Patent Application
20240263159
CRISPR-Cas systems provide a valuable tool for gene editing. However, most methods for editing primary T cells require electroporation, can cause off-target genomic effects, and can be costly. There is a need in the art for CRISPR-Cas systems that achieve high gene editing efficiency both in vitro and in vivo, and are less expensive and easily implemented into experimental workflows. The present invention addresses this need.
As described herein, the present disclosure provides compositions and methods for Peptide-Assisted Genome Editing (PAGE). In one aspect, the disclosure provides a Peptide-Assisted Genome Editing (PAGE) system comprising a) a CRISPR associated (Cas) protein linked to a Cell Penetrating Peptide (CPP), and b) an endosomal escape peptide linked to a CPP.
In certain embodiments, the Cas is Cas9, or Cas12a, or a Cas derivative. In certain embodiments, the Cas derivative is a Cas protein linked to another protein or catalytic domain. In certain embodiments, the protein or catalytic domain is selected from the group consisting of an AID deaminase, an APOBEC deaminase, a TadA deaminase, a TET enzyme, a DNA methyltransferase, a transactivation domain, a reverse transcriptase, a histone acetyltransferase, a histone deacetylase, a sirtuin, a histone methyltransferase, a histone demethylase, a kinase, and a phosphatase.
In certain embodiments, the endosomal escape peptide comprises any of the amino acid sequences set forth in SEQ ID NOs: 1434-1523. In certain embodiments, the endosomal escape peptide comprises dTAT-HA2.
In certain embodiments, the Cas comprises a Nuclear Localization Signal (NLS) sequence. In certain embodiments, the NLS sequence comprises the amino acid sequence PAAKRVKLD (SEQ ID NO: 1). In certain embodiments, the NLS sequence further comprises a GGS linker.
In certain embodiments, the CPP comprises any of the amino acid sequences set forth in SEQ ID NOs: 10-1422. In certain embodiments, the CPP comprises a sequence derived from the trans-activating transcriptional activator (Tat) from HIV-1. In certain embodiments, the Tat sequence comprises the amino acid sequence GRKKRRQRRRPQ (SEQ ID NO: 2).
Another aspect of the disclosure provides an in vitro method of gene editing comprising introducing into a cell a PAGE system and at least one sgRNA or crRNA, wherein the PAGE system comprises a Cas protein linked to a CPP and an endosomal escape peptide linked to a CPP.
Another aspect of the disclosure provides an in vivo method of gene editing comprising introducing into a cell a PAGE system and at least one sgRNA or crRNA, wherein the PAGE system comprises a Cas protein linked to a CPP and an endosomal escape peptide linked to a CPP, and administering the cell to a subject.
In certain embodiments, the Cas is Cas9, or Cas12a, or a Cas derivative. In certain embodiments, the Cas derivative is a Cas protein linked to another protein or catalytic domain. In certain embodiments, the protein or catalytic domain is selected from the group consisting of an AID deaminase, an APOBEC deaminase, a TadA deaminase, a TET enzyme, a DNA methyltransferase, a transactivation domain, a reverse transcriptase, a histone acetyltransferase, a histone deacetylase, a sirtuin, a histone methyltransferase, a histone demethylase, a kinase, and a phosphatase.
In certain embodiments, the endosomal escape peptide comprises any of the amino acid sequences set forth in SEQ ID NOs: 1434-1523. In certain embodiments, the endosomal escape peptide comprises dTAT-HA2.
In certain embodiments, the Cas comprises a NLS sequence. In certain embodiments, the NLS sequence comprises the amino acid sequence PAAKRVKLD (SEQ ID NO: 1). In certain embodiments, the NLS sequence further comprises a GGS linker.
In certain embodiments, the CPP comprises any of the amino acid sequences set forth in SEQ ID NOs: 10-1422. In certain embodiments, the CPP comprises a sequence derived from the trans-activating transcriptional activator (Tat) from HIV-1. In certain embodiments, the Tat sequence comprises the amino acid sequence GRKKRRQRRRPQ (SEQ ID NO: 2).
In certain embodiments, the method does not require electroporation. In certain embodiments, the PAGE system is introduced into the cell in a medium that does not contain serum. In certain embodiments, the endosomal escape peptide is introduced into the cell at a concentration of about 25-75 μM. In certain embodiments, the Cas is introduced into the cell at a concentration of about 0.5-5 μM.
In certain embodiments, cell is an immune cell.
In certain embodiments, the cell is selected from the group consisting of a primary human CD8 T cell, a human iPSC, and a CAR T cell.
In certain embodiments, the sgRNA targets Ano9, Pdcd1, Thy1, Ptprc, PTPRC, or B2M.
In certain embodiments, the subject is in need of a treatment for a disease or disorder, and wherein when the edited cell is administered to the subject, the disease or disorder is treated in the subject. In certain embodiments, the disease or disorder is an infection. In certain embodiments, the disease or disorder is related to T cell exhaustion.
The foregoing and other features and advantages of the present invention will be more fully understood from the following detailed description of illustrative embodiments taken in conjunction with the accompanying drawings.
Herein, an optimized, highly efficient, inexpensive, and novel gene editing method was established in cells using a cell penetrating Cas protein linked to an endosomal escape peptide. This work has generated a novel composition of matter for this cell penetrating Cas tool. Compared to the published gene editing methods using cell penetrating CRISPR-Cas systems (Ramakrishna et al., (2014) Genome Res 24, 1020-1027; Staahl et al., (2017) Nat Biotechnol 35, 431-434), this method achieves high gene editing efficiency both in vitro and in vivo. Compared to the published gene editing method for mouse primary T cell using CRISPR-Cas system that requires electroporation of Ribonucleoprotein (RNP) complex (Kornete et al., (2018) J Immunol 200, 2489-2501; Nussing et al., (2020) J. Immunol), this method is less expensive and more easily implemented into experimental workflows. The present method does not require electroporation, but instead requires either (1) incubating the cell penetrating Cas protein and endosomal escape peptide with the cells infected with an sgRNA expressing construct or (2) incubating the cell penetrating Cas-sgRNA ribonucleoprotein (RNP) complex and endosomal escape peptide with the cells. Furthermore, since this method does not require transgenic mice expressing Cas protein to achieve gene editing, it saves the time and expense of generating a specific Cas transgenic mouse line. Importantly, since the cells lose the majority of cell penetrating Cas protein in two days after incubation, this reduces the Cas protein immunogenicity and/or decreases off-target genomic effects observed in other studies.
The method can be used by researchers to achieve gene editing in primary mouse and human T cells or other primary immune cells (including human immune cells) and enable CRISPR-CAS screening. The settings used in this method can also be applied to other Cas proteins in addition to Cas9, i.e. Cas12a, and Cas9-Base Editor.
It is to be understood that the methods described in this disclosure are not limited to particular methods and experimental conditions disclosed herein as such methods and conditions may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting.
Furthermore, the experiments described herein, unless otherwise indicated, use conventional molecular and cellular biological and immunological techniques within the skill of the art. Such techniques are well known to the skilled worker, and are explained fully in the literature. See, e.g., Ausubel, et al., ed., Current Protocols in Molecular Biology, John Wiley & Sons, Inc., NY, N.Y. (1987-2008), including all supplements, Molecular Cloning: A Laboratory Manual (Fourth Edition) by M R Green and J. Sambrook, and Harlow et al., Antibodies: A Laboratory Manual, Chapter 14, Cold Spring Harbor Laboratory, Cold Spring Harbor (2013, 2nd edition).
Unless otherwise defined, scientific and technical terms used herein have the meanings that are commonly understood by those of ordinary skill in the art. In the event of any latent ambiguity, definitions provided herein take precedent over any dictionary or extrinsic definition. Unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular. The use of “or” means “and/or” unless stated otherwise. The use of the term “including,” as well as other forms, such as “includes” and “included,” is not limiting.
Generally, nomenclature used in connection with cell and tissue culture, molecular biology, immunology, microbiology, genetics and protein and nucleic acid chemistry and hybridization described herein is well-known and commonly used in the art. The methods and techniques provided herein are generally performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated. Enzymatic reactions and purification techniques are performed according to manufacturer's specifications, as commonly accomplished in the art or as described herein. The nomenclatures used in connection with, and the laboratory procedures and techniques of, analytical chemistry, synthetic organic chemistry, and medicinal and pharmaceutical chemistry described herein are those well-known and commonly used in the art. Standard techniques are used for chemical syntheses, chemical analyses, pharmaceutical preparation, formulation, and delivery, and treatment of patients.
That the disclosure may be more readily understood, select terms are defined below.
The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” means one element or more than one element.
“About” as used herein when referring to a measurable value such as an amount, a temporal duration, and the like, is meant to encompass variations of ±20% or ±10%, more preferably ±5%, even more preferably ±1%, and still more preferably ±0.1% from the specified value, as such variations are appropriate to perform the disclosed methods.
“Activation,” as used herein, refers to the state of a T cell that has been sufficiently stimulated to induce detectable cellular proliferation. Activation can also be associated with induced cytokine production, and detectable effector functions. The term “activated T cells” refers to, among other things, T cells that are undergoing cell division.
As used herein, to “alleviate” a disease means reducing the severity of one or more symptoms of the disease.
The term “antigen” as used herein is defined as a molecule that provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both. The skilled artisan will understand that any macromolecule, including virtually all proteins or peptides, can serve as an antigen.
Furthermore, antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein. Furthermore, one skilled in the art will understand that an antigen need not be encoded solely by a full length nucleotide sequence of a gene. It is readily apparent that the present invention includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be generated synthesized or can be derived from a biological sample. Such a biological sample can include, but is not limited to a tissue sample, a tumor sample, a cell or a biological fluid.
As used herein, the term “autologous” is meant to refer to any material derived from the same individual to which it is later to be re-introduced into the individual.
A “co-stimulatory molecule” refers to the cognate binding partner on a T cell that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the T cell, such as, but not limited to, proliferation. Co-stimulatory molecules include, but are not limited to an MHC class I molecule, BTLA and a Toll ligand receptor.
A “co-stimulatory signal”, as used herein, refers to a signal, which in combination with a primary signal, such as TCR/CD3 ligation, leads to T cell proliferation and/or upregulation or downregulation of key molecules.
A “disease” is a state of health of an animal wherein the animal cannot maintain homeostasis, and wherein if the disease is not ameliorated then the animal's health continues to deteriorate. In contrast, a “disorder” in an animal is a state of health in which the animal is able to maintain homeostasis, but in which the animal's state of health is less favorable than it would be in the absence of the disorder. Left untreated, a disorder does not necessarily cause a further decrease in the animal's state of health.
The term “downregulation” as used herein refers to the decrease or elimination of gene expression of one or more genes.
“Effective amount” or “therapeutically effective amount” are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological result or provides a therapeutic or prophylactic benefit. Such results may include, but are not limited to an amount that when administered to a mammal, causes a detectable level of immune suppression or tolerance compared to the immune response detected in the absence of the composition of the invention. The immune response can be readily assessed by a plethora of art-recognized methods. The skilled artisan would understand that the amount of the composition administered herein varies and can be readily determined based on a number of factors such as the disease or condition being treated, the age and health and physical condition of the mammal being treated, the severity of the disease, the particular compound being administered, and the like.
“Encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (i.e., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom. Thus, a gene encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system. Both the coding strand, the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
As used herein “endogenous” refers to any material from or produced inside an organism, cell, tissue or system.
The term “epitope” as used herein is defined as a small chemical molecule on an antigen that can elicit an immune response, inducing B and/or T cell responses. An antigen can have one or more epitopes. Most antigens have many epitopes; i.e., they are multivalent. In general, an epitope is roughly about 10 amino acids and/or sugars in size. Preferably, the epitope is about 4-18 amino acids, more preferably about 5-16 amino acids, and even more most preferably 6-14 amino acids, more preferably about 7-12, and most preferably about 8-10 amino acids. One skilled in the art understands that generally the overall three-dimensional structure, rather than the specific linear sequence of the molecule, is the main criterion of antigenic specificity and therefore distinguishes one epitope from another. Based on the present disclosure, a peptide used in the present invention can be an epitope.
As used herein, the term “exogenous” refers to any material introduced from or produced outside an organism, cell, tissue or system.
The term “expand” as used herein refers to increasing in number, as in an increase in the number of T cells. In one embodiment, the T cells that are expanded ex vivo increase in number relative to the number originally present in the culture. In another embodiment, the T cells that are expanded ex vivo increase in number relative to other cell types in the culture. The term “ex vivo,” as used herein, refers to cells that have been removed from a living organism, (e.g., a human) and propagated outside the organism (e.g., in a culture dish, test tube, or bioreactor).
The term “expression” as used herein is defined as the transcription and/or translation of a particular nucleotide sequence driven by its promoter.
“Expression vector” refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed. An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system. Expression vectors include all those known in the art, such as cosmids, plasmids (e.g., naked or contained in liposomes) and viruses (e.g., Sendai viruses, lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
“Identity” as used herein refers to the subunit sequence identity between two polymeric molecules particularly between two amino acid molecules, such as, between two polypeptide molecules. When two amino acid sequences have the same residues at the same positions; e.g., if a position in each of two polypeptide molecules is occupied by an arginine, then they are identical at that position. The identity or extent to which two amino acid sequences have the same residues at the same positions in an alignment is often expressed as a percentage. The identity between two amino acid sequences is a direct function of the number of matching or identical positions; e.g., if half (e.g., five positions in a polymer ten amino acids in length) of the positions in two sequences are identical, the two sequences are 50% identical; if 90% of the positions (e.g., 9 of 10), are matched or identical, the two amino acids sequences are 90% identical.
The term “immune response” as used herein is defined as a cellular response to an antigen that occurs when lymphocytes identify antigenic molecules as foreign and induce the formation of antibodies and/or activate lymphocytes to remove the antigen.
The term “immunosuppressive” is used herein to refer to reducing overall immune response.
“Insertion/deletion”, commonly abbreviated “indel,” is a type of genetic polymorphism in which a specific nucleotide sequence is present (insertion) or absent (deletion) in a genome.
“Isolated” means altered or removed from the natural state. For example, a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.” An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
The term “knockdown” as used herein refers to a decrease in gene expression of one or more genes.
The term “knockin” as used herein refers to an exogenous nucleic acid sequence that has been inserted into a target sequence (e.g., endogenous gene locus. In some embodiments, where the target sequence is a gene, a knockin is generated resulting in the exogenous nucleic acid sequence being in operable linkage with any upstream and/or downstream regulatory elements controlling expression of the target gene. In some embodiments, the knockin is generated resulting in the exogenous nucleic acid sequence not being in operable linkage with any upstream and/or downstream regulatory elements controlling expression of the target gene.
The term “knockout” as used herein refers to the ablation of gene expression of one or more genes.
A “lentivirus” as used herein refers to a genus of the Retroviridae family. Lentiviruses are unique among the retroviruses in being able to infect non-dividing cells; they can deliver a significant amount of genetic information into the DNA of the host cell, so they are one of the most efficient methods of a gene delivery vector. HIV, SIV, and FIV are all examples of lentiviruses. Vectors derived from lentiviruses offer the means to achieve significant levels of gene transfer in vivo.
By the term “modified” as used herein, is meant a changed state or structure of a molecule or cell of the invention. Molecules may be modified in many ways, including chemically, structurally, and functionally. Cells may be modified through the introduction of nucleic acids.
By the term “modulating,” as used herein, is meant mediating a detectable increase or decrease in the level of a response in a subject compared with the level of a response in the subject in the absence of a treatment or compound, and/or compared with the level of a response in an otherwise identical but untreated subject. The term encompasses perturbing and/or affecting a native signal or response thereby mediating a beneficial therapeutic response in a subject, preferably, a human.
In the context of the present invention, the following abbreviations for the commonly occurring nucleic acid bases are used. “A” refers to adenosine, “C” refers to cytosine, “G” refers to guanosine, “T” refers to thymidine, and “U” refers to uridine.
The term “oligonucleotide” typically refers to short polynucleotides. It will be understood that when a nucleotide sequence is represented by a DNA sequence (i.e., A, T, C, G), this also includes an RNA sequence (i.e., A, U, C, G) in which “U” replaces “T.”
Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some version contain an intron(s).
“Parenteral” administration of an immunogenic composition includes, e.g., subcutaneous (s.c.), intravenous (i.v.), intramuscular (i.m.), or intrasternal injection, or infusion techniques.
The term “polynucleotide” as used herein is defined as a chain of nucleotides. Furthermore, nucleic acids are polymers of nucleotides. Thus, nucleic acids and polynucleotides as used herein are interchangeable. One skilled in the art has the general knowledge that nucleic acids are polynucleotides, which can be hydrolyzed into the monomeric “nucleotides.” The monomeric nucleotides can be hydrolyzed into nucleosides. As used herein polynucleotides include, but are not limited to, all nucleic acid sequences which are obtained by any means available in the art, including, without limitation, recombinant means, i.e., the cloning of nucleic acid sequences from a recombinant library or a cell genome, using ordinary cloning technology and PCR, and the like, and by synthetic means.
As used herein, the terms “peptide,” “polypeptide,” and “protein” are used interchangeably, and refer to a compound comprised of amino acid residues covalently linked by peptide bonds. A protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein's or peptide's sequence. Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds. As used herein, the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types. “Polypeptides” include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others. The polypeptides include natural peptides, recombinant peptides, synthetic peptides, or a combination thereof.
By the term “specifically binds,” as used herein with respect to an antibody, is meant an antibody which recognizes a specific antigen, but does not substantially recognize or bind other molecules in a sample. For example, an antibody that specifically binds to an antigen from one species may also bind to that antigen from one or more species. But, such cross-species reactivity does not itself alter the classification of an antibody as specific. In another example, an antibody that specifically binds to an antigen may also bind to different allelic forms of the antigen. However, such cross reactivity does not itself alter the classification of an antibody as specific. In some instances, the terms “specific binding” or “specifically binding,” can be used in reference to the interaction of an antibody, a protein, or a peptide with a second chemical species, to mean that the interaction is dependent upon the presence of a particular structure (e.g., an antigenic determinant or epitope) on the chemical species; for example, an antibody recognizes and binds to a specific protein structure rather than to proteins generally. If an antibody is specific for epitope “A”, the presence of a molecule containing epitope A (or free, unlabeled A), in a reaction containing labeled “A” and the antibody, will reduce the amount of labeled A bound to the antibody.
By the term “stimulation,” is meant a primary response induced by binding of a stimulatory molecule (e.g., a TCR/CD3 complex) with its cognate ligand thereby mediating a signal transduction event, such as, but not limited to, signal transduction via the TCR/CD3 complex. Stimulation can mediate altered expression of certain molecules, such as downregulation of TGF-beta, and/or reorganization of cytoskeletal structures, and the like.
A “stimulatory molecule,” as the term is used herein, means a molecule on a T cell that specifically binds with a cognate stimulatory ligand present on an antigen presenting cell.
A “stimulatory ligand,” as used herein, means a ligand that when present on an antigen presenting cell (e.g., an aAPC, a dendritic cell, a B-cell, and the like) can specifically bind with a cognate binding partner (referred to herein as a “stimulatory molecule”) on a T cell, thereby mediating a primary response by the T cell, including, but not limited to, activation, initiation of an immune response, proliferation, and the like. Stimulatory ligands are well-known in the art and encompass, inter alia, an MHC Class I molecule loaded with a peptide, an anti-CD3 antibody, a superagonist anti-CD28 antibody, and a superagonist anti-CD2 antibody.
The term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). A “subject” or “patient,” as used therein, may be a human or non-human mammal. Non-human mammals include, for example, livestock and pets, such as ovine, bovine, porcine, canine, feline and murine mammals. Preferably, the subject is human.
A “target site” or “target sequence” refers to a nucleic acid sequence that defines a portion of a nucleic acid to which a binding molecule may specifically bind under conditions sufficient for binding to occur. In some embodiments, a target sequence refers to a genomic nucleic acid sequence that defines a portion of a nucleic acid to which a binding molecule may specifically bind under conditions sufficient for binding to occur.
The term “therapeutic” as used herein means a treatment and/or prophylaxis. A therapeutic effect is obtained by suppression, remission, or eradication of a disease state.
“Transplant” refers to a biocompatible lattice or a donor tissue, organ or cell, to be transplanted. An example of a transplant may include but is not limited to skin cells or tissue, bone marrow, and solid organs such as heart, pancreas, kidney, lung and liver. A transplant can also refer to any material that is to be administered to a host. For example, a transplant can refer to a nucleic acid or a protein.
The term “transfected” or “transformed” or “transduced” as used herein refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid. The cell includes the primary subject cell and its progeny.
To “treat” a disease as the term is used herein, means to reduce the frequency or severity of at least one sign or symptom of a disease or disorder experienced by a subject.
A “vector” is a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell. Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses. Thus, the term “vector” includes an autonomously replicating plasmid or a virus. The term should also be construed to include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, polylysine compounds, liposomes, and the like. Examples of viral vectors include, but are not limited to, Sendai viral vectors, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like.
Ranges: throughout this disclosure, various aspects of the invention can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the invention. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6. This applies regardless of the breadth of the range.
Provided herein are methods of gene editing (in vitro, ex vivo, and in vivo) using a novel CRISPR-Cas system termed Peptide-Assisted Genome Editing (PAGE) system. The PAGE system comprises a cell penetrating Cas (e.g. a Cas (e.g. Cas 9 or Cas12a) linked to a cell penetrating peptide (CPP)), and an endosomal escape peptide (e.g. dTAT-HA2) linked to a CPP. Using this method, the Cas is introduced into a cell (e.g. a primary resting T cell) in a non-viral, non-electroporation dependent manner. A single-guide RNA (sgRNA) or CRISPR RNA (crRNA); or a plurality of sgRNAs or crRNAs can then be introduced into the cell (e.g. via a retroviral expression construct or RNP) to achieve in vitro, ex vivo, and in vivo editing of the cell (e.g primary CD8 T cell).
In one aspect, the disclosure provides an in vitro method of gene editing comprising introducing into a cell a PAGE system comprising a cell penetrating Cas and an endosomal escape peptide, and at least one sgRNA or crRNA. The cell penetrating Cas comprises a Cas (e.g. Cas9, Cas12a) linked to a CPP. The endosomal escape peptide is linked to a CPP.
In another aspect, the disclosure provides an ex vivo or in vivo method of gene editing comprising introducing into a cell a PAGE system comprising a cell penetrating Cas and an endosomal escape peptide, and at least one sgRNA or crRNA, and administering the cell to a subject. The cell penetrating Cas comprises a Cas (e.g. Cas9, Cas12a) linked to a CPP. The endosomal escape peptide is linked to a CPP.
In certain embodiments, the Cas is Cas9. Exemplary Cas9 nucleases that may be used in the present invention include, but are not limited to, S. pyogenes Cas9 (SpCas9), S. aureus Cas9 (SaCas9), S. thermophilus Cas9 (StCas9), N. meningitidis Cas9 (NmCas9), C. jejuni Cas9 (CjCas9), and Geobacillus Cas9 (GeoCas9). In certain embodiments, the Cas is Cas12a (Cpf1), including but not limited to Butyrivibrio sp (BsCas12a), Thiomicrospira sp). XS5 (TsCas12a, Moraxella bovoculi (MbCas12a), Prevotella bryantii (PbCas12a), Bacteroidetes oral (BoCas12a), Lachnospiraceae bacterium (LbCas12a), and Acidaminococcus sp (AsCas12a). In certain embodiments, the Cas is Cas12a. In certain embodiments, the Cas is selected from the group consisting of Cas12b, Cas12d, Cas12f, T7, Cas3, Cas8a, Cas8b, Cas10d, Cse1, Csy1, Csn2, Cas4, Cas10, Csm2, Cmr5, and Fok1.
In certain embodiments, the Cas is a Cas derivative. In certain embodiments, the Cas derivative is a Cas protein linked to another protein or catalytic domain. The Cas protein can be linked to another protein or catalytic domain by any means known in the art, such as, but not limited to chemical linkage, fusion, or post-translational modification. In certain embodiments, the protein or catalytic domain is selected from the group consisting of an AID deaminase, an APOBEC deaminase, a TadA deaminase, a TET enzyme, a DNA methyltransferase, a transactivation domain, a reverse transcriptase, a histone acetyltransferase, a histone deacetylase, a sirtuin, a histone methyltransferase, a histone demethylase, a kinase, and a phosphatase.
In certain embodiments, the Cas comprises a Nuclear Localization Signal (NLS) sequence. Any NLS known in the art or disclosed herein can be used. In certain embodiments, the Cas comprises a Myc NLS sequence. In certain embodiments, the Myc NLS sequence comprises or consists of the amino acid sequence PAAKRVKLD (SEQ ID NO: 1). In certain embodiments, the Cas comprises a 4×Myc or 6×Myc NLS sequence. In certain embodiments, the NLS (i.e. 4×Myc or 6×Myc) sequence further comprises a GGS linker.
In certain embodiments, the cell penetrating Cas comprises a nucleotide sequence encoding, or amino acid sequence comprising, a Cell Penetrating Peptide. Cell Penetrating Peptides (CPPs, also known as Protein Transduction Domains, PTDs), are carriers with small peptide domains (generally less than 40 amino acids) that can easily cross cell membranes. Multiple cell permeable peptides have been identified that facilitate cellular uptake of various molecular cargo, ranging from nanosize particles to small chemical molecules. Cell penetrating sequences can be used as extensions to peptide sequences thereby making them more permeable to cell membranes, or cell penetrating peptide can be attached to other cargo molecules to enhance their cellular uptake. Cell penetrating sequences can be either fused directly to the cargo molecules or chemically linked to cargo molecules. Examples of such cell penetrating peptides include, but are not limited to trans-activating transcriptional activator (Tat) from HIV-1, Oligo-Arg, KALA, Transportan, Penetratin, Penetratin-Arg, TAT-HA2, and dTAT-HA2E5. The PAGE system may comprise two different CPPs or two of the same CPPs. The CPP can be linked to the Cas or endosomal escape peptide by any means known in the art, such as, but not limited to chemical linkage, fusion, or post-translational modification. In certain embodiments, the CPP comprises a peptide listed in Table 2. In certain embodiments, the Cas is linked to a CPP listed in Table 2. In certain embodiments, the endosomal escape peptide is linked to a CPP listed in Table 2. In certain embodiments, the CPP comprises any of the amino acid sequences set forth in SEQ ID NOs: 10-1422. In certain embodiments, the Cas is linked to a CPP comprising any of the amino acid sequences set forth in SEQ ID NOs: 10-1422. In certain embodiments, the endosomal escape peptide is linked to a CPP comprising any of the amino acid sequences set forth in SEQ ID NOs: 10-1422.
In certain embodiments, the cell penetrating Cas comprises a sequence derived from the trans-activating transcriptional activator (Tat) from HIV-1. In certain embodiments, the Tat sequence comprises the amino acid sequence GRKKRRQRRRPQ (SEQ ID NO: 2).
In certain embodiments, the cell penetrating Cas is introduced into the cell at a concentration between 0.05 μM and 10 μM. In certain embodiments, the cell penetrating Cas is introduced into the cell at a concentration of about 0.5 μM.
In certain embodiments, the endosomal escape peptide comprises dTAT-HA2. Other endosomal escape peptides that could be used include, but are not limited to, EEDs, HA2-penetratin, GALA, INF-7, and the like. In certain embodiments, the endosomal escape peptide comprises any one of the peptides or sequences listed in Table 1. The endosomal escape peptide can include any and all chemical modifications to the peptide, or chemically-modified derivatives of the peptide, or special chemical-linkers within the peptide, or D form of amino acids, listed in Table 1. In certain embodiments, the endosomal escape peptide comprises any one of the sequences set forth in SEQ ID NOs: 1434-1523. In certain embodiments, the endosomal escape peptide comprises any one of the sequences set forth in SEQ ID NOs: 1434-1523 and a chemical modification and/or a chemical-linker. Examples of chemical modifications include but are not limited to: phosphate (PO3), trifluoromethyl-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg), amino isobutyric acid (Aib), stearylation (Stearyl), 6-aminohexanoic acid (Ahx), L-2-naphthylalanine (Φ), and 3-amino-3-carboxypropyl (acp).
In certain embodiments, the endosomal escape peptide is introduced into the cell at a concentration between 10 μM to 100 μM. In certain embodiments, the endosomal escape peptide is introduced into the cell at a concentration of about 75 μM.
In certain embodiments, the cell is an immune cell. In certain embodiments, the cell is a murine primary CD8 T cell, human primary T cell, or human iPSC (induced pluripotent stem cell).
In certain embodiments, the method does not require electroporation. In certain embodiments, the PAGE system is introduced into the cell in a medium that does not contain Fetal Bovine Serum (FBS) or serum. In certain embodiments, the PAGE system is introduced into the cell in a medium contains FBS or serum.
The methods should be construed to target any gene/genomic region/nucleotide sequence in a cell (e.g. a eukaryotic/human cell). Thus, an sgRNA or crRNA, or plurality of sgRNAs or crRNAs can be designed to target any gene/genomic region/nucleotide sequence in a cell (e.g. a eukaryotic/human cell) for use with the methods herein. In certain embodiments, the sgRNA targets Ano9 or Pdcd1. In certain embodiments, the sgRNA targets human Ano9 or Pdcd1. In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence GCCTGGCTCACAGTGTCAGA (SEQ ID NO: 8; Pdcd1 Ig_44). In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence GGTATCATGAGTGCCCTAGT (SEQ ID NO: 9; Pdcd1 Tm_1). In certain embodiments, the sgRNA targets Ptprc or Thy1. In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence CGTGTGCTCGGGTATCCCAA (SEQ ID NO: 1424; Thy1 IG1). In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence CCGCCATGAGAATAACACCA (SEQ ID NO: 1425; Thy1 IG2). In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence CCTTGGTGTTATTCTCATGG (SEQ ID NO: 1426; Thy1 IG3). In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence TTGTCAAGCTAAGGCGACAG (SEQ ID NO: 1427; Ptprc CAT1). In certain embodiments, the sgRNA comprises or consists of the nucleotide sequence TCACAATAATCAGAAACACC (SEQ ID NO: 1428; Ptprc TM1). In certain embodiments, the crRNA targets PTPRC or B2M. In certain embodiments, the crRNA comprises or consists of the nucleotide sequence TTCAGTGGTCCCATTGTGGT (SEQ ID NO: 1429; PTPRC CAT1). In certain embodiments, the crRNA comprises or consists of the nucleotide sequence GTGGAATACAATCAGTTTGG (SEQ ID NO: 1430; PTPRC CAT2). In certain embodiments, the crRNA comprises or consists of the nucleotide sequence TTCTCGGCTTCCAGGCCTTC (SEQ ID NO: 1431; PTPRC CAT3). In certain embodiments, the crRNA comprises or consists of the nucleotide sequence CATTCTCTGCTGGATGACGT (SEQ ID NO: 1432; B2M IG1). In certain embodiments, the crRNA comprises or consists of the nucleotide sequence AATTCTCTCTCCATTCTTCA (SEQ ID NO: 1433; B2M IG2).
In certain embodiments, the methods disclosed herein are used to treat a subject for a disease or disorder. The method comprises introducing into a cell a PAGE system comprising a cell penetrating Cas and an endosomal escape peptide and at least one sgRNA or crRNA, then administering the cell to a subject. When the edited cell is administered to the subject, the disease or disorder is treated in the subject. In certain embodiments, the disease or disorder to be treated in the subject is an infection. In certain embodiments, the disease or disorder is related to T cell exhaustion.
In certain embodiments, the PAGE system comprises a CRISPR/Cas9 system. The CRISPR/Cas9 system is a facile and efficient system for inducing targeted genetic alterations. Target recognition by the Cas9 protein requires a ‘seed’ sequence within the guide RNA (gRNA) and a conserved di-nucleotide containing protospacer adjacent motif (PAM) sequence upstream of the gRNA-binding region. The CRISPR/Cas9 system can thereby be engineered to cleave virtually any DNA sequence by redesigning the gRNA in cell lines (such as 293T cells) and primary cells. The CRISPR/Cas9 system can simultaneously target multiple genomic loci by co-expressing a single Cas9 protein with two or more gRNAs, making this system suited for multiple gene editing or synergistic activation of target genes.
The Cas9 protein and guide RNA form a complex that identifies and cleaves target sequences. Cas9 is comprised of six domains: REC I, REC II, Bridge Helix, PAM interacting, HNH, and RuvC. The REC I domain binds the guide RNA, while the Bridge helix binds to target DNA. The HNH and RuvC domains are nuclease domains. Guide RNA is engineered to have a 5′ end that is complementary to the target DNA sequence. Upon binding of the guide RNA to the Cas9 protein, a conformational change occurs activating the protein. Once activated, Cas9 searches for target DNA by binding to sequences that match its protospacer adjacent motif (PAM) sequence. A PAM is a two or three nucleotide base sequence within one nucleotide downstream of the region complementary to the guide RNA. In one non-limiting example, the PAM sequence is 5′-NGG-3′. When the Cas9 protein finds its target sequence with the appropriate PAM, it melts the bases upstream of the PAM and pairs them with the complementary region on the guide RNA. Then the RuvC and HNH nuclease domains cut the target DNA after the third nucleotide base upstream of the PAM.
One non-limiting example of a CRISPR/Cas system used to inhibit gene expression, CRISPRi, is described in U.S. Patent Appl. Publ. No. US20140068797. CRISPRi induces permanent gene disruption that utilizes the RNA-guided Cas9 endonuclease to introduce DNA double stranded breaks which trigger error-prone repair pathways to result in frame shift mutations. A catalytically dead Cas9 lacks endonuclease activity. When coexpressed with a guide RNA, a DNA recognition complex is generated that specifically interferes with transcriptional elongation, RNA polymerase binding, or transcription factor binding. This CRISPRi system efficiently represses expression of targeted genes.
CRISPR/Cas gene disruption occurs when a guide nucleic acid sequence specific for a target gene and a Cas endonuclease are introduced into a cell and form a complex that enables the Cas endonuclease to introduce a double strand break at the target gene. In certain embodiments, the CRISPR/Cas system comprises an expression vector, such as, but not limited to, a pAd5F35-CRISPR vector. In other embodiments, the Cas expression vector induces expression of Cas9 endonuclease. Other endonucleases may also be used, including but not limited to, Cas12a (Cpf1), T7, Cas3, Cas8a, Cas8b, Cas10d, Cse1, Csy1, Csn2, Cas4, Cas10, Csm2, Cmr5, Fok1, other nucleases known in the art, and any combinations thereof.
In certain embodiments, inducing the Cas expression vector comprises exposing the cell to an agent that activates an inducible promoter in the Cas expression vector. In such embodiments, the Cas expression vector includes an inducible promoter, such as one that is inducible by exposure to an antibiotic (e.g., by tetracycline or a derivative of tetracycline, for example doxycycline). Other inducible promoters known by those of skill in the art can also be used. The inducing agent can be a selective condition (e.g., exposure to an agent, for example an antibiotic) that results in induction of the inducible promoter. This results in expression of the Cas expression vector.
As used herein, the term “guide RNA” or “gRNA” refer to any nucleic acid that promotes the specific association (or “targeting”) of an RNA-guided nuclease such as a Cas9 to a target sequence (e.g., a genomic or episomal sequence) in a cell.
As used herein, a “modular” or “dual RNA” guide comprises more than one, and typically two, separate RNA molecules, such as a CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA), which are usually associated with one another, for example by duplexing. gRNAs and their component parts are described throughout the literature (see, e.g., Briner et al. Mol. Cell, 56(2), 333-339 (2014), which is incorporated by reference).
As used herein, a “unimolecular gRNA,” “chimeric gRNA,” or “single guide RNA (sgRNA)” comprises a single RNA molecule. The sgRNA may be a crRNA and tracrRNA linked together. For example, the 3′ end of the crRNA may be linked to the 5′ end of the tracrRNA. A crRNA and a tracrRNA may be joined into a single unimolecular or chimeric gRNA, for example, by means of a four nucleotide (e.g., GAAA) “tetraloop” or “linker” sequence bridging complementary regions of the crRNA (at its 3′ end) and the tracrRNA (at its 5′ end).
As used herein, a “repeat” sequence or region is a nucleotide sequence at or near the 3′ end of the crRNA which is complementary to an anti-repeat sequence of a tracrRNA.
As used herein, an “anti-repeat” sequence or region is a nucleotide sequence at or near the 5′ end of the tracrRNA which is complementary to the repeat sequence of a crRNA.
Additional details regarding guide RNA structure and function, including the gRNA/Cas9 complex for genome editing may be found in, at least, Mali et al. Science, 339(6121), 823-826 (2013); Jiang et al. Nat. Biotechnol. 31(3). 233-239 (2013); and Jinek et al. Science, 337(6096), 816-821 (2012); which are incorporated by reference herein.
As used herein, a “guide sequence” or “targeting sequence” refers to the nucleotide sequence of a gRNA, whether unimolecular or modular, that is fully or partially complementary to a target domain or target polynucleotide within a DNA sequence in the genome of a cell where editing is desired. Guide sequences are typically 10-30 nucleotides in length, preferably 16-24 nucleotides in length (for example, 16, 17, 18, 19, 20, 21, 22, 23 or 24 nucleotides in length), and are at or near the 5′ terminus of a Cas9 gRNA.
As used herein, a “target domain” or “target polynucleotide sequence” or “target sequence” is the DNA sequence in a genome of a cell that is complementary to the guide sequence of the gRNA.
In the context of formation of a CRISPR complex, “target sequence” refers to a sequence to which a guide sequence is designed to have some complementarity, where hybridization between a target sequence and a guide sequence promotes the formation of a CRISPR complex. Full complementarity is not necessarily required, provided there is sufficient complementarity to cause hybridization and promote formation of a CRISPR complex. A target sequence may comprise any polynucleotide, such as DNA or RNA polynucleotides. In certain embodiments, a target sequence is located in the nucleus or cytoplasm of a cell. In other embodiments, the target sequence may be within an organelle of a eukaryotic cell, for example, mitochondrion or nucleus. Typically, in the context of a CRISPR system, formation of a CRISPR complex (comprising a guide sequence hybridized to a target sequence and complexed with one or more Cas proteins) results in cleavage of one or both strands in or near (e.g., within about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50 or more base pairs) the target sequence. As with the target sequence, it is believed that complete complementarity is not needed, provided this is sufficient to be functional.
In certain embodiments, one or more vectors driving expression of one or more elements of a CRISPR system are introduced into a host cell, such that expression of the elements of the CRISPR system direct formation of a CRISPR complex at one or more target sites. For example, a Cas nuclease, a crRNA, and a tracrRNA could each be operably linked to separate regulatory elements on separate vectors. Alternatively, two or more of the elements expressed from the same or different regulatory elements may be combined in a single vector, with one or more additional vectors providing any components of the CRISPR system not included in the first vector. CRISPR system elements that are combined in a single vector may be arranged in any suitable orientation, such as one element located 5′ with respect to (“upstream” of) or 3′ with respect to (“downstream” of) a second element. The coding sequence of one element may be located on the same or opposite strand of the coding sequence of a second element, and oriented in the same or opposite direction. In certain embodiments, a single promoter drives expression of a transcript encoding a CRISPR enzyme and one or more of the guide sequence, tracr mate sequence (optionally operably linked to the guide sequence), and a tracr sequence embedded within one or more intron sequences (e.g., each in a different intron, two or more in at least one intron, or all in a single intron).
In certain embodiments, the CRISPR associated (Cas) enzyme is part of a fusion protein comprising one or more heterologous protein domains (e.g. about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more domains in addition to the CRISPR enzyme). A CRISPR enzyme fusion protein may comprise any additional protein sequence, and optionally a linker sequence between any two domains. Examples of protein domains that may be fused to a CRISPR enzyme include, without limitation, epitope tags, reporter gene sequences, and protein domains having one or more of the following activities: methylase activity, demethylase activity, transcription activation activity, transcription repression activity, transcription release factor activity, histone modification activity, RNA cleavage activity and nucleic acid binding activity. Additional domains that may form part of a fusion protein comprising a CRISPR enzyme are described in U.S. Patent Appl. Publ. No. US20110059502, incorporated herein by reference. In certain embodiments, a tagged CRISPR enzyme is used to identify the location of a target sequence.
Conventional viral and non-viral based gene transfer methods can be used to introduce nucleic acids in mammalian and non-mammalian cells or target tissues. Such methods can be used to administer nucleic acids encoding components of a CRISPR system to cells in culture, or in a host organism. Non-viral vector delivery systems include DNA plasmids, RNA (e.g., a transcript of a vector described herein), naked nucleic acid, and nucleic acid complexed with a delivery vehicle, such as a liposome. Viral vector delivery systems include DNA and RNA viruses, which have either episomal or integrated genomes after delivery to the cell (Anderson, 1992, Science 256:808-813; and Yu, et al., 1994, Gene Therapy 1:13-26).
In some embodiments, the CRISPR/Cas is derived from a type II CRISPR/Cas system. In other embodiments, the CRISPR/Cas system is derived from a Cas9 nuclease. Exemplary Cas9 nucleases that may be used in the present invention include, but are not limited to, S. pyogenes Cas9 (SpCas9), S. aureus Cas9 (SaCas9), S. thermophilus Cas9 (StCas9), N. meningitidis Cas9 (NmCas9), C. jejuni Cas9 (CjCas9), and Geobacillus Cas9 (GeoCas9).
In general, Cas proteins comprise at least one RNA recognition and/or RNA binding domain. RNA recognition and/or RNA binding domains interact with the guiding RNA. Cas proteins can also comprise nuclease domains (i.e., DNase or RNase domains), DNA binding domains, helicase domains, RNAse domains, protein-protein interaction domains, dimerization domains, as well as other domains. The Cas proteins can be modified to increase nucleic acid binding affinity and/or specificity, alter an enzymatic activity, and/or change another property of the protein. In certain embodiments, the Cas-like protein of the fusion protein can be derived from a wild type Cas9 protein or fragment thereof. In other embodiments, the Cas can be derived from modified Cas9 protein. For example, the amino acid sequence of the Cas9 protein can be modified to alter one or more properties (e.g., nuclease activity, affinity, stability, and so forth) of the protein. Alternatively, domains of the Cas9 protein not involved in RNA-guided cleavage can be eliminated from the protein such that the modified Cas9 protein is smaller than the wild type Cas9 protein. In general, a Cas9 protein comprises at least two nuclease (i.e., DNase) domains. For example, a Cas9 protein can comprise a RuvC-like nuclease domain and a HNH-like nuclease domain. The RuvC and HNH domains work together to cut single strands to make a double-stranded break in DNA. (Jinek, et al., 2012, Science, 337:816-821). In certain embodiments, the Cas9-derived protein can be modified to contain only one functional nuclease domain (either a RuvC-like or a HNH-like nuclease domain). For example, the Cas9-derived protein can be modified such that one of the nuclease domains is deleted or mutated such that it is no longer functional (i.e., the nuclease activity is absent). In some embodiments in which one of the nuclease domains is inactive, the Cas9-derived protein is able to introduce a nick into a double-stranded nucleic acid (such protein is termed a “nickase”), but not cleave the double-stranded DNA. In any of the above-described embodiments, any or all of the nuclease domains can be inactivated by one or more deletion mutations, insertion mutations, and/or substitution mutations using well-known methods, such as site-directed mutagenesis, PCR-mediated mutagenesis, and total gene synthesis, as well as other methods known in the art.
In one non-limiting embodiment, a vector drives the expression of the CRISPR system. The art is replete with suitable vectors that are useful in the present invention. The vectors to be used are suitable for replication and, optionally, integration in eukaryotic cells. Typical vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence. The vectors of the present invention may also be used for nucleic acid standard gene delivery protocols. Methods for gene delivery are known in the art (U.S. Pat. Nos. 5,399,346, 5,580,859 & 5,589,466, incorporated by reference herein in their entireties).
Further, the vector may be provided to a cell in the form of a viral vector. Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (4th Edition, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York, 2012), and in other virology and molecular biology manuals. Viruses, which are useful as vectors include, but are not limited to, retroviruses, adenoviruses, adeno-associated viruses, herpes viruses, Sindbis virus, gammaretrovirus and lentiviruses. In general, a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers (e.g., WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193).
Any type of cell can be edited with the methods disclosed herein. In certain embodiments, the cell is an immune cell. Immune cells are cells of the immune system, such as cells of the innate or adaptive immunity, e.g., myeloid or lymphoid cells, including lymphocytes, typically T cells and/or NK cells. Other exemplary cells include stem cells, such as multipotent and pluripotent stem cells, including induced pluripotent stem cells (iPSCs). In some aspects, the cells are human cells. Immune cells can be obtained from a number of sources, including blood, peripheral blood mononuclear cells, bone marrow, lymph node tissue, spleen tissue, umbilical cord, lymph, or lymphoid organs.
In certain embodiments, the immune cell is a T cell, e.g., a CD8+ T cell (e.g., a primary CD8+ T cell, a CD8+ naive T cell, central memory T cell, or effector memory T cell), a CD4+ T cell, a natural killer T cell (NKT cells), a regulatory T cell (Treg), a stem cell memory T cell, a lymphoid progenitor cell a hematopoietic stem cell, a natural killer cell (NK cell) or a dendritic cell. In certain embodiments, the cell is a monocyte or granulocyte, e.g., myeloid cell, macrophage, neutrophil, dendritic cell, mast cell, eosinophil, and/or basophil. In certain embodiments, the cell is an induced pluripotent stem (iPS) cell or a cell derived from an iPS cell, e.g., an iPS cell generated from a subject, manipulated to alter (e.g., induce a mutation in) or manipulate the expression of one or more target genes, and differentiated into, e.g., a T cell, e.g., a CD8+ T cell (e.g., a primary CD8+ T cell, a CD8+ naive T cell, central memory T cell, or effector memory T cell), a CD4+ T cell, a stem cell memory T cell, a lymphoid progenitor cell or a hematopoietic stem cell.
In some embodiments, the cells include one or more subsets of T cells or other cell types, such as whole T cell populations, CD4+ cells, CD8+ cells, and subpopulations thereof, such as those defined by function, activation state, maturity, potential for differentiation, expansion, recirculation, localization, and/or persistence capacities, antigen-specificity, type of antigen receptor, presence in a particular organ or compartment, marker or cytokine secretion profile, and/or degree of differentiation. Among the sub-types and subpopulations of T cells and/or of n CD4+ and/or of CD8+ T cells are naive T (TN) cells, effector T cells (TEFF), memory T cells and sub-types thereof, such as stem cell memory T (TSCM), central memory T (TCM), effector memory T (TEM), or terminally differentiated effector memory T cells, tumor-infiltrating lymphocytes (TIL), immature T cells, mature T cells, helper T cells, cytotoxic T cells, mucosa-associated invariant T (MAIT) cells, naturally occurring and adaptive regulatory T (Treg) cells, helper T cells, such as TH1 cells, TH2 cells, TH3 cells, TH17 cells, TH9 cells, TH22 cells, follicular helper T cells, alpha/beta T cells, and delta/gamma T cells. In certain embodiments, any number of T cell lines available in the art, may be used.
In certain embodiments, the cell comprises a Chimeric Antigen Receptor (CAR). In certain embodiments, the cell is a CAR T cell. Exemplary CARs include, but are not limited to, those disclosed herein, those disclosed in U.S. Pat. Nos. 10,357,514B2, 10,221,245B2, 10,603,378B2, 8,916,381B1, 9,394,368B2, US20140050708A1, U.S. Pat. Nos. 9,598,489B2, 9,365,641B2, US20210079059A1, U.S. Pat. No. 9,783,591B2, WO2016028896A1, U.S. Pat. No. 9,446,105B2, WO2016014576A1, US20210284752A1, WO2016014565A2, WO2016014535A1, and U.S. Pat. No. 9,272,002B2, and any other CAR generally disclosed in the art. The disclosure should be construed to include any CAR known in the art.
In some embodiments, the methods include isolating immune cells from a subject, preparing, processing, culturing, and/or engineering them. In some embodiments, preparation of the cells includes one or more culture and/or preparation steps. The cells for engineering as described may be isolated from a sample, such as a biological sample, e.g., one obtained from or derived from a subject. In some embodiments, the subject from which the cell is isolated is one having a disease or condition or in need of a cell therapy or to which cell therapy will be administered. The subject in some embodiments is a human in need of a particular therapeutic intervention, such as the adoptive cell therapy for which cells are being isolated, processed, and/or engineered. Accordingly, the cells in some embodiments are primary cells, e.g., primary human cells, e.g., primary human CD8+ cells. The samples include tissue, fluid, and other samples taken directly from the subject, as well as samples resulting from one or more processing steps, such as separation, centrifugation, genetic engineering (e.g. transduction with viral vector), washing, and/or incubation. The biological sample can be a sample obtained directly from a biological source or a sample that is processed. Biological samples include, but are not limited to, body fluids, such as blood, plasma, serum, cerebrospinal fluid, synovial fluid, urine and sweat, tissue and organ samples, including processed samples derived therefrom.
In certain embodiments, a source of immune cells is obtained from a subject for ex vivo manipulation. Sources of cells for ex vivo manipulation may also include, e.g., autologous or heterologous donor blood, cord blood, or bone marrow. For example the source of immune cells may be from a subject to be treated with the modified immune cells of the invention, e.g., the subject's blood, the subject's cord blood, or the subject's bone marrow. Non-limiting examples of subjects include humans, dogs, cats, mice, rats, and transgenic species thereof. Preferably, the subject is a human.
In certain embodiments, a cell is modified with a method contemplated herein; e.g. by introducing into the cell a cell penetrating CRISPR-Cas9 or -Cas12a system comprising a cell penetrating Cas9 or Cas12a and an endosomal escape peptide, then the modified cell is administered to a subject. In certain embodiments, the subject is in need of a treatment for a disease or condition. With reference to the subject to be treated, the cells may be allogeneic and/or autologous. The cells typically are primary cells, such as those isolated directly from a subject and/or isolated from a subject and frozen.
In some aspects, the sample from which the cells are derived or isolated is blood or a blood-derived sample, or is or is derived from an apheresis or leukapheresis product. Exemplary samples include whole blood, peripheral blood mononuclear cells (PBMCs), leukocytes, bone marrow, thymus, tissue biopsy, tumor, leukemia, lymphoma, lymph node, gut associated lymphoid tissue, mucosa associated lymphoid tissue, spleen, other lymphoid tissues, liver, lung, stomach, intestine, colon, kidney, pancreas, breast, bone, prostate, cervix, testes, ovaries, tonsil, or other organ, and/or cells derived therefrom. Samples include, in the context of cell therapy, e.g., adoptive cell therapy, samples from autologous and allogeneic sources.
In some embodiments, the cells are derived from cell lines, e.g., T cell lines. The cells in some embodiments are obtained from a xenogeneic source, for example, from mouse, rat, non-human primate, and pig. In some embodiments, isolation of the cells includes one or more preparation and/or non-affinity based cell separation steps. In some examples, cells are washed, centrifuged, and/or incubated in the presence of one or more reagents, for example, to remove unwanted components, enrich for desired components, lyse or remove cells sensitive to particular reagents. In some examples, cells are separated based on one or more property, such as density, adherent properties, size, sensitivity and/or resistance to particular components.
In some examples, cells from the circulating blood of a subject are obtained, e.g., by apheresis or leukapheresis. The samples, in some aspects, contain lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and/or platelets, and in some aspects contains cells other than red blood cells and platelets. In some embodiments, the blood cells collected from the subject are washed, e.g., to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps. In some embodiments, the cells are washed with phosphate buffered saline (PBS). In some aspects, a washing step is accomplished by tangential flow filtration (TFF) according to the manufacturer's instructions. In some embodiments, the cells are resuspended in a variety of biocompatible buffers after washing. In certain embodiments, components of a blood cell sample are removed and the cells directly resuspended in culture media. In some embodiments, the methods include density-based cell separation methods, such as the preparation of white blood cells from peripheral blood by lysing the red blood cells and centrifugation through a Percoll or Ficoll gradient.
In one embodiment, immune are obtained cells from the circulating blood of an individual are obtained by apheresis or leukapheresis. The apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets. The cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media, such as phosphate buffered saline (PBS) or wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations, for subsequent processing steps. After washing, the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca-free, Mg-free PBS. Alternatively, the undesirable components of the apheresis sample may be removed and the cells directly resuspended in culture media.
In some embodiments, the isolation methods include the separation of different cell types based on the expression or presence in the cell of one or more specific molecules, such as surface markers, e.g., surface proteins, intracellular markers, or nucleic acids. In some embodiments, any known method for separation based on such markers may be used. In some embodiments, the separation is affinity- or immunoaffinity-based separation. For example, the isolation in some aspects includes separation of cells and cell populations based on the cells' expression or expression level of one or more markers, typically cell surface markers, for example, by incubation with an antibody or binding partner that specifically binds to such markers, followed generally by washing steps and separation of cells having bound the antibody or binding partner, from those cells having not bound to the antibody or binding partner.
Such separation steps can be based on positive selection, in which the cells having bound the reagents are retained for further use, and/or negative selection, in which the cells having not bound to the antibody or binding partner are retained. In some examples, both fractions are retained for further use. In some aspects, negative selection can be particularly useful where no antibody is available that specifically identifies a cell type in a heterogeneous population, such that separation is best carried out based on markers expressed by cells other than the desired population. The separation need not result in 100% enrichment or removal of a particular cell population or cells expressing a particular marker. For example, positive selection of or enrichment for cells of a particular type, such as those expressing a marker, refers to increasing the number or percentage of such cells, but need not result in a complete absence of cells not expressing the marker. Likewise, negative selection, removal, or depletion of cells of a particular type, such as those expressing a marker, refers to decreasing the number or percentage of such cells, but need not result in a complete removal of all such cells.
In some examples, multiple rounds of separation steps are carried out, where the positively or negatively selected fraction from one step is subjected to another separation step, such as a subsequent positive or negative selection. In some examples, a single separation step can deplete cells expressing multiple markers simultaneously, such as by incubating cells with a plurality of antibodies or binding partners, each specific for a marker targeted for negative selection. Likewise, multiple cell types can simultaneously be positively selected by incubating cells with a plurality of antibodies or binding partners expressed on the various cell types.
In some embodiments, one or more of the T cell populations is enriched for or depleted of cells that are positive for (marker+) or express high levels (markerhigh) of one or more particular markers, such as surface markers, or that are negative for (marker−) or express relatively low levels (markerlow) of one or more markers. For example, in some aspects, specific subpopulations of T cells, such as cells positive or expressing high levels of one or more surface markers, e.g., CD28+, CD62L+, CCR7+, CD27+, CD127+, CD4+, CD8+, CD45RA+, and/or CD45RO+ T cells, are isolated by positive or negative selection techniques. In some cases, such markers are those that are absent or expressed at relatively low levels on certain populations of T cells (such as non-memory cells) but are present or expressed at relatively higher levels on certain other populations of T cells (such as memory cells). In one embodiment, the cells (such as the CD8+ cells or the T cells, e.g., CD3+ cells) are enriched for (i.e., positively selected for) cells that are positive or expressing high surface levels of CD45RO, CCR7, CD28, CD27, CD44, CD 127, and/or CD62L and/or depleted of (e.g., negatively selected for) cells that are positive for or express high surface levels of CD45RA. In some embodiments, cells are enriched for or depleted of cells positive or expressing high surface levels of CD 122, CD95, CD25, CD27, and/or IL7-Ra (CD 127). In some examples, CD8+ T cells are enriched for cells positive for CD45RO (or negative for CD45RA) and for CD62L. For example, CD3+, CD28+ T cells can be positively selected using CD3/CD28 conjugated magnetic beads (e.g., DYNABEADS® M-450 CD3/CD28 T Cell Expander).
In some embodiments, T cells are separated from a PBMC sample by negative selection of markers expressed on non-T cells, such as B cells, monocytes, or other white blood cells, such as CD14. In some aspects, a CD4+ or CD8+ selection step is used to separate CD4+ helper and CD8+ cytotoxic T cells. Such CD4+ and CD8+ populations can be further sorted into sub-populations by positive or negative selection for markers expressed or expressed to a relatively higher degree on one or more naive, memory, and/or effector T cell subpopulations. In some embodiments, CD8+ cells are further enriched for or depleted of naive, central memory, effector memory, and/or central memory stem cells, such as by positive or negative selection based on surface antigens associated with the respective subpopulation. In some embodiments, enrichment for central memory T (TCM) cells is carried out to increase efficacy, such as to improve long-term survival, expansion, and/or engraftment following administration, which in some aspects is particularly robust in such sub-populations. In some embodiments, combining TCM-enriched CD8+ T cells and CD4+ T cells further enhances efficacy.
In some embodiments, memory T cells are present in both CD62L+ and CD62L− subsets of CD8+ peripheral blood lymphocytes. PBMC can be enriched for or depleted of CD62L−CD8+ and/or CD62L+CD8+ fractions, such as using anti-CD8 and anti-CD62L antibodies. In some embodiments, a CD4+ T cell population and a CD8+ T cell sub-population, e.g., a sub-population enriched for central memory (TCM) cells. In some embodiments, the enrichment for central memory T (TCM) cells is based on positive or high surface expression of CD45RO, CD62L, CCR7, CD28, CD3, and/or CD 127; in some aspects, it is based on negative selection for cells expressing or highly expressing CD45RA and/or granzyme B. In some aspects, isolation of a CD8+ population enriched for TCM cells is carried out by depletion of cells expressing CD4, CD 14, CD45RA, and positive selection or enrichment for cells expressing CD62L. In one aspect, enrichment for central memory T (TCM) cells is carried out starting with a negative fraction of cells selected based on CD4 expression, which is subjected to a negative selection based on expression of CD 14 and CD45RA, and a positive selection based on CD62L. Such selections in some aspects are carried out simultaneously and in other aspects are carried out sequentially, in either order. In some aspects, the same CD4 expression-based selection step used in preparing the CD8+ cell population or subpopulation, also is used to generate the CD4+ cell population or sub-population, such that both the positive and negative fractions from the CD4-based separation are retained and used in subsequent steps of the methods, optionally following one or more further positive or negative selection steps.
CD4+ T helper cells are sorted into naive, central memory, and effector cells by identifying cell populations that have cell surface antigens. CD4+ lymphocytes can be obtained by standard methods. In some embodiments, naive CD4+ T lymphocytes are CD45RO−, CD45RA+, CD62L+, CD4+ T cells. In some embodiments, central memory CD4+ cells are CD62L+ and CD45RO+. In some embodiments, effector CD4+ cells are CD62L− and CD45RO. In one example, to enrich for CD4+ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CDI 1b, CD16, HLA-DR, and CD8. In some embodiments, the antibody or binding partner is bound to a solid support or matrix, such as a magnetic bead or paramagnetic bead, to allow for separation of cells for positive and/or negative selection.
In some embodiments, the cells are incubated and/or cultured prior to or in connection with genetic engineering. The incubation steps can include culture, cultivation, stimulation, activation, and/or propagation. In some embodiments, the compositions or cells are incubated in the presence of stimulating conditions or a stimulatory agent. Such conditions include those designed to induce proliferation, expansion, activation, and/or survival of cells in the population, to mimic antigen exposure, and/or to prime the cells for genetic engineering, such as for the introduction of a recombinant antigen receptor. The conditions can include one or more of particular media, temperature, oxygen content, carbon dioxide content, time, agents, e.g., nutrients, amino acids, antibiotics, ions, and/or stimulatory factors, such as cytokines, chemokines, antigens, binding partners, fusion proteins, recombinant soluble receptors, and any other agents designed to activate the cells. In some embodiments, the stimulating conditions or agents include one or more agent, e.g., ligand, which is capable of activating an intracellular signaling domain of a TCR complex. In some aspects, the agent turns on or initiates TCR/CD3 intracellular signaling cascade in a T cell. Such agents can include antibodies, such as those specific for a TCR component and/or costimulatory receptor, e.g., anti-CD3, anti-CD28, for example, bound to solid support such as a bead, and/or one or more cytokines. Optionally, the expansion method may further comprise the step of adding anti-CD3 and/or anti CD28 antibody to the culture medium (e.g., at a concentration of at least about 0.5 ng/ml). In some embodiments, the stimulating agents include IL-2 and/or IL-15, for example, an IL-2 concentration of at least about 10 units/mL.
In another embodiment, T cells are isolated from peripheral blood by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL™ gradient. Alternatively, T cells can be isolated from an umbilical cord. In any event, a specific subpopulation of T cells can be further isolated by positive or negative selection techniques.
The cord blood mononuclear cells so isolated can be depleted of cells expressing certain antigens, including, but not limited to, CD34, CD8, CD14, CD19, and CD56. Depletion of these cells can be accomplished using an isolated antibody, a biological sample comprising an antibody, such as ascites, an antibody bound to a physical support, and a cell bound antibody.
Enrichment of a T cell population by negative selection can be accomplished using a combination of antibodies directed to surface markers unique to the negatively selected cells. A preferred method is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected. For example, to enrich for CD4+ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CD11b, CD16, HLA-DR, and CD8.
For isolation of a desired population of cells by positive or negative selection, the concentration of cells and surface (e.g., particles such as beads) can be varied. In certain embodiments, it may be desirable to significantly decrease the volume in which beads and cells are mixed together (i.e., increase the concentration of cells), to ensure maximum contact of cells and beads. For example, in one embodiment, a concentration of 2 billion cells/ml is used. In one embodiment, a concentration of 1 billion cells/ml is used. In a further embodiment, greater than 100 million cells/ml is used. In a further embodiment, a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/ml is used. In yet another embodiment, a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/ml is used. In further embodiments, concentrations of 125 or 150 million cells/ml can be used. Using high concentrations can result in increased cell yield, cell activation, and cell expansion.
T cells can also be frozen after the washing step, which does not require the monocyte-removal step. While not wishing to be bound by theory, the freeze and subsequent thaw step provides a more uniform product by removing granulocytes and to some extent monocytes in the cell population. After the washing step that removes plasma and platelets, the cells may be suspended in a freezing solution. While many freezing solutions and parameters are known in the art and will be useful in this context, in a non-limiting example, one method involves using PBS containing 20% DMSO and 8% human serum albumin, or other suitable cell freezing media. The cells are then frozen to −80° C. at a rate of 1° C. per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at −20° C. or in liquid nitrogen.
In one embodiment, the population of T cells is comprised within cells such as peripheral blood mononuclear cells, cord blood cells, a purified population of T cells, and a T cell line. In another embodiment, peripheral blood mononuclear cells comprise the population of T cells. In yet another embodiment, purified T cells comprise the population of T cells.
In certain embodiments, T regulatory cells (Tregs) can be isolated from a sample. The sample can include, but is not limited to, umbilical cord blood or peripheral blood. In certain embodiments, the Tregs are isolated by flow-cytometry sorting. The sample can be enriched for Tregs prior to isolation by any means known in the art. The isolated Tregs can be cryopreserved, and/or expanded prior to use. Methods for isolating Tregs are described in U.S. Pat. Nos. 7,754,482, 8,722,400, and 9,555,105, and U.S. patent application Ser. No. 13/639,927, contents of which are incorporated herein in their entirety.
In one aspect, the disclosure provides a novel cell penetrating PAGE system capable of efficiently editing a cell (e.g. a primary CD8 T cell). The PAGE system comprises a cell penetrating Cas (e.g. a Cas (e.g. Cas9 or Cas12a) linked to a CPP) and an endosomal escape peptide linked to a CPP (e.g. dTAT-HA2).
In certain embodiments, the Cas is Cas9. Exemplary Cas9 nucleases that may be used in the present invention include, but are not limited to, S. pyogenes Cas9 (SpCas9), S. aureus Cas9 (SaCas9), S. thermophilus Cas9 (StCas9), N. meningitidis Cas9 (NmCas9), C. jejuni Cas9 (CjCas9), and Geobacillus Cas9 (GeoCas9). In certain embodiments, the Cas is Cas12a (Cpf1), including but not limited to, Butyrivibrio sp (BsCas12a), Thiomicrospira sp). XS5 (TsCas12a, Moraxella bovoculi (MbCas12a), Prevotella bryantii (PbCas12a), Bacteroidetes oral (BoCas12a), Lachnospiraceae bacterium (LbCas12a), and Acidaminococcus sp (AsCas12a). In certain embodiments, the Cas is selected from the group consist Cas12b, Cas12d, Cas12f, T7, Cas3, Cas8a, Cas8b, Cas10d, Cse1, Csy1, Csn2, Cas4, Cas10, Csm2, Cmr5, and Fok1.
In certain embodiments, the Cas protein (i.e. Cas9, Cas12a, Cas derivative) is either fused or chemically linked or post-translationally attached to DNA modifiers or catalytic domains thereof, including but not limited to, AID deaminase, an APOBEC deaminase, a TadA deaminase, a TET enzyme, a DNA methyltransferase, a transactivation domain, a reverse transcriptase, a histone acetyltransferase, a histone deacetylase, a sirtuin, a histone methyltransferase, a histone demethylase, a kinase, a phosphatase, and the like.
In certain embodiments, the endosomal escape peptide comprises dTAT-HA2. Other endosomal escape peptides that could be used include, but are not limited to, EEDs, HA2-penetratin, GALA, INF-7, and the like. In certain embodiments, the endosomal escape peptide is any one of the peptides listed in Table 1. In certain embodiments, the endosomal escape peptide comprises any one of the sequences set forth in SEQ ID NOs: 1434-1523. In certain embodiments, the endosomal escape peptide is linked to any of the CPPs listed in Table 2. In certain embodiments, the endosomal escape peptide is linked to a CPP comprising any of the amino acid sequences set forth in SEQ ID NOs: 10-1422.
In certain embodiments, the Cas comprises a nuclear localization sequence (NLS). The NLS can include any NLS known in the art or disclosed herein. In certain embodiments, the Cas comprises a 4× or 6×Myc NLS sequence. In certain embodiments, the Myc NLS sequence comprises the amino acid sequence PAAKRVKLD (SEQ ID NO: 1). In certain embodiments, the NLS (i.e. 4× or 6×Myc NLS) sequence further comprises a GGS linker.
In certain embodiments, the cell penetrating Cas comprises a nucleotide sequence encoding, or amino acid sequence comprising, a Cell Penetrating Peptide. Examples of CPPs include, but are not limited to trans-activating transcriptional activator (Tat) from HIV-1, Oligo-Arg, KALA, Transportan, Penetratin, Penetratin-Arg, TAT-HA2, and dTAT-HA2E5. Examples of CPPs are also listed in Table 2 herein. In certain embodiments, the CPP comprises any of the amino acid sequences set forth in SEQ ID NOs: 10-1422. In certain embodiments, the cell penetrating Cas comprises a sequence derived from the trans-activating transcriptional activator (Tat) from HIV-1. In certain embodiments, the Tat sequence comprises the amino acid sequence GRKKRRQRRRPQ (SEQ ID NO: 2). Other truncated or modified Tat peptides that could be used include, but are not limited to, Truncated Tat: YGRKKRRQRRR (SEQ ID NO: 3), CGRKKRRQRRR (SEQ ID NO: 4), GRKKRRQRRRPPQ (SEQ ID NO: 5), RKKRRQRRRPQ (SEQ ID NO: 6), and RKKRRQRRR (SEQ ID NO: 7), and Modified Tat: 2×Tat, 3×Tat, 4×Tat, n×Tat, and the like.
The PAGE system may comprise two different CPPs or two of the same CPPs. The CPP can be linked to the Cas or endosomal escape peptide by any means known in the art, such as, but not limited to chemical linkage, fusion, or post-translational modification.
Also provided are kits comprising the composition and/or for practicing the methods of the invention, as described herein. For example, in some embodiments, kits for practicing the invention methods include a composition comprising a cell penetrating PAGE system comprising a cell penetrating Cas and an endosomal escape peptide.
Furthermore, additional reagents that are required or desired in the protocol to be practiced with the kit components may be present, which additional reagents include, but are not limited to: sgRNAs, nuclease-free water, carriers, and reagents (e.g., nucleotides, buffers, cations, etc.), and the like. The kit components may be present in separate containers, or one or more of the components may be present in the same container, where the containers may be storage containers and/or containers that are employed during the assay for which the kit is designed.
In addition to the above components, the kit may further include instructions for practicing the methods described herein. These instructions may be present in the subject kits in a variety of forms, one or more of which may be present in the kit. One form in which these instructions may be present is as printed information on a suitable medium or substrate, e.g., a piece or pieces of paper on which the information is printed, in the packaging of the kit, in a package insert, etc. Yet another form of instructions may include a computer readable medium, e.g., CD, etc., on which the information has been recorded. Yet another form of instructions may include a website address which may be used via the internet to access the information at a removed site. Any convenient means may be present in the kits.
The contents of the articles, patents, and patent applications, and all other documents and electronically available information mentioned or cited herein, are hereby incorporated by reference in their entirety to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference. Applicants reserve the right to physically incorporate into this application any and all materials and information from any such articles, patents, patent applications, or other physical and electronic documents.
While the present invention has been described with reference to the specific embodiments thereof, it should be understood by those skilled in the art that various changes may be made and equivalents may be substituted without departing from the true spirit and scope of the invention. It will be readily apparent to those skilled in the art that other suitable modifications and adaptations of the methods described herein may be made using suitable equivalents without departing from the scope of the embodiments disclosed herein. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process step or steps, to the objective, spirit and scope of the present invention. All such modifications are intended to be within the scope of the claims appended hereto. Having now described certain embodiments in detail, the same will be more clearly understood by reference to the following examples, which are included for purposes of illustration only and are not intended to be limiting.
The invention is now described with reference to the following Examples. These Examples are provided for the purpose of illustration only, and the invention is not limited to these Examples, but rather encompasses all variations that are evident as a result of the teachings provided herein.
TAT-4×Myc NLS-Cas9 expression construct was created by replacing the 4×SV40 NLS (PKKKRKV (SEQ ID NO: 1423)) at the N-terminus of Cas9 (Staahl et al., (2017) Nat Biotechnol 35, 431-434) with 4×Myc NLS (PAAKRVKLD (SEQ ID NO: 1)) with linker -G-G-S- between Myc NLS. The sequence of the TAT cell penetrating peptide (GRKKRRQRRRPQ (SEQ ID NO: 2)), derived from the trans-activating transcriptional activator (Tat) from HIV-1 (Frankel and Pabo, 1988; Green and Loewenstein, 1988), was added to the N-terminus, and TAT-4×Myc NLS-Cas9 was cloned into a bacterial recombinant protein expression vector (Gootenberg et al., 2017) with a Twin-Strep and SUMO tag (
To determine whether TAT-4×Myc NLS-Cas9 has the ability to edit a genome, the EL4 thymoma cell line was used. EL4 cells were infected with a lentiviral reporter construct stably expressing mCherry and sgRNA targeting mCherry. If TAT-4×Myc NLS-Cas9 penetrates the cell membrane and edits mCherry in EL4 reporter cells, the frequency of mCherry cells increases due to loss of mCherry fluorescence, as measured by flow cytometry (
It was also tested whether the percentage of FBS during incubation has an effect on TAT-4×Myc NLS-Cas9 editing efficiency. When the percentage of FBS decreased from 10% to 0, and the cells were co-treated with 10 μM dTAT-HA2 and 0.5 μM TAT-4×Myc NLSCas9, the percentage of mCherry− cells increased from 4.26% to 15.9% (
Before testing TAT-4×Myc NLS-Cas9 in vitro editing in mouse primary T cells, the editing efficiency of two sgRNAs targeting cell surface marker CD45.2 were designed and tested in RN2-Cas9 cells, which stably express Cas9. RN2-Cas9 cells were infected with retrovirus expressing sgRNA and mCherry, and CD45.2 expression level was measured by flow cytometry after 3 days of infection. Both sgRNAs targeting CD45.2 efficiently knocked down CD45.2 compared to sgRNAs targeting Rosa26 (
A schematic workflow for testing the in vivo editing efficiency of TAT-4×Myc-NLS Cas9 is shown in
A schematic workflow for testing the in vitro editing efficiency of TAT-4×Myc NLS-Cas9 in human primary T cells is shown in
iPSCs were infected by the same lentiviral reporter construct and treated as in
This disclosure provides a new method for in vitro and in vivo CRISPR editing of mouse and human CD8 T cells, human primary T cells, and human iPSCs. The efficiency of this editing can reach up to 90% for in vitro CD90.2 editing and in vivo PD-1 editing, which is much higher than other published methods using cell penetrating Cas9 for genome editing (Staahl et al., (2017) Nat Biotechnol 35, 431-434). In addition, this method can achieve genome editing in a timely and economic manner, since it does not require electroporation or Cas9 transgenic mice required by previously described methods for mouse CD8 T cell genome editing. Therefore, this disclosure describes a simple, efficient, and economic way to edit CD8 T cell genomes both in vitro and in vivo.
PAGE system constructs were generated comprising cell penetrating CRISPR-associated (Cas) proteins (Cas9, Cas12) and assisting/endosomal escape peptide(s) (TAT, HA2) (
The editing efficiency of Cas9-T6NCPP (TAT-4×NLSMYC-Cas9-2×NLSSV40-sfGFP) was quantified with various endosomal escaping or cell penetrating chemical compounds and peptides in EL4-mChe reporter cells (
EL4 cells were treated with 5 μM of Cas9-T6NCPP and 75 μM of TH at 37° C. for 30 minutes, then cells were washed with PBS and trypsinized to remove cell surface-bound Cas9-T6NCPP. Nuclear and cytosolic fractions were separated and subject to immunoblotting analyses using antibodies against Cas9, nuclear marker Lamin B1, and cytosolic marker a-Tubulin. Western blots of Cas9-T6NCPP, Lamin-B1, and α-Tubulin levels in nuclear fraction, cytosolic fraction, and whole-cell lysates prepared from EL4 cells treated with Cas9-T6NCPP and TH are shown in
The Cas9-PAGE system was optimized in EL4 reporter cells (
TH (dTAT-HA2) supports the PAGE system in trans. Gene editing efficiency was quantified after truncation of TH. EL4 mCherry reporter cells were incubated with 0.5 μM Cas9-T6NCPP in the presence of 75 μM T, H, or TH peptides. The percentage of cells with loss of mCherry was measured by flow cytometry at day 4 post-treatment. TH (dTAT-HA2), but neither T (dTAT) nor H (dHA2) peptides alone, enhanced Cas9-T6NCPP editing efficiency in EL4 mCherry reporter cells (
Cas9-PAGE system-mediated gene editing efficiency was quantified in various cell types (
The PAGE system was evaluated in murine primary CD8 T cells ex vivo. Murine primary T cells were activated with anti-CD3, anti-CD28 and IL-2, followed by retroviral transduction with a sgRNA expression vector linked with mCherry fluorescent marker. The FACS-sorted enriched mCherry positive cells were incubated with Cas9-T6NCPP and TH peptide, which were then washed out after 30 minutes incubation. Gene editing was evaluated at various time points by flow cytometry against indicated gene products or via direct sanger sequencing of the targeted genomic regions (
A cell penetrating ribonucleoprotein (RNP) complex for PAGE genome editing was tested in murine primary T cells ex vivo (
opCas12a-RNP-PAGE genome editing was demonstrated in human chimeric antigen receptor (CAR) T cells ex vivo (
Highly efficient in vivo editing of clinically relevant genes by the Cas9-PAGE system was demonstrated in murine primary T cells (
Cas9-BE PAGE base editing was demonstrated in a K562 d2GFP reporter cell line (
The following enumerated embodiments are provided, the numbering of which is not to be construed as designating levels of importance.
Embodiment 1 provides a Peptide-Assisted Genome Editing (PAGE) system comprising a) a CRISPR associated (Cas) protein linked to a Cell Penetrating Peptide (CPP), and b) an endosomal escape peptide linked to a CPP.
Embodiment 2 provides the PAGE system of embodiment 1, wherein the Cas is Cas9, or Cas12a, or a Cas derivative.
Embodiment 3 provides the PAGE system of embodiment 2, wherein the Cas derivative is a Cas protein linked to another protein or catalytic domain.
Embodiment 4 provides the PAGE system of embodiment 3, wherein the protein or catalytic domain is selected from the group consisting of an AID deaminase, an APOBEC deaminase, a TadA deaminase, a TET enzyme, a DNA methyltransferase, a transactivation domain, a reverse transcriptase, a histone acetyltransferase, a histone deacetylase, a sirtuin, a histone methyltransferase, a histone demethylase, a kinase, and a phosphatase.
Embodiment 5 provides the PAGE system of any of the preceding embodiments, wherein the endosomal escape peptide comprises any of the amino acid sequences set forth in SEQ ID NOs: 1434-1523.
Embodiment 6 provides the PAGE system of any of the preceding embodiments, wherein the endosomal escape peptide comprises dTAT-HA2.
Embodiment 7 provides the PAGE system of any of the preceding embodiments, wherein the Cas comprises a Nuclear Localization Signal (NLS) sequence.
Embodiment 8 provides the PAGE system of embodiment 7, wherein the NLS sequence comprises the amino acid sequence PAAKRVKLD (SEQ ID NO: 1).
Embodiment 9 provides the PAGE system of embodiment 7 or 8, wherein the NLS sequence further comprises a GGS linker.
Embodiment 10 provides the PAGE system of any of the preceding embodiments, wherein the CPP comprises any of the amino acid sequences set forth in SEQ ID NOs: 10-1422.
Embodiment 11 provides the PAGE system of any of the preceding embodiments, wherein the CPP comprises a sequence derived from the trans-activating transcriptional activator (Tat) from HIV-1.
Embodiment 12 provides the PAGE system of embodiment, 11, wherein the Tat sequence comprises the amino acid sequence GRKKRRQRRRPQ (SEQ ID NO: 2).
Embodiment 13 provides an in vitro method of gene editing comprising introducing into a cell a PAGE system and at least one sgRNA or crRNA, wherein the PAGE system comprises a Cas protein linked to a CPP and an endosomal escape peptide linked to a CPP.
Embodiment 14 provides an in vivo method of gene editing comprising introducing into a cell a PAGE system and at least one sgRNA or crRNA, wherein the PAGE system comprises a Cas protein linked to a CPP and an endosomal escape peptide linked to a CPP, and administering the cell to a subject.
Embodiment 15 provides the method of embodiment 13 or 14, wherein the Cas is Cas9, or Cas12a, or a Cas derivative.
Embodiment 16 provides the method of embodiment 15, wherein the Cas derivative is a Cas protein linked to another protein or catalytic domain.
Embodiment 17 provides the method of embodiment 16, wherein the protein or catalytic domain is selected from the group consisting of an AID deaminase, an APOBEC deaminase, a TadA deaminase, a TET enzyme, a DNA methyltransferase, a transactivation domain, a reverse transcriptase, a histone acetyltransferase, a histone deacetylase, a sirtuin, a histone methyltransferase, a histone demethylase, a kinase, and a phosphatase.
Embodiment 18 provides the method of any of embodiments 13-17, wherein the endosomal escape peptide comprises any of the amino acid sequences set forth in SEQ ID NOs: 1434-1523.
Embodiment 19 provides the method of any of embodiments 13-18, wherein the endosomal escape peptide comprises dTAT-HA2.
Embodiment 20 provides the method of any of embodiments 13-19, wherein the Cas comprises a NLS sequence.
Embodiment 21 provides the method of embodiment 20, wherein the NLS sequence comprises the amino acid sequence PAAKRVKLD (SEQ ID NO: 1).
Embodiment 22 provides the method of embodiments 20 or 21, wherein the NLS sequence further comprises a GGS linker.
Embodiment 23 provides the method of any of embodiments 13-22, wherein the CPP comprises any of the amino acid sequences set forth in SEQ ID NOs: 10-1422.
Embodiment 24 provides the method of any of embodiments 13-23, wherein the CPP comprises a sequence derived from the trans-activating transcriptional activator (Tat) from HIV-1.
Embodiment 25 provides the method of embodiment 24, wherein the Tat sequence comprises the amino acid sequence GRKKRRQRRRPQ (SEQ ID NO: 2).
Embodiment 26 provides the method of any of embodiments 13-25, wherein the method does not require electroporation.
Embodiment 27 provides the method of any of embodiments 13-26, wherein the PAGE system is introduced into the cell in a medium that does not contain serum.
Embodiment 28 provides the method of any of embodiments 13-27, wherein the endosomal escape peptide is introduced into the cell at a concentration of about 25-75 μM.
Embodiment 29 provides the method of any of embodiments 13-28, wherein the Cas is introduced into the cell at a concentration of about 0.5-5 μM.
Embodiment 30 provides the method of any of embodiments 13-29, wherein the cell is an immune cell.
Embodiment 31 provides the method of any of embodiments 13-30, wherein the cell is selected from the group consisting of a primary human CD8 T cell, a human iPSC, and a CAR T cell.
Embodiment 32 provides the method of any of embodiments 13-31, wherein the sgRNA targets Ano9, Pdcd1, Thy1, Ptprc, PTPRC, or B2M.
Embodiment 33 provides the method of any of embodiments 13-32, wherein the subject is in need of a treatment for a disease or disorder, and wherein when the edited cell is administered to the subject, the disease or disorder is treated in the subject.
Embodiment 34 provides the method of embodiment 33, wherein the disease or disorder is an infection.
Embodiment 35 provides the method of embodiment 34, wherein the disease or disorder is related to T cell exhaustion.
The contents of the articles, patents, and patent applications, and all other documents and electronically available information mentioned or cited herein, are hereby incorporated by reference in their entirety to the same extent as if each individual publication was specifically and individually indicated to be incorporated by reference. Applicants reserve the right to physically incorporate into this application any and all materials and information from any such articles, patents, patent applications, or other physical and electronic documents.
While this invention has been disclosed with reference to specific embodiments, it is apparent that other embodiments and variations of this invention may be devised by others skilled in the art without departing from the true spirit and scope of the invention. The appended claims are intended to be construed to include all such embodiments and equivalent variations.
The present application is entitled to priority under 35 U.S.C. § 119(e) to U.S. Provisional Patent Application No. 63/196,144, filed Jun. 2, 2021, which is incorporated by reference in its entirety herein.
This invention was made with government support under AI117950, AI108565, and CA077831 awarded by the National Institutes of Health. The government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/US22/31983 | 6/2/2022 | WO |
| Number | Date | Country | |
|---|---|---|---|
| 63196144 | Jun 2021 | US |
