficiency virus (HIV) 2 vector, a modified human immunodeficiency virus (HIV) 2 vector, a sooty mangabey simian immunodeficiency virus (SIVSM) vector, a modified sooty mangabey simian immunodeficiency virus (SIVSM) vector, a African green monkey simian immunodeficiency virus (SIV AGM ) vector, a modified African green monkey simian immunodeficiency virus (SIV AGM ) vector, an equine infectious anemia virus (EIAV) vector, a modified equine infectious anemia virus (EIAV) vector, a feline immunodeficiency virus (FIV) vector, a modified feline immuno
  • a vector of the disclosure is a non-viral vector.
  • the vector comprises or consists of a nanoparticle, a micelle, a liposome or lipoplex, a polymersome, a polyplex or a dendrimer.
  • nucleic acid sequences encoding the fusion proteins disclosed herein for use in gene transfer and expression techniques described herein. It should be understood, although not always explicitly stated that the sequences provided herein can be used to provide the expression product as well as substantially identical sequences that produce a protein that has the same biological properties. These“biologically equivalent” or“biologically active” or“equivalent” polypeptides are encoded by equivalent polynucleotides as described herein.
  • polypeptides may possess at least 60%, or alternatively, at least 65%, or alternatively, at least 70%, or alternatively, at least 75%, or alternatively, at least 80%, or alternatively at least 85%, or alternatively at least 90%, or alternatively at least 95% or alternatively at least 98%, identical primary amino acid sequence to the reference polypeptide when compared using sequence identity methods run under default conditions.
  • Specific polypeptide sequences are provided as examples of particular embodiments.
  • an equivalent polynucleotide is one that hybridizes under stringent conditions to the reference polynucleotide or its complement or in reference to a polypeptide, a polypeptide encoded by a polynucleotide that hybridizes to the reference encoding polynucleotide under stringent conditions or its complementary strand.
  • an equivalent polypeptide or protein is one that is expressed from an equivalent polynucleotide.
  • nucleic acid sequences e.g., polynucleotide sequences
  • exemplary Cas sequences such as e.g., SEQ ID NO: 46 (Cas13d) are codon optimized for expression in human cells. Codon optimization refers to the fact that different cells differ in their usage of particular codons. This codon bias corresponds to a bias in the relative abundance of particular tRNAs in the cell type. By altering the codons in the sequence to match with the relative abundance of corresponding tRNAs, it is possible to increase expression.
  • nucleic acid sequences coding for, e.g., a Cas protein can be generated.
  • such a sequence is optimized for expression in a host or target cell, such as a host cell used to express the Cas protein or a cell in which the disclosed methods are practiced (such as in a mammalian cell, e.g., a human cell).
  • Codon preferences and codon usage tables for a particular species can be used to engineer isolated nucleic acid molecules encoding a Cas protein (such as one encoding a protein having at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type protein) that takes advantage of the codon usage preferences of that particular species.
  • the Cas proteins disclosed herein can be designed to have codons that are preferentially used by a particular organism of interest.
  • an Cas nucleic acid sequence is optimized for expression in human cells, such as one having at least 70%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 98%, or at least 99% sequence identity to its corresponding wild-type or originating nucleic acid sequence.
  • an isolated nucleic acid molecule encoding at least one Cas protein (which can be part of a vector) includes at least one Cas protein coding sequence that is codon optimized for expression in a eukaryotic cell, or at least one Cas protein coding sequence codon optimized for expression in a human cell.
  • such a codon optimized Cas coding sequence has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating sequence.
  • a eukaryotic cell codon optimized nucleic acid sequence encodes a Cas protein having at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating protein.
  • clones containing functionally equivalent nucleic acids may be routinely generated, such as nucleic acids which differ in sequence but which encode the same Cas protein sequence.
  • Silent mutations in the coding sequence result from the degeneracy (i.e., redundancy) of the genetic code, whereby more than one codon can encode the same amino acid residue.
  • leucine can be encoded by CTT, CTC, CTA, CTG, TTA, or TTG; serine can be encoded by TCT, TCC, TCA, TCG, AGT, or AGC; asparagine can be encoded by AAT or AAC; aspartic acid can be encoded by GAT or GAC; cysteine can be encoded by TGT or TGC; alanine can be encoded by GCT, GCC, GCA, or GCG; glutamine can be encoded by CAA or CAG; tyrosine can be encoded by TAT or TAC; and isoleucine can be encoded by ATT, ATC, or ATA. Tables showing the standard genetic code can be found in various sources (see, for example, Stryer, 1988, Biochemistry, 3.sup.rd Edition, W.H.5 Freeman and Co., NY).
  • Hybridization refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues.
  • the hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PC reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Examples of stringent hybridization conditions include: incubation temperatures of about 25°C to about 37°C; hybridization buffer concentrations of about 6x SSC to about 10x SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4x SSC to about 8x SSC.
  • Examples of moderate hybridization conditions include: incubation temperatures of about 40°C to about 50°C; buffer concentrations of about 9x SSC to about 2x SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5x SSC to about 2x SSC.
  • high stringency conditions include: incubation temperatures of about 55°C to about 68°C; buffer concentrations of about lx SSC to about 0.1x SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about lx SSC, 0.1x SSC, or deionized water.
  • hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes.
  • SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
  • Homology or“identity” or“similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or“non-homologous” sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present invention.
  • a cell of the disclosure is a prokaryotic cell.
  • a cell of the disclosure is a eukaryotic cell. In some embodiments, a cell of the disclosure is a somatic cell. In some embodiments, a cell of the disclosure is a germline cell. In some embodiments, a germline cell of the disclosure is not a human cell.
  • a cell of the disclosure is a stem cell.
  • a cell of the disclosure is an embryonic stem cell.
  • an embryonic stem cell of the disclosure is not a human cell.
  • a cell of the disclosure is a multipotent stem cell or a pluripotent stem cell.
  • a cell of the disclosure is an adult stem cell.
  • a cell of the disclosure is an induced pluripotent stem cell (iPSC).
  • a cell of the disclosure is a hematopoietic stem cell (HSC).
  • a somatic cell of the disclosure is an immune cell.
  • an immune cell of the disclosure is a lymphocyte
  • an immune cell of the disclosure is a T lymphocyte (also referred to herein as a T-cell).
  • Exemplary T-cells of the disclosure include, but are not limited to, na ⁇ ve T cells, effector T cells, helper T cells, memory T cells, regulatory T cells (Tregs) and Gamma delta T cells.
  • an immune cell of the disclosure is a B lymphocyte.
  • an immune cell of the disclosure is a natural killer cell.
  • an immune cell of the disclosure is an antigen- presenting cell.
  • a somatic cell of the disclosure is a muscle cell.
  • a muscle cell of the disclosure is a myoblast or a myocyte.
  • a muscle cell of the disclosure is a cardiac muscle cell, skeletal muscle cell or smooth muscle cell.
  • a muscle cell of the disclosure is a striated cell.
  • a somatic cell of the disclosure is an epithelial cell.
  • an epithelial cell of the disclosure forms a squamous cell epithelium, a cuboidal cell epithelium, a columnar cell epithelium, a stratified cell epithelium, a pseudostratified columnar cell epithelium or a transitional cell epithelium.
  • an epithelial cell of the disclosure forms a gland including, but not limited to, a pineal gland, a thymus gland, a pituitary gland, a thyroid gland, an adrenal gland, an apocrine gland, a holocrine gland, a merocrine gland, a serous gland, a mucous gland and a sebaceous gland.
  • an epithelial cell of the disclosure contacts an outer surface of an organ including, but not limited to, a lung, a spleen, a stomach, a pancreas, a bladder, an intestine, a kidney, a gallbladder, a liver, a larynx or a pharynx.
  • an epithelial cell of the disclosure contacts an outer surface of a blood vessel or a vein.
  • a somatic cell of the disclosure is a neuronal cell.
  • a neuron cell of the disclosure is a neuron of the central nervous system.
  • a neuron cell of the disclosure is a neuron of the brain or the spinal cord.
  • a neuron cell of the disclosure is a neuron of the retina.
  • a neuron cell of the disclosure is a neuron of a cranial nerve or an optic nerve.
  • a neuron cell of the disclosure is a neuron of the peripheral nervous system.
  • a neuron cell of the disclosure is a neuroglial or a glial cell.
  • a glial of the disclosure is a glial cell of the central nervous system including, but not limited to, oligodendrocytes, astrocytes, ependymal cells and microglia
  • a glial of the disclosure is a glial cell of the peripheral nervous system including, but not limited to, Schwann cells and satellite cells.
  • a somatic cell of the disclosure is a primary cell.
  • a somatic cell of the disclosure is a cultured cell.
  • a somatic cell of the disclosure is in vivo, in vitro, ex vivo or in situ.
  • a somatic cell of the disclosure is autologous or allogeneic.
  • the disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the RNA-binding protein or fusion protein thereof (or a portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a RNA-binding portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein.
  • the disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the RNA-binding protein or fusion protein thereof (or a portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the RNA- binding protein or fusion protein thereof (or a portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA or a single guide RNA of the disclosure and a fusion protein of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof or portion thereof induces a break in the RNA molecule and provides immune masking activity specific to the RNA-binding protein.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof (or a portion thereof) induces a break to the RNA molecule and provides immune masking activity specific to the RNA-binding protein.
  • the disclosure provides a method of modifying a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule and provides immune masking activity specific to the RNA-binding protein comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof induces a break in the RNA molecule.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and an RNA-binding protein of the disclosure and a mutated non-cleavable FasL of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof or portion thereof induces a break in the RNA molecule.
  • the cell is in vivo, in vitro, ex vivo or in situ.
  • the composition comprises a vector comprising composition comprising a guide RNA sequence or a single guide RNA of the disclosure and a sequence encoding an RNA-binding protein of the disclosure and sequence encoding a mutated non-cleavable FasL of the disclosure.
  • the vector is an AAV.
  • the disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure.
  • the disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising a guide RNA sequence of the disclosure, a sequence encoding an RNA-binding protein of the disclosure, and a sequence encoding a mutated non-cleavable FasL of the disclosure, and wherein the composition modifies a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule and provides immune masking activity specific to the RNA- binding protein.
  • the disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising composition comprising a compositions of the disclosure.
  • a disease or disorder of the disclosure includes, but is not limited to, a genetic disease or disorder.
  • the genetic disease or disorder is a single-gene disease or disorder.
  • the single-gene disease or disorder is an autosomal dominant disease or disorder, an autosomal recessive disease or disorder, an X-chromosome linked (X-linked) disease or disorder, an X-linked dominant disease or disorder, an X-linked recessive disease or disorder, a Y-linked disease or disorder or a mitochondrial disease or disorder.
  • the genetic disease or disorder is a multiple-gene disease or disorder.
  • the genetic disease or disorder is a multiple-gene disease or disorder.
  • the single-gene disease or disorder is an autosomal dominant disease or disorder including, but not limited to, Huntington's disease, neurofibromatosis type 1, neurofibromatosis type 2, Marfan syndrome, hereditary nonpolyposis colorectal cancer, hereditary multiple exostoses, Von Willebrand disease, and acute intermittent porphyria.
  • the single-gene disease or disorder is an autosomal recessive disease or disorder including but not limited to Albinism Medium-chain acyl-CoA dehydrogenase deficiency, cystic fibrosis, sickle-cell disease, Tay-Sachs disease, Niemann-Pick disease, spinal muscular atrophy, and Roberts syndrome.
  • the single-gene disease or disorder is X-linked disease or disorder including, but not limited to, muscular dystrophy, Duchenne muscular dystrophy, Hemophilia, Adrenoleukodystrophy (ALD), Rett syndrome, and Hemophilia A.
  • the single-gene disease or disorder is a mitochondrial disorder including, but not limited to, Leber's hereditary optic neuropathy.
  • a disease or disorder of the disclosure includes, but is not limited to, an immune disease or disorder.
  • the immune disease or disorder is an immunodeficiency disease or disorder including, but not limited to, B-cell deficiency, T-cell deficiency, neutropenia, asplenia, complement deficiency, acquired immunodeficiency syndrome (AIDS) and immunodeficiency due to medical intervention (immunosuppression as an intended or adverse effect of a medical therapy).
  • the immune disease or disorder is an autoimmune disease or disorder including, but not limited to, Achalasia, Addison’s disease, Adult Still's disease, Agammaglobulinemia, Alopecia areata, Amyloidosis, Anti- GBM/Anti-TBM nephritis, Antiphospholipid syndrome, Autoimmune angioedema,
  • Autoimmune dysautonomia Autoimmune encephalomyelitis, Autoimmune hepatitis, Autoimmune inner ear disease (AIED), Autoimmune myocarditis, Autoimmune oophoritis, Autoimmune orchitis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmune urticaria, Axonal & neuronal neuropathy (AMAN), Baló disease, Behcet’s disease, Benign mucosal pemphigoid, Bullous pemphigoid, Castleman disease (CD), Celiac disease, Chagas disease, Chronic inflammatory demyelinating polyneuropathy (CIDP), Chronic recurrent multifocal osteomyelitis (CRMO), Churg-Strauss Syndrome (CSS) or Eosinophilic
  • Granulomatosis Cicatricial pemphigoid, Cogan’s syndrome, Cold agglutinin disease, Congenital heart block, Coxsackie myocarditis, CREST syndrome, Crohn’s disease, Dermatitis herpetiformis, Dermatomyositis, Devic’s disease (neuromyelitis optica), Discoid lupus, Dressler’s syndrome, Endometriosis, Eosinophilic esophagitis (EoE), Eosinophilic fasciitis, Erythema nodosum, Essential mixed cryoglobulinemia, Evans syndrome,
  • Fibromyalgia Fibrosing alveolitis
  • Giant cell arteritis temporary arteritis
  • Giant cell myocarditis Glomerulonephritis
  • Goodpasture’s syndrome Granulomatosis with
  • hemoglobinuria PNH
  • Parry Romberg syndrome Pars planitis (peripheral uveitis)
  • PA Pernicious anemia
  • POEMS syndrome Polyarteritis nodosa
  • Polyglandular syndromes type I, II, III Polymyalgia rheumatica
  • Polymyositis
  • Postmyocardial infarction syndrome Postpericardiotomy syndrome, Primary biliary cirrhosis, Primary sclerosing cholangitis, Progesterone dermatitis, Psoriasis, Psoriatic arthritis, Pure red cell aplasia (PRCA), Pyoderma gangrenosum, Raynaud’s phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy, Relapsing polychondritis, Restless legs syndrome (RLS), Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis,
  • Sarcoidosis Schmidt syndrome, Scleritis, Scleroderma, Sjögren’s syndrome, Sperm & testicular autoimmunity, Stiff person syndrome (SPS), Subacute bacterial endocarditis (SBE), Susac’s syndrome, Sympathetic ophthalmia (SO), Takayasu’s arteritis, Temporal
  • TTP Thrombocytopenic purpura
  • TSS Tolosa-Hunt syndrome
  • Transverse myelitis Type 1 diabetes
  • Ulcerative colitis UC
  • Undifferentiated connective tissue disease UCTD
  • Vasculitis Vitiligo
  • Vogt-Koyanagi-Harada Disease or Wegener’s granulomatosis.
  • a disease or disorder of the disclosure includes, but is not limited to, an inflammatory disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a metabolic disease or disorder.
  • a disease or disorder of the disclosure includes but is not limited to a degenerative or a progressive disease or disorder.
  • the degenerative or a progressive disease or disorder includes, but is not limited to, amyotrophic lateral sclerosis (ALS), Huntington’s disease, Alzheimer’s disease, and aging.
  • ALS amyotrophic lateral sclerosis
  • Huntington’s disease Huntington’s disease
  • Alzheimer’s disease and aging.
  • a disease or disorder of the disclosure includes, but is not limited to, an infectious disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a pediatric or a developmental disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a cardiovascular disease or disorder.
  • a disease or disorder of the disclosure includes, but is not limited to, a proliferative disease or disorder.
  • the proliferative disease or disorder is a cancer.
  • the cancer includes, but is not limited to, Acute Lymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML), Adrenocortical Carcinoma, AIDS-Related Cancers, Kaposi Sarcoma (Soft Tissue Sarcoma), AIDS-Related Lymphoma (Lymphoma), Primary CNS Lymphoma (Lymphoma), Anal Cancer, Appendix Cancer, Gastrointestinal Carcinoid Tumors, Astrocytomas, Atypical Teratoid/Rhabdoid Tumor, Central Nervous System (Brain Cancer), Basal Cell Carcinoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Ewing Sarcoma, Osteosarcoma, Malignant
  • CML Myelogenous Leukemia
  • Chronic Myeloproliferative Neoplasms Colorectal Cancer
  • Craniopharyngioma Cutaneous T-Cell Lymphoma
  • Ductal Carcinoma In situ Embryonal Tumors
  • Endometrial Cancer Uterine Cancer
  • Ependymoma Esophageal Cancer
  • Extracranial Germ Cell Tumor Extragonadal Germ Cell Tumor, Eye Cancer, Childhood Intraocular Melanoma, Intraocular Melanoma, Retinoblastoma, Fallopian Tube Cancer, Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma, Gallbladder Cancer, Gastric (Stomach) Cancer, Gastrointestinal Carcinoid Tumor, Gastrointestinal Stromal Tumors (GIST) (Soft Tissue Sarcoma) Childhood Gastrointestinal Stromal Tumors Germ Cell Tumors, Childhood Extracranial Germ Cell Tumors, Extragonadal Germ Cell Tumors, Ovarian Germ Cell Tumors, Testicular Cancer, Gestational Trophoblastic Disease, Hairy Cell Leukemia, Head and Neck Cancer, Heart Tumors, Hepatocellular (Liver) Cancer,
  • Nasopharyngeal Cancer Head and Neck Cancer
  • Neuroblastoma Non-Hodgkin Lymphoma
  • Non-Small Cell Lung Cancer Oral Cancer
  • Lip and Oral Cavity Cancer and Oropharyngeal Cancer Osteosarcoma and Malignant Fibrous Histiocytoma of Bone, Ovarian Cancer, Pancreatic Cancer, Pancreatic Neuroendocrine Tumors (Islet Cell Tumors), Papillomatosis, Paraganglioma, Parathyroid Cancer, Penile Cancer, Pharyngeal Cancer (Head and Neck Cancer), Pheochromocytoma , Plasma Cell Neoplasm/Multiple Myeloma, Pleuropulmonary Blastoma, Pregnancy and Breast Cancer, Primary Central Nervous System (CNS)
  • CNS Central Nervous System
  • Lymphoma Primary Peritoneal Cancer, Prostate Cancer, Rectal Cancer, Recurrent Cancer, Renal Cell (Kidney) Cancer, Retinoblastoma, Rhabdomyosarcoma, Childhood (Soft Tissue Sarcoma), Salivary Gland Cancer (Head and Neck Cancer), Sarcoma, Childhood
  • Osteosarcoma (Bone Cancer), Uterine Sarcoma, Sézary Syndrome, Lymphoma, Skin Cancer, Small Cell Lung Cancer, Small Intestine Cancer, Soft Tissue Sarcoma, Squamous Cell Carcinoma of the Skin, Squamous Neck Cancer, Stomach (Gastric) Cancer, T-Cell
  • Lymphoma Testicular Cancer, Throat Cancer (Head and Neck Cancer), Nasopharyngeal Cancer, Oropharyngeal Cancer, Hypopharyngeal Cancer, Thymoma and Thymic Carcinoma , Thyroid Cancer Transitional Cell Cancer of the Renal Pelvis and Ureter Renal Cell Cancer, Urethral Cancer, Uterine Sarcoma, Vaginal Cancer, Vascular Tumors (Soft Tissue Sarcoma), Vulvar Cancer, Wilms Tumor and Other Childhood Kidney Tumors.
  • a subject of the disclosure has been diagnosed with the disease or disorder.
  • the subject of the disclosure presents at least one sign or symptom of the disease or disorder.
  • the subject has a biomarker predictive of a risk of developing the disease or disorder.
  • the biomarker is a genetic mutation.
  • a subject of the disclosure is female. In some embodiments of the methods of the disclosure, a subject of the disclosure is male. In some embodiments, a subject of the disclosure has two XX or XY chromosomes. In some embodiments, a subject of the disclosure has two XX or XY chromosomes and a third chromosome, either an X or a Y.
  • a subject of the disclosure is a neonate, an infant, a child, an adult, a senior adult, or an elderly adult. In some embodiments of the methods of the disclosure, a subject of the disclosure is a neonate, an infant, a child, an adult, a senior adult, or an elderly adult. In some
  • a subject of the disclosure is at least 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30 or 31 days old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or any number of years or partial years in between of age.
  • a subject of the disclosure is a mammal. In some embodiments, a subject of the disclosure is a non-human mammal.
  • a subject of the disclosure is a human.
  • a therapeutically effective amount comprises a single dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises at least one dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises one or more dose(s) of a composition of the disclosure.
  • a therapeutically effective amount eliminates a sign or symptom of the disease or disorder In some embodiments, a therapeutically effective amount reduces a severity of a sign or symptom of the disease or disorder.
  • a therapeutically effective amount eliminates the disease or disorder.
  • a therapeutically effective amount prevents an onset of a disease or disorder. In some embodiments, a therapeutically effective amount delays the onset of a disease or disorder. In some embodiments, a therapeutically effective amount reduces the severity of a sign or symptom of the disease or disorder. In some embodiments, a therapeutically effective amount improves a prognosis for the subject.
  • a composition of the disclosure is administered to the subject systemically. In some embodiments, the composition of the disclosure is administered to the subject by an intravenous route. In some
  • composition of the disclosure is administered to the subject by an injection or an infusion.
  • composition of the disclosure is administered to the subject locally.
  • composition of the disclosure is administered to the subject by an intraosseous, intraocular,
  • composition of the disclosure is administered directly to the cerebral spinal fluid of the central nervous system. In some embodiments, the composition of the disclosure is administered directly to a tissue or fluid of the eye and does not have bioavailability outside of ocular structures. In some embodiments, the composition of the disclosure is administered to the subject by an injection or an infusion.
  • a composition comprising:
  • a composition comprising: (a) a sequence encoding a non-self polypeptide, and
  • a composition comprising:
  • a composition comprising an adeno-associated virus (AAV) vector comprising:
  • composition comprising:
  • gRNA guide RNA
  • composition of any one of embodiments 1-15, wherein one or more sequence(s) encoding the promoter comprises a sequence isolated or derived from a U6 promoter. [0371] 17. The composition of any one of embodiments 1-15, wherein one or more sequence(s) encoding the promoter comprises a sequence isolated or derived from a promoter capable of diving expression of a transfer RNA (tRNA). [0372] 18.
  • composition of embodiment 17, wherein the sequence encoding the promoter comprises a sequence isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter.
  • composition of embodiment 17, wherein the sequence encoding the promoter comprises a sequence isolated or derived from a valine tRNA promoter.
  • 20. The composition of any one of embodiment 1-3 or 6-19, wherein a delivery vector comprises the composition.
  • 21. The composition of embodiment 20, wherein the delivery vector isan adeno- associated viral (AAV) vector.
  • AAV adeno- associated viral
  • the AAV comprises a sequence isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12.
  • composition of embodiment 4 or 5 wherein the AAV comprises a sequence isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12.
  • AAV comprises a sequence isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12.
  • IRS Internal Ribosomal Entry Site
  • 26. The composition of any one of embodiments 8-23, wherein the vector comprises a sequence encoding IRES or a sequence encoding a self-cleaving peptide.
  • 27. The composition of embodiment 24 or 26, wherein the sequence encoding IRES or the sequence encoding a self-cleaving peptide is positioned between the sequence of (a) and the sequence of (b). [0382] 28.
  • 29. The composition of any one of embodiments 24-28, wherein the self-cleaving peptide comprises a 2A self-cleaving peptide.
  • 30. The composition of any one of embodiments 1-29, wherein the non-cleavable FASL comprises a mutation in a metalloproteinase cleavage site.
  • composition of embodiment 31, wherein the mutation comprises one or more of a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition of the amino acid sequence ELAELR.
  • the non- cleavable FASL comprises the amino acid sequence of:
  • composition of embodiment 6, wherein the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence.
  • the composition of embodiment 35, wherein the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
  • 37. The composition of embodiment 35, wherein the spacer sequence has 100% complementarity to the target RNA sequence.
  • 38. The composition of any one of embodiments 35-37, wherein the spacer sequence comprises or consists of 20 nucleotides. [0393] 39.
  • GCCCCGGCCCCGGCCCCGGCCCCGGC (SEQ ID NO: 11)
  • GCTGCTGCTGCTGCTGCTGC (SEQ ID NO: 12)
  • GGGGCCGGGGCCGGGGCCGG (SEQ ID NO: 74)
  • composition of embodiment 45, wherein the spacer sequence comprises the sequence GUGAUAAGUGGAAUGCCAUG (SEQ ID NO: 14),
  • composition of embodiment 41 or 42, wherein the scaffold sequence comprises or consists of 85 nucleotides.
  • composition of embodiment 47, wherein the scaffold sequence comprises the sequence
  • composition of embodiment 48 wherein the spacer sequence comprises the sequence at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
  • the composition of embodiment 41 or 42, wherein the scaffold sequence comprises the sequence
  • a fusion protein comprises the RNA-binding polypeptide.
  • the fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA- binding polypeptide,
  • neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity
  • first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and
  • RNA-binding polypeptide comprises an RNA-nuclease activity.
  • the composition of embodiment 56, wherein the CRISPR-Cas protein is a Type II CRISPR-Cas protein.
  • the composition of embodiment 57, wherein the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof.
  • 59 The composition of embodiment 56, wherein the CRISPR-Cas protein is a Type V CRISPR-Cas protein. [0414] 60.
  • composition of embodiment 59, wherein the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof.
  • CRISPR-Cas protein is a Type VI CRISPR-Cas protein.
  • first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
  • composition of any one of embodiments 56-66, wherein the CRISPR-Cas protein comprises a mutation.
  • 68 The composition of embodiment 67, wherein a nuclease domain of the CRISPR-Cas protein comprises the mutation.
  • 69 The composition of embodiment 67 or 68, wherein the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein [0425] 70.
  • 70 The composition of any one of embodiments 67-69, wherein the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a
  • 71 The composition of any one of embodiments 67-69, wherein the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
  • 72 The composition of embodiment 55, wherein the first RNA binding protein comprises a Pumilio and FBF (PUF) protein.
  • PPF Pumilio and FBF
  • 73 The composition of embodiment 72, wherein the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein.
  • PUMBY Pumilio-based assembly
  • 75. The composition of any one of embodiments 55-74, wherein the first RNA binding protein is not a monomer of a multimer complex
  • 76. The composition of any one of embodiments 55-75, wherein a multimer protein complex does not comprise the first RNA binding protein.
  • 77. The composition of any one of embodiments 55-76, wherein the first RNA binding protein selectively binds to a target sequence within the RNA molecule. [0433] 78.
  • composition of any one of embodiments 55-77, wherein the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule.
  • 79. The composition of any one of embodiments 55-78, wherein the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
  • 80. The composition of any one of embodiments 55-79, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule.
  • composition of any one of embodiments 55-80, wherein the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints. [0437] 82.
  • composition of any one of embodiments 55-81, wherein the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS).
  • sequence encoding a nuclear localization signal is positioned 3’ to the sequence encoding the first RNA binding protein.
  • first RNA binding protein comprises an NLS at a C-terminus of the protein.
  • sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS.
  • a non-self therapeutic transgene is delivered to a target issue via viral or nonviral means.
  • vector with DNA encoding mutant FASL (mFASL) is co-delivered by AAV.
  • mFASL expression is driven by a promoter that is activated by TNFa or IL-6 signaling ( Figure 3A).
  • TNFa or IL-6 signaling Figure 3A.
  • This regulated expression of mFASL induces expression of mFASL only in the presence of activated T cells. In turn, T cells become sensitive to mFASL-mediated death only when activated.
  • Two AAV-9 transfer vectors were produced that 1) encode Cas13d and guide RNA, and 2) encode mFASL driven by an IL-6-regualated promoter. The following IL-6-regulated promoters were compared:
  • CALCB promoter i. CALCB promoter
  • AAV-9 preparations were generated according to standard techniques (triple- transfection method) and purified by IDX gradient ultracentrifugation. AAV was titered by qPCR after dialysis against PBS.
  • One of the three AAV versions described above is next injected into the tibialis anterior muscles of wildtype FVB strain mice (30 ⁇ L total volume, 2*10 ⁇ 10 vg, 1*10 ⁇ 11 vg or 4*10 ⁇ 12 vg) and subjected to daily clinical observation subsequently. (Contralateral injection of vector 1 and either vector 2, 3, or PBS.4 mice for each combination, 1/2, 1/3, 1/PBS). Mice are sacrificed at 1w, 4w, and 6w after
  • the proximal half of the tibialis anterior muscle (injection site), heart, spleen, liver (representative portion, i.e. piece of a lobe) and kidneys are collected, placed individually (except pair organs) into cryovials and flash frozen in liquid nitrogen for RNA/protein assessment and changes in gene expressions.
  • the other half of the tibialis anterior muscle is embedded in OCT and frozen. The tibialis anterior muscle is cut in a transverse fashion.
  • RNA isolations from frozen tissue is carried out with RNAeasy columns (Qiagen) according to the manufacturer’s protocol. RNA quality and concentrations are estimated using the Nanodrop spectrophotometer. cDNA preparation is done using Superscript III (Thermo) with random primers according to the manufacturer’s protocol. qPCR is carried out to assess the levels of Cas9 in tissue among the three mouse groups (vector 1/2, 1/3, 1/PBS).
  • Immunofluorescence with sectioned tibialis anterior muscle is conducted to measure infiltration of immune cells (CD3 and CD45 staining).
  • EXAMPLE 2 Preventing adaptive immune response to a non-self therapeutic transgene
  • a non-self therapeutic transgene is delivered to a target issue via viral or nonviral means.
  • vector with DNA enconding mutant FASL (mFASL) is co-delivered by viral or nonviral means.
  • the mFASL mRNA contains an intron that splits the coding sequence of FASL ( Figure 3B). This intron is bound by an RNA-binding protein Cas13d with a single guide RNA that is partially complementary to the intron which prevents splicing of the adjacent exons.
  • the Cas13d guide RNA is perfectly complementary to genes whose expression is regulated by TNFa or IL-6 signaling so that mFASL splicing is released from blockage upon TNFa or IL-6 signaling.
  • Systems where the guide RNA is perfectly complementary to mRNAs encoded by the following genes were constructed: BCAR3, CALCB, CCR6, COL6A3, CXCR5, DHRS9, FLT1, FNBP1L, FNDC9, GBP4, GPR87, GZMB, HOPX, HSD11B1, IFIT2, IFNL1, IGFBP6, IL12RB2, IL1R1, IL1R2, IL23R, IL24, KCNK18, MAF, NAPSA, PALLD, PRG4, PSD3, RORA, TNFSF1, TNFSF13B, TSHZ2.
  • Two AAV-9 transfer vectors were produced that 1) encode Cas13d and guide RNA, and 2) encode the mFASL construct with the intervening intron.
  • AAV-9 preparations were generated according to standard techniques (triple- transfection method) and purified by IDX gradient ultracentrifugation. AAV was titered by qPCR after dialysis against PBS. The AAV encoding the non-self transgene along with a vector containing the engineered mFASL construct and Cas13d were next injected into the tibialis anterior muscles of wildtype FVB strain mice (30 ⁇ L total volume, 2*10 ⁇ 10 vg, 1*10 ⁇ 11 vg or 4*10 ⁇ 12 vg) and subjected to daily clinical observation subsequently.
  • RNA/protein assessment and changes in gene expressions The other half of the tibialis anterior muscle is embedded in OCT and frozen. The tibialis anterior muscle is cut in a transverse fashion.
  • RNA isolations from frozen tissue is carried out with RNAeasy columns (Qiagen) according to the manufacturer’s protocol. RNA quality and concentrations are estimated using the Nanodrop spectrophotometer. cDNA preparation is done using Superscript III (Thermo) with random primers according to the manufacturer’s protocol. qPCR is carried out to assess the levels of Cas9 in tissue among the three mouse groups (vector 1/2, 1/3, 1/PBS).
  • Immunofluorescence with sectioned tibialis anterior muscle is conducted to measure infiltration of immune cells (CD3 and CD45 staining).
  • compositions of the disclosure are used for the treatment of myotonic dystrophy type I (DM1) wherein an RNA-targeting CRISPR system composed of a therapeutic transgene (Cas9 or Cas13d and corresponding single guide RNA targeting the CUG repeats that cause DM1) is delivered to patient muscle or the central nervous system.
  • DM1 myotonic dystrophy type I
  • an RNA-targeting CRISPR system composed of a therapeutic transgene (Cas9 or Cas13d and corresponding single guide RNA targeting the CUG repeats that cause DM1) is delivered to patient muscle or the central nervous system.
  • mFASL causes the elimination of T cells that are specific to Cas9 or Cas13d and potentially cytotoxic against treated cells.
  • compositions of the disclosure are used for the treatment of hemophilia.
  • a secreted transgene such as Factor IX is used for the treatment of hemophilia.
  • a vector carrying an expression cassette for factor IX along with mFASL reduces, eliminates, or prevents an adaptive immune response to Factor IX-expressing cells.
  • EXAMPLE 5 Preventing adaptive immune response to a non-self therapeutic transgene while simultaneously preventing immune response to repeated AAV administrations
  • compositions of the disclosure may comprise an AAV vector containing an expressed polypeptide composed of all or part of AAV viral capsid protein.
  • the AAV capsid polypeptide is identical to the serotype used to deliver the system. Co-expression of this AAV capsid polypeptide causes the elimination of T cells that are specific to the AAV capsid in a manner described above. This causes depletion of T cells that can regulate both cellular and humoral immunity to the AAV capsid. This allows repeated dosing of the same AAV serotype.
  • an individual AAV serotype could not be used in more than once in a patient due to the formation of adaptive immune response against the viral capsid.
  • compositions of the disclosure may be useful in situations wherein incomplete therapeutic transfer occurs during the first administration of a gene therapy or wherein a second dose is desired.
  • the second dose of the gene therapy does not require the presence of the mFASL and AAV capsid polypeptide unless subsequent doses beyond the second dose are desired.
  • One situation could be during the treatment of large organs such as skeletal muscle where the volume of virus required to transduce muscle in a single dose is prohibitively high.
  • Another situation could be during treatment involving complicated administration methods in the brain or spine where initial treatments do not provide satisfactory infection of targeted cells.

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Abstract

Disclosed are compositions comprising a sequence encoding a non-self polypeptide of interest (POI), and a sequence encoding a non-cleavable FASL, wherein expression of the non-cleavable FASL in the presence of IL-6 or TNF-alpha eliminates MHC-mediated immunogenic peptides and helper T cells specific to the expression of the POI. Methods of making and methods of using compositions of the disclosure are also provided. For example, compositions of the disclosure may be used in the combined treatment of a disease or disorder in a subject and immune masking activity specific to the treatment. Exemplary disease or disorders of the disclosure include genetic and epigenetic diseases or disorders.

Description

FASL IMMUNOMODULATORY GENE THERAPY COMPOSITIONS AND
METHODS FOR USE FIELD OF THE DISCLOSURE
[01] The disclosure is directed to molecular biology, gene therapy, and/or modifying expression and activity of RNA molecules, and more, specifically, to compositions and methods for attenuating the immune response to cells subjected to RNA modification and/or gene therapies via elimination of immune effector cells. RELATED APPLICATIONS
[02] This application claims priority to U.S. Patent Application No.62/722,550, filed August 24, 2018, the contents of which are herein incorporated by reference in their entirety. INCORPORATION OF SEQUENCE LISTING
[03] The contents of the text file named“LOCN_004_001WO_SeqList_ST25”, which was created on August 24, 2019 and is 20.7 MB in size, are hereby incorporated by reference in their entirety.
BACKGROUND
[04] There has been a long-felt but unmet need in the art for attenuating the detrimental immune response to non-self gene therapies. The disclosure provides compositions and methods for promoting the elimination of immune effector cells specific to cells treated or modified by gene therapy techniques.
[05] The importance of the role of FasL (Fas Ligand) in the pathway for immune regulation is well established. Activated T-cells upregulate Fas and become sensitive to FasL-mediated apoptosis in the process of activation-induced cell death and tolerance to self- antigens. Deficiencies in Fas or FasL often cause autoimmune pathologies or aberrant lymphoproliferation demonstrating the apparent lack of compensatory mechanisms in the pathway. While local presentation of mutated FasL has been shown to prevent rejection of transplanted cells in mice, ectopic expression of FASL in certain transplantation settings has had mixed results in achieving graft survival. In many instances, gene therapies delivering a non-self therapeutic transgene, such as a CRISPR/Cas complex, to a patient in need of such treatment can trigger an undesirable immune response to the therapeutic transgene and/or to the vector delivering the transgene. As such, there is a need to provide compositions and methods for masking immune activity and thereby promoting elimination of immune effector cells specific to cells treated and/or modified by gene therapy techniques. SUMMARY
[06] The disclosure provides a composition comprising: a sequence encoding a non-self polypeptide of interest (POI), and a sequence encoding a non-cleavable FasL, wherein expression of the non-cleavable FasL eliminates MHC-mediated immunogenic peptides and helper T cells specific to the expression of the POI. In some embodiments, the POI is a CRISPR-Cas protein. In some embodiments, the POI is a viral capsid polypeptide such as an AAV viral capsid. In other embodiments, the POI is a heterologous non-self (foreign) protein antigen, fragment or variant thereof. In another embodiment, non-self proteins or POIs are selected from the group consisting of bacterial proteins, archaeal proteins, viral proteins, parasitic proteins, tumor proteins, mycoplasma proteins, yeast proteins or allergen proteins. In one embodiment, a non-self POI is a bacterially-derived CRISPR/Cas protein or an archaeal-derived CRISPR/Cas protein.
[07] The disclosure also provides a composition comprising a sequence comprising: a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule, a sequence encoding an RNA-binding polypeptide, and a sequence encoding a non-cleavable FASL, wherein expression of the non-cleavable FASL eliminates MHC-mediated
immunogenic peptides and helper T cells specific to the expression of the RNA-binding polypeptide.
[08] In some embodiments of the compositions of the disclosure, the target sequence comprises at least one repeated sequence.
[09] In some embodiments of the compositions of the disclosure, the sequences are within the same vector.
[010] In some embodiments of the compositions of the disclosure, the vector is a viral vector. In some embodiments, the viral vector is an AAV vector, an adenoviral vector, or a retroviral vector such as a lentiviral vector.
[011] In some embodiments of the compositions of the disclosure, the vector is an AAV vector and the vector comprises sequences encoding the AAV capsid.
[012] In some embodiments of the compositions of the disclosure, the sequences comprise an IRES (Internal Ribosomal Entry Site) or a 2A ribosomal site [013] In some embodiments of the compositions of the disclosure, the mutated non- cleavable FasL comprises at least one mutation or deletion in its metalloproteinase cleavage site. In some embodiments, the mutated non-cleavable FasL comprises at least one mutation or deletion in its protease recognition region. In another embodiment, the protease recognition region is at least amino acid residues 119 to 154 of wild-type human FasL.
[014] In some embodiments, the metalloproteinase cleavage site comprises the amino acid sequence ELAELR. In another embodiment, the mutation comprises one or more of a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition of the amino acid sequence ELAELR.
[015] In some embodiments, the non-cleavable FASL comprises the amino acid sequence of:
MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLPPPPP PPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKX1X2X3X4 X5X6ESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGIV LLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLVM MEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGLY KL (SEQ ID NO: 210), wherein X1 is not a glutamic acid (E), X2 is not an leucine (L), X3 is not an alanine (A), X4 is not an glutamic acid (E), X5 is not an leucine (L) or X6 is not an arginine (R).
[016] In some embodiments, the non-cleavable FASL comprises the amino acid sequence of:
MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLPPPPP PPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKX1X2X3X4 X5X6ESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGIV LLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLVM MEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGLY KL (SEQ ID NO: 210), wherein X1 is not a glutamic acid (E), X2 is not an leucine (L), X3 is not an alanine (A), X4 is not an glutamic acid (E), X5 is not an leucine (L) and X6 is not an arginine (R).
[017] In some embodiments, expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the non-self polypeptide, and wherein expression of FASL is in the presence of IL-6 or TNF- alpha. [018] In some embodiments, the non-cleavable FASL comprises an intron, wherein the intron blocks FASL splicing in the absence of IL-6 or TNF-alpha.
In some embodiments, the non-cleavable FASL comprises an intron, wherein the intron blocks FASL splicing in the absence of IL-6 or TNF-alpha. In a further embodiment, the composition comprises synthetic mRNA target sites which are expressed in the presence of IL-6 or TNF-alpha.
[019] In some embodiments, the compositions comprise 1) a synthetic notch system, 2) microRNA target sites, or a 3) split intein and engineered IL-6 or TNF-alpha receptors for regulating expression of FASL in the presence of IL-6 or TNF-alpha.
[020] In some embodiments of the compositions of the disclosure, the RNA-binding polypeptide or RNA-binding portion thereof is selected from the group consisting of Cas9, Cas13d, PUF, PUMBY, and PPR.
[021] In some embodiments of the compositions of the disclosure, the sequences comprise a promoter or promoters.
[022] In some embodiments, the promoter driving expression of FASL is regulated by the presence of IL-6 receptor or TNF-alpha receptor. In some embodiments, a promoter capable of driving FASL expression in the presence of IL-6 receptor or TNF-alpha receptor is a promoter listed in Table 1 or Table 2.
[023] In some embodiments, the non-self POI is a nucleoprotein complex encoded by (i) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule, and (ii) a sequence encoding an RNA-binding polypeptide.
[024] In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a sequence encoding a promoter capable of expressing the gRNA in a eukaryotic cell.
[025] In some embodiments of the compositions of the disclosure, the eukaryotic cell is an animal cell. In some embodiments, the animal cell is a mammalian cell. In some
embodiments, the animal cell is a human cell.
[026] In some embodiments of the compositions of the disclosure, the promoter is a constitutively active promoter. In some embodiments, the promoter comprises a sequence isolated or derived from a promoter capable of diving expression of an RNA polymerase. In some embodiments, the promoter sequence comprises a sequence isolated or derived from a U6 promoter. In some embodiments, the promoter sequence comprises a sequence isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA) In some embodiments, the promoter sequence comprises a sequence isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter. In some embodiments, the promoter comprises a sequence isolated or derived from a valine tRNA promoter. BRIEF DESCRIPTION OF THE DRAWINGS
[027] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
[028] Figure 1A-B are schematic diagrams relevant to the compositions of the disclosure. (A) Depicts typical therapeutic non-self transgene delivery via AAV which result in presentation of non-self polypeptides that can activate T helper cells and potentiate a cytotoxic effect against treated tissue or cells. (B) Depicts various embodiments of the compositions of the disclosure by including sequences encoding mutated (metalloproteinase non-cleavable) versions of FasL in vector constructs comprising therapeutic transgenes (Tx genes), such as transgene components encoding a CRISPR/Cas9 complex, thereby resulting in the promotion of programmed death of T-cells that interrogate treated tissue or cells and preventing cytotoxic activity against the treated tissue or cells.
[029] Figure 2A-B are schematic diagrams relevant to the compositions of the disclosure. (A) Depicts repeated AAV administration in humans which results in formation of adaptive immunity against the AAV capsid in the form of both humoral and cellular responses. (B) Depicts compositions of the disclosure by including sequences encoding both mutated non- cleavable FasL and polypeptides from the AAV vector capsid in the vector constructs additionally comprising a therapeutic transgene (self or non-self). This results in elimination of T-cells specific to the viral capsid and prevention of the formation of adaptive immunity against the viral capsid which allows for efficient and safe redosing with the AAV vector.
[030] Figure 3A-F are schematic diagrams relevant to embodiments of the compositions disclosed herein that are capable of detecting the activity of T cells (A) Depicts a construct configuration embodiment comprising FASL driven by a promoter that is regulated by IL-6 receptor or TNF-alpha receptor. (B) Depicts a construct configuration embodiment comprising a Cas13d RNA-targeting system and FASL. The FASL comprises an intron whose splicing is negatively regulated by Cas13d. Upon gene expression changes mediated by IL-6 or TNF-alpha, Cas13d is titrated away from the FASL construct so that splicing of FASL is allowed and FASL protein is produced. (C) Depicts a construct configuration embodiment similar to the construct configuration in (B) but with the addition of another component: engineered mRNA that is regulated by TNF-alpha receptor or IL-6 receptor that contains concatenated sites which titrate Cas13d away from the FASL pre-mRNA. (D) Depicts a construct configuration embodiment comprising an engineered receptor such as Syn-notch that detects IL-6 or TNF-alpha and subsequently releases a transcription factor such as GAL4 thereby promoting expression of a GAL4-regulated FASL gene. (E) Depicts a construct configuration embodiment comprising an engineered mRNA that codes for FASL and also contains concatenated target sites in the 3’UTR for a microRNA (miRNA) that is downregulated upon stimulation by TNF-alpha or IL-6. (F) Depicts a construct configuration embodiment comprising an engineered version of IL-6 receptor or TNF-alpha receptor that carries an intein on the intracellular domain along with a Cas13d-intein fusion present in the nucleus. This construct embodiment is similar to the embodiment of (B) in that the Cas13d regulates splicing of FASL but the release of the intein from the cell membrane and translocation to the nucleus upon IL-6 or TNF-alpha detection results in intein activity on Cas13d thereby releasing the splicing block on FASL. DETAILED DESCRIPTION
[031] The disclosure provides compositions and methods for combined therapeutic and immune masking activity. The immune masking activity eliminates MHC-mediated immunogenic peptides and helper T-cells specific to the expression of a non-self therapeutic activity, i.e., a non-self therapeutic protein such as a CRISPR/Cas ribonucleoprotein complex. The compositions comprise nucleic acid sequences which encode at least two functional components– a non-self protein of interest (POI) and a non-cleavable mutated FasL. In one embodiment of the compositions of the disclosure, the compositions comprise nucleic acid sequences comprising a gRNA that specifically binds a target sequence within an RNA molecule, a sequence encoding an RNA-binding polypeptide or RNA-binding portion thereof and a sequence encoding a non-cleavable FasL In another embodiment, the compositions comprise vector constructs. In other embodiments, the sequences comprise a promoter driving the functional components or separate promoters driving expression of each or certain of the functional components. Additional elements often used in the expression of multiple coding sequences such as 2A ribosomal skipping sites, or IRESs can be incorporated in the compositions comprising the vector constructs.
[032] An important feature of the compositions and methods of the disclosure is controlling the timing and levels associated with FASL expression. Constitutive expression of FASL is associated with toxicity but by expressing FASL when cells are challenged by activated T cells, selective T cell elimination is achieved while avoiding these toxicity issues.
[033] In one embodiment, temporal control of FASL expression is achieved by utilizing delivery modes that promote short-term expression of the FASL system. Specifically, nonviral delivery modes such as lipid nanoparticles carrying DNA or RNA encoding the FASL system promotes transient expression of the system in the target tissue.
[034] In another embodiment, AAV vectors or other viral delivery or nonviral delivery modes comprise built-in temporal controls. One such approach involves promoters that cycle with circadian rhythms such as the clock gene. Another could involve the use of drug- inducible promoters such as, without limitation, tetracycline, cumate, galactose (GAL), alcohol oxidase (AOX), cellobiohydrolase, or glucoamylase.
[035] In another embodiment, integrated sensors promote FASL expression only under controlled conditions. Specifically, a genetic circuit that recognizes expression of specific genes is used to identify the activity of cytotoxic T cells and subsequently promote FASL expression only in the presence of these activated T cells.
[036] Accordingly, the disclosure provides compositions and methods for regulating and/or controlling expression of mutant (mFASL). In one embodiment, the composition produces mFASL only in the presence of activated T cells via detection of the cytokines, IL-6 or TNFalpha. This mFASL protein protects the therapeutic-treated cells via specific killing of the activated T cell. In the absence of the cytokines, the cells downregulate FASL which avoids safety issues associated with broad, constitutive expression of FASL.
[037] In one embodiment, the production of mFASL is only in the presence of activated T cells via use of a construct configuration, such as Fig 3A, comprising a promoter which is specifically activated by one or both of IL-6 and/or TNF-alpha. Exemplary promoters which are specifically activated by one or both IL-6 and/or TNF-alpha include, without limitation, promoters listed in Table 1 and/or Table 2 [038] Table 1: Genes with promoters regulated by TNF-alpha
Figure imgf000010_0001
Figure imgf000011_0001
Figure imgf000012_0001
Figure imgf000013_0001
Figure imgf000014_0001
Figure imgf000015_0001
Figure imgf000016_0001
Figure imgf000017_0001
Figure imgf000018_0001
Figure imgf000019_0001
Figure imgf000020_0001
Figure imgf000021_0001
Figure imgf000022_0001
Figure imgf000023_0001
Figure imgf000024_0001
Figure imgf000025_0001
Figure imgf000026_0001
[039] Table 2: Promoters regulated by IL6 (STAT3)
Figure imgf000026_0002
Figure imgf000027_0001
[040] In another embodiment, mFASL expression is regulated by a construct
configuration, such as Fig.3B, comprising an RNA-targeting system (e.g., Cas13d) that prevents splicing of mFASL. Specifically, the FASL comprises an intron whose splicing is negatively regulated by the RNA-binding protein (e.g., Cas13d). Upon TNFalpha or IL-6 signaling, the RNA-targeting system is drawn to a stronger binding site in an RNA that is expressed upon TNFalpha or IL-6 signaling, that is, Cas13d is titrated away from the FASL construct. This releases the splicing block on mFASL (and splicing of FASL is permitted) and promotes production of the protein. In one embodiment, the Cas13d guide RNA (gRNA) is antisense to the mRNA of the regulated FASL construct configuration (such as in Fig 3A). Spacer sequences for gRNAs targeting the IL6 or TNF-alpha-regulated mRNAs are listed in Table 3. [041] Table 3. Spacer sequences for gRNAs targeting the IL6 or TNF-alpha-regulated mRNAs
Figure imgf000028_0001
Figure imgf000029_0001
[042] In a similar embodiment, a construct configuration, such as Fig.3C, comprises an engineered RNA comprising concatenated sites that titrate Cas13d away from the FASL pre- mRNA and which is regulated by TNFalpha or IL-6 via use of an appropriate promoter (such as, without limitation, a promoter in Table 1 or Table 2). In this case, the engineered RNA contains multiple target sites for the RNA-targeting system. As such, expression of the engineered RNA releases the splicing block on the mFASL mRNA.
[043] In another embodiment, a construct configuration, such as Fig.3D, comprises an engineered receptor such as synthetic notch detects IL-6 or TNFalpha and regulates expression of a promoter that drives mFASL. In this manner, mFASL is only produced in the presence of TNFalpha or IL-6 signaling.
[044] For example, such an engineered Syn-notch receptor would detect IL-6 or TNF- alpha and subsequently release a transcription factor such as GAL4 which promotes expression of a GAL4-regulated FASL gene. In one embodiment, the engineered receptor comprises three modules (from N- to C-terminus):
[045] 1) an IL-6 or TNF-alpha binding section such as, without limitation, an IL-6 scFV having an amino acid sequence as follows:
[046] MSTVILSAAAPLSGVYAAMERGSHHHHHHGSGSGSGIEGRPYNGTGSACEL GTQVQLKESGPGLVPSQSLSITCTVSDFSLTNYGVHWVRQSPGKGLEWLGVIWSGGS TDYNAAFISRLSISKDNSKSQVFFEMNSLQADDTAIYYCARNGNRYYGYALDYWGQ GTSVTVSSGGGGSGGGGSGGGGSDVVMTQTPLSLPVSLGDQASISCRSSQSIVHSNG NTYLEWYLQKPGQSPKLLIYTVSNRLSGVPDRFSGSGSGTDFTLKISRVEAEDLGVY YCFQGSHGPYTFGGGTKLEIKLQTCGRKLSLNQN (SEQ ID NO: 227)
[047] 2) A synthetic notch such as, without limitation, having an amino acid sequence as follows:
[048] ILDYSFTGGAGRDIPPPQIEEACELPECQVDAGNKVCNLQCNNHACGWDGG DCSLNFNDPWKNCTQSLQCWKYFSDGHCDSQCNSAGCLFDGFDCQLTEGQCNPLY DQYCKDHFSDGHCDQGCNSAECEWDGLDCAEHVPERLAAGTLVLVVLLPPDQLRN NSFHFLRELSHVLHTNVVFKRDAQGQQMIFPYYGHEEELRKHPIKRSTVGWATSSLL PGTSGGRQRRELDPMDIRGSIVYLEIDNRQCVQSSSQCFQSATDVAAFLGALASLGSL NIPYKIEAVKSEPVEPPLPSQLHLMYVAAAAFVLLFFVGCGVLLSRKRRR (SEQ ID NO: 228)
[049] and 3) a transcription factor such as, without limitation, GAL4 having the amino acid sequence as follows:
[050] MKLLSSIEQACDICRLKKLKCSKEKPKCAKCLKNNWECRYSPKTKRSPLTR AHLTEVESRLERLEQLFLLIFPREDLDMILKMDSLQDIKALLTGLFVQDNVNKDAVT DRLASVETDMPLTLRQHRISATSSSEESSNKGQRQLTVSAAAGGSGGSGGSDALDDF DLDMLGSDALDDFDLDMLGSDALDDFDLDMLGSDALDDFDLDMLGS (SEQ ID NO: 229)
[051] In another embodiment, in a construct configuration, such as Fig.3E, mFASL is regulated via placement of microRNA (miRNA) binding sites of interest in the mRNA 3’UTR. The engineered mRNA comprises concatenated target sites (for an miRNA or miRNAs of interest) and are selected so that these microRNAs are expressed in cells that are not subjected to TNFalpha or IL-6. Cells that experience TNF-alpha or IL-6 reduce expression of the microRNA (i.e., the miRNA is downregulated upon stimulation by TNF- alpha or IL-6), resulting in mFASL expression only in the presence of cytokine signaling. In one embodiment, the engineered mRNA comprises target sites for miRNA, without limitation, selected from the group consisting of hsa-miR-934, hsa-miR-1269a, hsa-miR-671- 5p, hsa-miR-663a, hsa-miR-1292, hsa-miR-615-5p, hsa-miR-2276, hsa-miR-1307-3p, hsa- miR-3654, hsa-miR-4741, hsa-miR-100-5p, hsa-miR-3189-3p, hsa-miR-548t-5p, hsa-miR- 769-3p, hsa-miR-1307-5p, hsa-miR-3687, hsa-miR-324-5p, hsa-miR-449c-5p, hsa-miR-532- 5p, hsa-miR-122-5p, hsa-miR-301b, hsa-miR-652-3p, hsa-miR-181a-5p, hsa-miR-140-3p, hsa-miR-331-3p, hsa-miR-10a-5p, hsa-miR-3656, hsa-miR-146a-5p, hsa-miR-1246, hsa- miR-143-3p, hsa-miR-23a-5p, hsa-miR-4508, hsa-miR-4488, hsa-miR-548o-3p, hsa-miR- 29c-5p, hsa-miR-21-3p, hsa-miR-215, hsa-miR-139-3p, hsa-miR-720, hsa-miR-3141, hsa- miR-29b-1-5p, hsa-miR-141-5p, hsa-miR-25-5p, hsa-miR-197-5p, hsa-miR-1260b, hsa-miR- 22-5p, and hsa-miR-628-5p.
[052] In another embodiment, a construct configuration, such as Fig.3F, comprises an engineered receptor that detects IL-6 or TNFalpha and comprises a split intein (e.g., an intein on the intracellular domain along with a Cas13d-intein fusion that is present in the nucleus). The RNA-targeting system (such as Cas13d) regulates the splicing of an mRNA encoding mFASL and releases the intein from the cell membrane. Accordingly, upon activation of the synthetic receptor, the fused split intein translocates to the nucleus where it interacts with the split intein fused to the RNA-targeting system. The result is the destruction of a functional RNA-targeting system, correct mFASL mRNA splicing, and the production of mFASL protein.
[053] The disclosure provides vectors, compositions and cells comprising the therapeutic and FasL immune masking nucleic acid sequences. The disclosure provides methods of using the vectors, compositions and cells of the disclosure to treat a disease or disorder and at the same time eliminate the MHC-mediated immunogenic response specific to the vectors and/or compositions and treated cells. Preventing adaptive immune response to a non-self therapeutic transgene
[054] An AAV vector carrying a therapeutic, non-self transgene is packaged with mutant FALS (mFASL) so that both genes are expressed. After administration of the AAV vector, treated cells begin to express both the transgene and mFASL. Peptides derived from the transgene are displayed by MHC as part of the typical and typical process of antigen presentation conducted by many cell types. The formation of regulatory and effector T cells that target the non-self peptides occurs. These transgene-specific T cells interrogate infected (treated) cells that display the non-self peptides and simultaneously encounter mFASL. The presence of this non-self peptide display and mFASL results in apoptosis of the transgene- specific T cells. This eliminates this facet of adaptive immune response against the therapeutic transgene and the cells that harbor it.
Treatment of myotonic dystrophy type I (DM1)
[055] Compositions of the disclosure are used for the treatment of myotonic dystrophy type I (DM1) wherein an RNA-targeting CRISPR system composed of a therapeutic transgene (Cas9) and single guide RNA targeting the CUG repeats that cause DM1 are delivered to patient muscle or the central nervous system. The presence of mFASL causes the elimination of T cells that are specific to Cas9 and potentially cytotoxic against treated cells. Treatment of hemophilia
[056] Compositions of the disclosure are used for the treatment of hemophilia. A secreted transgene such as Factor IX is used for the treatment of hemophilia. A vector carrying an expression cassette for factor IX along with mFASL reduces, eliminates, or prevents an adaptive immune response to Factor IX-expressing cells Preventing adaptive immune response to a non-self therapeutic transgene while simultaneously preventing immune response to repeated AAV administrations
[057] Compositions of the disclosure may comprise an AAV vector containing an expressed polypeptide composed of all or part of AAV viral capsid protein. The AAV capsid polypeptide is identical to the serotype used to deliver the system. Co-expression of this AAV capsid polypeptide causes the elimination of T cells that are specific to the AAV capsid in a manner described above. This causes depletion of T cells that can regulate both cellular and humoral immunity to the AAV capsid. This allows repeated dosing of the same AAV serotype. In the absence of the compositions of the disclosure, and using the standard of care prior to development of the compositions of the disclosure, an individual AAV serotype could not be used in more than once in a patient due to the formation of adaptive immune response against the viral capsid.
[058] The compositions of the disclosure may be useful in situations wherein incomplete therapeutic transfer occurs during the first administration of a gene therapy or wherein a second dose is desired. In this case, the second dose of the gene therapy does not require the presence of the mFASL and AAV capsid polypeptide unless subsequent doses beyond the second dose are desired. One situation could be during the treatment of large organs such as skeletal muscle where the volume of virus required to transduce muscle in a single dose is prohibitively high. Another situation could be during treatment involving complicated administration methods in the brain or spine where initial treatments do not provide satisfactory infection of targeted cells. Non-cleavable FasL
[059] The Fas/FasL interaction is well established with regards to the immune system. The activation of T cells through the T cell receptor (TCR) upregulates both Fas and FasL. In circumstances of low to moderate TCR stimulation, T cells proliferate. Under conditions of repetitive or high levels of TCR stimulation, T cells are driven toward apoptosis. This phenomenon has been termed Antigen Induced Cell Death (AICD). The importance of AICD in regulating the immune system has been demonstrated in the LPR mouse. Nagata et al., Immunol. Today 16:39-43 (1995).
[060] That the Fas/FasL interaction contributes to immune privilege is also well established. In particular, a number of studies demonstrate engineered immune privilege via the induction of FasL expression in transplantation settings Bellgrau et al Nature 377:630- 632 (1995); Griffith et al., Science 270:1189-1192 (1995), Lau et al., Science 273:109-112 (1996).
[061] FasL is proteolytically cleaved by matrix metalloproteases and bound to the cell membrane. Because soluble FasL is released into and circulated widely throughout the circulatory system, it is known to cause non-specific and widespread cell death. Ogasawara et al., Nature 364:806-809 (1993), published erratum, Nature 365:568 (1993), Tanaka et al., Nature Med.2:317-322 (1996), Rodriguez et al., J. Exp. Med.183:1031-1036 (1996). As such, selective modulation of Fas/FasL and the subsequent selective induction of apoptosis to specific target tissues and cells has been achieved by the mutation of the FasL protease recognition region. This is because it has been found that making at least one mutation or deletion in the wild-type FasL protease recognition region inhibits proteolytic cleavage of the FasL polypeptide from the cell membrane and minimizes the production of and the deleterious non-selective effects of soluble FasL. The sequence of the wild-type, full-length human FasL is known in the art. The extracellular domain of the wild-type, full-length human FasL is defined by amino acid residues 103 to 281, and the protease recognition region of wild-type human FasL comprises at least amino acid residues 119 to 154. Residues are numbered by reference to the known amino acid sequence of wild-type human FasL. See Takahashi et al., Int'l Immunol.6:1567-1574 (1994). Moreover, non-cleavable mutated FasL polypeptides and methods of generating the same can be found, e.g., in WO 1999/036079, which is incorporated herein by reference in its entirety.
[062] The terminology“FASL” and“mFasL” are used interchangeably herein to refer to non-cleavable mutated FasL.
[063] In one embodiment, an exemplary mutated non-cleavable FasL (mus musculus) (MMP cleavage site in bold) can be generated by making one or more mutations or deletions in the following amino acid sequence:
[064] PGSVFPCPSCGPRGPDQRRPPPPPPPVSPLPPPSQPLPLPPLTPLKKKDHNTNL WLPVVFFMVLVALVGMGLGMYQLFHLQKELAELREFTNQSLKVSSFEKQIANPSTP SEKKEPRSVAHLTGNPHSRSIPLEWEDTYGTALISGVKYKKGGLVINETGLYFVYSK VYFRGQSCNNQPLNHKVYMRNSKYPEDLVLMEEKRLNYCTTGQIWAHSSYLGAVF NLTSADHLYVNISQLSLINFEESKTFFGLYKL (SEQ ID NO: 209).
[065] In another embodiment, an exemplary mutated non-cleavable FasL (homo sapiens) (MMP cleavage site in bold) can be generated by making one or more mutations or deletions in the following amino acid sequence: [066] MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPP LPPPPPPPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKEL AELRESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGI VLLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLV MMEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGL YKL (SEQ ID NO: 210).
Non-Self POIs
[067] With regard to an embodiment relating to one component of the compositions of the disclosure, a nucleic acid sequence of the composition encodes a non-self protein of interest (POI). In one embodiment, a non-self POI is a heterologous non-self (or foreign) protein antigen, fragment or variant thereof. Exemplary non-self proteins or POIs include, without limitation, bacterial proteins, archaeal proteins, viral proteins (e.g., viral capsids), parasitic proteins, tumor proteins, mycoplasma proteins, yeast proteins or allergen proteins. In one embodiment, a non-self POI is a bacterially-derived CRISPR/Cas protein or an archaeal- derived CRISPR/Cas protein. In another embodiment, a non-self POI is a viral capsid specific to the viral vector carrying a therapeutic transgene (self or non-self transgene).
AAV Capsids– Repeated Administration of Self or Non-Self Gene Therapy
[068] Repeated AAV administration in humans and animal models typically results in formation of adaptive immunity against the AAV capsid in the form of both humoral and cellular responses (Fig.2A). As a result, repeated doses of AAV result in attenuated gene transduction after the initial dose with the potential for toxic effects. By include both FASL and polypeptides from the AAV capsid in the transgene payload (self or non-self transgenes) carried within the AAV vector used in the initial treatment, T-cells specific to the viral capsid can be eliminated (Fig.2B). Elimination of these capsid-specific T-cells prevents the formation of adaptive immunity against the viral capsid and allows efficient and safe redosing. Specifically, the expression of the viral capsid polypeptide causes infected cells to display peptides specific to the viral capsid via MHC which will promote interaction among capsid-specific T cells (with TCRs for the viral capsid peptides) and infected cells. The co- expression of FASL on the infected cells will promote killing of these capsid-specific T-cells. As the T-cells are required for mounting of both cellular and humoral immunity against the capsid, subsequent treatments with the same AAV serotype will not be attenuated by the adaptive immune system. [069] AAV biology has been extensively studied and is well known in the art. AAV capsids for use in the compositions disclosed herein are derived from AAV serotypes which include, without limitation, AAV1, AAV2, AAV4, AAV5, AAV6 (a hybrid of AAV1 and AAV2), AAV7, AAV8, AAV9, AAV10, AAV11, AAV12, and synthetic AAV serotypes, such as, without limitation, Anc80 AAV (an ancestor of AAV 1, 2, 6, 8 and 9).
[070] In one embodiment, the AAV capsid is derived from the AAV9 VP1 amino acid sequence which is:
[071] MAADGYLPDWLEDNLSEGIREWWALKPGAPQPKANQQHQDNARGLVLPG YKYLGPGNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLKYNHADAEFQER LKEDTSFGGNLGRAVFQAKKRLLEPLGLVEEAAKTAPGKKRPVEQSPQEPDSSAGIG KSGAQPAKKRLNFGQTGDTESVPDPQPIGEPPAAPSGVGSLTMASGGGAPVADNNE GADGVGSSSGNWHCDSQWLGDRVITTSTRTWALPTYNNHLYKQISNSTSGGSSNDN AYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTDN NGVKTIANNLTSTVQVFTDSDYQLPYVLGSAHEGCLPPFPADVFMIPQYGYLTLNDG SQAVGRSSFYCLEYFPSQMLRTGNNFQFSYEFENVPFHSSYAHSQSLDRLMNPLIDQ YLYYLSKTINGSGQNQQTLKFSVAGPSNMAVQGRNYIPGPSYRQQRVSTTVTQNNN SEFAWPGASSWALNGRNSLMNPGPAMASHKEGEDRFFPLSGSLIFGKQGTGRDNVD ADKVMITNEEEIKTTNPVATESYGQVATNHQSAQAQAQTGWVQNQGILPGMVWQD RDVYLQGPIWAKIPHTDGNFHPSPLMGGFGMKHPPPQILIKNTPVPADPPTAFNKDK LNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSNNVEFAVNTEGVYSE PRPIGTRYLTRNL (SEQ ID NO: 211).
[072] In another embodiment, the predicted surface residues of AAV9 capsid (subset of VP1) is:
[073] AKTAPGKKRPVEQSPQEPDSSAGIGKSGAQPAKKRLNFGQTGDTESVPDPQP IGEPPAAPSGVGSLTMASWHCDSQWLGDRVITTSTRTWALPTYNNHLYKQISNSTSG GSSNDNAYFGYSTPWGYFDFNRFWHCDSQWLGDRVITTSTRTWALPTYNNHLYKQI SNSTSGGSSNDNAYFGYSTPWGYFDFNRFDVFMIPQYGYLTLNDGSQAVGRSSFYCL EYFPSQMLRTGNNFQFSYEFENVPFHSSYAHSQSLDRLMNPLIDQYLYYLSKTINGSG QNQQTLKFSVAGPSNMAVQGRNYIPGPSYRQQRVSTTVTQNNNSEFAWPGASSWA LNGRNSLMNPGPAMASHKEGEDRFFPLSGSLIFGKQGTGRDNVDADKVMITNEEEIK TTNPVATESYGQVATNHQSAQAQAQTGWVQNQGILPGMVWIKNTPVPADPPTAFN KDKLNSFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSNNVEFAVNTEGV YSEPRPIGTRYLTRNL (SEQ ID NO: 212) [074] In one embodiment, the AAV capsid is derived from the Anc80 AAV VP1 amino acid sequence which is:
AADGYLPDWLEDNLSEGIREWDLKPGAPKPKANQQKQDDGRGLVLPGYYLGPFNG LDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTSFGGN LGRAVFQAKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKKGQQPAXK RLNFGQTGDSESVPDPQPLGEPPAAPSGVGSNTMXAGGGAPADNNEGADGVGNAS GNWHCDSTWLGDRVITTSTRTALPTYNNHLYKQISSQSGXSTNDNTYFGYSTPWGY FDFNRFHCHFSPRDWQRLINNNWGFRPKXLNFKLFNIQVKEVTTNDGTTTIANNLTS TVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRSSFYCL EYFPSQMLRTGNNFXFSYTFEDVPFHSSYAHSQSLDRLNPLIDQYLYYLSRTQTTSGT AGNRXLQFSQAGPSSANQAKNWLPGPCYRQQRVSKTXNQNNNSNFAWTGATKYH LNGRDSLVNPGPAMATHKDDEDKFFPMSGVLIFGKQGAGNSNVDLDNVITXEEEIKT TNPVATEXYGTVATNLQSXNTAPATGTVNSQGALPGVWQXRDVYLQGPIWAKIPHT DGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPTTFSPAKFASFITQYSTGQVSVEIEE LQKENSKRWNPEIQYTSNYNKSTNVDFAVDTNGVYSEPRPIGTRYLTRNL (SEQ ID NO: 213)
[075] In one embodiment, the AAV capsid is derived from the AAV12 VP1 amino acid sequence which is:
MAADGYLPDWLEDNLSEGIREWWALKPGAPQPKANQQHQDNGRGLVLPGYKYLG PFNGLDKGEPVNEADAAALEHDKAYDKQLEQGDNPYLKYNHADAEFQQRLATDTS FGGNLGRAVFQAKKRILEPLGLVEEGVKTAPGKKRPLEKTPNRPTNPDSGKAPAKKK QKDGEPADSARRTLDFEDSGAGDGPPEGSSSGEMSHDAEMRAAPGGNAVEAGQGA DGVGNASGDWHCDSTWSEGRVTTTSTRTWVLPTYNNHLYLRIGTTANSNTYNGFST PWGYFDFNRFHCHFSPRDWQRLINNNWGLRPKSMRVKIFNIQVKEVTTSNGETTVA NNLTSTVQIFADSTYELPYVMDAGQEGSFPPFPNDVFMVPQYGYCGVVTGKNQNQT DRNAFYCLEYFPSQMLRTGNNFEVSYQFEKVPFHSMYAHSQSLDRMMNPLLDQYL WHLQSTTTGNSLNQGTATTTYGKITTGDFAYYRKNWLPGACIKQQKFSKNANQNY KIPASGGDALLKYDTHTTLNGRWSNMAPGPPMATAGAGDSDFSNSQLIFAGPNPSG NTTTSSNNLLFTSEEEIATTNPRDTDMFGQIADNNQNATTAPHIANLDAMGIVPGMV WQNRDIYYQGPIWAKVPHTDGHFHPSPLMGGFGLKHPPPQIFIKNTPVPANPNTTFS AARINSFLTQYSTGQVAVQIDWEIQKEHSKRWNPEVQFTSNYGTQNSMLWAPDNAG NYHELRAIGSRFLTHHL (SEQ ID NO: 214) [076] In one embodiment, the AAV capsid is derived from the AAV1 VP1 amino acid sequence which is:
MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLG PFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTS FGGNLGRAVFQAKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQP AKKRLNFGQTGDSESVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGV GNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYS TPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIA NNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRS SFYCLEYFPSQMLRTGNNFTFSYTFEEVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRT QNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWT GASKYNLNGRESIINPGTAMASHKDDEDKFFPMSGVMIFGKESAGASNTALDNVMIT DEEEIKATNPVATERFGTVAVNFQSSSTDPATGDVHAMGALPGMVWQDRDVYLQG PIWAKIPHTDGHFHPSPLMGGFGLKNPPPQILIKNTPVPANPPAEFSATKFASFITQYST GQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTRYL TRPL (SEQ ID NO: 215)
[077] In one embodiment, the AAV capsid is derived from the AAV2 VP1 amino acid sequence which is:
MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPF NGLDKGEPVNEADAAALEHDKAYDRQLDSGDNPYLKYNHADAEFQERLKEDTSFG GNLGRAVFQAKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTGKAGQQPA RKRLNFGQTGDADSVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVG NSSGNWHCDSTWMGDRVITTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTP WGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTQNDGTTTIAN NLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRS SFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRT NTPSGTTTQSRLQFSQAGASDIRDQSRNWLPGPCYRQQRVSKTSADNNNSEYSWTG ATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMITD EEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPI WAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTG QVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVYSEPRPIGTRYLTR NL (SEQ ID NO: 216) [078] In one embodiment, the AAV capsid is derived from the AAV6 VP1 amino acid sequence which is:
MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLG PFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTS FGGNLGRAVFQAKKRVLEPFGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQP AKKRLNFGQTGDSESVPDPQPLGEPPATPAAVGPTTMASGGGAPMADNNEGADGV GNASGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISSASTGASNDNHYFGYS TPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNDGVTTIA NNLTSTVQVFSDSEYQLPYVLGSAHQGCLPPFPADVFMIPQYGYLTLNNGSQAVGRS SFYCLEYFPSQMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLNRT QNQSGSAQNKDLLFSRGSPAGMSVQPKNWLPGPCYRQQRVSKTKTDNNNSNFTWT GASKYNLNGRESIINPGTAMASHKDDKDKFFPMSGVMIFGKESAGASNTALDNVMI TDEEEIKATNPVATERFGTVAVNLQSSSTDPATGDVHVMGALPGMVWQDRDVYLQ GPIWAKIPHTDGHFHPSPLMGGFGLKHPPPQILIKNTPVPANPPAEFSATKFASFITQY STGQVSVEIEWELQKENSKRWNPEVQYTSNYAKSANVDFTVDNNGLYTEPRPIGTR YLTRPL (SEQ ID NO: 217)
[079] In one embodiment, the AAV capsid is derived from the AAV8 VP1 amino acid sequence which is:
MAADGYLPDWLEDNLSEGIREWWDLKPGAPKPKANQQKQDDGRGLVLPGYKYLG PFNGLDKGEPVNAADAAALEHDKAYDQQLKAGDNPYLRYNHADAEFQERLQEDTS FGGNLGRAVFQAKKRVLEPLGLVEEGAKTAPGKKRPVEQSPQEPDSSSGIGKTGQQP AKKRLNFGQTGDSESVPDPQPLGEPPAAPSGLGPNTMASGGGAPMADNNEGADGV GNSSGNWHCDSTWLGDRVITTSTRTWALPTYNNHLYKQISNGTSGGSTNDNTYFGY STPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQVKEVTTNEGTKTI ANNLTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQALG RSSFYCLEYFPSQMLRTGNNFQFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYL VRTQTTGTGGTQTLAFSQAGPSSMANQARNWVPGPCYRQQRVSTTTNQNNNSNFA WTGAAKFKLNGRDSLMNPGVAMASHKDDDDRFFPSSGVLIFGKQGAGNDGVDYSQ VLITDEEEIKATNPVATEEYGAVAINNQAANTQAQTGLVHNQGVIPGMVWQNRDVY LQGPIWAKIPHTDGNFHPSPLMGGFGLKHPPPQILIKNTPVPADPPLTFNQAKLNSFIT QYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYYKSTNVDFAVNTEGVYSEPRPIGT RYLTRNL (SEQ ID NO: 218) RNA-Binding Proteins
[080] An RNA-binding protein, polypeptide, or domain of the disclosure includes, without limitation, an RNA-binding portion or portions of the RNA-binding protein or polypeptide or domain.
[081] In some embodiments of the compositions of the disclosure, the sequence encoding an RNA-binding protein or RNA-binding portion thereof comprises a sequence isolated or derived from a CRISPR Cas protein. In some embodiments, the CRISPR Cas protein comprises a Type II CRISPR Cas protein. In some embodiments, the Type II CRISPR Cas protein comprises a Cas9 protein. Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea.
Exemplary Cas9 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Streptococcus pyogenes, Haloferax mediteranii, Mycobacterium tuberculosis, Francisella tularensis subsp. novicida, Pasteurella multocida, Neisseria meningitidis, Campylobacter jejune, Streptococcus thermophilus, Campylobacter lari CF89- 12, Mycoplasma gallisepticum str. F, Nitratifractor salsuginis str. DSM 16511,
Parvibaculum lavamentivorans, Roseburia intestinalis, Neisseria cinerea, a
Gluconacetobacter diazotrophicus, an Azospirillum B510, a Sphaerochaeta globus str.
Buddy, Flavobacterium columnare, Fluviicola taffensis, Bacteroides coprophilus,
Mycoplasma mobile, Lactobacillus farciminis, Streptococcus pasteurianus, Lactobacillus johnsonii, Staphylococcus pseudintermedius, Filifactor alocis, Treponema denticola, Legionella pneumophila str. Paris, Sutterella wadsworthensis, Corynebacter diphtherias, Streptococcus aureus, and Francisella novicida.
[082] Exemplary wild type S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence:
1 MDKKYSIGLD IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE 61 ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG 121 NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD 181 VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN 241 LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI 301 LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA 361 GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH 421 AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE 481 VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL 541 SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI 601 IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG 661 RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL 721 HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER 781 MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH 841 IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL 901 TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS 961 KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK 1021 MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF 1081 ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA 1141 YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK 1201 YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE 1261 QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA 1321 PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD. (SEQ ID NO: 147) ^
[083] Nuclease inactivated S. pyogenes Cas9 proteins may comprise a substitution of an Alanine (A) for an Aspartic Acid (D) at position 10 and an alanine (A) for a Histidine (H) at position 840. Exemplary nuclease inactivated S. pyogenes Cas9 proteins of the disclosure may comprise or consist of the amino acid sequence (D10A and H840A bolded and
underlined):
1 MDKKYSIGLA IGTNSVGWAV ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE 61 ATRLKRTARR RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG 121 NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD 181 VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP GEKKNGLFGN 241 LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA QIGDQYADLF LAAKNLSDAI 301 LLSDILRVNT EITKAPLSAS MIKRYDEHHQ DLTLLKALVR QQLPEKYKEI FFDQSKNGYA 361 GYIDGGASQE EFYKFIKPIL EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH 421 AILRRQEDFY PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE 481 VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL 541 SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS LGTYHDLLKI 601 IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA HLFDDKVMKQ LKRRRYTGWG 661 RLSRKLINGI RDKQSGKTIL DFLKSDGFAN RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL 721 HEHIANLAGS PAIKKGILQT VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER 781 MKRIEEGIKE LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDA
841 IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL 901 TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI REVKVITLKS 961 KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK YPKLESEFVY GDYKVYDVRK 1021 MIAKSEQEIG KATAKYFFYS NIMNFFKTEI TLANGEIRKR PLIETNGETG EIVWDKGRDF 1081 ATVRKVLSMP QVNIVKKTEV QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA 1141 YSVLVVAKVE KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK 1201 YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE 1261 QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII HLFTLTNLGA 1321 PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI DLSQLGGD . (SEQ ID NO: 148)
[084] Nuclease inactivated S. pyogenes Cas9 proteins may comprise deletion of a RuvC nuclease domain or a portion thereof, an HNH domain, a DNAse active site, a bba-metal fold or a portion thereof comprising a DNAse active site or any combination thereof.
[085] Other exemplary Cas9 proteins or portions thereof may comprise or consist of the following amino acid sequences.
[086] In some embodiments the Cas9 protein can be S. pyogenes Cas9 and may comprise or consist of the amino acid sequence:
MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTAR
RRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLR
KKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDA
KAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDN
LL AQIGDQY ADLFL AAKNL SD AILL SDILRVNTEITKAPL S ASMIKRYDEHHQDLTLLKAL VRQQLPEK
YKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHL
GET .HAII .RROF.DFYPFI .KDNRFK IFK II TFRTPYYVGPT ARGNSRF A WMTRK SEETTTP WNFEEVVDK G
ASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLF
KTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTL
TLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANR
NFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKWDELVKVMGRHKPENI
VIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQ
ELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEWKKMKNYWRQLLNAKLITQ
RKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLV
SDFRKDFQFYKVREINNYHHAHDAYLNAWGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIG
KATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTE
VQTGGF SKESILPKRN SDKLI ARKKD WDPKKY GGFD SPTVAY S VL WAKVEKGKSKKLKS VKELLGITI
MERS SFEKNPIDFLEAKGYKEVKKDLIIKLPKY SLFELENGRKRML AS AGELQKGNEL ALP SKYVNFLY
LASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQA
ENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD (SEQ ID NO:
149)
[087] In some embodiments the Cas9 protein can be S. aureus Cas9 and may comprise or consist of the amino acid sequence:
MKRNYILGLDIGITSVGYGIIDYETRDVIDAGVRLFKEANVENNEGRRSKRGARRLKRRRRHRIQRVKK
LLFDYNLLTDHSELSGINPYEARVKGLSQKLSEEEFSAALLHLAKRRGVHNVNEVEEDTGNELSTKEQI
SRNSKALEEKYVAELQLERLKKDGEVRGSINRFKTSDYVKEAKQLLKVQKAYHQLDQSFIDTYIDLLE
TRRTYYEGPGEGSPFGWKDIKEWYEMLMGHCTYFPEELRSVKYAYNADLYNALNDLNNLVITRDENE
KLEYYEKFQIIENVFKQKKKPTLKQIAKEILVNEEDIKGYRVTSTGKPEFTNLKVYHDIKDITARKEIIEN AELLDQIAKILTIYQSSEDIQEELTNLNSELTQEEIEQISNLKGYTGTHNLSLKAINLILDELWHTNDNQIA IFNRLKLVPKKVDLSQQKEIPTTLVDDFILSPVVKRSFIQSIKVINAIIKKYGLPNDIIIELAREKNSKDAQK MINEMQKRNRQTNERIEEIIRTTGKENAKYLIEKIKLHDMQEGKCLYSLEAIPLEDLLNNPFNYEVDHIIP RSVSFDNSFNNKVLVKQEENSKKGNRTPFQYLSSSDSKISYETFKKHILNLAKGKGRISKTKKEYLLEER DINRFSVQKDFINRNLVDTRYATRGLMNLLRSYFRVNNLDVKVKSINGGFTSFLRRKWKFKKERNKGY KHHAEDALIIANADFIFKEWKKLDKAKKVMENQMFEEKQAESMPEIETEQEYKEIFITPHQIKHIKDFK DYKYSHRVDKKPNRELINDTLYSTRKDDKGNTLIVNNLNGLYDKDNDKLKKLINKSPEKLLMYHHDP QTYQKLKLIMEQYGDEKNPLYKYYEETGNYLTKYSKKDNGPVIKKIKYYGNKLNAHLDITDDYPNSR NKVVKLSLKPYRFDVYLDNGVYKFVTVKNLDVIKKENYYEVNSKCYEEAKKLKKISNQAEFIASFYN NDLIKINGELYRVIGVNNDLLNRIEVNMIDITYREYLENMNDKRPPRIIKTIASKTQSIKKYSTDILGNLY EVKSKKHPQIIKKG (SEQ ID NO:150)
[088] In some embodiments the Cas9 protein can be S. thermophiles CRISPR1 Cas9 and may comprise or consist of the amino acid sequence:
MSDLVLGLDIGIGSVGVGILNKVTGEIIHKNSRIFPAAQAENNLVRRTNRQGRRLARRKKHRRVRLNRL FEESGLITDFTKISINLNPYQLRVKGLTDELSNEELFIALKNMVKHRGISYLDDASDDGNSSVGDYAQIV KENSKQLETKTPGQIQLERYQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALRILQTQQEFNPQIT DEFINRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSGETLDNIFGILIGKCTFYPDEFRAAKASYTAQEF NLLNDLNNLTVPTETKKLSKEQKNQIINYVKNEKAMGPAKLFKYIAKLLSCDVADIKGYRIDKSGKAEI HTFEAYRKMKTLETLDIEQMDRETLDKLAYVLTLNTEREGIQEALEHEFADGSFSQKQVDELVQFRKA NSSIFGKGWHNFSVKLMMELIPELYETSEEQMTILTRLGKQKTTSSSNKTKYIDEKLLTEEIYNPVVAKS VRQAIKIVNAAIKEYGDFDNIVIEMARETNEDDEKKAIQKIQKANKDEKDAAMLKAANQYNGKAELP HSVFHGHKQLATKIRLWHQQGERCLYTGKTISIHDLINNSNQFEVDHILPLSITFDDSLANKVLVYATA NQEKGQRTPYQALDSMDDAWSFRELKAFVRESKTLSNKKKEYLLTEEDISKFDVRKKFIERNLVDTRY ASRVVLNALQEHFRAHKIDTKVSVVRGQFTSQLRRHWGIEKTRDTYHHHAVDALIIAASSQLNLWKK QKNTLVSYSEDQLLDIETGELISDDEYKESVFKAPYQHFVDTLKSKEFEDSILFSYQVDSKFNRKISDATI YATRQAKVGKDKADETYVLGKIKDIYTQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEPILENYPN KQINDKGKEVPCNPFLKYKEEHGYIRKYSKKGNGPEIKSLKYYDSKLGNHIDITPKDSNNKVVLQSVSP WRADVYFNKTTGKYEILGLKYADLQFDKGTGTYKISQEKYNDIKKKEGVDSDSEFKFTLYKNDLLLV KDTETKEQQLFRFLSRTMPKQKHYVELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLGKSNISIYKV RTDVLGNQHIIKNEGDKPKLDF (SEQ ID NO: 151)
[089] In some embodiments the Cas9 protein can be N. meningitidis Cas9 and may comprise or consist of the amino acid sequence:
MAAFKPNPINYILGLDIGIASVGWAMVEIDEDENPICLIDLGVRVFERAEVPKTGDSLAMARRLARSVR RLTRRRAHRLLRARRLLKREGVLQAADFDENGLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKH RGYLSQRKNEGETADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYSHTFS RKDLQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDAVQKMLGHCTFEPAEPKAAKNTY TAERFIWLTKLNNLRILEQGSERPLTDTERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLRYGKD NAEASTLMEMKAYHAISRALEKEGLKDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLKDRIQPEILEA LLKHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYGDHYGKKNTEEKIYLPPIPADEIRNPVVLRA LSQARKVINGVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENRKDREKAAAKFREYFPNFVGEPK SKDILKLRLYEQQHGKCLYSGKEINLGRLNEKGYVEIDHALPFSRTWDDSFNNKVLVLGSENQNKGNQ TPYEYFNGKDNSREWQEFKARVETSRFPRSKKQRILLQKFDEDGFKERNLNDTRYVNRFLCQFVADR MRLTGKGKKRVFASNGQITNLLRGFWGLRKVRAENDRHHALDAVVVACSTVAMQQKITRFVRYKEM NAFDGKTIDKETGEVLHQKTHFPQPWEFFAQEVMIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSSRPE AVHEYVTPLFVSRAPNRKMSGQGHMETVKSAKRLDEGVSVLRVPLTQLKLKDLEKMVNREREPKLYE ALKARLEAHKDDPAKAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVRNHNGIADNATMVRV DVFEKGDKYYLVPIYSWQVAKGILPDRAVVQGKDEEDWQLIDDSFNFKFSLHPNDLVEVITKKARMF GYFASCHRGTGNINIRIHDLDHKIGKNGILEGIGVKTALSFQKYQIDELGKEIRPCRLKKRPPVR (SEQ ID NO: 152)
[090] In some embodiments the Cas9 protein can be Parvibaculum. lavamentivorans Cas9 and may comprise or consist of the amino acid sequence:
MERIFGFDIGTTSIGFSVIDYSSTQSAGNIQRLGVRIFPEARDPDGTPLNQQRRQKRMMRRQLRRRRIRR KALNETLHEAGFLPAYGSADWPVVMADEPYELRRRGLEEGLSAYEFGRAIYHLAQHRHFKGRELEES DTPDPDVDDEKEAANERAATLKALKNEQTTLGAWLARRPPSDRKRGIHAHRNVVAEEFERLWEVQSK FHPALKSEEMRARISDTIFAQRPVFWRKNTLGECRFMPGEPLCPKGSWLSQQRRMLEKLNNLAIAGGN ARPLDAEERDAILSKLQQQASMSWPGVRSALKALYKQRGEPGAEKSLKFNLELGGESKLLGNALEAK LADMFGPDWPAHPRKQEIRHAVHERLWAADYGETPDKKRVIILSEKDRKAHREAAANSFVADFGITG EQAAQLQALKLPTGWEPYSIPALNLFLAELEKGERFGALVNGPDWEGWRRTNFPHRNQPTGEILDKLP SPASKEERERISQLRNPTVVRTQNELRKVVNNLIGLYGKPDRIRIEVGRDVGKSKREREEIQSGIRRNEK QRKKATEDLIKNGIANPSRDDVEKWILWKEGQERCPYTGDQIGFNALFREGRYEVEHIWPRSRSFDNSP RNKTLCRKDVNIEKGNRMPFEAFGHDEDRWSAIQIRLQGMVSAKGGTGMSPGKVKRFLAKTMPEDFA ARQLNDTRYAAKQILAQLKRLWPDMGPEAPVKVEAVTGQVTAQLRKLWTLNNILADDGEKTRADHR HHAIDALTVACTHPGMTNKLSRYWQLRDDPRAEKPALTPPWDTIRADAEKAVSEIVVSHRVRKKVSG PLHKETTYGDTGTDIKTKSGTYRQFVTRKKIESLSKGELDEIRDPRIKEIVAAHVAGRGGDPKKAFPPYP CVSPGGPEIRKVRLTSKQQLNLMAQTGNGYADLGSNHHIAIYRLPDGKADFEIVSLFDASRRLAQRNPI VQRTRADGASFVMSLAAGEAIMIPEGSKKGIWIVQGVWASGQVVLERDTDADHSTTTRPMPNPILKDD AKKVSIDPIGRVRPSND (SEQ ID NO: 153)
[091] In some embodiments the Cas9 protein can be Corynebacter diphtheria Cas9 and may comprise or consist of the amino acid sequence:
MKYHVGIDVGTFSVGLAAIEVDDAGMPIKTLSLVSHIHDSGLDPDEIKSAVTRLASSGIARRTRRLYRR KRRRLQQLDKFIQRQGWPVIELEDYSDPLYPWKVRAELAASYIADEKERGEKLSVALRHIARHRGWRN PYAKVSSLYLPDGPSDAFKAIREEIKRASGQPVPETATVGQMVTLCELGTLKLRGEGGVLSARLQQSDY AREIQEICRMQEIGQELYRKIIDVVFAAESPKGSASSRVGKDPLQPGKNRALKASDAFQRYRIAALIGNL RVRVDGEKRILSVEEKNLVFDHLVNLTPKKEPEWVTIAEILGIDRGQLIGTATMTDDGERAGARPPTHD TNRSIVNSRIAPLVDWWKTASALEQHAMVKALSNAEVDDFDSPEGAKVQAFFADLDDDVHAKLDSLH LPVGRAAYSEDTLVRLTRRMLSDGVDLYTARLQEFGIEPSWTPPTPRIGEPVGNPAVDRVLKTVSRWL ESATKTWGAPERVIIEHVREGFVTEKRAREMDGDMRRRAARNAKLFQEMQEKLNVQGKPSRADLWR YQSVQRQNCQCAYCGSPITFSNSEMDHIVPRAGQGSTNTRENLVAVCHRCNQSKGNTPFAIWAKNTSI EGVSVKEAVERTRHWVTDTGMRSTDFKKFTKAVVERFQRATMDEEIDARSMESVAWMANELRSRVA QHFASHGTTVRVYRGSLTAEARRASGISGKLKFFDGVGKSRLDRRHHAIDAAVIAFTSDYVAETLAVR SNLKQSQAHRQEAPQWREFTGKDAEHRAAWRVWCQKMEKLSALLTEDLRDDRVVVMSNVRLRLGN GSAHKETIGKLSKVKLSSQLSVSDIDKASSEALWCALTREPGFDPKEGLPANPERHIRVNGTHVYAGDN IGLFPVSAGSIALRGGYAELGSSFHHARVYKITSGKKPAFAMLRVYTIDLLPYRNQDLFSVELKPQTMS MRQAEKKLRDALATGNAEYLGWLVVDDELVVDTSKIATDQVKAVEAELGTIRRWRVDGFFSPSKLRL RPLQMSKEGIKKESAPELSKIIDRPGWLPAVNKLFSDGNVTVVRRDSLGRVRLESTAHLPVTWKVQ
(SEQ ID NO: 154)
[092] In some embodiments the Cas9 protein can be Streptococcus pasteurianus Cas9 and may comprise or consist of the amino acid sequence:
MTNGKILGLDIGIASVGVGIIEAKTGKVVHANSRLFSAANAENNAERRGFRGSRRLNRRKKHRVKRVR DLFEKYGIVTDFRNLNLNPYELRVKGLTEQLKNEELFAALRTISKRRGISYLDDAEDDSTGSTDYAKSID ENRRLLKNKTPGQIQLERLEKYGQLRGNFTVYDENGEAHRLINVFSTSDYEKEARKILETQADYNKKIT AEFIDDYVEILTQKRKYYHGPGNEKSRTDYGRFRTDGTTLENIFGILIGKCNFYPDEYRASKASYTAQE YNFLNDLNNLKVSTETGKLSTEQKESLVEFAKNTATLGPAKLLKEIAKILDCKVDEIKGYREDDKGKPD LHTFEPYRKLKFNLESINIDDLSREVIDKLADILTLNTEREGIEDAIKRNLPNQFTEEQISEIIKVRKSQSTA FNKGWHSFSAKLMNELIPELYATSDEQMTILTRLEKFKVNKKSSKNTKTIDEKEVTDEIYNPVVAKSVR QTIKIINAAVKKYGDFDKIVIEMPRDKNADDEKKFIDKRNKENKKEKDDALKRAAYLYNSSDKLPDEV FHGNKQLETKIRLWYQQGERCLYSGKPISIQELVHNSNNFEIDHILPLSLSFDDSLANKVLVYAWTNQE KGQKTPYQVIDSMDAAWSFREMKDYVLKQKGLGKKKRDYLLTTENIDKIEVKKKFIERNLVDTRYAS RVVLNSLQSALRELGKDTKVSVVRGQFTSQLRRKWKIDKSRETYHHHAVDALIIAASSQLKLWEKQD NPMFVDYGKNQVVDKQTGEILSVSDDEYKELVFQPPYQGFVNTISSKGFEDEILFSYQVDSKYNRKVS DATIYSTRKAKIGKDKKEETYVLGKIKDIYSQNGFDTFIKKYNKDKTQFLMYQKDSLTWENVIEVILRD YPTTKKSEDGKNDVKCNPFEEYRRENGLICKYSKKGKGTPIKSLKYYDKKLGNCIDITPEESRNKVILQS INPWRADVYFNPETLKYELMGLKYSDLSFEKGTGNYHISQEKYDAIKEKEGIGKKSEFKFTLYRNDLILI KDIASGEQEIYRFLSRTMPNVNHYVELKPYDKEKFDNVQELVEALGEADKVGRCIKGLNKPNISIYKVR TDVLGNKYFVKKKGDKPKLDFKNNKK (SEQ ID NO: 155)
[093] In some embodiments the Cas9 protein can be Neisseria cinerea Cas9 and may comprise or consist of the amino acid sequence:
MAAFKPNPMNYILGLDIGIASVGWAIVEIDEEENPIRLIDLGVRVFERAEVPKTGDSLAAARRLARSVRR LTRRRAHRLLRARRLLKREGVLQAADFDENGLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKHR GYLSQRKNEGETADKELGALLKGVADNTHALQTGDFRTPAELALNKFEKESGHIRNQRGDYSHTFNR KDLQAELNLLFEKQKEFGNPHVSDGLKEGIETLLMTQRPALSGDAVQKMLGHCTFEPTEPKAAKNTYT AERFVWLTKLNNLRILEQGSERPLTDTERATLMDEPYRKSKLTYAQARKLLDLDDTAFFKGLRYGKD NAEASTLMEMKAYHAISRALEKEGLKDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLKDRVQPEILEA LLKHISFDKFVQISLKALRRIVPLMEQGNRYDEACTEIYGDHYGKKNTEEKIYLPPIPADEIRNPVVLRA LSQARKVINGVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENRKDREKSAAKFREYFPNFVGEPK SKDILKLRLYEQQHGKCLYSGKEINLGRLNEKGYVEIDHALPFSRTWDDSFNNKVLALGSENQNKGNQ TPYEYFNGKDNSREWQEFKARVETSRFPRSKKQRILLQKFDEDGFKERNLNDTRYINRFLCQFVADHM LLTGKGKRRVFASNGQITNLLRGFWGLRKVRAENDRHHALDAVVVACSTIAMQQKITRFVRYKEMN AFDGKTIDKETGEVLHQKAHFPQPWEFFAQEVMIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSSRPEA VHKYVTPLFISRAPNRKMSGQGHMETVKSAKRLDEGISVLRVPLTQLKLKDLEKMVNREREPKLYEAL KARLEAHKDDPAKAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVHNHNGIADNATIVRVDVF EKGGKYYLVPIYSWQVAKGILPDRAVVQGKDEEDWTVMDDSFEFKFVLYANDLIKLTAKKNEFLGYF VSLNRATGAIDIRTHDTDSTKGKNGIFQSVGVKTALSFQKYQIDELGKEIRPCRLKKRPPVR (SEQ ID NO: 156)
[094] In some embodiments the Cas9 protein can be Campylobacter lari Cas9 and may comprise or consist of the amino acid sequence:
MRILGFDIGINSIGWAFVENDELKDCGVRIFTKAENPKNKESLALPRRNARSSRRRLKRRKARLIAIKRIL AKELKLNYKDYVAADGELPKAYEGSLASVYELRYKALTQNLETKDLARVILHIAKHRGYMNKNEKKS NDAKKGKILSALKNNALKLENYQSVGEYFYKEFFQKYKKNTKNFIKIRNTKDNYNNCVLSSDLEKELK LILEKQKEFGYNYSEDFINEILKVAFFQRPLKDFSHLVGACTFFEEEKRACKNSYSAWEFVALTKIINEIK SLEKISGEIVPTQTINEVLNLILDKGSITYKKFRSCINLHESISFKSLKYDKENAENAKLIDFRKLVEFKKA LGVHSLSRQELDQISTHITLIKDNVKLKTVLEKYNLSNEQINNLLEIEFNDYINLSFKALGMILPLMREGK RYDEACEIANLKPKTVDEKKDFLPAFCDSIFAHELSNPVVNRAISEYRKVLNALLKKYGKVHKIHLELA RDVGLSKKAREKIEKEQKENQAVNAWALKECENIGLKASAKNILKLKLWKEQKEICIYSGNKISIEHLK DEKALEVDHIYPYSRSFDDSFINKVLVFTKENQEKLNKTPFEAFGKNIEKWSKIQTLAQNLPYKKKNKI LDENFKDKQQEDFISRNLNDTRYIATLIAKYTKEYLNFLLLSENENANLKSGEKGSKIHVQTISGMLTSV LRHTWGFDKKDRNNHLHHALDAIIVAYSTNSIIKAFSDFRKNQELLKARFYAKELTSDNYKHQVKFFE PFKSFREKILSKIDEIFVSKPPRKRARRALHKDTFHSENKIIDKCSYNSKEGLQIALSCGRVRKIGTKYVE NDTIVRVDIFKKQNKFYAIPIYAMDFALGILPNKIVITGKDKNNNPKQWQTIDESYEFCFSLYKNDLILL QKKNMQEPEFAYYNDFSISTSSICVEKHDNKFENLTSNQKLLFSNAKEGSVKVESLGIQNLKVFEKYIIT PLGDKIKADFQPRENISLKTSKKYGLR (SEQ ID NO: 157)
[095] In some embodiments the Cas9 protein can be T. denticola Cas9 and may comprise or consist of the amino acid sequence:
MKKEIKDYFLGLDVGTGSVGWAVTDTDYKLLKANRKDLWGMRCFETAETAEVRRLHRGARRRIERR KKRIKLLQELFSQEIAKTDEGFFQRMKESPFYAEDKTILQENTLFNDKDFADKTYHKAYPTINHLIKAWI ENKVKPDPRLLYLACHNIIKKRGHFLFEGDFDSENQFDTSIQALFEYLREDMEVDIDADSQKVKEILKDS SLKNSEKQSRLNKILGLKPSDKQKKAITNLISGNKINFADLYDNPDLKDAEKNSISFSKDDFDALSDDLA SILGDSFELLLKAKAVYNCSVLSKVIGDEQYLSFAKVKIYEKHKTDLTKLKNVIKKHFPKDYKKVFGY NKNEKNNNNYSGYVGVCKTKSKKLIINNSVNQEDFYKFLKTILSAKSEIKEVNDILTEIETGTFLPKQISK SNAEIPYQLRKMELEKILSNAEKHFSFLKQKDEKGLSHSEKIIMLLTFKIPYYIGPINDNHKKFFPDRCWV VKKEKSPSGKTTPWNFFDHIDKEKTAEAFITSRTNFCTYLVGESVLPKSSLLYSEYTVLNEINNLQIIIDG KNICDIKLKQKIYEDLFKKYKKITQKQISTFIKHEGICNKTDEVIILGIDKECTSSLKSYIELKNIFGKQVDE ISTKNMLEEIIRWATIYDEGEGKTILKTKIKAEYGKYCSDEQIKKILNLKFSGWGRLSRKFLETVTSEMP GFSEPVNIITAMRETQNNLMELLSSEFTFTENIKKINSGFEDAEKQFSYDGLVKPLFLSPSVKKMLWQTL KLVKEISHITQAPPKKIFIEMAKGAELEPARTKTRLKILQDLYNNCKNDADAFSSEIKDLSGKIENEDNL RLRSDKLYLYYTQLGKCMYCGKPIEIGHVFDTSNYDIDHIYPQSKIKDDSISNRVLVCSSCNKNKEDKY PLKSEIQSKQRGFWNFLQRNNFISLEKLNRLTRATPISDDETAKFIARQLVETRQATKVAAKVLEKMFPE TKIVYSKAETVSMFRNKFDIVKCREINDFHHAHDAYLNIVVGNVYNTKFTNNPWNFIKEKRDNPKIAD TYNYYKVFDYDVKRNNITAWEKGKTIITVKDMLKRNTPIYTRQAACKKGELFNQTIMKKGLGQHPLK KEGPFSNISKYGGYNKVSAAYYTLIEYEEKGNKIRSLETIPLYLVKDIQKDQDVLKSYLTDLLGKKEFKI LVPKIKINSLLKINGFPCHITGKTNDSFLLRPAVQFCCSNNEVLYFKKIIRFSEIRSQREKIGKTISPYEDLS FRSYIKENLWKKTKNDEIGEKEFYDLLQKKNLEIYDMLLTKHKDTIYKKRPNSATIDILVKGKEKFKSLI IENQFEVILEILKLFSATRNVSDLQHIGGSKYSGVAKIGNKISSLDNCILIYQSITGIFEKRIDLLKV (SEQ ID NO: 158)
[096] In some embodiments the Cas9 protein can be S. mutans Cas9 and may comprise or consist of the amino acid sequence:
MKKPYSIGLDIGTNSVGWAVVTDDYKVPAKKMKVLGNTDKSHIEKNLLGALLFDSGNTAEDRRLKRT ARRRYTRRRNRILYLQEIFSEEMGKVDDSFFHRLEDSFLVTEDKRGERHPIFGNLEEEVKYHENFPTIYH LRQYLADNPEKVDLRLVYLALAHIIKFRGHFLIEGKFDTRNNDVQRLFQEFLAVYDNTFENSSLQEQNV QVEEILTDKISKSAKKDRVLKLFPNEKSNGRFAEFLKLIVGNQADFKKHFELEEKAPLQFSKDTYEEELE VLLAQIGDNYAELFLSAKKLYDSILLSGILTVTDVGTKAPLSASMIQRYNEHQMDLAQLKQFIRQKLSD KYNEVFSDVSKDGYAGYIDGKTNQEAFYKYLKGLLNKIEGSGYFLDKIEREDFLRKQRTFDNGSIPHQI HLQEMRAIIRRQAEFYPFLADNQDRIEKLLTFRIPYYVGPLARGKSDFAWLSRKSADKITPWNFDEIVD KESSAEAFINRMTNYDLYLPNQKVLPKHSLLYEKFTVYNELTKVKYKTEQGKTAFFDANMKQEIFDGV FKVYRKVTKDKLMDFLEKEFDEFRIVDLTGLDKENKVFNASYGTYHDLCKILDKDFLDNSKNEKILEDI VLTLTLFEDREMIRKRLENYSDLLTKEQVKKLERRHYTGWGRLSAELIHGIRNKESRKTILDYLIDDGN SNRNFMQLINDDALSFKEEIAKAQVIGETDNLNQVVSDIAGSPAIKKGILQSLKIVDELVKIMGHQPENI VVEMARENQFTNQGRRNSQQRLKGLTDSIKEFGSQILKEHPVENSQLQNDRLFLYYLQNGRDMYTGE ELDIDYLSQYDIDHIIPQAFIKDNSIDNRVLTSSKENRGKSDDVPSKDVVRKMKSYWSKLLSAKLITQRK FDNLTKAERGGLTDDDKAGFIKRQLVETRQITKHVARILDERFNTETDENNKKIRQVKIVTLKSNLVSN FRKEFELYKVREINDYHHAHDAYLNAVIGKALLGVYPQLEPEFVYGDYPHFHGHKENKATAKKFFYS NIMNFFKKDDVRTDKNGEIIWKKDEHISNIKKVLSYPQVNIVKKVEEQTGGFSKESILPKGNSDKLIPRK TKKFYWDTKKYGGFDSPIVAYSILVIADIEKGKSKKLKTVKALVGVTIMEKMTFERDPVAFLERKGYR NVQEENIIKLPKYSLFKLENGRKRLLASARELQKGNEIVLPNHLGTLLYHAKNIHKVDEPKHLDYVDK HKDEFKELLDVVSNFSKKYTLAEGNLEKIKELYAQNNGEDLKELASSFINLLTFTAIGAPATFKFFDKNI DRKRYTSTTEILNATLIHQSITGLYETRIDLNKLGGD (SEQ ID NO: 159)
[097] In some embodiments the Cas9 protein can be S. thermophilus CRISPR 3 Cas9 and may comprise or consist of the amino acid sequence:
MTKPYSIGLDIGTNSVGWAVTTDNYKVPSKKMKVLGNTSKKYIKKNLLGVLLFDSGITAEGRRLKRTA RRRYTRRRNRILYLQEIFSTEMATLDDAFFQRLDDSFLVPDDKRDSKYPIFGNLVEEKAYHDEFPTIYHL RKYLADSTKKADLRLVYLALAHMIKYRGHFLIEGEFNSKNNDIQKNFQDFLDTYNAIFESDLSLENSKQ LEEIVKDKISKLEKKDRILKLFPGEKNSGIFSEFLKLIVGNQADFRKCFNLDEKASLHFSKESYDEDLETL LGYIGDDYSDVFLKAKKLYDAILLSGFLTVTDNETEAPLSSAMIKRYNEHKEDLALLKEYIRNISLKTY NEVFKDDTKNGYAGYIDGKTNQEDFYVYLKKLLAEFEGADYFLEKIDREDFLRKQRTFDNGSIPYQIH LQEMRAILDKQAKFYPFLAKNKERIEKILTFRIPYYVGPLARGNSDFAWSIRKRNEKITPWNFEDVIDKE SSAEAFINRMTSFDLYLPEEKVLPKHSLLYETFNVYNELTKVRFIAESMRDYQFLDSKQKKDIVRLYFK DKRKVTDKDIIEYLHAIYGYDGIELKGIEKQFNSSLSTYHDLLNIINDKEFLDDSSNEAIIEEIIHTLTIFED REMIKQRLSKFENIFDKSVLKKLSRRHYTGWGKLSAKLINGIRDEKSGNTILDYLIDDGISNRNFMQLIH DDALSFKKKIQKAQIIGDEDKGNIKEVVKSLPGSPAIKKGILQSIKIVDELVKVMGGRKPESIVVEMARE NQYTNQGKSNSQQRLKRLEKSLKELGSKILKENIPAKLSKIDNNALQNDRLYLYYLQNGKDMYTGDD LDIDRLSNYDIDHIIPQAFLKDNSIDNKVLVSSASNRGKSDDVPSLEVVKKRKTFWYQLLKSKLISQRKF DNLTKAERGGLSPEDKAGFIQRQLVETRQITKHVARLLDEKFNNKKDENNRAVRTVKIITLKSTLVSQF RKDFELYKVREINDFHHAHDAYLNAVVASALLKKYPKLEPEFVYGDYPKYNSFRERKSATEKVYFYS NIMNIFKKSISLADGRVIERPLIEVNEETGESVWNKESDLATVRRVLSYPQVNVVKKVEEQNHGLDRGK PKGLFNANLSSKPKPNSNENLVGAKEYLDPKKYGGYAGISNSFTVLVKGTIEKGAKKKITNVLEFQGISI LDRINYRKDKLNFLLEKGYKDIELIIELPKYSLFELSDGSRRMLASILSTNNKRGEIHKGNQIFLSQKFVK LLYHAKRISNTINENHRKYVENHKKEFEELFYYILEFNENYVGAKKNGKLLNSAFQSWQNHSIDELCSS FIGPTGSERKGLFELTSRGSAADFEFLGVKIPRYRDYTPSSLLKDATLIHQSVTGLYETRIDLAKLGEG
(SEQ ID NO: 160)
[098] In some embodiments the Cas9 protein can be C. jejuni Cas9 and may comprise or consist of the amino acid sequence:
MARILAFDIGISSIGWAFSENDELKDCGVRIFTKVENPKTGESLALPRRLARSARKRLARRKARLNHLK HLIANEFKLNYEDYQSFDESLAKAYKGSLISPYELRFRALNELLSKQDFARVILHIAKRRGYDDIKNSDD KEKGAILKAIKQNEEKLANYQSVGEYLYKEYFQKFKENSKEFTNVRNKKESYERCIAQSFLKDELKLIF KKQREFGFSFSKKFEEEVLSVAFYKRALKDFSHLVGNCSFFTDEKRAPKNSPLAFMFVALTRIINLLNNL KNTEGILYTKDDLNALLNEVLKNGTLTYKQTKKLLGLSDDYEFKGEKGTYFIEFKKYKEFIKALGEHN LSQDDLNEIAKDITLIKDEIKLKKALAKYDLNQNQIDSLSKLEFKDHLNISFKALKLVTPLMLEGKKYDE ACNELNLKVAINEDKKDFLPAFNETYYKDEVTNPVVLRAIKEYRKVLNALLKKYGKVHKINIELAREV GKNHSQRAKIEKEQNENYKAKKDAELECEKLGLKINSKNILKLRLFKEQKEFCAYSGEKIKISDLQDEK MLEIDHIYPYSRSFDDSYMNKVLVFTKQNQEKLNQTPFEAFGNDSAKWQKIEVLAKNLPTKKQKRILD KNYKDKEQKNFKDRNLNDTRYIARLVLNYTKDYLDFLPLSDDENTKLNDTQKGSKVHVEAKSGMLTS ALRHTWGFSAKDRNNHLHHAIDAVIIAYANNSIVKAFSDFKKEQESNSAELYAKKISELDYKNKRKFFE PFSGFRQKVLDKIDEIFVSKPERKKPSGALHEETFRKEEEFYQSYGGKEGVLKALELGKIRKVNGKIVK NGDMFRVDIFKHKKTNKFYAVPIYTMDFALKVLPNKAVARSKKGEIKDWILMDENYEFCFSLYKDSLI LIQTKDMQEPEFVYYNAFTSSTVSLIVSKHDNKFETLSKNQKILFKNANEKEVIAKSIGIQNLKVFEKYIV SALGEVTKAEFRQREDFKK (SEQ ID NO: 161)
[099] In some embodiments the Cas9 protein can be P. multocida Cas9 and may comprise or consist of the amino acid sequence: MQTTNLSYILGLDLGIASVGWAVVEINENEDPIGLIDVGVRIFERAEVPKTGESLALSRRLARSTRRLIRR RAHRLLLAKRFLKREGILSTIDLEKGLPNQAWELRVAGLERRLSAIEWGAVLLHLIKHRGYLSKRKNES QTNNKELGALLSGVAQNHQLLQSDDYRTPAELALKKFAKEEGHIRNQRGAYTHTFNRLDLLAELNLLF AQQHQFGNPHCKEHIQQYMTELLMWQKPALSGEAILKMLGKCTHEKNEFKAAKHTYSAERFVWLTK LNNLRILEDGAERALNEEERQLLINHPYEKSKLTYAQVRKLLGLSEQAIFKHLRYSKENAESATFMELK AWHAIRKALENQGLKDTWQDLAKKPDLLDEIGTAFSLYKTDEDIQQYLTNKVPNSVINALLVSLNFDK FIELSLKSLRKILPLMEQGKRYDQACREIYGHHYGEANQKTSQLLPAIPAQEIRNPVVLRTLSQARKVIN AIIRQYGSPARVHIETGRELGKSFKERREIQKQQEDNRTKRESAVQKFKELFSDFSSEPKSKDILKFRLYE QQHGKCLYSGKEINIHRLNEKGYVEIDHALPFSRTWDDSFNNKVLVLASENQNKGNQTPYEWLQGKIN SERWKNFVALVLGSQCSAAKKQRLLTQVIDDNKFIDRNLNDTRYIARFLSNYIQENLLLVGKNKKNVF TPNGQITALLRSRWGLIKARENNNRHHALDAIVVACATPSMQQKITRFIRFKEVHPYKIENRYEMVDQE SGEIISPHFPEPWAYFRQEVNIRVFDNHPDTVLKEMLPDRPQANHQFVQPLFVSRAPTRKMSGQGHMET IKSAKRLAEGISVLRIPLTQLKPNLLENMVNKEREPALYAGLKARLAEFNQDPAKAFATPFYKQGGQQ VKAIRVEQVQKSGVLVRENNGVADNASIVRTDVFIKNNKFFLVPIYTWQVAKGILPNKAIVAHKNEDE WEEMDEGAKFKFSLFPNDLVELKTKKEYFFGYYIGLDRATGNISLKEHDGEISKGKDGVYRVGVKLAL SFEKYQVDELGKNRQICRPQQRQPVR (SEQ ID NO: 162)
[0100] In some embodiments the Cas9 protein can be F. novicida Cas9 and may comprise or consist of the amino acid sequence:
MNFKILPIAIDLGVKNTGVFSAFYQKGTSLERLDNKNGKVYELSKDSYTLLMNNRTARRHQRRGIDRK QLVKRLFKLIWTEQLNLEWDKDTQQAISFLFNRRGFSFITDGYSPEYLNIVPEQVKAILMDIFDDYNGED DLDSYLKLATEQESKISEIYNKLMQKILEFKLMKLCTDIKDDKVSTKTLKEITSYEFELLADYLANYSES LKTQKFSYTDKQGNLKELSYYHHDKYNIQEFLKRHATINDRILDTLLTDDLDIWNFNFEKFDFDKNEEK LQNQEDKDHIQAHLHHFVFAVNKIKSEMASGGRHRSQYFQEITNVLDENNHQEGYLKNFCENLHNKK YSNLSVKNLVNLIGNLSNLELKPLRKYFNDKIHAKADHWDEQKFTETYCHWILGEWRVGVKDQDKK DGAKYSYKDLCNELKQKVTKAGLVDFLLELDPCRTIPPYLDNNNRKPPKCQSLILNPKFLDNQYPNWQ QYLQELKKLQSIQNYLDSFETDLKVLKSSKDQPYFVEYKSSNQQIASGQRDYKDLDARILQFIFDRVKA SDELLLNEIYFQAKKLKQKASSELEKLESSKKLDEVIANSQLSQILKSQHTNGIFEQGTFLHLVCKYYKQ RQRARDSRLYIMPEYRYDKKLHKYNNTGRFDDDNQLLTYCNHKPRQKRYQLLNDLAGVLQVSPNFL KDKIGSDDDLFISKWLVEHIRGFKKACEDSLKIQKDNRGLLNHKINIARNTKGKCEKEIFNLICKIEGSED KKGNYKHGLAYELGVLLFGEPNEASKPEFDRKIKKFNSIYSFAQIQQIAFAERKGNANTCAVCSADNA HRMQQIKITEPVEDNKDKIILSAKAQRLPAIPTRIVDGAVKKMATILAKNIVDDNWQNIKQVLSAKHQL HIPIITESNAFEFEPALADVKGKSLKDRRKKALERISPENIFKDKNNRIKEFAKGISAYSGANLTDGDFDG AKEELDHIIPRSHKKYGTLNDEANLICVTRGDNKNKGNRIFCLRDLADNYKLKQFETTDDLEIEKKIAD TIWDANKKDFKFGNYRSFINLTPQEQKAFRHALFLADENPIKQAVIRAINNRNRTFVNGTQRYFAEVLA NNIYLRAKKENLNTDKISFDYFGIPTIGNGRGIAEIRQLYEKVDSDIQAYAKGDKPQASYSHLIDAMLAF CIAADEHRNDGSIGLEIDKNYSLYPLDKNTGEVFTKDIFSQIKITDNEFSDKKLVRKKAIEGFNTHRQMT RDGIYAENYLPILIHKELNEVRKGYTWKNSEEIKIFKGKKYDIQQLNNLVYCLKFVDKPISIDIQISTLEE LRNILTTNNIAATAEYYYINLKTQKLHEYYIENYNTALGYKKYSKEMEFLRSLAYRSERVKIKSIDDVK QVLDKDSNFIIGKITLPFKKEWQRLYREWQNTTIKDDYEFLKSFFNVKSITKLHKKVRKDFSLPISTNEG KFLVKRKTWDNNFIYQILNDSDSRADGTKPFIPAFDISKNEIVEAIIDSFTSKNIFWLPKNIELQKVDNKNI FAIDTSKWFEVETPSDLRDIGIATIQYKIDNNSRPKVRVKLDYVIDDDSKINYFMNHSLLKSRYPDKVLE ILKQSTIIEFESSGFNKTIKEMLGMKLAGIYNETSNN (SEQ ID NO: 163)
[0101] In some embodiments the Cas9 protein can be Lactobacillus buchneri Cas9 and may comprise or consist of the amino acid sequence:
MKVNNYHIGLDIGTSSIGWVAIGKDGKPLRVKGKTAIGARLFQEGNPAADRRMFRTTRRRLSRRKWRL KLLEEIFDPYITPVDSTFFARLKQSNLSPKDSRKEFKGSMLFPDLTDMQYHKNYPTIYHLRHALMTQDK KFDIRMVYLAIHHIVKYRGNFLNSTPVDSFKASKVDFVDQFKKLNELYAAINPEESFKINLANSEDIGHQ FLDPSIRKFDKKKQIPKIVPVMMNDKVTDRLNGKIASEIIHAILGYKAKLDVVLQCTPVDSKPWALKFD DEDIDAKLEKILPEMDENQQSIVAILQNLYSQVTLNQIVPNGMSLSESMIEKYNDHHDHLKLYKKLIDQ LADPKKKAVLKKAYSQYVGDDGKVIEQAEFWSSVKKNLDDSELSKQIMDLIDAEKFMPKQRTSQNGV IPHQLHQRELDEIIEHQSKYYPWLVEINPNKHDLHLAKYKIEQLVAFRVPYYVGPMITPKDQAESAETV FSWMERKGTETGQITPWNFDEKVDRKASANRFIKRMTTKDTYLIGEDVLPDESLLYEKFKVLNELNMV RVNGKLLKVADKQAIFQDLFENYKHVSVKKLQNYIKAKTGLPSDPEISGLSDPEHFNNSLGTYNDFKK LFGSKVDEPDLQDDFEKIVEWSTVFEDKKILREKLNEITWLSDQQKDVLESSRYQGWGRLSKKLLTGIV NDQGERIIDKLWNTNKNFMQIQSDDDFAKRIHEANADQMQAVDVEDVLADAYTSPQNKKAIRQVVK VVDDIQKAMGGVAPKYISIEFTRSEDRNPRRTISRQRQLENTLKDTAKSLAKSINPELLSELDNAAKSKK GLTDRLYLYFTQLGKDIYTGEPINIDELNKYDIDHILPQAFIKDNSLDNRVLVLTAVNNGKSDNVPLRM FGAKMGHFWKQLAEAGLISKRKLKNLQTDPDTISKYAMHGFIRRQLVETSQVIKLVANILGDKYRNDD TKIIEITARMNHQMRDEFGFIKNREINDYHHAFDAYLTAFLGRYLYHRYIKLRPYFVYGDFKKFREDKV TMRNFNFLHDLTDDTQEKIADAETGEVIWDRENSIQQLKDVYHYKFMLISHEVYTLRGAMFNQTVYP ASDAGKRKLIPVKADRPVNVYGGYSGSADAYMAIVRIHNKKGDKYRVVGVPMRALDRLDAAKNVSD ADFDRALKDVLAPQLTKTKKSRKTGEITQVIEDFEIVLGKVMYRQLMIDGDKKFMLGSSTYQYNAKQL VLSDQSVKTLASKGRLDPLQESMDYNNVYTEILDKVNQYFSLYDMNKFRHKLNLGFSKFISFPNHNVL DGNTKVSSGKREILQEILNGLHANPTFGNLKDVGITTPFGQLQQPNGILLSDETKIRYQSPTGLFERTVSL KDL (SEQ ID NO: 164)
[0102] In some embodiments the Cas9 protein can be Listeria innocua Cas9 and may comprise or consist of the amino acid sequence:
MKKPYTIGLDIGTNSVGWAVLTDQYDLVKRKMKIAGDSEKKQIKKNFWGVRLFDEGQTAADRRMAR TARRRIERRRNRISYLQGIFAEEMSKTDANFFCRLSDSFYVDNEKRNSRHPFFATIEEEVEYHKNYPTIY HLREELVNSSEKADLRLVYLALAHIIKYRGNFLIEGALDTQNTSVDGIYKQFIQTYNQVFASGIEDGSLK KLEDNKDVAKILVEKVTRKEKLERILKLYPGEKSAGMFAQFISLIVGSKGNFQKPFDLIEKSDIECAKDS YEEDLESLLALIGDEYAELFVAAKNAYSAVVLSSIITVAETETNAKLSASMIERFDTHEEDLGELKAFIK LHLPKHYEEIFSNTEKHGYAGYIDGKTKQADFYKYMKMTLENIEGADYFIAKIEKENFLRKQRTFDNG AIPHQLHLEELEAILHQQAKYYPFLKENYDKIKSLVTFRIPYFVGPLANGQSEFAWLTRKADGEIRPWNI EEKVDFGKSAVDFIEKMTNKDTYLPKENVLPKHSLCYQKYLVYNELTKVRYINDQGKTSYFSGQEKE QIFNDLFKQKRKVKKKDLELFLRNMSHVESPTIEGLEDSFNSSYSTYHDLLKVGIKQEILDNPVNTEML ENIVKILTVFEDKRMIKEQLQQFSDVLDGVVLKKLERRHYTGWGRLSAKLLMGIRDKQSHLTILDYLM NDDGLNRNLMQLINDSNLSFKSIIEKEQVTTADKDIQSIVADLAGSPAIKKGILQSLKIVDELVSVMGYP PQTIVVEMARENQTTGKGKNNSRPRYKSLEKAIKEFGSQILKEHPTDNQELRNNRLYLYYLQNGKDMY TGQDLDIHNLSNYDIDHIVPQSFITDNSIDNLVLTSSAGNREKGDDVPPLEIVRKRKVFWEKLYQGNLM SKRKFDYLTKAERGGLTEADKARFIHRQLVETRQITKNVANILHQRFNYEKDDHGNTMKQVRIVTLKS ALVSQFRKQFQLYKVRDVNDYHHAHDAYLNGVVANTLLKVYPQLEPEFVYGDYHQFDWFKANKAT AKKQFYTNIMLFFAQKDRIIDENGEILWDKKYLDTVKKVMSYRQMNIVKKTEIQKGEFSKATIKPKGN SSKLIPRKTNWDPMKYGGLDSPNMAYAVVIEYAKGKNKLVFEKKIIRVTIMERKAFEKDEKAFLEEQG YRQPKVLAKLPKYTLYECEEGRRRMLASANEAQKGNQQVLPNHLVTLLHHAANCEVSDGKSLDYIES NREMFAELLAHVSEFAKRYTLAEANLNKINQLFEQNKEGDIKAIAQSFVDLMAFNAMGAPASFKFFET TIERKRYNNLKELLNSTIIYQSITGLYESRKRLDD (SEQ ID NO: 165)
[0103] In some embodiments the Cas9 protein can be L. pneumophilia Cas9 and may comprise or consist of the amino acid sequence:
MESSQILSPIGIDLGGKFTGVCLSHLEAFAELPNHANTKYSVILIDHNNFQLSQAQRRATRHRVRNKKR NQFVKRVALQLFQHILSRDLNAKEETALCHYLNNRGYTYVDTDLDEYIKDETTINLLKELLPSESEHNFI DWFLQKMQSSEFRKILVSKVEEKKDDKELKNAVKNIKNFITGFEKNSVEGHRHRKVYFENIKSDITKD NQLDSIKKKIPSVCLSNLLGHLSNLQWKNLHRYLAKNPKQFDEQTFGNEFLRMLKNFRHLKGSQESLA VRNLIQQLEQSQDYISILEKTPPEITIPPYEARTNTGMEKDQSLLLNPEKLNNLYPNWRNLIPGIIDAHPFL EKDLEHTKLRDRKRIISPSKQDEKRDSYILQRYLDLNKKIDKFKIKKQLSFLGQGKQLPANLIETQKEME THFNSSLVSVLIQIASAYNKEREDAAQGIWFDNAFSLCELSNINPPRKQKILPLLVGAILSEDFINNKDKW AKFKIFWNTHKIGRTSLKSKCKEIEEARKNSGNAFKIDYEEALNHPEHSNNKALIKIIQTIPDIIQAIQSHL GHNDSQALIYHNPFSLSQLYTILETKRDGFHKNCVAVTCENYWRSQKTEIDPEISYASRLPADSVRPFD GVLARMMQRLAYEIAMAKWEQIKHIPDNSSLLIPIYLEQNRFEFEESFKKIKGSSSDKTLEQAIEKQNIQ WEEKFQRIINASMNICPYKGASIGGQGEIDHIYPRSLSKKHFGVIFNSEVNLIYCSSQGNREKKEEHYLLE HLSPLYLKHQFGTDNVSDIKNFISQNVANIKKYISFHLLTPEQQKAARHALFLDYDDEAFKTITKFLMSQ QKARVNGTQKFLGKQIMEFLSTLADSKQLQLEFSIKQITAEEVHDHRELLSKQEPKLVKSRQQSFPSHAI DATLTMSIGLKEFPQFSQELDNSWFINHLMPDEVHLNPVRSKEKYNKPNISSTPLFKDSLYAERFIPVWV KGETFAIGFSEKDLFEIKPSNKEKLFTLLKTYSTKNPGESLQELQAKSKAKWLYFPINKTLALEFLHHYF HKEIVTPDDTTVCHFINSLRYYTKKESITVKILKEPMPVLSVKFESSKKNVLGSFKHTIALPATKDWERL FNHPNFLALKANPAPNPKEFNEFIRKYFLSDNNPNSDIPNNGHNIKPQKHKAVRKVFSLPVIPGNAGTM MRIRRKDNKGQPLYQLQTIDDTPSMGIQINEDRLVKQEVLMDAYKTRNLSTIDGINNSEGQAYATFDN WLTLPVSTFKPEIIKLEMKPHSKTRRYIRITQSLADFIKTIDEALMIKPSDSIDDPLNMPNEIVCKNKLFGN ELKPRDGKMKIVSTGKIVTYEFESDSTPQWIQTLYVTQLKKQP (SEQ ID NO: 166)
[0104] In some embodiments the Cas9 protein can be N. lactamica Cas9 and may comprise or consist of the amino acid sequence:
MAAFKPNPMNYILGLDIGIASVGWAMVEVDEEENPIRLIDLGVRVFERAEVPKTGDSLAMARRLARSV RRLTRRRAHRLLRARRLLKREGVLQDADFDENGLVKSLPNTPWQLRAAALDRKLTCLEWSAVLLHLV KHRGYLSQRKNEGETADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYSHT FSRKDLQAELNLLFEKQKEFGNPHVSDGLKEDIETLLMAQRPALSGDAVQKMLGHCTFEPAEPKAAKN TYTAERFIWLTKLNNLRILEQGSERPLTDTERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLRYG KDNAEASTLMEMKAYHAISRALEKEGLKDKKSPLNLSTELQDEIGTAFSLFKTDKDITGRLKDRVQPEI LEALLKHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYGDHYCKKNAEEKIYLPPIPADEIRNPVV LRALSQARKVINCVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENRKDREKAAAKFREYFPNFVG EPKSKDILKLRLYEQQHGKCLYSGKEINLVRLNEKGYVEIDHALPFSRTWDDSFNNKVLVLGSENQNK GNQTPYEYFNGKDNSREWQEFKARVETSRFPRSKKQRILLQKFDEEGFKERNLNDTRYVNRFLCQFVA DHILLTGKGKRRVFASNGQITNLLRGFWGLRKVRTENDRHHALDAVVVACSTVAMQQKITRFVRYKE MNAFDGKTIDKETGEVLHQKAHFPQPWEFFAQEVMIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSSR PEAVHEYVTPLFVSRAPNRKMSGQGHMETVKSAKRLDEGISVLRVPLTQLKLKGLEKMVNREREPKL YDALKAQLETHKDDPAKAFAEPFYKYDKAGSRTQQVKAVRIEQVQKTGVWVRNHNGIADNATMVR VDVFEKGGKYYLVPIYSWQVAKGILPDRAVVAFKDEEDWTVMDDSFEFRFVLYANDLIKLTAKKNEF LGYFVSLNRATGAIDIRTHDTDSTKGKNGIFQSVGVKTALSFQKNQIDELGKEIRPCRLKKRPPVR (SEQ ID NO: 167)
[0105] In some embodiments the Cas9 protein can be N. meningitides Cas9 and may comprise or consist of the amino acid sequence:
MAAFKPNPINYILGLDIGIASVGWAMVEIDEDENPICLIDLGVRVFERAEVPKTGDSLAMARRLARSVR RLTRRRAHRLLRARRLLKREGVLQAADFDENGLIKSLPNTPWQLRAAALDRKLTPLEWSAVLLHLIKH RGYLSQRKNEGETADKELGALLKGVADNAHALQTGDFRTPAELALNKFEKESGHIRNQRGDYSHTFS RKDLQAELILLFEKQKEFGNPHVSGGLKEGIETLLMTQRPALSGDAVQKMLGHCTFEPAEPKAAKNTY TAERFIWLTKLNNLRILEQGSERPLTDTERATLMDEPYRKSKLTYAQARKLLGLEDTAFFKGLRYGKD NAEASTLMEMKAYHAISRALEKEGLKDKKSPLNLSPELQDEIGTAFSLFKTDEDITGRLKDRIQPEILEA LLKHISFDKFVQISLKALRRIVPLMEQGKRYDEACAEIYGDHYGKKNTEEKIYLPPIPADEIRNPVVLRA LSQARKVINGVVRRYGSPARIHIETAREVGKSFKDRKEIEKRQEENRKDREKAAAKFREYFPNFVGEPK SKDILKLRLYEQQHGKCLYSGKEINLGRLNEKGYVEIDHALPFSRTWDDSFNNKVLVLGSENQNKGNQ TPYEYFNGKDNSREWQEFKARVETSRFPRSKKQRILLQKFDEDGFKERNLNDTRYVNRFLCQFVADR MRLTGKGKKRVFASNGQITNLLRGFWGLRKVRAENDRHHALDAVVVACSTVAMQQKITRFVRYKEM NAFDGKTIDKETGEVLHQKTHFPQPWEFFAQEVMIRVFGKPDGKPEFEEADTPEKLRTLLAEKLSSRPE AVHEYVTPLFVSRAPNRKMSGQGHMETVKSAKRLDEGVSVLRVPLTQLKLKDLEKMVNREREPKLYE ALKARLEAHKDDPAKAFAEPFYKYDKAGNRTQQVKAVRVEQVQKTGVWVRNHNGIADNATMVRV DVFEKGDKYYLVPIYSWQVAKGILPDRAVVQGKDEEDWQLIDDSFNFKFSLHPNDLVEVITKKARMF GYFASCHRGTGNINIRIHDLDHKIGKNGILEGIGVKTALSFQKYQIDELGKEIRPCRLKKRPPVR(SEQ ID NO: 168)
[0106] In some embodiments the Cas9 protein can be B. longum Cas9 and may comprise or consist of the amino acid sequence:
MLSRQLLGASHLARPVSYSYNVQDNDVHCSYGERCFMRGKRYRIGIDVGLNSVGLAAVEVSDENSPV RLLNAQSVIHDGGVDPQKNKEAITRKNMSGVARRTRRMRRRKRERLHKLDMLLGKFGYPVIEPESLD KPFEEWHVRAELATRYIEDDELRRESISIALRHMARHRGWRNPYRQVDSLISDNPYSKQYGELKEKAK AYNDDATAAEEESTPAQLVVAMLDAGYAEAPRLRWRTGSKKPDAEGYLPVRLMQEDNANELKQIFR VQRVPADEWKPLFRSVFYAVSPKGSAEQRVGQDPLAPEQARALKASLAFQEYRIANVITNLRIKDASA ELRKLTVDEKQSIYDQLVSPSSEDITWSDLCDFLGFKRSQLKGVGSLTEDGEERISSRPPRLTSVQRIYES DNKIRKPLVAWWKSASDNEHEAMIRLLSNTVDIDKVREDVAYASAIEFIDGLDDDALTKLDSVDLPSG RAAYSVETLQKLTRQMLTTDDDLHEARKTLFNVTDSWRPPADPIGEPLGNPSVDRVLKNVNRYLMNC QQRWGNPVSVNIEHVRSSFSSVAFARKDKREYEKNNEKRSIFRSSLSEQLRADEQMEKVRESDLRRLE AIQRQNGQCLYCGRTITFRTCEMDHIVPRKGVGSTNTRTNFAAVCAECNRMKSNTPFAIWARSEDAQT RGVSLAEAKKRVTMFTFNPKSYAPREVKAFKQAVIARLQQTEDDAAIDNRSIESVAWMADELHRRID WYFNAKQYVNSASIDDAEAETMKTTVSVFQGRVTASARRAAGIEGKIHFIGQQSKTRLDRRHHAVDA SVIAMMNTAAAQTLMERESLRESQRLIGLMPGERSWKEYPYEGTSRYESFHLWLDNMDVLLELLNDA LDNDRIAVMQSQRYVLGNSIAHDATIHPLEKVPLGSAMSADLIRRASTPALWCALTRLPDYDEKEGLPE DSHREIRVHDTRYSADDEMGFFASQAAQIAVQEGSADIGSAIHHARVYRCWKTNAKGVRKYFYGMIR VFQTDLLRACHDDLFTVPLPPQSISMRYGEPRVVQALQSGNAQYLGSLVVGDEIEMDFSSLDVDGQIGE YLQFFSQFSGGNLAWKHWVVDGFFNQTQLRIRPRYLAAEGLAKAFSDDVVPDGVQKIVTKQGWLPPV NTASKTAVRIVRRNAFGEPRLSSAHHMPCSWQWRHE (SEQ ID NO: 169)
[0107] In some embodiments the Cas9 protein can be A. muciniphila Cas9 and may comprise or consist of the amino acid sequence:
MSRSLTFSFDIGYASIGWAVIASASHDDADPSVCGCGTVLFPKDDCQAFKRREYRRLRRNIRSRRVRIER IGRLLVQAQIITPEMKETSGHPAPFYLASEALKGHRTLAPIELWHVLRWYAHNRGYDNNASWSNSLSE DGGNGEDTERVKHAQDLMDKHGTATMAETICRELKLEEGKADAPMEVSTPAYKNLNTAFPRLIVEKE VRRILELSAPLIPGLTAEIIELIAQHHPLTTEQRGVLLQHGIKLARRYRGSLLFGQLIPRFDNRIISRCPVTW AQVYEAELKKGNSEQSARERAEKLSKVPTANCPEFYEYRMARILCNIRADGEPLSAEIRRELMNQARQ EGKLTKASLEKAISSRLGKETETNVSNYFTLHPDSEEALYLNPAVEVLQRSGIGQILSPSVYRIAANRLR RGKSVTPNYLLNLLKSRGESGEALEKKIEKESKKKEADYADTPLKPKYATGRAPYARTVLKKVVEEIL DGEDPTRPARGEAHPDGELKAHDGCLYCLLDTDSSVNQHQKERRLDTMTNNHLVRHRMLILDRLLKD LIQDFADGQKDRISRVCVEVGKELTTFSAMDSKKIQRELTLRQKSHTDAVNRLKRKLPGKALSANLIRK CRIAMDMNWTCPFTGATYGDHELENLELEHIVPHSFRQSNALSSLVLTWPGVNRMKGQRTGYDFVEQ EQENPVPDKPNLHICSLNNYRELVEKLDDKKGHEDDRRRKKKRKALLMVRGLSHKHQSQNHEAMKEI GMTEGMMTQSSHLMKLACKSIKTSLPDAHIDMIPGAVTAEVRKAWDVFGVFKELCPEAADPDSGKIL KENLRSLTHLHHALDACVLGLIPYIIPAHHNGLLRRVLAMRRIPEKLIPQVRPVANQRHYVLNDDGRM MLRDLSASLKENIREQLMEQRVIQHVPADMGGALLKETMQRVLSVDGSGEDAMVSLSKKKDGKKEK NQVKASKLVGVFPEGPSKLKALKAAIEIDGNYGVALDPKPVVIRHIKVFKRIMALKEQNGGKPVRILKK GMLIHLTSSKDPKHAGVWRIESIQDSKGGVKLDLQRAHCAVPKNKTHECNWREVDLISLLKKYQMKR YPTSYTGTPR (SEQ ID NO: 170)
[0108] In some embodiments the Cas9 protein can be O. laneus Cas9 and may comprise or consist of the amino acid sequence:
METTLGIDLGTNSIGLALVDQEEHQILYSGVRIFPEGINKDTIGLGEKEESRNATRRAKRQMRRQYFRK KLRKAKLLELLIAYDMCPLKPEDVRRWKNWDKQQKSTVRQFPDTPAFREWLKQNPYELRKQAVTED VTRPELGRILYQMIQRRGFLSSRKGKEEGKIFTGKDRMVGIDETRKNLQKQTLGAYLYDIAPKNGEKY RFRTERVRARYTLRDMYIREFEIIWQRQAGHLGLAHEQATRKKNIFLEGSATNVRNSKLITHLQAKYGR GHVLIEDTRITVTFQLPLKEVLGGKIEIEEEQLKFKSNESVLFWQRPLRSQKSLLSKCVFEGRNFYDPVH QKWIIAGPTPAPLSHPEFEEFRAYQFINNIIYGKNEHLTAIQREAVFELMCTESKDFNFEKIPKHLKLFEK FNFDDTTKVPACTTISQLRKLFPHPVWEEKREEIWHCFYFYDDNTLLFEKLQKDYALQTNDLEKIKKIR LSESYGNVSLKAIRRINPYLKKGYAYSTAVLLGGIRNSFGKRFEYFKEYEPEIEKAVCRILKEKNAEGEV IRKIKDYLVHNRFGFAKNDRAFQKLYHHSQAITTQAQKERLPETGNLRNPIVQQGLNELRRTVNKLLA TCREKYGPSFKFDHIHVEMGRELRSSKTEREKQSRQIRENEKKNEAAKVKLAEYGLKAYRDNIQKYLL YKEIEEKGGTVCCPYTGKTLNISHTLGSDNSVQIEHIIPYSISLDDSLANKTLCDATFNREKGELTPYDFY QKDPSPEKWGASSWEEIEDRAFRLLPYAKAQRFIRRKPQESNEFISRQLNDTRYISKKAVEYLSAICSDV KAFPGQLTAELRHLWGLNNILQSAPDITFPLPVSATENHREYYVITNEQNEVIRLFPKQGETPRTEKGEL LLTGEVERKVFRCKGMQEFQTDVSDGKYWRRIKLSSSVTWSPLFAPKPISADGQIVLKGRIEKGVFVCN QLKQKLKTGLPDGSYWISLPVISQTFKEGESVNNSKLTSQQVQLFGRVREGIFRCHNYQCPASGADGNF WCTLDTDTAQPAFTPIKNAPPGVGGGQIILTGDVDDKGIFHADDDLHYELPASLPKGKYYGIFTVESCD PTLIPIELSAPKTSKGENLIEGNIWVDEHTGEVRFDPKKNREDQRHHAIDAIVIALSSQSLFQRLSTYNAR RENKKRGLDSTEHFPSPWPGFAQDVRQSVVPLLVSYKQNPKTLCKISKTLYKDGKKIHSCGNAVRGQL HKETVYGQRTAPGATEKSYHIRKDIRELKTSKHIGKVVDITIRQMLLKHLQENYHIDITQEFNIPSNAFF KEGVYRIFLPNKHGEPVPIKKIRMKEELGNAERLKDNINQYVNPRNNHHVMIYQDADGNLKEEIVSFW SVIERQNQGQPIYQLPREGRNIVSILQINDTFLIGLKEEEPEVYRNDLSTLSKHLYRVQKLSGMYYTFRH HLASTLNNEREEFRIQSLEAWKRANPVKVQIDEIGRITFLNGPLC (SEQ ID NO: 171).
[0109] In some embodiments of the compositions of the disclosure, the sequence encoding the fRNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein. In some embodiments, the CRISPR Cas protein comprises a Type V CRISPR Cas protein. In some embodiments, the Type V CRISPR Cas protein comprises a Cpf1 protein. Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea. Exemplary Cpf1 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Francisella tularensis subsp. novicida, Acidaminococcus sp. BV3L6 and Lachnospiraceae bacterium sp. ND2006. Exemplary Cpf1 proteins of the disclosure may be nuclease inactivated.
[0110] Exemplary wild type Francisella tularensis subsp. Novicida Cpf1 (FnCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
1 MSIYQEFVNK YSLSKTLRFE LIPQGKTLEN IKARGLILDD EKRAKDYKKA KQIIDKYHQF 61 FIEEILSSVC ISEDLLQNYS DVYFKLKKSD DDNLQKDFKS AKDTIKKQIS EYIKDSEKFK 121 NLFNQNLIDA KKGQESDLIL WLKQSKDNGI ELFKANSDIT DIDEALEIIK SFKGWTTYFK 181 GFHENRKNVY SSNDIPTSII YRIVDDNLPK FLENKAKYES LKDKAPEAIN YEQIKKDLAE 241 ELTFDIDYKT SEVNQRVFSL DEVFEIANFN NYLNQSGITK FNTIIGGKFV NGENTKRKGI 301 NEYINLYSQQ INDKTLKKYK MSVLFKQILS DTESKSFVID KLEDDSDVVT TMQSFYEQIA 361 AFKTVEEKSI KETLSLLFDD LKAQKLDLSK IYFKNDKSLT DLSQQVFDDY SVIGTAVLEY 421 ITQQIAPKNL DNPSKKEQEL IAKKTEKAKY LSLETIKLAL EEFNKHRDID KQCRFEEILA 481 NFAAIPMIFD EIAQNKDNLA QISIKYQNQG KKDLLQASAE DDVKAIKDLL DQTNNLLHKL 541 KIFHISQSED KANILDKDEH FYLVFEECYF ELANIVPLYN KIRNYITQKP YSDEKFKLNF 601 ENSTLANGWD KNKEPDNTAI LFIKDDKYYL GVMNKKNNKI FDDKAIKENK GEGYKKIVYK 661 LLPGANKMLP KVFFSAKSIK FYNPSEDILR IRNHSTHTKN GSPQKGYEKF EFNIEDCRKF 721 IDFYKQSISK HPEWKDFGFR FSDTQRYNSI DEFYREVENQ GYKLTFENIS ESYIDSVVNQ 781 GKLYLFQIYN KDFSAYSKGR PNLHTLYWKA LFDERNLQDV VYKLNGEAEL FYRKQSIPKK 841 ITHPAKEAIA NKNKDNPKKE SVFEYDLIKD KRFTEDKFFF HCPITINFKS SGANKFNDEI 901 NLLLKEKAND VHILSIDRGE RHLAYYTLVD GKGNIIKQDT FNIIGNDRMK TNYHDKLAAI 961 EKDRDSARKD WKKINNIKEM KEGYLSQVVH EIAKLVIEYN AIVVFEDLNF GFKRGRFKVE 1021 KQVYQKLEKM LIEKLNYLVF KDNEFDKTGG VLRAYQLTAP FETFKKMGKQ TGIIYYVPAG 1081 FTSKICPVTG FVNQLYPKYE SVSKSQEFFS KFDKICYNLD KGYFEFSFDY KNFGDKAAKG 1141 KWTIASFGSR LINFRNSDKN HNWDTREVYP TKELEKLLKD YSIEYGHGEC IKAAICGESD 1201 KKFFAKLTSV LNTILQMRNS KTGTELDYLI SPVADVNGNF FDSRQAPKNM PQDADANGAY 1261 HIGLKGLMLL GRIKNNQEGK KLNLVIKNEE YFEFVQNRNN (SEQ ID NO: 172)
[0111] Exemplary wild type Lachnospiraceae bacterium sp. ND2006 Cpf1 (LbCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
1 AASKLEKFTN CYSLSKTLRF KAIPVGKTQE NIDNKRLLVE DEKRAEDYKG VKKLLDRYYL 61 SFINDVLHSI KLKNLNNYIS LFRKKTRTEK ENKELENLEI NLRKEIAKAF KGAAGYKSLF 121 KKDIIETILP EAADDKDEIA LVNSFNGFTT AFTGFFDNRE NMFSEEAKST SIAFRCINEN 181 LTRYISNMDI FEKVDAIFDK HEVQEIKEKI LNSDYDVEDF FEGEFFNFVL TQEGIDVYNA 241 IIGGFVTESG EKIKGLNEYI NLYNAKTKQA LPKFKPLYKQ VLSDRESLSF YGEGYTSDEE 301 VLEVFRNTLN KNSEIFSSIK KLEKLFKNFD EYSSAGIFVK NGPAISTISK DIFGEWNLIR 361 DKWNAEYDDI HLKKKAVVTE KYEDDRRKSF KKIGSFSLEQ LQEYADADLS VVEKLKEIII 421 QKVDEIYKVY GSSEKLFDAD FVLEKSLKKN DAVVAIMKDL LDSVKSFENY IKAFFGEGKE 481 TNRDESFYGD FVLAYDILLK VDHIYDAIRN YVTQKPYSKD KFKLYFQNPQ FMGGWDKDKE 541 TDYRATILRY GSKYYLAIMD KKYAKCLQKI DKDDVNGNYE KINYKLLPGP NKMLPKVFFS 601 KKWMAYYNPS EDIQKIYKNG TFKKGDMFNL NDCHKLIDFF KDSISRYPKW SNAYDFNFSE 661 TEKYKDIAGF YREVEEQGYK VSFESASKKE VDKLVEEGKL YMFQIYNKDF SDKSHGTPNL 721 HTMYFKLLFD ENNHGQIRLS GGAELFMRRA SLKKEELVVH PANSPIANKN PDNPKKTTTL 781 SYDVYKDKRF SEDQYELHIP IAINKCPKNI FKINTEVRVL LKHDDNPYVI GIDRGERNLL 841 YIVVVDGKGN IVEQYSLNEI INNFNGIRIK TDYHSLLDKK EKERFEARQN WTSIENIKEL 901 KAGYISQVVH KICELVEKYD AVIALEDLNS GFKNSRVKVE KQVYQKFEKM LIDKLNYMVD 961 KKSNPCATGG ALKGYQITNK FESFKSMSTQ NGFIFYIPAW LTSKIDPSTG FVNLLKTKYT 1021 SIADSKKFIS SFDRIMYVPE EDLFEFALDY KNFSRTDADY IKKWKLYSYG NRIRIFAAAK 1081 KNNVFAWEEV CLTSAYKELF NKYGINYQQG DIRALLCEQS DKAFYSSFMA LMSLMLQMRN 1141 SITGRTDVDF LISPVKNSDG IFYDSRNYEA QENAILPKNA DANGAYNIAR KVLWAIGQFK 1201 KAEDEKLDKV KIAISNKEWL EYAQTSVK (SEQ ID NO: 173)
[0112] Exemplary wild type Acidaminococcus sp. BV3L6 Cpf1 (AsCpf1) proteins of the disclosure may comprise or consist of the amino acid sequence:
1 MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT 61 YADQCLQLVQ LDWENLSAAI DSYRKEKTEE TRNALIEEQA TYRNAIHDYF IGRTDNLTDA 121 INKRHAEIYK GLFKAELFNG KVLKQLGTVT TTEHENALLR SFDKFTTYFS GFYENRKNVF 181 SAEDISTAIP HRIVQDNFPK FKENCHIFTR LITAVPSLRE HFENVKKAIG IFVSTSIEEV 241 FSFPFYNQLL TQTQIDLYNQ LLGGISREAG TEKIKGLNEV LNLAIQKNDE TAHIIASLPH 301 RFIPLFKQIL SDRNTLSFIL EEFKSDEEVI QSFCKYKTLL RNENVLETAE ALFNELNSID 361 LTHIFISHKK LETISSALCD HWDTLRNALY ERRISELTGK ITKSAKEKVQ RSLKHEDINL 421 QEIISAAGKE LSEAFKQKTS EILSHAHAAL DQPLPTTLKK QEEKEILKSQ LDSLLGLYHL 481 LDWFAVDESN EVDPEFSARL TGIKLEMEPS LSFYNKARNY ATKKPYSVEK FKLNFQMPTL 541 ASGWDVNKEK NNGAILFVKN GLYYLGIMPK QKGRYKALSF EPTEKTSEGF DKMYYDYFPD 601 AAKMIPKCST QLKAVTAHFQ THTTPILLSN NFIEPLEITK EIYDLNNPEK EPKKFQTAYA 661 KKTGDQKGYR EALCKWIDFT RDFLSKYTKT TSIDLSSLRP SSQYKDLGEY YAELNPLLYH 721 ISFQRIAEKE IMDAVETGKL YLFQIYNKDF AKGHHGKPNL HTLYWTGLFS PENLAKTSIK 781 LNGQAELFYR PKSRMKRMAH RLGEKMLNKK LKDQKTPIPD TLYQELYDYV NHRLSHDLSD 841 EARALLPNVI TKEVSHEIIK DRRFTSDKFF FHVPITLNYQ AANSPSKFNQ RVNAYLKEHP 901 ETPIIGIDRG ERNLIYITVI DSTGKILEQR SLNTIQQFDY QKKLDNREKE RVAARQAWSV 961 VGTIKDLKQG YLSQVIHEIV DLMIHYQAVV VLENLNFGFK SKRTGIAEKA VYQQFEKMLI 1021 DKLNCLVLKD YPAEKVGGVL NPYQLTDQFT SFAKMGTQSG FLFYVPAPYT SKIDPLTGFV 1081 DPFVWKTIKN HESRKHFLEG FDFLHYDVKT GDFILHFKMN RNLSFQRGLP GFMPAWDIVF 1141 EKNETQFDAK GTPFIAGKRI VPVIENHRFT GRYRDLYPAN ELIALLEEKG IVFRDGSNIL 1201 PKLLENDDSH AIDTMVALIR SVLQMRNSNA ATGEDYINSP VRDLNGVCFD SRFQNPEWPM 1261 DADANGAYHI ALKGQLLLNH LKESKDLKLQ NGISNQDWLA YIQELRN(SEQ ID NO: 174)
[0113] In some embodiments of the compositions of the disclosure, the sequence encoding the RNA binding protein comprises a sequence isolated or derived from a CRISPR Cas protein or RNA-binding portion thereof. In some embodiments, the CRISPR Cas protein comprises a Type VI CRISPR Cas protein. In some embodiments, the Type VI CRISPR Cas protein comprises a Cas13 protein. Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, a bacteria or an archaea. Exemplary Cas13 proteins of the disclosure may be isolated or derived from any species, including, but not limited to, Leptotrichia wadei, Listeria seeligeri serovar 1/2b (strain ATCC 35967 / DSM 20751 / CIP 100100 / SLCC 3954), Lachnospiraceae bacterium, Clostridium aminophilum DSM 10710, Carnobacterium gallinarum DSM 4847, Paludibacter propionicigenes WB4, Listeria weihenstephanensis FSL R9-0317, Listeria
weihenstephanensis FSL R9-0317, bacterium FSL M6-0635 (Listeria newyorkensis), Leptotrichia wadei F0279, Rhodobacter capsulatus SB 1003, Rhodobacter capsulatus R121, Rhodobacter capsulatus DE442 and Corynebacterium ulcerans. Exemplary Cas13 proteins of the disclosure may be DNA nuclease inactivated. Exemplary Cas13 proteins of the disclosure include, but are not limited to, Cas13a, Cas13b, Cas13c, Cas13d and orthologs thereof. Exemplary Cas13b proteins of the disclosure include, but are not limited to, subtypes 1 and 2 referred to herein as Csx27 and Csx28, respectively.
[0114] Exemplary Cas13a proteins include, but are not limited to:
Figure imgf000055_0001
Figure imgf000056_0001
[0115] Exemplary wild type Cas13a proteins of the disclosure may comprise or consist of the amino acid sequence:
1 MGNLFGHKRW YEVRDKKDFK IKRKVKVKRN YDGNKYILNI NENNNKEKID NNKFIRKYIN 61 YKKNDNILKE FTRKFHAGNI LFKLKGKEGI IRIENNDDFL ETEEVVLYIE AYGKSEKLKA 121 LGITKKKIID EAIRQGITKD DKKIEIKRQE NEEEIEIDIR DEYTNKTLND CSIILRIIEN 181 DELETKKSIY EIFKNINMSL YKIIEKIIEN ETEKVFENRY YEEHLREKLL KDDKIDVILT 241 NFMEIREKIK SNLEILGFVK FYLNVGGDKK KSKNKKMLVE KILNINVDLT VEDIADFVIK 301 ELEFWNITKR IEKVKKVNNE FLEKRRNRTY IKSYVLLDKH EKFKIERENK KDKIVKFFVE 361 NIKNNSIKEK IEKILAEFKI DELIKKLEKE LKKGNCDTEI FGIFKKHYKV NFDSKKFSKK 421 SDEEKELYKI IYRYLKGRIE KILVNEQKVR LKKMEKIEIE KILNESILSE KILKRVKQYT 481 LEHIMYLGKL RHNDIDMTTV NTDDFSRLHA KEELDLELIT FFASTNMELN KIFSRENINN 541 DENIDFFGGD REKNYVLDKK ILNSKIKIIR DLDFIDNKNN ITNNFIRKFT KIGTNERNRI 601 LHAISKERDL QGTQDDYNKV INIIQNLKIS DEEVSKALNL DVVFKDKKNI ITKINDIKIS 661 EENNNDIKYL PSFSKVLPEI LNLYRNNPKN EPFDTIETEK IVLNALIYVN KELYKKLILE 721 DDLEENESKN IFLQELKKTL GNIDEIDENI IENYYKNAQI SASKGNNKAI KKYQKKVIEC 781 YIGYLRKNYE ELFDFSDFKM NIQEIKKQIK DINDNKTYER ITVKTSDKTI VINDDFEYII 841 SIFALLNSNA VINKIRNRFF ATSVWLNTSE YQNIIDILDE IMQLNTLRNE CITENWNLNL 901 EEFIQKMKEI EKDFDDFKIQ TKKEIFNNYY EDIKNNILTE FKDDINGCDV LEKKLEKIVI 961 FDDETKFEID KKSNILQDEQ RKLSNINKKD LKKKVDQYIK DKDQEIKSKI LCRIIFNSDF 1021 LKKYKKEIDN LIEDMESENE NKFQEIYYPK ERKNELYIYK KNLFLNIGNP NFDKIYGLIS 1081 NDIKMADAKF LFNIDGKNIR KNKISEIDAI LKNLNDKLNG YSKEYKEKYI KKLKENDDFF 1141 AKNIQNKNYK SFEKDYNRVS EYKKIRDLVE FNYLNKIESY LIDINWKLAI QMARFERDMH 1201 YIVNGLRELG IIKLSGYNTG ISRAYPKRNG SDGFYTTTAY YKFFDEESYK KFEKICYGFG 1261 IDLSENSEIN KPENESIRNY ISHFYIVRNP FADYSIAEQI DRVSNLLSYS TRYNNSTYAS 1321 VFEVFKKDVN LDYDELKKKF KLIGNNDILE RLMKPKKVSV LELESYNSDY IKNLIIELLT 1381 KIENTNDTL (SEQ ID NO: 190) [0116] Exemplary Cas13b proteins include, but are not limited to:
Figure imgf000057_0001
Figure imgf000058_0001
[0117] Exemplary wild type Bergeyella zoohelcum ATCC 43767 Cas13b (BzCas13b) proteins of the disclosure may comprise or consist of the amino acid sequence:
1 menktslgnn iyynpfkpqd ksyfagyfna amentdsvfr elgkrlkgke ytsenffdai 61 fkenislvey eryvkllsdy fpmarlldkk evpikerken fkknfkgiik avrdlrnfyt 121 hkehgeveit deifgvldem lkstvltvkk kkvktdktke ilkksiekql dilcqkkley 181 lrdtarkiee krrnqrerge kelvapfkys dkrddliaai yndafdvyid kkkdslkess 241 kakyntksdp qqeegdlkip iskngvvfll slfltkqeih afkskiagfk atvideatvs 301 eatvshgkns icfmatheif shlaykklkr kvrtaeinyg eaenaeqlsv yaketlmmqm 361 ldelskvpdv vyqnlsedvq ktfiedwney lkenngdvgt meeeqvihpv irkryedkfn 421 yfairfldef aqfptlrfqv hlgnylhdsr pkenlisdrr ikekitvfgr lselehkkal 481 fikntetned rehyweifpn pnydfpkeni svndkdfpia gsildrekqp vagkigikvk 541 llnqqyvsev dkavkahqlk qrkaskpsiq niieeivpin esnpkeaivf ggqptaylsm 601 ndihsilyef fdkwekkkek lekkgekelr keigkelekk ivgkiqaqiq qiidkdtnak 661 ilkpyqdgns taidkeklik dlkqeqnilq klkdeqtvre keyndfiayq dknreinkvr 721 drnhkqylkd nlkrkypeap arkevlyyre kgkvavwlan dikrfmptdf knewkgeqhs 781 llqkslayye qckeelknll pekvfqhlpf klggyfqqky lyqfytcyld krleyisglv 841 qqaenfksen kvfkkvenec fkflkkqnyt hkeldarvqs ilgypifler gfmdekptii 901 kgktfkgnea lfadwfryyk eyqnfqtfyd tenyplvele kkqadrkrkt kiyqqkkndv 961 ftllmakhif ksvfkqdsid qfsledlyqs reerlgnqer arqtgerntn yiwnktvdlk 1021 lcdgkitven vklknvgdfi kyeydqrvqa flkyeeniew qaflikeske eenypyvver 1081 eieqyekvrr eellkevhli eeyilekvkd keilkkgdnq nfkyyilngl lkqlknedve 1141 sykvfnlnte pedvninqlk qeatdleqka fvltyirnkf ahnqlpkkef wdycqekygk 1201 iekektyaey faevfkkeke alik. (SEQ ID NO: 191)
[0118] In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a
CasRX/Cas13d protein. CasRX/Cas13d is an effector of the type VI-D CRISPR-Cas systems. In some embodiments, the CasRX/Cas13d protein is an RNA-guided RNA endonuclease enzyme that can cut or bind RNA. In some embodiments, the CasRX/Cas13d protein can include one or more higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domains. In some embodiments, the CasRX/Cas13d protein can include either a wild-type or mutated HEPN domain. In some embodiments, the CasRX/Cas13d protein includes a mutated HEPN domain that cannot cut RNA but can process guide RNA. In some embodiments, the CasRX/Cas13d protein does not require a protospacer flanking sequence. Also see WO Publication No. WO2019/040664 & US2019/0062724, which is incorporated herein by reference in its entirety, for further examples and sequences of CasRX/Cas13d protein, without limitation, specific reference is made to
[0119] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence:
CasRX/Cas13d Gut_metagenome_contig6049000251:
LYLTSFGKGN AAVIEQKIEP ENGYRVTGMQ ITPSITVNKA TDESVRFRVK RKIAQKDEFI 60
ADNPMHEGRH RIEPSAGSDM LGLKTKLEKY YFGKEFDDNL HIQIIYNILD IEKILAVYST 120
NITA 124
(SEQ ID NO: 54). [0120] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig546000275:
MDSYRPKLYK LIDFCIFKHY HEYTEISEKN VDTLRAAVSE EQKESFYADE AKRLWGIFDK 60 QFLGFCKKIN VWVNGSHEKE ILGYIDKDAY RKKSDVSYFS KFLYAMSFFL DGKEINDLLT 120 TLINKFDNIA SFISTAKELD AEIDRILEKK LDPVTGKPLK GKNSFRNFIA NNVIENKRFI 180 YVIKFCNPKN VLKLVKNTKV TEFVLKRMPE SQIDRYYSSC IDTEKNPSVD KKISDLAEMI 240 KKIAFDDFRN VRQKTRTREE SLEKERFKAV IGLYLTVVYL LIKNLVNVNS RYVMAFHCLE 300 RDAKLYGINI GKNYIELTED LCRENENSRS AYLARNKRLR DCVKQNIDNA KNMKSKEK 358 (SEQ ID NO: 57).
[0121] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4114000374:
DTKINPQTWL YQLENTPDLD NEYRDTLDHF FDERFNEINE HFVTQNATNL CIMKEVFPDE 60 DFKSIADLYY DFIVVKSYKN IGFSIKKLRE KMLELPEAKR VTSTEMDSVR SKLYKLIDFC 120 IFKHYHEKPE TVEMIVSMLR AYTSEDMKE 149 (SEQ ID NO: 61).
[0122] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig721000619:
KEGSTMAKNE KKKSTAKALG LKSSFVVNND IYMTSFGKGN KAVLEKKITE NTIENKSDTT 60 YFDVINRDPK GFTLEGRRIA DMTAFSNDPK YHVNVVNGKF LEDQLGARSE LEKKVFGRTF 120 DDNVHIQLIH NILDIEKIMA QYVSDIVYLL HNTIKRDMND DIMGYISIRN SFDDFCHPER 180 IPDRKAKDNL QKQHDIFFDE ILKCGRLAYF GNAFFEDGSD NKEIAKLKRY KEIYHIIALM 240 GSLRQSYFHG ENSDKNFQGP TWAYTLESNL TGKYKEFKDT LDKTFDERYE MISKDFGSTN 300 MVNLQILEEL LKMLYGNVSP 320 (SEQ ID NO: 67).
[0123] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2002000411:
EKQNKAKYQA IISLYLMVMY QIVKNMIYVN SRYVIAFHCL ERDSNQLLGR FNSRDASMYN 60 KLTQKFITDK YLNDGAQGCS KKVGNYLSHN ITCCSDELRK EYRNQVDHFA VVRMIGKYAA 120 DIGKFSTWFE LYHYVMQRII FDKRNPLSET ERTYKQLIAK HHTYCKDLVK ALNTPFGYNL 180 ARYKNLSIGE LFDRNNYNAK TKET 204 (SEQ ID NO: 69).
[0124] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig13552000311:
LIDFLIYDLY YNRKPARIEE IVDKLRESVN DEEKESIYSA ETKYVYEALG KVLVRSLKKY 60 LNGATIRDLK NRYDAKTANR IWDISEHSKS GHVNCFCKLI YMMTLMLDGK EINDLLTTLV 120 NKFDNIASFI DVMDELGLEH SFTDNYKMFA DSKAICLDLQ FINSFARMSK IDDEKSKRQL 180 FRDALVVLDI GDKNEDWIEK YLTSDIFKRD ENGNKIDGEK RDFRNFIANN VIKSARFKYL 240 VKYSSADGMI KLKKNEKLIS FVLEQLPETQ IDRYYESCGL DCAVADRKVR IEKLTGLIRD 300 MRFDNFRGVN YSNDACKKDK QAKAKYQAII SLYLMVLYQI VKNMIYVNSR YVIAFHCLER 360 DLLFFNIELD NSYQYSNCNE LTEKFIKDKY MKEGALGFNM KAGRYLTKNI GNCSNELRKI 420 YRNQVDHFAV VRKIGNYAAD IASVGSWFE 449 (SEQ ID NO: 71).
[0125] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig10037000527:
YMDQNFANSD AWAIHVYRNK IQHLDAVRHA DMYIGDIREF HSWFELYHYI IQRRIIDQYA 60 YESTPGSSRD GSAIIDEERL NPATRRYFRL ITTYKT 96 (SEQ ID NO: 72).
[0126] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig238000329:
RYDKDRSKIY TMMDFVIYRY YIDNNNDSID FINKLRSSID EKSKEKLYNE EANRLWNKLK 60 EYMLYIKEFN GKLASRTPDR DGNISEFVES LPKIHRLLPR GQKISNFSKL MYLLTMFLDG 120 KEINDLLTTL INKFENIQGF LDIMPEINVN AKFEPEYVFF NKSHEIAGEL KLIKGFAQMG 180 EPAATLKLEM TADAIKILGT EKEDAELIKL AESLFKDENG KLLGNKQHGM RNFIGNNVIK 240 SKRFHYLIRY GDPAHLHKIA TNKNVVRFVL GRIADMQKKQ GQKGKNQIDR YYEVCVGNKD 300 IKKTIEEKID ALTDIIVNMN YDQFEKKKAV IENQNRGKTF EEKNKYKRDN AEREKFKKII 360 SLYLTVIYHI LKNIVNVNSR YILGFHCLER DKQLYIEKYN KDKLDGFVAL TKFCLGDEER 420 YEDLKAKAQA SIQALETANP KLYAKYMNYS DEEKKEEFKK QLNRERVKNA RNAYLKNIKN 480 YIMIRLQLRD QTDSSGYLCG EFRDKVAHLE VARHAHEYI 519 (SEQ ID NO: 73).
[0127] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig2643000492:
NGEIVSLAEK EAFSAKIADK NIGCKIENKQ FRHPKGYDVI ADNPIYKGSP RQDMLGLKET 60 LEKRYFSPSD SIDNVRVQVA HNILDIEKIL AEYITNAVYS FDNIAGFGKD IIGDDFSPVY 120 TYDKFEKSDR YEYFKNLLNN SRLGYYGQAF FECDDSKENK KKKDAIKCYN IIALLSGLRH 180 W 181 (SEQ ID NO: 84).
[0128] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig874000057:
MSKNKESYAK GMGLKSALVS GSKVYMTSFE GGNDAKLEKV VENSEIVSLA EKESFSAEIF 60 KKNIGCKIEN KKFKHPKRYD VIADNPLYKG SVRQDMLGLK ETLEKRYFNS ADGTDNVCIQ 120 VIHNILDIEK ILAEYITNAV YSFDNIAGFG EDIIGMGGFK PIYTYKQFKE PDKYNKKFDD 180 ILNNSRLGYY GKAFFEKNDL KHNPNKKKRD KNPYILKYDN ECYYIIALLS GLRHWNIHSH 240 AKDDLVSYRW LYNLDSILNR EYISTLNYLY DDIADELTES FSKNSSANVN YIAETLNIDP 300 SEFAQQYFRF SIMKEQKNMG FNVSKLREIM LDRKELSDIR DNHRVFDSIR SKLYTMMDFV 360 IYRYYIEEAA KTEAENRNLP ENEKKISEKD FFVINLRGSF DENQKEKLYI EEAKRLWEKL 420 KDIMLKIKEF RGEKVKEYKK 440 (SEQ ID NO: 85).
[0129] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig4781000489:
LDKQLDYEYI RTLNYMFNDI ADELTRTFSK NSAANVNYIA ETLNIDPNKF AEQYFRFSIM 60 KEQKNLGFNL TKLRESMLDR RELSDIRDNH NVFDSIRPKL YTMMDFVIYK HYIDEAKKTE 120 AENKSLPDDR KNLSEKD 137 (SEQ ID NO: 86).
[0130] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig12144000352:
RMGEPVANTK RVMMIDAVKI LGTDLSDDEL KEMADSFFKD SDGNLLKKGK HGMRNFITNN 60 VIKNKRFHYL IRYGDPAHLH EIAKNEA 87 (SEQ ID NO: 87).
[0131] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig5590000448:
VHNNEEKDLI KYTWLYNLDK YLDAEYITTL NYMYNDIGDE LTDSFSKNSA ANINYIAETL 60 GIDPKTFAEQ YFRFSIMKEQ KNLGFNLTKL REVMLDRKDM SEIRENHNDF DSIRAKVYTM 120 MDFVIYRYYI EEAAKVNAAN KSLPDNEKSL SEKDIFVISL RGSFNEDQKD RLYYDEAQRL 180 WSKVGKLMLK IKKFRGKDTR KYKNMGTPRI RRLIPEGRDI STFSKLMYAL TMFLDGKEIN 240 DLLTTLINKF DNIQSFLKVM PLIGVNAKFA EEYSFFNNSE KIADELRLIK SFARMGEPVA 300 DARRAMYIDA IRILGTDLSD DELKALADSF SLDENGNKLG KGKHGMRNFI INNVITNKRF 360 HYLIRYGNPV HLHEIAKNEA VVKFVLGRIA DIQKKQGQNG KNQIDRYYET CIGK 414 (SEQ ID NO: 88).
[0132] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig525000349:
MSKKENRKSY VKGLGLKSTL VSDSKVYLTT FADGSNAKLE KCVENNKIIC ISNDKEAFAA 60 SIANKNVGYK IKNDEKFRHP KGYDIISNNP LLHNNSVQQD MLGLKNVLEK RYFGKSSGGD 120 NNLCIQIIHN IIDIEKILSE YIPNVVYAFN NIAGFKDEHN NIIDIIGTQT YNSSYTYADF 180 SKDKSDKKYI EFQKLLKNKR LGYWGKAFFT GQGNNAKVRQ ENQCFHIIAL LISLRNWATH 240 SNELDKHTKR TWLYKLDDTN ILNAEYVKTL NYLYDTIADE LTKSFSKNGA VNVNYLAKKY 300 NIKDDLPGFS EQYFRFSIMK EQKNLGFNIS KLRENMLDFK DMSVI 345 (SEQ ID NO: 89).
[0133] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7229000302:
KKISSLTKFC LGESDEKKLK ALAKKSLEEL KTTNSKLYEN YIKYSDERKA EEAKRQINRE 60 RAKTAMNAHL RNTKWNDIMY GQLKDLADSK SRICSEFRNK AAHLEVARYA HMYINDISEV 120 KSYFRLYHYI MQRRIIDVIE NNPKAKYEGK VKVYFEDVKK NKKYNKNLLK LMCVPFGYCI 180 PRFKNLSIEQ MFDMNETDNS DKKKEK 206 (SEQ ID NO: 90).
[0134] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig3227000343:
IGDISEVNSY FQLYHYIMQR ILIDKIGSKT TGKAKEYFDS VIVNKKYDDR LLKLLCSPLG 60 YCLTRYKDLS IEALFDMNEA AKYDKLNKER KNKKK 95 (SEQ ID NO: 91).
[0135] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Gut_metagenome_contig7030000469:
SIRSKLYTMM DFVIYRYYIE ESAKAAAENK PSESDSFVIR LRGSFNENQK EELYIEEAER 60
LWKKFGEIML KIKEFRGEKV KEYKKEVPRI ERILPHGKDI SAFSKLMYML SMFLD 115 (SEQ ID NO: 92).
[0136] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d gut_metagenome_P17E0k2120140920, c87000043:
MYFSKMIYML TYFLDGKEIN DLLTTLISKF DNIKEFLKIM KSSAVDVECE LTAGYKLFND 60
SQRITNELFI VKNIASMRKP AASAKLTMFR DALTILGIDD KITDDRISEI LKLKEKGKGI 120
HGLRNFITNN VIESSRFVYL IKYANAQKIR EVAKNEKVVM FVLGGIPDTQ IERYYKSCVE 180
FPDMNSSLEA KRSELARMIK NISFDDFKNV KQQAKGRENV AKERAKAVIG LYLT 234
(SEQ ID NO: 93).
[0137] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OBVH01003037.1, human gut metagenome sequence (also found in WGS contigs emb|OBXZ01000094.1| and emb|OBJF01000033.1|):
MAKKKRITAK ERKQNHRELL MKKADSNAEK EKAKKPVVEN KPDTAISKDN TPKPNKEIKK 60
SKAKLAGVKW VIKANDDVAY ISSFGKGNNS VLEKRIMGDV SSNVNKDSHM YVNPKYTKKN 120
YEIKNGFSSG SSLVTYPNKP DKNSGMDALC LKPYFEKDFF GHIFTDNMHI QAIYNIFDIE 180
KILAKHITNI IYTVNSFDRN YNQSGNDTIG FGLNYRVPYS EYGGGKDSNG EPKNQSKWEK 240
RDNFIKFYNE SKPHLGYYEN IFYDHGEPIS EEKFYNYLNI LNFIRNNTFH YKDDDIELYS 300
ENYSEEFVFI NCLNKFVKNK FKNVNKNFIS NEKNNLYIIL NAYGKDTENV EVVKKYSKEL 360
YKLSVLKTNK NLGVNVKKLR ESAIEYGYCP LPYDKEKEVA KLSSVKHKLY KTYDFVITHY 420
LNSNDKLLLE IVETLRLSKN DDEKENVYKK YAEKLFKADD VINPIKAISK LFARKGNKLF 480
KEKIIIKKEY IEDVSIDKNI YDFTKVIFFM TCFLDGKEIN DLLTNIISKL QVIEDHNNVI 540
KFISNNKDAV YKDYSDKYAI FRNAGKIATE LEAIKSIARM ENKIENAPQE PLLKDALLSL 600
GVSDDTKVLE NTYNKYFDSK EKTDKQSQKV STFLMNNVIN NNRFKYVIKY INPADINGLA 660
KNRYLVKFVL SKIPEEQIDS YYKLFSNEEE PGCEEKIKLL TKKISKLNFQ TLFENNKIPN 720
VEKEKKKAII TLYFTIVYIL VKNLVNINGL YTLALYFVER DGYFYKDICG KKDKKKSYND 780
VDYLLLPEIF SGSKYREETK NLKLPKEKDR DIMKKYLPND KDREKYNKFF TAYRNNIVHL 840
NIIAKLSELT KNIDKDINSY FDIYHYCTQR VMFNYCKEKN DVVLAKMKDL AHIKSDCNEF 900
SSKHTYPFSS AVLRFMNLPF AYNVPRFKNL SYKKFFDKQ 939
(SEQ ID NO: 94).
[0138] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg|DJXD01000002.1| (uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome):
MKKQKSKKTV SKTSGLKEAL SVQGTVIMTS FGKGNMANLS YKIPSSQKPQ NLNSSAGLKN 60
VEVSGKKIKF QGRHPKIATT DNPLFKPQPG MDLLCLKDKL EMHYFGKTFD DNIHIQLIYQ 120
ILDIEKILAV HVNNIVFTLD NVLHPQKEEL TEDFIGAGGW RINLDYQTLR GQTNKYDRFK 180
NYIKRKELLY FGEAFYHENE RRYEEDIFAI LTLLSALRQF CFHSDLSSDE SDHVNSFWLY 240
QLEDQLSDEF KETLSILWEE VTERIDSEFL KTNTVNLHIL CHVFPKESKE TIVRAYYEFL 300 IKKSFKNMGF SIKKLREIML EQSDLKSFKE DKYNSVRAKL YKLFDFIITY YYDHHAFEKE 360
ALVSSLRSSL TEENKEEIYI KTARTLASAL GADFKKAAAD VNAKNIRDYQ KKANDYRISF 420
EDIKIGNTGI GYFSELIYML TLLLDGKEIN DLLTTLINKF DNIISFIDIL KKLNLEFKFK 480
PEYADFFNMT NCRYTLEELR VINSIARMQK PSADARKIMY RDALRILGMD NRPDEEIDRE 540
LERTMPVGAD GKFIKGKQGF RNFIASNVIE SSRFHYLVRY NNPHKTRTLV KNPNVVKFVL 600
EGIPETQIKR YFDVCKGQEI PPTSDKSAQI DVLARIISSV DYKIFEDVPQ SAKINKDDPS 660
RNFSDALKKQ RYQAIVSLYL TVMYLITKNL VYVNSRYVIA FHCLERDAFL HGVTLPKMNK 720
KIVYSQLTTH LLTDKNYTTY GHLKNQKGHR KWYVLVKNNL QNSDITAVSS FRNIVAHISV 780
VRNSNEYISG IGELHSYFEL YHYLVQSMIA KNNWYDTSHQ PKTAEYLNNL KKHHTYCKDF 840
VKAYCIPFGY VVPRYKNLTI NELFDRNNPN PEPKEEV 877
(SEQ ID NO: 95).
[0139] An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig tpg|DJXD01000002.1| (uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome) (SEQ ID NO: 95) comprises or consists of the nucleic acid sequence:
CasRX/Cas13d DR:
caactacaac cccgtaaaaa tacggggttc tgaaac 36
[0140] (SEQ ID NO: 96).
[0141] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OGZC01000639.1 (human gut metagenome assembly):
MKKKNIRATR EALKAQKIKK SQENEALKKQ KLAEEAAQKR REELEKKNLA QWEETSAEGR 60
RSRVKAVGVK SVFVVGDDLY LATFGNGNET VLEKKITPDG KITTFPEEET FTAKLKFAQT 120
EPTVATSIGI SNGRIVLPEI SVDNPLHTTM QKNTIKRSAG EDILQLKDVL ENRYFDRSFN 180
DDLHIRLIYN ILDIEKILAE YTTNAVFAID NVSGCSDDFL SNFSTRNQWD EFQNPEQHRE 240
HFGNKDNVIC SVKKQQDLFF NFFKNNRIGY FGKAFFHAES ERKIVKKTEK EVYHILTLIG 300
SLRQWITHST EGGISRLWLY QLEDALSREY QETMNNCYNS TIYGLQKDFE KTNAPNLNFL 360
AEILGKNASE LAEPYFRFII TKEYKNLGFS IKTLREMLLD QPDLQEIREN HNVYDSIRSK 420
LYKMIDFVLV YAYSNERKSK ADALASNLRS AITEDAKKRI YQNEADQLWT SYQELFKRIR 480
GFKGAQVKEY SSKNMPIPIQ KQIQNILKPA EQVTYFTKLM YLLTMFLDGK EINDLLTTLI 540
NKFDNISSLL KTMEQLELQT TFKEDYTFFQ QSSRLCKEIT QLKSFARMGN PISNLKEVMM 600
VDAIQILGTE KSEQELQSMA CFFFRDKNGK KLNTGEHGMR NFIGNNVISN TRFQYLIRYG 660
NPQKLHTLSQ NETVVRFVLS RIAKNQRVQG MNGKNQIDRY YETCGGTNSW SVSEEEKINF 720
LCKILTNMSY DQFQDVKQSG AEITAEEKRK KERYKAIISL YLTVLYQLIK NLVNINARYI 780
IAFHCLERDA ILYSSKFNTS INLKKRYTAL TEMILGYETD EKARRKDTRT VYEKAEAAKN 840
RHLKNVKWNC KTRENLENAD KNAIVAFRNI VAHLWIIRDA DRFITGMGAM KRYFDCYHYL 900
LQRELGYILE KSNQGSEYTK KSLEKVQQYH SYCKDFLHML CLPFAYCIPR YKNLSIAELF 960
DRHEPEAEPK EEASSVNNSQ FITT 984
(SEQ ID NO: 97).
[0142] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OHBM01000764.1 (human gut metagenome assembly):
XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX 60 XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX 120 XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX 180 XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXXXXXXXXX XXHPLQKRYR YLTSTNLKSF 240 ETYKNNLVNK KKFDLDRVKK IPQLAYFGSA FYNTPEDTSA KITKTKIKSN EEIYYTFMLL 300 STARNFSAHY LDRNRAKSSD AEDFDGTSVI MYNLDNEELY KKLYNKKVHM ALTGMKKVLD 360 ANFNKKVEHL NNSFIKNSAK DFVILCEVLG IKSRDEKTKF VKDYYDFVVR KNYKHLGFSV 420 KELRELLFAN HDSNKYIKEF DKISNKKFDS VRSRLNRLAD YIIYDYYNKN NAKVSDLVKY 480 LRAAADDEQK KKIYLNESIN LVKSGILERI KKILPKLNGK IIGNMQPDST ITASMLHNTG 540 KDWHPISENA HYFTKWIYTL TLFMDGKEIN DLVTTLINKF DNIASFIEVL KSQSVCTHFS 600 EERKMFIDSA EICSELSAMN SFARMEAPGA SSKRAMFVEA ARILGDNRSK EELEEYFDTL 660 FDKSASKKEK GFRNFIRNNV VDSNRFKYLT RYTDTSSVKA FSNNKALVKF AIKDIPQEQI 720 LRYYNSCFGA SERYYNDGMS DKLVEAIGKI NLMQFNGVIQ QADRNMLPEE KKKANAQKEK 780 YKSIIRLYLT VCYLFFKNLV YVNSRYYSAF YNLEKDRSLF EINGELKPTG KFDEGHYTGL 840 VKLFIDNGWI NPRASAYLTV NLANSDETAI RTFRNTAEHL EALRNADKYL NDLKQFDSYF 900 EIYHYITQRN IKEKCEMLKE QTVKYNNDLL KYHGYSKDFV KALCVPFGYN LPRFKNLSID 960 ALFDKNDKRE KLKKGFED 978 (SEQ ID NO: 98).
[0143] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OHCP01000044.1 (human gut metagenome assembly):
MAKKITAKQK REEKERLNKQ KWAKNDSVII VPETKEEIKT GEIQDNNRKR SRQKSQAKAM 60 GLKAVLSFDN KIAIASFVSS KNAKSSHIER ITDKEGTTIS VNSKMFESSV NKRDINIEKR 120 ITIEEPQQDG TIKKEEKGVK STTCNPYFKV GGKDYIGIKE IAEEHFFGRA FPNENLRVQI 180 AYNIFDVQKI LGTFVNNIIY SFYNLSRDEV QSDNDVIGML YSISDYDRQK ETETFLQAKS 240 LLKQTEAYYA YFDDVFKKNK KPDKNKEGDN SKQYQENLRH NFNILRVLSF LRQICMHAEV 300 HVSDDEGCTR TQNYTDSLEA LFNISKAFGK KMPELKTLID NIYSKGINAI NDEFVKNGKN 360 NLYILSKVYP NEKREVLLRE YYNFVVCKEG SNIGISTRKL KETMIAQNMP SLKEENTYRN 420 KLYTVMNFIL VRELKNCATI REQMIKELRA NMDEEEGRDR IYSKYAKEIY LYVKDKLKLM 480 LNVFKEEAEG IIIPGKEDPV KFSHGKLDKK EIESFCLTTK NTEDITKVIY FLCKFLDGKE 540 INELCCAMMN KLDGISDLIE TAKQCGEDVE FVDQFKCLSK CATMSNQIRI VKNISRMKKE 600 MTIDNDTIFL DALELLGRKI EKYQKDKNGD YVKDEKGKKV YTKDYNNFQD MFFEGKNHRV 660 RNFVSNNVIK SKWFSYVVRY NKPAECQALM RNSKLVKFAL DELPDSQIEK YYISVFGEKS 720 SSSNEEMRRE LLKKLCDFSV RGFLDEIVLL SEDEMKQKDK FSEKEKKKSL IRLYLTIVYL 780 ITKSMVKINT RFSIACATYE RDYILLCQSE KAERAWEKGA TAFALTRKFL NHDKPTFEQY 840 YTREREISAM PQEKRKELRK ENDQLLKKTH YSKHAYCYIV DNVNNLTGAV ANDNGRGLPC 900 LSEKNDNANL FLEMRNKIVH LNVVHDMVKY INEIKNITSY YAFFCYVLQR MIIGNNSNEQ 960 NKFKAKYSKT LQEFGTYSKD LMWVLNLPFA YNLPRYKNLS NEQLFYDEEE RMEKIVGRKN 1020 DSR 1023 (SEQ ID NO: 99).
[0144] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OGDF01008514.1| (human gut metagenome assembly):
MTETKPKRED IAKTPAAKSR SKAAGLKSTF AVNGSVLLTS FGRGNDAVPE KLITEKAVSE 60 INTVKPRFSV EKPATSYSSS FGIKSHISAT ADNPLAGRAP VGEDAIHAKE VLEQRVFGKT 120 FSDDNIHIQL IYNILDIRKI LSTYANNVVF TINSMRRLDE YDREQDYLGY LYTGNSYERL 180 LDIADKYAVD GEDWRNTAAG ISNDFEKKQF QTINGFWDLL DMIEPYMCYF SEAFFCETTV 240 KDPDSGRIVP CLEQRSDGDI YNILRILSIV RQTCMHDNAS MRTVMFTLGQ NSVRDRKNGF 300 DELAELLDYL YDEKIDIVNR DFLRNQKNNI ELLSRIYGSS ADSPERDRLV QNFYDFRVLS 360 QDKNLGFSIK KLREKLLDSP ALSVVRSKKY DTMRSKIYSL IDFMIYRKFS ENHVAVDDFV 420 EELRSLLTED EKESAYSRWA ETLINDGFAQ EILVKLLPQT DPAVIGKIKG KKLLNDSIAG 480 IKLKKDASFF TKIINVLCMF QDGKEINELV SSLVNKFANI QSFVDVMRSQ GIDSGFTADY 540 AMFAESGRIS RELHILKGIA RMQHSIAGLG DVKIYGSDDK FHGVSRRVYT DAAYILGFGE 600 RSEDNDGYVD DYVSSKLLGG ADKNLRNFIT NNVIKNRRFL YTVRYMNPKR AKKLVQNDAL 660 VVLALSGIPE TQIDRYYKSC IEKRSFNPDL NEKIAALSEM ITTLKIDDFE DVKQNPEKNA 720 NYEAKKNQRI SKERYKACIG LYLTVLYLIC KNLVKINARY SIAIGCLERD TQLHGVDFKG 780 AAYMTRDVFI AKGWINPKKP TVKSIKEQYA FLTPYIFTTY RNMIAHLAAV TNAYKYIPQM 840 DRFKSWFHLY HTVIQHSLIQ QYEYDRDYGR KGAPVVSERV LQLLEQCREH SNYSRDLLHI 900 LNLPFGYNLP RYLNLSSEKY FDANAI 926
[0145] (SEQ ID NO: 100).
[0146] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OGPN01002610.1 (human gut metagenome assembly):
MAKKITAKQK REEKERLNKQ KWAKQDTPVV PKSKTEEKPV AASDDKLLKT TQVKKVQTKS 60 KAKAMGLKTV LSFDDKIAIA SFVNDKKTKL PHIERITDKS GTTIHENARM FDSSVDEQNV 120 NIEKRMTIEE KQNDGTFKKD EKDVKATICN PYFKTCGKDY IGIKDVAEKY FFGKTFPNEN 180 LRVQIAYNVF DIQKILGTYV NNIIYSFYNL RRDGKSDVDI IGSLYAFADF DNQLKDKPAF 240 REAKDLLKNT EAYFSYFGDV FKKSKKGKKD ENNEDYEKNL RHNFNVLRVL SFLRQICTHA 300 YVKCTGGAKN NGDSTKVEAE SLDALFNITE YFAKTAPELS KTINEIYKEG IDRINNDFVT 360 NGKNNLYILS KVYPDMQRNE LVKKYYQFVV CKEGNNVGIN TRKLKESIIS QHPWITTPQD 420 NNKANDYESC RHKLYTIMCF ILVAELDAHE SIRDNMVAEL RANMDGDDGR DAIYEKYAKD 480 IYHIVKDKLL AMQKVFDEEL VPVKVEGKND PQQFTHGKLG KKEIESFCLS DKNTSDIAKV 540 VYFLCNFLDG KEINELCCAM MNKFDGIGDL IDTAKQCGEE VKFIEEFACL SNCRKITNDI 600 RVAKSISKMK NKVNIDNDII YLDAIELLGR KIEKYQKDEN GKILLGTDGK RLYTQEYKYF 660 NDMFFNAGNH KVRNFIANNV MQSKWFFYVV RYNKPAECQI IMRNKTLVKF TLDDLPDMQI 720 QRYYSSVFGD NNMPAVDEMR KRLLDKINQF SVRGFLDELD EIVLMSDEES KRNKSSEKEQ 780 KKSLIRLYLT IAYLITKSMV KINTRFSIAC AMYERDYALL CQSEMKGGPW DGGAQALAVT 840 RKFLNHDREV FDRYCAREAE IARLPSEERK PLRKANDKLL KQTHYTNHSY TYIVNNLNSF 900 TDIDYCAKDV GLPAPNDKND NASILGEMRN DIAHLNIVHD MVKYIEELKD ISSYYAFYCY 960 VLQRRLVGKD PNCQNKFKAK YAKELNDYGT YNKNLMWMLN LPFAYNLPRY KNLSSEFLFY 1020 DMEYNKKDDE 1030 (SEQ ID NO: 101).
[0147] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): from contig emb|OBLI01020244 and emb|OBLI01038679 (from pig gut metagenome):
MAKKITAKQR REERERQNKQ KWAKKQADAT AVFECEADIK PADSKDEDCT NIYIKREKKK 60
TQAKAMGLKT VLGFDNKIAI ASFMSSKDSK SSHIERITDP NGKTIREDVR MFDSNVDECS 120
INLEKRMTVE ERQKDGTIKK DEKDVKSTIC NPYSNECGKD YIGIKSVAEE LFFGRTFPND 180
NLRVQIAYNI FDIQKILGTY INNIIYSFYN LSRDESQSDN DVIGTLYMLK DFDGQKETDT 240
FRQARALLER TEAYYSYFDN VFKKIDKNKK KSDDCKRERN EILRYNFNVL RVLSFLRQIC 300
AHAQVKISNE HDREKGGGLV DSLDALFNIS RFFDAVAPEL NEVINSVYSK GIDDINDNFV 360
KNGKNNFYIL SKIYPEVARE DLLREYYYFV VSKEGNNIGI STKKLKEAII VQDMSYIKSE 420
DYDTYRNKLY TVLCFILVKE LNERTTIREQ MVADLRANMN GDIGREDIYS KYAKIIYAQV 480
KPRFDTMKSA FEEEAKDVIV PDKKKPVKFS HGKLDKNEIE RFCITSANTD SVAKIIYFLC 540
KFLDGKEINE LCCAMMNKLD GINDLIETAE QCGAKVEFVD KFSVLSNCET ISDQIRIVKS 600
ISKMKKEIAI DNDTIFLDAL ELLGRKIDKY KKDATGKYLK DENGKYLYSK EYDDFQYMFF 660
KDSHRVRNFI SNSVIKSKWF SYIVRYNQPS ECRAIMKNKT LVKFALDELP DLQIQRYFVA 720
LYGDEDLPSY GEMRKILLKK LHDFSIKGFL DEIVLLSDLD MESQDKYCEK EQKKSLFRLY 780
LTIAYLITKS MVKINTRFSI ACATYERDYA LLCASNKQER AWSSGATALA LTRRFLNQDK 840
LIFEKHYARE GEISKLPKEE RKAMRKVNDQ LLKRTHFSKH SYCYIVDNVN RLTGGECRTD 900
KRVLPVLNEK NDNAGILLDF RKTIAHLNVV HKMVDYVDEI KGITSYYAFF CYVLQRMLVG 960
NNLNEKNAIK EKYSATVKSF GTYSKDFMWL INLPFAYNLP RYKNLSNEQL FYDEEERNET 1020
EEQIDRL 1027
(SEQ ID NO: 102).
[0148] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OIZX01000427.1:
MAKKKKTARQ LREEMQQQRK QAIQKQQEQR QEKAAAARET AAPEQPAAAP VPKRQRKSLA 60
KAAGLKSNFI LDPQRRTTVM TAFGQGSTAI LEKQIVDRAI SDLQPVQQFQ VEPASAAKYR 120
LKNSRVRFPN VTADDPLYRR KDGGFVPGMD ALRRKNVLEQ RFFGKSFADN IHIQMIYSIL 180
DIHKILAAAS GHIVHLLNIV NGSKDRDFIG MLAAHVLYNE LNEEAKRSIA DFCKSPRLIY 240
YSAAFYETLD NGKSERRSNE DIFNILALMT CLRNFSSHHS IAIKVKDYSA AGLYNLRRLG 300
PDMKKMLDTF YTEAFIQLNQ SFQDHNTTNL TCLFDILNIS DSARQKQLAE EFYRYVVFKE 360
QKNLGFSVRK LREEMLLLPD AAVIADKRYD TCRSKLYNLM DFLILRVYRT GRADRCDKLP 420
EALRAALTDE EKAVVYHKEA LSLWNEMRTL ILDGLLPQMT PENLSRLSGQ KRKGELSLDD 480
AMLKECLYEP GPVPEDAAPE EANAEYFCRM IYLATLFMDG KEINTLLTTL ISKFENIAAF 540
LQTMEQLNIE AELGPEYAMF TRSRAVAEQL RVINSFALMK KPQVNAKQQL YRAAVTLLGT 600
EDPDGVTDEM LCIDPVTGKM LPPNQRHHGD TGLRNFIANN VVESRRFQYL IRYSDPAQLH 660
QLASNKKLVR FVLSSIPDTQ INRYYETCGQ TRLAGRAAKV EFLTDMIAAI RFDQFRDVNQ 720
KERGANTQKE RYKAMLGLYQ TVLYLAVKNL VNINARYVMA FHCVERDMFL YDGELTDPKG 780
ESVSAFLAVN GKKGVQPQYL LLTQLFIRRD YLKRSACEQI QHNMENISDR LLREYRNAVA 840
HLNVIAHLAD YSADMREITS YYGLYHYLMQ RHLFKRHAWQ IRQPERPTEE EQKLIEQEQK 900
QLAWEKALFD KTLQYHSYNK DLVKALNAPF GYNLARYKNL SIEPLFSKEA APAAEIKATH 960
A 961
(SEQ ID NO: 103).
[0149] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig OCTW011587266.1: MKQNDRENNN KIKKSAAKAV GVKSLARLSD GSTVVSSFGK GAAAELESLI TGGEIRKLSD 60
KAILEITDDT QNKNAYNVKS SRIPNLTART DKLSDKSGMD DLGFKRELEL EVFGQCFDDS 120
IHIQIAHAVF DIQKSLAAVI PNVLYTLNNL DRSYSTDNTS DKKDIIGNTL NYQHSYESFN 180
VEKRGEFTEY YNAAKDRFSY FPDILCVLEK VNGKDRYQPK SEKDAFNVLS SVNMLRNSLF 240
HFAPKSNDGK ARIAVFKNQF DSDFSHITST VNKIYSAKIA GVNENFLNNE GNNLYIILKA 300
TNWDIKKIVP QLYRFSVLKS DKNMGFNMRK LREFAVESKN IDLSRLNDKF LTNNRKKLYK 360
VIDFIIYYHL NKVLKDSFVD DFVAALRASQ SEEEKEKLYA QYSERLFADE GLKSAIKKAV 420
DMISDTKSNI FKMKTPLDKA LIENIKVNSD ASDFCKLIYV FTRFLDGKEI NILLNSLIKK 480
FQDIHSFNTT VKKLSENNLI INADYVDDYS LFEQSGTVAR ELMLIKSISK MDFGLDNINL 540
SFMYDDALRT LGVSDENLPE VKREYFGKTK NLSAYIRNNV LENRRFKYVI KYIHPSDVQK 600
IACNKAIAGF VLNRMPDTQI KRYYDSLINK GATDIQAQAK ALLDCITGIS FDAIKDDKHL 660
HKSKEKSPQR SADRERKKAM LTLYYTIVYI FVKQMLHINS LYTIGFFYLE RDQRFIYSRA 720
KKENKNPSKN SYLNDFRSVT AYFIPSEIMK RIEKNENKGF LEDFEALWNS CGKTSRLRKE 780
DVLLYARYIS PDHALKNYKM ILNSYRNKIA HINVIMSAGK YTGGIKRMDS YFSVFQHLVQ 840
CDILSNPNNK GKCFESESLK PLLLDMKFDG TDEKLYSKRL TRALNIPFGY NVPRYKNLTF 900
EKIYLKSSIN E 911 (SEQ ID NO: 104).
[0150] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OGNF01009141.1: MADIDKKKSS AKAAGLKSTF VLENNKLLMT SFGNGNKAVI EKIIDEKVDS INEPEVFSVT 60
PCDKKFELQP AKRGLAADSL VDNPLKSKKT AGDDAIHSRK FLERQFFDGN TFNDNIHIQL 120
IYNILDIEKI LSVHVNDIVY SVNNILSRGE GMEYNDYIGT LNLKSFETYK NNLVNKKKFD 180
LDRVKKIPQL AYFGSAFYNT PEDTSAKITK TKIKSNEEIY YTFMLLSTAR NFSAHYLDRN 240
RAKSSDAEDF DGTSVIMYNL DNEELYKKLY NKKVHMALTG MKKVLDANFN KKVEHLNNSF 300
IKNSAKDFVI LCEVLGIKSR DEKTKFVKDY YDFVVRKNYK HLGFSVKELR ELLFANHDSN 360
KYIKEFDKIS NKKFDSVRSR LNRLADYIIY DYYNKNNAKV SDLVKYLRAA ADDEQKKKIY 420
LNESINLVKS GILERIKKIL PKLNGKIIGN MQPDSTITAS MLHNTGKDWH PISENAHYFT 480
KWIYTLTLFM DGKEINDLVT TLINKFDNIA SFIEVLKSQS VCTHFSEERK MFIDSAEICS 540
ELSAMNSFAR MEAPGASSKR AMFVEAARIL GDNRSKEELE EYFDTLFDKS ASKKEKGFRN 600
FIRNNVVDSN RFKYLTRYTD TSSVKAFSNN KALVKFAIKD IPQEQILRYY NSCFGASERY 660
YNDGMSDKLV EAIGKINLMQ FNGVIQQADR NMLPEEKKKA NAQKEKYKSI IRLYLTVCYL 720
FFKNLVYVNS RYYSAFYNLE KDRSLFEING ELKPTGKFDE GHYTGLVKLF IDNGWINPRA 780
SAYLTVNLAN SDETAIRTFR NTAEHLEALR NADKYLNDLK QFDSYFEIYH YITQRNIKEK 840
CEMLKEQTVK YNNDLLKYHG YSKDFVKALC VPFGYNLPRF KNLSIDALFD KNDKREKLKK 900
GFED 904
(SEQ ID NO: 105).
[0151] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig emb|OIEN01002196.1: MERQKRKMKS KSKMAGVKSV FVIGDELLMT SFGDGDDAVL EKDIDENGVV NDCRNPAAYD 60
AVYGTDSIRV KKTNNNIRAK VNNPLAKSNI RSEESALFRT RVNEYKREQK DKYETLFFGK 120
TFDDNIHIQL ISKILDIEKT FSVVIGNIVY AINNLSLEQS IDRPIDIFGD KNTQGISLRE 180
DNDYLKTMLP RCEYLFHNIL NSDSDNNSKM NYNKVNKGKE EKDNRNNENI EKLKKALEVI 240
KIIRVDSFHG VDGIKGDQKF PRSKYNLAVN YNEEIQKTIS EPFNRKVEEV QQDFYRNSCV 300
NIDFLKEIMY GSNYTDRGSD SLECSYFNFA ILKQNKNMGF SITSIRECLL DLYELNFESM 360 QNLRPRANSF CDFLIYDYYC KNESERANLV DCLRSAASEE EKKNIYFQTA ERVKEKFRNA 420 FNRISRFDAS YIKNSREKNL SGGSSLPKYS FIEGFTKRSK KINDNDEKNA DLFCNMLYYL 480
AQFLDGKEIN IFLTSIHNIF QNIDSFLKVM KEKGMECKFQ KDFKMFSHAG HVAKKIEIVI 540
SLAKMKKTLD FYNAQALKDA VTILGVSKKH QYLDMNSYLD FYMFDNRSGA TGKNAGKDHN 600
LRNFLVSNVI RSRKFNYLSR YSNLAEVKKL AQNPSLVQFV LSRIEPSLIC RYYESSQGIS 660
SEGITIDEQI KKLTGIIVDM NIDSFENINN GEIGMRYSKA TPQSIERRNQ MRVCVGLYLN 720
VLYQIEKNLM NVNARYVLAF AFAERDALML NFTLEECKKN KKRSSGGFSF IEMTQFFIDK 780
KLFKVATEAI KKNVLKYNGN PESLNHIPGE YICKNMEGYH ENTVRNFRNM VAHLTAVARV 840
PLYISEVTQI DSYYALYHYC MQMNILQGIE QSGKILDNIK LKNALENARV HRTYSKDAVK 900
YLCLPFAYNI SRYKALTIKD LFDWTEYSCK KDE 933
(SEQ ID NO: 106).
[0152] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736:
MKRQKTFAKR IGIKSTVAYG QGKYAITTFG KGSKAEIAVR SADPPEETLP TESDATLSIH 60
AKFAKAGRDG REFKCGDVDE TRIHTSRSEY ESLISNPAES PREDYLGLKG TLERKFFGDE 120
YPKDNLRIQI IYSILDIQKI LGLYVEDILH FVDGLQDEPE DLVGLGLGDE KMQKLLSKAL 180
PYMGFFGSTD VFKVTKKREE RAAADEHNAK VFRALGAIRQ KLAHFKWKES LAIFGANANM 240
PIRFFQGATG GRQLWNDVIA PLWKKRIERV RKSFLSNSAK NLWVLYQVFK DDTDEKKKAR 300
ARQYYHFSVL KEGKNLGFNL TKTREYFLDK FFPIFHSSAP DVKRKVDTFR SKFYAILDFI 360
IYEASVSVAN SGQMGKVAPW KGAIDNALVK LREAPDEEAK EKIYNVLAAS IRNDSLFLRL 420
KSACDKFGAE QNRPVFPNEL RNNRDIRNVR SEWLEATQDV DAAAFVQLIA FLCNFLEGKE 480
INELVTALIK KFEGIQALID LLRNLEGVDS IRFENEFALF NDDKGNMAGR IARQLRLLAS 540
VGKMKPDMTD AKRVLYKSAL EILGAPPDEV SDEWLAENIL LDKSNNDYQK AKKTVNPFRN 600
YIAKNVITSR SFYYLVRYAK PTAVRKLMSN PKIVRYVLKR LPEKQVASYY SAIWTQSESN 660
SNEMVKLIEM IDRLTTEIAG FSFAVLKDKK DSIVSASRES RAVNLEVERL KKLTTLYMSI 720
AYIAVKSLVK VNARYFIAYS ALERDLYFFN EKYGEEFRLH FIPYELNGKT CQFEYLAILK 780
YYLARDEETL KRKCEICEEI KVGCEKHKKN ANPPYEYDQE WIDKKKALNS ERKACERRLH 840
FSTHWAQYAT KRDENMAKHP QKWYDILASH YDELLALQAT GWLATQARND AEHLNPVNEF 900
DVYIEDLRRY PEGTPKNKDY HIGSYFEIYH YIRQRAYLEE VLAKRKEYRD SGSFTDEQLD 960
KLQKILDDIR ARGSYDKNLL KLEYLPFAYN LPRYKNLTTE ALFDDDSVSG KKRVAEWRER 1020
EKTREAEREQ RRQR 1034
(SEQ ID NO: 107).
An exemplary direct repeat sequence of CasRX/Cas13d Metagenomic hit (no protein accession): contig e-k87_11092736 (SEQ ID NO: 107) comprises or consists of the nucleic acid sequence: CasRX/Cas13d Direct repeat 1: gtgagaagtc tccttatggg gagatgctac
(SEQ ID NO: 108).
[0153] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129306_1000735:
MQKQREQQTV TDESERKKKP LKSGAKAAGL KSVFVLSEGK ELLTSFGRGN EAVPEKRVTG 60
GTIANARTDN KEAFSAALQN KRFEVFGRTA GSSDDPLAVS RAPGQDLIGA KTALEERYFG 120
RAFADNIHMQ VIYAIQDINK ILAVHANNIV YTLNNLDREA DPETDDFIGS GYLTLKNTFE 180
TYCDPAALNE REREKVTVSK QHFDAFMQNP RLAYYGNAFF RKLSKAERLA RGREIFDKES 240 PERRQEILGS RGKNKSVDDE IRALAPEWVK REERDVYSEL VLMSELRQSC FHGQQKNSAR 300 IFRLDNDLGP GVDGARELLD RLYAEKINDL RSFDKTSASS NFRLLFNAYH ADNEKKKELA 360 QEFYRFSVLK VSKNTGFSIR TLREKIIEDH AAQYRDKIYD SMRKKLFSTF DFFLWRFYEE 420 REDEAEELRA CLRAARSDEE KEQIYAEAAA SCWPSVKPFV ESVAATLCDV VKGRTKLNKL 480 KLSADESTLV RNAIDGVRIS PRASYFTKLI YLMTLFLDGK EINDLLTTLI HAFENIDSFL 540 SVLGSERLER TFDANYRIFA DSGVIAQELR AVNSFARMTT EPFNSKLVMF EDAAQLFGMS 600 GGLVEHAEEL REYLDNKMLD KTKLRLLPDG KVDTGFRNFI ISNVTESRRF RYLVRYCEPR 660 AVRDYMSCRP LIRLTLRDMP DTILRRYYEQ SVGAATVDRE RILDTLADKL LSLRFTDFEN 720 VNQRANAERN REKQKMMGII SLYLNVAYQI VKNLVYVNAR YTMAYHCAER DTELLLNAAG 780 EGNLLRRDRS WPARLHLPRR ALARRRDRVE VMERDVARGP EAYNRDEWLG LVRTLRREKR 840 VCDNLHNNYA YLCGADAEPG DASLSLLFVY RNKAAHLSVL NKGGRLSGDL KEAKSWFYVY 900 HFLMQRVLEE EFRNTQALPE RLRELLMMAE RYRGCSKDLI KVLNLTFAYN LPRYKNLSID 960 GRFDKNHPDP SDE 973 (SEQ ID NO: 109).
[0154] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0129317_1008067:
MKKQKKSLVK AAGLKSAFVV GDSVYLTSFG KGNAARLDTK INPDNSTERY VSDSEKHTLK 60 INSITDTELR LSGPFPKQAE AKNPTHKKDN EQKNTRQDML GLKSTLEKFY FGSTFDDNIH 120 IQIIHNIQDI AKILAAHSNN AGYALDNMLA YQGVEFSDMI GYMGTSRTFD NYDPNHKNNK 180 DFFRFLKLPR LGYFGSAFYS QKGKDFEKRS DEEVYNICAL MGQIRQCCFH GKQEKYQLKW 240 LYNFHNFKSN KPFLDTLDKH FDEMIDRINK NFIKNNTPDL IILSGLYPDM AKKELVRLFY 300 DFTTVKEYKN MGFSVKKLRE KMLESEEASD FRDKDYDSVR RKLYKLMDFC IYYLYYSDSE 360 RNENLVSRLR ESLTDENKDI IYSKEAKIVW NELRKKFSTI LDNVKGSNIK KLENVKEKFI 420 SEDEFDDIKL DIDISYFSKL MYVMCYFLDG KEINDLLTTL VSKFDNIGSI IEAATQIGIN 480 IEFIDDFKFF DRSKDISVEL NIIRNFARMQ APVPNAKRAM QEDAIRILGG SEEDIFSILD 540 DMTGYDKSGK KLAQSKKGFR NFIINNVVES SRFKYIVRYS NPQKIRKLAN NSVVVGFVLG 600 KLPDAQIESY FNSCLPNRVY STPDKARESL RDMLHNISFN DFADVKQDDR RATPEEKVEK 660 ERYKAIIGLY LTVMYHLVKN LVYVNSRYVM AFHCLERDAM HYDVSLDNYR DLIRHLISEG 720 DSSCNHFISH NRRMRDCIEE NVKNSEQLIF GKEDAVIRFR NNVAHLSAIR NANEYIGDIR 780 EITSYFALYH YLMQRKLIDD CKVNDTAHKY FEQLTKYKTY VMDMVKALCS PFGYNLPRFK 840 NLSIEGKFDM HESK 854 (SEQ ID NO: 110).
[0155] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d Ga0224415_10048792:
MSKKENRKSY VKGLGLKSTL VSDSKVYLTT FADGSNAKLE KCVENNKIIC ISNDKEAFAA 60 SIANKNVGYK IKNDEKFRHP KGYDIISNNP LLHNNSVQQD MLGLKNVLEK RYFGKSSGGD 120 NNLCIQIIHN IIDIEKILSE YIPNVVYAFN NIAGFKDEHN NIIDIIGTQT YNSSYTYADF 180 SKDKSDKKYI EFQKLLKNKR LGYWGKAFFT GQGNNAKVRQ ENQCFHIIAL LISLRNWATH 240 SNELDKHTKR TWLYKLDDTN ILNAEYVKTL NYLYDTIADE LTKSFSKNGA VNVNYLAKKY 300 NIKDDLPGFS EQYFRFSIMK EQKNLGFNIS KLRENMLDFK DMSVIRDDHN RYDKDRSKIY 360 TMMDFVIYRY YIDNNNDSID FINKLRSSID EKSKEKLYNE EANRLWNKLK EYMLYIKEFN 420 GKLASRTPDR DGNISEFVES LPKIHRLLPR GQKISNFSKL MYLLTMFLDG KEINDLLTTL 480 INKFENIQGF LDIMPEINVN AKFEPEYVFF NKSHEIAGEL KLIKGFAQMG EPAATLKLEM 540 TADAIKILGT EKEDAELIKL AESLFKDENG KLLGNKQHGM RNFIGNNVIK SKRFHYLIRY 600 GDPAHLHKIA TNKNVVRFVL GRIADMQKKQ GQKGKNQIDR YYEVCVGNKD IKKTIEEKID 660
ALTDIIVNMN YDQFEKKKAV IENQNRGKTF EEKNKYKRDN AEREKFKKII SLYLTVIYHI 720
LKNIVNVNSR YILGFHCLER DKQLYIEKYN KDKLDGFVAL TKFCLGDEER FEDLKAKAQA 780
SIQALETANP KLYAKYMNYS DEEKKEEFKK QLNRERVKNA RNAYLKNIKN YIMIRLQLRD 840
QTDSSGYLCG EFRDKVAHLE VARHAHEYIG NIKEVNSYFQ LYHYIMQCRL YDVLKNNTKA 900
EAMVKGKAKE YFEALEKEGT YNDKLLKIAC VPFGYCIPRY KNLSMEELFD MNEEKKFKKK 960
APENT 965 (SEQ ID NO: 111).
[0156] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence CasRX/Cas13d 160582958 _gene49834:
MKNSVTFKLI QAQENKEAAR KKAKDIAEQA RIAKRNGVVK KEENRINRIQ IEIQTQKKSN 60
TQNAYHLKSL AKAAGVKSVF AIGNDLLMTG FGPGNDATIE KRVFQNRAIE TLSSPEQYSA 120
EFQNKQFKIK GNIKVLNHST QKMEEIQTEL QDNYNRPHFD LLGCKNVLEQ KYFGRTFSDN 180
IHVQIAYNIM DIEKLLTPYI NNIIYTLNEL MRDNSKDDFF GCDSHFSVAY LYDELKAGYS 240
DRLKTKPNLS KNIDRIWNNF CNYMNSDSGN TEARLAYFGE LFYKPKETGD AKSDYKTHLS 300
NNQKEEWELK SDKEVYNIFA ILCDLRHFCT HGESITPSGK PFPYNLEKNL FPEAKQVLNS 360
LFEEKAESLG AEAFGKTAGK TDVSILLKVF EKEQASQKEQ QALLKEYYDF KVQKTYKNMG 420
FSIKKLREAI MEIPDAAKFK DDLYSSLRHK LYGLFDFILV KHFLDTSDSE NLQNNDIFRQ 480
LRACRCEEEK DQVYRSIAVK VWEKVKKKEL NMFKQVVVIP SLSKDELKQM EMTKNTELLS 540
SIETISTQAS LFSEMIFMMT YLLDGKEINL LCTSLIEKFE NIASFNEVLK SPQIGYETKY 600
TEGYAFFKNA DKTAKELRQV NNMARMTKPL GGVNTKCVMY NEAAKILGAK PMSKAELESV 660
FNLDNHDYTY SPSGKKIPNK NFRNFIINNV ITSRRFLYLI RYGNPEKIRK IAINPSIISF 720
VLKQIPDEQI KRYYPPCIGK RTDDVTLMRD ELGKMLQSVN FEQFSRVNNK QNAKQNPNGE 780
KARLQACVRL YLTVPYLFIK NMVNINARYV LAFHCLERDH ALCFNSRKLN DDSYNEMANK 840
FQMVRKAKKE QYEKEYKCKK QETGTAHTKK IEKLNQQIAY IDKDIKNMHS YTCRNYRNLV 900
AHLNVVSKLQ NYVSELPNDY QITSYFSFYH YCMQLGLMEK VSSKNIPLVE SLKNEANDAQ 960
SYSAKKTLEY FDLIEKNRTY CKDFLKALNA PFSYNLPRFK NLSIEALFDK NIVYEQADLK 1020
KE 1022
(SEQ ID NO: 112).
[0157] An exemplary direct repeat sequence of CasRX/Cas13d proteins may comprise or consist of the sequence
CasRX/Cas13d 160582958 _gene49834 (SEQ ID NO: 112) comprises or consists of the nucleic acid sequence: CasRX/Cas13d DR:
gaactacacc cctctgttct tgtaggggtc taacac 36
(SEQ ID NO: 113).
[0158] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence: CasRX/Cas13d 250twins_35838_GL0110300:
MGNKQRVSAQ KRRENAKLCN QQKARQAESQ RDKIKNMNVE KMKNINTNDI KHTKTTAKKL 60
GLKSTIIADK KIILTSFINE QSSKTANIEK VAGFKGDTID TISYTPRMFR SEINPGEIVI 120
SKGDDLSEFA NPANFPIGRD YVKIRSALEK QYFGKEFPED NLHVQIAYNV ADIKKILSVY 180
INNIIYMFYN LARSEEYDIF YNSQSENSGR DCDVIGSLYY QASYRNQDAN RFEKDGKKKA 240 IDSLLDDTRA YYTYFDGLFS VPKREDDGKI KESEKEKAKD QNFDVLRLLS VGRQLTFHSD 300 KSNNEAYLFD LSKLTRAAQD ENRRQDIQSL LNILNSTCRS NLEGVNGDFV KHAKNNLYVL 360
NQLYPSLKAN DLIGEYYNFI VKKENRNIGI RLITVRELII EHNYTNLKDS KYDTYRNKIY 420
TVLNFILFRE IQENSIAIKN FREKLRSTEK AEQPALYQAF ANKIYPMVQA KFAKAIDLFE 480
EQYKTKFKSE FKGGISIENM QQQNILLQTE NIDYFSKYVL FLTKFLDGKE INELLCALIN 540
KFDNIADLLD ISKQIGTPVV FCADYESLND AAKIAENIRL IKNIAHLRPA IQEAQSSKDN 600
ADAAGTPATL LIDAYNMLNT DIQLVYGEAA YEELRKDLFE RKNGTKYNKK GKKVDVYDHK 660
FRNFLINNVI KSKWFFYIAK YVKPADCAKM MSNKKMIEFA LRDLPETQIK RYYYTITGNE 720
ALGDAESLKG VIIEQLHAFS IKNTLLSIKN MGEGEYKIQQ IGSSKEKLKA IVNLYLTVAY 780
LLTKSLVKVN IRFSIAFGCL ERDLVLQKKS EKKFDAIINE ILLEDDKIRK ECDKERAQAK 840
TLPRELAQER FAQIKRRESG CYFKSYHVYD YLSKNSNEFK QNHIDFAVTS YRNNVEHLNV 900
VHCMTKYFSE VKDVKSYYGV YCYIMQRMLC DELIIKNQDK PDVRQTFEEY NRLLKDHGTY 960
SKNLMWLLNF PFAYNLARYK NLSNEDLFNA KNNDQKSK 998
(SEQ ID NO: 114).
[0159] Exemplary CasRX/Cas13d proteins may comprise or consist of the sequence:
CasRX/Cas13d 250twins_36050_GL0158985:
MKKKHQSAAE KRQVKKLKNQ EKAQKYASEP SPLQSDTAGV ECSQKKTVVS HIASSKTLAK 60
AMGLKSTLVM GDKLVITSFA ASKAVGGAGY KSANIEKITD LQGRVIEEHE RMFSADVGEK 120
NIELSKNDCH TNVNNPVVTN IGKDYIGLKS RLEQEFFGKT FENDNLHVQL AYNILDIKKI 180
LGTYVNNIIY IFYNLNRAGT GRDERMYDDL IGTLYAYKPM EAQQTYLLKG DKDMRRFEEV 240
KQLLQNTSAY YVYYGTLFEK VKAKSKKEQR AKEAEIDACT AHNYDVLRLL SLMRQLCMHS 300
VAGTAFKLAE SALFNIEDVL SADLKEILDE AFSGAVNKLN DGFVQHSGNN LYVLQQLYPN 360
ETIERIAEKY YRLTVRKEDL NMGVNIKKLR ELIVGQYFPE VLDKEYDLSK NGDSVVTYRS 420
KIYTVMNYIL LYYLEDHDSS RESMVEALRQ NREGDEGKEE IYRQFAKKVW NGVSGLFGVC 480
LNLFKTEKRN KFRSKVALPD VSGAAYMLSS ENIDYFVKML FFVCKFLDGK EINELLCALI 540
NKFDNIADIL DAAAQCGSSV WFVDSYRFFE RSRRISAQIR IVKNIASKDF KKSKKDSDES 600
YPEQLYLDAL ALLGDVISKY KQNRDGSVVI DDQGNAVLTE QYKRFRYEFF EEIKRDESGG 660
IKYKKSGKPE YNHQRRNFIL NNVLKSKWFF YVVKYNRPSS CRELMKNKEI LRFVLRDIPD 720
SQVRRYFKAV QGEEAYASAE AMRTRLVDAL SQFSVTACLD EVGGMTDKEF ASQRAVDSKE 780
KLRAIIRLYL TVAYLITKSM VKVNTRFSIA FSVLERDYYL LIDGKKKSSD YTGEDMLALT 840
RKFVGEDAGL YREWKEKNAE AKDKYFDKAE RKKVLRQNDK MIRKMHFTPH SLNYVQKNLE 900
SVQSNGLAAV IKEYRNAVAH LNIINRLDEY IGSARADSYY SLYCYCLQMY LSKNFSVGYL 960
INVQKQLEEH HTYMKDLMWL LNIPFAYNLA RYKNLSNEKL FYDEEAAAEK ADKAENERGE 1020
(SEQ ID NO: 115).
[0160] Yan et al. (2018) Mol Cell.70(2):327-339 (doi: 10.1016/j.molcel.2018.02.2018) and Konermann et al. (2018) Cell 173(3):665-676 (doi: 10.1016/j.cell/2018.02.033) have described CasRX/Cas13d proteins and both of which are incorporated by reference herein in their entireties. Also see WO Publication Nos. WO2018/183703 (CasM) and
WO2019/006471 (Cas13d), which are incorporated herein by reference in their entirety.
[0161]
[0162] Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence: [0163] Cas13d (Ruminococcus flavefaciens XPD3002) sequence:
1 IEKKKSFAKG MGVKSTLVSG SKVYMTTFAE GSDARLEKIV EGDSIRSVNE GEAFSAEMAD 61 KNAGYKIGNA KFSHPKGYAV VANNPLYTGP VQQDMLGLKE TLEKRYFGES ADGNDNICIQ 121 VIHNILDIEK ILAEYITNAA YAVNNISGLD KDIIGFGKFS TVYTYDEFKD PEHHRAAFNN 181 NDKLINAIKA QYDEFDNFLD NPRLGYFGQA FFSKEGRNYI INYGNECYDI LALLSGLAHW 241 VVANNEEESR ISRTWLYNLD KNLDNEYIST LNYLYDRITN ELTNSFSKNS AANVNYIAET 301 LGINPAEFAE QYFRFSIMKE QKNLGFNITK LREVMLDRKD MSEIRKNHKV FDSIRTKVYT 361 MMDFVIYRYY IEEDAKVAAA NKSLPDNEKS LSEKDIFVIN LRGSFNDDQK DALYYDEANR 421 IWRKLENIMH NIKEFRGNKT REYKKKDAPR LPRILPAGRD VSAFSKLMYA LTMFLDGKEI 481 NDLLTTLINK FDNIQSFLKV MPLIGVNAKF VEEYAFFKDS AKIADELRLI KSFARMGEPI 541 ADARRAMYID AIRILGTNLS YDELKALADT FSLDENGNKL KKGKHGMRNF IINNVISNKR 601 FHYLIRYGDP AHLHEIAKNE AVVKFVLGRI ADIQKKQGQN GKNQIDRYYE TCIGKDKGKS 661 VSEKVDALTK IITGMNYDQF DKKRSVIEDT GRENAEREKF KKIISLYLTV IYHILKNIVN 721 INARYVIGFH CVERDAQLYK EKGYDINLKK LEEKGFSSVT KLCAGIDETA PDKRKDVEKE 781 MAERAKESID SLESANPKLY ANYIKYSDEK KAEEFTRQIN REKAKTALNA YLRNTKWNVI 841 IREDLLRIDN KTCTLFANKA VALEVARYVH AYINDIAEVN SYFQLYHYIM QRIIMNERYE 901 KSSGKVSEYF DAVNDEKKYN DRLLKLLCVP FGYCIPRFKN LSIEALFDRN EAAKFDKEKK 961 SGNS. (SEQ ID NO: 45)
[0164] Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
[0165] Cas13d (contig e‐k87_11092736): 
MKRQKTFAKRIGIKSTVAYGQGKYAITTFGKGSKAEIAVRSADPPEETLPTESDATLSIHAK FAKAGRDGREFKCGDVDETRIHTSRSEYESLISNPAESPREDYLGLKGTLERKFFGDEYPKD NLRIQIIYSILDIQKILGLYVEDILHFVDGLQDEPEDLVGLGLGDEKMQKLLSKALPYMGFF GSTDVFKVTKKREERAAADEHNAKVFRALGAIRQKLAHFKWKESLAIFGANANMPIRFFQGA TGGRQLWNDVIAPLWKKRIERVRKSFLSNSAKNLWVLYQVFKDDTDEKKKARARQYYHFSVL KEGKNLGFNLTKTREYFLDKFFPIFHSSAPDVKRKVDTFRSKFYAILDFIIYEASVSVANSG QMGKVAPWKGAIDNALVKLREAPDEEAKEKIYNVLAASIRNDSLFLRLKSACDKFGAEQNRP VFPNELRNNRDIRNVRSEWLEATQDVDAAAFVQLIAFLCNFLEGKEINELVTALIKKFEGIQ ALIDLLRNLEGVDSIRFENEFALFNDDKGNMAGRIARQLRLLASVGKMKPDMTDAKRVLYKS ALEILGAPPDEVSDEWLAENILLDKSNNDYQKAKKTVNPFRNYIAKNVITSRSFYYLVRYAK PTAVRKLMSNPKIVRYVLKRLPEKQVASYYSAIWTQSESNSNEMVKLIEMIDRLTTEIAGFS FAVLKDKKDSIVSASRESRAVNLEVERLKKLTTLYMSIAYIAVKSLVKVNARYFIAYSALER DLYFFNEKYGEEFRLHFIPYELNGKTCQFEYLAILKYYLARDEETLKRKCEICEEIKVGCEK HKKNANPPYEYDQEWIDKKKALNSERKACERRLHFSTHWAQYATKRDENMAKHPQKWYDILA SHYDELLALQATGWLATQARNDAEHLNPVNEFDVYIEDLRRYPEGTPKNKDYHIGSYFEIYH YIRQRAYLEEVLAKRKEYRDSGSFTDEQLDKLQKILDDIRARGSYDKNLLKLEYLPFAYNLP RYKNLTTEALFDDDSVSGKKRVAEWREREKTREAEREQRRQR (SEQ ID NO: 46).
[0166] An exemplary direct repeat sequence of Cas13d (contig e‐k87_11092736) (SEQ ID NO: 46) comprises or consists of the nucleic acid sequence:Cas13d (contig e‐k87_11092736)  Direct Repeat Sequence): GTGAGAAGTCTCCTTATGGGGAGATGCTAC (SEQ ID NO: 47).
[0167] Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
[0168] Cas13d (160582958_gene49834): 
MKNSVTFKLIQAQENKEAARKKAKDIAEQARIAKRNGVVKKEENRINRIQIEIQTQKKSNTQ NAYHLKSLAKAAGVKSVFAIGNDLLMTGFGPGNDATIEKRVFQNRAIETLSSPEQYSAEFQN KQFKIKGNIKVLNHSTQKMEEIQTELQDNYNRPHFDLLGCKNVLEQKYFGRTFSDNIHVQIA YNIMDIEKLLTPYINNIIYTLNELMRDNSKDDFFGCDSHFSVAYLYDELKAGYSDRLKTKPN LSKNIDRIWNNFCNYMNSDSGNTEARLAYFGELFYKPKETGDAKSDYKTHLSNNQKEEWELK SDKEVYNIFAILCDLRHFCTHGESITPSGKPFPYNLEKNLFPEAKQVLNSLFEEKAESLGAE AFGKTAGKTDVSILLKVFEKEQASQKEQQALLKEYYDFKVQKTYKNMGFSIKKLREAIMEIP DAAKFKDDLYSSLRHKLYGLFDFILVKHFLDTSDSENLQNNDIFRQLRACRCEEEKDQVYRS IAVKVWEKVKKKELNMFKQVVVIPSLSKDELKQMEMTKNTELLSSIETISTQASLFSEMIFM MTYLLDGKEINLLCTSLIEKFENIASFNEVLKSPQIGYETKYTEGYAFFKNADKTAKELRQV NNMARMTKPLGGVNTKCVMYNEAAKILGAKPMSKAELESVFNLDNHDYTYSPSGKKIPNKNF RNFIINNVITSRRFLYLIRYGNPEKIRKIAINPSIISFVLKQIPDEQIKRYYPPCIGKRTDD VTLMRDELGKMLQSVNFEQFSRVNNKQNAKQNPNGEKARLQACVRLYLTVPYLFIKNMVNIN ARYVLAFHCLERDHALCFNSRKLNDDSYNEMANKFQMVRKAKKEQYEKEYKCKKQETGTAHT KKIEKLNQQIAYIDKDIKNMHSYTCRNYRNLVAHLNVVSKLQNYVSELPNDYQITSYFSFYH YCMQLGLMEKVSSKNIPLVESLKNEANDAQSYSAKKTLEYFDLIEKNRTYCKDFLKALNAPF SYNLPRFKNLSIEALFDKNIVYEQADLKKE (SEQ ID NO: 48).
[0169] An exemplary direct repeat sequence of Cas13d (160582958_gene49834) (SEQ ID NO: 48) comprises or consists of the nucleic acid sequence:
[0170] Cas13d (160582958_gene49834) Direct Repeat Sequence:
GAACTACACCCCTCTGTTCTTGTAGGGGTCTAACAC (SEQ ID NO: 49).
[0171] Exemplary wild type Cas13d proteins of the disclosure may comprise or consist of the amino acid sequence:
[0172] Cas13d (contig tpg|DJXD01000002.1| ; uncultivated Ruminococcus assembly,  UBA7013, from sheep gut metagenome):
MKKQKSKKTVSKTSGLKEALSVQGTVIMTSFGKGNMANLSYKIPSSQKPQNLNSSAGLKNVE VSGKKIKFQGRHPKIATTDNPLFKPQPGMDLLCLKDKLEMHYFGKTFDDNIHIQLIYQILDI EKILAVHVNNIVFTLDNVLHPQKEELTEDFIGAGGWRINLDYQTLRGQTNKYDRFKNYIKRK ELLYFGEAFYHENERRYEEDIFAILTLLSALRQFCFHSDLSSDESDHVNSFWLYQLEDQLSD EFKETLSILWEEVTERIDSEFLKTNTVNLHILCHVFPKESKETIVRAYYEFLIKKSFKNMGF SIKKLREIMLEQSDLKSFKEDKYNSVRAKLYKLFDFIITYYYDHHAFEKEALVSSLRSSLTE ENKEEIYIKTARTLASALGADFKKAAADVNAKNIRDYQKKANDYRISFEDIKIGNTGIGYFS ELIYMLTLLLDGKEINDLLTTLINKFDNIISFIDILKKLNLEFKFKPEYADFFNMTNCRYTL EELRVINSIARMQKPSADARKIMYRDALRILGMDNRPDEEIDRELERTMPVGADGKFIKGKQ GFRNFIASNVIESSRFHYLVRYNNPHKTRTLVKNPNVVKFVLEGIPETQIKRYFDVCKGQEI PPTSDKSAQIDVLARIISSVDYKIFEDVPQSAKINKDDPSRNFSDALKKQRYQAIVSLYLTV MYLITKNLVYVNSRYVIAFHCLERDAFLHGVTLPKMNKKIVYSQLTTHLLTDKNYTTYGHLK NQKGHRKWYVLVKNNLQNSDITAVSSFRNIVAHISVVRNSNEYISGIGELHSYFELYHYLVQ SMIAKNNWYDTSHQPKTAEYLNNLKKHHTYCKDFVKAYCIPFGYVVPRYKNLTINELFDRNN PNPEPKEEV (SEQ ID NO: 50).
[0173] An exemplary direct repeat sequence of Cas13d (contig tpg|DJXD01000002.1| ;  uncultivated Ruminococcus assembly, UBA7013, from sheep gut metagenome) (SEQ ID NO: 50) comprises or consists of the nucleic acid sequence:Cas13d (contig 
tpg|DJXD01000002.1| ; uncultivated Ruminococcus assembly, UBA7013, from sheep gut  metagenome) Direct Repeat Sequence:
CAACTACAACCCCGTAAAAATACGGGGTTCTGAAAC (SEQ ID NO: 51).
[0174] In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. In some embodiments, the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence. In some embodiments, the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of the sequence UGGAGCGAGCAUCCCCCAAA (SEQ ID NO: 1), GUUUGGGGGAUGCUCGCUCCA (SEQ ID NO: 2), CCCUCACUGCUGGGGAGUCC (SEQ ID NO: 3), GGACUCCCCAGCAGUGAGGG (SEQ ID NO: 4),
GCAACUGGAUCAAUUUGCUG (SEQ ID NO: 5), GCAGCAAAUUGAUCCAGUUGC (SEQ ID NO: 6), GCAUUCUUAUCUGGUCAGUGC (SEQ ID NO: 7), GCACUGACCAGAUAAGAAUG (SEQ ID NO: 8), GAGCAGCAGCAGCAGCAGCAG (SEQ ID NO: 9), GCAGGCAGGCAGGCAGGCAGG (SEQ ID NO: 10),
GCCCCGGCCCCGGCCCCGGC (SEQ ID NO: 11) , or GCTGCTGCTGCTGCTGCTGC (SEQ ID NO: 12), GGGGCCGGGGCCGGGGCCGG (SEQ ID NO: 74),
GGGCCGGGGCCGGGGCCGGG (SEQ ID NO: 75), GGCCGGGGCCGGGGCCGGGG (SEQ ID NO: 76), GCCGGGGCCGGGGCCGGGGC (SEQ ID NO: 77),
CCGGGGCCGGGGCCGGGGCC (SEQ ID NO: 78), or CGGGGCCGGGGCCGGGGCCG (SEQ ID NO: 79).
[0175] In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. In some embodiments, the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence.
[0176] In some embodiments, the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of the sequence GUGAUAAGUGGAAUGCCAUG (SEQ ID NO: 14),
CUGGUGAACUUCCGAUAGUG (SEQ ID NO: 15), or GAGATATAGCCTGGTGGTTC (SEQ ID NO: 16).
[0177] In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. In some embodiments, the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence. In some embodiments, the spacer sequence has 100% complementarity to the target RNA sequence. In some embodiments, the spacer sequence comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence comprises or consists of 21 nucleotides. In some embodiments, the spacer sequence comprises or consists of a sequence comprising at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof.
[0178] In some embodiments of the compositions of the disclosure, the sequence comprising the gRNA further comprises a scaffold sequence that specifically binds to the first RNA binding protein. In some embodiments, the scaffold sequence comprises a stem- loop structure. In some embodiments, the scaffold sequence comprises or consists of 90 nucleotides. In some embodiments, the scaffold sequence comprises or consists of 93 nucleotides. In some embodiments, the scaffold sequence comprises or consists of the sequence
GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCG UUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 13). In some embodiments, the scaffold sequence comprises or consists of the sequence
GGACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGCUUUUU (SEQ ID NO: 17). In some embodiments, the scaffold sequence comprises or consists of the sequence
GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCG UUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 82) or
GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUU GAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 83).
[0179] In some embodiments of the compositions of the disclosure, the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule.
[0180] In some embodiments of the compositions of the disclosure, an RNA genome or an RNA transcriptome comprises the RNA molecule.
[0181] In some embodiments of the compositions of the disclosure, the sequence encoding the RNA-binding protein encodes a CRISPR-Cas protein or RNA-binding portion thereof. In some embodiments, the RNA-binding protein is a fusion protein. In some embodiments, the CRISPR-Cas protein is a Type II CRISPR-Cas protein. In some embodiments, the RNA- binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited. In some
embodiments, the native RNA nuclease activity is increased or induced. In some
embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited. In some embodiments, the CRISPR-Cas protein comprises a mutation. In some embodiments, a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein In some embodiments the mutation occurs in an amino acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
[0182] In some embodiments of the compositions of the disclosure, the RNA binding protein comprises a CRISPR-Cas protein or RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein is a Type V CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cpf1 polypeptide or an RNA- binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited. In some embodiments, the native RNA nuclease activity is increased or induced. In some embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited. In some embodiments, the CRISPR-Cas protein comprises a mutation. In some embodiments, a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein. In some embodiments, the mutation occurs in an amino acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
[0183] In some embodiments of the compositions of the disclosure, the RNA binding protein comprises a CRISPR-Cas protein or RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein is a Type VI CRISPR-Cas protein. In some embodiments, the RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof. In some embodiments, the RNA binding protein comprises a Cas13d polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity. In some embodiments, the native RNA nuclease activity is reduced or inhibited. In some embodiments, the native RNA nuclease activity is increased or induced. In some embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and the native DNA nuclease activity is inhibited. In some embodiments the CRISPR-Cas protein comprises a mutation In some embodiments a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein. In some
embodiments, the mutation occurs in an amino acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
[0184] In some embodiments, a target RNA-binding fusion protein is not an RNA-guided target RNA-binding fusion protein and as such comprises at least one RNA-binding polypeptide which is capable of binding a target RNA without a corresponding gRNA sequence. Such non-guided RNA-binding polypeptides include, without limitation, at least one RNA-binding protein or RNA-binding portion thereof which is a PUF (Pumilio and FBF homology family). This type RNA-binding polypeptide can be used in place of a gRNA- guided RNA binding protein such as CRISPR/Cas. In some embodiments of the
compositions of the disclosure, the RNA-binding protein or RNA-binding portion thereof is a PUF (Pumilio and FBF homology family). The unique RNA recognition mode of PUF proteins (named for Drosophila Pumilio and C. elegans fem-3 binding factor) that are involved in mediating mRNA stability and translation are well known in the art. The PUF domain of human Pumilio1, also known in the art, binds tightly to cognate RNA sequences and its specificity can be modified. It contains eight PUF repeats that recognize eight consecutive RNA bases with each repeat recognizing a single base. Since two amino acid side chains in each repeat recognize the Watson-Crick edge of the corresponding base and determine the specificity of that repeat, a PUF domain can be designed to specifically bind most 8-nt RNA. Wang et al., Nat Methods.2009; 6(11): 825-830. See also WO2012/068627 which is incorporated by reference herein in its entirety.
[0185] In some embodiments of the compositions of the disclosure, the RNA-binding protein or RNA-binding portion thereof is a PUMBY (Pumilio-based assembly) protein. RNA-binding protein PumHD (Pumilio homology domain, a member of the PUF family), which has been widely used in native and modified form for targeting RNA, has been engineered to yield a set of four canonical protein modules, each of which targets one RNA base. These modules (i.e., Pumby, for Pumilio-based assembly) can be concatenated in chains of varying composition and length to bind desired target RNAs The specificity of such Pumby–RNA interactions is high, with undetectable binding of a Pumby chain to RNA sequences that bear three or more mismatches from the target sequence. Katarzyna et al., PNAS, 2016; 113(19): E2579-E2588.
[0186] In some embodiments of the compositions of the disclosure, the first RNA binding protein comprises a Pumilio and FBF (PUF) protein. In some embodiments, the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein. In some
embodiments, a PUF1 protein of the disclosure comprises or consists of the amino acid sequence of
MDKSKQMNIN NLSNIPEVID PGITIPIYEE EYENNGESNS QLQQQPQKLG SYRSRAGKFS 60 NTLSNLLPSI SAKLHHSKKN SHGKNGAEFS SSNNSSQSTV ASKTPRASPS RSKMMESSID 120 GVTMDRPGSL TPPQDMEKLV HFPDSSNNFL IPAPRGSSDS FNLPHQISRT RNNTMSSQIT 180 SISSIAPKPR TSSGIWSSNA SANDPMQQHL LQQLQPTTSN NTTNSNTLND YSTKTAYFDN 240 MVSTSGSQMA DNKMNTNNLA IPNSVWSNTR QRSQSNASSI YTDAPLYEQP ARASISSHYT 300 IPTQESPLIA DEIDPQSINW VTMDPTVPSI NQISNLLPTN TISISNVFPL QHQQPQLNNA 360 INLTSTSLAT LCSKYGEVIS ARTLRNLNMA LVEFSSVESA VKALDSLQGK EVSMIGAPSK 420 ISFAKILPMH QQPPQFLLNS QGLPLGLENN NLQPQPLLQE QLFNGAVTFQ QQGNVSIPVF 480 NQQSQQSQHQ NHSSGSAGFS NVLHGYNNNN SMHGNNNNSA NEKEQCPFPL PPPNVNEKED 540 LLREIIELFE ANSDEYQINS LIKKSLNHKG TSDTQNFGPL PEPLSGREFD PPKLRELRKS 600 IDSNAFSDLE IEQLAIAMLD ELPELSSDYL GNTIVQKLFE HSSDIIKDIM LRKTSKYLTS 660 MGVHKNGTWA CQKMITMAHT PRQIMQVTQG VKDYCTPLIN DQFGNYVIQC VLKFGFPWNQ 720 FIFESIIANF WVIVQNRYGA RAVRACLEAH DIVTPEQSIV LSAMIVTYAE YLSTNSNGAL 780 LVTWFLDTSV LPNRHSILAP RLTKRIVELC GHRLASLTIL KVLNYRGDDN ARKIILDSLF 840 GNVNAHDSSP PKELTKLLCE TNYGPTFVHK VLAMPLLEDD LRAHIIKQVR KVLTDSTQIQ 900 PSRRLLEEVG LASPSSTHNK TKQQQQQHHN SSISHMFATP DTSGQHMRGL SVSSVKSGGS 960 KHTTMNTTTT NGSSASTLSP GQPLNANSNS SMGYFSYPGV FPVSGFSGNA SNGYAMNNDD 1020 LSSQFDMLNF NNGTRLSLPQ LSLTNHNNTT MELVNNVGSS QPHTNNNNNN NNTNYNDDNT 1080 VFETLTLHSA N
1091SEQ ID NO: 219). In some embodiments, a PUF3 protein of the disclosure comprises or consists of the amino acid sequence of
1 MEMNMDMDMD MELASIVSSL SALSHSNNNG GQAAAAGIVN GGAAGSQQIG GFRRSSFTTA 61 NEVDSEILLL HGSSESSPIF KKTALSVGTA PPFSTNSKKF FGNGGNYYQY RSTDTASLSS 121 ASYNNYHTHH TAANLGKNNK VNHLLGQYSA SIAGPVYYNG NDNNNSGGEG FFEKFGKSLI 181 DGTRELESQD RPDAVNTQSQ FISKSVSNAS LDTQNTFEQN VESDKNFNKL NRNTTNSGSL 241 YHSSSNSGSS ASLESENAHY PKRNIWNVAN TPVFRPSNNP AAVGATNVAL PNQQDGPANN 301 NFPPYMNGFP PNQFHQGPHY QNFPNYLIGS PSNFISQMIS VQIPANEDTE DSNGKKKKKA 361 NRPSSVSSPS SPPNNSPFPF AYPNPMMFMP PPPLSAPQQQ QQQQQQQQQE DQQQQQQQEN 421 PYIYYPTPNP IPVKMPKDEK TFKKRNNKNH PANNSNNANK QANPYLENSI PTKNTSKKNA 481 SSKSNESTAN NHKSHSHSHP HSQSLQQQQQ TYHRSPLLEQ LRNSSSDKNS NSNMSLKDIF 541 GHSLEFCKDQ HGSRFIQREL ATSPASEKEV IFNEIRDDAI ELSNDVFGNY VIQKFFEFGS 601 KIQKNTLVDQ FKGNMKQLSL QMYACRVIQK ALEYIDSNQR IELVLELSDS VLQMIKDQNG 661 NHVIQKAIET IPIEKLPFIL SSLTGHIYHL STHSYGCRVI QRLLEFGSSE DQESILNELK 721 DFIPYLIQDQ YGNYVIQYVL QQDQFTNKEM VDIKQEIIET VANNVVEYSK HKFASNVVEK 781 SILYGSKNQK DLIISKILPR DKNHALNLED DSPMILMIKD QFANYVIQKL VNVSEGEGKK 841 LIVIAIRAYL DKLNKSNSLG NRHLASVEKL AALVENAEV (SEQ ID NO: 220). In some embodiments, a PUF4 protein of the disclosure comprises or consists of the amino acid sequence of
1 MSTKGLKEEI DDVPSVDPVV SETVNSALEQ LQLDDPEENA TSNAFANKVS QDSQFANGPP 61 SQMFPHPQMM GGMGFMPYSQ MMQVPHNPCP FFPPPDFNDP TAPLSSSPLN AGGPPMLFKN 121 DSLPFQMLSS GAAVATQGGQ NLNPLINDNS MKVLPIASAD PLWTHSNVPG SASVAIEETT 181 ATLQESLPSK GRESNNKASS FRRQTFHALS PTDLINAANN VTLSKDFQSD MQNFSKAKKP 241 SVGANNTAKT RTQSISFDNT PSSTSFIPPT NSVSEKLSDF KIETSKEDLI NKTAPAKKES 301 PTTYGAAYPY GGPLLQPNPI MPGHPHNISS PIYGIRSPFP NSYEMGAQFQ PFSPILNPTS 361 HSLNANSPIP LTQSPIHLAP VLNPSSNSVA FSDMKNDGGK PTTDNDKAGP NVRMDLINPN 421 LGPSMQPFHI LPPQQNTPPP PWLYSTPPPF NAMVPPHLLA QNHMPLMNSA NNKHHGRNNN 481 SMSSHNDNDN IGNSNYNNKD TGRSNVGKMK NMKNSYHGYY NNNNNNNNNN NNNNNSNATN 541 SNSAEKQRKI EESSRFADAV LDQYIGSIHS LCKDQHGCRF LQKQLDILGS KAADAIFEET 601 KDYTVELMTD SFGNYLIQKL LEEVTTEQRI VLTKISSPHF VEISLNPHGT RALQKLIECI 661 KTDEEAQIVV DSLRPYTVQL SKDLNGNHVI QKCLQRLKPE NFQFIFDAIS DSCIDIATHR 721 HGCCVLQRCL DHGTTEQCDN LCDKLLALVD KLTLDPFGNY VVQYIITKEA EKNKYDYTHK 781 IVHLLKPRAI ELSIHKFGSN VIEKILKTAI VSEPMILEIL NNGGETGIQS LLNDSYGNYV 841 LQTALDISHK QNDYLYKRLS EIVAPLLVGP IRNTPHGKRI IGMLHLDS (SEQ ID NO: 221).
In some embodiments, a PUF5 protein of the disclosure comprises or consists of the amino acid sequence of
1 MSDSTGRINS KASDSSSISD HQTADLSIFN GSFDGGAFSS SNIPLFNFMG TGNQRFQYSP 61 HPFAKSSDPC RLAALTPSTP KGPLNLTPAD FGLADFSVGN ESFADFTANN TSFVGNVQSN 121 VRSTRLLPAW AVDNSGNIRD DLTLQDVVSN GSLIDFAMDR TGVKFLERHF PEDHDNEMHF 181 VLFDKLTEQG AVFTSLCRSA AGNFIIQKFV EHATLDEQER LVRKMCDNGL IEMCLDKFAC 241 RVVQMSIQKF DVSIAMKLVE KISSLDFLPL CTDQCAIHVL QKVVKLLPIS AWSFFVKFLC 301 RDDNLMTVCQ DKYGCRLVQQ TIDKLSDNPK LHCFNTRLQL LHGLMTSVAR NCFRLSSNEF 361 ANYVVQYVIK SSGVMEMYRD TIIEKCLLRN ILSMSQDKYA SHVVEGAFLF APPLLLSEMM 421 DEIFDGYVKD QETNRDALDI LLFHQYGNYV VQQMISICIS ALLGKEERKM VASEMRLYAK 481 WFDRIKNRVN RHSGRLERFS SGKKIIESLQ KLNVPMTMTN EPMPYWAMPT PLMDISAHFM 541 NKLNFQKNSV FDE (SEQ ID NO: 222). In some embodiments, a PUF6 protein of the disclosure comprises or consists of the amino acid sequence of
1 MTPNRRSTDS YNMLGASFDF DPDFSLLSNK THKNKNPKPP VKLLPYRHGS NTTSSDLDNY 61 IFNSGSGSSD DETPPPAAPI FISLEEVLLN GLLIDFAIDP SGVKFLEANY PLDSEDQIRK 121 AVFEKLTEST TLFVGLCHSR NGNFIVQKLV ELATPAEQRE LLRQMIDGGL LVMCKDKFAC 181 RVVQLALQKF DHSNVFQLIQ ELSTFDLAAM CTDQISIHVI QRVVKQLPVD MWTFFVHFLS 241 SGDSLMAVCQ DKYGCRLVQQ VIDRLAENPK LPCFKFRIQL LHSLMTCIVR NCYRLSSNEF 301 ANYVIQYVIK SSGIMEMYRD TIIDKCLLRN LLSMSQDKYA SHVIEGAFLF APPALLHEMM 361 EEIFSGYVKD VELNRDALDI LLFHQYGNYV VQQMISICTA ALIGKEERQL PPAILLLYSG 421 WYEKMKQRVL QHASRLERFS SGKKIIDSVM RHGVPTAAAI NAQAAPSLME LTAQFDAMFP 481 SFLAR (SEQ ID NO: 223). In some embodiments, a PUF7 protein of the disclosure comprises or consists of the amino acid sequence of
1 MTPNRRSTDS YNMLGASFDF DPDFSLLSNK THKNKNPKPP VKLLPYRHGS NTTSSDSDSY 61 IFNSGSGSSD AETPAPVAPI FISLEDVLLN GQLIDFAIDP SGVKFLEANY PLDSEDQIRK 121 AVFEKFTEST TLFVGLCHSR NGNFIVQKLV ELATPAEQRE LLRQMIDGGL LAMCKDKFAC 181 RVVQLALQKF DHSNVFQLIQ ELSTFDLAAM CTDQISIHVI QRVVKQLPVD MWTFFVHFLS 241 SGDSLMAVCQ DKYGCRLVQQ VIDRLAENPK LPCFKFRIQL LHSLMTCIVR NCYRLSSNEF 301 ANYVIQYVIK SSGIMEMYRD TIIDKCLLRN LLSMSQDKYA SHVIEGAFLF APPALLHEMM 361 EEIFSGYVKD VESNRDALDI LLFHQYGNYV VQQMISICTA ALIGKEEREL PPAILLLYSG 421 WYEKMKQRVL QHASRLERFS SGKKIIDSVM RHGVPTAAAV NAQAAPSLME LTAQFDAMFP 481 SFLAR (SEQ ID NO: 224). In some embodiments, a PUF8 protein of the disclosure comprises or consists of the amino acid sequence of
1 MSRPISIGNT CTFDPSASPI ESLGRSIGAQ KIVDSVCGSP IRSYGRHIST NPKNERLPDT 61 PEFQFATYMH QGGKVIGQNT LHMFGTPPSC YCAQENIPIS SNVGHVLSTI NNNYMNHQYN 121 GSNMFSNQMT QMLQAQAYND LQMHQAHSQS IRVPVQPSAT GIFSNPYREP TTTDDLLTRY 181 RANPAMMKNL KLSDIRGALL KFAKDQVGSR FIQQELASSK DRFEKDSIFD EVVSNADELV 241 DDIFGNYVVQ KFFEYGEERH WARLVDAIID RVPEYAFQMY ACRVLQKALE KINEPLQIKI 301 LSQIRHVIHR CMKDQNGNHV VQKAIEKVSP QYVQFIVDTL LESSNTIYEM SVDPYGCRVV 361 QRCLEHCSPS QTKPVIGQIH KRFDEIANNQ YGNYVVQHVI EHGSEEDRMV IVTRVSNNLF 421 EFATHKYSSN VIEKCLEQGA VYHKSMIVGA ACHHQEGSVP IVVQMMKDQY ANYVVQKMFD 481 QVTSEQRREL ILTVRPHIPV LAKLEKYFQK PAVMSYPYQD MQGSH (SEQ ID NO: 225). In some embodiments, a PUF9 protein of the disclosure comprises or consists of the amino acid sequence of
1 MADPNWAYAP PTNYYADHSI AKPIMISGGH PSQDQGHSPK SESFGQSVTT AFNGMVDNLV 61 GSPSSSVQQR NYFTTTPFPI SRSPNDRNDD KIMGNGSYGV PIPIPQDGVP QGTPDFQMTP 121 FLQQGGHLIG GSPNGPVQVS GNWYSGGAGI FSTMQQADPS NGMPGMAAEF VNNENGMPGP 181 NGMHQQAMIS GSPPFPYQNM MNLTTSFGAM GLGPQQIQQR DPQMFQQPIL HEPIQGMAQN 241 GFGQQVFFTQ MQNQQHPQGQ AQQQLQQLAQ QHQQQQNSQQ FFGQGPNGMG NGGVMNDWSQ 301 RSFGMPQQQA QQNGLPPNFS QNPPRRRGPE DPNGQTPKTL QDIKNNVIEF AKDQHGSRFI 361 QQKLERASLR DKAAIFTPVL ENAEELMTDV FGNYVIQKFF EFGNNEQRNQ LVGTIRGNVM 421 KLALQMYGCR VIQKALEYVE EKYQHEILGE MEGQVLKCVK DQNGNHVIQK VIERVEPERL 481 QFIIDAFTKN NSDNVYTLSV HPYGCRVIQR VLEYCNEEQK QPVLDALQIH LKQLVLDQYG 541 NYVIQHVIEH GSPSDKEQIV QDVISDDLLK FAQHKFASNV IEKCLTFGGH AERNLIIDKV 601 CGDPNDPSPP LLQMMKDPFA NYVVQKMLDV ADPQHRKKIT LTIKPHIATL RKYNFGKHIL 661 LKLEKYFAKQ APANSSNSSS NDQIYEHSPF DIPLGADFSN HPF (SEQ ID NO: 226).
[0187] In some embodiments of the compositions of the disclosure, the RNA-binding protein or RNA-binding portion thereof is a PPR protein. PPR proteins (proteins with pentatricopeptide repeat (PPR) motifs derived from plants) are nuclear-encoded and exclusively controlled at the RNA level organelles (chloroplasts and mitochondria), cutting, translation, splicing, RNA editing, genes specifically acting on RNA stability. PPR proteins are typically a motif of 35 amino acids and have a structure in which a PPR motif is about 10 contiguous amino acids. The combination of PPR motifs can be used for sequence-selective binding to RNA. PPR proteins are often comprised of PPR motifs of about 10 repeat domains. PPR domains or RNA-binding domains may be configured to be catalytically inactive. WO 2013/058404 incorporated herein by reference in its entirety.
[0188] In some embodiments of the compositions of the disclosure, a fusion protein comprises the RNA-binding polypeptide. In some embodiments, the fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity, wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity.
[0189] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the first RNA binding protein comprises a CRISPR-Cas protein. In some embodiments, the CRISPR-Cas protein is a Type II CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR- Cas protein is a Type V CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof. In some embodiments, the CRISPR-Cas protein is a Type VI CRISPR-Cas protein. In some embodiments, the first RNA binding protein comprises a Cas13 polypeptide or an RNA- binding portion thereof. In some embodiments, the CRISPR-Cas protein comprises a native RNA nuclease activity.
[0190] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the native RNA nuclease activity is reduced or inhibited. In some embodiments, the native RNA nuclease activity is increased or induced. In some embodiments, the CRISPR-Cas protein comprises a native DNA nuclease activity and wherein the native DNA nuclease activity is inhibited. In some embodiments, the CRISPR-Cas protein comprises a mutation. In some embodiments, a nuclease domain of the CRISPR-Cas protein comprises the mutation. In some embodiments, the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein. In some embodiments, the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a
transposition. In some embodiments, the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain.
[0191] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide or RNA- binding portion thereof and a sequence encoding a second RNA-binding polypeptide or RNA-binding portion thereof, the first RNA binding protein comprises a Pumilio and FBF (PUF) protein. In some embodiments, the first RNA binding protein comprises a Pumilio- based assembly (PUMBY) protein. In some embodiments, the first RNA binding protein comprises a PPR (pentatricopeptide repeat) protein.
[0192] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the first RNA binding protein does not require multimerization for RNA-binding activity. In some embodiments, the first RNA binding protein is not a monomer of a multimer complex. In some embodiments, a multimer protein complex does not comprise the first RNA binding protein [0193] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the first RNA binding protein selectively binds to a target sequence within the RNA molecule. In some embodiments, the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule. In some embodiments, the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule.
[0194] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, an RNA genome or an RNA transcriptome comprises the RNA molecule.
[0195] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
[0196] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS). In some embodiments, the sequence encoding a nuclear localization signal (NLS) is positioned 3’ to the sequence encoding the first RNA binding protein. In some embodiments, the first RNA binding protein comprises an NLS at a C-terminus of the protein. In some
embodiments, the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. In some embodiments, the sequence encoding the first NLS or the second NLS is positioned 3’ to the sequence encoding the first RNA binding protein. In some embodiments, the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein. RNA-Binding Endonucleases
[0197] In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the second RNA binding protein binds RNA in a manner in which it associates with RNA. In some embodiments, the second RNA binding protein associates with RNA in a manner in which it cleaves RNA [0198] In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of an RNAse.
[0199] In some embodiments of the compositions of the disclosure, including those wherein a fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA-binding polypeptide, the second RNA binding protein comprises or consists of a nuclease domain. In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an RNAse. In some embodiments, the second RNA binding protein comprises or consists of an RNAse1. In some embodiments, the sequence encoding the RNAse1 comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGLCKPVNTFVHEPLVDVQ NVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEG SPYVPVHFDASVEDST (SEQ ID NO: 20). In some embodiments, the second RNA binding protein comprises or consists of an RNAse4. In some embodiments, the sequence encoding the RNAse4 comprises or consists of:
QDGMYQRFLRQHVHPEETGGSDRYCDLMMQRRKMTLYHCKRFNTFIHEDIWNIRSI CSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRRVVIACEGNPQ VPVHFDG (SEQ ID NO: 21). In some embodiments, the second RNA binding protein comprises or consists of an RNAse6. In some embodiments, the sequence encoding the RNAse6 comprises or consists of:
WPKRLTKAHWFEIQHIQPSPLQCNRAMSGINNYTQHCKHQNTFLHDSFQNVAAVCD LLSIVCKNRRHNCHQSSKPVNMTDCRLTSGKYPQCRYSAAAQYKFFIVACDPPQKSD PPYKLVPVHLDSIL (SEQ ID NO: 22). In some embodiments, the second RNA binding protein comprises or consists of an RNAse7. In some embodiments, the sequence encoding the RNAse7 comprises or consists of:
APARAGFCPLLLLLLLGLWVAEIPVSAKPKGMTSSQWFKIQHMQPSPQACNSAMKNI NKHTKRCKDLNTFLHEPFSSVAATCQTPKIACKNGDKNCHQSHGPVSLTMCKLTSG KYPNCRYKEKRQNKSYVVACKPPQKKDSQQFHLVPVHLDRVL (SEQ ID NO: 23). In some embodiments, the second RNA binding protein comprises or consists of an RNAse8. In some embodiments, the sequence encoding the RNAse8 comprises or consists of:
TSSQWFKTQHVQPSPQACNSAMSIINKYTERCKDLNTFLHEPFSSVAITCQTPNIACK NSCKNCHQSHGPMSLTMGELTSGKYPNCRYKEKHLNTPYIVACDPPQQGDPGYPLV PVHLDKVV (SEQ ID NO: 24). In some embodiments, the second RNA binding protein comprises or consists of an RNAse2. In some embodiments, the sequence encoding the RNAse2 comprises or consists of:
KPPQFTWAQWFETQHINMTSQQCTNAMQVINNYQRRCKNQNTFLLTTFANVVNVC GNPNMTCPSNKTRKNCHHSGSQVPLIHCNLTTPSPQNISNCRYAQTPANMFYIVACD NRDQRRDPPQYPVVPVHLDRII (SEQ ID NO: 25). In some embodiments, the second RNA binding protein comprises or consists of an RNAse6PL. In some embodiments, the sequence encoding the RNAse6PL comprises or consists of:
DKRLRDNHEWKKLIMVQHWPETVCEKIQNDCRDPPDYWTIHGLWPDKSEGCNRSW PFNLEEIKKNWMEITDSSLPSPSMGPAPPRWMRSTPRRSTLAEAWNSTGSWTSTGGC ALPPAALPSGDLCCRPSLTAGSRGVGVDLTALHQLLHVHYSATGIIPEECSEPTKPFQI ILHHDHTEWVQSIGMPIWGTISSSESAIGKNEESQPACAVLSHDS (SEQ ID NO: 26). In some embodiments, the second RNA binding protein comprises or consists of an RNAseL. In some embodiments, the sequence encoding the RNAseL comprises or consists of:
AAVEDNHLLIKAVQNEDVDLVQQLLEGGANVNFQEEEGGWTPLHNAVQMSREDIV ELLLRHGADPVLRKKNGATPFILAAIAGSVKdLLKLFLSKGADVNECDFYGFTAFME AAVYGKVKALKFLYKRGANVNLRRKTKEDQERLRKGGATALMDAAEKGHVEVLK ILLDEMGADVNACDNMGRNALIHALLSSDDSDVEAITHLLLDHGADVNVRGERGKT PLILAVEKKHLGLVQRLLEQEHIEINDTDSDGKTALLLAVELKLKKIAELLCKRGAST DCGDLVMTARRNYDHSLVKVLLSHGAKEDFHPPAEDWKPQSSHWGAALKDLHRIY RPMIGKLKFFIDEKYKIADTSEGGIYLGFYEKQEVAVKTFCEGSPRAQREVSCLQSSR ENSHLVTFYGSESHRGHLFVCVTLCEQTLEACLDVHRGEDVENEEDEFARNVLSSIF KAVQELHLSCGYTHQDLQPQNILIDSKKAAHLADFDKSIKWAGDPQEVKRDLEDLG RLVLYVVKKGSISFEDLKAQSNEEVVQLSPDEETKDLIHRLFHPGEHVRDCLSDLLG HPFFWTWESRYRTLRNVGNESDIKTRKSESEILRLLQPGPSEHSKSFDKWTTKINECV MKKMNKFYEKRGNFYQNTVGDLLKFIRNLGEHIDEEKHKKMKLKIGDPSLYFQKTF PDLVIYVYTKLQNTEYRKHFPQTHSPNKPQCDGAGGASGLASPGC (SEQ ID NO: 27). In some embodiments, the second RNA binding protein comprises or consists of an
RNAseT2. In some embodiments, the sequence encoding the RNAseT2 comprises or consists of:
VQHWPETVCEKIQNDCRDPPDYWTIHGLWPDKSEGCNRSWPFNLEEIKDLLPEMRA YWPDVIHSFPNRSRFWKHEWEKHGTCAAQVDALNSQKKYFGRSLELYRELDLNSVL LKLGIKPSINYYQVADFKDALARVYGVIPKIQCLPPSQDEEVQTIGQIELCLTKQDQQ LQNCTEPGEQPSPKQEVWLANGAAESRGLRVCEDGPVFYPPPKKTKH (SEQ ID NO: 28). In some embodiments, the second RNA binding protein comprises or consists of an RNAse11. In some embodiments, the sequence encoding the RNAse11 comprises or consists of:
EASESTMKIIKEEFTDEEMQYDMAKSGQEKQTIEILMNPILLVKNTSLSMSKDDMSST LLTFRSLHYNDPKGNSSGNDKECCNDMTVWRKVSEANGSCKWSNNFIRSSTEVMR RVHRAPSCKFVQNPGISCCESLELENTVCQFTTGKQFPRCQYHSVTSLEKILTVLTGH SLMSWLVCGSKL (SEQ ID NO: 29). In some embodiments, the second RNA binding protein comprises or consists of an RNAseT2-like. In some embodiments, the sequence encoding the RNAseT2-like comprises or consists of:
XLGGADKRLRDNHEWKKLIMVQHWPETVCEKIQNDCRDPPDYWTIHGLWPDKSEG CNRSWPFNLEEIKDLLPEMRAYWPDVIHSFPNRSRFWKHEWEKHGTCAAQVDALNS QKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQTTEEDLNLDVEPTTEDTAEEVTIH VLLHSALFGEIGPRRW (SEQ ID NO: 30).
[0200] In some embodiments of the compositions of the disclosure, the second RNA binding protein comprises or consists of a mutated RNAse.
[0201] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R)) polypeptide. In some embodiments, the Rnase1(K41R) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCRPVNTFVHEPLVDVQ NVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEG SPYVPVHFDASVEDST (SEQ ID NO: 116).
[0202] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E)) polypeptide. In some embodiments, the Rnase1 (Rnase1(K41R, D121E)) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCRPVNTFVHEPLVDVQ NVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEG SPYVPVHFEASVEDST (SEQ ID NO: 117).
[0203] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(K41R, D121E, H119N)) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCRPVNTFVHEPLVDVQ NVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEG SPYVPVNFEASVEDST (SEQ ID NO: 118) [0204] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1. In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(H119N)) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQ NVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEG SPYVPVNFDASVEDST (SEQ ID NO: 119).
[0205] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCKPVNTFVHEPLVDVQ NVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEG SPYVPVNFDASVEDST (SEQ ID NO: 120). In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide.
[0206] In some embodiments, the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCRPVNTFVHEPLVDVQ NVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEG SPYVPVNFEASVEDST (SEQ ID NO: 121).
[0207] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D, H119N)) polypeptide. In some embodiments, the Rnase1 (Rnase1(R39D, N67D, N88A, G89D, R91D)) polypeptide comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCKPVNTFVHEPLVDVQ NVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEG SPYVPVHFDASVEDST (SEQ ID NO: 122).
[0208] In some embodiments, the second RNA binding protein comprises or consists of a mutated Rnase1 (Rnase1 (R39D, N67D, N88A, G89D, R91D, H119N, K41R, D121E)) polypeptide that comprises or consists of: KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGDCRPVNTFVHEPLVDVQ NVCFQEKVTCKDGQGNCYKSNSSMHITDCRLTADSDYPNCAYRTSPKERHIIVACEG SPYVPVNFEASVEDST (SEQ ID NO: 208).
[0209] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a NOB1 polypeptide. The composition of claim 101, wherein the sequence encoding the NOB1 polypeptide comprises or consists of:
APVEHVVADAGAFLRHAALQDIGKNIYTIREVVTEIRDKATRRRLAVLPYELRFKEPL PEYVRLVTEFSKKTGDYPSLSATDIQVLALTYQLEAEFVGVSHLKQEPQKVKVSSSIQ HPETPLHISGFHLPYKPKPPQETEKGHSACEPENLEFSSFMFWRNPLPNIDHELQELLI DRGEDVPSEEEEEEENGFEDRKDDSDDDGGGWITPSNIKQIQQELEQCDVPEDVRVG CLTTDFAMQNVLLQMGLHVLAVNGMLIREARSYILRCHGCFKTTSDMSRVFCSHCG NKTLKKVSVTV (SEQ ID NO: 31).
[0210] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an endonuclease. In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an endonuclease V (ENDOV). In some embodiments, the sequence encoding the ENDOV comprises or consists of:
AFSGLQRVGGVDVSFVKGDSVRACASLVVLSFPELEVVYEESRMVSLTAPYVSGFL AFREVPFLLELVQQLREKEPGLMPQVLLVDGNGVLHHRGFGVACHLGVLTDLPCVG VAKKLLQVDGLENNALHKEKIRLLQTRGDSFPLLGDSGTVLGMALRSHDRSTRPLYI SVGHRMSLEAAVRLTCCCCRFRIPEPVRQADICSREHIRKS (SEQ ID NO: 32).
[0211] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an endonuclease G (ENDOG). In some embodiments, the sequence encoding the ENDOG comprises or consists of:
AELPPVPGGPRGPGELAKYGLPGLAQLKSRESYVLCYDPRTRGALWVVEQLRPERL RGDGDRRECDFREDDSVHAYHRATNADYRGSGFDRGHLAAAANHRWSQKAMDDT FYLSNVAPQVPHLNQNAWNNLEKYSRSLTRSYQNVYVCTGPLFLPRTEADGKSYVK YQVIGKNHVAVPTHFFKVLILEAAGGQIELRTYVMPNAPVDEAIPLERFLVPIESIERA SGLLFVPNILARAGSLKAITAGSK (SEQ ID NO: 33).
[0212] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an endonuclease D1 (ENDOD1). In some embodiments, sequence encoding the ENDOD1 comprises or consists of:
RLVGEEEAGFGECDKFFYAGTPPAGLAADSHVKICQRAEGAERFATLYSTRDRIPVY SAFRAPRPAPGGAEQRWLVEPQIDDPNSNLEEAINEAEAITSVNSLGSKQALNTDYLD SDYQRGQLYPFSLSSDVQVATFTLTNSAPMTQSFQERWYVNLHSLMDRALTPQCGS GEDLYILTGTVPSDYRVKDKVAVPEFVWLAACCAVPGGGWAMGFVKHTRDSDIIED VMVKDLQKLLPFNPQLFQNNCGETEQDTEKMKKILEVVNQIQDEERMVQSQKSSSP LSSTRSKRSTLLPPEASEGSSSFLGKLMGFIATPFIKLFQLIYYLVVAILKNIVYFLWCV TKQVINGIESCLYRLGSATISYFMAIGEELVSIPWKVLKVVAKVIRALLRILCCLLKAI CRVLSIPVRVLVDVATFPVYTMGAIPIVCKDIALGLGGTVSLLFDTAFGTLGGLFQVV FSVCKRIGYKVTFDNSGEL (SEQ ID NO: 34).
[0213] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Human flap endonuclease-1 (hFEN1). In some embodiments, the sequence encoding the hFEN1 comprises or consists of:
MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEG ETTSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQA QAAGAEQEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAG KVYAAATEDMDCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLC ILLGSDYCESIRGIGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEP EVLDPESVELKWSEPNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTQGRLDDFF KVTGSLSSAKRKEPEPKGSTKKKAKTGAAGKFKRGK (SEQ ID NO: 35).
[0214] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a human Schlafen 14 (hSLFN14) polypeptide. In some
embodiments, the sequence encoding the hSLFN14 comprises or consists of:
ESTHVEFKRFTTKKVIPRIKEMLPHYVSAFANTQGGYVLIGVDDKSKEVVGCKWEK VNPDLLKKEIENCIEKLPTFHFCCEKPKVNFTTKILNVYQKDVLDGYVCVIQVEPFCC VVFAEAPDSWIMKDNSVTRLTAEQWVVMMLDTQSAPPSLVTDYNSCLISSASSARK SPGYPIKVHKFKEALQ (SEQ ID NO: 36).
[0215] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a human beta-lactamase-like protein 2 (hLACTB2) polypeptide. In some embodiments, the sequence encoding the hLACTB2 comprises or consists of:
TLQGTNTYLVGTGPRRILIDTGEPAIPEYISCLKQALTEFNTAIQEIVVTHWHRDHSGG IGDICKSINNDTTYCIKKLPRNPQREEIIGNGEQQYVYLKDGDVIKTEGATLRVLYTPG HTDDHMALLLEEENAIFSGDCILGEGTTVFEDLYDYMNSLKELLKIKADIIYPGHGPV IHNAEAKIQQYISHRNIREQQILTLFRENFEKSFTVMELVKIIYKNTPENLHEMAKHNL LLHLKKLEKEGKIFSNTDPDKKWKAHL (SEQ ID NO: 37). [0216] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an apurinic/apyrimidinic (AP) endodeoxyribonuclease (APEX2) polypeptide. In some embodiments, the sequence encoding the APEX2 comprises or consists of:
MLRVVSWNINGIRRPLQGVANQEPSNCAAVAVGRILDELDADIVCLQETKVTRDAL TEPLAIVEGYNSYFSFSRNRSGYSGVATFCKDNATPVAAEEGLSGLFATQNGDVGCY GNMDEFTQEELRALDSEGRALLTQHKIRTWEGKEKTLTLINVYCPHADPGRPERLVF KMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECFEEDPGRKWMD SLLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGD RTLVIDTFQASFLLPEVMGSDHCPVGAVLSVSSVPAKQCPPLCTRFLPEFAGTQLKIL RFLVPLEQSPVLEQSTLQHNNQTRVQTCQNKAQVRSTRPQPSQVGSSRGQKNLKSYF QPSPSCPQASPDIELPSLPLMSALMTPKTPEEKAVAKVVKGQAKTSEAKDEKELRTSF WKSVLAGPLRTPLCGGHREPCVMRTVKKPGPNLGRRFYMCARPRGPPTDPSSRCNF FLWSRPS (SEQ ID NO: 38).
[0217] In some embodiments, the sequence encoding the APEX2 comprises or consists of: MLRVVSWNINGIRRPLQGVANQEPSNCAAVAVGRILDELDADIVCLQETKVTRDAL TEPLAIVEGYNSYFSFSRNRSGYSGVATFCKDNATPVAAEEGLSGLFATQNGDVGCY GNMDEFTQEELRALDSEGRALLTQHKIRTWEGKEKTLTLINVYCPHADPGRPERLVF KMRFYRLLQIRAEALLAAGSHVIILGDLNTAHRPIDHWDAVNLECFEEDPGRKWMD SLLSNLGCQSASHVGPFIDSYRCFQPKQEGAFTCWSAVTGARHLNYGSRLDYVLGD RTLVIDTFQASFLLPEVMGSDHCPVGAVLSVSSVPAKQCPPLCTRFLPEFAGTQLKIL RFLVPLEQSP (SEQ ID NO: 39).
[0218] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an angiogenin (ANG) polypeptide. In some embodiments, the sequence encoding the ANG comprises or consists of:
QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICE NKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVH LDQSIFRRP (SEQ ID NO: 40).
[0219] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a heat responsive protein 12 (HRSP12) polypeptide. In some embodiments, the sequence encoding the HRSP12 comprises or consists of: SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGVAEEAKQALK NMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAALP KGSRIEIEAVAIQGPLTTASL (SEQ ID NO: 41).
[0220] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12A (ZC3H12A) polypeptide. In some embodiments, the sequence encoding the ZC3H12A comprises or consists of:
GGGTPKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFL ERGHTDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDD RFIVKLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGR HGPSLDNFLRKKPLTLE (SEQ ID NO: 42). In some embodiments, the sequence encoding the ZC3H12A comprises or consists of:
SGPCGEKPVLEASPTMSLWEFEDSHSRQGTPRPGQELAAEEASALELQMKVDFFRKL GYSSTEIHSVLQKLGVQADTNTVLGELVKHGTATERERQTSPDPCPQLPLVPRGGGT PKAPNLEPPLPEEEKEGSDLRPVVIDGSNVAMSHGNKEVFSCRGILLAVNWFLERGH TDITVFVPSWRKEQPRPDVPITDQHILRELEKKKILVFTPSRRVGGKRVVCYDDRFIV KLAYESDGIVVSNDTYRDLQGERQEWKRFIEERLLMYSFVNDKFMPPDDPLGRHGP SLDNFLRKKPLTLEHRKQPCPYGRKCTYGIKCRFFHPERPSCPQRSVADELRANALLS PPRAPSKDKNGRRPSPSSQSSSLLTESEQCSLDGKKLGAQASPGSRQEGLTQTYAPSG RSLAPSGGSGSSFGPTDWLPQTLDSLPYVSQDCLDSGIGSLESQMSELWGVRGGGPG EPGPPRAPYTGYSPYGSELPATAAFSAFGRAMGAGHFSVPADYPPAPPAFPPREYWS EPYPLPPPTSVLQEPPVQSPGAGRSPWGRAGSLAKEQASVYTKLCGVFPPHLVEAVM GRFPQLLDPQQLAAEILSYKSQHPSE (SEQ ID NO: 43).
[0221] In some embodiments, wherein the sequence encoding the second RNA binding protein comprises or consists of a Reactive Intermediate Imine Deaminase A (RIDA) polypeptide. In some embodiments, the sequence encoding the RIDA comprises or consists of:
SSLIRRVISTAKAPGAIGPYSQAVLVDRTIYISGQIGMDPSSGQLVSGGVAEEAKQALK NMGEILKAAGCDFTNVVKTTVLLADINDFNTVNEIYKQYFKSNFPARAAYQVAALP KGSRIEIEAVAIQGPLTTASL (SEQ ID NO: 44).
[0222] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Phospholipase D Family Member 6 (PDL6) polypeptide. In some embodiments the sequence encoding the PDL6 comprises or consists of: EALFFPSQVTCTEALLRAPGAELAELPEGCPCGLPHGESALSRLLRALLAARASLDLC LFAFSSPQLGRAVQLLHQRGVRVRVVTDCDYMALNGSQIGLLRKAGIQVRHDQDPG YMHHKFAIVDKRVLITGSLNWTTQAIQNNRENVLITEDDEYVRLFLEEFERIWEQFNP TKYTFFPPKKSHGSCAPPVSRAGGRLLSWHRTCGTSSESQT (SEQ ID NO: 126).
[0223] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Endonuclease III-like protein 1 (NTHL) polypeptide. In some embodiments, the sequence encoding the NTHL comprises or consists of:
CSPQESGMTALSARMLTRSRSLGPGAGPRGCREEPGPLRRREAAAEARKSHSPVKRP RKAQRLRVAYEGSDSEKGEGAEPLKVPVWEPQDWQQQLVNIRAMRNKKDAPVDH LGTEHCYDSSAPPKVRRYQVLLSLMLSSQTKDQVTAGAMQRLRARGLTVDSILQTD DATLGKLIYPVGFWRSKVKYIKQTSAILQQHYGGDIPASVAELVALPGVGPKMAHL AMAVAWGTVSGIAVDTHVHRIANRLRWTKKATKSPEETRAALEEWLPRELWHEIN GLLVGFGQQTCLPVHPRCHACLNQALCPAAQGL (SEQ ID NO: 123).
[0224] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Mitochondrial ribonuclease P catalytic subunit(KIAA0391) polypeptide. In some embodiments, the sequence encoding the KIAA0391 comprises or consists of:
KARYKTLEPRGYSLLIRGLIHSDRWREALLLLEDIKKVITPSKKNYNDCIQGALLHQD VNTAWNLYQELLGHDIVPMLETLKAFFDFGKDIKDDNYSNKLLDILSYLRNNQLYP GESFAHSIKTWFESVPGKQWKGQFTTVRKSGQCSGCGKTIESIQLSPEEYECLKGKIM RDVIDGGDQYRKTTPQELKRFENFIKSRPPFDVVIDGLNVAKMFPKVRESQLLLNVV SQLAKRNLRLLVLGRKHMLRRSSQWSRDEMEEVQKQASCFFADDISEDDPFLLYAT LHSGNHCRFITRDLMRDHKACLPDAKTQRLFFKWQQGHQLAIVNRFPGSKLTFQRIL SYDTVVQTTGDSWHIPYDEDLVERCSCEVPTKWLCLHQKT (SEQ ID NO: 127).
[0225] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an apurinic or apyrimidinic site lyase (APEX1) polypeptide. In some embodiments, the sequence encoding the APEX1 comprises or consists of:
PKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSG KPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGL SHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAY VPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNK KNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRL DYFLLS (SEQ ID NO: 125) [0226] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an argonaute 2 (AGO2) polypeptide. In some embodiments, the sequence encoding the AGO2 comprises or consists of:
SVEPMFRHLKNTYAGLQLVVVILPGKTPVYAEVKRVGDTVLGMATQCVQMKNVQR TTPQTLSNLCLKINVKLGGVNNILLPQGRPPVFQQPVIFLGADVTHPPAGDGKKPSIA AVVGSMDAHPNRYCATVRVQQHRQEIIQDLAAMVRELLIQFYKSTRFKPTRIIFYRD GVSEGQFQQVLHHELLAIREACIKLEKDYQPGITFIVVQKRHHTRLFCTDKNERVGKS GNIPAGTTVDTKITHPTEFDFYLCSHAGIQGTSRPSHYHVLWDDNRFSSDELQILTYQ LCHTYVRCTRSVSIPAPAYYAHLVAFRARYHLVDKEHDSAEGSHTSGQSNGRDHQA LAKAVQVHQDTLRTMYFA (SEQ ID NO: 128).
[0227] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a mitochondrial nuclease EXOG (EXOG) polypeptide. In some embodiments, the sequence encoding the EXOG comprises or consists of:
QGAEGALTGKQPDGSAEKAVLEQFGFPLTGTEARCYTNHALSYDQAKRVPRWVLE HISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYVGSGWSRGHMAPAGNNKFSSKA MAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTERFEDVWVVSGPLTLPQTRGDGK KIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPLALGAFVVPNEAIGFQPQLTEFQVS LQDLEKLSGLVFFPHLDRTSDIRNICSVDTCKLLDFQEFTLYLSTRKIEGARSVLRLEK IMENLKNAEIEPDDYFMSRYEKKLEELKAKEQSGTQIRKPS (SEQ ID NO: 129).
[0228] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Zinc Finger CCCH-Type Containing 12D (ZC3H12D)
polypeptide. In some embodiments, the sequence encoding the ZC3H12D comprises or consists of:
EHPSKMEFFQKLGYDREDVLRVLGKLGEGALVNDVLQELIRTGSRPGALEHPAAPRL VPRGSCGVPDSAQRGPGTALEEDFRTLASSLRPIVIDGSNVAMSHGNKETFSCRGIKL AVDWFRDRGHTYIKVFVPSWRKDPPRADTPIREQHVLAELERQAVLVYTPSRKVHG KRLVCYDDRYIVKVAYEQDGVIVSNDNYRDLQSENPEWKWFIEQRLLMFSFVNDRF MPPDDPLGRHGPSLSNFLSRKPKPPEPSWQHCPYGKKCTYGIKCKFYHPERPHHAQL AVADELRAKTGARPGAGAEEQRPPRAPGGSAGARAAPREPFAHSLPPARGSPDLAA LRGSFSRLAFSDDLGPLGPPLPVPACSLTPRLGGPDWVSAGGRVPGPLSLPSPESQFSP GDLPPPPGLQLQPRGEHRPRDLHGDLLSPRRPPDDPWARPPRSDRFPGRSVWAEPAW GDGATGGLSVYATEDDEGDARARARIALYSVFPRDQVDRVMAAFPELSDLARLILL VQRCQSAGAPLGKP (SEQ ID NO: 130) [0229] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an endoplasmic reticulum to nucleus signaling 2 (ERN2) polypeptide. In some embodiments, the sequence encoding the ERN2 comprises or consists of:
RQQQPQVVEKQQETPLAPADFAHISQDAQSLHSGASRRSQKRLQSPSKQAQPLDDPE AEQLTVVGKISFNPKDVLGRGAGGTFVFRGQFEGRAVAVKRLLRECFGLVRREVQL LQESDRHPNVLRYFCTERGPQFHYIALELCRASLQEYVENPDLDRGGLEPEVVLQQL MSGLAHLHSLHIVHRDLKPGNILITGPDSQGLGRVVLSDFGLCKKLPAGRCSFSLHSG IPGTEGWMAPELLQLLPPDSPTSAVDIFSAGCVFYYVLSGGSHPFGDSLYRQANILTG APCLAHLEEEVHDKVVARDLVGAMLSPLPQPRPSAPQVLAHPFFWSRAKQLQFFQD VSDWLEKESEQEPLVRALEAGGCAVVRDNWHEHISMPLQTDLRKFRSYKGTSVRDL LRAVRNKKHHYRELPVEVRQALGQVPDGFVQYFTNRFPRLLLHTHRAMRSCASESL FLPYYPPDSEARRPCPGATGR (SEQ ID NO: 131).
[0230] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a pelota mRNA surveillance and ribosome rescue factor (PELO) polypeptide. In some embodiments, the sequence encoding the PELO comprises or consists of:
KLVRKNIEKDNAGQVTLVPEEPEDMWHTYNLVQVGDSLRASTIRKVQTESSTGSVG SNRVRTTLTLCVEAIDFDSQACQLRVKGTNIQENEYVKMGAYHTIELEPNRQFTLAK KQWDSVVLERIEQACDPAWSADVAAVVMQEGLAHICLVTPSMTLTRAKVEVNIPRK RKGNCSQHDRALERFYEQVVQAIQRHIHFDVVKCILVASPGFVREQFCDYLFQQAV KTDNKLLLENRSKFLQVHASSGHKYSLKEALCDPTVASRLSDTKAAGEVKALDDFY KMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKE NAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED (SEQ ID NO: 132).
[0231] In some embodiments, wherein the sequence encoding the second RNA binding protein comprises or consists of a YBEY metallopeptidase (YBEY) polypeptide. In some embodiments, the sequence encoding the YBEY comprises or consists of:
SLVIRNLQRVIPIRRAPLRSKIEIVRRILGVQKFDLGIICVDNKNIQHINRIYRDRNVPTD VLSFPFHEHLKAGEFPQPDFPDDYNLGDIFLGVEYIFHQCKENEDYNDVLTVTATHG LCHLLGFTHGTEAEWQQMFQKEKAVLDELGRRTGTRLQPLTRGLFGGS (SEQ ID NO: 133). [0232] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a cleavage and polyadenylation specific factor 4 like (CPSF4L) polypeptide. In some embodiments, the sequence encoding the CPSF4L comprises or consists of:
QEVIAGLERFTFAFEKDVEMQKGTGLLPFQGMDKSASAVCNFFTKGLCEKGKLCPF RHDRGEKMVVCKHWLRGLCKKGDHCKFLHQYDLTRMPECYFYSKFGDCSNKECSF LHVKPAFKSQDCPWYDQGFCKDGPLCKYRHVPRIMCLNYLVGFCPEGPKCQFAQKI REFKLLPGSKI (SEQ ID NO: 134).
[0233] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an hCG_2002731polypeptide. In some embodiments, the sequence encoding the hCG_2002731 comprises or consists of:
KLVRKNIEKDNAGQVTLVPEEPEDMWHTYNLVQVGDSLRASTIRKVQTESSTGSVG SNRVRTTLTLCVEAIDFDSQACQLRVKGTNIQENEYVKMGAYHTIELEPNRQFTLAK KQWDSVVLERIEQACDPAWSADVAAVVMQEGLAHICLVTPSMTLTRAKVEVNIPRK RKGNCSQHDRALERFYEQVVQAIQRHIHFDVVKCILVASPGFVREQFCDYMFQQAV KTDNKLLLENRSKFLQVHASSGHKYSLKEALCDPTVASRLSDTKAAGEVKALDDFY KMLQHEPDRAFYGLKQVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKE NAGTVRIFSSLHVSGEQLSQLTGVAAILRFPVPELSDQEGDSSSEED (SEQ ID NO: 135).
[0234] In some embodiments, the sequence encoding the hCG_2002731 comprises or consists of:
DPAWSADVAAVVMQEGLAHICLVTPSMTLTRAKVEVNIPRKRKGNCSQHDRALERF YEQVVQAIQRHIHFDVVKCILVASPGFVREQFCDYMFQQAVKTDNKLLLENRSKFLQ VHASSGHKYSLKEALCDPTVASRLSDTKAAGEVKALDDFYKMLQHEPDRAFYGLK QVEKANEAMAIDTLLISDELFRHQDVATRSRYVRLVDSVKENAGTVRIFSSLHVSGE QLSQLTGVAAILRFPVPELSDQEGDSSSEED (SEQ ID NO: 136).
[0235] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of an Excision Repair Cross-Complementation Group 1 (ERCC1) polypeptide. In some embodiments, the sequence encoding the ERCC1 comprises or consists of:
MDPGKDKEGVPQPSGPPARKKFVIPLDEDEVPPGVRGNPVLKFVRNVPWEFGDVIPD YVLGQSTCALFLSLRYHNLHPDYIHGRLQSLGKNFALRVLLVQVDVKDPQQALKEL AKMCILADCTLILAWSPEEAGRYLETYKAYEQKPADLLMEKLEQDFVSRVTECLTT VKSVNKTDSQTLLTTFGSLEQLIAASREDLALCPGLGPQK (SEQ ID NO: 137).
[0236] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a ras-related C3 botulinum toxin substrate 1 isoform (RAC1) polypeptide. In some embodiments, the sequence encoding the RAC1 comprises or consists of:
KESRAKKFQRQHMDSDSSPSSSSTYCNQMMRRRNMTQGRCKPVNTFVHEPLVDVQ NVCFQEKVTCKNGQGNCYKSNSSMHITDCRLTNGSRYPNCAYRTSPKERHIIVACEG SPYVPVHFDASVEDST (SEQ ID NO: 138).
[0237] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Ribonuclease A A1 (RAA1) polypeptide. In some embodiments, the sequence encoding the RAA1 comprises or consists of:
QDNSRYTHFLTQHYDAKPQGRDDRYCESIMRRRGLTSPCKDINTFIHGNKRSIKAICE NKNGNPHRENLRISKSSFQVTTCKLHGGSPWPPCQYRATAGFRNVVVACENGLPVH LDQSIFRRP (SEQ ID NO: 139).
[0238] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a Ras Related Protein (RAB1) polypeptide. In some embodiments, the sequence encoding the RAB1 comprises or consists of:
GLGLVQPSYGQDGMYQRFLRQHVHPEETGGSDRYCNLMMQRRKMTLYHCKRFNT FIHEDIWNIRSICSTTNIQCKNGKMNCHEGVVKVTDCRDTGSSRAPNCRYRAIASTRR VVIACEGNPQVPVHFDG (SEQ ID NO: 140).
[0239] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a DNA Replication Helicase/Nuclease 2 (DNA2) polypeptide. In some embodiments, the sequence encoding the DNA2 comprises or consists of:
XSAVDNILLKLAKFKIGFLRLGQIQKVHPAIQQFTEQEICRSKSIKSLALLEELYNSQLI VATTCMGINHPIFSRKIFDFCIVDEASQISQPICLGPLFFSRRFVLVGDHQQLPPLVLNR EARALGMSESLFKRLEQNKSAVVQLTVQYRMNSKIMSLSNKLTYEGKLECGSDKVA NAVINLRHFKDVKLELEFYADYSDNPWLMGVFEPNNPVCFLNTDKVPAPEQVEKGG VSNVTEAKLIVFLTSIFVKAGCSPSDIGIIAPYRQQLKIINDLLARSIGMVEVNTVDKY QGRDKSIVLVSFVRSNKDGTVGELLKDWRRLNVAITRAKHKLILLGCVPSLNCYPPL EKLLNHLNSEKLISFFFCIWSHLIALL (SEQ ID NO: 141).
[0240] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a FLJ35220 polypeptide In some embodiments the sequence encoding the FLJ35220 comprises or consists of:
MALRSHDRSTRPLYISVGHRMSLEAAVRLTCCCCRFRIPEPVRQADICSREHIRKSLG LPGPPTPRSPKAQRPVACPKGDSGESSALC (SEQ ID NO: 142).
[0241] In some embodiments, wherein the sequence encoding the second RNA binding protein comprises or consists of a FLJ13173 polypeptide. In some embodiments, the sequence encoding the FLJ13173 comprises or consists of:
CYTNHALSYDQAKRVPRWVLEHISKSKIMGDADRKHCKFKPDPNIPPTFSAFNEDYV GSGWSRGHMAPAGNNKFSSKAMAETFYLSNIVPQDFDNNSGYWNRIEMYCRELTE RFEDVWVVSGPLTLPQTRGDGKKIVSYQVIGEDNVAVPSHLYKVILARRSSVSTEPL ALGAFVVPNEAIGFQPQLTEFQVSLQDLEKLSGLVFFPHLDRT (SEQ ID NO: 143).
[0242] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of a DNA repair endonuclease XPF (ERCC4) polypeptide. In some embodiments, the sequence encoding the ERCC4 comprises or consists of:
MESGQPARRIAMAPLLEYERQLVLELLDTDGLVVCARGLGADRLLYHFLQLHCHPA CLVLVLNTQPAEEEYFINQLKIEGVEHLPRRVTNEITSNSRYEVYTQGGVIFATSRILV VDFLTDRIPSDLITGILVYRAHRIIESCQEAFILRLFRQKNKRGFIKAFTDNAVAFDTGF CHVERVMRNLFVRKLYLWPRFHVAVNSFLEQHKPEVVEIHVSMTPTMLAIQTAILDI LNACLKELKCHNPSLEVEDLSLENAIGKPFDKTIRHYLDPLWHQLGAKTKSLVQDLK ILRTLLQYLSQYDCVTFLNLLESLRATEKAFGQNSGWLFLDSSTSMFINARARVYHLP DAKMSKKEKISEKMEIKEGEGILWG (SEQ ID NO: 64).
In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 1 (TENM1) polypeptide. In some embodiments, the sequence encoding the TENM1 comprises or consists of:
[0243] VTVSQMTSVLNGKTRRFADIQLQHGALCFNIRYGTTVEEEKNHVLEIARQR AVAQAWTKEQRRLQEGEEGIRAWTEGEKQQLLSTGRVQGYDGYFVLSVEQYLELS DSANNIHFMRQSEIGRR (SEQ ID NO: 144).
[0244] In some embodiments, the sequence encoding the second RNA binding protein comprises or consists of Teneurin Transmembrane Protein 2 (TENM2) polypeptide. In some embodiments, the sequence encoding the TENM2 comprises or consists of:
[0245] TVSQPTLLVNGKTRRFTNIEFQYSTLLLSIRYGLTPDTLDEEKARVLDQARQR ALGTAWAKEQQKARDGREGSRLWTEGEKQQLLSTGRVQGYEGYYVLPVEQYPELA DSSSNIQFLRQNEMGKR (SEQ ID NO: 145). [0246] In some embodiments, the second RNA binding protein comprises or consists of a transcription activator-like effector nuclease (TALEN) polypeptide or a nuclease domain thereof. In some embodiments, the sequence encoding the TALEN polypeptide comprises or consists of:
1 MRIGKSSGWL NESVSLEYEH VSPPTRPRDT RRRPRAAGDG GLAHLHRRLA VGYAEDTPRT 61 EARSPAPRRP LPVAPASAPP APSLVPEPPM PVSLPAVSSP RFSAGSSAAI TDPFPSLPPT 121 PVLYAMAREL EALSDATWQP AVPLPAEPPT DARRGNTVFD EASASSPVIA SACPQAFASP 181 PRAPRSARAR RARTGGDAWP APTFLSRPSS SRIGRDVFGK LVALGYSREQ IRKLKQESLS 241 EIAKYHTTLT GQGFTHADIC RISRRRQSLR VVARNYPELA AALPELTRAH IVDIARQRSG 301 DLALQALLPV ATALTAAPLR LSASQIATVA QYGERPAIQA LYRLRRKLTR APLHLTPQQV 361 VAIASNTGGK RALEAVCVQL PVLRAAPYRL STEQVVAIAS NKGGKQALEA VKAHLLDLLG 421 APYVLDTEQV VAIASHNGGK QALEAVKADL LDLRGAPYAL STEQVVAIAS HNGGKQALEA 481 VKADLLELRG APYALSTEQV VAIASHNGGK QALEAVKAHL LDLRGVPYAL STEQVVAIAS 541 HNGGKQALEA VKAQLLDLRG APYALSTAQV VAIASNGGGK QALEGIGEQL LKLRTAPYGL 601 STEQVVAIAS HDGGKQALEA VGAQLVALRA APYALSTEQV VAIASNKGGK QALEAVKAQL 661 LELRGAPYAL STAQVVAIAS HDGGNQALEA VGTQLVALRA APYALSTEQV VAIASHDGGK 721 QALEAVGAQL VALRAAPYAL NTEQVVAIAS SHGGKQALEA VRALFPDLRA APYALSTAQL 781 VAIASNPGGK QALEAVRALF RELRAAPYAL STEQVVAIAS NHGGKQALEA VRALFRGLRA 841 APYGLSTAQV VAIASSNGGK QALEAVWALL PVLRATPYDL NTAQIVAIAS HDGGKPALEA 901 VWAKLPVLRG APYALSTAQV VAIACISGQQ ALEAIEAHMP TLRQASHSLS PERVAAIACI 961 GGRSAVEAVR QGLPVKAIRR IRREKAPVAG PPPASLGPTP QELVAVLHFF RAHQQPRQAF 1021 VDALAAFQAT RPALLRLLSS VGVTEIEALG GTIPDATERW QRLLGRLGFR PATGAAAPSP 1081 DSLQGFAQSL ERTLGSPGMA GQSACSPHRK RPAETAIAPR SIRRSPNNAG QPSEPWPDQL 1141 AWLQRRKRTA RSHIRADSAA SVPANLHLGT RAQFTPDRLR AEPGPIMQAH TSPASVSFGS 1201 HVAFEPGLPD PGTPTSADLA SFEAEPFGVG PLDFHLDWLL QILET(SEQ ID NO:
205).
In some embodiments, the sequence encoding the TALEN polypeptide comprises or consists of:
1 mdpirsrtps parellpgpq pdrvqptadr ggappaggpl dglparrtms rtrlpsppap 61 spafsagsfs dllrqfdpsl ldtslldsmp avgtphtaaa paecdevqsg lraaddpppt 121 vrvavtaarp prakpaprrr aaqpsdaspa aqvdlrtlgy sqqqqekikp kvgstvaqhh 181 ealvghgfth ahivalsrhp aalgtvavky qdmiaalpea thedivgvgk qwsgaralea 241 lltvagelrg pplqldtgql vkiakrggvt aveavhasrn altgaplnlt paqvvaiasn 301 nggkqaletv qrllpvlcqa hgltpaqvva iashdggkqa letmqrllpv lcqahglppd 361 qvvaiasnig gkqaletvqr llpvlcqahg ltpdqvvaia shgggkqale tvqrllpvlc 421 qahgltpdqv vaiashdggk qaletvqrll pvlcqahglt pdqvvaiasn gggkqaletv 481 qrllpvlcqa hgltpdqvva iasnggkqal etvqrllpvl cqahgltpdq vvaiashdgg 541 kqaletvqrl lpvlcqthgl tpaqvvaias hdggkqalet vqqllpvlcq ahgltpdqvv 601 aiasniggkq alatvqrllp vlcqahgltp dqvvaiasng ggkqaletvq rllpvlcqah 661 gltpdqvvai asngggkqal etvqrllpvl cqahgltqvq vvaiasnigg kqaletvqrl 721 lpvlcqahgl tpaqvvaias hdggkqalet vqrllpvlcq ahgltpdqvv aiasngggkq 781 aletvqrllp vlcqahgltq eqvvaiasnn ggkqaletvq rllpvlcqah gltpdqvvai 841 asngggkqal etvqrllpvl cqahgltpaq vvaiasnigg kqaletvqrl lpvlcqdhgl 901 tlaqvvaias niggkqalet vqrllpvlcq ahgltqdqvv aiasniggkq aletvqrllp 961 vlcqdhgltp dqvvaiasni ggkqaletvq rllpvlcqdh gltldqvvai asnggkqale 1021 tvqrllpvlc qdhgltpdqv vaiasnsggk qaletvqrll pvlcqdhglt pnqvvaiasn 1081 ggkqalesiv aqlsrpdpal aaltndhlva laclggrpam davkkglpha pelirrvnrr 1141 igertshrva dyaqvvrvle ffqchshpay afdeamtqfg msrnglvqlf rrvgvtelea 1201 rggtlppasq rwdrilqasg mkrakpspts aqtpdqaslh afadslerdl dapspmhegd 1261 qtgassrkrs rsdravtgps aqhsfevrvp eqrdalhlpl swrvkrprtr iggglpdpgt 1321 piaadlaass tvmweqdaap fagaaddfpa fneeelawlm ellpqsgsvg gti (SEQ ID NO: 206). In some embodiments, the second RNA binding protein comprises or consists of a zinc finger nuclease polypeptide or a nuclease domain thereof. In some embodiments, the sequence encoding the zinc finger nuclease polypeptide comprises or consists of:
1 MSRPRFNPRG DFPLQRPRAP NPSGMRPPGP FMRPGSMGLP RFYPAGRARG IPHRFAGHES 61 YQNMGPQRMN VQVTQHRTDP RLTKEKLDFH EAQQKKGKPH GSRWDDEPHI SASVAVKQSS 121 VTQVTEQSPK VQSRYTKESA SSILASFGLS NEDLEELSRY PDEQLTPENM PLILRDIRMR 181 KMGRRLPNLP SQSRNKETLG SEAVSSNVID YGHASKYGYT EDPLEVRIYD PEIPTDEVEN 241 EFQSQQNISA SVPNPNVICN SMFPVEDVFR QMDFPGESSN NRSFFSVESG TKMSGLHISG 301 GQSVLEPIKS VNQSINQTVS QTMSQSLIPP SMNQQPFSSE LISSVSQQER IPHEPVINSS 361 NVHVGSRGSK KNYQSQADIP IRSPFGIVKA SWLPKFSHAD AQKMKRLPTP SMMNDYYAAS 421 PRIFPHLCSL CNVECSHLKD WIQHQNTSTH IESCRQLRQQ YPDWNPEILP SRRNEGNRKE 481 NETPRRRSHS PSPRRSRRSS SSHRFRRSRS PMHYMYRPRS RSPRICHRFI SRYRSRSRSR 541 SPYRIRNPFR GSPKCFRSVS PERMSRRSVR SSDRKKALED VVQRSGHGTE FNKQKHLEAA 601 DKGHSPAQKP KTSSGTKPSV KPTSATKSDS NLGGHSIRCK SKNLEDDTLS ECKQVSDKAV 661 SLQRKLRKEQ SLHYGSVLLI TELPEDGCTE EDVRKLFQPF GKVNDVLIVP YRKEAYLEME 721 FKEAITAIMK YIETTPLTIK GKSVKICVPG KKKAQNKEVK KKTLESKKVS ASTLKRDADA 781 SKAVEIVTST SAAKTGQAKA SVAKVNKSTG KSASSVKSVV TVAVKGNKAS IKTAKSGGKK 841 SLEAKKTGNV KNKDSNKPVT IPENSEIKTS IEVKATENCA KEAISDAALE ATENEPLNKE 901 TEEMCVMLVS NLPNKGYSVE EVYDLAKPFG GLKDILILSS HKKAYIEINR KAAESMVKFY 961 TCFPVLMDGN QLSISMAPEN MNIKDEEAIF ITLVKENDPE ANIDTIYDRF VHLDNLPEDG 1021 LQCVLCVGLQ FGKVDHHVFI SNRNKAILQL DSPESAQSMY SFLKQNPQNI GDHMLTCSLS 1081 PKIDLPEVQI EHDPELEKES PGLKNSPIDE SEVQTATDSP SVKPNELEEE STPSIQTETL 1141 VQQEEPCEEE AEKATCDSDF AVETLELETQ GEEVKEEIPL VASASVSIEQ FTENAEECAL 1201 NQQMFNSDLE KKGAEIINPK TALLPSDSVF AEERNLKGIL EESPSEAEDF ISGITQTMVE 1261 AVAEVEKNET VSEILPSTCI VTLVPGIPTG DEKTVDKKNI SEKKGNMDEK EEKEFNTKET 1321 RMDLQIGTEK AEKNEGRMDA EKVEKMAAMK EKPAENTLFK AYPNKGVGQA NKPDETSKTS 1381 ILAVSDVSSS KPSIKAVIVS SPKAKATVSK TENQKSFPKS VPRDQINAEK KLSAKEFGLL 1441 KPTSARSGLA ESSSKFKPTQ SSLTRGGSGR ISALQGKLSK LDYRDITKQS QETEARPSIM 1501 KRDDSNNKTL AEQNTKNPKS TTGRSSKSKE EPLFPFNLDE FVTVDEVIEE VNPSQAKQNP 1561 LKGKRKETLK NVPFSELNLK KKKGKTSTPR GVEGELSFVT LDEIGEEEDA AAHLAQALVT 1621 VDEVIDEEEL NMEEMVKNSN SLFTLDELID QDDCISHSEP KDVTVLSVAE EQDLLKQERL 1681 VTVDEIGEVE ELPLNESADI TFATLNTKGN EGDTVRDSIG FISSQVPEDP STLVTVDEIQ 1741 DDSSDLHLVT LDEVTEEDED SLADFNNLKE ELNFVTVDEV GEEEDGDNDL KVELAQSKND 1801 HPTDKKGNRK KRAVDTKKTK LESLSQVGPV NENVMEEDLK TMIERHLTAK TPTKRVRIGK 1861 TLPSEKAVVT EPAKGEEAFQ MSEVDEESGL KDSEPERKRK KTEDSSSGKS VASDVPEELD 1921 FLVPKAGFFC PICSLFYSGE KAMTNHCKST RHKQNTEKFM AKQRKEKEQN EAEERSSR (SEQ ID NO: 52). Guide RNA
[0247] The terms guide RNA (gRNA) and single guide RNA (sgRNA) are used
interchangeably throughout the disclosure.
[0248] Guide RNAs (gRNAs) of the disclosure may comprise of a spacer sequence and a scaffolding sequence. In some embodiments, a guide RNA is a single guide RNA (sgRNA) comprising a contiguous spacer sequence and scaffolding sequence. In some embodiments, the spacer sequence and the scaffolding sequence are not contiguous. In some embodiments, a sequence encoding a guide RNA or single guide RNA of the disclosure comprises or consists of a spacer sequence and a scaffolding sequence, that are separated by a linker sequence. In some embodiments, the linker sequence may comprise or consist of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between. In some embodiments, the linker sequence may comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50 or any number of nucleotides in between.
[0249] Guide RNAs (gRNAs) of the disclosure may comprise non-naturally occurring nucleotides. In some embodiments, a guide RNA of the disclosure or a sequence encoding the guide RNA comprises or consists of modified or synthetic RNA nucleotides. Exemplary modified RNA nucleotides include, but are not limited to, pseudouridine (Y), dihydrouridine (D), inosine (I), and 7-methylguanosine (m7G), hypoxanthine, xanthine, xanthosine, 7- methylguanine, 5, 6-Dihydrouracil, 5-methylcytosine, 5-methylcytidine, 5- hydropxymethylcytosine, isoguanine, and isocytosine.
[0250] Guide RNAs (gRNAs) of the disclosure may bind modified RNA within a target sequence. Within a target sequence, guide RNAs (gRNAs) of the disclosure may bind modified RNA. Exemplary epigenetically or post-transcriptionally modified RNA include, but are not limited to, 2’-O-Methylation (2’-OMe) (2’-O-methylation occurs on the oxygen of the free 2’-OH of the ribose moiety), N6-methyladenosine (m6A), and 5-methylcytosine (m5C).
[0251] In some embodiments of the compositions of the disclosure, a guide RNA of the disclosure comprises at least one sequence encoding a non-coding C/D box small nucleolar RNA (snoRNA) sequence. In some embodiments, the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the target sequence of the RNA molecule comprises at least one 2’-OMe. In some embodiments, the snoRNA sequence comprises at least one sequence that is complementary to the target RNA, wherein the at least one sequence that is complementary to the target RNA comprises a box C motif (RUGAUGA) and a box D motif (CUGA).
[0252] Spacer sequences of the disclosure bind to the target sequence of an RNA molecule. Spacer sequences of the disclosure may comprise a CRISPR RNA (crRNA). Spacer sequences of the disclosure comprise or consist of a sequence having sufficient
complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence. Upon binding to a target sequence of an RNA molecule, the spacer sequence may guide one or more of a scaffolding sequence and a fusion protein to the RNA molecule. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence.
[0253] Scaffolding sequences of the disclosure bind the first RNA-binding polypeptide of the disclosure. Scaffolding sequences of the disclosure may comprise a trans acting RNA (tracrRNA). Scaffolding sequences of the disclosure comprise or consist of a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence. Upon binding to a target sequence of an RNA molecule, the scaffolding sequence may guide a fusion protein to the RNA molecule. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96, 97%, 98%, 99%, or any percentage identity in between to the target sequence. In some embodiments, a sequence having sufficient complementarity to a target sequence of an RNA molecule to bind selectively to the target sequence has 100% identity the target sequence. Alternatively or in addition, in some embodiments, scaffolding sequences of the disclosure comprise or consist of a sequence that binds to a first RNA binding protein or a second RNA binding protein of a fusion protein of the disclosure. In some embodiments, scaffolding sequences of the disclosure comprise a secondary structure or a tertiary structure. Exemplary secondary structures include, but are not limited to, a helix, a stem loop, a bulge, a tetraloop and a pseudoknot. Exemplary tertiary structures include, but are not limited to, an A-form of a helix, a B-form of a helix, and a Z-form of a helix.
Exemplary tertiary structures include but are not limited to a twisted or helicized stem loop. Exemplary tertiary structures include, but are not limited to, a twisted or helicized pseudoknot. In some embodiments, scaffolding sequences of the disclosure comprise at least one secondary structure or at least one tertiary structure. In some embodiments, scaffolding sequences of the disclosure comprise one or more secondary structure(s) or one or more tertiary structure(s).
[0254] In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof selectively binds to a tetraloop motif in an RNA molecule of the disclosure. In some embodiments, a target sequence of an RNA molecule comprises a tetraloop motif. In some embodiments, the tetraloop motif is a“GRNA” motif comprising or consisting of one or more of the sequences of GAAA, GUGA, GCAA or GAGA.
[0255] In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof that binds to a target sequence of an RNA molecule hybridizes to the target sequence of the RNA molecule. In some embodiments, a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein covalently binds to the first RNA binding protein or to the second RNA binding protein. In some embodiments, a guide RNA or a portion thereof that binds to a first RNA binding protein or to a second RNA binding protein non-covalently binds to the first RNA binding protein or to the second RNA binding protein.
[0256] In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints. In some embodiments, a spacer sequence of the disclosure comprises or consists of between 10 and 30 nucleotides, inclusive of the endpoints. In some embodiments, a spacer sequence of the disclosure comprises or consists of 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 nucleotides. In some embodiments, the spacer sequence of the disclosure comprises or consists of 20 nucleotides. In some embodiments, the spacer sequence of the disclosure comprises or consists of 21 nucleotides. In some embodiments, a scaffold sequence of the disclosure comprises or consists of between 10 and 100 nucleotides, inclusive of the endpoints. In some embodiments, a spacer sequence of the disclosure comprises or consists of 30, 35, 40, 45, 50, 55, 60, 65, 70, 76, 80, 87, 90, 95, 100 or any number of nucleotides in between. In some embodiments, the scaffold sequence of the disclosure comprises or consists of between 85 and 95 nucleotides, inclusive of the endpoints. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 85 nucleotides In some embodiments the scaffold sequence of the disclosure comprises or consists of 90 nucleotides. In some embodiments, the scaffold sequence of the disclosure comprises or consists of 93 nucleotides.
[0257] In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof does not comprise a nuclear localization sequence (NLS).
[0258] In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof does not comprise a sequence complementary to a protospacer adjacent motif (PAM).
[0259] Therapeutic or pharmaceutical compositions of the disclosure do not comprise a PAMmer oligonucleotide. In other embodiments, optionally, non-therapeutic or non- pharmaceutical compositions may comprise a PAMmer oligonucleotide.
[0260] In some embodiments of the compositions of the disclosure, a guide RNA or a portion thereof comprises a sequence complementary to a protospacer flanking sequence (PFS). In some embodiments, including those wherein a guide RNA or a portion thereof comprises a sequence complementary to a PFS, the first RNA binding protein may comprise a sequence isolated or derived from a Cas13 protein. In some embodiments, including those wherein a guide RNA or a portion thereof comprises a sequence complementary to a PFS, the first RNA binding protein may comprise a sequence encoding a Cas13 protein or an RNA- binding portion thereof. In some embodiments, the guide RNA or a portion thereof does not comprise a sequence complementary to a PFS.
[0261] In some embodiments of the compositions of the disclosure, a sequence encoding a guide RNA of the disclosure further comprises a sequence encoding a promoter to drive expression of the guide RNA. In some embodiments, a vector comprising a sequence encoding a guide RNA of the disclosure further comprises a sequence encoding a promoter to drive expression of the guide RNA. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a constitutive promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding an inducible promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a hybrid or a recombinant promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a promoter capable of expressing the guide RNA in a mammalian cell. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a promoter capable of expressing the guide RNA in a human cell In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a promoter capable of expressing the guide RNA and restricting the guide RNA to the nucleus of the cell. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a human RNA polymerase promoter or a sequence isolated or derived from a sequence encoding a human RNA polymerase promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a U6 promoter or a sequence isolated or derived from a sequence encoding a U6 promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a human tRNA promoter or a sequence isolated or derived from a sequence encoding a human tRNA promoter. In some embodiments, a sequence encoding a promoter to drive expression of the guide RNA comprises a sequence encoding a human valine tRNA promoter or a sequence isolated or derived from a sequence encoding a human valine tRNA promoter.
[0262] In some embodiments of the compositions of the disclosure, a sequence encoding a promoter to drive expression of the guide RNA further comprises a regulatory element. In some embodiments, a vector comprising a sequence encoding a promoter to drive expression of the guide RNA further comprises a regulatory element. In some embodiments, a regulatory element enhances expression of the guide RNA. Exemplary regulatory elements include, but are not limited to, an enhancer element, an intron, an exon, or a combination thereof.
[0263] In some embodiments of the compositions of the disclosure, a vector of the disclosure comprises one or more of a sequence encoding a guide RNA, a sequence encoding a promoter to drive expression of the guide RNA and a sequence encoding a regulatory element. In some embodiments of the compositions of the disclosure, the vector further comprises a sequence encoding a fusion protein of the disclosure.
Fusion Proteins
[0264] Fusion proteins in the context of the compositions of the disclosure may comprise a first RNA binding protein and a second RNA binding protein. In some embodiments, along a sequence encoding the fusion protein, the sequence encoding the first RNA binding protein is positioned 5’ of the sequence encoding the second RNA binding protein. In some
embodiments, along a sequence encoding the fusion protein, the sequence encoding the first RNA binding protein is positioned 3’ of the sequence encoding the second RNA binding protein. [0265] In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of selectively binding an RNA molecule and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule and inducing a break in the RNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and not binding a DNA molecule, a mammalian DNA molecule or any DNA molecule. In some embodiments, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein capable of binding an RNA molecule, inducing a break in the RNA molecule, and neither binding nor inducing a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule.
[0266] In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein with no DNA nuclease activity.
[0267] In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure.
[0268] In some embodiments of the compositions of the disclosure, the sequence encoding the first RNA binding protein comprises a sequence isolated or derived from a protein having DNA nuclease activity, wherein the DNA nuclease activity is inactivated and wherein the DNA nuclease activity does not induce a break in a DNA molecule, a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure. In some embodiments, the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity to a level at which the DNA nuclease activity does not induce a break in a DNA molecule a mammalian DNA molecule or any DNA molecule when a composition of the disclosure is contacted to an RNA molecule or introduced into a cell or into a subject of the disclosure. In some embodiments, the sequence encoding the first RNA binding protein comprises a mutation that inactivates or decreases the DNA nuclease activity and the mutation comprises one or more of a substitution, inversion, transposition, insertion, deletion, or any combination thereof to a nucleic acid sequence or amino acid sequence encoding the first RNA binding protein or a nuclease domain thereof.
[0269] In some embodiments, the fusion protein disclosed herein comprises a linker between the at least two RNA-binding polypeptides. In some embodiments, the linker is a peptide linker. In some embodiments, the peptide linker comprises one or more repeats of the tri-peptide GGS. In other embodiments, the linker is a non-peptide linker. In some embodiments, the non-peptide linker comprises polyethylene glycol (PEG), polypropylene glycol (PPG), co-poly(ethylene/propylene) glycol, polyoxyethylene (POE), polyurethane, polyphosphazene, polysaccharides, dextran, polyvinyl alcohol, polyvinylpyrrolidones, polyvinyl ethyl ether, polyacryl amide, polyacrylate, polycyanoacrylates, lipid polymers, chitins, hyaluronic acid, heparin, or an alkyl linker.
[0270] In some embodiments, the at least one RNA-binding protein does not require multimerization for RNA-binding activity. In some embodiments, the at least one RNA- binding protein is not a monomer of a multimer complex. In some embodiments, a multimer protein complex does not comprise the RNA binding protein. In some embodiments, the at least one of RNA-binding protein selectively binds to a target sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein does not comprise an affinity for a second sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule. In some embodiments, the at least one RNA-binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints.
[0271] In some embodiments, the at least one RNA-binding protein of the fusion proteins disclosed herein further comprises a sequence encoding a nuclear localization signal (NLS). In some embodiments, a nuclear localization signal (NLS) is positioned 3’ to the RNA binding protein. In some embodiments, the at least one RNA-binding protein comprises an NLS at a C-terminus of the protein. In some embodiments, the at least one RNA-binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. In some embodiments, the first NLS or the second NLS is positioned 3’ to the RNA-binding protein In some embodiments the at least one RNA- binding protein comprises the first NLS or the second NLS at a C-terminus of the protein. In some embodiments, the at least one RNA-binding protein further comprises an NES (nuclear export signal) or other peptide tag or secretory signal.
[0272] In some embodiments, a fusion protein disclosed herein comprises the at least one RNA-binding protein as a first RNA-binding protein together with a second RNA-binding protein comprising or consisting of a nuclease domain.
[0273] In some embodiments, the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the C-terminus of the first RNA-binding polypeptide. In some embodiments, the second RNA-binding polypeptide is operably configured to the first RNA-binding polypeptide at the N-terminus of the first RNA-binding polypeptide. For example, one such exemplary fusion protein is E99 which is configured so that
RNAse1(R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the N-terminus of SpyCas9 whereas another exemplary fusion protein, E100, is configured so that
RNAse1(R39D, N67D, N88A, G89D, R19D, H119N, K41R) is located at the C-terminus of SpyCas9.
gRNA Target Sequences
[0274] In some embodiments of the compositions of the disclosure, a target sequence of an RNA molecule comprises a sequence motif corresponding to the RNA binding protein and/or the RNA binding proteins and/or fusion protein thereof.
[0275] In some embodiments of the compositions and methods of the disclosure, the sequence motif is a signature of a disease or disorder.
[0276] A sequence motif of the disclosure may be isolated or derived from a sequence of foreign or exogenous sequence found in a genomic sequence, and therefore translated into an mRNA molecule of the disclosure or a sequence of foreign or exogenous sequence found in an RNA sequence of the disclosure.
[0277] A sequence motif of the disclosure may comprise or consist of a mutation in an endogenous sequence that causes a disease or disorder. The mutation may comprise or consist of a sequence substitution, inversion, deletion, insertion, transposition, or any combination thereof.
[0278] A sequence motif of the disclosure may comprise or consist of a repeated sequence. In some embodiments, the repeated sequence may be associated with a microsatellite instability (MSI). MSI at one or more loci results from impaired DNA mismatch repair mechanisms of a cell of the disclosure A hypervariable sequence of DNA may be transcribed into an mRNA of the disclosure comprising a target sequence comprising or consisting of the hypervariable sequence.
[0279] A sequence motif of the disclosure may comprise or consist of a biomarker. The biomarker may indicate a risk of developing a disease or disorder. The biomarker may indicate a healthy gene (low or no determinable risk of developing a disease or disorder. The biomarker may indicate an edited gene. Exemplary biomarkers include, but are not limited to, single nucleotide polymorphisms (SNPs), sequence variations or mutations, epigenetic marks, splice acceptor sites, exogenous sequences, heterologous sequences, and any combination thereof.
[0280] A sequence motif of the disclosure may comprise or consist of a secondary, tertiary or quaternary structure. The secondary, tertiary or quaternary structure may be endogenous or naturally occurring. The secondary, tertiary or quaternary structure may be induced or non- naturally occurring. The secondary, tertiary or quaternary structure may be encoded by an endogenous, exogenous, or heterologous sequence.
[0281] In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule comprises or consists of between 2 and 100 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 50 nucleotides or nucleic acid bases, inclusive of the endpoints. In some embodiments, the target sequence of an RNA molecule comprises or consists of between 2 and 20 nucleotides or nucleic acid bases, inclusive of the endpoints.
[0282] In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule is continuous. In some embodiments, the target sequence of an RNA molecule is discontinuous. For example, the target sequence of an RNA molecule may comprise or consist of one or more nucleotides or nucleic acid bases that are not contiguous because one or more intermittent nucleotides are positioned in between the nucleotides of the target sequence.
[0283] In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule is naturally occurring. In some embodiments, the target sequence of an RNA molecule is non-naturally occurring. Exemplary non-naturally occurring target sequences may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
[0284] In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule binds to a guide RNA of the disclosure.
[0285] In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule binds to a first RNA binding protein of the disclosure.
[0286] In some embodiments of the compositions and methods of the disclosure, a target sequence of an RNA molecule binds to a second RNA binding protein of the disclosure. RNA Molecules
[0287] In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure comprises a target sequence. In some embodiments, the RNA molecule of the disclosure comprises at least one target sequence. In some embodiments, the RNA molecule of the disclosure comprises one or more target sequence(s). In some embodiments, the RNA molecule of the disclosure comprises two or more target sequences.
[0288] In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure is a naturally occurring RNA molecule. In some embodiments, the RNA molecule of the disclosure is a non-naturally occurring molecule. Exemplary non- naturally occurring RNA molecules may comprise or consist of sequence variations or mutations, chimeric sequences, exogenous sequences, heterologous sequences, chimeric sequences, recombinant sequences, sequences comprising a modified or synthetic nucleotide or any combination thereof.
[0289] In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a virus.
[0290] In some embodiments of the compositions and methods of the disclosure, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a prokaryotic organism. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species or strain of archaea or a species or strain of bacteria.
[0291] In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a eukaryotic organism. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a species of protozoa parasite protist algae, fungi, yeast, amoeba, worm, microorganism, invertebrate, vertebrate, insect, rodent, mouse, rat, mammal, or a primate. In some embodiments, an RNA molecule of the disclosure comprises or consists of a sequence isolated or derived from a human.
[0292] In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure comprises or consists of a sequence derived from a coding sequence from a genome of an organism or a virus. In some embodiments, the RNA molecule of the disclosure comprises or consists of a primary RNA transcript, a precursor messenger RNA (pre-mRNA) or messenger RNA (mRNA). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has not been processed (e.g. a transcript). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to post-transcriptional processing (e.g. a transcript comprising a 5’cap and a 3’ polyadenylation signal). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to alternative splicing (e.g. a splice variant). In some embodiments, the RNA molecule of the disclosure comprises or consists of a gene product that has been subject to removal of non-coding and/or intronic sequences (e.g. a messenger RNA (mRNA)).
[0293] In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure comprises or consists of a sequence derived from a non-coding sequence (e.g. a non-coding RNA (ncRNA)). In some embodiments, the RNA molecule of the disclosure comprises or consists of a ribosomal RNA. In some embodiments, the RNA molecule of the disclosure comprises or consists of a small ncRNA molecule. Exemplary small RNA molecules of the disclosure include, but are not limited to, microRNAs
(miRNAs), small interfering (siRNAs), piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs), extracellular or exosomal RNAs
(exRNAs), and small Cajal body-specific RNAs (scaRNAs). In some embodiments, the RNA molecule of the disclosure comprises or consists of a long ncRNA molecule. Exemplary long RNA molecules of the disclosure include, but are not limited to, X-inactive specific transcript (Xist) and HOX transcript antisense RNA (HOTAIR).
[0294] In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure contacted by a composition of the disclosure in an intracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a
composition of the disclosure in a cytosolic space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a nucleus In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a vesicle, membrane-bound compartment of a cell, or an organelle.
[0295] In some embodiments of the compositions and methods of the disclosure, the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular space. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an exosome. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a liposome, a polymersome, a micelle or a nanoparticle. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in an extracellular matrix. In some
embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a droplet. In some embodiments, the RNA molecule of the disclosure contacted by a composition of the disclosure in a microfluidic droplet.
[0296] In some embodiments of the compositions and methods of the disclosure, a RNA molecule of the disclosure comprises or consists of a single-stranded sequence. In some embodiments, the RNA molecule of the disclosure comprises or consists of a double-stranded sequence. In some embodiments, the double-stranded sequence comprises two RNA molecules. In some embodiments, the double-stranded sequence comprises one RNA molecule and one DNA molecule. In some embodiments, including those wherein the double-stranded sequence comprises one RNA molecule and one DNA molecule, compositions of the disclosure selectively bind and, optionally, selectively cut the RNA molecule.
Vectors
[0297] In some embodiments of the compositions and methods of the disclosure, a vector comprises a guide RNA of the disclosure. In some embodiments, the vector comprises at least one guide RNA of the disclosure. In some embodiments, the vector comprises one or more guide RNA(s) of the disclosure. In some embodiments, the vector comprises two or more guide RNAs of the disclosure. In some embodiments, the vector further comprises a fusion protein of the disclosure. In some embodiments, the fusion protein comprises a first RNA binding protein and a second RNA binding protein.
[0298] In some embodiments of the compositions and methods of the disclosure, a first vector comprises a guide RNA of the disclosure and a second vector comprises a fusion protein of the disclosure. In some embodiments, the first vector comprises at least one guide RNA of the disclosure In some embodiments the first vector comprises one or more guide RNA(s) of the disclosure. In some embodiments, the first vector comprises two or more guide RNA(s) of the disclosure. In some embodiments, the fusion protein comprises a first RNA binding protein and a second RNA binding protein. In some embodiments, the first vector and the second vector are identical. In some embodiments, the first vector and the second vector are not identical.
[0299] In some embodiments of the compositions and methods of the disclosure, the vector is or comprises a component of a“2-component RNA targeting system” comprising (a) nucleic acid sequence encoding a RNA-targeted fusion protein of the disclosure; and (b) a single guide RNA (sgRNA) sequence comprising: on its 5’ end, an RNA sequence (or spacer sequence) that hybridizes to or binds to a target RNA sequence; and on its 3’ end, an RNA sequence (or scaffold sequence) capable of binding to or associating with the CRISPR/Cas protein of the fusion protein; and wherein the 2-component RNA targeting system recognizes and alters the target RNA in a cell in the absence of a PAMmer. In some embodiments, the sequences of the 2-component system are in a single vector. In some embodiments, the spacer sequence of the 2-component system targets a repeat sequence selected from the group consisting of CUG, CCUG, CAG, and GGGGCC.
[0300] In some embodiments of the compositions and methods of the disclosure, a vector of the disclosure is a viral vector. In some embodiments, the viral vector comprises a sequence isolated or derived from a retrovirus. In some embodiments, the viral vector comprises a sequence isolated or derived from a lentivirus. In some embodiments, the viral vector comprises a sequence isolated or derived from an adenovirus. In some embodiments, the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV). In some embodiments, the viral vector is replication incompetent. In some embodiments, the viral vector is isolated or recombinant. In some embodiments, the viral vector is self- complementary.
[0301] In some embodiments of the compositions and methods of the disclosure, the viral vector comprises a sequence isolated or derived from an adeno-associated virus (AAV). In some embodiments, the viral vector comprises an inverted terminal repeat sequence or a capsid sequence that is isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12, or the vector and/or components are derived from a synthetic AAV serotype, such as, without limitation, Anc80 AAV (an ancestor of AAV 1, 2, 6, 8 and 9). In some embodiments, the viral vector is replication incompetent. In some embodiments, the viral vector is isolated or recombinant (rAAV). In some embodiments, the viral vector is self-complementary (scAAV).
[0302] In some embodiments of the compositions and methods of the disclosure, a vector of the disclosure is a non-viral vector. In some embodiments, the vector comprises or consists of a nanoparticle, a micelle, a liposome or lipoplex, a polymersome, a polyplex or a dendrimer. In some embodiments, the vector is an expression vector or recombinant expression system. As used herein, the term“recombinant expression system” refers to a genetic construct for the expression of certain genetic material formed by recombination.
[0303] In some embodiments of the compositions and methods of the disclosure, an expression vector, viral vector or non-viral vector provided herein, includes without limitation, an expression control element. An“expression control element” as used herein refers to any sequence that regulates the expression of a coding sequence, such as a gene. Exemplary expression control elements include but are not limited to promoters, enhancers, microRNAs, post-transcriptional regulatory elements, polyadenylation signal sequences, and introns. Expression control elements may be constitutive, inducible, repressible, or tissue- specific, for example. A“promoter” is a control sequence that is a region of a polynucleotide sequence at which initiation and rate of transcription are controlled. It may contain genetic elements at which regulatory proteins and molecules may bind such as RNA polymerase and other transcription factors. In some embodiments, expression control by a promoter is tissue- specific. Non-limiting exemplary promoters include CMV, CBA, CAG, Cbh, EF-1a, PGK, UBC, GUSB, UCOE, hAAT, TBG, Desmin, MCK, C5-12, NSE, Synapsin, PDGF, MecP2, CaMKII, mGluR2, NFL, NFH, nb2, PPE, ENK, EAAT2, GFAP, MBP, and U6 promoters. An“enhancer” is a region of DNA that can be bound by activating proteins to increase the likelihood or frequency of transcription. Non-limiting exemplary enhancers and
posttranscriptional regulatory elements include the CMV enhancer and WPRE.
[0304] In some embodiments of the compositions and methods of the disclosure, an expression vector, viral vector or non-viral vector provided herein, includes without limitation, vector elements such as an IRES or 2A peptide sites for configuration of “multicistronic” or“polycistronic” or“bicistronic” or tricistronic” constructs, i.e., having double or triple or multiple coding areas or exons, and as such will have the capability to express from mRNA two or more proteins from a single construct. Multicistronic vectors simultaneously express two or more separate proteins from the same mRNA. The two strategies most widely used for constructing multicistronic configurations are through the use of an IRES or a 2A self-cleaving site. An“IRES” refers to an internal ribosome entry site or portion thereof of viral, prokaryotic, or eukaryotic origin which are used within polycistronic vector constructs. In some embodiments, an IRES is an RNA element that allows for translation initiation in a cap-independent manner. The term“self-cleaving peptides” or“sequences encoding self-cleaving peptides” or“2A self-cleaving site” refer to linking sequences which are used within vector constructs to incorporate sites to promote ribosomal skipping and thus to generate two polypeptides from a single promoter, such self- cleaving peptides include without limitation, T2A, and P2A peptides or sequences encoding the self-cleaving peptides.
[0305] In some embodiments, the vector is a viral vector. In some embodiments, the vector is an adenoviral vector, an adeno-associated viral (AAV) vector, or a lentiviral vector. In some embodiments, the vector is a retroviral vector, an adenoviral/retroviral chimera vector, a herpes simplex viral I or II vector, a parvoviral vector, a reticuloendotheliosis viral vector, a polioviral vector, a papillomaviral vector, a vaccinia viral vector, or any hybrid or chimeric vector incorporating favorable aspects of two or more viral vectors. In some embodiments, the vector further comprises one or more expression control elements operably linked to the polynucleotide. In some embodiments, the vector further comprises one or more selectable markers. In some embodiments, the AAV vector has low toxicity. In some embodiments, the AAV vector does not incorporate into the host genome, thereby having a low probability of causing insertional mutagenesis. In some embodiments, the AAV vector can encode a range of total polynucleotides from 4.5 kb to 4.75 kb. In some embodiments, exemplary AAV vectors that may be used in any of the herein described compositions, systems, methods, and kits can include an AAV1 vector, a modified AAV1 vector, an AAV2 vector, a modified AAV2 vector, an AAV3 vector, a modified AAV3 vector, an AAV4 vector, a modified AAV4 vector, an AAV5 vector, a modified AAV5 vector, an AAV6 vector, a modified AAV6 vector, an AAV7 vector, a modified AAV7 vector, an AAV8 vector, an AAV9 vector, an AAV.rh10 vector, a modified AAV.rh10 vector, an AAV.rh32/33 vector, a modified AAV.rh32/33 vector, an AAV.rh43 vector, a modified AAV.rh43 vector, an AAV.rh64R1 vector, and a modified AAV.rh64R1 vector and any combinations or equivalents thereof. In some embodiments, the lentiviral vector is an integrase-competent lentiviral vector (ICLV). In some embodiments, the lentiviral vector can refer to the transgene plasmid vector as well as the transgene plasmid vector in conjunction with related plasmids (e g a packaging plasmid a rev expressing plasmid an envelope plasmid) as well as a lentiviral-based particle capable of introducing exogenous nucleic acid into a cell through a viral or viral-like entry mechanism. Lentiviral vectors are well-known in the art (see, e.g., Trono D. (2002) Lentiviral vectors, New York: Spring-Verlag Berlin Heidelberg and Durand et al. (2011) Viruses 3(2):132-159 doi: 10.3390/v3020132). In some
embodiments, exemplary lentiviral vectors that may be used in any of the herein described compositions, systems, methods, and kits can include a human immunodeficiency virus (HIV) 1 vector, a modified human immunodeficiency virus (HIV) 1 vector, a human immunodeficiency virus (HIV) 2 vector, a modified human immunodeficiency virus (HIV) 2 vector, a sooty mangabey simian immunodeficiency virus (SIVSM) vector, a modified sooty mangabey simian immunodeficiency virus (SIVSM) vector, a African green monkey simian immunodeficiency virus (SIVAGM) vector, a modified African green monkey simian immunodeficiency virus (SIVAGM) vector, an equine infectious anemia virus (EIAV) vector, a modified equine infectious anemia virus (EIAV) vector, a feline immunodeficiency virus (FIV) vector, a modified feline immunodeficiency virus (FIV) vector, a Visna/maedi virus (VNV/VMV) vector, a modified Visna/maedi virus (VNV/VMV) vector, a caprine arthritis- encephalitis virus (CAEV) vector, a modified caprine arthritis-encephalitis virus (CAEV) vector, a bovine immunodeficiency virus (BIV), or a modified bovine immunodeficiency virus (BIV).
[0306] In some embodiments of the compositions and methods of the disclosure, a vector of the disclosure is a non-viral vector. In some embodiments, the vector comprises or consists of a nanoparticle, a micelle, a liposome or lipoplex, a polymersome, a polyplex or a dendrimer. Nucleic Acids
[0307] Provided herein are the nucleic acid sequences encoding the fusion proteins disclosed herein for use in gene transfer and expression techniques described herein. It should be understood, although not always explicitly stated that the sequences provided herein can be used to provide the expression product as well as substantially identical sequences that produce a protein that has the same biological properties. These“biologically equivalent” or“biologically active” or“equivalent” polypeptides are encoded by equivalent polynucleotides as described herein. They may possess at least 60%, or alternatively, at least 65%, or alternatively, at least 70%, or alternatively, at least 75%, or alternatively, at least 80%, or alternatively at least 85%, or alternatively at least 90%, or alternatively at least 95% or alternatively at least 98%, identical primary amino acid sequence to the reference polypeptide when compared using sequence identity methods run under default conditions. Specific polypeptide sequences are provided as examples of particular embodiments.
Modifications to the sequences to amino acids with alternate amino acids that have similar charge. Additionally, an equivalent polynucleotide is one that hybridizes under stringent conditions to the reference polynucleotide or its complement or in reference to a polypeptide, a polypeptide encoded by a polynucleotide that hybridizes to the reference encoding polynucleotide under stringent conditions or its complementary strand. Alternatively, an equivalent polypeptide or protein is one that is expressed from an equivalent polynucleotide.
[0308] The nucleic acid sequences (e.g., polynucleotide sequences) disclosed herein may be codon-optimized which is a technique well known in the art. In some embodiments disclosed herein, exemplary Cas sequences, such as e.g., SEQ ID NO: 46 (Cas13d), are codon optimized for expression in human cells. Codon optimization refers to the fact that different cells differ in their usage of particular codons. This codon bias corresponds to a bias in the relative abundance of particular tRNAs in the cell type. By altering the codons in the sequence to match with the relative abundance of corresponding tRNAs, it is possible to increase expression. It is also possible to decrease expression by deliberately choosing codons for which the corresponding tRNAs are known to be rare in a particular cell type. Codon usage tables are known in the art for mammalian cells, as well as for a variety of other organisms. Based on the genetic code, nucleic acid sequences coding for, e.g., a Cas protein, can be generated. In some embodiments, such a sequence is optimized for expression in a host or target cell, such as a host cell used to express the Cas protein or a cell in which the disclosed methods are practiced (such as in a mammalian cell, e.g., a human cell). Codon preferences and codon usage tables for a particular species can be used to engineer isolated nucleic acid molecules encoding a Cas protein (such as one encoding a protein having at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type protein) that takes advantage of the codon usage preferences of that particular species. For example, the Cas proteins disclosed herein can be designed to have codons that are preferentially used by a particular organism of interest. In one example, an Cas nucleic acid sequence is optimized for expression in human cells, such as one having at least 70%, at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 98%, or at least 99% sequence identity to its corresponding wild-type or originating nucleic acid sequence. In some embodiments, an isolated nucleic acid molecule encoding at least one Cas protein (which can be part of a vector) includes at least one Cas protein coding sequence that is codon optimized for expression in a eukaryotic cell, or at least one Cas protein coding sequence codon optimized for expression in a human cell. In one embodiment, such a codon optimized Cas coding sequence has at least 80%, at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating sequence. In another embodiment, a eukaryotic cell codon optimized nucleic acid sequence encodes a Cas protein having at least 85%, at least 90%, at least 92%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99%, or 100% sequence identity to its corresponding wild-type or originating protein. In another embodiment, a variety of clones containing functionally equivalent nucleic acids may be routinely generated, such as nucleic acids which differ in sequence but which encode the same Cas protein sequence. Silent mutations in the coding sequence result from the degeneracy (i.e., redundancy) of the genetic code, whereby more than one codon can encode the same amino acid residue. Thus, for example, leucine can be encoded by CTT, CTC, CTA, CTG, TTA, or TTG; serine can be encoded by TCT, TCC, TCA, TCG, AGT, or AGC; asparagine can be encoded by AAT or AAC; aspartic acid can be encoded by GAT or GAC; cysteine can be encoded by TGT or TGC; alanine can be encoded by GCT, GCC, GCA, or GCG; glutamine can be encoded by CAA or CAG; tyrosine can be encoded by TAT or TAC; and isoleucine can be encoded by ATT, ATC, or ATA. Tables showing the standard genetic code can be found in various sources (see, for example, Stryer, 1988, Biochemistry, 3.sup.rd Edition, W.H.5 Freeman and Co., NY).
[0309] “Hybridization” refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi-stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PC reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
[0310] Examples of stringent hybridization conditions include: incubation temperatures of about 25°C to about 37°C; hybridization buffer concentrations of about 6x SSC to about 10x SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4x SSC to about 8x SSC. Examples of moderate hybridization conditions include: incubation temperatures of about 40°C to about 50°C; buffer concentrations of about 9x SSC to about 2x SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5x SSC to about 2x SSC. Examples of high stringency conditions include: incubation temperatures of about 55°C to about 68°C; buffer concentrations of about lx SSC to about 0.1x SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about lx SSC, 0.1x SSC, or deionized water. In general, hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes. SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
[0311] “Homology” or“identity” or“similarity” refers to sequence similarity between two peptides or between two nucleic acid molecules. Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. An “unrelated” or“non-homologous” sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences of the present invention.
Cells
[0312] In some embodiments of the compositions and methods of the disclosure, a cell of the disclosure is a prokaryotic cell.
[0313] In some embodiments of the compositions and methods of the disclosure, a cell of the disclosure is a eukaryotic cell. In some embodiments, a cell of the disclosure is a somatic cell. In some embodiments, a cell of the disclosure is a germline cell. In some embodiments, a germline cell of the disclosure is not a human cell.
[0314] In some embodiments of the compositions and methods of the disclosure, a cell of the disclosure is a stem cell. In some embodiments, a cell of the disclosure is an embryonic stem cell. In some embodiments, an embryonic stem cell of the disclosure is not a human cell. In some embodiments, a cell of the disclosure is a multipotent stem cell or a pluripotent stem cell. In some embodiments, a cell of the disclosure is an adult stem cell. In some embodiments, a cell of the disclosure is an induced pluripotent stem cell (iPSC). In some embodiments, a cell of the disclosure is a hematopoietic stem cell (HSC).
[0315] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is an immune cell. In some embodiments, an immune cell of the disclosure is a lymphocyte In some embodiments an immune cell of the disclosure is a T lymphocyte (also referred to herein as a T-cell). Exemplary T-cells of the disclosure include, but are not limited to, naïve T cells, effector T cells, helper T cells, memory T cells, regulatory T cells (Tregs) and Gamma delta T cells. In some embodiments, an immune cell of the disclosure is a B lymphocyte. In some embodiments, an immune cell of the disclosure is a natural killer cell. In some embodiments, an immune cell of the disclosure is an antigen- presenting cell.
[0316] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a muscle cell. In some embodiments, a muscle cell of the disclosure is a myoblast or a myocyte. In some embodiments, a muscle cell of the disclosure is a cardiac muscle cell, skeletal muscle cell or smooth muscle cell. In some embodiments, a muscle cell of the disclosure is a striated cell.
[0317] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is an epithelial cell. In some embodiments, an epithelial cell of the disclosure forms a squamous cell epithelium, a cuboidal cell epithelium, a columnar cell epithelium, a stratified cell epithelium, a pseudostratified columnar cell epithelium or a transitional cell epithelium. In some embodiments, an epithelial cell of the disclosure forms a gland including, but not limited to, a pineal gland, a thymus gland, a pituitary gland, a thyroid gland, an adrenal gland, an apocrine gland, a holocrine gland, a merocrine gland, a serous gland, a mucous gland and a sebaceous gland. In some embodiments, an epithelial cell of the disclosure contacts an outer surface of an organ including, but not limited to, a lung, a spleen, a stomach, a pancreas, a bladder, an intestine, a kidney, a gallbladder, a liver, a larynx or a pharynx. In some embodiments, an epithelial cell of the disclosure contacts an outer surface of a blood vessel or a vein.
[0318] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a neuronal cell. In some embodiments, a neuron cell of the disclosure is a neuron of the central nervous system. In some embodiments, a neuron cell of the disclosure is a neuron of the brain or the spinal cord. In some embodiments, a neuron cell of the disclosure is a neuron of the retina. In some embodiments, a neuron cell of the disclosure is a neuron of a cranial nerve or an optic nerve. In some embodiments, a neuron cell of the disclosure is a neuron of the peripheral nervous system. In some embodiments, a neuron cell of the disclosure is a neuroglial or a glial cell. In some embodiments, a glial of the disclosure is a glial cell of the central nervous system including, but not limited to, oligodendrocytes, astrocytes, ependymal cells and microglia In some embodiments a glial of the disclosure is a glial cell of the peripheral nervous system including, but not limited to, Schwann cells and satellite cells.
[0319] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a primary cell.
[0320] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is a cultured cell.
[0321] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is in vivo, in vitro, ex vivo or in situ.
[0322] In some embodiments of the compositions and methods of the disclosure, a somatic cell of the disclosure is autologous or allogeneic.
Methods of Use
[0323] The disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the RNA-binding protein or fusion protein thereof (or a portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein.
[0324] The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the fusion protein (or a RNA-binding portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein.
[0325] The disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the RNA-binding protein or fusion protein thereof (or a portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and a fusion protein of the disclosure. In some embodiments, the vector is an AAV.
[0326] The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for binding of one or more of the guide RNA or the RNA- binding protein or fusion protein thereof (or a portion thereof) to the RNA molecule and providing immune masking activity specific to the RNA-binding protein. In some
embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA or a single guide RNA of the disclosure and a fusion protein of the disclosure. In some embodiments, the vector is an AAV.
[0327] The disclosure provides a method of modifying level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof or portion thereof induces a break in the RNA molecule and provides immune masking activity specific to the RNA-binding protein.
[0328] The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof (or a portion thereof) induces a break to the RNA molecule and provides immune masking activity specific to the RNA-binding protein.
[0329] The disclosure provides a method of modifying a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule and provides immune masking activity specific to the RNA-binding protein comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof induces a break in the RNA molecule. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA of the disclosure and an RNA-binding protein of the disclosure and a mutated non-cleavable FasL of the disclosure. In some embodiments, the vector is an AAV.
[0330] The disclosure provides a method of modifying an activity of a protein encoded by an RNA molecule comprising contacting the composition and a cell comprising the RNA molecule under conditions suitable for RNA nuclease activity wherein the RNA-binding protein or fusion protein thereof or portion thereof induces a break in the RNA molecule. In some embodiments, the cell is in vivo, in vitro, ex vivo or in situ. In some embodiments, the composition comprises a vector comprising composition comprising a guide RNA sequence or a single guide RNA of the disclosure and a sequence encoding an RNA-binding protein of the disclosure and sequence encoding a mutated non-cleavable FasL of the disclosure. In some embodiments, the vector is an AAV.
[0331] The disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure.
[0332] The disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising a guide RNA sequence of the disclosure, a sequence encoding an RNA-binding protein of the disclosure, and a sequence encoding a mutated non-cleavable FasL of the disclosure, and wherein the composition modifies a level of expression of an RNA molecule of the disclosure or a protein encoded by the RNA molecule and provides immune masking activity specific to the RNA- binding protein.
[0333] The disclosure provides a method of treating a disease or disorder comprising administering to a subject a therapeutically effective amount of a composition of the disclosure, wherein the composition comprises a vector comprising composition comprising a compositions of the disclosure.
[0334] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a genetic disease or disorder. In some embodiments, the genetic disease or disorder is a single-gene disease or disorder. In some embodiments, the single-gene disease or disorder is an autosomal dominant disease or disorder, an autosomal recessive disease or disorder, an X-chromosome linked (X-linked) disease or disorder, an X-linked dominant disease or disorder, an X-linked recessive disease or disorder, a Y-linked disease or disorder or a mitochondrial disease or disorder. In some embodiments, the genetic disease or disorder is a multiple-gene disease or disorder. In some embodiments, the genetic disease or disorder is a multiple-gene disease or disorder. In some embodiments, the single-gene disease or disorder is an autosomal dominant disease or disorder including, but not limited to, Huntington's disease, neurofibromatosis type 1, neurofibromatosis type 2, Marfan syndrome, hereditary nonpolyposis colorectal cancer, hereditary multiple exostoses, Von Willebrand disease, and acute intermittent porphyria. In some embodiments, the single-gene disease or disorder is an autosomal recessive disease or disorder including but not limited to Albinism Medium-chain acyl-CoA dehydrogenase deficiency, cystic fibrosis, sickle-cell disease, Tay-Sachs disease, Niemann-Pick disease, spinal muscular atrophy, and Roberts syndrome. In some embodiments, the single-gene disease or disorder is X-linked disease or disorder including, but not limited to, muscular dystrophy, Duchenne muscular dystrophy, Hemophilia, Adrenoleukodystrophy (ALD), Rett syndrome, and Hemophilia A. In some embodiments, the single-gene disease or disorder is a mitochondrial disorder including, but not limited to, Leber's hereditary optic neuropathy.
[0335] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, an immune disease or disorder. In some embodiments, the immune disease or disorder is an immunodeficiency disease or disorder including, but not limited to, B-cell deficiency, T-cell deficiency, neutropenia, asplenia, complement deficiency, acquired immunodeficiency syndrome (AIDS) and immunodeficiency due to medical intervention (immunosuppression as an intended or adverse effect of a medical therapy). In some embodiments, the immune disease or disorder is an autoimmune disease or disorder including, but not limited to, Achalasia, Addison’s disease, Adult Still's disease, Agammaglobulinemia, Alopecia areata, Amyloidosis, Anti- GBM/Anti-TBM nephritis, Antiphospholipid syndrome, Autoimmune angioedema,
Autoimmune dysautonomia, Autoimmune encephalomyelitis, Autoimmune hepatitis, Autoimmune inner ear disease (AIED), Autoimmune myocarditis, Autoimmune oophoritis, Autoimmune orchitis, Autoimmune pancreatitis, Autoimmune retinopathy, Autoimmune urticaria, Axonal & neuronal neuropathy (AMAN), Baló disease, Behcet’s disease, Benign mucosal pemphigoid, Bullous pemphigoid, Castleman disease (CD), Celiac disease, Chagas disease, Chronic inflammatory demyelinating polyneuropathy (CIDP), Chronic recurrent multifocal osteomyelitis (CRMO), Churg-Strauss Syndrome (CSS) or Eosinophilic
Granulomatosis (EGPA), Cicatricial pemphigoid, Cogan’s syndrome, Cold agglutinin disease, Congenital heart block, Coxsackie myocarditis, CREST syndrome, Crohn’s disease, Dermatitis herpetiformis, Dermatomyositis, Devic’s disease (neuromyelitis optica), Discoid lupus, Dressler’s syndrome, Endometriosis, Eosinophilic esophagitis (EoE), Eosinophilic fasciitis, Erythema nodosum, Essential mixed cryoglobulinemia, Evans syndrome,
Fibromyalgia, Fibrosing alveolitis, Giant cell arteritis (temporal arteritis), Giant cell myocarditis, Glomerulonephritis, Goodpasture’s syndrome, Granulomatosis with
Polyangiitis, Graves’ disease, Guillain-Barre syndrome, Hashimoto’s thyroiditis, Hemolytic anemia, Henoch-Schonlein purpura (HSP), Herpes gestationis or pemphigoid gestationis (PG), Hidradenitis Suppurativa (HS) (Acne Inversa) Hypogammalglobulinemia IgA Nephropathy, IgG4-related sclerosing disease, Immune thrombocytopenic purpura (ITP), Inclusion body myositis (IBM), Interstitial cystitis (IC), Juvenile arthritis, Juvenile diabetes (Type 1 diabetes), Juvenile myositis (JM), Kawasaki disease, Lambert-Eaton syndrome, Leukocytoclastic vasculitis, Lichen planus, Lichen sclerosus, Ligneous conjunctivitis, Linear IgA disease (LAD), Lupus, Lyme disease chronic, Meniere’s disease, Microscopic polyangiitis (MPA), Mixed connective tissue disease (MCTD), Mooren’s ulcer, Mucha- Habermann disease, Multifocal Motor Neuropathy (MMN) or MMNCB, Multiple sclerosis, Myasthenia gravis, Myositis, Narcolepsy, Neonatal Lupus, Neuromyelitis optica,
Neutropenia, Ocular cicatricial pemphigoid, Optic neuritis, Palindromic rheumatism (PR), PANDAS, Paraneoplastic cerebellar degeneration (PCD), Paroxysmal nocturnal
hemoglobinuria (PNH), Parry Romberg syndrome, Pars planitis (peripheral uveitis),
Parsonnage-Turner syndrome, Pemphigus, Peripheral neuropathy, Perivenous
encephalomyelitis, Pernicious anemia (PA), POEMS syndrome, Polyarteritis nodosa, Polyglandular syndromes type I, II, III, Polymyalgia rheumatica, Polymyositis,
Postmyocardial infarction syndrome, Postpericardiotomy syndrome, Primary biliary cirrhosis, Primary sclerosing cholangitis, Progesterone dermatitis, Psoriasis, Psoriatic arthritis, Pure red cell aplasia (PRCA), Pyoderma gangrenosum, Raynaud’s phenomenon, Reactive Arthritis, Reflex sympathetic dystrophy, Relapsing polychondritis, Restless legs syndrome (RLS), Retroperitoneal fibrosis, Rheumatic fever, Rheumatoid arthritis,
Sarcoidosis, Schmidt syndrome, Scleritis, Scleroderma, Sjögren’s syndrome, Sperm & testicular autoimmunity, Stiff person syndrome (SPS), Subacute bacterial endocarditis (SBE), Susac’s syndrome, Sympathetic ophthalmia (SO), Takayasu’s arteritis, Temporal
arteritis/Giant cell arteritis, Thrombocytopenic purpura (TTP), Tolosa-Hunt syndrome (THS), Transverse myelitis, Type 1 diabetes, Ulcerative colitis (UC), Undifferentiated connective tissue disease (UCTD), Uveitis, Vasculitis, Vitiligo, Vogt-Koyanagi-Harada Disease, or Wegener’s granulomatosis.
[0336] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, an inflammatory disease or disorder.
[0337] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a metabolic disease or disorder.
[0338] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes but is not limited to a degenerative or a progressive disease or disorder. In some embodiments, the degenerative or a progressive disease or disorder includes, but is not limited to, amyotrophic lateral sclerosis (ALS), Huntington’s disease, Alzheimer’s disease, and aging.
[0339] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, an infectious disease or disorder.
[0340] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a pediatric or a developmental disease or disorder.
[0341] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a cardiovascular disease or disorder.
[0342] In some embodiments of the compositions and methods of the disclosure, a disease or disorder of the disclosure includes, but is not limited to, a proliferative disease or disorder. In some embodiments, the proliferative disease or disorder is a cancer. In some embodiments, the cancer includes, but is not limited to, Acute Lymphoblastic Leukemia (ALL), Acute Myeloid Leukemia (AML), Adrenocortical Carcinoma, AIDS-Related Cancers, Kaposi Sarcoma (Soft Tissue Sarcoma), AIDS-Related Lymphoma (Lymphoma), Primary CNS Lymphoma (Lymphoma), Anal Cancer, Appendix Cancer, Gastrointestinal Carcinoid Tumors, Astrocytomas, Atypical Teratoid/Rhabdoid Tumor, Central Nervous System (Brain Cancer), Basal Cell Carcinoma, Bile Duct Cancer, Bladder Cancer, Bone Cancer, Ewing Sarcoma, Osteosarcoma, Malignant Fibrous Histiocytoma, Brain Tumors, Breast Cancer, Burkitt Lymphoma, Carcinoid Tumor, Carcinoma, Cardiac (Heart) Tumors, Embryonal Tumors, Germ Cell Tumor, Primary CNS Lymphoma, Cervical Cancer,
Cholangiocarcinoma, Chordoma, Chronic Lymphocytic Leukemia (CLL), Chronic
Myelogenous Leukemia (CML), Chronic Myeloproliferative Neoplasms, Colorectal Cancer , Craniopharyngioma, Cutaneous T-Cell Lymphoma, Ductal Carcinoma In Situ, Embryonal Tumors, Endometrial Cancer (Uterine Cancer), Ependymoma, Esophageal Cancer,
Esthesioneuroblastoma (Head and Neck Cancer), Ewing Sarcoma (Bone Cancer),
Extracranial Germ Cell Tumor, Extragonadal Germ Cell Tumor, Eye Cancer, Childhood Intraocular Melanoma, Intraocular Melanoma, Retinoblastoma, Fallopian Tube Cancer, Fibrous Histiocytoma of Bone, Malignant, and Osteosarcoma, Gallbladder Cancer, Gastric (Stomach) Cancer, Gastrointestinal Carcinoid Tumor, Gastrointestinal Stromal Tumors (GIST) (Soft Tissue Sarcoma) Childhood Gastrointestinal Stromal Tumors Germ Cell Tumors, Childhood Extracranial Germ Cell Tumors, Extragonadal Germ Cell Tumors, Ovarian Germ Cell Tumors, Testicular Cancer, Gestational Trophoblastic Disease, Hairy Cell Leukemia, Head and Neck Cancer, Heart Tumors, Hepatocellular (Liver) Cancer,
Histiocytosis, Hodgkin Lymphoma, Hypopharyngeal Cancer (Head and Neck Cancer), Intraocular Melanoma, Islet Cell Tumors, Pancreatic Neuroendocrine Tumors, Kaposi Sarcoma (Soft Tissue Sarcoma), Kidney (Renal Cell) Cancer, Langerhans Cell Histiocytosis, Laryngeal Cancer (Head and Neck Cancer), Leukemia, Lip and Oral Cavity Cancer (Head and Neck Cancer), Liver Cancer, Lung Cancer (Non-Small Cell and Small Cell), Childhood Lung Cancer, Lymphoma, Male Breast Cancer, Malignant Fibrous Histiocytoma of Bone and Osteosarcoma, Melanoma, Merkel Cell Carcinoma (Skin Cancer), Mesothelioma, Metastatic Squamous Neck Cancer with Occult Primary (Head and Neck Cancer), Midline Tract Carcinoma With NUT Gene Changes, Mouth Cancer (Head and Neck Cancer), Multiple Endocrine Neoplasia Syndromes, Multiple Myeloma/Plasma Cell Neoplasms, Mycosis Fungoides (Lymphoma), Myelodysplastic Syndromes, Myelodysplastic/Myeloproliferative Neoplasms, Nasal Cavity and Paranasal Sinus Cancer (Head and Neck Cancer),
Nasopharyngeal Cancer (Head and Neck Cancer), Neuroblastoma, Non-Hodgkin Lymphoma, Non-Small Cell Lung Cancer, Oral Cancer, Lip and Oral Cavity Cancer and Oropharyngeal Cancer, Osteosarcoma and Malignant Fibrous Histiocytoma of Bone, Ovarian Cancer, Pancreatic Cancer, Pancreatic Neuroendocrine Tumors (Islet Cell Tumors), Papillomatosis, Paraganglioma, Parathyroid Cancer, Penile Cancer, Pharyngeal Cancer (Head and Neck Cancer), Pheochromocytoma , Plasma Cell Neoplasm/Multiple Myeloma, Pleuropulmonary Blastoma, Pregnancy and Breast Cancer, Primary Central Nervous System (CNS)
Lymphoma, Primary Peritoneal Cancer, Prostate Cancer, Rectal Cancer, Recurrent Cancer, Renal Cell (Kidney) Cancer, Retinoblastoma, Rhabdomyosarcoma, Childhood (Soft Tissue Sarcoma), Salivary Gland Cancer (Head and Neck Cancer), Sarcoma, Childhood
Rhabdomyosarcoma (Soft Tissue Sarcoma), Childhood Vascular Tumors (Soft Tissue Sarcoma), Ewing Sarcoma (Bone Cancer), Kaposi Sarcoma (Soft Tissue Sarcoma),
Osteosarcoma (Bone Cancer), Uterine Sarcoma, Sézary Syndrome, Lymphoma, Skin Cancer, Small Cell Lung Cancer, Small Intestine Cancer, Soft Tissue Sarcoma, Squamous Cell Carcinoma of the Skin, Squamous Neck Cancer, Stomach (Gastric) Cancer, T-Cell
Lymphoma, Testicular Cancer, Throat Cancer (Head and Neck Cancer), Nasopharyngeal Cancer, Oropharyngeal Cancer, Hypopharyngeal Cancer, Thymoma and Thymic Carcinoma , Thyroid Cancer Transitional Cell Cancer of the Renal Pelvis and Ureter Renal Cell Cancer, Urethral Cancer, Uterine Sarcoma, Vaginal Cancer, Vascular Tumors (Soft Tissue Sarcoma), Vulvar Cancer, Wilms Tumor and Other Childhood Kidney Tumors.
[0343] In some embodiments of the methods of the disclosure, a subject of the disclosure has been diagnosed with the disease or disorder. In some embodiments, the subject of the disclosure presents at least one sign or symptom of the disease or disorder. In some embodiments, the subject has a biomarker predictive of a risk of developing the disease or disorder. In some embodiments, the biomarker is a genetic mutation.
[0344] In some embodiments of the methods of the disclosure, a subject of the disclosure is female. In some embodiments of the methods of the disclosure, a subject of the disclosure is male. In some embodiments, a subject of the disclosure has two XX or XY chromosomes. In some embodiments, a subject of the disclosure has two XX or XY chromosomes and a third chromosome, either an X or a Y.
[0345] In some embodiments of the methods of the disclosure, a subject of the disclosure is a neonate, an infant, a child, an adult, a senior adult, or an elderly adult. In some
embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5,6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27,28, 29, 30 or 31 days old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 or 12 months old. In some embodiments of the methods of the disclosure, a subject of the disclosure is at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100 or any number of years or partial years in between of age.
[0346] In some embodiments of the methods of the disclosure, a subject of the disclosure is a mammal. In some embodiments, a subject of the disclosure is a non-human mammal.
[0347] In some embodiments of the methods of the disclosure, a subject of the disclosure is a human.
[0348] In some embodiments of the methods of the disclosure, a therapeutically effective amount comprises a single dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises at least one dose of a composition of the disclosure. In some embodiments, a therapeutically effective amount comprises a therapeutically effective amount comprises one or more dose(s) of a composition of the disclosure.
[0349] In some embodiments of the methods of the disclosure, a therapeutically effective amount eliminates a sign or symptom of the disease or disorder In some embodiments, a therapeutically effective amount reduces a severity of a sign or symptom of the disease or disorder.
[0350] In some embodiments of the methods of the disclosure, a therapeutically effective amount eliminates the disease or disorder.
[0351] In some embodiments of the methods of the disclosure, a therapeutically effective amount prevents an onset of a disease or disorder. In some embodiments, a therapeutically effective amount delays the onset of a disease or disorder. In some embodiments, a therapeutically effective amount reduces the severity of a sign or symptom of the disease or disorder. In some embodiments, a therapeutically effective amount improves a prognosis for the subject.
[0352] In some embodiments of the methods of the disclosure, a composition of the disclosure is administered to the subject systemically. In some embodiments, the composition of the disclosure is administered to the subject by an intravenous route. In some
embodiments, the composition of the disclosure is administered to the subject by an injection or an infusion.
[0353] In some embodiments of the methods of the disclosure, a composition of the disclosure is administered to the subject locally. In some embodiments, the composition of the disclosure is administered to the subject by an intraosseous, intraocular,
intracerebrospinal or intraspinal route. In some embodiments, the composition of the disclosure is administered directly to the cerebral spinal fluid of the central nervous system. In some embodiments, the composition of the disclosure is administered directly to a tissue or fluid of the eye and does not have bioavailability outside of ocular structures. In some embodiments, the composition of the disclosure is administered to the subject by an injection or an infusion.
Numbered Embodiments
[0354] 1. A composition comprising:
(a)^a^sequence^encoding^a^non‐self^polypeptide^of^interest^(POI),^and^
(b)^a^sequence^encoding^a^non‐cleavable^Fas^Ligand^(FASL),^^
wherein^expression^of^the^non‐cleavable^FASL^eliminates^MHC‐mediated^immunogenic^ peptides^and^helper^T^cells^specific^to^the^expression^of^the^POI.^ [0355] 2. A composition comprising: (a) a sequence encoding a non-self polypeptide, and
(b) a sequence encoding a non-cleavable FASL,
wherein expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the non-self polypeptide. [0356] 3. A composition comprising:
(a) a sequence encoding a therapeutic polypeptide, and
(b) a sequence encoding a non-cleavable FASL,
wherein expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the therapeutic polypeptide. [0357] 4. A composition comprising an adeno-associated virus (AAV) vector comprising:
a sequence encoding an AAV capsid polypeptide, and
a composition comprising
(a) a sequence encoding a human polypeptide, and
(b) a sequence encoding a non-cleavable FASL,
wherein expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the human polypeptide and/or the AAV capsid polypeptide. [0358] 5. The composition of embodiment 4, wherein the human polypeptide is a self polypeptide and wherein the peptide is derived from the AAV capsid polypeptide. [0359] 6. A composition comprising:
(a) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule,
(b) a sequence encoding an RNA-binding polypeptide, and
(c) a sequence encoding a non-cleavable FASL,
[0360] wherein expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the RNA- binding polypeptide. [0361] 7. The composition of any one of embodiments 1-5, wherein a vector comprises the sequence of (a) and the sequence of (b). [0362] 8. The composition of embodiment 6, wherein a vector comprises the sequence of (a), the sequence of (b) and the sequence of (c). [0363] 9. The composition of embodiment 7 or 8, wherein the vector is an expression vector. [0364] 10. The composition of embodiment 9, wherein the expression vector is a plasmid. [0365] 11. The composition of any one of embodiments 1-10, wherein a promoter drives expression of the sequence of (a). [0366] 12. The composition of any one of embodiments 1-5 and 7-11, wherein the promoter drives expression of the sequence of (b). [0367] 13. The composition of embodiment 6, wherein a first promoter drives expression of the sequence of (a) and a second promoter drives expression of the sequence of (b). [0368] 14. The composition of embodiment 13, wherein the second promoter drives expression of the sequence of (b) and the sequence of (c). [0369] 15. The composition of embodiment 11, wherein a first promoter drives expression of the sequence of (a) and a second promoter drives expression of the sequence of (b). [0370] 16. The composition of any one of embodiments 1-15, wherein one or more sequence(s) encoding the promoter comprises a sequence isolated or derived from a U6 promoter. [0371] 17. The composition of any one of embodiments 1-15, wherein one or more sequence(s) encoding the promoter comprises a sequence isolated or derived from a promoter capable of diving expression of a transfer RNA (tRNA). [0372] 18. The composition of embodiment 17, wherein the sequence encoding the promoter comprises a sequence isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter. [0373] 19. The composition of embodiment 17, wherein the sequence encoding the promoter comprises a sequence isolated or derived from a valine tRNA promoter. [0374] 20. The composition of any one of embodiment 1-3 or 6-19, wherein a delivery vector comprises the composition. [0375] 21. The composition of embodiment 20, wherein the delivery vector isan adeno- associated viral (AAV) vector. [0376] 22. The composition of embodiment 20, wherein the AAV comprises a sequence isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12. [0377] 23. The composition of embodiment 4 or 5, wherein the AAV comprises a sequence isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12. [0378] 24. The composition of any one of embodiments 1-5, 7-14 or 16-23, wherein the sequence of (a) or the sequence of (b) further comprises a sequence encoding an Internal Ribosomal Entry Site (IRES) or a sequence encoding a self-cleaving peptide. [0379] 25. The composition of embodiment 6, wherein the sequence of (b) or the sequence of (c) further comprises a sequence encoding IRES or a sequence encoding a self- cleaving peptide. [0380] 26. The composition of any one of embodiments 8-23, wherein the vector comprises a sequence encoding IRES or a sequence encoding a self-cleaving peptide. [0381] 27. The composition of embodiment 24 or 26, wherein the sequence encoding IRES or the sequence encoding a self-cleaving peptide is positioned between the sequence of (a) and the sequence of (b). [0382] 28. The composition of embodiment 25 or 26, wherein the sequence encoding IRES or the sequence encoding a self-cleaving peptide is positioned between the sequence of (b) and the sequence of (c). [0383] 29. The composition of any one of embodiments 24-28, wherein the self-cleaving peptide comprises a 2A self-cleaving peptide. [0384] 30. The composition of any one of embodiments 1-29, wherein the non-cleavable FASL comprises a mutation in a metalloproteinase cleavage site. [0385] 31. The composition of embodiment 30, wherein the metalloproteinase cleavage site comprises the amino acid sequence ELAELR. [0386] 32. The composition of embodiment 31, wherein the mutation comprises one or more of a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition of the amino acid sequence ELAELR. [0387] 33. The composition of any one of embodiments 30-32, wherein the non- cleavable FASL comprises the amino acid sequence of:
MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLPPPPP PPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKX1X2X3X 4X5X6ESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGI VLLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLV MMEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGL YKL (SEQ ID NO: 210), wherein X1 is not a glutamic acid (E), X2 is not an leucine (L), X3 is not an alanine (A), X4 is not an glutamic acid (E), X5 is not an leucine (L) or X6 is not an arginine (R). [0388] 34. The composition of any one of embodiments 30-32, wherein the non- cleavable FASL comprises the amino acid sequence of:
MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLPPPPP PPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKX1X2X3X 4X5X6ESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGI VLLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLV MMEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGL YKL (SEQ ID NO: 210), wherein X1 is not a glutamic acid (E), X2 is not an leucine (L), X3 is not an alanine (A), X4 is not an glutamic acid (E), X5 is not an leucine (L) and X6 is not an arginine (R). [0389] 35. The composition of embodiment 6, wherein the sequence comprising the gRNA further comprises a spacer sequence that specifically binds to the target RNA sequence. [0390] 36. The composition of embodiment 35, wherein the spacer sequence has at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 87%, 90%, 95%, 97%, 99% or any percentage in between of complementarity to the target RNA sequence. [0391] 37. The composition of embodiment 35, wherein the spacer sequence has 100% complementarity to the target RNA sequence. [0392] 38. The composition of any one of embodiments 35-37, wherein the spacer sequence comprises or consists of 20 nucleotides. [0393] 39. The composition of any one of embodiments 35-37, wherein the spacer sequence comprises or consists of 21 nucleotides. [0394] 40. The composition of embodiment 39, wherein the spacer sequence comprises the sequence UGGAGCGAGCAUCCCCCAAA (SEQ ID NO: 1),
GUUUGGGGGAUGCUCGCUCCA (SEQ ID NO: 2), CCCUCACUGCUGGGGAGUCC (SEQ ID NO: 3), GGACUCCCCAGCAGUGAGGG (SEQ ID NO: 4),
GCAACUGGAUCAAUUUGCUG (SEQ ID NO: 5), GCAGCAAAUUGAUCCAGUUGC (SEQ ID NO: 6), GCAUUCUUAUCUGGUCAGUGC (SEQ ID NO: 7),
GCACUGACCAGAUAAGAAUG (SEQ ID NO: 8), GAGCAGCAGCAGCAGCAGCAG (SEQ ID NO: 9), GCAGGCAGGCAGGCAGGCAGG (SEQ ID NO: 10),
GCCCCGGCCCCGGCCCCGGC (SEQ ID NO: 11) , or GCTGCTGCTGCTGCTGCTGC (SEQ ID NO: 12), GGGGCCGGGGCCGGGGCCGG (SEQ ID NO: 74),
GGGCCGGGGCCGGGGCCGGG (SEQ ID NO: 75), GGCCGGGGCCGGGGCCGGGG (SEQ ID NO: 76), GCCGGGGCCGGGGCCGGGGC (SEQ ID NO: 77),
CCGGGGCCGGGGCCGGGGCC (SEQ ID NO: 78), CGGGGCCGGGGCCGGGGCCG (SEQ ID NO: 79). [0395] 41. The composition of any one of embodiments 6, 11, 13-14, 17-23, 25, and 28- 40, wherein the sequence comprising the gRNA further comprises a scaffold sequence that specifically binds to the RNA binding protein. [0396] 42. The composition of embodiment 41, wherein the scaffold sequence comprises a stem-loop structure. [0397] 43. The composition of embodiment 41 or 42, wherein the scaffold sequence comprises or consists of 90 nucleotides. [0398] 44. The composition of embodiment 41 or 42, wherein the scaffold sequence comprises or consists of 93 nucleotides [0399] 45. The composition of embodiment 44, wherein the scaffold sequence comprises the sequence
GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCG UUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 13). [0400] 46. The composition of embodiment 45, wherein the spacer sequence comprises the sequence GUGAUAAGUGGAAUGCCAUG (SEQ ID NO: 14),
CUGGUGAACUUCCGAUAGUG (SEQ ID NO: 15), or GAGATATAGCCTGGTGGTTC (SEQ ID NO: 16). [0401] 47. The composition of embodiment 41 or 42, wherein the scaffold sequence comprises or consists of 85 nucleotides. [0402] 48. The composition of embodiment 47, wherein the scaffold sequence comprises the sequence
GGACAGCAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUUGAAAAAGU GGCACCGAGUCGGUGCUUUUU (SEQ ID NO: 17). [0403] 49. The composition of embodiment 48, wherein the spacer sequence comprises the sequence at least 1, 2, 3, 4, 5, 6, or 7 repeats of the sequence CUG (SEQ ID NO: 18), CCUG (SEQ ID NO: 19), CAG (SEQ ID NO: 80), GGGGCC (SEQ ID NO: 81) or any combination thereof. [0404] 50. The composition of embodiment 41 or 42, wherein the scaffold sequence comprises the sequence
GUUUAAGAGCUAUGCUGGAAACAGCAUAGCAAGUUUAAAUAAGGCUAGUCCG UUAUCAACUUGAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 82) or
GUUUUAGAGCUAGAAAUAGCAAGUUAAAAUAAGGCUAGUCCGUUAUCAACUU GAAAAAGUGGCACCGAGUCGGUGCUUUUUUU (SEQ ID NO: 83). [0405] 51. The composition of any one of embodiments 6, 11, 13-14, 17-23, 25, and 28- 50, wherein the gRNA does not bind or does not selectively bind to a second sequence within the RNA molecule. [0406] 52. The composition of any one of embodiments 6, 11, 13-14, 17-23, 25, and 28- 51, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule. [0407] 53. The composition of any one of embodiments 6, 11, 13-14, 17-23, 25, and 28- 52, wherein the RNA-binding polypeptide is selected from the group consisting of CRISPR- Cas, PUF, Pumilio, and PPR. [0408] 54. The composition of embodiment 53, wherein a fusion protein comprises the RNA-binding polypeptide. [0409] 55. The composition of embodiment 54, wherein the fusion protein comprises a sequence encoding a first RNA-binding polypeptide and a sequence encoding a second RNA- binding polypeptide,
wherein neither the first RNA-binding polypeptide nor the second RNA-binding polypeptide comprises a significant DNA-nuclease activity,
wherein the first RNA-binding polypeptide and the second RNA-binding polypeptide are not identical, and
wherein the second RNA-binding polypeptide comprises an RNA-nuclease activity. [0410] 56. The composition embodiment 55, wherein the first RNA binding protein comprises a CRISPR-Cas protein. [0411] 57. The composition of embodiment 56, wherein the CRISPR-Cas protein is a Type II CRISPR-Cas protein. [0412] 58. The composition of embodiment 57, wherein the first RNA binding protein comprises a Cas9 polypeptide or an RNA-binding portion thereof. [0413] 59. The composition of embodiment 56, wherein the CRISPR-Cas protein is a Type V CRISPR-Cas protein. [0414] 60. The composition of embodiment 59, wherein the first RNA binding protein comprises a Cpf1 polypeptide or an RNA-binding portion thereof. [0415] 61. The composition of embodiment 56, wherein the CRISPR-Cas protein is a Type VI CRISPR-Cas protein. [0416] 62. The composition of embodiment 61, wherein the first RNA binding protein comprises a Cas13 polypeptide or an RNA-binding portion thereof.
[0417]
[0418] 63. The composition of any one of embodiments 56-62, wherein the CRISPR-Cas protein comprises a native RNA nuclease activity. [0419] 64. The composition of embodiment 63, wherein the native RNA nuclease activity is reduced or inhibited. [0420] 65. The composition of embodiment 63, wherein the native RNA nuclease activity is increased or induced. [0421] 66. The composition of any one of embodiments 56-63, wherein the CRISPR-Cas protein comprises a native DNA nuclease activity and wherein the native DNA nuclease activity is inhibited. [0422] 67. The composition of any one of embodiments 56-66, wherein the CRISPR-Cas protein comprises a mutation. [0423] 68. The composition of embodiment 67, wherein a nuclease domain of the CRISPR-Cas protein comprises the mutation. [0424] 69. The composition of embodiment 67 or 68, wherein the mutation occurs in a nucleic acid encoding the CRISPR-Cas protein [0425] 70. The composition of any one of embodiments 67-69, wherein the mutation comprises a substitution, an insertion, a deletion, a frameshift, an inversion, or a
transposition. [0426] 71. The composition of any one of embodiments 67-69, wherein the mutation comprises a deletion of a nuclease domain, a binding site within the nuclease domain, an active site within the nuclease domain, or at least one essential amino acid residue within the nuclease domain. [0427] 72. The composition of embodiment 55, wherein the first RNA binding protein comprises a Pumilio and FBF (PUF) protein. [0428] 73. The composition of embodiment 72, wherein the first RNA binding protein comprises a Pumilio-based assembly (PUMBY) protein. [0429] 74. The composition of any one of embodiments 55-73, wherein the first RNA binding protein does not require multimerization for RNA-binding activity. [0430] 75. The composition of any one of embodiments 55-74, wherein the first RNA binding protein is not a monomer of a multimer complex [0431] 76. The composition of any one of embodiments 55-75, wherein a multimer protein complex does not comprise the first RNA binding protein. [0432] 77. The composition of any one of embodiments 55-76, wherein the first RNA binding protein selectively binds to a target sequence within the RNA molecule. [0433] 78. The composition of any one of embodiments 55-77, wherein the first RNA binding protein does not comprise an affinity for a second sequence within the RNA molecule. [0434] 79. The composition of any one of embodiments 55-78, wherein the first RNA binding protein does not comprise a high affinity for or selectively bind a second sequence within the RNA molecule. [0435] 80. The composition of any one of embodiments 55-79, wherein an RNA genome or an RNA transcriptome comprises the RNA molecule. [0436] 81. The composition of any one of embodiments 55-80, wherein the first RNA binding protein comprises between 2 and 1300 amino acids, inclusive of the endpoints. [0437] 82. The composition of any one of embodiments 55-81, wherein the sequence encoding the first RNA binding protein further comprises a sequence encoding a nuclear localization signal (NLS). [0438] 83. The composition of embodiment 82, wherein the sequence encoding a nuclear localization signal (NLS) is positioned 3’ to the sequence encoding the first RNA binding protein. [0439] 84. The composition of embodiment 82, wherein the first RNA binding protein comprises an NLS at a C-terminus of the protein. [0440] 85. The composition of any one of embodiments 55-81, wherein the sequence encoding the first RNA binding protein further comprises a first sequence encoding a first NLS and a second sequence encoding a second NLS. [0441] 86. The composition of embodiment 85, wherein the sequence encoding the first NLS or the second NLS is positioned 3’ to the sequence encoding the first RNA binding protein. [0442] 87. The composition of embodiment 85, wherein the first RNA binding protein comprises the first NLS or the second NLS at a C-terminus of the protein. [0443] 88. The composition of any one of embodiments 55-87, wherein the second RNA binding protein comprises or consists of a nuclease domain. [0444] 89. The composition of embodiment 88, wherein the sequence encoding the second RNA binding protein comprises or consists of an RNAse. EXAMPLES EXAMPLE 1: Preventing adaptive immune response to a non-self therapeutic transgene
[0445] A non-self therapeutic transgene is delivered to a target issue via viral or nonviral means. In order to prevent adaptive immune response to this therapeutic, vector with DNA encoding mutant FASL (mFASL) is co-delivered by AAV. mFASL expression is driven by a promoter that is activated by TNFa or IL-6 signaling (Figure 3A). This regulated expression of mFASL induces expression of mFASL only in the presence of activated T cells. In turn, T cells become sensitive to mFASL-mediated death only when activated. Two AAV-9 transfer vectors were produced that 1) encode Cas13d and guide RNA, and 2) encode mFASL driven by an IL-6-regualated promoter. The following IL-6-regulated promoters were compared:
[0446]
i. CALCB promoter:
tcctggtgtggtactacaaaggtcctggaagtcctcctgccttacttcgagtccgccacaggccgga gctacttctagaacagttctgactgccttcccaggggagggggcgactgcaggtcaccctgcctcag tgcacgctgcgcatctgagttgcaggccgggcggcagtcacccgagtcagcggtcccgattcttcg tgggtgttacctggagtttccattgcacgggtgctggaggccaacccgccctagtcccaccagctgg gtcctgccacaagaaaaggacccagagggcctagacagatatcccctgaacttttttctgacccgca gaaacagtgagcatcacctgcaggggttccgccagcctctggctttgcttcctgcccggcagcctcc agcaagttttcccgaatgctctccaggagtgcagtgggcgccggcggacttatttagggtcgctgct gccaagcgtcagagagcgaaccggaggcccggggctgggggctgtggtgagaggcgccccttt ctttcttgccatcgcccctacccccagctccttcctagcctattctgccaaagctgggatcttctcctgg aacccgggagcaagaagagctggcagtgccgactcccagaacccggctttccttcagaaaagatg gataggccgagtttgtgtgcgtggacgtgcatgtgtcggtgtgcatgtttaggggacagtatgtaccc ccaattgcataaaacacgcctgtttttggaaacagaaacacacggggttgctttcgggtatgggtgtg gttagtttgggttcctgcgcacgctcccttttcggagcagctggtgagggcgcatctgttccagtgagt gctggctgtctgatggactgtctgtgaatgcagaaggcagagcgtgtggtgggggtcctgccatgtg agtgatgatgcgcgcactggctggtctgtagtcgcgagtggaacttgtgtgaaaattctcaggctgac tctcgcgctgcagcacctgctcccctccgtgggtggcagctggaccccagcgcgctcagctctcag gcgcttcagcgaagtggggtaggggtgtggaacgagagagatagagacccgggcatagaccatc tccgccaggcagcttggcaaacaggtggcagagttgcagggcagctgtgtaagccaacttcggcg cagcagtggagggtcctggcttggcgtgggggatgctggacccgcggtcgaggatttggggatat aggggaagagggaggaggtggatgctgagccttgtatgcaggctatgtcagtttagccctctcccc aacctctcttcggctcctgcccgtcccagaggagtgaggtggagaagggctggctgccagactgg caccaaaacagccttctttgggtgcccaggttgccagggctcgaggggtcggaggatatccaggg aagcaccccaggtggtccaaaaagatcaaattttgaggacccctccctccccttttccctcccccccc ctccttccctgccgtgggctctttcagctgtggtccctttagaacccaggactactactgctcaacctcg ctgggggttcgggtggctggattcgggtccctcactggcgtgacaggagggagtgcgaggcagg aatttaggagccaaggaggtgagagcagctctggcccctcactgtaggtgacgccaaactctcctc gacttgccccgactcttagttgaaaaatctctgtcctctcccaggctctccagcttcccaagcaatgac ctcaatgaaaaaaatgacagcggggcggactgcccccgctccagagtaccagtgccggcagtgc gagctatgacgcaatcggagctcggtcggtcctttgattggctagtcctggccactttggattggccg cgcgggctggtggggaccccccccctccagctatctctgtaataagagcggggtctccgcgggga aggcGCCCACAGCAGGTGTGGTGTTCATCCCGGGTCGACCGGC CGCTCGCGCTGCCCTGAAACTCTAGTCGCCAGGTGAGGAAC TTCCCATTCCCCATTCCGCTC (SEQ ID NO: 192)
ii. BCAR3 promoter:
taaatagaatattatcagcatgcagaagtcacctctgggatccctttctgtcataatccacagctcaata taaccactgtcttcacttttaacatcacagatatgctttgactatttttgaagtttatgtaaatggaatcatat agtatgtacccatttgcggccagcttctttcactcaatatcctatttgtaagattcactcatcttgttgagtg taaatgagttcatgcattcttattactatgttgtatgttacacagtttatctctcttctgctgatggacatttgg gttgttttctttttggccgtcataaagagatacattataaacatttttcaacatcttttggtgaatatgtgtata catctctgttgggtgcacacttaggggtggaattgctgggtcataggatacatgttaatttagcttttcta gataatgccaagcaggtttttaaagtggttgtaaaaagttcattttgacgagcagtatggtcaggccctt taattttagtcattctgggtggtatgaagttagatcacattgaaatatcaatttgcatttttgggatggttaa taaattgagatattttccatatgtttattggcttttttgagaaatgcctgtttgtcctctcttgaggacagttg aaatattctgcctgtttttaattggattttctgccttattctggctgatccgtaggtgttctttatatatctgtaa acaaaccttttttggatgtatgtgttgcaattatgttttctcactctgcggtttgccttttcactcgtggtgtct tttcatgaacagaagctcttaattttaatcttgtccaatgatgagttttttttctttatattagtactacatgtgt ttaagacatcgtctttgtctaccccaaggtaatgaagatttttttggacattttctttggatcgtgttattggt ttactttttacctttaaaatccatctggaggccgggcgcggtggctcacacctgtaatcccagcactttg ggaggccgaggtgggtggatcacctgaggtcaggagttcgagaccagcctgaccaaaatggtga acccgtctctactaaaaatacaaaaattagccgggcatagtggcgtgcgcctgtaatcccagctactt gggaagctgaggcaagataattgcttgaacccgggaggcggaggttgcagtgagccaagatcatg ccgttgcacaacagcttgggcaacaagaccgaaactctgtctcgaaaagaaaaattccatctggaat tgactggggatggggggattcagttgatccagcatcatttactggaaagagagagctaatctgaccc ccaatacagcacagcagcacctgacataaatcaagtgaccacatattgtaaatctgtttttggactttat tccattggtcagtttgtctatccttctactatttctatgactttataatggatcttgatataagatagtgttaag tcttttccagtgggctccaatttttcaccccaccaaatcatctagtgctgaagtgccaccgccaactcgc actttgctttcaatacgtccatacgagtgcaattgatttgcctgttcccgtggatggttcatttgtggttac ctggggctttgtctcatcaaagcccttcacattgaaagccagccaggtgtctgcagacgagcaaagc agatctgttgggtaattaaataacgcggggaaggggaaggagtggattcgacgaggctgtctctgg agagagcttcagaaaggaagtgatcgagctatacttgaggactggctccttggggagatacgaaga gagccaaactctaaaatccgggcagaggagggcctggctaggtcaccgaatgtaaatgtctcggg gggttccgcaaggcagcgcgaatcggctcgccggggtggggccgcggagccgcaaatcaccag ttgagggccggagtgcgcgccgccggctcAGAGCTGCGCCTGCTGCTGGCC GGGCGGGGGACGGGGCCGGGACCGGAGCCGGAGCTGCGGG GCGCACCGGCTAGACGCGCGCGGGATTCTCGGCGGGCAC
(SEQ ID NO: 193)
iii. CCAR6 promoter:
ccacattcctcgccttttatgcacctcacagtgtctatgcaaatgaacagtgtgattttaaatttgaggaa gtttcaataagagtgagatctaagaggatctttaatataggggcatttttagagagctaaaaaccaaat aggtctcagctttctcagggtgacatataatttagatttgacttggaactacagaaggaatatggggca aaggacatgagaaacattgcagaggtcagtgccatatggagcttccacctcagctctcgaagtaaag gcaaccagcccaggctgggagccagtcagcagcagggtctcaatctccatccactaccttcccctct ggggcagggagggtgttgcagggaggaggccactcttggagacctccagatccctgcctctgtgc agtctaacagaaggggcccccacagtggccatgaatctctttgttctgcaaggaagggggtgtcatt gggcctcctgggtccctcagcatctgcgtggccacacaacgcggttttgttcaacacgttacatttctg cttaattaatgttcatttttggtccccagcaaagtccaatctgtttttcgttttctttcttttctttccaggcagg cattgccagggctaatcatctataaaagggcttactttcttaccttcacgctaagcaagaccatccaag ggcagtgttagagggcacctgagaacgcaggaggggtgtgttacctggtggcctgtttcttcctccta tgggcagcccttctacaggaagcagaagcctcaggggcgatggtagaaatgaggaggaggggat ggagctgaggtagcaggggaggggtcgtaagagcagaggggagggtcttgctttgttcgccatcc aataatcagcaggtttcgggttggggtgaactactggggaggagcgccccagggcttctctcagat ggaggagggacaggtcacccagagtgaaggaagttgtgagctctgttagaggaaaacagccagg acttagtcaggagaggctttgtttggaaggattgttgtaaggcagggagaggaatgatggcagcaag aggaccccgtgaccataggtctgcaagcacttcaaacagaaaaggcccttcttttatccagtaaggg ggagccactggggccagcagagtctttggaggggaccctggacaaacccgggaaaatggccagt ggggttgagcaggacacaggtcctgctgtgtctagctggttccccagagagatgataaggggtgcg ctccagcttctcaggctcactcaggcgtgaggacgtggagctcagggctctgcaggaaggagcga cccaggtgaggtgtggtcaagatagagcagagctgggcagcgggcagtggagcctcgtgggcag cctgggggtggggaggcacagtgcactgggaagtggagaaagtgtgagtccatcaggctggctg agaattgatcacgaacctattgtctgtaaaacttttgttatttcctgagacgtggttcacagcaacccag gtgcgaacagccttgtgattctagggttcttttctattttttaagcacttgcatctacaaataaatttctgag tgacttgtcgtcagctgctttccttgatatgtctaaagacagggcagtgacccgcatcgtcacccaga gattctgtctctgtgccacatgaagattaggtgcccgcttttgattgaggagctcctctgttgctctcaaa gtatcttgtaataatagctgagatgcatggagaaccacctctccttcaggcgctgctcctcggcttccg tggacgggcatggctatttctcggaaccctctgaggttagagctgtcatggtctttcttctgaaagagg aaaccgaggcttgctggggctcagtggcccttctgtggctgcacagctttcggggtggggccagga ctgactgactccacacaaaagtgctcccggcccatgtctttAACTCACACGGCCTCTT GCAAACGTTCCCAAATCTTCCCAGTCGGCTTGCAGAGACTCC TTGCTCCCAGGAGATAACCAGGTAAAGGAGTATGAAAGTTT
G (SEQ ID NO: 194)
iv. COL6A3 promoter:
agtgtatttgtatttgaaagaaaccgtggagtggaaacacctaaaacgtgcttgttcagttaacctcagt ttgctgagctgcttggagcatggggttgtaatcaaagattgtcttcttcgcagcagacaatgttctggg agaaatagtcctccttagtgctgaagttgcagactctaaccaagggggtggcagcaagtatccccgg tctctgtaggggcttgagtcaacgcctgcactgtgcagagaggatgagggcagagaattggatgcc gctggaggggcgtgttgtccttctacatgtcatgcaggcagcgcggttctatactcggagcctctgct cagcgtgtcttcacctaagaaccccataattcaggttccatccttgttccctactccagtgctctgcaag tgagccctttggtttagagatgggttgggcttctttatgggagaggaagggagccctggagctgcag aggggagcaggcattctctctggggtgctgtctcctttcttccctaaattggagggagataatccatgg aaaggagttaatgatttctttgctcttcaaacttggtttggaaggatctctcagtcaaaaagaacctttcg gatgtctcttgatatttcacattaatggacttttcataaggaccacatgatgggagagcagtgagaagtt tggggatggccaaagctgggttgtcatttgagctctgttactaacccagactggacaatgacgatgtc acttactctctcggaacttcttttcttttcttcttttcttttctttttttcttttttctcttctcttctcttctcttctcttct cttctcttcttttcttttcatttcttttctttctttcctttttctcttttttggagtctcactctgttgcccaggctaga gtgcagtggcgccatctcggctcactgcaacctctgcctcctgggttcaagcaattgtcctgcctcag cctcccaaatagctgggactacaagcgcctgccaccatgcctggctaatttttatatttttagtagagat ttagtaggggtttcaccatgttggccaggctggtctccaactcctgaccttgtgatctgcctgccttagc ctcccgaagtgctgagattacaggcataagccaccgtgcccagcctgtttctttcatctgtaaaatggg accacaatttcacctaataaaagaagacatctttctatttaaaagggcttagggtgttgatgtttgtgata aaggagagaatgtatattgaagtgttttgaaatgtgcaaagctttctagaaacagaagttcttactcaag tattttcccgaagctttggcaagataaccatttttattaccccgtctgtgcctagaatgggcctataagcg ccacaatcagaatcattagatatagaaattaagagaaatgtagcctccttttttttgccggtgaacagag ctttggttaacagaaaaccaaggcgattttaattgctggtttttctatttgaagggggaagttattagtag aagtctcaattcagaaacttcaagaagaaatgggagggtgtggtgagggtaagcgggggactgcat ttcctgttttcctttcagatggtgttggaaaacattgcaggaaaaccatggatacccacgaagaaattcc aaaatttattctttttgacgccaagggcccagcccaaaaggtgacgagtaggagtggtcaatttttttttt taagagttggggcttgcaggagtccagctaaacgcttgtagggtgaagacagaattcagagggtga catcagcctgagcgggggccagaagaaacagagtggaggagtctggtttcatttacagttttgggtc agttctgcagtgaggagggggagaggaggggtccgggagggaggaggaggaggaggaggag ctggaggaagccctgactggtatccctggccccagtccagtttggagctcAGTCTTCCACC AAAGGCCGTTCAGTTCTCCTGGGCTCCAGCCTCCTGCAAGGA CTGCAAGAGTTTTCCTCCGCAGCTCTGAGTCTCCACTTTTTTG GTGGA (SEQ ID NO: 195)
v. CXCR5 promoter:
atggaatcttttttttttttttttttgagtgtcaccaaggctagagggcagtggtgtgatcatggctcattgc agcctcaacctcctgggctcaagcgatccgcctatctcagcctcctgagtagctgggactacaggtg tgtgccaccatgcccagctaatttttgaattttttgtagagacgaggtttcaccatgttgcccaggctagt ctcaaattcctgggctcaaaggattctcccatcttgacctcccaaagtgctgggattacaggcatgag caaccacgccctgccaagtatagagtcttgaacaaggaaatgcatatcgtcctatattttttcctagtca gataatatctagaccattaaccagaaatcacccagaggtcaaaaaacagggcgtcaaaggacccag aaaccaagtctgcaaataacgactgaagacactgtggaagtgtgtttgggagacaacaagactctca ggatgtgctggctgtcttcagaggatgcttattggaagaggagtcagacagtccagacagaaggca cagccaggacctctggagaggagttacaggaagacatattttgactcatcataaggaataagtttcta atcatgaaaccatcctccactgaaacatgatctattgaaaggagcaaatgtctcaccttcattgatgttc gtattcattgattctgggtgatcatctgataaggatgcagtgacgagaatcttgcatttgctgggggtgg gggtgtggttgaggatagtctggtttatattccaaagttcctttcaattcctctatgattctatacgctgtac tccttcctgatcaatgtccctagccagggtggccaaggctaagtcaagtatgctaagggattggagg ggcagggatattgagaatagggtgaatggaaggatgaggagttcccagcaagcttgggacacagg aaaccttggggcagcttcctcctggaggtttcaggactgtacgtgctggagaagaagtgtgatgcctt gtcctgaaagccgtcttctttgaaagcagcttctaaaggcagtgaatggagaagagcgaggaaacg accccaataccaccaacagaggctggaaactcctcaggctgtttaatcctaagaatgatgcatctgtt ggccgggcacggtggttcacatctgtaatcctagcactttgggaggctgaggcaggcggatcacctt aggtcaggaattcaagaccagactgaccaacatggagaaaccccatttctactaaaaatacaaaatt agccgggcgtggtagcgcatgcctgtaatcccagctactcgggaggctgaagcaggagaattgctt gaatccgggaggtggagtttgtggtgagctgagatctcgccattgcactccagcctgggcaacgag agcaaaattctgtctcaaaataaataaataaaaatacaaaattagccgggcgtggtggtgcatgcctg taatcccagatgctcgggaggctgaggcaggagaatcgcttgaacctgggaggtggaggttgtggt gagccaagatcatgccattgcactccagcctgggcaagaagtgcaaaactctgtctcaaaaaaaaa aaaaaaaaaaaaaaaaaagaatgatgcatctgttggggatgcagtggggtaagcatcttcagtaagc aaggtgtgaagaggggaaagagggaaggtgaatatggaggagagggtgaaggagggcactgg aaagggtagtaggatcccagcaaagggcgatttggctgaaagggagcgtgataacaagggtggg ggtggggccaagaagcagccaccatgtgtgggtgcctctgtgcgtgcagtcatctttctcacatcatt gtggatcaagagaggaaatgcccacttctggaagaaaaagccacaaaatgagacttggaagggaa attgatcaacatctacaaaacggcttcttaaaggaagcggccctcAGACAGGACAGAG TTGAGGGAAAGGACAGAGGTTATGAGTGCCTGCAAGAGTGG CAGCCTGGAGTAGAGAAAACACTAAAGGTGGAGTCAAAAG ACCTGAG (SEQ ID NO: 196)
[0447] AAV-9 preparations were generated according to standard techniques (triple- transfection method) and purified by IDX gradient ultracentrifugation. AAV was titered by qPCR after dialysis against PBS. One of the three AAV versions described above is next injected into the tibialis anterior muscles of wildtype FVB strain mice (30µL total volume, 2*10^10 vg, 1*10^11 vg or 4*10^12 vg) and subjected to daily clinical observation subsequently. (Contralateral injection of vector 1 and either vector 2, 3, or PBS.4 mice for each combination, 1/2, 1/3, 1/PBS). Mice are sacrificed at 1w, 4w, and 6w after
injection. For each animal, the proximal half of the tibialis anterior muscle (injection site), heart, spleen, liver (representative portion, i.e. piece of a lobe) and kidneys are collected, placed individually (except pair organs) into cryovials and flash frozen in liquid nitrogen for RNA/protein assessment and changes in gene expressions. The other half of the tibialis anterior muscle is embedded in OCT and frozen. The tibialis anterior muscle is cut in a transverse fashion.
[0448] RNA isolations from frozen tissue is carried out with RNAeasy columns (Qiagen) according to the manufacturer’s protocol. RNA quality and concentrations are estimated using the Nanodrop spectrophotometer. cDNA preparation is done using Superscript III (Thermo) with random primers according to the manufacturer’s protocol. qPCR is carried out to assess the levels of Cas9 in tissue among the three mouse groups (vector 1/2, 1/3, 1/PBS).
[0449] Immunofluorescence with sectioned tibialis anterior muscle is conducted to measure infiltration of immune cells (CD3 and CD45 staining).
EXAMPLE 2: Preventing adaptive immune response to a non-self therapeutic transgene
[0450] A non-self therapeutic transgene is delivered to a target issue via viral or nonviral means. In order to prevent adaptive immune response to this therapeutic, vector with DNA enconding mutant FASL (mFASL) is co-delivered by viral or nonviral means. The mFASL mRNA contains an intron that splits the coding sequence of FASL (Figure 3B). This intron is bound by an RNA-binding protein Cas13d with a single guide RNA that is partially complementary to the intron which prevents splicing of the adjacent exons. The Cas13d guide RNA is perfectly complementary to genes whose expression is regulated by TNFa or IL-6 signaling so that mFASL splicing is released from blockage upon TNFa or IL-6 signaling. Systems where the guide RNA is perfectly complementary to mRNAs encoded by the following genes were constructed: BCAR3, CALCB, CCR6, COL6A3, CXCR5, DHRS9, FLT1, FNBP1L, FNDC9, GBP4, GPR87, GZMB, HOPX, HSD11B1, IFIT2, IFNL1, IGFBP6, IL12RB2, IL1R1, IL1R2, IL23R, IL24, KCNK18, MAF, NAPSA, PALLD, PRG4, PSD3, RORA, TNFSF1, TNFSF13B, TSHZ2. Two AAV-9 transfer vectors were produced that 1) encode Cas13d and guide RNA, and 2) encode the mFASL construct with the intervening intron.
[0451] AAV-9 preparations were generated according to standard techniques (triple- transfection method) and purified by IDX gradient ultracentrifugation. AAV was titered by qPCR after dialysis against PBS. The AAV encoding the non-self transgene along with a vector containing the engineered mFASL construct and Cas13d were next injected into the tibialis anterior muscles of wildtype FVB strain mice (30µL total volume, 2*10^10 vg, 1*10^11 vg or 4*10^12 vg) and subjected to daily clinical observation subsequently.
(Contralateral injection of vector 1 and either vector 2 3 or PBS 4 mice for each combination, 1/2, 1/3, 1/PBS). Mice are sacrificed at 1w, 4w, and 6w after injection. For each animal, the proximal half of the tibialis anterior muscle (injection site), heart, spleen, liver (representative portion, i.e. piece of a lobe) and kidneys are collected, placed
individually (except pair organs) into cryovials and flash frozen in liquid nitrogen for RNA/protein assessment and changes in gene expressions. The other half of the tibialis anterior muscle is embedded in OCT and frozen. The tibialis anterior muscle is cut in a transverse fashion.
[0452] RNA isolations from frozen tissue is carried out with RNAeasy columns (Qiagen) according to the manufacturer’s protocol. RNA quality and concentrations are estimated using the Nanodrop spectrophotometer. cDNA preparation is done using Superscript III (Thermo) with random primers according to the manufacturer’s protocol. qPCR is carried out to assess the levels of Cas9 in tissue among the three mouse groups (vector 1/2, 1/3, 1/PBS).
[0453] Immunofluorescence with sectioned tibialis anterior muscle is conducted to measure infiltration of immune cells (CD3 and CD45 staining).
EXAMPLE 3: Treatment of myotonic dystrophy type (DM1)
Figure imgf000148_0001
[0454] Compositions of the disclosure are used for the treatment of myotonic dystrophy type I (DM1) wherein an RNA-targeting CRISPR system composed of a therapeutic transgene (Cas9 or Cas13d and corresponding single guide RNA targeting the CUG repeats that cause DM1) is delivered to patient muscle or the central nervous system. The presence of mFASL causes the elimination of T cells that are specific to Cas9 or Cas13d and potentially cytotoxic against treated cells.
EXAMPLE 4: Treatment of hemophilia
[0455] Compositions of the disclosure are used for the treatment of hemophilia. A secreted transgene such as Factor IX is used for the treatment of hemophilia. A vector carrying an expression cassette for factor IX along with mFASL reduces, eliminates, or prevents an adaptive immune response to Factor IX-expressing cells.
EXAMPLE 5: Preventing adaptive immune response to a non-self therapeutic transgene while simultaneously preventing immune response to repeated AAV administrations
[0456] Compositions of the disclosure may comprise an AAV vector containing an expressed polypeptide composed of all or part of AAV viral capsid protein. The AAV capsid polypeptide is identical to the serotype used to deliver the system. Co-expression of this AAV capsid polypeptide causes the elimination of T cells that are specific to the AAV capsid in a manner described above. This causes depletion of T cells that can regulate both cellular and humoral immunity to the AAV capsid. This allows repeated dosing of the same AAV serotype. In the absence of the compositions of the disclosure, and using the standard of care prior to development of the compositions of the disclosure, an individual AAV serotype could not be used in more than once in a patient due to the formation of adaptive immune response against the viral capsid.
[0457] The compositions of the disclosure may be useful in situations wherein incomplete therapeutic transfer occurs during the first administration of a gene therapy or wherein a second dose is desired. In this case, the second dose of the gene therapy does not require the presence of the mFASL and AAV capsid polypeptide unless subsequent doses beyond the second dose are desired. One situation could be during the treatment of large organs such as skeletal muscle where the volume of virus required to transduce muscle in a single dose is prohibitively high. Another situation could be during treatment involving complicated administration methods in the brain or spine where initial treatments do not provide satisfactory infection of targeted cells. INCORPORATION BY REFERENCE
[0458] Every document cited herein, including any cross referenced or related patent or application is hereby incorporated herein by reference in its entirety unless expressly excluded or otherwise limited. The citation of any document is not an admission that it is prior art with respect to any invention disclosed or claimed herein or that it alone, or in any combination with any other reference or references, teaches, suggests or discloses any such invention. Further, to the extent that any meaning or definition of a term in this document conflicts with any meaning or definition of the same term in a document incorporated by reference, the meaning or definition assigned to that term in this document shall govern. OTHER EMBODIMENTS
[0459] While particular embodiments of the disclosure have been illustrated and described, various other changes and modifications can be made without departing from the spirit and scope of the disclosure. The scope of the appended claims includes all such changes and modifications that are within the scope of this disclosure.

Claims

What is claimed is: 1. A composition comprising:
(a) a sequence encoding a non-self polypeptide of interest (POI), and
(b) a sequence encoding a non-cleavable Fas Ligand (FASL),
wherein expression of the non-cleavable FASL eliminates MHC-mediated immunogenic peptides and helper T cells specific to the expression of the POI.
2. The composition of claim 1, wherein expression of the non-cleavable FASL selectively eliminates a T-cell that recognizes a MHC-peptide complex, wherein the peptide is derived from the non-self polypeptide, and wherein expression of FASL is in the presence of IL-6 or TNF-alpha.
3. The composition of claim 1, wherein the non-self POI is a nucleoprotein complex encoded by (i) a sequence comprising a guide RNA (gRNA) that specifically binds a target sequence within an RNA molecule, and (ii) a sequence encoding an RNA-binding polypeptide.
4. The composition of any one of claims 1-3, wherein a vector comprises the sequence of (a) and the sequence of (b).
5. The composition of claim 4, wherein the vector is an expression vector.
6. The composition of claim 5, wherein the expression vector is a plasmid.
7. The composition of claim 1, wherein a promoter drives expression of the sequence of (a).
8. The composition of claim 1, wherein the promoter drives expression of the sequence of (b).
9. The composition of claim 8, wherein the promoter is a promoter regulated by the presence of IL-6 receptor or TNF-alpha receptor.
10. The composition of claim 1, wherein a first promoter drives expression of the sequence of (a) and a second promoter drives expression of the sequence of (b).
11. The composition of claim 3, wherein a first promoter drives expression of the sequences encoding the nucleoprotein complex and a second promoter drives expression of the sequence of (b).
12. The composition of claim 11, the first promoter comprises a sequence isolated or derived from a U6 promoter.
13. The composition of claim 11, wherein the first promoter comprises a sequence isolated or derived from a promoter capable of driving expression of a transfer RNA (tRNA).
14. The composition of claim 13, wherein the promoter comprises a sequence isolated or derived from an alanine tRNA promoter, an arginine tRNA promoter, an asparagine tRNA promoter, an aspartic acid tRNA promoter, a cysteine tRNA promoter, a glutamine tRNA promoter, a glutamic acid tRNA promoter, a glycine tRNA promoter, a histidine tRNA promoter, an isoleucine tRNA promoter, a leucine tRNA promoter, a lysine tRNA promoter, a methionine tRNA promoter, a phenylalanine tRNA promoter, a proline tRNA promoter, a serine tRNA promoter, a threonine tRNA promoter, a tryptophan tRNA promoter, a tyrosine tRNA promoter, or a valine tRNA promoter.
15. The composition of claim 14, wherein the sequence encoding the promoter comprises a sequence isolated or derived from a valine tRNA promoter.
16. The composition of claim 1, wherein a delivery vector comprises the composition.
17. The composition of claim 16, wherein the delivery vector is an adeno-associated viral (AAV) vector.
18. The composition of claim 17, wherein the AAV comprises a sequence isolated or derived from an AAV of serotype AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, AAV10, AAV11, or AAV12.
19. The composition of any one of claim 1, wherein the sequence of (a) or the sequence of (b) further comprises an Internal Ribosomal Entry Site (IRES) or sequence encoding a self-cleaving peptide.
20. The composition of claim 19, wherein the IRES or the sequence encoding a self- cleaving peptide is positioned between the sequence of (a) and the sequence of (b).
21. The composition of claims 19 or 20, wherein the self-cleaving peptide comprises a 2A self-cleaving peptide.
22. The composition of claim 1, wherein the non-cleavable FASL comprises a mutation in a metalloproteinase cleavage site.
23. The composition of claim 22, wherein the metalloproteinase cleavage site comprises the amino acid sequence ELAELR.
24. The composition of claim 23, wherein the mutation comprises one or more of a substitution, an insertion, a deletion, a frameshift, an inversion, or a transposition of the amino acid sequence ELAELR.
25. The composition of claim 22, wherein the non-cleavable FASL comprises the amino acid sequence of:
MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLPPPPP PPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKX1X2X3X4 X5X6ESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGIV LLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLVM MEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGLY KL (SEQ ID NO: 210), wherein X1 is not a glutamic acid (E), X2 is not an leucine (L), X3 is not an alanine (A), X4 is not an glutamic acid (E), X5 is not an leucine (L) or X6 is not an arginine (R).
26. The composition of claim 22, wherein the non-cleavable FASL comprises the amino acid sequence of:
MQQPFNYPYPQIYWVDSSASSPWAPPGTVLPCPTSVPRRPGQRRPPPPPPPPPLPPPPP PPPLPPLPLPPLKKRGNHSTGLCLLVMFFMVLVALVGLGLGMFQLFHLQKX1X2X3X4 X5X6ESTSQMHTASSLEKQIGHPSPPPEKKELRKVAHLTGKSNSRSMPLEWEDTYGIV LLSGVKYKKGGLVINETGLYFVYSKVYFRGQSCNNLPLSHKVYMRNSKYPQDLVM MEGKMMSYCTTGQMWARSSYLGAVFNLTSADHLYVNVSELSLVNFEESQTFFGLY KL (SEQ ID NO: 210), wherein X1 is not a glutamic acid (E), X2 is not an leucine (L), X3 is not an alanine (A), X4 is not an glutamic acid (E), X5 is not an leucine (L) and X6 is not an arginine (R).
27. The composition of claim 1, wherein the non-cleavable FASL comprises an intron, wherein the intron blocks FASL splicing in the absence of IL-6 or TNF-alpha.
28. The composition of claim 27, further comprising synthetic mRNA target sites which are expressed in the presence of IL-6 or TNF-alpha.
29. The composition of claim 1, further comprising 1) a synthetic notch system, 2) microRNA target sites, or a 3) split intein and engineered IL-6 or TNF-alpha receptors for regulating expression of FASL in the presence of IL-6 or TNF-alpha.
30. The composition of claim 3, wherein the RNA-binding polypeptide is a CRISPR/Cas polypeptide selected from the group consisting of Cas9, Cpfl, Cas13a, Cas13b, Cas13c, and Cas13d.
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Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021195025A1 (en) * 2020-03-25 2021-09-30 City Of Hope Antisense rna for treatment of sars-associated coronavirus
WO2023004365A1 (en) * 2021-07-20 2023-01-26 Sio Gene Therapies Inc. Vector constructs for delivery of nucleic acids encoding therapeutic proteasome activator complex subunits and methods of using the same
WO2023073661A3 (en) * 2021-11-01 2023-06-22 Ionis Pharmaceuticals, Inc. Compounds and methods for reducing psd3 expression
WO2023242469A1 (en) * 2022-06-13 2023-12-21 Turun Yliopisto Oligonucleotides for modulating regulatory t cell mediated immunosuppression

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9499805B2 (en) 2010-06-18 2016-11-22 The University Of North Carolina At Chapel Hill Methods and compositions for synthetic RNA endonucleases
KR20210058806A (en) * 2018-06-08 2021-05-24 로카나바이오 인크. RNA targeting fusion protein composition and method of use

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030211509A1 (en) * 2002-03-26 2003-11-13 Wiley Steven R. TNF-delta ligand and uses thereof
US20090239240A1 (en) * 1996-11-13 2009-09-24 Keting Chu Mutant Forms of Fas Ligand and Uses Thereof
WO2017123556A1 (en) * 2016-01-11 2017-07-20 The Board Of Trustees Of The Leland Stanford Junior University Chimeric proteins and methods of immunotherapy
US20180100163A1 (en) * 2015-04-27 2018-04-12 Ucl Business Plc Nucleic acid construct

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1998052615A1 (en) * 1997-05-22 1998-11-26 Uab Research Foundation Controlling immune response to specific antigens
US6451759B1 (en) * 1998-01-14 2002-09-17 The Regents Of The University Of California Noncleavable Fas ligand
AU2002250333A1 (en) * 2001-03-13 2002-09-24 Johns Hopkins University School Of Medicine Fas ligand-expressing hematopoietic cells for transplantation
WO2003092723A1 (en) * 2002-05-03 2003-11-13 Nikolai Rainov Use of fasl for the treatment of neurodegenerative diseases
WO2018013932A1 (en) * 2016-07-15 2018-01-18 Salk Institute For Biological Studies Methods and compositions for genome editing in non-dividing cells

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20090239240A1 (en) * 1996-11-13 2009-09-24 Keting Chu Mutant Forms of Fas Ligand and Uses Thereof
US20030211509A1 (en) * 2002-03-26 2003-11-13 Wiley Steven R. TNF-delta ligand and uses thereof
US20180100163A1 (en) * 2015-04-27 2018-04-12 Ucl Business Plc Nucleic acid construct
WO2017123556A1 (en) * 2016-01-11 2017-07-20 The Board Of Trustees Of The Leland Stanford Junior University Chimeric proteins and methods of immunotherapy

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
ABUDAYYEH ET AL.: "RNA targeting with CRISPR-Cas13a", NATURE, vol. 550, no. 7675, 4 October 2017 (2017-10-04), pages 280 - 284, XP055529736, DOI: 10.1038/nature24049 *
See also references of EP3841116A4 *
SYMES ET AL.: "Retrovirally transduced murine T lymphocytes expressing FasL mediate effective killing of prostate cancer cells", CANCER GENE THERAPY, vol. 16, no. 5, 19 December 2008 (2008-12-19), pages 439 - 452, XP055694401 *
VARGO-GOGOLA ET AL.: "Identification of novel matrix metalloproteinase-7 (matrilysin) cleavage sites in murine and human Fas ligand", ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, vol. 408, no. 2, 15 December 2002 (2002-12-15), pages 155 - 161, XP055694404 *

Cited By (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021195025A1 (en) * 2020-03-25 2021-09-30 City Of Hope Antisense rna for treatment of sars-associated coronavirus
WO2023004365A1 (en) * 2021-07-20 2023-01-26 Sio Gene Therapies Inc. Vector constructs for delivery of nucleic acids encoding therapeutic proteasome activator complex subunits and methods of using the same
WO2023073661A3 (en) * 2021-11-01 2023-06-22 Ionis Pharmaceuticals, Inc. Compounds and methods for reducing psd3 expression
WO2023242469A1 (en) * 2022-06-13 2023-12-21 Turun Yliopisto Oligonucleotides for modulating regulatory t cell mediated immunosuppression

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