WO2018236909A1 - Engineered t-cell receptors and methods of their use in modulating inflammatory responses and treating atherosclerosis - Google Patents

Engineered t-cell receptors and methods of their use in modulating inflammatory responses and treating atherosclerosis Download PDF

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Publication number
WO2018236909A1
WO2018236909A1 PCT/US2018/038340 US2018038340W WO2018236909A1 WO 2018236909 A1 WO2018236909 A1 WO 2018236909A1 US 2018038340 W US2018038340 W US 2018038340W WO 2018236909 A1 WO2018236909 A1 WO 2018236909A1
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cell
polynucleotide
cells
vector
drb1
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PCT/US2018/038340
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French (fr)
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Patrick Ho
Klaus Ley
Ravi KOLLA
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La Jolla Institute For Allergy And Immunology
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P9/00—Drugs for disorders of the cardiovascular system
    • A61P9/10—Drugs for disorders of the cardiovascular system for treating ischaemic or atherosclerotic diseases, e.g. antianginal drugs, coronary vasodilators, drugs for myocardial infarction, retinopathy, cerebrovascula insufficiency, renal arteriosclerosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/462—Cellular immunotherapy characterized by the effect or the function of the cells
    • A61K39/4621—Cellular immunotherapy characterized by the effect or the function of the cells immunosuppressive or immunotolerising
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4631—Chimeric Antigen Receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4632—T-cell receptors [TCR]; antibody T-cell receptor constructs
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P1/00—Drugs for disorders of the alimentary tract or the digestive system
    • A61P1/16—Drugs for disorders of the alimentary tract or the digestive system for liver or gallbladder disorders, e.g. hepatoprotective agents, cholagogues, litholytics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P37/00—Drugs for immunological or allergic disorders
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70517—CD8
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70521—CD28, CD152
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70596—Molecules with a "CD"-designation not provided for elsewhere
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/775—Apolipopeptides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/31—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by the route of administration
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/03—Fusion polypeptide containing a localisation/targetting motif containing a transmembrane segment

Definitions

  • CAR-T Chimeric Antigen Receptor T-Cell Therapy
  • Atherosclerosis is a pervasive human disease causing 31% of deaths worldwide. Often characterized as a silent killer, atherosclerosis of the cardiovascular arteries can trigger heart attacks from a process in which lipids, leukocytes, and other factors build up along the arterial lining to form deposits called plaques. Plaques can reduce blood flow to vital organs and tissues, and/or block arteries. If an artery becomes occluded or ruptured, this can lead to blood clots and death of affected tissues and organs. Inadequate removal of lipids lining the artery walls by specialized leukocytes (e.g., macrophages) contributes to plaque formation and growth.
  • leukocytes e.g., macrophages
  • LDL low-density lipoprotein
  • This disclosure relates to novel polynucleotides, cells, compositions and methods of their use.
  • a polynucleotide encoding an engineered T-cell receptor comprising, consisting of, or alternatively consisting essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the athero-relevant antigen is bound to the MHC molecule.
  • the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
  • an engineered T-cell receptor comprising, consisting of, or alternatively consisting essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the athero-relevant antigen is bound to the MHC molecule.
  • the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule.
  • Another aspect of the disclosure relates to a vector comprising the polynucleotide according to any of the embodiments disclosed herein, optionally operatively linked to a promoter.
  • the vector further comprises an enhancer, a polynucleotide encoding FoxP3 optionally operatively linked to a promoter, a polynucleotide encoding IL-10 optionally operatively linked to a promoter, a suicide gene optionally operatively linked to a promoter, a ubiquitin binding domain, and/or STUB1 optionally operatively linked to a promoter.
  • the vector is from the group of: a plasmid, a retroviral vector, a lentiviral vector, an adenoviral vector, or an adeno-associated viral vector. Also provided herein are the expression product(s) of the vector comprising the polynucleotide encoding an engineered T-cell receptor.
  • the disclosure relates to a cell comprising or expressing the polynucleotide or vector according to any one of the embodiments disclosed herein.
  • the cell comprises two or more distinct polynucleotides or two or more distinct vectors according to the embodiments disclosed herein, and wherein the engineered T-cell receptors encoded by the two or more polynucleotides or two or more vectors bind distinct antigens.
  • the cell is an isolated cell.
  • the cell is a leukocyte, a T-cell, or an NK cell.
  • the cell is a regulatory T-cell, a regulatory memory T-cell, a central memory T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell.
  • a cell comprising the expression product(s) of the polynucleotide or vector encoding an engineered T-cell receptor.
  • the engineered T-cell receptor is expressed on the surface of the cell.
  • a population of cells or modified cells according to any of the embodiments described herein.
  • the population can be homogenous or
  • the disclosure provides a non-human animal comprising one or more of a polynucleotide, and/or vector, and/or cell, and/or a population of cells according to any of the embodiments described herein.
  • the non-human animal comprises two or more polynucleotides, two or more vectors, two or more cells, or two or more populations of cells that encode distinct engineered T-cell receptors that bind distinct athero- relevant antigen targets.
  • composition comprising a carrier and one or more of: a polynucleotide, vector, engineered T cell receptor, cell, modified cell, or population comprising said cells or modified cells according to any of the embodiments described herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero- relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the disclosure provides a kit comprising a composition according to any of the embodiments described herein and instructions for use.
  • Another aspect of the disclosure relates to a method of producing a modified cell, the method comprising: (i) introducing a polynucleotide or vector according to any of the embodiments described herein into a cell or a population of cells, and optionally culturing the cell or population of cells under conditions that favor expression the polynucleotide or vector; and (ii) optionally selecting a cell or enriching a cell or a subpopulation of cells that have been successfully modified with the polynucleotide or vector of step (i).
  • step (i) comprises CRISPR mediated gene editing.
  • the cell is a leukocyte, a T-cell, or an K cell.
  • the cell is a regulatory T-cell, a regulatory memory T-cell, a central memory T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell.
  • the method further comprises inducing a regulatory T-cell phenotype in the cell or subpopulation of modified cells by inducing FoxP3 expression.
  • the method further comprises introducing a polynucleotide encoding IL-10 and/or a suicide gene to the cell or subpopulation of modified cells.
  • the method further comprises contacting the cell or subpopulation of modified cells with activation-induced soluble anti- ⁇ antibody and/or anti-IL-5 antibody. Also provided are the cells prepared by these methods, that are optionally isolated.
  • provided herein are one or more of: methods of inducing an antiinflammatory response in a cell or tissue, mediating an immune response in a cell or tissue, or mediating an inflammatory response in a cell or tissue, comprising administering an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the subject is murine, canine, feline, simian, equine, rat or human.
  • a method of inducing an antiinflammatory response, mediating an immune response, or mediating an inflammatory response in a subject in need thereof comprising administering an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein.
  • the response is characterized by suppression of pathogenic T-cells.
  • the response is characterized by decreased expression of one or more pro-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more pro-inflammatory cytokines comprise IL- ⁇ , TNF-a, IFN- ⁇ , IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL- 21, IL-23, IL-27, and/or TGF- ⁇ .
  • the one or more pro-inflammatory cytokines comprise IL- ⁇ , TNF-a, IFN- ⁇ , IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL- 21, IL-23, IL-27, and/or TGF- ⁇ .
  • the response is characterized by increased expression of one or more anti-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more anti-inflammatory cytokines comprise TGF- ⁇ , IL-lRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL-35, and/or INF-a.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T- cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the subject is murine, canine, feline, simian, equine, rat or human.
  • Also provided herein is a method of enhancing the activity of a regulatory T-cell or a memory regulatory T-cell, comprising administering an effective amount of of a
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T- cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the enhanced activity of the regulatory T-cell is characterized by increased expression of IL-10.
  • the administration is to a cell or tissue.
  • Administration to a cell or tissue may be in vivo, ex vivo, or in vitro.
  • the administration is to a subject.
  • the subject is murine, canine, feline, simian, or human.
  • a method of protecting a subject against an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage comprising administering to the subject an effective amount of an effective amount of a polynucleotide, engineered T-cell receptor, vector, cell, modified cell, population, or composition according to any of the embodiments described herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T- cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the subject is murine, canine, feline, simian, equine, rat or human.
  • a method of treating an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage in a subject in need thereof comprising administering to the subject an effective amount of an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T- cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the subject is murine, canine, feline, simian, equine, rat or human.
  • the adverse cardiovascular event or cardiovascular disease, disorder, or damage is from the group of: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
  • the adverse cardiovascular event or cardiovascular disease, disorder, or damage comprises atherosclerosis.
  • Another aspect of this disclosure relates to a method of treating a disease or condition involving an inflammatory response or related to inflammation in a subject in need thereof, comprising administering to the subject an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T- cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the subject is murine, canine, feline, simian, equine, rat or human.
  • the cell, modified cell, or population is autologous to the subject being treated. In other aspects, the cell is allogenic to the subject.
  • the cell can be from any appropriate species, e.g., mammalian, canine, feline, murine, rat, equine or human.
  • the term "4- IBB costimulatory signaling region" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the 4- IBB costimulatory signaling region sequence as shown herein.
  • the example sequence of the 4-lBB costimulatory signaling region is provided in U.S. Pub. No. US20130266551A1.
  • the sequence of the 4-lBB costimulatory signaling region associated disclosed in the U.S. Pub. No. US20130266551A1 is listed as follows:
  • the term "about” is used to indicate that a value includes the standard deviation of error for the device or method being employed to determine the value.
  • AAV adeno-associated virus
  • AAV adeno-associated virus
  • Non-limiting exemplary serotypes useful in the methods disclosed herein include any of the 11 serotypes, e.g., AAV2, AAV8, AAV9, or variant serotypes, e.g., AAV- DJ.
  • Nonlimiting exemplary AAV vectors are disclosed in U.S. Pub. Nos.
  • administer and “administering” are used to mean introducing the therapeutic agent (e.g., polynucleotide, vector, cell, modified cell, population) into a subject.
  • the therapeutic administration of this substance serves to attenuate any symptom, or prevent additional symptoms from arising.
  • administration is for the purposes of preventing or reducing the likelihood of developing an autoimmune disease or disorder, the substance is provided in advance of any visible or detectable symptom.
  • Routes of administration include, but are not limited to, oral (such as a tablet, capsule or suspension), topical, transdermal, intranasal, vaginal, rectal, subcutaneous intravenous, intraarterial, intramuscular, intraosseous, intraperitoneal, epidural and intrathecal.
  • affinity refers to the strength of the reversible
  • affinity refers to the interaction between the MHC molecule (or the antigen binding domain (e.g., peptide binding cleft) of an MHC molecule) and an antigen, antigen fragment, peptide, or epitope.
  • affinity refers to the interaction between the TCR's variable domain regions and an antigen or antigen- MHC complex.
  • K D equilibrium dissociation constant
  • antigen-MHC affinities reported herein reflect K D and were calculated according to the method disclosed in Sidney, J. et al. J. Immunol. 185: 4189-4198 (2010). Affinity and K D are inversely related - the smaller the K D value, the greater the binding affinity.
  • high affinity refers to a KD of less than or equal to 1000 nM. Antigens bound to MHC with intermediate high affinity exhibit a KD of between 10-100 nM. Antigens bound to MHC with very high affinity exhibit a K D of less than or equal to 10 nM.
  • animal refers to living multi-cellular vertebrate organisms, a category that includes, for example, mammals and birds.
  • mammal includes both human and non-human mammals.
  • antibody As used herein, the term “antibody” ( or “Ab”) collectively refers to
  • immunoglobulins or "Ig" or immunoglobulin-like molecules including but not limited to antibodies of the following isotypes: IgM, IgA, IgD, IgE, IgG, and combinations thereof.
  • Immunoglobulin-like molecules include but are not limited to similar molecules produced during an immune response in a vertebrate, for example, in mammals such as humans, rats, goats, rabbits and mice, as well as non-mammalian species, such as shark immunoglobulins (see Feige, M. et al. Proc. Nat. Ac. Sci. 41(22): 8155-60 (2014)).
  • the term “antibody” includes intact immunoglobulins and "antibody fragments” or "antigen binding fragments” that specifically bind to a molecule of interest (or a group of highly similar molecules of interest) to the substantial exclusion of binding to other molecules (for example, antibodies and antibody fragments that have a binding constant for the molecule of interest that is at least 10 3 M "1 greater, at least 10 4 M _1 greater or at least 10 5 M “1 greater than a binding constant for other molecules in a biological sample).
  • the term “antibody” also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, 111.); Kuby, J., Immunology, 3 rd Ed., W.H. Freeman & Co., New York, 1997.
  • the general structure of an antibody is comprised of heavy (H) chains and light (L) chains connected by disulfide bonds.
  • the structure can also comprise glycans attached at conserved amino acid residues.
  • Each heavy and light chain contains a constant region and a variable region (also known as "domains").
  • the constant regions of the heavy chain also contribute to the effector function of the antibody molecule.
  • Antibodies comprising the heavy chains ⁇ , ⁇ , ⁇ 3, ⁇ , ⁇ , ⁇ 2, ⁇ 4, ⁇ , and ⁇ 2 result in the following isotypes: IgM, IgD, IgG3, IgGl, IgAl, IgG2, IgG4, IgE, and IgA2,
  • Class switching is the process by which the constant region of an immunoglobulin heavy chain is replaced with a different immunoglobulin heavy chain through recombination of the heavy chain locus of a B-cell to produce an antibody of a different isotype.
  • Antibodies may exist as monomers (e.g., IgG), dimers (e.g., IgA), tetramers (e.g., fish IgM), pentamers (e.g., mammalian IgM), and/or in complexes with other molecules.
  • antibodies can be bound to the surface of a cell or secreted by a cell.
  • the variable regions of the immunoglobulin heavy and the light chains specifically bind the antigen.
  • the "framework" region is a portion of the Fab that acts as a scaffold for three hypervariable regions called “complementarity-determining regions” (CDRs).
  • CDRs complementarity-determining regions
  • a set of CDRs is known as a paratope.
  • the framework regions of different light or heavy chains are relatively conserved within a species.
  • the combined framework region of an antibody (comprising regions from both light and heavy chains), largely adopts a ⁇ -sheet conformation and the CDRs form loops which connect, and in some cases form part of, the ⁇ -sheet structure.
  • framework regions act to position the CDRs in correct orientation by interchain, non-covalent interactions.
  • the framework region and CDRs for numerous antibodies have been defined and are available in a database maintained online (Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991).
  • the CDRs of the variable regions of heavy and light chains are responsible for binding to an epitope of an antigen.
  • a limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs).
  • the CDRs of a heavy or light chain are numbered sequentially starting from the N-terminal end (i.e. CDR1, CDR2, and CDR3).
  • a V L CDR3 is the middle CDR located in the variable domain of the light chain of an antibody.
  • a V H CDRl is the first CDR in the variable domain of a heavy chain of an antibody.
  • An antibody that binds a specific antigen will have specific V H and V L region sequences, and thus specific CDR sequences.
  • Antibodies with different specificities i.e. different combining sites for different antigens) have different CDRs.
  • Fab antigen-binding fragment
  • the Fab fragment comprises the region that binds to an antigen and is composed of one variable region and one constant region from both a heavy chain and a light chain.
  • An F(ab') 2 fragment refers to a fragment of an antibody digested by pepsin or the enzyme IdeS (immunoglobulin degrading enzyme from S. pyogenes) comprising two Fab regions connected by disulfide bonds.
  • a single chain variable fragment (“scFv”) refers to a fusion protein comprising at least one V H and at least one V L region connected by a linker of between 5 to 30 amino acids.
  • the term "antigen” refers to a compound, composition, or substance that may be specifically bound and/or recognized by the products of specific humoral or cellular immunity and antigen recognition molecules, including but not limited to an antibody molecule, single-chain variable fragment (scFv), cell surface immunoglobulin receptor, B- cell receptor (BCR), T-cell receptor (TCR), engineered TCR, modified TCR, or CAR.
  • the term “antigen” may also refer to an epitope of an antigen.
  • epitope of an antigen refers to an antigen or a fragment, peptide, region, site, or domain of an antigen that is recognized by an antigen recognition molecule.
  • Antigens can be any type of molecule including but not limited to peptides, proteins, lipids, phospholipids haptens, simple intermediary metabolites, sugars (e.g., monosaccharides or oligosaccharides), hormones, and macromolecules such as complex carbohydrates (e.g., polysaccharides).
  • Common categories of antigens include, but are not limited to microbial antigens such as viral antigens, bacterial antigens, fungal antigens, protozoa, and other parasitic antigens, antigens involved in autoimmune disease (including autoantigens), allergy, and graft rejection, tumor antigens, toxins, and other miscellaneous antigens.
  • antigen binding domain refers to any protein or polypeptide domain that can specifically bind to an antigen target (including target complexes of antigens and MHC molecules).
  • autologous in reference to cells, tissue, and/or grafts refers to cells, tissue, and/or grafts that are isolated from and then and administered back into the same subject, patient, recipient, and/or host.
  • Allogeneic refers to non-autologous cells, tissue, and/or grafts.
  • Atherosclerosis is a systemic disease characterized by narrowing of blood vessels due to the formation of atheromatous plaques or atheromata. Atheroma is the deposition of lipids and cholesterol within the inner wall of arteries that makes arterial lumen stenotic.
  • the major clinical manifestations of atherosclerosis are angina, myocardial infarction , transient cerebral ischemic attacks, and strokes.
  • B cell refers to a type of lymphocyte in the humoral immunity of the adaptive immune system. B cells principally function to make antibodies, serve as antigen presenting cells, release cytokines, and develop memory B cells after activation by antigen interaction. B cells are distinguished from other lymphocytes, such as T cells, by the presence of a B-cell receptor on the cell surface. B cells may either be isolated or obtained from a commercially available source.
  • Non-limiting examples of commercially available B cell lines include lines AHH-1 (ATCC® CRL-8146TM), BC-1 (ATCC® CRL- 2230TM), BC-2 (ATCC® CRL-2231TM), BC-3 (ATCC® CRL-2277TM), CA46 (ATCC® CRL-1648TM), DG-75 [D.G.-75] (ATCC® CRL-2625TM), DS-1 (ATCC® CRL-11102TM), EB-3 [EB3] (ATCC® CCL-85TM), Z-138 (ATCC #CRL-3001), DB (ATCC CRL-2289), Toledo (ATCC CRL-2631), Pfiffer (ATCC CRL-2632), SR (ATCC CRL-2262), JM-1 (ATCC CRL-10421), NFS-5 C-l (ATCC CRL-1693); NFS-70 CIO (ATCC CRL-1694), FS-25 C-3 (ATCC CRL-1695), AND SUP-B15 (ATCC CRL-1929).
  • AHH-1
  • cell lines derived from anaplastic and large cell lymphomas e.g., DEL, DL-40, FE-PD, JB6, Karpas 299, Ki-JK, Mac-2A Plyl, SR-786, SU-DHL-1, -2, - 4,-5,-6,-7,-8,-9,-10, and -16, DOHH-2, NU-DHL-1, U-937, Granda 519, USC-DHL-1, RL; Hodgkin's lymphomas, e.g., DEV, HD-70, HDLM-2, HD-MyZ, HKB-1, KM-H2, L 428, L 540, LI 236, SBH-1, SUP-HD1, SU/RH-HD-1.
  • Non-limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection, or ATCC, (www.atcc.org/) and the German Collection of Microorganisms and Cell Cultures
  • Cas9 refers to a CRISPR associated endonuclease referred to by this name.
  • Non-limiting exemplary Cas9s include Staphylococcus aureus Cas9, nuclease dead Cas9, and orthologs and biological equivalents each thereof.
  • Orthologs include but are not limited to Streptococcus pyogenes Cas9 ("spCas9"), Cas 9 from Streptococcus thermophiles, Legionella pneumophilia, Neisseria lactamica, Neisseria meningitides, Francisella novicida; and Cpfl (which performs cutting functions analogous to Cas9) from various bacterial species including Acidaminococcus spp. and Francisella novicida U112.
  • CD3 zeta signaling domain refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD3 zeta signaling domain sequence as shown herein.
  • Non-limiting exemplary sequences of the CD3 zeta signaling domain are provided in U.S. Pub. No. US
  • CD3 zeta signaling domain sequence is:
  • CD8 a hinge domain refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD8 a hinge domain sequence as shown herein.
  • the example sequences of CD8 a hinge domain for human, mouse, and other species are provided in Pinto, R.D. et al. (2006) Vet. Immunol. Immunopathol. 110: 169-177.
  • Non-limiting examples of such include: Human CD8 alpha hinge domain:
  • CD8 a transmembrane domain refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD8 a transmembrane domain sequence as shown herein.
  • the fragment sequences associated with the amino acid positions 183 to 203 of the human T-cell surface glycoprotein CD8 alpha chain (NCBI Reference Sequence: NP 001759.3), or the amino acid positions 197 to 217 of the mouse T-cell surface glycoprotein CD8 alpha chain (NCBI Reference
  • CD28 costimulatory signaling region refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD28 costimulatory signaling region sequence shown herein.
  • Exemplary CD28 costimulatory signaling domains are provided in U.S. Pat. No. 5,686,281; Geiger, T. L. et al., Blood 98: 2364-2371 (2001); Hombach, A. et al., J Immunol 167: 6123-6131 (2001); Maher, J. et al.
  • Non-limiting examples include residues 114-220 of the below CD28 Sequence: MLRLLLALNL FPSIQVTGNK
  • CD28 transmembrane domain refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, at least 90% sequence identity, or alternatively at least 95% sequence identity with the CD28 transmembrane domain sequence as shown herein.
  • GenBank Accession Nos: XM_006712862.2 and XM_009444056.1 provide additional, non-limiting, example sequences of the CD28 transmembrane domain.
  • the sequences associated with each of the listed accession numbers are incorporated herein.
  • chimeric intends that the sequence contains is comprised of at least one substitutent unit (e.g., fragment, region, portion, domain, polynucleotide, or polypeptide) that is derived from, obtained or isolated from, or based upon other distinct physical or chemical entities.
  • substitutent unit e.g., fragment, region, portion, domain, polynucleotide, or polypeptide
  • a chimera of two or more different proteins may comprise the sequence of a variable region domain from an antibody fused to the transmembrane domain of a cell signaling molecule.
  • a "chimeric" sequence intends that the sequence is comprised of sequences from at least two distinct species (e.g., humanized antibodies).
  • chimeric antigen receptor refers to a fused protein comprising an extracellular domain capable of binding to an antigen, a
  • transmembrane domain derived from a polypeptide different from a polypeptide from which the extracellular domain is derived, and at least one intracellular domain.
  • the "chimeric antigen receptor (CAR)” is also known as a “T-body”, “chimeric receptor”, or “chimeric immune receptor (CIR).”
  • the "extracellular domain capable of binding to an antigen” means any oligopeptide or polypeptide that can bind to a certain antigen.
  • the "intracellular domain” means any oligopeptide or polypeptide known to function as a domain that transmits a signal to cause activation or inhibition of a biological process in a cell.
  • the intracellular domain may comprise, alternatively consist essentially of, or yet further comprise one or more costimulatory signaling domains in addition to the primary signaling domain.
  • the "transmembrane domain” means any oligopeptide or polypeptide known to span the cell membrane and that can function to link the extracellular and signaling domains.
  • a chimeric antigen receptor may optionally comprise a "hinge domain” which serves as a linker between the extracellular and transmembrane domains.
  • Hinge domain IgGl heavy chain hinge sequence:
  • CD28 transmembrane region CD28 transmembrane region
  • CD28 co-stimulatory signaling region CD28 co-stimulatory signaling region
  • each exemplary domain component includes other proteins that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the proteins encoded by the above disclosed nucleic acid sequences. Further, non-limiting examples of such domains are provided herein.
  • a "composition” typically intends a combination of the active agent, e.g., an engineered T-cell receptor, a modified T-cell receptor, a chimeric antigen receptor, a cell comprising an engineered T-cell receptor, a CAR T cell or a CAR NK cell, an antibody, a compound or composition, and a naturally-occurring or non-naturally-occurring carrier, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like and include pharmaceutically acceptable carriers.
  • the active agent e.g., an engineered T-cell receptor, a modified T-cell receptor, a chimeric antigen receptor, a cell comprising an engineered T-cell receptor, a CAR T cell or a CAR NK cell, an antibody, a compound or composition, and a naturally-occurring or non-natural
  • Carriers also include pharmaceutical excipients and additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, tetra-oligosaccharides, and oligosaccharides; derivatized sugars such as alditols, aldonic acids, esterified sugars and the like; and polysaccharides or sugar polymers), which can be present singly or in combination, comprising alone or in
  • Exemplary protein excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein, and the like.
  • Representative amino acid/antibody components which can also function in a buffering capacity, include alanine, arginine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame, and the like.
  • Carbohydrate excipients are also intended within the scope of this technology, examples of which include but are not limited to monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose, and the like; disaccharides, such as lactose, sucrose, trehalose, cellobiose, and the like;
  • polysaccharides such as raffinose, melezitose, maltodextrins, dextrans, starches, and the like
  • alditols such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoinositol.
  • compositions and methods shall mean excluding other elements of any essential significance to the combination for the stated purpose.
  • a composition consisting essentially of the elements as defined herein would not exclude other materials or steps that do not materially affect the basic and novel characteristic(s) of the claimed disclosure, such as compositions for treating or preventing multiple sclerosis.
  • Consisting of shall mean excluding more than trace elements of other ingredients and substantial method steps. Embodiments defined by each of these transition terms are within the scope of this disclosure.
  • consensus sequence refers to an amino acid or nucleic acid sequence that is determined by aligning a series of multiple sequences and that defines an idealized sequence that represents the predominant choice of amino acid or base at each corresponding position of the multiple sequences.
  • the consensus sequence for the series can differ from each of the sequences by zero, one, a few, or more substitutions. Also, depending on the sequences of the series of multiple sequences, more than one consensus sequence may be determined for the series. The generation of consensus sequences has been subjected to intensive mathematical analysis. Various software programs can be used to determine a consensus sequence.
  • CRISPR refers to a technique of sequence specific genetic manipulation relying on the clustered regularly interspaced short palindromic repeats pathway. CRISPR can be used to perform gene editing and/or gene regulation, as well as to simply target proteins to a specific genomic location.
  • Gene editing refers to a type of genetic engineering in which the nucleotide sequence of a target polynucleotide is changed through introduction of deletions, insertions, single stranded or double stranded breaks, or base substitutions to the polynucleotide sequence.
  • CRISPR-mediated gene editing utilizes the pathways of nonhomologous end-joining (HEJ) or homologous recombination to perform the edits.
  • Gene regulation refers to increasing or decreasing the production of specific gene products such as protein or RNA.
  • a "cytotoxic cell” intends a cell that is capable of killing other cells or microbes.
  • cytotoxic cells include but are not limited to CD8+ T cells, natural-killer (NK) cells, NKT cells, and neutrophils, which cells are capable of mediating cytotoxicity responses.
  • the term "detectable marker” refers to at least one marker capable of directly or indirectly, producing a detectable signal.
  • a non-exhaustive list of this marker includes enzymes which produce a detectable signal, for example by colorimetry,
  • luminescence such as horseradish peroxidase, alkaline phosphatase, ⁇ - galactosidase, glucose-6-phosphate dehydrogenase, chromophores such as fluorescent, luminescent dyes, groups with electron density detected by electron microscopy or by their electrical property such as conductivity, amperometry, voltammetry, impedance, detectable groups, for example whose molecules are of sufficient size to induce detectable modifications in their physical and/or chemical properties, such detection may be accomplished by optical methods such as diffraction, surface plasmon resonance, surface variation, the contact angle change or physical methods such as atomic force spectroscopy, tunnel effect, or radioactive molecules such as 32 P, 35 S or 125 I.
  • optical methods such as diffraction, surface plasmon resonance, surface variation, the contact angle change or physical methods such as atomic force spectroscopy, tunnel effect, or radioactive molecules such as 32 P, 35 S or 125 I.
  • disease-relevant antigen refers to an antigen, epitope, or fragment thereof involved in the disease process or mechanism.
  • an inflammation- relevant antigen is an antigen or fragment thereof that, when presented, produces an immune response.
  • An inflammation-relevant antigen producing such an effect is selected to treat the inflammation.
  • an autoimmunity-related antigen is an antigen that is relevant to an autoimmune disease and would not be selected for the treatment of a disorder or disease other than autoimmunity, e.g., cancer.
  • Non-limiting, exemplary disease-relevant antigens are disclosed herein and further, such antigens may be determined for a particular disease based on the epitope screening techniques, mechanisms, and methods described herein.
  • the term "athero-relevant antigen” refers to a disease-relevant antigen that is relevant to the etiology of an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage.
  • the adverse cardiovascular event or cardiovascular disease, disorder, or damage includes but is not limited to coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
  • ApoBlOO is an athero-relevant antigen involved in atherosclerosis.
  • Additional athero- relevant antigens include but are not limited to heat shock proteins (Xu, Q. et al. Am. J.
  • an effective amount or “efficacious amount” is an amount sufficient to achieve the intended purpose, non-limiting examples of such include: initiation of the immune response, modulation of the immune response, suppression of an inflammatory response and modulation of T cell activity or T cell populations.
  • the effective amount is one that functions to achieve a stated therapeutic purpose, e.g., a therapeutically effective amount.
  • the effective amount, or dosage depends on the purpose and the composition, and can be determined according to the present disclosure.
  • encode refers to a polynucleotide which is said to "encode” an RNA or polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, the nucleic acid can be transcribed and/or translated to produce a functional RNA (e.g., miRNA, siRNA, RNAi, tRNA, rRNA, snRNA, etc), an mRNA, or a polypeptide and/or a fragment thereof.
  • the antisense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom.
  • an engineered T-cell receptor refers to a molecule comprising the elements of (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain.
  • an engineered T-cell receptor is a genetically modified TCR, a modified TCR, a recombinant TCR, a transgenic TCR, a partial TCR, a chimeric fusion protein, a CAR, a first generation CAR, a second generation CAR, a third generation CAR, or a fourth generation TRUCK.
  • the engineered T-cell receptor comprises an antibody or a fragment of an antibody.
  • the engineered T-cell receptor is a genetically modified TCR or a CAR.
  • the term "enhancer,” as used herein, denotes regulatory sequence elements that augment, improve or ameliorate transcription of a nucleic acid sequence irrespective of its location and orientation in relation to the nucleic acid sequence to be expressed.
  • An enhancer may enhance transcription from a single promoter or simultaneously from more than one promoter. As long as this functionality of improving transcription is retained or substantially retained (e.g., at least 70%, at least 80%, at least 90% or at least 95% of wild-type activity, that is, activity of a full-length sequence), any truncated, mutated or otherwise modified variants of a wild-type enhancer sequence are also within the above definition.
  • the term "equivalent” or “biological equivalent” of an antigen binding domain means the domain to selectively bind its epitope protein or fragment thereof as measured by ELISA or other suitable methods.
  • Biologically equivalent antigen binding domains include, but are not limited to, those antibodies, peptides, antibody fragments, antibody variant, antibody derivative and antibody mimetics that bind to the same epitope as the reference antibody. It is to be inferred without explicit recitation and unless otherwise intended, that when the present disclosure relates to a polypeptide, protein, peptide polynucleotide or antibody, an equivalent or a biologically equivalent of such is intended within the scope of this disclosure.
  • the term "biological equivalent thereof is intended to be synonymous with "equivalent thereof when referring to a reference protein, antibody, polypeptide or nucleic acid, intends those having minimal homology while still maintaining desired structure or functionality. Unless specifically recited herein, it is contemplated that any polynucleotide, polypeptide or protein mentioned herein also includes equivalents thereof. For example, an equivalent intends at least about 70% homology or identity, or at least 80 % homology or identity and alternatively, or at least about 85 %, or alternatively at least about 90 %, or alternatively at least about 95 %, or alternatively 98 % percent homology or identity and exhibits substantially equivalent biological activity to the reference protein, polypeptide or nucleic acid.
  • an equivalent thereof is a polynucleotide that hybridizes under stringent conditions to the reference polynucleotide or its complement.
  • the term "equivalent” also includes but is not limited to a sub-sequence, portion, homologue, variant or derivative thereof.
  • polynucleotides are transcribed into mRNA and/or the process by which the transcribed mRNA is subsequently being translated into peptides, polypeptides, or proteins.
  • expression may include splicing of the mRNA in a eukaryotic cell.
  • the expression level of a gene may be determined by measuring the amount of mRNA or protein in a cell or tissue sample.
  • the expression level of a gene from one sample may be directly compared to the expression level of that gene from a control or reference sample.
  • the expression level of a gene from one sample may be directly compared to the expression level of that gene from the same sample following administration of a compound.
  • a “first generation CAR” refers to a CAR comprising an
  • a “second generation CAR” refers to a first generation CAR further comprising one costimulation domain (e.g., 4-1BB or CD28).
  • a “third generation CAR” refers to a first generation CAR further comprising two costimulation domains (e.g., CD27, CD28, ICOS, 4-1BB, or OX40).
  • a "fourth generation CAR” (also known as a “TRUCK”) refers to a CAR T-cell further engineered to secrete an additional factor (e.g., proinflammatory cytokine IL-12).
  • TRUCK a CAR T-cell further engineered to secrete an additional factor (e.g., proinflammatory cytokine IL-12).
  • gRNA or "guide RNA” as used herein refers to guide RNA sequences used to target specific polynucleotide sequences for gene editing employing the CRISPR technique.
  • Techniques of designing gRNAs and donor therapeutic polynucleotides for target specificity are well known in the art. For example, Doench, J., et al. Nature biotechnology 2014; 32(12): 1262-7, Mohr, S. et al. (2016) FEBS Journal 283 : 3232-38, and Graham, D., et al. Genome Biol. 2015; 16: 260.
  • gRNA comprises or alternatively consists essentially of, or yet further consists of a fusion polynucleotide comprising CRISPR RNA (crRNA) and trans- activating CRIPSPR RNA (tracrRNA); or a polynucleotide comprising CRISPR RNA (crRNA) and trans-activating CRIPSPR RNA (tracrRNA).
  • a gRNA is synthetic (Kelley, M. et al. (2016) J of Biotechnology 233 (2016) 74-83).
  • HLA-A refers to an MHC class I cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-A variant, including but not limited to any one of its several variants, including but not limited to HLA-A serotypes Al to A69.
  • the gene locus of HLA-A is located at chromosome 6p21.3 (mRNA:
  • HLA-A is a heterodimer composed of an a chain (encoded by the HLA-A gene) and a ⁇ chain.
  • the ⁇ chain (“ ⁇ 2 microglobulin") is encoded by the B2M gene located at chromosome 15:44.71-44.72 in humans and chromosome 2: 122.15 in mice (mRNA: NM_004048).
  • Examples of the HLA-A sequences are known in the art and a non- limited example is HLA-A*03 :01 :0:01 precursor:
  • HLA-A serotypes and/or alleles are known in the art to be associated with disease including but not limited to Al (type I diabetes), A2 (spontaneous abortion), A3 (hemochromatosis, myasthenia gravis, and multiple sclerosis), Al 1 (papilloma virus susceptibility), A24
  • HLA-A2 is associated with HLA graft compatibility (e.g., HLA-A*02:01 to HLA-A*02:426).
  • HLA-B refers to an MHC class I cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-B variant, including but not limited to any one of its several variants, including but not limited to HLA-B serotypes Bl to B83.
  • the gene locus of HLA-B is located at chromosome 6:31.35-36 (mRNA: M 005514).
  • HLA-B is a heterodimer composed of an a chain (encoded by the HLA-B gene) and a ⁇ chain.
  • the ⁇ chain (“ ⁇ 2 microglobulin”) is encoded by the B2M gene located at chromosome 15:44.71-44.72 in humans and chromosome 2: 122.15 in mice (mRNA:
  • HLA-B sequences are known in the art and a non-limited example of an HLA-B protein sequence is provided:
  • HLA-B serotypes and/or alleles are known in the art to be associated with disease.
  • B27 is associated with ankylosing spondylitis, inflammatory joint diseases, psoriasis, inflammatory bowel disorders, reactive arthritis.
  • HLA-B is also associated with HLA graft compatibility (e.g., HLA-A*02:01 to HLA-A*02:426).
  • HLA-C refers to an MHC class I cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-C variant, including but not limited to any one of its several variants, including but not limited to HLA-C serotypes Cwl to Cwl 1 and C12 to C18.
  • the gene locus of HLA-C is located at chromosome 6:31.21 (mRNA: NM_002117, NM_001243042).
  • HLA-C is a heterodimer composed of an a chain (encoded by the HLA-C gene) and a ⁇ chain.
  • the ⁇ chain (“ ⁇ 2 microglobulin”) is encoded by the B2M gene located at chromosome 15:44.71-44.72 in humans and
  • HLA-Cw-1 precursor MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL EDLRSWTAA DTAAQITQRK LEAARAAEQL RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP SSQPTTPFMG IVAGLAV
  • HLA-C HLA-C serotypes and/or alleles are known in the art to be associated with disease including but not limited to Cwl (multinodular goiters) and C* 16 (chronic B-cell lymphocytic leukemia). HLA-C is associated with HLA graft compatibility.
  • HLA-DP refers to an MHC class II cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-DP variant, including but not limited to any one of its several variants, including but not limited to HLA-DP serotypes Al and Bl and HLA-DP alleles Al *01 to Al *04 and Bl *01 to Bl * l l .
  • the gene locus of HLA-DP is located at chromosome 6p21.31 (mRNA: M 002117,
  • HLA-DP is a heterodimer composed of an a chain (encoded by the HLA- DPA1 gene) and a ⁇ chain (encoded by the HLA-DPBl gene). Examples of HLA-DP sequences are known in the art.
  • a non-limited example of HLA-DPA1 is:
  • TLIQRS HTQATNDPPEVTVFPKEPVELGQPNTLICHIDKFFPPVLNVTWLCNGELVT EGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLDQPLLKHWEAQEPIQ MP ETTETVLCALGLVLGLVGIIVGTVLIIKSLRSGHDPRAQGTL.
  • HLA-DPBl is: MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR RVQPRVNVSP SKKGPLQHHN LLVCHVTDFY PGSIQVRWFL NGQEETAGVV STNLIRNGDW TFQILVMLEM TPQQGDVYTC QVEHTSLDSP VTVEWKAQSD SARSKTLTGA GGFVLGLIIC GVGIFMHRRS KKVQRGSA.
  • GenBank Accession Nos. are herein incorporated by reference.
  • HLA-DR refers to an MHC class II cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any ULA-DR variant, including but not limited to any one of its several variants, including but not limited to HLA-DR serotypes DR1 to DR 75 comprising a combination of ULA-DRA and ULA-DRB haplotypes.
  • HLA-DR sequences are known in the art and non-limited examples of such are disclosed in Rose, L.M. et al. (1996) Cancer Immunol. Immunother. 43 :26-30: HLA- DRB1 * 1001 [DR10]:
  • HLA-DR specific antibody may bind and therefore can serve as an immunogen for the generation of additional antibodies, monoclonal antibodies and antigen binding fragments of each thereof.
  • sequences associated with each of the listed reference(s) and GenBank Accession Numbers that correspond to the name HLA-DR or its equivalents including but not limited to the specified HLA-DR subtypes are herein incorporated by reference as additional non-limiting examples.
  • HLA-G refers to a specific molecule associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with HLA-G, including but not limited to any one of its several isoforms, including by not limited to membrane-bound isoforms (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4), soluble isoforms (e.g., HLA-G5, HLA-G6, HLA-G7) , and soluble forms generated by proteolytic cleavage of membrane- bound isoforms (e.g., sHLA-Gl).
  • membrane-bound isoforms e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4
  • soluble isoforms e.g., HLA-G5, HLA-G6, HLA-G7
  • HLA-G is a nonclassical MHC class I paralogue consisting of a heterodimer of a heavy chain and a ⁇ 2 microglobulin.
  • the genetic locus for HLA-G is found at chromosome 6:29.83 in humans and at chromosome 17:37.27 in mice. Examples of the HLA-G sequence are provided herein.
  • the mRNA sequences associated with GenBan Accession Nos. are exemplary: NM_002127.5 XM_006715080.1 XM 006725041.1 XM_006725700.1 XM 006725909.1.
  • An example of the protein translation of M_002127.5 is:
  • homology or “identical”, percent “identity” or “similarity”, when used in the context of two or more nucleic acids or polypeptide sequences, refers to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, e.g., at least 60% identity, preferably at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region (e.g., nucleotide sequence encoding an antibody described herein or amino acid sequence of an antibody described herein).
  • Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences.
  • the alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in Current Protocols in Molecular Biology (Ausubel et al., eds. 1987) Supplement 30, section 7.7.18, Table 7.7.1.
  • default parameters are used for alignment.
  • a preferred alignment program is BLAST, using default parameters.
  • the terms also include sequences that have deletions and/or additions, as well as those that have substitutions.
  • the preferred algorithms can account for gaps and the like.
  • identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is at least 50-100 amino acids or nucleotides in length.
  • An "unrelated” or “non-homologous” sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences disclosed herein.
  • Hybridization refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues.
  • the hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner.
  • the complex may comprise two strands forming a duplex structure, three or more strands forming a multi- stranded complex, a single self-hybridizing strand, or any combination of these.
  • a hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
  • Examples of stringent hybridization conditions include: incubation temperatures of about 25°C to about 37°C; hybridization buffer concentrations of about 6x SSC to about lOx SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4x SSC to about 8x SSC.
  • Examples of moderate hybridization conditions include: incubation temperatures of about 40°C to about 50°C; buffer concentrations of about 9x SSC to about 2x SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5x SSC to about 2x SSC.
  • Examples of high stringency conditions include: incubation temperatures of about 55°C to about 68°C; buffer concentrations of about lx SSC to about O.
  • lx SSC formamide concentrations of about 55% to about 75%
  • wash solutions of about lx SSC, O. lx SSC, or deionized water.
  • hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes.
  • SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
  • ICOS costimulatory signaling region refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the ICOS costimulatory signaling region sequence as shown herein.
  • Non-limiting example sequences of the ICOS costimulatory signaling region are provided in U.S.
  • immune response refers to the development of a cell-mediated response (e.g., mediated by antigen- specific T cells or their secretion products).
  • a cellular immune response is elicited by the presentation of polypeptide epitopes in association with Class I or Class II MHC molecules, to treat or prevent a viral infection, expand antigen-specific Breg cells, TCI, CD4 + T helper cells and/or CD8+ cytotoxic T cells and/or disease generated, autoregulatory T cell and B cell "memory" cells.
  • the response may also involve activation of other components.
  • the term “immune response” may be used to encompass the formation of a regulatory network of immune cells.
  • regulatory network formation may refer to an immune response elicited such that an immune cell, preferably a T cell, more preferably a T regulatory cell, triggers further differentiation of other immune cells, such as but not limited to, B cells or antigen-presenting cells - non limiting examples of which include dendritic cells, monocytes, and macrophages.
  • regulatory network formation involves B cells being differentiated into regulatory B cells; in certain embodiments, regulatory network formation involves the formation of tolerogenic antigen-presenting cells.
  • Immunoblasts include all cells that are produced by hematopoietic stem cells (HSC) including, but not limited to, HSCs, white blood cells (leukocytes), lymphocytes (including T cells, B cells, and natural killer (NK) cells) and myeloid-derived cells
  • HSC hematopoietic stem cells
  • leukocytes white blood cells
  • lymphocytes including T cells, B cells, and natural killer (NK) cells
  • myeloid-derived cells myeloid-derived cells
  • lymphocytes include but are not limited to lymphocytes, granulocytes, monocytes, and macrophages.
  • inflammatory response and "inflammation” as used herein indicate the complex biological response of immune cells, humoral factors, and vascular tissues of an individual or subject to exogenous or endogenous stimuli, such as pathogens, damaged cells, or irritants, and/or inflammatory signals such as pro-inflammatory cytokines.
  • the inflammatory response includes secretion of cytokines and, more particularly, of proinflammatory cytokines, i.e. cytokines which are produced predominantly by activated immune cells and are involved in the amplification of inflammatory reactions.
  • pro-inflammatory cytokines and chemokines include but are not limited to IL- ⁇ , T F-a, IFN- ⁇ , IL-8, IL-6, IL-12, IL-15, IL-16, IL-17 (including family members IL17A, IL17B, IL- 17C, IL-17D, IL-17E, IL-17F), IL-18, GM-CSF, IL-21, IL-23, IL-27 and TGF- ⁇ .
  • anti-inflammatory cytokines include but are not limited to TGF- ⁇ , IL-lRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL-35, INF-a.
  • a cytokine may have either pro-inflammatory and antiinflammatory properties depending on the particular biological context (Cavaillon, J.M (2001) Cell Mol Biol 47(4): 695-702).
  • Exemplary inflammations include acute inflammation and chronic inflammation.
  • Acute inflammation indicates a short-term process characterized by the classic signs of inflammation (swelling, redness, pain, heat, and loss of function) due to the infiltration of the tissues by plasma and leukocytes.
  • An acute inflammation typically occurs as long as the injurious stimulus is present and ceases once the stimulus has been removed, broken down, or walled off by scarring (fibrosis).
  • Chronic inflammation indicates a condition characterized by concurrent active inflammation, tissue destruction, and attempts at repair. Chronic inflammation is not characterized by the classic signs of acute
  • inflammation listed above. Instead, chronically inflamed tissue is characterized by the infiltration of mononuclear immune cells (monocytes, macrophages, lymphocytes, and plasma cells), tissue destruction, and attempts at healing, which include angiogenesis and fibrosis.
  • An inflammation can be inhibited in the sense of the present disclosure by affecting and in particular inhibiting any one of the events that form the complex biological response associated with an inflammation in an individual.
  • exemplary diseases or conditions associated with or related to inflammation and/or inflammatory responses include but are not limited to autoimmune diseases or disorders, adverse cardiovascular events, cardiovascular or liver disease, disorder, or damage, coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
  • introduce refers to the process whereby a foreign (i.e. extrinsic or extracellular) agent is introduced into a host cell thereby producing a cell comprising the foreign agent.
  • Methods of introducing nucleic acids include but are not limited to
  • transduction is done via a vector (e.g., a viral vector).
  • transfection is done via a chemical carrier, DNA/liposome complex, or micelle (e.g., Lipofectamine (Invitrogen)).
  • viral infection is done via infecting the cells with a viral particle comprising the polynucleotide of interest (e.g., AAV).
  • introduction further comprises CRISPR mediated or Transcription activator-like effector nuclease (TALEN) mediated gene editing.
  • TALEN Transcription activator-like effector nuclease
  • Methods of introducing non-nucleic acid foreign agents include but are not limited to culturing the cells in the presence of the foreign agent, contacting the cells with the agent, contacting the cells with a composition comprising the agent and an excipient, and contacting the cells with vesicles or viral particles comprising the agent.
  • non-nucleic acid foreign agents e.g., soluble factors, cytokines, proteins, peptides, enzymes, growth factors, signaling molecules, small molecule inhibitors
  • isolated refers to molecules or biologicals or cellular materials being substantially free from other materials.
  • isolated refers to nucleic acid, such as DNA or RNA, or protein or polypeptide (e.g., an antibody or derivative thereof), or cell or cellular organelle, or tissue or organ, separated from other DNAs or RNAs, or proteins or polypeptides, or cells or cellular organelles, or tissues or organs, respectively, that are present in the natural source.
  • isolated also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized.
  • an "isolated nucleic acid” is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state.
  • isolated is also used herein to refer to polypeptides which are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides.
  • isolated is also used herein to refer to cells or tissues that are isolated from other cells or tissues and substantially separated from other cells of a tissue. "Isolated cell” is meant to encompass both cultured and engineered cells or tissues.
  • linker sequence relates to any amino acid sequence comprising from 1 to 10, or alternatively, 8 amino acids, or alternatively 6 amino acids, or alternatively 5 amino acids that may be repeated from 1 to 10, or alternatively to about 8, or alternatively to about 6, or alternatively about 5, or 4 or alternatively 3, or alternatively 2 times.
  • the linker may comprise up to 15 amino acid residues consisting of a pentapeptide repeated three times.
  • the linker sequence is a (Glycine4Serine)3 flexible polypeptide linker comprising three copies of gly-gly-gly-gly-ser, or equivalents thereof.
  • Non-limiting examples of linker sequences are known in the art, e.g.,
  • a "flexible linker” intends a linker characterized by minimal rigidity.
  • a flexible linker facilitates improved, preferred, or optimal secondary conformation, tertiary conformation, and/or quaternary conformation of the linked protein domains or full length polypeptide.
  • a flexible linker reduces or minimizes negative steric effects.
  • MHC major histocompatibility complex
  • MHC may be used interchangeably with the term "human leukocyte antigen" (HLA) when used in reference to human MHC; thus, MHC refers to all HLA subtypes including, but not limited to, the classical MHC genes disclosed herein: HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-DM, HLA-DO, HLA-DP, HLA- DQ, and HLA-DR, in addition to all variants, isoforms, isotypes, and other biological equivalents thereof.
  • MHC class I (MHC-I) and MHC class II (MHC-II) molecules utilize distinct antigen processing pathways.
  • peptides derived from intracellular antigens are presented to CD8+ T cells by MHC class I molecules, which are expressed on virtually all cells, while extracellular antigen-derived peptides are presented to CD4+ T cells by MHC-II molecules.
  • MHC class I molecules which are expressed on virtually all cells
  • extracellular antigen-derived peptides are presented to CD4+ T cells by MHC-II molecules.
  • MHC-II molecules extracellular antigen-derived peptides
  • MHC-II molecules extracellular antigen-derived peptides
  • a particular antigen, peptide, and/or epitope is identified and presented in an antigen-MHC complex in the context of an appropriate MHC class I or II protein.
  • the genetic makeup of a subject may be assessed to determine which MHC allele is suitable for a particular patient, disease, or condition with a particular set of antigens.
  • the MHC genes are known as the histocompatibility 2 (H-2) genes.
  • Murine classical MHC class I subtypes include H-2D, H-2K, and H-2L.
  • Murine non-classical MHC class I subtypes include H-2Q, H-2M, and H-2T.
  • Murine classical MHC class II subtypes include H-2A (I- A), and H-2E (1-E).
  • Non-classical murine MHC class II subtypes include H-2M and H-20.
  • Canine MHC molecules are known as Dog Leukocyte Antigens (DLA).
  • Feline MHC molecules are known as Feline Leukocyte Antigens (FLA).
  • an orthologous or homologous MHC molecule is selected to transition a therapy or treatment involving a specific antigen-MHC complex from one species to a different species.
  • Non-classical MHC molecules are non-polymorphic, conserved among species, and possess narrow, deep, hydrophobic ligand binding pockets. These binding pockets are capable of presenting glycolipids and phospholipids to Natural Killer T (NKT) cells or certain subsets of CD 8+ T-cells.
  • NKT Natural Killer T
  • MHCs for use according to the present disclosure may be produced, isolated, or purified through techniques known in the art. Common protocols for obtaining MHCs involve steps such as, but not limited to, electrophoresis or other techniques of charge or size based separation, biotinylation or other tagging methods and purification, or transfection and induction of vector constructs expressing MHC proteins. Purified animal antibodies are also available through commercially available sources, including retailers such as eBioscience, Biolegend, or Tonbo Biosciences.
  • the MHC may be classical MHC I, non-classical MHC I, classical MHC II, non-classical MHC II, dimers (Fc fusions), MHC tetramers, or a polymeric form of MHC.
  • MHC multimers are generated according to methods well documented in the art, see, e.g., Bakker et al. "MHC Multimer Technology: Current Status and Future Prospects," Current Opinion in
  • MHC restriction refers to an antigen, antigen fragment, peptide, or epitope that is only specifically recognized and bound by an antigen binding domain when the antigen is bound to a particular MHC molecule.
  • an MHC-restricted antigen is not specifically recognized and bound by an antigen binding domain outside of the context of a particular MHC molecule.
  • the particular MHC molecule is a specific allele or subtype of HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-DM, HLA-DO, HLA-DP, HLA-DQ, or HLA-DR.
  • the antigen binding domain is the antigen binding domain of an antibody, an antibody fragment, a CAR, an engineered TCR, or a B-cell receptor ("BCR").
  • the term "monoclonal antibody” refers to an antibody produced by a cell into which the light and heavy chain genes of a single antibody have been transfected or, more traditionally, by a single clone of B-lymphocytes.
  • Monoclonal antibodies generally have affinity for a single epitope (i.e. they are monovalent) but may be engineered to be specific for two or more epitopes (e.g., bispecific).
  • Monoclonal antibodies include recombinant antibodies, chimeric antibodies, humanized antibodies, and human antibodies.
  • NK cell also known as natural killer cell, refers to a type of lymphocyte that originates in the bone marrow and play a critical role in the innate immune system. NK cells provide rapid immune responses against viral-infected cells, tumor cells or other stressed cell, even in the absence of antibodies and major
  • NK cells may either be isolated or obtained from a commercially available source.
  • NK cell lines include lines NK-92 (ATCC® CRL-2407TM), NK-92MI (ATCC® CRL-2408TM). Further examples include but are not limited to NK lines HANKl, KHYG-1, NKL, NK-YS, NOI-90, and YT.
  • Non-limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection, or ATCC, (http://www.atcc.org/) and the German Collection of Microorganisms and Cell Cultures (https://www.dsmz.de/).
  • the term "overexpress" with respect to a cell, a tissue, or an organ expresses a protein to an amount that is greater than the amount that is produced in a control cell, a control issue, or an organ.
  • a protein that is overexpressed may be endogenous to the host cell or exogenous to the host cell.
  • OX40 costimulatory signaling region refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, or alternatively 90% sequence identity, or alternatively at least 95% sequence identity with the OX40 costimulatory signaling region sequence as shown herein.
  • Non-limiting example sequences of the OX40 costimulatory signaling region are disclosed in U.S. Publication 2012/20148552A1, and include the exemplary sequence provided below.
  • CCGATGCCCA CAAGCCCCCT GGGGGAGGCA GTTTCCGGAC CCCCATCCAA GAGGAGCAGG CCGACGCCCA CTCCACCCTG GCCAAGATC.
  • a "pathogenic T cell” is a T cell that is harmful to a subject containing the T cell. Whereas, a non-pathogenic T cell is not substantially harmful to a subject, and an anti- pathogenic T cells reduces, ameliorates, inhibits, or negates the harm of a pathogenic T cell.
  • plaque regression refers to the overall reduction in plaque volume and a return of the arterial endothelium to its normal functional state. Plaque regression can comprise a decrease in the size, incidence, severity, and/or thickness of plaques on the inner walls of arteries. Plaque regression can also comprise stabilization of a vulnerable plaque. Techniques for measuring plaque regression are known in the art and include but are not limited to coronary angiography, intravascular ultrasound, ultrasound measurement of the carotid intima media thickness, magnetic resonance imaging, computed tomography luminal coronary stenosis assessment, ECG-gated single photon emission computed mography, infared spectroscopy, and intra-coronary thermography (reviewed in Dave, T. et al. Indian J. Endocrinol. Metab. 17(6): 983-989 (2013)).
  • protein protein
  • peptide and “polypeptide” are used interchangeably and in their broadest sense to refer to a compound of two or more subunit amino acids, amino acid analogs or peptidomimetics.
  • the subunits may be linked by peptide bonds.
  • the subunit may be linked by other bonds, e.g., ester, ether, etc.
  • a protein or peptide must contain at least two amino acids and no limitation is placed on the maximum number of amino acids which may comprise a protein's or peptide's sequence.
  • amino acid refers to either natural and/or unnatural or synthetic amino acids, including glycine and both the D and L optical isomers, amino acid analogs and peptidomimetics.
  • polynucleotide and “oligonucleotide” are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. Polynucleotides can have any three-dimensional structure and may perform any function, known or unknown.
  • polynucleotides a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, RNAi, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers.
  • a polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs.
  • modifications to the nucleotide structure can be imparted before or after assembly of the polynucleotide.
  • the sequence of nucleotides can be interrupted by non-nucleotide components.
  • a polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component.
  • the term also refers to both double- and single-stranded molecules. Unless otherwise specified or required, any aspect of this technology that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.
  • a polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for thymine when the polynucleotide is RNA.
  • polynucleotide sequence is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching.
  • nucleic acid sequence and “polynucleotide” are used interchangeably to refer to a polymeric form of nucleotides of any length, either ribonucleotides or
  • a polypeptide may contain a contiguous nucleic acid sequence of the following lengths: 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860
  • promoter refers to any sequence that regulates the expression of a coding sequence, such as a gene. Promoters may be constitutive, inducible, repressible, or tissue-specific, for example.
  • a "promoter” is a control sequence that is a region of a polynucleotide sequence at which initiation and rate of transcription are controlled. It may contain genetic elements at which regulatory proteins and molecules may bind such as RNA polymerase and other transcription factors.
  • Non- limiting exemplary promoters include CMV, U6, EFla, SV40, PGK1 (human or mouse), P5, Ubc, human beta actin, CAG, TRE, UAS, Ac5, Polyhedrin, CaMKIIa, Gall, 10, TEF1, GDS, ADH1, CaMV35S, Ubi, HI, U6, and Alpha- 1 -antitrypsin.
  • Synthetically- derived promoters may be used for ubiquitous or tissue specific expression.
  • virus-derived promoters some of which are noted above, may be useful in the methods disclosed herein, e.g., CMV, HIV, adenovirus, and AAV promoters.
  • purification marker refers to at least one marker useful for purification or identification.
  • a non-exhaustive list of this marker includes His, lacZ, GST, maltose-binding protein, NusA, BCCP, c-myc, CaM, FLAG, GFP, YFP, cherry, thioredoxin, poly(NANP), V5, Snap, HA, chitin-binding protein, Softag 1, Softag 3,
  • Suitable direct or indirect fluorescence marker comprise FLAG, GFP, YFP, RFP, dTomato, cherry, Cy3, Cy 5, Cy 5.5, Cy 7, DNP, AMCA, Biotin, Digoxigenin, Tamra, Texas Red, rhodamine, Alexa fluors, FITC, TRITC or any other fluorescent dye or hapten.
  • a purified nucleic acid, peptide, protein, biological complexes or other active compound is one that is isolated in whole or in part from proteins or other contaminants.
  • substantially purified peptides, proteins, biological complexes, or other active compounds for use within the disclosure comprise more than 80% of all macromolecular species present in a preparation prior to admixture or formulation of the peptide, protein, biological complex or other active compound with a pharmaceutical carrier, excipient, buffer, absorption enhancing agent, stabilizer, preservative, adjuvant or other co-ingredient in a complete pharmaceutical formulation for therapeutic administration.
  • the peptide, protein, biological complex or other active compound is purified to represent greater than 90%, often greater than 95% of all macromolecular species present in a purified preparation prior to admixture with other formulation ingredients.
  • the purified preparation may be essentially homogeneous, wherein other macromolecular species are not detectable by conventional techniques.
  • the term “recognizes and specifically binds” or “antibody binding” or “specific binding” means the contact between the antigen binding domain of an antibody, antibody fragment, CAR, TCR, engineered TCR, BCR, MHC, immunoglobulin-like molecule, scFv, CDR or other antigen presentation molecule and an antigen, epitope, or peptide with a binding affinity (K D ) of less than 10 ⁇ 5 M.
  • an antigen binding domain binds to both a complex of both an antigen and an MHC molecule.
  • antigen binding domains bind with affinities of less than about 10 ⁇ 6 M, 10 ⁇ 7 M, and preferably 10 "8 M, 10 "9 M, 10 "10 M, 10 "U M, or 10 "12 M.
  • specific binding refers to the binding of an antigen to an MHC molecule, or the binding of an antigen binding domain of an engineered T-cell receptor to an antigen or antigen-MHC complex.
  • recombinant protein refers to a polypeptide which is produced by recombinant DNA techniques, wherein generally, DNA encoding the polypeptide is inserted into a suitable expression vector which is in turn used to transform a host cell to produce the heterologous protein.
  • a polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) having a certain percentage (for example, 80%, 85%, 90%, or 95%) of "sequence identity" to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences.
  • the alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in Current Protocols in Molecular Biology (Ausubel et al., eds. 1987) Supplement 30, section 7.7.18, Table 7.7.1.
  • default parameters are used for alignment.
  • a preferred alignment program is BLAST, using default parameters.
  • signal peptide or “signal polypeptide” intends an amino acid sequence usually present at the N-terminal end of newly synthesized secretory or membrane polypeptides or proteins. It acts to direct the polypeptide across or into a cell membrane and is then subsequently removed. Examples of such are well known in the art. Non-limiting examples are those described in U.S. Patent Nos. 8,853,381 and 5,958,736.
  • subject refers to human and veterinary subjects, for example, humans, animals, non-human primates, dogs, cats, sheep, mice, horses, and cows.
  • subject is a human.
  • subject is suffering from a disease or condition to be treated by one of the methods disclosed herein.
  • suicide gene refers to a gene encoding a factor that is capable of inducing death in a cell that expresses it.
  • a suicide gene provides a strategy to regulate cell persistence by providing a mechanism for specific depletion of cells expressing the suicide gene. Once activated, the suicide gene kills the cell through, for example, apoptosis or cell- mediated cytotoxicity.
  • Non limiting examples of suicide genes include (1) iCasp9 which is activated by administration of API 903 to cause apoptosis, (2) CD20 which is activated by administration of CD-20 specific antibody rituximab causing depletion through antibody- dependent cellular cytotoxicity, and (3) herpesvirus thymidine kinase which is activated by ganciclovir.
  • T-cell refers to a type of lymphocyte that matures in the thymus. T cells play an important role in cell-mediated immunity and are distinguished from other lymphocytes, such as B cells, by the presence of a T-cell receptor (TCR) on the cell surface. T-cells may either be isolated or obtained from a commercially available source.
  • T cell includes all types of immune cells expressing CD3 including T-helper cells (CD4+ cells), cytotoxic T-cells (CD8+ cells), natural killer T-cells, naive T cells (CCR7+,
  • NKT Natural killer T cells
  • TCR co-express NK cell markers and a semi-invariant T cell receptor (TCR). They are implicated in the regulation of immune responses associated with a broad range of diseases.
  • Non-limiting examples of commercially available T-cell lines include lines BCL2 (AAA) Jurkat (ATCC® CRL-2902TM), BCL2 (S70A) Jurkat (ATCC® CRL-2900TM), BCL2 (S87A) Jurkat (ATCC® CRL-2901TM), BCL2 Jurkat (ATCC® CRL-2899TM), Neo Jurkat (ATCC® CRL-2898TM), TALL- 104 cytotoxic human T cell line (ATCC # CRL-11386).
  • T-cell lines e.g., such as Deglis, EBT-8, HPB-MLp-W, HUT 78, HUT 102, Karpas 384, Ki 225, My-La, Se-Ax, SKW-3, SMZ-1 and T34; and immature T- cell lines, e.g., ALL- SIL, Bel3, CCRF-CEM, CML-T1, D D-41, DU.528, EU-9, HD-Mar, HPB-ALL, H-SB2, HT-1, JK-T1, Jurkat, Karpas 45, KE-37, KOPT-K1, K-Tl, L-KAW, Loucy, MAT, MOLT-1, MOLT 3, MOLT-4, MOLT 13, MOLT- 16, MT-1, MT-ALL, P12/Ichikawa, Peer, PER0117, PER-255, PF-382, PFI-285, RPMI-8402, ST-4, SUP-T1 to
  • Null leukemia cell lines including but not limited to REH, NALL-1, KM-3, L92-221, are a another commercially available source of immune cells, as are cell lines derived from other leukemias and lymphomas, such as K562 erythroleukemia, THP-1 monocytic leukemia, U937 lymphoma, HEL
  • Non- limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection, or ATCC, (http://www.atcc.org/) and the German Collection of Microorganisms and Cell Cultures (https://www.dsmz.de/).
  • T-cell receptor refers to a cell surface molecule found on T-cells that functions to recognize and bind antigens presented by antigen presenting molecules.
  • a TCR is a heterodimer of an alpha chain (TRA) and a beta chain (TRB).
  • TRG alternative gamma
  • TRD delta
  • T-cells expressing this version of a TCR are known as ⁇ T-cells.
  • TCRs are part of the immunoglobulin superfamily. Accordingly, like an antibody, the TCR comprises three hypervariable CDR regions per chain. There is also an additional area of hypervari ability on the beta-chain (HV4).
  • the TCR heterodimer is generally present in an octomeric complex that further comprises three dimeric signaling modules ⁇ 3 ⁇ / ⁇ , CD35/8, and CD247 ⁇ / ⁇ or ⁇ / ⁇ .
  • Nonlimiting exemplary amino acid sequence of the human TCR-beta chain is
  • modified TCR refers to a TCR that has been genetically engineered, and/or a transgenic TCR, and/or a recombinant TCR.
  • modified TCRs include single-chain VaVP TCRs (scTv), full-length TCRs produced through use of a T cell display system, and TCRs wherein the CDR regions have been engineered to recognize a specific antigen, peptide, fragment, and/or MHC molecule.
  • scTv single-chain VaVP TCRs
  • Methods of developing and engineering modified TCRs are known in the art. For example, see Stone, J.D. et al. Methods in Enzymology 503 : 189-222 (2012), PCT Application WO2014018863 Al .
  • Type-1 T Regulatory (T R 1) cells are a subset of CD4+ T cells that have regulatory properties and are able to suppress antigen-specific immune responses in vitro and in vivo. These T R 1 cells are defined by their unique profile of cytokine production and make high levels of IL-10 and TGF-beta, but no IL-4 or IL-2. The IL-10 and TGF-beta produced by these cells mediate the inhibition of primary naive T cells in vitro. There is also evidence that T R cells exist in vivo, and the presence of high IL-10-producing CD4(+) T cells in patients with severe combined immunodeficiency who have received allogeneic stem-cell transplants have been documented.
  • T R 1 cells are involved in the regulation of peripheral tolerance and they could potentially be used as a cellular therapy to modulate immune responses in vivo. See, for example, Levings, M. et al. J. Allergy Clin. Immunol. 106(1 Pt2): S 109-12 (2000).
  • TRI cells are defined by their ability to produce high levels of IL-10 and TGF-beta. Trl cells specific for a variety of antigens arise in vivo, but may also differentiate from naive CD4+ T cells in the presence of IL-10 in vitro. T R 1 cells have a low proliferative capacity, which can be overcome by IL-15. T R 1 cells suppress naive and memory T helper type 1 or 2 responses via production of IL-10 and TGF-beta. Further characterization of T R 1 cells at the molecular level will define their mechanisms of action and clarify their relationship with other subsets of Tr cells.
  • T R 1 cells to identify novel targets for the development of new therapeutic agents, and as a cellular therapy to modulate peripheral tolerance, can be foreseen. See, for example, Roncarolo, M. et al. Immunol. Rev. 182:68-79 (2001).
  • "treating" or “treatment” of a disease or condition in a subject refers to (1) preventing the symptoms or disease or condition from occurring in a subject that is predisposed or does not yet display symptoms of the disease; (2) inhibiting the disease or condition or arresting its development; or (3) ameliorating or causing regression of the disease or condition or the symptoms of the disease or condition.
  • treatment is an approach for obtaining beneficial or desired results, including clinical results.
  • beneficial or desired results can include one or more, but are not limited to, alleviation or amelioration of one or more symptoms, diminishment of extent of a condition (including a disease), stabilized (i.e., not worsening) state of a condition (including disease), delay or slowing of condition (including disease), progression, amelioration or palliation of the condition (including disease), states and remission (whether partial or total), whether detectable or undetectable.
  • the clinical endpoints will vary by the specific tissue targeted or affected by the immune response.
  • the clinical endpoints for successful treatment include but are not limited to an incremental improvement or a partial reduction in an adverse symptom, disorder, illness, disease or complication caused by or associated with an adverse cardiovascular event or cardiovascular disease or an inhibition, decrease, reduction, suppression, prevention, limit or control of worsening or progression of one or more adverse symptoms, disorders, illnesses, diseases or complications caused by or associated with an adverse cardiovascular event or cardiovascular disease over a short or long duration (hours, days, weeks, months, etc.).
  • a beneficial or desired result of treatment also includes reducing or eliminating the need, dosage frequency or amount of additional therapeutics such as another drug or other agent used for treating a subject having or at risk of having an adverse cardiovascular event or cardiovascular disease. For example, reducing an amount of an adjunct therapy, for example, a reduction or decrease of a treatment for an adverse cardiovascular event or cardiovascular disease.
  • unit dose refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the composition calculated to produce the desired responses in association with its administration, i.e., the appropriate route and regimen.
  • the quantity to be administered both according to number of treatments and unit dose, depends on the result and/or protection desired. Precise amounts of the
  • composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the subject, route of administration, intended goal of treatment (alleviation of symptoms versus cure), and potency, stability, and toxicity of the particular composition.
  • solutions Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically or prophylactically effective.
  • the formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described herein.
  • vector refers to a nucleic acid construct deigned for transfer between different hosts, including but not limited to a plasmid, a virus, a cosmid, a phage, a BAC, a YAC, etc.
  • a "viral vector” is defined as a recombinantly produced virus or viral particle that comprises a polynucleotide to be delivered into a host cell, either in vivo, ex vivo or in vitro.
  • plasmid vectors may be prepared from commercially available vectors.
  • viral vectors may be produced from baculoviruses, retroviruses, adenoviruses, AAVs, etc.
  • the viral vector is a lentiviral vector.
  • viral vectors include retroviral vectors, adenovirus vectors, adeno-associated virus vectors, alphavirus vectors and the like.
  • Infectious tobacco mosaic virus (TMV)-based vectors can be used to manufacturer proteins and have been reported to express Griffithsin in tobacco leaves (O'Keefe et al.
  • a vector construct refers to the polynucleotide comprising the retroviral genome or part thereof, and a gene of interest such as a polynucleotide encoding a CAR.
  • Vectors that contain both a promoter and a cloning site into which a polynucleotide can be operatively linked are well known in the art. Such vectors are capable of transcribing RNA in vitro or in vivo, and are commercially available from sources such as Agilent Technologies (Santa Clara, Calif.) and Promega Biotech (Madison, Wis.).
  • the present disclosure provides polypeptides encoding an engineered T-cell receptor comprising, consisting essentially of, or yet further consisting of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T- cell receptor is a modified TCR.
  • the engineered T-cell receptor is a CAR.
  • the polynucleotide is the complement of a polynucleotide encoding an engineered T-cell receptor.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the athero-relevant antigen is bound to the MHC molecule.
  • the engineered T- cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
  • an engineered T-cell receptor comprising, consisting of, or alternatively consisting essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T- cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the athero-relevant antigen is bound to the MHC molecule.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the athero- relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
  • Extracellular Antigen Binding Domain the present disclosure provides an engineered T-cell receptor that comprises, consists, or alternatively consists essentially of an antigen binding domain that specifically recognizes and binds, binds, or is specific to an athero-relevant antigen bound to an MHC molecule.
  • the MHC binds to the athero-relevant antigen with high affinity, optionally an affinity less than 1000 nM.
  • the athero-relevant antigen binds to the MHC with high affinity, optionally an affinity less than 1000 nM.
  • the affinity of the interaction between the athero-relevant antigen and the MHC molecule is characterized by a dissociation constant (K D ) which is less than about 0.1 nM, less than than about 1 nM, less than about 5 nM, less than about 10 nM, less than about 15 nM, less than about 20 nM, less than about 50 nM, less than about 100 nM, less than about 150 nM, less than about 200 nM, less than about 250 nM, less than about 300 nM, less than about 350 nM, less than about 400 nM, less than about 450 nM, less than about 500 nM, less than about 550 nM, less than about 600 nM, less than about 650 nM, less than about 700 nM, less than about 750 nM, less than about 800 nM, less than about 850 nM, less than about 900 nM, less than about 950 nM, less than about 0.1 nM
  • the affinity of the interaction between the antigen and the MHC molecule ranges from: about 1 nM to about 10 nM, about 1 nM to about 15 nM, about 1 nM to about 50 nM, about 1 nM to about 100 nM, about 1 nM to about 200 nM, about 1 nM to about 300 nM, about 1 nM to about 400 nM, about 1 nM to about 500 nM, about 1 nM to about 600 nM, about 1 nM to about 700 nM, about 1 nM to about 800 nM, about 1 nM to about 900 nM, about 1 nm to about 1000 nM, about 1 nM to about 1100 nM, about 1 nM to about 1200 nM, about 1 nM to about 1300 nM, about 1 nM to about 1400 nM, about 1 nM to about 1500 nM, about 1 nM to about 2 ⁇ ,
  • the MHC's affinity for the antigen is less than about 1000 nM.
  • the athero-relevant antigen comprises all or part of an epitope derived from an antigen involved in an adverse cardiovascular event, or
  • cardiovascular or liver disease disorder, or damage including but not limited to: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
  • the antigen comprises, consists, or alternatively consists essentially of all or part of an epitope derived from ApoBlOO.
  • ApoBlOO polypeptide sequence from which peptides, sub-sequences, portions, homologues, variants, derivatives and T cell epitopes may be derived is as follows:
  • Athero-relevant antigens can be based upon or derived from an ApoBlOO amino acid sequence.
  • an athero-relevant antigen can comprise an amino acid sequence having 60% or more (e.g., 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%) sequence identity with a region of ApoBlOO.
  • the an athero-relevant antigens or equivalents thereof include those having at least partial sequence identity to one or more ApoBlOO peptides, subsequences, portions, homologues, variants or derivatives thereof set forth as any one of the peptides set forth in in Table 1.
  • the percent identity of such sequences can be as little as 60%, or can be greater (e.g., 60%, 65%, 70%, 75%, 75% 80%, 85%, 90%, 95%, 96%, 97%, 98%), 99%), etc.).
  • the percent identity can extend over the entire sequence length or a portion of the sequence.
  • the length of the sequence sharing the percent identity is 2, 3, 4, 5 or more contiguous amino acids, e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, etc.
  • the athero-relevant antigen comprises, consists, or alternatively consists essentially of the ApoB 100-derived peptides listed in the following Table 1, or an equivalent of each thereof:
  • the athero-relevant antigen comprises, consists, or alternatively consists essentially of the amino acid sequence SLFFSAQPFEITAST,
  • IKHIYAISSAALSAS or an equivalent of each thereof.
  • the length of the athero-relevant antigen disclosed herein may vary based on the particular MHC allele and/or the specific antigen recognition domain (e.g., TCR, scFv, etc.).
  • the length of the antigen peptides according to some embodiments described herein may vary from, for example, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, between 20 - 25, between 20-30, between 30-40 amino acids, or up to 50 amino acids in length.
  • the antigen includes a core of at least at least 5 amino acids, at least 6, at least 7, at least 8, at least 9 and more.
  • the length of the autoantigenic peptide does not exceed about 100 amino acids, does not exceed about 50 amino acids, does not exceed about 30 amino acids, or does not exceed 20 amino acids. According to some embodiments of the invention, the length of the autoantigenic peptide includes at least 5 and no more than 35 amino acids.
  • antigens or equivalents thereof may further comprise independently at least 2, or alternatively at least 3, or alternatively at least 4, or alternatively at least 5, or at least 6, or alternatively at least 7, or alternatively at least 8, or alternatively at least 9 or alternatively at least 10 amino acids at the amino and/or carboxyl terminus of the polypeptide.
  • the antigens listed in Table 1 or equivalents thereof further comprise independently at least 2, or alternatively at least 3, or alternatively at least 4, or alternatively at least 5, or at least 6, or alternatively at least 7, or alternatively at least 8, or alternatively at least 9 or alternatively at least 10 amino acids at the amino and/or carboxyl terminus of the polypeptide.
  • Athero-relevant antigen peptides or equivalents thereof that exhibit sequence identity to a reference ApoBlOO peptide, sub-sequence or portion, or modification thereof set forth as any one of the peptides in Table 1.
  • an athero-relevant antigen, or a sub-sequence, portion, homologue, variant or derivative thereof comprises, consists or consists essentially of a sequence at least 60% or more (e.g., 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, etc.) identical to a reference ApoBlOO protein or peptide, or sub-sequence, portion, homologue, variant or derivative thereof as set forth as any one of the peptides set forth in in Table 1.
  • Athero-relevant antigens, or equivalents thereof comprise, consist of, or consist essentially of include or consist of an ApoBlOO peptide, wherein the athero-relevant antigen or equivalent thereof has one or more modifications, such as an amino acid addition to, deletion of, or substitution of any amino acid residue in any peptide set forth as any one of the peptides set forth in in Table 1.
  • a modified sequence is at least 80% or more, e.g., 80-85%, 85-90%, 90-95%, 95-100% identical, to a ApoBlOO peptide, or sub-sequence, portion, homologue or derivative thereof set forth as any one of the peptides set forth in in Table 1 or has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100, or more, additions to, deletions of, or substitutions.
  • antigen binding domains that recognize and/or bind modified and variant forms of athero-relevant antigens including but not limited to ApoBlOO peptides and equivalents thereof.
  • modified and variant forms of athero-relevant antigens including but not limited to ApoBlOO peptides and equivalents thereof.
  • Modifications intend an ApoBlOO peptide or equivalent thereof that deviates from a reference sequence. Such modifications may have greater or less activity or function than a reference ApoBlOO peptide, sub-sequence or portion thereof, such as ability to elicit, stimulate, induce, promote, increase or enhance T-cell response or immune or inflammatory response.
  • Athero-antigens or equivalents include sequences having substantially the same, greater or less relative activity or function as a T-cell epitope than a reference epitope set forth in in Table 1, for example, an ability to elicit, stimulate, induce, promote, increase or enhance an immune response in vitro or in vivo.
  • Non-limiting examples of modifications include one or more amino acid
  • substitutions e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25- 30, 30-50, 50-100, or more residues
  • additions and insertions e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100, or more residues
  • deletions e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100
  • Additional modifications to the antigens and peptides contemplated herein include but are not limited to acetylation, amidation, azido group conjugated to the primary epsilon amino group on an inserted lysine or as 5-azidopentanoic acid on the N-terminus, biotinylation, carrier proteins and MAP peptides (e.g., KLH or BSA conjugated peptides), MAP peptides, modifications to increase cell penetration, conjugation to 5-azidopentanoic acid, azidogroup conjugated to lysine or propargylglycine can be conjugated to the peptide for reactivity with azido groups, counterions, cholesterol conjugation, C-terminal inserted cysteine, cyclization with disulfide bonds or amide bonds, conjugation of DOTA, DOPA and DTPA to the termini, Caprylic acid (C8), Capric acid (CIO), Why acid, (C12), Myristic acid (C14), Palm
  • Tyr(S03H2) and unnatural amino acids: D-amino acids, Aib, Abu, Ahx, Orn, pGlu, Nle, DAB, Cit, Hyp, Tyr(3-N02), or Met sulfoxide or sulfone.
  • Athero-relevant antigens or equivalents thereof can be a part of or contained within a larger molecule, such as another peptide sequence, or a fusion, heterologous domain, or chimera.
  • an addition is a chimeric fusion sequence or heterologous domain (i.e. an amino acid sequence having one or more molecules not normally present in a reference endogenous sequence covalently attached to the sequence).
  • the athero-relevant antigen is an MHC-restricted antigen.
  • the antigen binding domain specifically binds to both the antigen and the MHC molecule.
  • the antigen binding domain specifically binds a region spanning the athero-relevant antigen and MHC bound to the athero-relevant antigen (i.e. the antigen-MHC complex).
  • the MHC molecule comprises, consists, or alternatively consists essentially of all or part of an MHC class I molecule (e.g., HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, or CD1 molecule).
  • an MHC class I molecule e.g., HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, or CD1 molecule.
  • the MHC molecule comprises, consists of, or alternatively consists essentially of an MHC class II molecule (e.g., HLA-DM, HLA-DO, HLA-DP, HLA-DQ, and HLA-DR).
  • MHC class II molecule e.g., HLA-DM, HLA-DO, HLA-DP, HLA-DQ, and HLA-DR.
  • the MHC molecule is a classical MHC molecule. In other
  • the MHC molecule is a non-classical MHC molecule.
  • the extracellular antigen binding domain specifically binds and recognizes an antigen bound to a specific MHC allele or mutation.
  • specific peptide-MHC allele complexes are provided in Tables .
  • the MHC class II molecule comprises all or part of an HLA- DR, HLA-DQ, or HLA-DP molecule.
  • the MHC molecule is selected from the group of: DRB1*01:01, DRB1*01:02, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:03, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*10:01, DRB1*11:01, DRB1*11:04, DRB1*12:01, DRB1*13:01, DRB1*13:02, DRB1*14:01, DRB1*15:01, DRB3*01:01, DRB3*02:02, DRB4*01:01, DRB5*01:01, DPB1*04:01, DPB1*05:01, or DQB
  • the MHC molecule is selected from the group of: DPB1*02:01, DPB1*03:01, DPB1*04:02, DPB1*14:01, DQB1*02:01, DQB1*03:01, DQB1*06:02, DRB1*01:01, DRB1*04:01, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*09:01, DRB1*1101, DRB1*12:01, DRB1*13:02, DRB1*15:01, DRB3*01:01, DRB3*02:02, DRB4*01:01 or DRB5*01:01 or an equivalent of each thereof.
  • the athero-relevant antigen comprises, consists, or consists essentially any one of the peptides set forth in Table 1, or an equivalent of each thereof, and binds to one or more of the MHC molecules set forth in Table 4, or an equivalent of each thereof.
  • the athero-relevant antigen comprises all or part of the sequence SLFFSAQPFEITAST or an equivalent thereof and binds to either DRB 1*0101, DRB 1*0701, or an equivalent of each thereof.
  • the antigen binding domain comprises, consists, or consists essentially of Fab, variable regions of a TCR, BCR, or Ig, or a fragment of an scFv (e.g., a V H chain or V L chain).
  • An scFv region can comprise the variable regions of the heavy (V H ) and light chains (V L ) of immunoglobulins, connected with a short linker peptide.
  • the linker peptide may be from 1 to 50 amino acids, for instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids.
  • the linker is glycine rich, although it may also contain serine or threonine.
  • the heavy chain variable region of the Ig comprises, or consists essentially thereof, or consists of those disclosed herein or an equivalent of each thereof and/or comprises one or more CDR regions comprising those disclosed herein or an equivalent of each thereof.
  • the light chain variable region of the Ig comprises, or consists essentially thereof, or consists of those disclosed herein or an equivalent of each thereof and/or comprises one or more CDR regions comprising those disclosed herein or an equivalent of each thereof.
  • transmembrane Domain The transmembrane domain may be derived either from a natural or from a synthetic source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein. Transmembrane regions of particular use in this disclosure may be derived from CD 8 ( M_001768, M_170299), CD28
  • CD45 M_001267798, M_002838, NM 080921, NM_080922
  • CD4 M_000616, M_001195014, M_001195015, M_001195016, M_001195017), CD 5 ( M_014207, M_001346456), phosphatidate cytidylyltransferase 1 (CDS, M_001263), CD9 ( M_001769, M_001330312), CD16 ( M_000569), CD22 ( M_024916), CD33 ( M_001082618, M_001177608, M_001772), CD37 ( M_001040031, NM_001774), CD64 ( M_000566), CD80 ( M_005191), CD86 ( M_176892, M_001206924,
  • transmembrane domain is a CD3, CD8, or a CD28 transmembrane domain.
  • the transmembrane domain may be synthetic, in which case it will comprise predominantly hydrophobic residues such as leucine and valine.
  • a triplet of phenylalanine, tryptophan and valine will be found at each end of a synthetic transmembrane domain.
  • a short oligo- or polypeptide linker preferably between 2 and 10 amino acids in length may form the linkage between the transmembrane domain and the cytoplasmic signaling domain of the engineered t-cell receptor.
  • a glycine-serine doublet provides a particularly suitable linker.
  • Intracellular Signaling Domain The intracellular signaling domain (or cytoplasmic domain) of the engineered T-cell receptor is responsible for activation of at least one of the traditional effector functions of an immune cell in which an engineered T-cell receptor has been introduced.
  • the intracellular signaling domain comprises, consists, or consists essentially of the intracellular signaling domain of a co-stimulatory molecule.
  • the intracellular signaling domain refers to a portion of a protein which transmits the effector function signal and directs the immune cell to perform its specific function. An entire signaling domain or a portion thereof may be used so long as the portion is sufficient to transmit the effector function signal.
  • Cytoplasmic sequences of the T-cell receptor (TCR) and co-receptors, as well as derivatives or variants thereof, can function as intracellular signaling domains for use in a CAR or modified TCR.
  • Intracellular signaling domains of particular use in this disclosure may be derived from FcR (e.g., M 000566), TCR, CD3 ( M_000732, M_000733, M_000073), phosphatidate cytidylyltransferase 1 (CDS,
  • CD22 NM_024916
  • CD79a M_021601, M_001783
  • CD79b CD79b
  • the intracellular signaling domain of the engineered t-cell receptor can comprise the signaling domain of CD28, 4-1BB, CD3 zeta, CD27 ( M_001242), ICOS, or OX40.
  • the intracellular signaling domain is derived from a protein of the same species as the subject. In other embodiments, the intracellular signaling domain is derived from a protein of a different cell (e.g., macrophage, B cell) or a different species than the subject.
  • the intracellular region of at least one co-stimulatory signaling molecule including but not limited CD27 ( M_001242), CD28, 4- IBB, OX40, CD30 ( M_001243), CD40 ( M_001250), programmed cell death protein 1 (PD- 1, M 005018), ICOS, lymphocyte function-associated antigen- 1 (LFA-1, M_001114380), CD2 ( M_001767), CD7 (NM_006137), CD27 (NM_001242), CD276 ( M_001024736), or a ligand that specifically binds with CD83, may also be included in the cytoplasmic domain of the engineered T-cell receptor.
  • co-stimulatory signaling molecule including but not limited CD27 ( M_001242), CD28, 4- IBB, OX40, CD30 ( M_001243), CD40 ( M_001250), programmed cell death protein 1 (PD- 1, M 005018), ICOS, lymphocyte function-associated antigen- 1 (LFA-1
  • the engineered T-cell receptor of the present disclosure can comprise one or more co-stimulatory domain.
  • a CAR may comprise one, two, or more co-stimulatory domains.
  • the costimulatory domain can be derived from the costimulatory domain of CD28, 4- IBB, CD3 zeta, CD27, ICOS, or OX40.
  • the costimulatory domain is derived from a protein of the same species as the subject. In other embodiments, the costimulatory domain is derived from a protein of a different species than the subject.
  • the polynucleotide can further comprise a detectable marker or purification marker and/or a polynucleotide encoding a detectable marker or a purification marker, each conjugated to the polynucleotide.
  • Flexible spacer The engineered T-cell receptor may optionally further comprise a spacer domain of up to 300 amino acids, preferably 5 to 100 amino acids, more preferably 25 to 50 amino acids.
  • the spacer may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids.
  • a spacer domain may comprise, for example, a portion of a human Fc domain, a CH3 domain, or the hinge region of any immunoglobulin, such as IgA, IgD, IgE, IgG, or IgM, or variants thereof. Additional spacers include, but are not limited to, CD4, CD8, and CD28 hinge regions.
  • present disclosure provides vectors comprising, consisting, or alternatively consisting essential of a polynucleotide according to any of the embodiments described herein.
  • the polynucleotide is operatively linked to a promoter.
  • the vector is from the group of: a plasmid, a retroviral vector, a lentiviral vector, an adenoviral vector, or an adeno-associated viral vector.
  • the vector is an expression vector.
  • the vector is useful for integration in genomic DNA, replication, viral particle production, and/or infection or transduction with high efficiency.
  • the disclosed vectors comprise an element that enhances or induces a regulatory T-cell phenotype.
  • the disclosed vectors comprise an element that reduces or inhibits an effector T-cell phenotype.
  • the isolated nucleic acid sequence is comprised in a vector.
  • the vector is a plasmid.
  • the vector is a viral vector.
  • the vector is a lentiviral vector.
  • the term "vector” intends a recombinant vector that retains the ability to infect and transduce non-dividing and/or slowly-dividing cells and integrate into the target cell's genome.
  • the vector is derived from or based on a wild-type virus.
  • the vector is derived from or based on a wild-type lentivirus. Examples of such, include without limitation, human immunodeficiency virus (HIV), equine infectious anemia virus (EIAV), simian immunodeficiency virus (SIV) and feline immunodeficiency virus (FIV).
  • retrovirus can be used as a basis for a vector backbone such murine leukemia virus (MLV).
  • MLV murine leukemia virus
  • a viral vector according to the disclosure need not be confined to the components of a particular virus.
  • the viral vector may comprise components derived from two or more different viruses, and may also comprise synthetic components. Vector components can be manipulated to obtain desired characteristics, such as target cell specificity.
  • the recombinant vectors of this disclosure may be derived from primates and non- primates.
  • primate lentiviruses include the human immunodeficiency virus (HIV), the causative agent of human acquired immunodeficiency syndrome (AIDS), and the simian immunodeficiency virus (SIV).
  • the non-primate lentiviral group includes the prototype "slow virus” visna/maedi virus (VMV), as well as the related caprine arthritis- encephalitis virus (CAEV), equine infectious anemia virus (EIAV) and the more recently described feline immunodeficiency virus (FIV) and bovine immunodeficiency virus (BIV).
  • Recombinant lentiviral vectors are known in the art, e.g., see US Patent Nos. 6,924,123; 7,056,699; 7,07,993; 7,419,829 and 7,442,551.
  • Retroviral vectors for use in this disclosure include, but are not limited to pLenti series versions 4, 6, and 6.2 (Invitrogen); "ViraPower” system (Lentigen Corp.), pHIV-7- GFP, "Lenti-X", pLVX, (Clontech), pLKO. l-puro (Sigma-Aldrich), pLemiR (Open
  • assays include, for example, Southern and Northern blotting, RT-PCR and PCR; biochemical assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELlSAs and Western blots) or by assays described herein to identify agents falling within the scope of the disclosure.
  • assays include, for example, Southern and Northern blotting, RT-PCR and PCR; biochemical assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELlSAs and Western blots) or by assays described herein to identify agents falling within the scope of the disclosure.
  • the disclosed vectors can further comprise a regulatory element such as an enhancer element.
  • enhancers include, for example, WPRE, the human cytomegalovirus (HCMV) immediate early (IE) enhancer, the enhancer of the Moloney Murine Sarcoma Virus (MMSV), the U3 region of Rous Sarcoma Virus (RSV), the U3 region of Spleen Focus Forming Virus (SFFV), and the HCMV IE enhancer.
  • the disclosed vectors can further comprise a polynucleotide encoding all or part of forkhead box P3 ("FoxP3," NM_001114377, NM_014009), or an equivalent thereof.
  • FoxP3 may be operatively linked to a regulatory control element such as a promoter or an internal ribosome entry site (IRES).
  • IRS internal ribosome entry site
  • FoxP3 is fused to a detectable marker such as GFP.
  • the ubiquitin binding sites in FoxP3 are mutated to reduce degradation and/or stabilize the protein.
  • the STUB1 gene (NM_005861, M_001293197, or an equivalent thereof) is included in the vector to reduce degradation and/or stabilize the protein.
  • a nonlimiting example of the nucleotide sequence of FoxP3 is: GCACACACTC ATCGAAAAAA ATTTGGATTA TTAGAAGAGA
  • the disclosed vectors can further comprise a polynucleotide encoding all or part of IL-10 ( M 000572) or an equivalent thereof.
  • IL-10 may be operatively linked to a regulatory control element such as a promoter or an internal ribosome entry site (IRES).
  • IL-10 is fused to a detectable marker such as GFP.
  • the IL-10 is activation inducible.
  • expression of IL-10 may be under the control of a promoter activated by an inflammatory response (e.g., mxl promoter activated by interferon).
  • a nonlimiting example of the nucleotide sequence of IL-10 is: ACACATCAGG
  • the disclosed vectors can further comprise a suicide gene to induce cell death in cells comprising and/or expressing the vector.
  • the suicide gene is operatively linked to a promoter.
  • the promoter is inducible (e.g., tetracycline-inducible).
  • the suicide gene is triggered following adoptive cell treatment (Buddee et al., PLoS One, (2013)).
  • the suicide gene may function to downregulate expression of the engineered T-cell receptor following binding to the target antigen (WO 2016/011210).
  • Non-limiting examples of suicide genes include caspase-9 (NM_001229, NM_001278054, NM_032996, or its equivalent) and thymidine kinase (NM_003258 or its equivalent).
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T- cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the cells express the polynucleotide or vector according to any of the embodiments disclosed herein.
  • the cells comprise two or more polynucleotides encoding distinct engineered T-cell receptors.
  • the cells comprise two or more vectors encoding distinct engineered T-cell receptors.
  • the cells comprising two or more vectors or polynucleotides may express engineered T-cell receptors that bind a plurality of antigens (e.g., the cells comprise a plurality of engineered T-cell receptors have distinct antigen specificities).
  • the cell is an isolated cell.
  • the cell is isolated or purified from a subject's peripheral blood mononuclear cells and in other aspects it is a cultured cell from a cell population that optionally is commercially available.
  • the cell is of any appropriate species for the subject being treating, e.g., mammalian, canine, feline, murine or human.
  • the cell is a leukocyte.
  • the leukocyte may be murine, canine, feline, simian, or human.
  • the cell is a T-cell.
  • the T-cell may be regulatory T-cell, a regulatory memory T-cell, a central memory T-cell, a naive T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell, preferably a regulatory T-cell.
  • the cell is an K cell that is isolated or a cultured cell from a cell population that optionally is commercially available.
  • the cell is of any appropriate species for the subject being treating, e.g., mammalian, canine, feline, murine or human.
  • the cell comprises and/or expresses an engineered T-cell receptor on the cell surface.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds an antigen that binds an MHC molecule, wherein the antigen binds to the MHC molecule with high affinity, and/or wherein the antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T- cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell further comprises the athero-relevant antigen-MHC complex bound to the extracellular antigen binding domain.
  • the population is substantially homogenous.
  • substantially homogenous intends a plurality of cells of greater than 50%, 60%>, 70%, 80%>, or 95% purity or homogeneity.
  • the population is a heterogenous mixture of two or more cells comprising and/or expressing distinct engineered T-cell receptors with distinct antigen specificities.
  • non-human animal comprising, consisting, or alternatively consisting essentially of the polynucleotide or vector of any one of the embodiments described herein.
  • compositions comprising, consisting of, or alternatively consisting essentially of a carrier and one or more of the products disclosed herein: a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, isolated cell, or population comprising an engineered T-cell receptor according to any of the embodiments disclosed herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero- relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the carrier is a pharmaceutically acceptable carrier.
  • the composition comprises a pharmaceutically or physiologically acceptable carrier, diluent, or excipient.
  • Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives.
  • Compositions of the present disclosure may be formulated for oral, intravenous, intranasal, intramuscular, intrathecal, topical, enteral, and/or parenteral administration. In particular embodiments, the compositions of the present disclosure are formulated for intravenous administration.
  • the buffers such as neutral buffered saline, phosphate buffered saline and the like
  • carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol
  • compositions are administered systemically.
  • one or more antimicrobial agents such as chlorobutanol, ascorbic acid, parabens, thermerosal, or the like can be used to prevent the growth of microorganisms. It may also be preferable to include agents that alter the tonicity such as sugars or salts.
  • suitable diluents such as saline, phosphate-buffered saline, hydrogel, nutrient carrier, albumin, recombinant albumin,
  • Administration of the cells or compositions can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosage of administration are known to those of skill in the art and will vary with the composition used for therapy, the purpose of the therapy and the subject being treated. In some aspects, a matrix and or catheter may be used. Preferably, the administration is in such an amount as will be therapeutically effective and immune modifying. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician. Suitable dosage formulations and methods of administering the agents are known in the art.
  • administrations of a composition about, at least about, or at most about 3, 4, 5, 6, 7, 8, 9, 10 or more administrations.
  • the administrations will normally range from 1, 2, 3, 4, 5, 6, or 7 days to annual intervals, more usually from one to two week intervals.
  • Periodic boosters at intervals of every other day, twice a week, weekly, biweekly, monthly, or 0.1, 0.2, 0.3, 0.4, 0.5, 1, 2, 3,4 or 5 years, usually two years, will be desirable to maintain the condition of the immune system.
  • the administration(s) may be followed by assays for autoreactive immune responses,
  • the carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid poly(ethylene glycol), and the like), suitable mixtures thereof, and vegetable oils.
  • the proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion, and by the use of surfactants.
  • the prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like.
  • isotonic agents for example, sugars or sodium chloride.
  • Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
  • the cells, populations, vectors, and polynucleotides of the disclosure can be administered in combination with other traditional therapies. These include, but are not limited to, the administration of immunosuppressive or modulating therapies or treatments and therapies to ameliorate the symptoms of and/or treat
  • Non-limiting examples of immunosuppressive agents or therapies include anti-inflammatory drugs such as sulfasalazine, corticosteroids such as prednisone, and immune system suppressors such as azathioprine and mercaptopurine.
  • Additional classes of immune modulating therapies or treatments include but are not limited to a calcineurin inhibitor, a chemokine receptor inhibitor, a glucocorticoid, an mTOR inhibitor, an anti- metabolic compound, a phosphodiesterase-5 inhibitor, an antibody, or a leukocyte function antigen-3/Fc fusion protein.
  • Therapies or treatments to ameliorate the symptoms of and/or treat cardiovascular disease include but are not limited to cholesterol medications such as statins, anti-platelet medications such as aspirin, angiotensin-converting enzyme inhibitors, calcium channel blockers, diuretics, and invasive procedures such as angioplasty, stent placement, endarterectomy, fibinolytic therapy, and/or bypass surgery.
  • cholesterol medications such as statins, anti-platelet medications such as aspirin, angiotensin-converting enzyme inhibitors, calcium channel blockers, diuretics, and invasive procedures such as angioplasty, stent placement, endarterectomy, fibinolytic therapy, and/or bypass surgery.
  • the cells and populations of cell are administered to the host using methods known in the art and described, for example, in International Application No. PCT/US2011/064191.
  • This administration of the cells or compositions of the invention can be performed to generate an animal model of the relevant disease, disorder, or condition for experimental assays and screens.
  • kits comprising, consisting of, or alternatively consisting essentially of a composition as described herein and instructions for use. Additional reagents and/or instructions can further be provided as necessary.
  • Also provided herein is a method of producing a modified cell, comprising, consisting, or alternatively consisting essentially of: (i) introducing a polynucleotide or vector according to any of the embodiments described herein into a cell or a population of cells, and optionally culturing the cell or population of cells under conditions that favor expression of the polynucleotide or the vector; (ii) and further optionally selecting a cell or enriching a cell or a subpopulation of cells that have been successfully modified with the polynucleotide or vector of step (i).
  • the cells are selected from or isolated from a group consisting of leukocytes, T-cells and NK-cells.
  • the T-cells are regulatory T-cells, naive T-cells, central memory T-cells, regulatory memory T-cells, effector memory T-cells, CD4+ T-cells, or a CD8+ T-cells.
  • the cell is isolated from a subject.
  • the subject may be a murine, canine, feline, simian, or a human.
  • step (i) comprises CRISPR mediated gene editing to introduce the polynucleotide into the genome of the target cell.
  • CRISPR CRISPR mediated gene editing to introduce the polynucleotide into the genome of the target cell.
  • Methods of using CRISPR to perform gene editing are known in the art.
  • the polynucleotide or vector is introduced to the target cell via a viral particle comprising, consisting of, or alternatively consisting essentially of a polynucleotide or vector according to the
  • cells expressing the disclosed engineered T-cell receptors may be further modified to express one or more of: FoxP3, IL-10, a detectable or selectable marker, a suicide gene, and/or an equivalent of each thereof as described herein.
  • one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene may be encoded on one or more vectors introduced to the cell or subpopulation of modified cells.
  • each gene may be operatively linked to an expression control element such as a promoter.
  • one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene are encoded on the same vector.
  • one or one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene are encoded on separate vectors.
  • one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene is encoded on the same vector that encodes an engineered T-cell receptor according to any of the embodiments described herein.
  • FoxP3 expression is induced by contacting the cell or subpopulation of modified cells with an effective amount of transforming growth factor beta 1-4 ("TGFp," e.g., TGFpl : P 000651; available from Peprotech rhTGFpl cat# 100-21, 100-21C) and/or IL-10 (available from Peprotech rhIL-10 cat# 200-10), thereby inducing FoxP3 expression in the cell or subpopulation of modified cells.
  • TGFp transforming growth factor beta 1-4
  • the culture conditions comprise about 1 to about 10 ng/mL, or alternatively about 5 to about 20 ng/mL, or alternatively about 5 to about 30 ng/mL, or alternatively about 5 to about 40 ng/mL, or alternatively about 5 to about 50 ng/mL, or alternatively about 5 to about 100 ng/mL, or alternatively about 5 to about 250 ng/mL, or alternatively about 5 to about 500 ng/mL, or alternatively about 25 to about 75 ng/mL, or alternatively about 50 to about 100 ng/mL, or alternatively about 100 to about 500 ng/mL, or or alternatively about 100 ng/mL to about 1 ⁇ g/mL, or alternatively about 1 ⁇ g/mL to about 10 ⁇ g/mL, or alternatively about 10 ⁇ g/mL to about 50 ⁇ g/mL, or alternatively about 50 ⁇ g/mL to about 100 ⁇ g/mL, or alternatively about 100 ⁇ g/mL to
  • the culture conditions comprise about 10 ng/mL, or alternatively about 15 ng/mL, or alternatively about 20 ng/mL, or alternatively about 25 ng/mL, or alternatively about 30 ng/mL, or alternatively about 40 ng/mL, or alternatively about 50 ng/ml, or alternatively about 100 ng/mL, or alternatively about 200 ng/mL, or alternatively about 250 ng/mL, or alternatively about 300 ng/mL, or alternatively about 400 ng/mL, or alternatively about 500 ng/mL, or alternatively about 1 ⁇ g/mL of TGFP and/or IL- 10.
  • TGFP and/or IL-10 is about 5 to about 100 ng/mL.
  • the cell or subpopulation of modified cells is contacted with an effective amount of anti -interferon ⁇ antibody (e.g., ThermoFisher cat# 16-7311- 81)(Skurkovich, S. et al. J. of Immune Based Therapies, Vaccines, and Antimicrobials, 4: 1-8 (2015)) anti IL-5 antibody (e.g., mepolizumab (GlaxoSmithKline)) (Mukhergee, M. et al. World Allergy Organ J.
  • anti -interferon ⁇ antibody e.g., ThermoFisher cat# 16-7311- 81
  • anti IL-5 antibody e.g., mepolizumab (GlaxoSmithKline)
  • mepolizumab GaxoSmithKline
  • anti-T F antibody or inhibitor e.g., infliximab, adalimumab, certolizumab pegol, golimumab, etenercept, or bupropion
  • anti-IL-7 antibody e.g., R&D Systems Human IL-7 antibody cat# MAB207.
  • the antibodies are activation-induced.
  • cells Prior to expansion and genetic modification of the cells disclosed herein, cells may be obtained from a subject - for instance, in embodiments involving autologous therapy - or a commercially available culture, that are available from the American Type Culture
  • ATCC ATCC Collection
  • Cells can be obtained from a number of sources in a subject, including peripheral blood mononuclear cells (PBMC), bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
  • PBMC peripheral blood mononuclear cells
  • Isolation methods for use in relation to this disclosure include, but are not limited to Life Technologies Dynabeads® system; STEMcell
  • cells may be obtained through commercially available cell lines, including but not limited to BCL2 (AAA) Jurkat (ATCC® CRL-2902TM), BCL2 (S70A) Jurkat (ATCC® CRL-2900TM), BCL2 (S87A) Jurkat (ATCC® CRL-2901TM), BCL2 Jurkat (ATCC® CRL-2899TM), Neo Jurkat (ATCC® CRL-2898TM), NK-92 (ATCC® CRL- 2407TM), NK-92MI (ATCC® CRL-2408TM).
  • BCL2 (S70A) Jurkat ATCC® CRL-2900TM
  • BCL2 (S87A) Jurkat ATCC® CRL-2901TM
  • BCL2 Jurkat ATCC® CRL-2899TM
  • Neo Jurkat ATCC® CRL-2898TM
  • NK-92 ATCC® CRL- 2407TM
  • NK-92MI ATCC®
  • appropriate cells may be derived from stem cells or lymphoid progenitors including iPS cells, ES cells, hematopoietic stem cells, common lymphoid progenitors (CLPs), DN1, DN2, DN3, DN4, or DP cells.
  • stem cells or lymphoid progenitors including iPS cells, ES cells, hematopoietic stem cells, common lymphoid progenitors (CLPs), DN1, DN2, DN3, DN4, or DP cells.
  • the cells are autologous to the subject being treated. In another aspect, the cells are allogeneic to the subject being treated.
  • Polypeptides encoding engineered T-cell receptors can be packaged into a lentiviral or retroviral packaging system by using a packaging vector and cell lines.
  • the packaging plasmid includes, but is not limited to retroviral vector, lentiviral vector, adenoviral vector, and adeno-associated viral vector.
  • the packaging vector contains elements and sequences that facilitate the delivery of genetic materials into cells.
  • the retroviral constructs are packaging plasmids comprising at least one retroviral helper DNA sequence derived from a replication-incompetent retroviral genome encoding in trans all virion proteins required to package a replication incompetent retroviral vector, and for producing virion proteins capable of packaging the replication-incompetent retroviral vector at high titer, without the production of replication-competent helper virus.
  • the retroviral DNA sequence lacks the region encoding the native enhancer and/or promoter of the viral 5' LTR of the virus, and lacks both the psi function sequence responsible for packaging helper genome and the 3' LTR, but encodes a foreign polyadenylation site, for example the SV40
  • the retrovirus is a leukemia virus such as a Moloney Murine Leukemia Virus (MMLV), the Human Immunodeficiency Virus (HIV), or the Gibbon Ape Leukemia virus (GALV).
  • MMLV Moloney Murine Leukemia Virus
  • HSV Human Immunodeficiency Virus
  • GALV Gibbon Ape Leukemia virus
  • the foreign enhancer and promoter may be the human cytomegalovirus (HCMV) immediate early (IE) enhancer and promoter, the enhancer and promoter (U3 region) of the Moloney Murine Sarcoma Virus (MMSV), the U3 region of Rous Sarcoma Virus (RSV), the U3 region of Spleen Focus Forming Virus (SFFV), or the HCMV IE enhancer joined to the native Moloney Murine Leukemia Virus (MMLV) promoter.
  • HCMV human cytomegalovirus
  • IE immediate early
  • IE Enhancr and promoter
  • U3 region of the Moloney Murine Sarcoma Virus
  • RSV Rous Sarcoma Virus
  • SFFV Spleen Focus Forming Virus
  • HCMV IE enhancer joined to the native Moloney Murine Leukemia Virus
  • the retroviral packaging plasmid may consist of two retroviral helper DNA sequences encoded by plasmid based expression vectors, for example where a first helper sequence contains a cDNA encoding the gag and pol proteins of ecotropic MMLV or GALV and a second helper sequence contains a cDNA encoding the env protein.
  • the Env gene which determines the host range, may be derived from the genes encoding xenotropic, amphotropic, ecotropic, polytropic (mink focus forming) or 10A1 murine leukemia virus env proteins, or the Gibbon Ape Leukemia Virus (GALV env protein, the Human Immunodeficiency Virus env (gpl60) protein, the Vesicular Stomatitus Virus (VSV) G protein, the Human T cell leukemia (HTLV) type I and II env gene products, chimeric envelope gene derived from combinations of one or more of the aforementioned env genes or chimeric envelope genes encoding the cytoplasmic and transmembrane of the aforementioned env gene products and a monoclonal antibody directed against a specific surface molecule on a desired target cell.
  • GLV env protein Gibbon Ape Leukemia Virus
  • gpl60 Human Immunodeficiency Virus env
  • VSV Ves
  • the cells can be activated and expanded using generally known methods such as those described in U.S. Patent Nos. 6,352,694; 6,534,055; 6,905,680;
  • Stimulation with the antigen and/or MHC ex vivo can activate and expand the selected engineered T-cell receptor expressing cell subpopulation.
  • PhosflowTM activation kits Miltenyi Biotec MACSTM activation/expansion kits, and other commercially available cell kits specific to activation moieties of the relevant cell.
  • Particular subpopulations of immune cells may be activated or expanded through the use of beads or other agents available in such kits.
  • a-CD3/a-CD28 Dynabeads® may be used to activate and expand a population of isolated T-cells.
  • the polynucleotides, cells, vectors, populations, and modified cells of the present disclosure may be used to induce an anti-inflammatory response in a cell, tissue, or subject, mediate an immune response in a cell, tissue, or subject or mediate an inflammatory response in a cell tissue, or subject in vitro, ex vivo, or in vivo.
  • the polynucleotides, cells, vectors, populations, and modified cells of the present invention may be administered either alone or in combination with diluents, known anti-cancer therapeutics, and/or with other components such as cytokines or other cell populations that are immunostimulatory to a subject in need thereof.
  • the cell, tissue, or subject may be canine, equine, murine, rat, simian, feline, or human.
  • Method aspects of the present disclosure relate to methods for inducing an antiinflammatory response, mediating an immune response, or mediating an inflammatory response in a subject in need thereof, the method comprising, consisting of, or alternatively consisting essentially of administering to a subject in need thereof an effective amount of the polynucleotides, vectors, cells, modified cells, compositions, or populations disclosed herein.
  • the response is characterized by suppression of pathogenic T-cells.
  • the response is characterized by increased or decreased expression of one or more pro-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more pro-inflammatory cytokines comprise IL- ⁇ , T F-a, IFN- ⁇ , IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL-21, IL-23, IL-27, and/or TGF- ⁇ .
  • the one or more pro-inflammatory cytokines comprise IL- ⁇ , T F-a, IFN- ⁇ , IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL-21, IL-23, IL-27, and/or TGF- ⁇ .
  • the response is characterized by increased or decreased expression of one or more antiinflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more anti-inflammatory cytokines comprise TGF- ⁇ , IL-IRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL- 35, and/or INF-a.
  • the cell, modified cell, or population is autologous to the subject.
  • the subject may be canine, equine, murine, rat, simian, feline, or human.
  • Additional method aspects of the present disclosure relate to methods for enhancing the activity of a regulatory T-cell, the methods comprising, consisting of, or alternatively consisting essentially of administering an effective amount of the polynucleotides, vectors, cells, modified cells, compositions, or populations disclosed herein.
  • the enhanced activity of the regulatory T-cell is characterized by increased expression of IL-10.
  • the subject may be canine, equine, murine, rat, simian, feline, or human.
  • the present disclosure provides a prophylactic method of protecting a subject against an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage, the method comprising, consisting of, or alternatively consisting essentially of administering to a subject an effective amount of the polynucleotides, vectors, engineered T-cell receptors, cells, modified cells, compositions, or populations disclosed herein.
  • Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero- relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the method reduces the chance that a subject will experience an adverse symptom of the adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis. In some aspects, the method reduces the chance that a subject will develop adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis.
  • the subject is at high risk for developing an adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis.
  • the method comprises plaque regression.
  • the subject may be canine, equine, murine, rat, simian, feline, or human.
  • Engineered T- cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the adverse cardiovascular event or cardiovascular disease, disorder, or damage is from the group of: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
  • the method reduces the chance that a subject will experience an adverse symptom of the adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis.
  • the method comprises plaque regression.
  • the subject may be canine, equine, murine, rat, simian, feline, or human.
  • a method of treating a disease or condition involving an inflammatory response or related to inflammation in a subject in need thereof comprising, consisting of, or alternatively consisting essentially of administering to a subject in need thereof an effective amount of the polynucleotides, vectors, engineered T-cell receptors, cells, modified cells, compositions, or populations disclosed herein.
  • Engineered T- cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule.
  • the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
  • the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ⁇ , and/or IL-5 response.
  • the engineered T-cell receptor is a modified T-cell receptor.
  • the engineered T-cell receptor is a chimeric antigen receptor (CAR).
  • the extracellular antigen binding domain binds both the antigen and the MHC molecule.
  • the polynucleotide or vector encodes the engineered T cell receptor.
  • the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
  • the subject may be canine, equine, murine, rat, simian, feline, or human.
  • the cell, modified cell, or population for use in any of the herein disclosed methods is autologous to the subject being treated and/or to whom the cell, modified cell, or population is administered. In other aspects, the cell, modified cell, or population is allogenic to the subject.
  • the methods described herein further comprise a combination therapy comprising, consisting, or consisting essentially of administration of an effective amount of one or more therapeutic compounds.
  • a combination therapy comprising, consisting, or consisting essentially of administration of an effective amount of one or more therapeutic compounds.
  • these include, but are not limited to, the immunosuppressive or modulating therapies or treatments and therapies to ameliorate the symptoms of and/or treat cardiovascular disease.
  • immunosuppressive agents or therapies include anti-inflammatory drugs such as
  • immune modulating therapies or treatments include but are not limited to a calcineurin inhibitor, a chemokine receptor inhibitor, a glucocorticoid, an mTOR inhibitor, an anti-metabolic compound, a
  • cardiovascular disease include but are not limited to cholesterol medications such as statins, anti-platelet medications such as aspirin, angiotensin-converting enzyme inhibitors, calcium channel blockers, and diuretics.
  • the subject has been treated with one or more surgical interventions such as angioplasty, stent placement, endarterectomy, fibinolytic therapy, and/or bypass surgery.
  • the endogenous T-cells and/or other lymphocytes of the patient are depleted prior to administration of an effective amount of the polynucleotides, vectors, cells, modified cells, compositions, or populations disclosed herein.
  • Methods of the present disclosure may be practiced by any mode of administration or delivery, or by any route, systemic, regional and local administration or delivery.
  • Exemplary administration and delivery routes include intravenous (i.v.), intraperitoneal (i.p.), intrarterial, intramuscular, mucosal, inhalation, respiration, intranasal, intubation, parenteral,
  • compositions of the present invention may be administered in a manner appropriate to the disease, condition, or symptom to be treated or prevented.
  • the quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined by clinical trials.
  • ApoBlOO is an apolipoprotein of about 4500 amino acids long and has been shown to be a component involved in the development of atherosclerosis. ApoBlOO has previously been suggested as being an autoantigen relevant to atherosclerosis. Regions of this apolipoprotein that activate T-cells through TCRs to induce inflammatory responses in atherosclerosis were recently identified. 30 peptides that could potentially be used in human patients were identified and screened for binding to 26 HLA alleles by competition assay and peptides were found that bound HLA alleles at 10 nM or better (see Tables 2 and 3 below).
  • Atherosclerosis is an inflammation-related disease characterized by monocytes entering the subendothelial space of the aterrial wall where they differentiate into macrophages and foam cells (Lusis, Nature 407: 233 (2000); Glass & Witztum, Cell 104: 503 (2001); and Galkina & Ley, Annu. Rev. Immunol. 27: 165 (2009); Li & Glass, Nat. Med. 8: 1235 (2002)).
  • Foam cell formation is induced by oxidized low density lipoprotein (oxLDL) and leads to production of pro-inflammatory factors and plaque formation.
  • oxLDL oxidized low density lipoprotein
  • oxLDL-induced foam cell formation is promoted by scavenger receptors such as CD36 and SR-A, which allow uncontrolled accumulation of modified LDL cholesterol in foam cells (Libby et al., Am. J. Med. 104: 14S (1998); and Kunjathoor et al., J. Biol. Chem. 277: 49982 (2002)).
  • scavenger receptors such as CD36 and SR-A
  • Chimeric antigen receptors (CARs) and modified T-cell receptors offer two distinct approaches to alter immune cell specificity. The primary structural difference between these two receptors is based on their origin.
  • CARs are typically derived from the small chain variable fragments (scFv) of antibody molecules.
  • modified TCRs are typically derived from sequenced, disease-relevant T cell receptors.
  • CARs recognize surface bound antigens expressed by targeted cells without regard to MHC presentation, while modified TCRs recognize peptides presented by MHC molecules, similar to
  • modified TCRs that recognize cognate antigen-MHC complexes. Because modified TCRs bind to antigen-MHC complexes, they can be used to target both extracellular and
  • the adoptive cell therapy described herein relates to regulatory T-cells that are isolated from an atherosclerotic patient and transduced with factors that direct regulatory T- cell specificity to an ApoB peptide:MHC complex to maintain and promote regulatory T- cell function.
  • the cells are intravenously transfused back into the diseased patient or subject to provide a first in class therapy to slow and/or halt the progression of atherosclerosis.
  • T-cell epitopes directed toward disease-relevant antigens are identified (e.g., through epitope screen and next generation sequencing). Briefly, samples comprising peripheral blood mononuclear cells (PBMCs) are obtained from the venous blood of human subjects suffering from the disease or condition of interest (e.g., atherosclerosis). These samples are compared to control samples from healthy donors with no personal or family history of heart disease. The MHC haplotypes of the samples are identified by next-generation sequencing.
  • PBMCs peripheral blood mononuclear cells
  • Peptides comprising epitopes derived from autoantigen targets or other disease-relevant antigen targets are synthesized (e.g., fragments of ApoB 100).
  • the peptides are predicted to bind specific subtypes and/or alleles of MHC molecules, e.g., those identified to be associated with disease.
  • the PBMCs are stimulated with the synthesized peptides in culture for about two weeks or an appropriate period to measure response.
  • inflammatory cytokines e.g., IFNy or IL-5
  • Complexes of peptides with MHC molecules are chosen if the affinity of the binding of the peptide to the MHC is less than about 1000 nM or, in some embodiments, if the peptide elicits a cytokine response despite restriction to a particular MHC allele (e.g., binds promiscuously to a panel or several MHC alleles).
  • donors of the HLADRB 1 *0101 or HLADRB 1 *0701 genotype are specifically identified. Tetramers/dextramers can be used to identify and characterize ApoB specific CD4+ T cells and sort based on Treg, Thl and Thl7 markers.
  • TCR TCR construct
  • CAR transgenic TCR
  • the variable regions of the T-cell receptor that recognizes the peptide-MHC are sequenced.
  • peptide specific T-cells e.g., CD4+ T-cells
  • T-cells that produce inflammatory cytokines upon stimulation with peptide are selected and sequenced to determine the amino acid sequence of the variable regions of their T-cell receptor (TCR).
  • HLA:peptide mulitmers tetramers, dextramers
  • the TCR of the present invention may target one or more of the MHC alleles listed in Table 4.
  • scFv single-chain variable fragments
  • scFv is a fusion protein of the variable regions of immunoglobulin heavy and light chains, connected by linker peptide.
  • scFv can be created from subcloned heavy and light chains derived from a monoclonal antibody or hybridoma, or by phage display.
  • Peptide-MHC complexes identified in the epitope screen are selected for monoclonal antibody development or scFv development. For example, in atherosclerosis, the following combinations are targeted for development:
  • the selection criteria for optimal scFv or antibodies includes clones that produce soluble recombinant IgGl for in vitro blocking assays. If a suitable rodent model for a disease or condition exists, labeled recombinant IgG produced is tested to determine cellular localization and efficacy in high-multi-dose PoC experiments. Tetramers are developed for cell selection and purification. Once suitable a scFv is identified, the amino acid sequence is determined.
  • the vector can further comprise a FoxP3 transcription factor to promote and maintain Treg function.
  • the FoxP3 can be mutated to deactivate STUB1 or ubiquitin binding domains.
  • additional gain of function mutations can be included.
  • the vector can further comprise GFP or another detectable marker.
  • the FoxP3 can be fused to GFP or another detectable marker to allow screening for FoxP3 positive cells.
  • the vector can further comprise a selection marker, killing marker, and/or a suicide gene (e.g., caspase 9) to attenuate the life of a cell transduced with the vector.
  • a selection marker e.g., caspase 9
  • a suicide gene e.g., caspase 9
  • Such marker or gene can be inducible (e.g., rapamycin or doxycycline inducible).
  • the vector can comprise activation-inducible IL-10.
  • the vector is then introduced (e.g., via transduction, CRISPR, transfection) into enriched regulatory T-cells of a subject.
  • Methods of enriching regulatory T-cells are known in the art and described herein.
  • the vector is introduced into NK cells, CD4+ T-cells, CD8+ T-cells, regulatory memory T-cell, regulatory memory T-cells, central memory T-cell, naive T-cells, effector T-cells, or cytotoxic T-cells.
  • the expression of the engineered T-cell receptor is measured in the modified cells.
  • the cells are stimulated with the peptide-MHC to measure IL-10 production in vitro.
  • Cell plasticity is assayed in inflammatory cell culture conditions (e.g., in the presence of inflammatory cytokines and/or with co-expression of transcription factors). Suitable modified cells or populations of modified cells are expanded.
  • a mouse model is used to determine whether cells comprising the engineered T-cell receptor can modulate the immune response in an appropriate disease model.
  • such models may include apoE-/- model and the LDLR-/- (Getz, G. et al. Arterioscler Throm. Vase. Biol. 32(5): 1104-1115). These mice may be crossed with mice carrying humanized alleles of MHC molecules. Additional models in various species are known in the art (see, e.g., Camacho, P. et al. Am. J. Cardiovasc. Dis. 6(3): 70-80 (2016)).
  • the peptide-MHC affinity is measured for the model. If the affinity is within an acceptable range (up to 1,000 nM), an engineered T-cell receptor is developed as described above. The CD4+ T-cell responses are characterized and compared to those measured in the human subjects.
  • mice comprising the engineered T-cell receptor are crossed to mice with MHC alleles of interest.
  • CAR transgenic mice may be crossed to DRB1 *0101 and DRB1 *0701.
  • the CD4 T-cell responses are characterized and compared to those measured in the human cells.
  • T-regulatory cells comprising the engineered T- cells are administered to the mice via any appropriate method. Treatment parameters are measured including decreased expression of pro-inflammatory cytokines, increased expression of anti-inflammatory cytokines, suppression of cytotoxic cells, expansion in vivo of regulatory T-cells, reduced inflammation in tissue, and/or amelioration of disease-specific symptoms.
  • adoptive cell therapy is performed in humans or other mammals.
  • PBMC samples are obtained from healthy donors and patients with cardiovascular disease.
  • ApoBlOO peptides are synthesized with measured affinity to a panel of HLA class II alleles.
  • the peptides can optionally be modified.
  • An addition can be the covalent or non- covalent attachment of any type of molecule to the sequence. Specific examples of additions include glycosylation, acetylation, phosphorylation, amidation, formylation, ubiquitination, and derivatization by protecting/blocking groups and any of numerous chemical
  • the peptides are phosphorylated or MDA modified.
  • An epitope screen is performed in healthy and disease patients and their respective HLA restriction for positively scoring peptide epitopes is determined.
  • Patient-specific CAR or modified T-cells are generated and administered to the patients. The mode of
  • administering the modified cells will vary by condition and target tissue. Administration may occur by any suitable method described herein.
  • the success of the therapy is measured by a reduction in clinical symptoms of the disease or condition, decrease in inflammation, decrease in expression of pro-inflammatory cytokines, increased expression of antiinflammatory cytokines, reduction or suppression of cytotoxic T-cells, expansion of regulatory T-cells, reduction in the infiltration of B and T-cells into the target tissue, or arresting or suppressing the development of clinical symptoms.
  • success is also measured by regression of plaque formation or by any of the clinical endpoints described herein.
  • the words “comprising” (and any form of comprising, such as “comprise” and “comprises”), “having” (and any form of having, such as “have” and “has”), "including” (and any form of including, such as “includes” and “include”) or “containing” (and any form of containing, such as “contains” and “contain”) are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

Abstract

Novel engineered T-cell receptors including modified TCRs and CARs targeting athero-relevant antigen-MHCs are disclosed. Also provided are novel methods for treating diseases or conditions related to inflammation and atherosclerosis.

Description

ENGINEERED T-CELL RECEPTORS AND METHODS OF THEIR USE IN MODULATING INFLAMMATORY RESPONSES AND TREATING
ATHEROSCLEROSIS
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority under 35 U.S.C. § 119(e) to U.S. Provisional Application No. 62/522,663, filed June 20, 2017, the contents of which are hereby incorporated by reference in its entirety.
BACKGROUND
[0002] Advances in cell therapy, most notably in cancer immunotherapy, are now offering hope to patients and doctors alike, with treatments that may be truly cancer curative. Over the past decade, tremendous efforts and resources have poured into the development of Chimeric Antigen Receptor T-Cell Therapy (CAR-T) to engineer patient-derived immune cells to recognize tumor cells expressing certain target proteins or antigens. Advances the gene and cell engineering industries are making clinical and commercial manufacturing of cell therapies more routine and cost efficient. The promises of CAR-T are in part evidenced by the nearly 3,700 publications and more than 300 clinical trials presently ongoing in the United States alone. In addition to cancer, opportunities for other disease exist, especially where expression of specific antigens on cells is a contributory factor to the pathology of the disease. However, despite the significant growth and activity in cancer cell therapy, application of CAR-T approaches to other disease indications is comparatively under developed.
[0003] Loss of immune tolerance is a hallmark of autoimmune disorders, which is characterized by the immune system's inability to distinguish between "self and "non-self antigens. If the immune system develops an aberrant response against self antigens, effector cells can target healthy cells or tissues for destruction. A sustained immune response to self antigens can lead to chronic inflammatory injury to tissues, which may prove lethal. In contrast to cancer, the mechanism of action for autoimmune cell therapy is founded upon reduction of inflammatory responses by down regulating both CD8+ and CD4+ T cell activities with a unique subset of CD4+ T cells called regulatory T cells. Upon antigen recognition through the T Cell Receptor (TCR), regulatory T cells are well known to produce anti-inflammatory cytokines that reduce immune cell activation. [0004] Epitope discovery and immune profiling presents a fertile ground for discovery of new antigen targets for the development of cell therapies. Immune profiling of autoimmune disease patients has defined volumes of epitopes, antigens, and post-translational
modifications as the foci of autoimmune responses and work from researchers worldwide has shown that patients with autoimmune disease often have shared responses to specific antigens. However, the breadth of antigens and epitopes, diversity of antigen presentation by major histocompatibility complexes, and the variability of epitopes that actually elicit immune responses present hurdles towards the development of cell therapies.
[0005] Atherosclerosis is a pervasive human disease causing 31% of deaths worldwide. Often characterized as a silent killer, atherosclerosis of the cardiovascular arteries can trigger heart attacks from a process in which lipids, leukocytes, and other factors build up along the arterial lining to form deposits called plaques. Plaques can reduce blood flow to vital organs and tissues, and/or block arteries. If an artery becomes occluded or ruptured, this can lead to blood clots and death of affected tissues and organs. Inadequate removal of lipids lining the artery walls by specialized leukocytes (e.g., macrophages) contributes to plaque formation and growth.
[0006] The link between inflammation and atherosclerosis is well established. For example it is known that plaques prone to ruptures contain rich amounts of macrophages that have engulfed low-density lipoprotein ("LDL"). When accumulated in plaques, macrophages can become activated and differentiate, producing necrotic centers that encourage arterial occlusion. Propagation of the necrotic centers is further driven by macrophage interaction with specialized lymphocytes that have the potential to exacerbate the disease.
[0007] Safe and effective therapies for diseases or conditions that involve inflammation or an improper immune response, particularly in cardiovascular diseases, disorders, or damage such as atherosclerosis are needed. This disclosure satisfies this need and provides related advantages as well.
SUMMARY
[0008] This disclosure relates to novel polynucleotides, cells, compositions and methods of their use.
[0009] In one aspect, provided herein is a polynucleotide encoding an engineered T-cell receptor comprising, consisting of, or alternatively consisting essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the athero-relevant antigen is bound to the MHC molecule. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
[0010] Also provided herein is a polynucleotide encoding an engineered T-cell receptor comprising, consisting of, or alternatively consisting essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the athero-relevant antigen is bound to the MHC molecule. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
[0011] In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule.
[0012] Another aspect of the disclosure relates to a vector comprising the polynucleotide according to any of the embodiments disclosed herein, optionally operatively linked to a promoter. In further aspects, the vector further comprises an enhancer, a polynucleotide encoding FoxP3 optionally operatively linked to a promoter, a polynucleotide encoding IL-10 optionally operatively linked to a promoter, a suicide gene optionally operatively linked to a promoter, a ubiquitin binding domain, and/or STUB1 optionally operatively linked to a promoter. In some aspects, the vector is from the group of: a plasmid, a retroviral vector, a lentiviral vector, an adenoviral vector, or an adeno-associated viral vector. Also provided herein are the expression product(s) of the vector comprising the polynucleotide encoding an engineered T-cell receptor.
[0013] In one aspect, the disclosure relates to a cell comprising or expressing the polynucleotide or vector according to any one of the embodiments disclosed herein. In some aspects, the cell comprises two or more distinct polynucleotides or two or more distinct vectors according to the embodiments disclosed herein, and wherein the engineered T-cell receptors encoded by the two or more polynucleotides or two or more vectors bind distinct antigens. In some aspects, the cell is an isolated cell. In some aspects, the cell is a leukocyte, a T-cell, or an NK cell. In further aspects, the cell is a regulatory T-cell, a regulatory memory T-cell, a central memory T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell. Also provided herein is a cell comprising the expression product(s) of the polynucleotide or vector encoding an engineered T-cell receptor. In some aspects, the engineered T-cell receptor is expressed on the surface of the cell.
[0014] In one aspect, provided herein is a population of cells or modified cells according to any of the embodiments described herein. The population can be homogenous or
heterogenous for the cells experessing the polynucleotide or vector.
[0015] In some aspects, the disclosure provides a non-human animal comprising one or more of a polynucleotide, and/or vector, and/or cell, and/or a population of cells according to any of the embodiments described herein. In some aspects, the non-human animal comprises two or more polynucleotides, two or more vectors, two or more cells, or two or more populations of cells that encode distinct engineered T-cell receptors that bind distinct athero- relevant antigen targets.
[0016] Also provided herein is a composition comprising a carrier and one or more of: a polynucleotide, vector, engineered T cell receptor, cell, modified cell, or population comprising said cells or modified cells according to any of the embodiments described herein. Engineered T-cell receptors described herein may comprise, consist of, or
alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero- relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell.
[0017] In one aspect, the disclosure provides a kit comprising a composition according to any of the embodiments described herein and instructions for use.
[0018] Another aspect of the disclosure relates to a method of producing a modified cell, the method comprising: (i) introducing a polynucleotide or vector according to any of the embodiments described herein into a cell or a population of cells, and optionally culturing the cell or population of cells under conditions that favor expression the polynucleotide or vector; and (ii) optionally selecting a cell or enriching a cell or a subpopulation of cells that have been successfully modified with the polynucleotide or vector of step (i). In some aspects, step (i) comprises CRISPR mediated gene editing. In some aspects, the cell is a leukocyte, a T-cell, or an K cell. In further aspects, the cell is a regulatory T-cell, a regulatory memory T-cell, a central memory T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell. In some aspects, the method, further comprises inducing a regulatory T-cell phenotype in the cell or subpopulation of modified cells by inducing FoxP3 expression. In another aspect, the method further comprises introducing a polynucleotide encoding IL-10 and/or a suicide gene to the cell or subpopulation of modified cells. In some aspects, the method further comprises contacting the cell or subpopulation of modified cells with activation-induced soluble anti- ΠΤΝΓγ antibody and/or anti-IL-5 antibody. Also provided are the cells prepared by these methods, that are optionally isolated.
[0019] In some aspects, provided herein are one or more of: methods of inducing an antiinflammatory response in a cell or tissue, mediating an immune response in a cell or tissue, or mediating an inflammatory response in a cell or tissue, comprising administering an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some embodiments, the subject is murine, canine, feline, simian, equine, rat or human.
[0020] In another aspect, provided herein is one or more of: a method of inducing an antiinflammatory response, mediating an immune response, or mediating an inflammatory response in a subject in need thereof, comprising administering an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein. In some aspects, the response is characterized by suppression of pathogenic T-cells. In some aspects, the response is characterized by decreased expression of one or more pro-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more pro-inflammatory cytokines comprise IL-Ιβ, TNF-a, IFN-γ, IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL- 21, IL-23, IL-27, and/or TGF-β. In further aspects, the response is characterized by increased expression of one or more anti-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more anti-inflammatory cytokines comprise TGF- β, IL-lRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL-35, and/or INF-a. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T- cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some
embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some embodiments, the subject is murine, canine, feline, simian, equine, rat or human.
[0021] Also provided herein is a method of enhancing the activity of a regulatory T-cell or a memory regulatory T-cell, comprising administering an effective amount of of a
polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T- cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some
embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some aspects, the enhanced activity of the regulatory T-cell is characterized by increased expression of IL-10. In some embodiments, the administration is to a cell or tissue.
Administration to a cell or tissue may be in vivo, ex vivo, or in vitro. In some embodiments, the administration is to a subject. In some embodiments, the subject is murine, canine, feline, simian, or human.
[0022] In one aspect, provided herein is a method of protecting a subject against an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage, comprising administering to the subject an effective amount of an effective amount of a polynucleotide, engineered T-cell receptor, vector, cell, modified cell, population, or composition according to any of the embodiments described herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T- cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some embodiments, the subject is murine, canine, feline, simian, equine, rat or human.
[0023] In another aspect, provided herein is a method of treating an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage in a subject in need thereof comprising administering to the subject an effective amount of an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T- cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some
embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some embodiments, the subject is murine, canine, feline, simian, equine, rat or human. In some aspects, the adverse cardiovascular event or cardiovascular disease, disorder, or damage is from the group of: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma. In a preferred aspect, the the adverse cardiovascular event or cardiovascular disease, disorder, or damage comprises atherosclerosis.
[0024] Another aspect of this disclosure relates to a method of treating a disease or condition involving an inflammatory response or related to inflammation in a subject in need thereof, comprising administering to the subject an effective amount of a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, population, or composition according to any of the embodiments described herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T- cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some embodiments, the subject is murine, canine, feline, simian, equine, rat or human.
[0025] In some aspects, the cell, modified cell, or population is autologous to the subject being treated. In other aspects, the cell is allogenic to the subject. The cell can be from any appropriate species, e.g., mammalian, canine, feline, murine, rat, equine or human.
DETAILED DESCRIPTION
[0026] It is to be understood that the present disclosure is not limited to particular aspects described, as such may, of course, 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, since the scope of the present disclosure will be limited only by the appended claims.
[0027] Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this technology belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present technology, the preferred methods, devices and materials are now described. All technical and patent publications cited herein are incorporated herein by reference in their entirety. Nothing herein is to be construed as an admission that the present technology is not entitled to antedate such disclosure by virtue of prior invention.
[0028] The practice of the present technology will employ, unless otherwise indicated, conventional techniques of tissue culture, immunology, molecular biology, microbiology, cell biology, and recombinant DNA, which are within the skill of the art. See, e.g., Green and Sambrook eds. (2012) Molecular Cloning: A Laboratory Manual, 4 edition; the series Ausubel et al. eds. (2015) Current Protocols in Molecular Biology; the series Methods in Enzymology (Academic Press, Inc., N.Y.); MacPherson et al. (2015) PCR 1 : A Practical Approach (IRL Press at Oxford University Press); MacPherson et al. (1995) PCR 2: A Practical Approach; McPherson et al. (2006) PCR: The Basics (Garland Science); Harlow and Lane eds. (1999) Antibodies, A Laboratory Manual; Greenfield ed. (2014) Antibodies, A Laboratory Manual; Freshney (2010) Culture of Animal Cells: A Manual of Basic Technique, 6th edition; Gait ed. (1984) Oligonucleotide Synthesis; U.S. Pat. No. 4,683,195; Hames and Higgins eds. (1984) Nucleic Acid Hybridization; Anderson (1999) Nucleic Acid
Hybridization; Herdewijn ed. (2005) Oligonucleotide Synthesis: Methods and Applications; Hames and Higgins eds. (1984) Transcription and Translation; Buzdin and Lukyanov ed. (2007) Nucleic Acids Hybridization: Modern Applications; Immobilized Cells and Enzymes (IRL Press (1986)); Grandi ed. (2007) In Vitro Transcription and Translation Protocols, 2nd edition; Guisan ed. (2006) Immobilization of Enzymes and Cells; Perbal (1988) A Practical Guide to Molecular Cloning, 2nd edition; Miller and Calos eds, (1987) Gene Transfer Vectors for Mammalian Cells (Cold Spring Harbor Laboratory); Makrides ed. (2003) Gene Transfer and Expression in Mammalian Cells; Mayer and Walker eds. (1987) Immunochemical Methods in Cell and Molecular Biology (Academic Press, London); Lundblad and
Macdonald eds. (2010) Handbook of Biochemistry and Molecular Biology, 4th edition; and Herzenberg et al. eds (1996) Weir's Handbook of Experimental Immunology, 5th edition.
[0029] It must be noted that as used herein and in the appended claims, the singular forms "a", "an", and "the" include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to "a peptide" includes a plurality of peptides, including mixtures thereof. The term "at least one" intends one or more.
[0030] All numerical designations, e.g., pH, temperature, time, concentration, and molecular weight, including ranges, are approximations which are varied ( + ) or ( - ) by increments of 1.0 or 0.1, as appropriate, or alternatively by a variation of +/- 15 %, or alternatively 10%, or alternatively 5%, or alternatively 2%. It is to be understood, although not always explicitly stated, that all numerical designations are preceded by the term "about." It also is to be understood, although not always explicitly stated, that the reagents described herein are merely exemplary and that equivalents of such are known in the art.
[0031] It is to be inferred without explicit recitation and unless otherwise intended, that when the present technology relates to a polypeptide, protein, polynucleotide or antibody, an equivalent or a biologically equivalent of such is intended within the scope of the present technology.
[0032] Throughout this disclosure, various publications, patents and published patent specifications are referenced by an identifying citation. All publications, patent applications, patents, and other references mentioned herein are expressly incorporated by reference in their entirety, to the same extent as if each were incorporated by reference individually. In case of conflict, the present specification, including definitions, will control.
Definitions
[0033] As used herein, the term "4- IBB costimulatory signaling region" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the 4- IBB costimulatory signaling region sequence as shown herein. The example sequence of the 4-lBB costimulatory signaling region is provided in U.S. Pub. No. US20130266551A1. The sequence of the 4-lBB costimulatory signaling region associated disclosed in the U.S. Pub. No. US20130266551A1 is listed as follows:
KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL.
[0034] As used herein, the term "about" is used to indicate that a value includes the standard deviation of error for the device or method being employed to determine the value. The term "about" when used before a numerical designation, e.g., temperature, time, amount, and concentration, including range, indicates approximations which may vary by ( + ) or ( - ) 15%, 10%, 5%, 3%, 2%, or 1 %.
[0035] The term "adeno-associated virus" or "AAV" as used herein refers to a member of the class of viruses belonging to the genus dependoparvovirus, family Parvoviridae. Multiple serotypes of this virus are known to be suitable for gene delivery; all known serotypes can infect cells from various tissue types. At least 11 sequentially numbered, AAV serotypes are known in the art. Non-limiting exemplary serotypes useful in the methods disclosed herein include any of the 11 serotypes, e.g., AAV2, AAV8, AAV9, or variant serotypes, e.g., AAV- DJ. Nonlimiting exemplary AAV vectors are disclosed in U.S. Pub. Nos.
US20070036760A1, US20120137379A1, and US20130195801A1.
[0036] As used herein, the term "administer" and "administering" are used to mean introducing the therapeutic agent (e.g., polynucleotide, vector, cell, modified cell, population) into a subject. The therapeutic administration of this substance serves to attenuate any symptom, or prevent additional symptoms from arising. When administration is for the purposes of preventing or reducing the likelihood of developing an autoimmune disease or disorder, the substance is provided in advance of any visible or detectable symptom. Routes of administration include, but are not limited to, oral (such as a tablet, capsule or suspension), topical, transdermal, intranasal, vaginal, rectal, subcutaneous intravenous, intraarterial, intramuscular, intraosseous, intraperitoneal, epidural and intrathecal.
[0037] As used herein, the term "affinity" refers to the strength of the reversible
biomolecular interaction between two molecules. For example, in the context of an antigen and MHC molecule, affinity refers to the interaction between the MHC molecule (or the antigen binding domain (e.g., peptide binding cleft) of an MHC molecule) and an antigen, antigen fragment, peptide, or epitope. In the context of a TCR and an antigen, affinity refers to the interaction between the TCR's variable domain regions and an antigen or antigen- MHC complex. Affinity is determined by calculating the equilibrium dissociation constant (KD) using a known method (e.g., surface plasmon resonance or oblique incidence reflectivity difference (see Landry, J. P., Fei, Y. & Zhu, X. Simultaneous Measurement of 10,000 Protein-Ligand Affinity Constants Using Microarray-Based Kinetic Constant Assays. Assay Drug Dev. Tech. 10, 250-259 (2012))).
[0038] The antigen-MHC affinities reported herein reflect KD and were calculated according to the method disclosed in Sidney, J. et al. J. Immunol. 185: 4189-4198 (2010). Affinity and KD are inversely related - the smaller the KD value, the greater the binding affinity. As used herein, "high affinity" refers to a KD of less than or equal to 1000 nM. Antigens bound to MHC with intermediate high affinity exhibit a KD of between 10-100 nM. Antigens bound to MHC with very high affinity exhibit a KD of less than or equal to 10 nM.
[0039] As used herein, the term "animal" refers to living multi-cellular vertebrate organisms, a category that includes, for example, mammals and birds. The term "mammal" includes both human and non-human mammals.
[0040] As used herein, the term "antibody" ( or "Ab") collectively refers to
immunoglobulins (or "Ig") or immunoglobulin-like molecules including but not limited to antibodies of the following isotypes: IgM, IgA, IgD, IgE, IgG, and combinations thereof. Immunoglobulin-like molecules include but are not limited to similar molecules produced during an immune response in a vertebrate, for example, in mammals such as humans, rats, goats, rabbits and mice, as well as non-mammalian species, such as shark immunoglobulins (see Feige, M. et al. Proc. Nat. Ac. Sci. 41(22): 8155-60 (2014)). Unless specifically noted otherwise, the term "antibody" includes intact immunoglobulins and "antibody fragments" or "antigen binding fragments" that specifically bind to a molecule of interest (or a group of highly similar molecules of interest) to the substantial exclusion of binding to other molecules (for example, antibodies and antibody fragments that have a binding constant for the molecule of interest that is at least 103 M"1 greater, at least 104 M_1 greater or at least 105 M"1 greater than a binding constant for other molecules in a biological sample). The term "antibody" also includes genetically engineered forms such as chimeric antibodies (for example, humanized murine antibodies), heteroconjugate antibodies (such as, bispecific antibodies). See also, Pierce Catalog and Handbook, 1994-1995 (Pierce Chemical Co., Rockford, 111.); Kuby, J., Immunology, 3rd Ed., W.H. Freeman & Co., New York, 1997.
[0041] The general structure of an antibody is comprised of heavy (H) chains and light (L) chains connected by disulfide bonds. The structure can also comprise glycans attached at conserved amino acid residues. Each heavy and light chain contains a constant region and a variable region (also known as "domains"). There are two types of light chain, lambda (λ) and kappa (κ). There are five primary types of heavy chains which determine the isotype (or class) of an antibody molecule: gamma (γ), delta (δ), alpha (a), mu (μ) and epsilon (ε). The constant regions of the heavy chain also contribute to the effector function of the antibody molecule. Antibodies comprising the heavy chains μ, δ, γ3, γΐ, αΐ, γ2, γ4, ε, and α2 result in the following isotypes: IgM, IgD, IgG3, IgGl, IgAl, IgG2, IgG4, IgE, and IgA2,
respectively. An IgY isotype, related to mammalian IgG, is found in reptiles and birds. An IgW isotype, related to mammalian IgD, is found in cartilaginous fish. Class switching is the process by which the constant region of an immunoglobulin heavy chain is replaced with a different immunoglobulin heavy chain through recombination of the heavy chain locus of a B-cell to produce an antibody of a different isotype. Antibodies may exist as monomers (e.g., IgG), dimers (e.g., IgA), tetramers (e.g., fish IgM), pentamers (e.g., mammalian IgM), and/or in complexes with other molecules. In some embodiments, antibodies can be bound to the surface of a cell or secreted by a cell.
[0042] The variable regions of the immunoglobulin heavy and the light chains specifically bind the antigen. The "framework" region is a portion of the Fab that acts as a scaffold for three hypervariable regions called "complementarity-determining regions" (CDRs). A set of CDRs is known as a paratope. The framework regions of different light or heavy chains are relatively conserved within a species. The combined framework region of an antibody (comprising regions from both light and heavy chains), largely adopts a β-sheet conformation and the CDRs form loops which connect, and in some cases form part of, the β-sheet structure. Thus, framework regions act to position the CDRs in correct orientation by interchain, non-covalent interactions. The framework region and CDRs for numerous antibodies have been defined and are available in a database maintained online (Kabat et al., Sequences of Proteins of Immunological Interest, U.S. Department of Health and Human Services, 1991).
[0043] The CDRs of the variable regions of heavy and light chains (VH and VL) are responsible for binding to an epitope of an antigen. A limited number of amino acid positions within the CDRs are directly involved in antigen binding. These positions within the CDRs are called specificity determining residues (SDRs). The CDRs of a heavy or light chain are numbered sequentially starting from the N-terminal end (i.e. CDR1, CDR2, and CDR3). For example, a VL CDR3 is the middle CDR located in the variable domain of the light chain of an antibody. A VH CDRl is the first CDR in the variable domain of a heavy chain of an antibody. An antibody that binds a specific antigen will have specific VH and VL region sequences, and thus specific CDR sequences. Antibodies with different specificities (i.e. different combining sites for different antigens) have different CDRs.
[0044] An "antigen-binding fragment" (Fab) refers to the regions of an antibody
corresponding to two of the three fragments produced by papain digestion. The Fab fragment comprises the region that binds to an antigen and is composed of one variable region and one constant region from both a heavy chain and a light chain. An F(ab')2 fragment refers to a fragment of an antibody digested by pepsin or the enzyme IdeS (immunoglobulin degrading enzyme from S. pyogenes) comprising two Fab regions connected by disulfide bonds. A single chain variable fragment ("scFv") refers to a fusion protein comprising at least one VH and at least one VL region connected by a linker of between 5 to 30 amino acids. Methods and techniques of developing scFv that bind to specific antigens are known in the art (see, e.g., Ahmad, Z. A. et al., Clinical and Developmental Immunology, 2012: 980250 (2012)).
[0045] As used herein, the term "antigen" refers to a compound, composition, or substance that may be specifically bound and/or recognized by the products of specific humoral or cellular immunity and antigen recognition molecules, including but not limited to an antibody molecule, single-chain variable fragment (scFv), cell surface immunoglobulin receptor, B- cell receptor (BCR), T-cell receptor (TCR), engineered TCR, modified TCR, or CAR. The term "antigen" may also refer to an epitope of an antigen. The term "epitope" refers to an antigen or a fragment, peptide, region, site, or domain of an antigen that is recognized by an antigen recognition molecule. Antigens can be any type of molecule including but not limited to peptides, proteins, lipids, phospholipids haptens, simple intermediary metabolites, sugars (e.g., monosaccharides or oligosaccharides), hormones, and macromolecules such as complex carbohydrates (e.g., polysaccharides). Common categories of antigens include, but are not limited to microbial antigens such as viral antigens, bacterial antigens, fungal antigens, protozoa, and other parasitic antigens, antigens involved in autoimmune disease (including autoantigens), allergy, and graft rejection, tumor antigens, toxins, and other miscellaneous antigens. As used herein, the term "antigen binding domain" refers to any protein or polypeptide domain that can specifically bind to an antigen target (including target complexes of antigens and MHC molecules).
[0046] As used herein, the term "autologous," in reference to cells, tissue, and/or grafts refers to cells, tissue, and/or grafts that are isolated from and then and administered back into the same subject, patient, recipient, and/or host. "Allogeneic" refers to non-autologous cells, tissue, and/or grafts.
[0047] Atherosclerosis is a systemic disease characterized by narrowing of blood vessels due to the formation of atheromatous plaques or atheromata. Atheroma is the deposition of lipids and cholesterol within the inner wall of arteries that makes arterial lumen stenotic. The major clinical manifestations of atherosclerosis are angina, myocardial infarction , transient cerebral ischemic attacks, and strokes.
[0048] As used herein, the term "B cell," refers to a type of lymphocyte in the humoral immunity of the adaptive immune system. B cells principally function to make antibodies, serve as antigen presenting cells, release cytokines, and develop memory B cells after activation by antigen interaction. B cells are distinguished from other lymphocytes, such as T cells, by the presence of a B-cell receptor on the cell surface. B cells may either be isolated or obtained from a commercially available source. Non-limiting examples of commercially available B cell lines include lines AHH-1 (ATCC® CRL-8146™), BC-1 (ATCC® CRL- 2230™), BC-2 (ATCC® CRL-2231™), BC-3 (ATCC® CRL-2277™), CA46 (ATCC® CRL-1648™), DG-75 [D.G.-75] (ATCC® CRL-2625™), DS-1 (ATCC® CRL-11102™), EB-3 [EB3] (ATCC® CCL-85™), Z-138 (ATCC #CRL-3001), DB (ATCC CRL-2289), Toledo (ATCC CRL-2631), Pfiffer (ATCC CRL-2632), SR (ATCC CRL-2262), JM-1 (ATCC CRL-10421), NFS-5 C-l (ATCC CRL-1693); NFS-70 CIO (ATCC CRL-1694), FS-25 C-3 (ATCC CRL-1695), AND SUP-B15 (ATCC CRL-1929). Further examples include but are not limited to cell lines derived from anaplastic and large cell lymphomas, e.g., DEL, DL-40, FE-PD, JB6, Karpas 299, Ki-JK, Mac-2A Plyl, SR-786, SU-DHL-1, -2, - 4,-5,-6,-7,-8,-9,-10, and -16, DOHH-2, NU-DHL-1, U-937, Granda 519, USC-DHL-1, RL; Hodgkin's lymphomas, e.g., DEV, HD-70, HDLM-2, HD-MyZ, HKB-1, KM-H2, L 428, L 540, LI 236, SBH-1, SUP-HD1, SU/RH-HD-1. Non-limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection, or ATCC, (www.atcc.org/) and the German Collection of Microorganisms and Cell Cultures
(https://www.dsmz.de/).
[0049] The term "Cas9" refers to a CRISPR associated endonuclease referred to by this name. Non-limiting exemplary Cas9s include Staphylococcus aureus Cas9, nuclease dead Cas9, and orthologs and biological equivalents each thereof. Orthologs include but are not limited to Streptococcus pyogenes Cas9 ("spCas9"), Cas 9 from Streptococcus thermophiles, Legionella pneumophilia, Neisseria lactamica, Neisseria meningitides, Francisella novicida; and Cpfl (which performs cutting functions analogous to Cas9) from various bacterial species including Acidaminococcus spp. and Francisella novicida U112.
[0050] As used herein, the term "CD3 zeta signaling domain" or "CD3 " refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD3 zeta signaling domain sequence as shown herein. Non-limiting exemplary sequences of the CD3 zeta signaling domain are provided in U.S. Pub. No. US
2013/0266551A1. An example of a CD3 zeta signaling domain sequence is:
RVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQ EGLYNELQKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALP PR.
[0051] As used herein, the term "CD8 a hinge domain" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD8 a hinge domain sequence as shown herein. The example sequences of CD8 a hinge domain for human, mouse, and other species are provided in Pinto, R.D. et al. (2006) Vet. Immunol. Immunopathol. 110: 169-177. Non-limiting examples of such include: Human CD8 alpha hinge domain:
PAKPTTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIY, Mouse CD8 alpha hinge domain:
KVNSTTTKPVLRTPSPVHPTGTSQPQRPEDCRPRGSVKGTGLDFACDIY, and Cat CD 8 alpha hinge domain:
PVKPTTTPAPRPPTQAPITTSQRVSLRPGTCQPSAGSTVEASGLDLSCDIY.
[0052] As used herein, the term "CD8 a transmembrane domain" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD8 a transmembrane domain sequence as shown herein. The fragment sequences associated with the amino acid positions 183 to 203 of the human T-cell surface glycoprotein CD8 alpha chain (NCBI Reference Sequence: NP 001759.3), or the amino acid positions 197 to 217 of the mouse T-cell surface glycoprotein CD8 alpha chain (NCBI Reference
Sequence: NP 001074579.1), and the amino acid positionsl90 to 210 of the rat T-cell surface glycoprotein CD8 alpha chain(NCBI Reference Sequence: NP_ 113726.1) provide additional example sequences of the CD8 a transmembrane domain. The sequences associated with each of the listed NCBI are provided as follows: Human CD8 alpha transmembrane domain: IYIWAPLAGTCGVLLLSLVIT; Mouse CD 8 alpha transmembrane domain:
IWAPLAGICVALLLSLIITLI; Rat CD8 alpha transmembrane domain:
IWAPLAGICAVLLLSLVITLI.
[0053] As used herein, the term "CD28 costimulatory signaling region" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the CD28 costimulatory signaling region sequence shown herein. Exemplary CD28 costimulatory signaling domains are provided in U.S. Pat. No. 5,686,281; Geiger, T. L. et al., Blood 98: 2364-2371 (2001); Hombach, A. et al., J Immunol 167: 6123-6131 (2001); Maher, J. et al. Nat Biotechnol 20: 70-75 (2002); Haynes, N. M. et al., J Immunol 169: 5780-5786 (2002); Haynes, N. M. et al., Blood 100: 3155-3163 (2002). Non-limiting examples include residues 114-220 of the below CD28 Sequence: MLRLLLALNL FPSIQVTGNK
ILVKQSPMLV AYDNAVNLSC KYSYNLFSRE FRASLHKGLDSAVEVCVVYG NYSQQLQVYS KTGFNCDGKL GNESVTFYLQ NLYVNQTDIY FCKIEVMYPPPYLD EKSNG TIIHV G HL CPSPLFPGPS KPFWVLVVVG
GVLAC YSLLVTVAFIIFWVR SKRSRLLHSD YMNMTPRRPG PTRKHYQPYA PPRDFAAYRS, and equivalents thereof.
[0054] As used herein, the term "CD28 transmembrane domain" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, at least 90% sequence identity, or alternatively at least 95% sequence identity with the CD28 transmembrane domain sequence as shown herein. The fragment sequences associated with the GenBank Accession Nos: XM_006712862.2 and XM_009444056.1 provide additional, non-limiting, example sequences of the CD28 transmembrane domain. The sequences associated with each of the listed accession numbers are incorporated herein.
[0055] In the context of a nucleic acid or amino acid sequence, the term "chimeric" intends that the sequence contains is comprised of at least one substitutent unit (e.g., fragment, region, portion, domain, polynucleotide, or polypeptide) that is derived from, obtained or isolated from, or based upon other distinct physical or chemical entities. For example, a chimera of two or more different proteins may comprise the sequence of a variable region domain from an antibody fused to the transmembrane domain of a cell signaling molecule. In particular aspects, a "chimeric" sequence intends that the sequence is comprised of sequences from at least two distinct species (e.g., humanized antibodies).
[0056] The term "chimeric antigen receptor" (CAR), as used herein, refers to a fused protein comprising an extracellular domain capable of binding to an antigen, a
transmembrane domain derived from a polypeptide different from a polypeptide from which the extracellular domain is derived, and at least one intracellular domain. The "chimeric antigen receptor (CAR)" is also known as a "T-body", "chimeric receptor", or "chimeric immune receptor (CIR)." The "extracellular domain capable of binding to an antigen" means any oligopeptide or polypeptide that can bind to a certain antigen. The "intracellular domain" means any oligopeptide or polypeptide known to function as a domain that transmits a signal to cause activation or inhibition of a biological process in a cell. In certain embodiments, the intracellular domain may comprise, alternatively consist essentially of, or yet further comprise one or more costimulatory signaling domains in addition to the primary signaling domain. The "transmembrane domain" means any oligopeptide or polypeptide known to span the cell membrane and that can function to link the extracellular and signaling domains. A chimeric antigen receptor may optionally comprise a "hinge domain" which serves as a linker between the extracellular and transmembrane domains. Non-limiting exemplary polynucleotide sequences that encode for components of each domain are disclosed herein, e.g. : Hinge domain: IgGl heavy chain hinge sequence:
CTCGAGCCCAAATCTTGTGACAAAACTCACACATGCCCACCGTGCCCG;
Transmembrane domain: CD28 transmembrane region:
TTTTGGGTGCTGGTGGTGGTTGGTGGAGTCCTGGCTTGCTATAGCTTGCTAGTAA CAGTGGCCTTTATTATTTTCTGGGTG; Intracellular domain: 4-1BB co-stimulatory signaling region:
AAACGGGGCAGAAAGAAACTCCTGTATATATTCAAACAACCATTTATGAGACCA
GTACAAACTACTCAAGAGGAAGATGGCTGTAGCTGCCGATTTCCAGAAGAAGAA
GAAGGAGGATGTGAACTG; Intracellular domain: CD28 co-stimulatory signaling region:
AGGAGTAAGAGGAGCAGGCTCCTGCACAGTGACTACATGAACATGACTCCCCGC
CGCCCCGGGCCCACCCGCAAGCATTACCAGCCCTATGCCCCACCACGCGACTTCG
CAGCCTATCGCTCC; Intracellular domain: CD3 zeta signaling region:
AGAGTGAAGTTCAGCAGGAGCGCAGACGCCCCCGCGTACCAGCAGGGCCAGAA
CCAGCTCTATAACGAGCTCAATCTAGGACGAAGAGAGGAGTACGATGTTTTGGA
CAAGAGACGTGGCCGGGACCCTGAGATGGGGGGAAAGCCGAGAAGGAAGAACC
CTCAGGAAGGCCTGTACAATGAACTGCAGAAAGATAAGATGGCGGAGGCCTACA
GTGAGATTGGGATGAAAGGCGAGCGCCGGAGGGGCAAGGGGCACGATGGCCTTT
ACCAGGGTCTCAGTACAGCCACCAAGGACACCTACGACGCCCTTCACATGCAGG
CCCTGCCCCCTCGCTAA.
[0057] Further embodiments of each exemplary domain component include other proteins that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the proteins encoded by the above disclosed nucleic acid sequences. Further, non-limiting examples of such domains are provided herein.
[0058] A "composition" typically intends a combination of the active agent, e.g., an engineered T-cell receptor, a modified T-cell receptor, a chimeric antigen receptor, a cell comprising an engineered T-cell receptor, a CAR T cell or a CAR NK cell, an antibody, a compound or composition, and a naturally-occurring or non-naturally-occurring carrier, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like and include pharmaceutically acceptable carriers. Carriers also include pharmaceutical excipients and additives proteins, peptides, amino acids, lipids, and carbohydrates (e.g., sugars, including monosaccharides, di-, tri-, tetra-oligosaccharides, and oligosaccharides; derivatized sugars such as alditols, aldonic acids, esterified sugars and the like; and polysaccharides or sugar polymers), which can be present singly or in combination, comprising alone or in
combination 1-99.99% by weight or volume. Exemplary protein excipients include serum albumin such as human serum albumin (HSA), recombinant human albumin (rHA), gelatin, casein, and the like. Representative amino acid/antibody components, which can also function in a buffering capacity, include alanine, arginine, glycine, arginine, betaine, histidine, glutamic acid, aspartic acid, cysteine, lysine, leucine, isoleucine, valine, methionine, phenylalanine, aspartame, and the like. Carbohydrate excipients are also intended within the scope of this technology, examples of which include but are not limited to monosaccharides such as fructose, maltose, galactose, glucose, D-mannose, sorbose, and the like; disaccharides, such as lactose, sucrose, trehalose, cellobiose, and the like;
polysaccharides, such as raffinose, melezitose, maltodextrins, dextrans, starches, and the like; and alditols, such as mannitol, xylitol, maltitol, lactitol, xylitol sorbitol (glucitol) and myoinositol.
[0059] As used herein, the term "comprising" or "comprises" is intended to mean that the compositions and methods that include the recited elements, but not excluding others.
"Consisting essentially of when used to define compositions and methods, shall mean excluding other elements of any essential significance to the combination for the stated purpose. Thus, a composition consisting essentially of the elements as defined herein would not exclude other materials or steps that do not materially affect the basic and novel characteristic(s) of the claimed disclosure, such as compositions for treating or preventing multiple sclerosis. "Consisting of shall mean excluding more than trace elements of other ingredients and substantial method steps. Embodiments defined by each of these transition terms are within the scope of this disclosure.
[0060] The term "consensus sequence" as used herein refers to an amino acid or nucleic acid sequence that is determined by aligning a series of multiple sequences and that defines an idealized sequence that represents the predominant choice of amino acid or base at each corresponding position of the multiple sequences. Depending on the sequences of the series of multiple sequences, the consensus sequence for the series can differ from each of the sequences by zero, one, a few, or more substitutions. Also, depending on the sequences of the series of multiple sequences, more than one consensus sequence may be determined for the series. The generation of consensus sequences has been subjected to intensive mathematical analysis. Various software programs can be used to determine a consensus sequence.
[0061] As used herein, the term "CRISPR" refers to a technique of sequence specific genetic manipulation relying on the clustered regularly interspaced short palindromic repeats pathway. CRISPR can be used to perform gene editing and/or gene regulation, as well as to simply target proteins to a specific genomic location. "Gene editing" refers to a type of genetic engineering in which the nucleotide sequence of a target polynucleotide is changed through introduction of deletions, insertions, single stranded or double stranded breaks, or base substitutions to the polynucleotide sequence. In some aspects, CRISPR-mediated gene editing utilizes the pathways of nonhomologous end-joining ( HEJ) or homologous recombination to perform the edits. Gene regulation refers to increasing or decreasing the production of specific gene products such as protein or RNA.
[0062] A "cytotoxic cell" intends a cell that is capable of killing other cells or microbes. Examples of cytotoxic cells include but are not limited to CD8+ T cells, natural-killer (NK) cells, NKT cells, and neutrophils, which cells are capable of mediating cytotoxicity responses.
[0063] As used herein, the term "detectable marker" refers to at least one marker capable of directly or indirectly, producing a detectable signal. A non-exhaustive list of this marker includes enzymes which produce a detectable signal, for example by colorimetry,
fluorescence, luminescence, such as horseradish peroxidase, alkaline phosphatase, β- galactosidase, glucose-6-phosphate dehydrogenase, chromophores such as fluorescent, luminescent dyes, groups with electron density detected by electron microscopy or by their electrical property such as conductivity, amperometry, voltammetry, impedance, detectable groups, for example whose molecules are of sufficient size to induce detectable modifications in their physical and/or chemical properties, such detection may be accomplished by optical methods such as diffraction, surface plasmon resonance, surface variation, the contact angle change or physical methods such as atomic force spectroscopy, tunnel effect, or radioactive molecules such as 32P, 35S or 125I.
[0064] As used herein, "disease-relevant antigen" refers to an antigen, epitope, or fragment thereof involved in the disease process or mechanism. For example, an inflammation- relevant antigen is an antigen or fragment thereof that, when presented, produces an immune response. An inflammation-relevant antigen producing such an effect is selected to treat the inflammation. Similarly, an autoimmunity-related antigen is an antigen that is relevant to an autoimmune disease and would not be selected for the treatment of a disorder or disease other than autoimmunity, e.g., cancer. Non-limiting, exemplary disease-relevant antigens are disclosed herein and further, such antigens may be determined for a particular disease based on the epitope screening techniques, mechanisms, and methods described herein. As used herein, the term "athero-relevant antigen" refers to a disease-relevant antigen that is relevant to the etiology of an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage. The adverse cardiovascular event or cardiovascular disease, disorder, or damage includes but is not limited to coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma. For example, as disclosed herein, ApoBlOO is an athero-relevant antigen involved in atherosclerosis. Additional athero- relevant antigens include but are not limited to heat shock proteins (Xu, Q. et al. Am. J.
Physiol. Heart Circ. Physiol. 302, H506-H514 (2012)), endothelial cells (ECs) (Narshi, C. et al. Lupus 20, 5-13 (2011) ), p2-glycoprotein I (Denas, G. et al. Autoimmun. Rev. 14, 214- 222 (2015); Hollan, I. et al. Autoimmun. Rev. 12, 1004-1015 (2013) ), and apolipoprotein A- I (Teizeira, P. et al. Clin. Dev. Immunol. 2012, 868251 (2012)).
[0065] An "an effective amount" or "efficacious amount" is an amount sufficient to achieve the intended purpose, non-limiting examples of such include: initiation of the immune response, modulation of the immune response, suppression of an inflammatory response and modulation of T cell activity or T cell populations. In one aspect, the effective amount is one that functions to achieve a stated therapeutic purpose, e.g., a therapeutically effective amount. As described herein in detail, the effective amount, or dosage, depends on the purpose and the composition, and can be determined according to the present disclosure.
[0066] The term "encode" as it is applied to nucleic acid sequences refers to a polynucleotide which is said to "encode" an RNA or polypeptide if, in its native state or when manipulated by methods well known to those skilled in the art, the nucleic acid can be transcribed and/or translated to produce a functional RNA (e.g., miRNA, siRNA, RNAi, tRNA, rRNA, snRNA, etc), an mRNA, or a polypeptide and/or a fragment thereof. The antisense strand is the complement of such a nucleic acid, and the encoding sequence can be deduced therefrom.
[0067] As used herein, the term "engineered T-cell receptor" refers to a molecule comprising the elements of (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain. In some aspects, an engineered T-cell receptor is a genetically modified TCR, a modified TCR, a recombinant TCR, a transgenic TCR, a partial TCR, a chimeric fusion protein, a CAR, a first generation CAR, a second generation CAR, a third generation CAR, or a fourth generation TRUCK. In some aspects, the engineered T-cell receptor comprises an antibody or a fragment of an antibody. In preferred aspects, the engineered T-cell receptor is a genetically modified TCR or a CAR.
[0068] As used herein, the term "enhancer," as used herein, denotes regulatory sequence elements that augment, improve or ameliorate transcription of a nucleic acid sequence irrespective of its location and orientation in relation to the nucleic acid sequence to be expressed. An enhancer may enhance transcription from a single promoter or simultaneously from more than one promoter. As long as this functionality of improving transcription is retained or substantially retained (e.g., at least 70%, at least 80%, at least 90% or at least 95% of wild-type activity, that is, activity of a full-length sequence), any truncated, mutated or otherwise modified variants of a wild-type enhancer sequence are also within the above definition.
[0069] In one aspect, the term "equivalent" or "biological equivalent" of an antigen binding domain means the domain to selectively bind its epitope protein or fragment thereof as measured by ELISA or other suitable methods. Biologically equivalent antigen binding domains include, but are not limited to, those antibodies, peptides, antibody fragments, antibody variant, antibody derivative and antibody mimetics that bind to the same epitope as the reference antibody. It is to be inferred without explicit recitation and unless otherwise intended, that when the present disclosure relates to a polypeptide, protein, peptide polynucleotide or antibody, an equivalent or a biologically equivalent of such is intended within the scope of this disclosure. As used herein, the term "biological equivalent thereof is intended to be synonymous with "equivalent thereof when referring to a reference protein, antibody, polypeptide or nucleic acid, intends those having minimal homology while still maintaining desired structure or functionality. Unless specifically recited herein, it is contemplated that any polynucleotide, polypeptide or protein mentioned herein also includes equivalents thereof. For example, an equivalent intends at least about 70% homology or identity, or at least 80 % homology or identity and alternatively, or at least about 85 %, or alternatively at least about 90 %, or alternatively at least about 95 %, or alternatively 98 % percent homology or identity and exhibits substantially equivalent biological activity to the reference protein, polypeptide or nucleic acid. Alternatively, when referring to polynucleotides, an equivalent thereof is a polynucleotide that hybridizes under stringent conditions to the reference polynucleotide or its complement. As used herein in the context of an antigen, epitope, or peptide sequence, the term "equivalent" also includes but is not limited to a sub-sequence, portion, homologue, variant or derivative thereof.
[0070] As used herein, the term "expression" refers to the process by which
polynucleotides are transcribed into mRNA and/or the process by which the transcribed mRNA is subsequently being translated into peptides, polypeptides, or proteins. If the polynucleotide is derived from genomic DNA, expression may include splicing of the mRNA in a eukaryotic cell. The expression level of a gene may be determined by measuring the amount of mRNA or protein in a cell or tissue sample. In one aspect, the expression level of a gene from one sample may be directly compared to the expression level of that gene from a control or reference sample. In another aspect, the expression level of a gene from one sample may be directly compared to the expression level of that gene from the same sample following administration of a compound.
[0071] As used herein, a "first generation CAR" refers to a CAR comprising an
extracellular domain capable of binding to an antigen, a transmembrane domain derived from a polypeptide different from a polypeptide from which the extracellular domain is derived, and at least one intracellular domain. A "second generation CAR" refers to a first generation CAR further comprising one costimulation domain (e.g., 4-1BB or CD28). A "third generation CAR" refers to a first generation CAR further comprising two costimulation domains (e.g., CD27, CD28, ICOS, 4-1BB, or OX40). A "fourth generation CAR" (also known as a "TRUCK") refers to a CAR T-cell further engineered to secrete an additional factor (e.g., proinflammatory cytokine IL-12). A review of these CAR technologies and cell therapy is found in Maus, M. et al. Clin. Cancer Res. 22(3): 1875-84 (2016).
[0072] The term "gRNA" or "guide RNA" as used herein refers to guide RNA sequences used to target specific polynucleotide sequences for gene editing employing the CRISPR technique. Techniques of designing gRNAs and donor therapeutic polynucleotides for target specificity are well known in the art. For example, Doench, J., et al. Nature biotechnology 2014; 32(12): 1262-7, Mohr, S. et al. (2016) FEBS Journal 283 : 3232-38, and Graham, D., et al. Genome Biol. 2015; 16: 260. gRNA comprises or alternatively consists essentially of, or yet further consists of a fusion polynucleotide comprising CRISPR RNA (crRNA) and trans- activating CRIPSPR RNA (tracrRNA); or a polynucleotide comprising CRISPR RNA (crRNA) and trans-activating CRIPSPR RNA (tracrRNA). In some aspects, a gRNA is synthetic (Kelley, M. et al. (2016) J of Biotechnology 233 (2016) 74-83).
[0073] As used herein, the term "HLA-A" refers to an MHC class I cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-A variant, including but not limited to any one of its several variants, including but not limited to HLA-A serotypes Al to A69. In humans, the gene locus of HLA-A is located at chromosome 6p21.3 (mRNA:
M_001242758, M_002116). HLA-A is a heterodimer composed of an a chain (encoded by the HLA-A gene) and a β chain. The β chain ("β2 microglobulin") is encoded by the B2M gene located at chromosome 15:44.71-44.72 in humans and chromosome 2: 122.15 in mice (mRNA: NM_004048). Examples of the HLA-A sequences are known in the art and a non- limited example is HLA-A*03 :01 :0:01 precursor:
MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQ FVRFDSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQ SEAGSHTIQFMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQIT KRKWEAAHEAEQLRAYLDGTCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHE ATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEE QRYTCHVQHEGLPKPLTLRWELSSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRK SSDRKGGSYTQAASSDSAQGSDVSLTACKV. The sequences associated with each of the above listed GenBank Accession Nos. are herein incorporated by reference. Several HLA-A serotypes and/or alleles are known in the art to be associated with disease including but not limited to Al (type I diabetes), A2 (spontaneous abortion), A3 (hemochromatosis, myasthenia gravis, and multiple sclerosis), Al 1 (papilloma virus susceptibility), A24
(ankylosing spondylitis, type I diabetes, and myasthenia gravis), A26 (adult T-cell leukemia), A30 (myasthenia gravis), and A68 (adult T-cell leukemia). HLA-A2 is associated with HLA graft compatibility (e.g., HLA-A*02:01 to HLA-A*02:426).
[0074] As used herein, the term "HLA-B" refers to an MHC class I cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-B variant, including but not limited to any one of its several variants, including but not limited to HLA-B serotypes Bl to B83. In humans, the gene locus of HLA-B is located at chromosome 6:31.35-36 (mRNA: M 005514). HLA-B is a heterodimer composed of an a chain (encoded by the HLA-B gene) and a β chain. The β chain ("β2 microglobulin") is encoded by the B2M gene located at chromosome 15:44.71-44.72 in humans and chromosome 2: 122.15 in mice (mRNA:
NM 004048). Examples of the HLA-B sequences are known in the art and a non-limited example of an HLA-B protein sequence is provided:
MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEP RFISVGYVDDTQFVRFDSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRES LR
NLRGY YNQ SEAGSHTLQ SM YGCD VGPDGRLLRGHDQ YAYDGKD YIALNEDLRS WT AA
DTAAQITQRKWEAAREAEQRRAYLEGECVEWLRRYLENGKDKLERADPPKTHVTH HPI
SDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRTFQKWAAVVV PSG
EEQRYTCH VQHEGLPKPLTLRWEP S S Q S T VPI VGI V AGL A VL A V V VIGA V V A A VMCR R KSSGGKGGSYSQAACSDSAQGSDVSLTA. The sequences associated with each of the above listed GenBank Accession Nos. are herein incorporated by reference.
Several HLA-B serotypes and/or alleles are known in the art to be associated with disease. For example, B27 is associated with ankylosing spondylitis, inflammatory joint diseases, psoriasis, inflammatory bowel disorders, reactive arthritis. HLA-B is also associated with HLA graft compatibility (e.g., HLA-A*02:01 to HLA-A*02:426).
[0075] As used herein, the term "HLA-C" refers to an MHC class I cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-C variant, including but not limited to any one of its several variants, including but not limited to HLA-C serotypes Cwl to Cwl 1 and C12 to C18. In humans, the gene locus of HLA-C is located at chromosome 6:31.21 (mRNA: NM_002117, NM_001243042). HLA-C is a heterodimer composed of an a chain (encoded by the HLA-C gene) and a β chain. The β chain ("β2 microglobulin") is encoded by the B2M gene located at chromosome 15:44.71-44.72 in humans and
chromosome 2: 122.15 in mice (mRNA: NM_004048). Examples of HLA-C sequences are known in the art and a non-limited example is HLA-Cw-1 precursor: MRVMAPRALL LLLSGGLALT ETWACSHSMR YFDTAVSRPG RGEPRFISVG YVDDTQFVRF DSDAASPRGE PRAPWVEQEG PEYWDRETQK YKRQAQADRV SLRNLRGYYN QSEDGSHTLQ RMSGCDLGPD GRLLRGYDQS AYDGKDYIAL EDLRSWTAA DTAAQITQRK LEAARAAEQL RAYLEGTCVE WLRRYLENGK ETLQRAEPPK THVTHHPLSD HEATLRCWAL GFYPAEITLT WQRDGEDQTQ DTELVETRPA GDGTFQKWAA VVVPSGQEQR YTCHMQHEGL QEPLTLSWEP SSQPTTPFMG IVAGLAVLVV LAVLGAVVTA MMCRRKSSGG KGGSCSQAAC SNSAQGSDES LITCKA. The sequences associated with each of the above listed GenBank Accession Nos. are herein incorporated by reference. Several HLA-C serotypes and/or alleles are known in the art to be associated with disease including but not limited to Cwl (multinodular goiters) and C* 16 (chronic B-cell lymphocytic leukemia). HLA-C is associated with HLA graft compatibility.
[0076] As used herein, the term "HLA-DP" refers to an MHC class II cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any HLA-DP variant, including but not limited to any one of its several variants, including but not limited to HLA-DP serotypes Al and Bl and HLA-DP alleles Al *01 to Al *04 and Bl *01 to Bl * l l . In humans, the gene locus of HLA-DP is located at chromosome 6p21.31 (mRNA: M 002117,
M 001243042). HLA-DP is a heterodimer composed of an a chain (encoded by the HLA- DPA1 gene) and a β chain (encoded by the HLA-DPBl gene). Examples of HLA-DP sequences are known in the art. A non-limited example of HLA-DPA1 is:
RPEDRMFHIRAVILRALSLAFLLSLRGAGAIKADHVSTYAAFV
QTHRPTGEFMFEFDEDEMFYVDLDKKETVWHLEEFGQAFSFEAQGGLANIAILNNNL N
TLIQRS HTQATNDPPEVTVFPKEPVELGQPNTLICHIDKFFPPVLNVTWLCNGELVT EGVAESLFLPRTDYSFHKFHYLTFVPSAEDFYDCRVEHWGLDQPLLKHWEAQEPIQ MP ETTETVLCALGLVLGLVGIIVGTVLIIKSLRSGHDPRAQGTL. A non- limited example of HLA-DPBl is: MMVLQVSAAP RTVALTALLM VLLTSVVQGR ATPENYLFQG RQECYAFNGT QRFLERYIYN REEFARFDSD VGEFRAVTEL GRPAAEYWNS QKDILEEKRA VPDRMCRHNY ELGGPMTLQR RVQPRVNVSP SKKGPLQHHN LLVCHVTDFY PGSIQVRWFL NGQEETAGVV STNLIRNGDW TFQILVMLEM TPQQGDVYTC QVEHTSLDSP VTVEWKAQSD SARSKTLTGA GGFVLGLIIC GVGIFMHRRS KKVQRGSA. The sequences associated with each of the above listed GenBank Accession Nos. are herein incorporated by reference.
[0077] As used herein, the term "HLA-DR" (refers to an MHC class II cell surface receptor associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, or alternatively at least 95% sequence identity with any ULA-DR variant, including but not limited to any one of its several variants, including but not limited to HLA-DR serotypes DR1 to DR 75 comprising a combination of ULA-DRA and ULA-DRB haplotypes.
Examples of the HLA-DR sequences are known in the art and non-limited examples of such are disclosed in Rose, L.M. et al. (1996) Cancer Immunol. Immunother. 43 :26-30: HLA- DRB1 * 1001 [DR10]:
GDTRPRFLEEVKFECHFFNGTERVRLLERRVHNQEEYARYDSDVGEYRAVTELGRP DAEYWNSQKDLLERRRAAVDTYCRHNYGVGESFTVQRRVQPKVTVYPSKTQPLQH HNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPQS GEVYTCQVEHPSVMSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRN QKGHSGLPPTGFLS; HLA-DRB3*0201 [DR52]:
GDTRPRFLELLKSECHFFNGTERVRFLERHFHNQEEYARFDSDVGEYRAVFELGRPD AEYWNSQKDLLEQKRGQVDNYCRHNYGVVESFTVQRRVHPQVTVYPAKTQPLQH HNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETFPRSG EVYTCQVEHPSVTSPLTVEWSARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQK GHSGLQPTGFLS; HLA-DRB1 *0301 [DR17 (3)]:
GDTRPRFLEYSTSECHFFNGTERVRYLDRYFHNQEENVRFDSDVGEFRAVTELGRPD AEYWNSQKDLLEQKRGRVDNYCRHNYGVVESFTVQRRVHPKVTVYPSKTQPLQHH LLVCSVSGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGE VYTCQVEHPSVTSPLTVEWRARSESAQSKMLSGVGGFVLGLLFLGAGLFIYFRNQKG HSGLQPRGFLS, as well as equivalents of each thereof. Rose et al. also discloses an exemplary epitope to which an HLA-DR specific antibody may bind and therefore can serve as an immunogen for the generation of additional antibodies, monoclonal antibodies and antigen binding fragments of each thereof. The sequences associated with each of the listed reference(s) and GenBank Accession Numbers that correspond to the name HLA-DR or its equivalents including but not limited to the specified HLA-DR subtypes are herein incorporated by reference as additional non-limiting examples. [0078] As used herein, the term "HLA-G" (also known as "MHC-G") refers to a specific molecule associated with this name and any other molecules that have analogous biological function that share at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with HLA-G, including but not limited to any one of its several isoforms, including by not limited to membrane-bound isoforms (e.g., HLA-G 1, HLA-G2, HLA-G3, HLA-G4), soluble isoforms (e.g., HLA-G5, HLA-G6, HLA-G7) , and soluble forms generated by proteolytic cleavage of membrane- bound isoforms (e.g., sHLA-Gl). HLA-G is a nonclassical MHC class I paralogue consisting of a heterodimer of a heavy chain and a β2 microglobulin. The genetic locus for HLA-G is found at chromosome 6:29.83 in humans and at chromosome 17:37.27 in mice. Examples of the HLA-G sequence are provided herein. In addition, the mRNA sequences associated with GenBan Accession Nos. are exemplary: NM_002127.5 XM_006715080.1 XM 006725041.1 XM_006725700.1 XM 006725909.1. An example of the protein translation of M_002127.5 is:
MVVMAPRTLFLLLSGALTLTETWAGSHSMRYFSAAVSRPGRGEPRFIAMGYVDDTQ F VRFD SD S ACPRMEPRAPW VEQEGPEYWEEETRNTKAHAQTDRMNLQTLRGYYNQ SEASSHTLQWMIGCDLGSDGRLLRGYEQYAYDGKDYLAL EDLRSWTAADTAAQIS KRKCEAANVAEQRRAYLEGTCVEWLHRYLENGKEMLQRADPPKTHVTHHPVFDYE ATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAGDGTFQKWAAVVVPSGEE QRYTCHVQHEGLPEPLMLRWKQ S SLPTIPF GIVAGL VVL AAVVTGAAVAAVLWRK KSSD. The sequences associated with each of the above listed GenBank Accession Nos. are herein incorporated by reference. HLA-G is known to be associated with immune tolerance in pregnancy.
[0079] As used herein, "homology" or "identical", percent "identity" or "similarity", when used in the context of two or more nucleic acids or polypeptide sequences, refers to two or more sequences or subsequences that are the same or have a specified percentage of nucleotides or amino acid residues that are the same, e.g., at least 60% identity, preferably at least 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or higher identity over a specified region (e.g., nucleotide sequence encoding an antibody described herein or amino acid sequence of an antibody described herein). Homology can be determined by comparing a position in each sequence which may be aligned for purposes of comparison. When a position in the compared sequence is occupied by the same base or amino acid, then the molecules are homologous at that position. A degree of homology between sequences is a function of the number of matching or homologous positions shared by the sequences. The alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in Current Protocols in Molecular Biology (Ausubel et al., eds. 1987) Supplement 30, section 7.7.18, Table 7.7.1. Preferably, default parameters are used for alignment. A preferred alignment program is BLAST, using default parameters. In particular, preferred programs are BLASTN and BLASTP, using the following default parameters: Genetic code = standard; filter = none; strand = both; cutoff = 60; expect = 10; Matrix = BLOSUM62; Descriptions = 50 sequences; sort by = HIGH SCORE; Databases = non-redundant, GenBank + EMBL + DDBJ + PDB + GenBank CDS translations + SwissProtein + SPupdate + PIR. Details of these programs can be found at the following Internet address: ncbi.nlm.nih.gov/cgi-bin/BLAST. The terms "homology" or "identical", percent "identity" or "similarity" also refer to, or can be applied to, the complement of a test sequence. The terms also include sequences that have deletions and/or additions, as well as those that have substitutions. As described herein, the preferred algorithms can account for gaps and the like. Preferably, identity exists over a region that is at least about 25 amino acids or nucleotides in length, or more preferably over a region that is at least 50-100 amino acids or nucleotides in length. An "unrelated" or "non-homologous" sequence shares less than 40% identity, or alternatively less than 25% identity, with one of the sequences disclosed herein.
[0080] "Hybridization" refers to a reaction in which one or more polynucleotides react to form a complex that is stabilized via hydrogen bonding between the bases of the nucleotide residues. The hydrogen bonding may occur by Watson-Crick base pairing, Hoogstein binding, or in any other sequence-specific manner. The complex may comprise two strands forming a duplex structure, three or more strands forming a multi- stranded complex, a single self-hybridizing strand, or any combination of these. A hybridization reaction may constitute a step in a more extensive process, such as the initiation of a PCR reaction, or the enzymatic cleavage of a polynucleotide by a ribozyme.
[0081] Examples of stringent hybridization conditions include: incubation temperatures of about 25°C to about 37°C; hybridization buffer concentrations of about 6x SSC to about lOx SSC; formamide concentrations of about 0% to about 25%; and wash solutions from about 4x SSC to about 8x SSC. Examples of moderate hybridization conditions include: incubation temperatures of about 40°C to about 50°C; buffer concentrations of about 9x SSC to about 2x SSC; formamide concentrations of about 30% to about 50%; and wash solutions of about 5x SSC to about 2x SSC. Examples of high stringency conditions include: incubation temperatures of about 55°C to about 68°C; buffer concentrations of about lx SSC to about O. lx SSC; formamide concentrations of about 55% to about 75%; and wash solutions of about lx SSC, O. lx SSC, or deionized water. In general, hybridization incubation times are from 5 minutes to 24 hours, with 1, 2, or more washing steps, and wash incubation times are about 1, 2, or 15 minutes. SSC is 0.15 M NaCl and 15 mM citrate buffer. It is understood that equivalents of SSC using other buffer systems can be employed.
[0082] As used herein, the term "ICOS costimulatory signaling region" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, preferably 90% sequence identity, more preferably at least 95% sequence identity with the ICOS costimulatory signaling region sequence as shown herein. Non-limiting example sequences of the ICOS costimulatory signaling region are provided in U.S.
Publication 2015/0017141A1 the following exemplary polynucleotide sequence:
ACAAAAAAGA AGTATTCATC CAGTGTGCAC GACCCTAACG GTGAATACAT GTTCATGAGA GCAGTGAACA CAGCCAAAAA ATCCAGACTC ACAGATGTGA CCCTA.
[0083] As used herein, the phrase "immune response" or its equivalent "immunological response" refers to the development of a cell-mediated response (e.g., mediated by antigen- specific T cells or their secretion products). A cellular immune response is elicited by the presentation of polypeptide epitopes in association with Class I or Class II MHC molecules, to treat or prevent a viral infection, expand antigen-specific Breg cells, TCI, CD4+ T helper cells and/or CD8+ cytotoxic T cells and/or disease generated, autoregulatory T cell and B cell "memory" cells. The response may also involve activation of other components. In some aspects, the term "immune response" may be used to encompass the formation of a regulatory network of immune cells. Thus, the term "regulatory network formation" may refer to an immune response elicited such that an immune cell, preferably a T cell, more preferably a T regulatory cell, triggers further differentiation of other immune cells, such as but not limited to, B cells or antigen-presenting cells - non limiting examples of which include dendritic cells, monocytes, and macrophages. In certain embodiments, regulatory network formation involves B cells being differentiated into regulatory B cells; in certain embodiments, regulatory network formation involves the formation of tolerogenic antigen-presenting cells. [0084] "Immune cells" include all cells that are produced by hematopoietic stem cells (HSC) including, but not limited to, HSCs, white blood cells (leukocytes), lymphocytes (including T cells, B cells, and natural killer (NK) cells) and myeloid-derived cells
(neutrophils, eosinophils, basophils, monocytes, macrophages, dendritic cells). "Leukocytes" include but are not limited to lymphocytes, granulocytes, monocytes, and macrophages.
[0085] The terms "inflammatory response" and "inflammation" as used herein indicate the complex biological response of immune cells, humoral factors, and vascular tissues of an individual or subject to exogenous or endogenous stimuli, such as pathogens, damaged cells, or irritants, and/or inflammatory signals such as pro-inflammatory cytokines. The inflammatory response includes secretion of cytokines and, more particularly, of proinflammatory cytokines, i.e. cytokines which are produced predominantly by activated immune cells and are involved in the amplification of inflammatory reactions. Exemplary pro-inflammatory cytokines and chemokines include but are not limited to IL-Ιβ, T F-a, IFN-γ, IL-8, IL-6, IL-12, IL-15, IL-16, IL-17 (including family members IL17A, IL17B, IL- 17C, IL-17D, IL-17E, IL-17F), IL-18, GM-CSF, IL-21, IL-23, IL-27 and TGF-β. Exemplary anti-inflammatory cytokines include but are not limited to TGF-β, IL-lRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL-35, INF-a. A cytokine may have either pro-inflammatory and antiinflammatory properties depending on the particular biological context (Cavaillon, J.M (2001) Cell Mol Biol 47(4): 695-702). Exemplary inflammations include acute inflammation and chronic inflammation. Acute inflammation indicates a short-term process characterized by the classic signs of inflammation (swelling, redness, pain, heat, and loss of function) due to the infiltration of the tissues by plasma and leukocytes. An acute inflammation typically occurs as long as the injurious stimulus is present and ceases once the stimulus has been removed, broken down, or walled off by scarring (fibrosis). Chronic inflammation indicates a condition characterized by concurrent active inflammation, tissue destruction, and attempts at repair. Chronic inflammation is not characterized by the classic signs of acute
inflammation listed above. Instead, chronically inflamed tissue is characterized by the infiltration of mononuclear immune cells (monocytes, macrophages, lymphocytes, and plasma cells), tissue destruction, and attempts at healing, which include angiogenesis and fibrosis. An inflammation can be inhibited in the sense of the present disclosure by affecting and in particular inhibiting any one of the events that form the complex biological response associated with an inflammation in an individual. [0086] As used herein, exemplary diseases or conditions associated with or related to inflammation and/or inflammatory responses include but are not limited to autoimmune diseases or disorders, adverse cardiovascular events, cardiovascular or liver disease, disorder, or damage, coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
[0087] The term "introduce" as applied to methods of producing modified cells such as chimeric antigen receptor cells refers to the process whereby a foreign (i.e. extrinsic or extracellular) agent is introduced into a host cell thereby producing a cell comprising the foreign agent. Methods of introducing nucleic acids include but are not limited to
transduction, retroviral gene transfer, transfection, electroporation, transformation, viral infection, and other recombinant DNA techniques known in the art. In some embodiments, transduction is done via a vector (e.g., a viral vector). In some embodiments, transfection is done via a chemical carrier, DNA/liposome complex, or micelle (e.g., Lipofectamine (Invitrogen)). In some embodiments, viral infection is done via infecting the cells with a viral particle comprising the polynucleotide of interest (e.g., AAV). In some embodiments, introduction further comprises CRISPR mediated or Transcription activator-like effector nuclease (TALEN) mediated gene editing. Methods of introducing non-nucleic acid foreign agents (e.g., soluble factors, cytokines, proteins, peptides, enzymes, growth factors, signaling molecules, small molecule inhibitors) include but are not limited to culturing the cells in the presence of the foreign agent, contacting the cells with the agent, contacting the cells with a composition comprising the agent and an excipient, and contacting the cells with vesicles or viral particles comprising the agent.
[0088] The term "isolated" as used herein refers to molecules or biologicals or cellular materials being substantially free from other materials. In one aspect, the term "isolated" refers to nucleic acid, such as DNA or RNA, or protein or polypeptide (e.g., an antibody or derivative thereof), or cell or cellular organelle, or tissue or organ, separated from other DNAs or RNAs, or proteins or polypeptides, or cells or cellular organelles, or tissues or organs, respectively, that are present in the natural source. The term "isolated" also refers to a nucleic acid or peptide that is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized. Moreover, an "isolated nucleic acid" is meant to include nucleic acid fragments which are not naturally occurring as fragments and would not be found in the natural state. The term "isolated" is also used herein to refer to polypeptides which are isolated from other cellular proteins and is meant to encompass both purified and recombinant polypeptides. The term "isolated" is also used herein to refer to cells or tissues that are isolated from other cells or tissues and substantially separated from other cells of a tissue. "Isolated cell" is meant to encompass both cultured and engineered cells or tissues.
[0089] As used herein the term "linker sequence" relates to any amino acid sequence comprising from 1 to 10, or alternatively, 8 amino acids, or alternatively 6 amino acids, or alternatively 5 amino acids that may be repeated from 1 to 10, or alternatively to about 8, or alternatively to about 6, or alternatively about 5, or 4 or alternatively 3, or alternatively 2 times. For example, the linker may comprise up to 15 amino acid residues consisting of a pentapeptide repeated three times. In one aspect, the linker sequence is a (Glycine4Serine)3 flexible polypeptide linker comprising three copies of gly-gly-gly-gly-ser, or equivalents thereof. Non-limiting examples of linker sequences are known in the art, e.g.,
GGGGSGGGGSGGGG (and equivalents thereof); the tripeptide EFM; or Glu-Phe-Gly-Ala- Gly-Leu-Val-Leu-Gly-Gly-Gln-Phe-Met, and equivalents of each thereof. A "flexible linker" intends a linker characterized by minimal rigidity. In some embodiments, a flexible linker facilitates improved, preferred, or optimal secondary conformation, tertiary conformation, and/or quaternary conformation of the linked protein domains or full length polypeptide. In some embodiments, a flexible linker reduces or minimizes negative steric effects.
[0090] As used herein, the term "major histocompatibility complex" (MHC) refers to an antigen presentation molecule that functions as part of the immune system to bind antigens and other peptide fragments and display them on the cell surface for recognition by antigen recognition molecules such as TCR. MHC may be used interchangeably with the term "human leukocyte antigen" (HLA) when used in reference to human MHC; thus, MHC refers to all HLA subtypes including, but not limited to, the classical MHC genes disclosed herein: HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-DM, HLA-DO, HLA-DP, HLA- DQ, and HLA-DR, in addition to all variants, isoforms, isotypes, and other biological equivalents thereof. MHC class I (MHC-I) and MHC class II (MHC-II) molecules utilize distinct antigen processing pathways. In general, peptides derived from intracellular antigens are presented to CD8+ T cells by MHC class I molecules, which are expressed on virtually all cells, while extracellular antigen-derived peptides are presented to CD4+ T cells by MHC-II molecules. However, several exceptions to this dichotomy have been observed. In certain embodiments disclosed herein, a particular antigen, peptide, and/or epitope is identified and presented in an antigen-MHC complex in the context of an appropriate MHC class I or II protein. The genetic makeup of a subject may be assessed to determine which MHC allele is suitable for a particular patient, disease, or condition with a particular set of antigens. In mice, the MHC genes are known as the histocompatibility 2 (H-2) genes. Murine classical MHC class I subtypes include H-2D, H-2K, and H-2L. Murine non-classical MHC class I subtypes include H-2Q, H-2M, and H-2T. Murine classical MHC class II subtypes include H-2A (I- A), and H-2E (1-E). Non-classical murine MHC class II subtypes include H-2M and H-20. Canine MHC molecules are known as Dog Leukocyte Antigens (DLA). Feline MHC molecules are known as Feline Leukocyte Antigens (FLA). In some embodiments, an orthologous or homologous MHC molecule is selected to transition a therapy or treatment involving a specific antigen-MHC complex from one species to a different species.
[0091] Non-classical MHC molecules are non-polymorphic, conserved among species, and possess narrow, deep, hydrophobic ligand binding pockets. These binding pockets are capable of presenting glycolipids and phospholipids to Natural Killer T (NKT) cells or certain subsets of CD 8+ T-cells.
[0092] MHCs for use according to the present disclosure may be produced, isolated, or purified through techniques known in the art. Common protocols for obtaining MHCs involve steps such as, but not limited to, electrophoresis or other techniques of charge or size based separation, biotinylation or other tagging methods and purification, or transfection and induction of vector constructs expressing MHC proteins. Purified animal antibodies are also available through commercially available sources, including retailers such as eBioscience, Biolegend, or Tonbo Biosciences. In certain embodiments, the MHC may be classical MHC I, non-classical MHC I, classical MHC II, non-classical MHC II, dimers (Fc fusions), MHC tetramers, or a polymeric form of MHC. In some embodiments, MHC multimers are generated according to methods well documented in the art, see, e.g., Bakker et al. "MHC Multimer Technology: Current Status and Future Prospects," Current Opinion in
Immunology, Vol. 17, No. 4 pp. 428-433 (2005) and references cited therein.
[0093] In the context of an antigen, peptide, or epitope, "MHC restriction" refers to an antigen, antigen fragment, peptide, or epitope that is only specifically recognized and bound by an antigen binding domain when the antigen is bound to a particular MHC molecule. Thus, an MHC-restricted antigen is not specifically recognized and bound by an antigen binding domain outside of the context of a particular MHC molecule. In some embodiments, the particular MHC molecule is a specific allele or subtype of HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-DM, HLA-DO, HLA-DP, HLA-DQ, or HLA-DR. In some embodiments, the antigen binding domain is the antigen binding domain of an antibody, an antibody fragment, a CAR, an engineered TCR, or a B-cell receptor ("BCR").
[0094] As used herein, the term "monoclonal antibody" refers to an antibody produced by a cell into which the light and heavy chain genes of a single antibody have been transfected or, more traditionally, by a single clone of B-lymphocytes. Monoclonal antibodies generally have affinity for a single epitope (i.e. they are monovalent) but may be engineered to be specific for two or more epitopes (e.g., bispecific). Methods of producing monoclonal antibodies are known to those of skill in the art, for example by creating a hybridoma through fusion of myeloma cells with immune spleen cells, phage display, single cell amplification from B-cell populations, single plasma cell interrogation technologies, and single B-cell culture. Monoclonal antibodies include recombinant antibodies, chimeric antibodies, humanized antibodies, and human antibodies.
[0095] As used herein, the term "NK cell," also known as natural killer cell, refers to a type of lymphocyte that originates in the bone marrow and play a critical role in the innate immune system. NK cells provide rapid immune responses against viral-infected cells, tumor cells or other stressed cell, even in the absence of antibodies and major
histocompatibility complex on the cell surfaces. NK cells may either be isolated or obtained from a commercially available source. Non-limiting examples of commercial NK cell lines include lines NK-92 (ATCC® CRL-2407™), NK-92MI (ATCC® CRL-2408™). Further examples include but are not limited to NK lines HANKl, KHYG-1, NKL, NK-YS, NOI-90, and YT. Non-limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection, or ATCC, (http://www.atcc.org/) and the German Collection of Microorganisms and Cell Cultures (https://www.dsmz.de/).
[0096] As used herein, the term "overexpress" with respect to a cell, a tissue, or an organ expresses a protein to an amount that is greater than the amount that is produced in a control cell, a control issue, or an organ. A protein that is overexpressed may be endogenous to the host cell or exogenous to the host cell.
[0097] As used herein, the term "OX40 costimulatory signaling region" refers to a specific protein fragment associated with this name and any other molecules that have analogous biological function that share at least 70%, or alternatively at least 80% amino acid sequence identity, or alternatively 90% sequence identity, or alternatively at least 95% sequence identity with the OX40 costimulatory signaling region sequence as shown herein. Non-limiting example sequences of the OX40 costimulatory signaling region are disclosed in U.S. Publication 2012/20148552A1, and include the exemplary sequence provided below. OX40 costimulatory signaling region: AGGGACCAG AGGCTGCCCC
CCGATGCCCA CAAGCCCCCT GGGGGAGGCA GTTTCCGGAC CCCCATCCAA GAGGAGCAGG CCGACGCCCA CTCCACCCTG GCCAAGATC.
[0098] A "pathogenic T cell" is a T cell that is harmful to a subject containing the T cell. Whereas, a non-pathogenic T cell is not substantially harmful to a subject, and an anti- pathogenic T cells reduces, ameliorates, inhibits, or negates the harm of a pathogenic T cell.
[0099] As used herein, the term "plaque regression" refers to the overall reduction in plaque volume and a return of the arterial endothelium to its normal functional state. Plaque regression can comprise a decrease in the size, incidence, severity, and/or thickness of plaques on the inner walls of arteries. Plaque regression can also comprise stabilization of a vulnerable plaque. Techniques for measuring plaque regression are known in the art and include but are not limited to coronary angiography, intravascular ultrasound, ultrasound measurement of the carotid intima media thickness, magnetic resonance imaging, computed tomography luminal coronary stenosis assessment, ECG-gated single photon emission computed mography, infared spectroscopy, and intra-coronary thermography (reviewed in Dave, T. et al. Indian J. Endocrinol. Metab. 17(6): 983-989 (2013)).
[0100] The term "protein", "peptide" and "polypeptide" are used interchangeably and in their broadest sense to refer to a compound of two or more subunit amino acids, amino acid analogs or peptidomimetics. The subunits may be linked by peptide bonds. In another aspect, the subunit may be linked by other bonds, e.g., ester, ether, etc. A protein or peptide must contain at least two amino acids and no limitation is placed on the maximum number of amino acids which may comprise a protein's or peptide's sequence. As used herein the term "amino acid" refers to either natural and/or unnatural or synthetic amino acids, including glycine and both the D and L optical isomers, amino acid analogs and peptidomimetics.
[0101] The terms "polynucleotide" and "oligonucleotide" are used interchangeably and refer to a polymeric form of nucleotides of any length, either deoxyribonucleotides or ribonucleotides or analogs thereof. Polynucleotides can have any three-dimensional structure and may perform any function, known or unknown. The following are non-limiting examples of polynucleotides: a gene or gene fragment (for example, a probe, primer, EST or SAGE tag), exons, introns, messenger RNA (mRNA), transfer RNA, ribosomal RNA, RNAi, ribozymes, cDNA, recombinant polynucleotides, branched polynucleotides, plasmids, vectors, isolated DNA of any sequence, isolated RNA of any sequence, nucleic acid probes and primers. A polynucleotide can comprise modified nucleotides, such as methylated nucleotides and nucleotide analogs. If present, modifications to the nucleotide structure can be imparted before or after assembly of the polynucleotide. The sequence of nucleotides can be interrupted by non-nucleotide components. A polynucleotide can be further modified after polymerization, such as by conjugation with a labeling component. The term also refers to both double- and single-stranded molecules. Unless otherwise specified or required, any aspect of this technology that is a polynucleotide encompasses both the double-stranded form and each of two complementary single-stranded forms known or predicted to make up the double-stranded form.
[0102] A polynucleotide is composed of a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); thymine (T); and uracil (U) for thymine when the polynucleotide is RNA. Thus, the term "polynucleotide sequence" is the alphabetical representation of a polynucleotide molecule. This alphabetical representation can be input into databases in a computer having a central processing unit and used for bioinformatics applications such as functional genomics and homology searching. As used herein, the terms "nucleic acid sequence" and "polynucleotide" are used interchangeably to refer to a polymeric form of nucleotides of any length, either ribonucleotides or
deoxyribonucleotides.
[0103] A polypeptide may contain a contiguous nucleic acid sequence of the following lengths: 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 210, 220, 230, 240, 250, 260, 270, 280, 290, 300, 310, 320, 330, 340, 350, 360, 370, 380, 390, 400, 410, 420, 430, 440, 441, 450, 460, 470, 480, 490, 500, 510, 520, 530, 540, 550, 560, 570, 580, 590, 600, 610, 620, 630, 640, 650, 660, 670, 680, 690, 700, 710, 720, 730, 740, 750, 760, 770, 780, 790, 800, 810, 820, 830, 840, 850, 860, 870, 880, 890, 900, 910, 920, 930, 940, 950, 960, 970, 980, 990, 1000, 1010, 1020, 1030, 1040, 1050, 1060, 1070, 1080, 1090, 1095, 1100, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 9000, 10000, or more nucleotides, nucleosides, or base pairs. It also is contemplated that a particular polypeptide from may be encoded by nucleic acids containing natural variations that having slightly different nucleic acid sequences but, nonetheless, encode the same or substantially similar protein, polypeptide, or peptide.
[0104] The term "promoter" as used herein refers to any sequence that regulates the expression of a coding sequence, such as a gene. Promoters may be constitutive, inducible, repressible, or tissue-specific, for example. A "promoter" is a control sequence that is a region of a polynucleotide sequence at which initiation and rate of transcription are controlled. It may contain genetic elements at which regulatory proteins and molecules may bind such as RNA polymerase and other transcription factors. Non- limiting exemplary promoters include CMV, U6, EFla, SV40, PGK1 (human or mouse), P5, Ubc, human beta actin, CAG, TRE, UAS, Ac5, Polyhedrin, CaMKIIa, Gall, 10, TEF1, GDS, ADH1, CaMV35S, Ubi, HI, U6, and Alpha- 1 -antitrypsin. Synthetically- derived promoters may be used for ubiquitous or tissue specific expression. Further, virus-derived promoters, some of which are noted above, may be useful in the methods disclosed herein, e.g., CMV, HIV, adenovirus, and AAV promoters.
[0105] As used herein, the term "purification marker" refers to at least one marker useful for purification or identification. A non-exhaustive list of this marker includes His, lacZ, GST, maltose-binding protein, NusA, BCCP, c-myc, CaM, FLAG, GFP, YFP, cherry, thioredoxin, poly(NANP), V5, Snap, HA, chitin-binding protein, Softag 1, Softag 3,
Strep, or S-protein. Suitable direct or indirect fluorescence marker comprise FLAG, GFP, YFP, RFP, dTomato, cherry, Cy3, Cy 5, Cy 5.5, Cy 7, DNP, AMCA, Biotin, Digoxigenin, Tamra, Texas Red, rhodamine, Alexa fluors, FITC, TRITC or any other fluorescent dye or hapten.
[0106] As used herein, the term "purified" does not require absolute purity; rather, it is intended as a relative term. Thus, for example, a purified nucleic acid, peptide, protein, biological complexes or other active compound is one that is isolated in whole or in part from proteins or other contaminants. Generally, substantially purified peptides, proteins, biological complexes, or other active compounds for use within the disclosure comprise more than 80% of all macromolecular species present in a preparation prior to admixture or formulation of the peptide, protein, biological complex or other active compound with a pharmaceutical carrier, excipient, buffer, absorption enhancing agent, stabilizer, preservative, adjuvant or other co-ingredient in a complete pharmaceutical formulation for therapeutic administration. More typically, the peptide, protein, biological complex or other active compound is purified to represent greater than 90%, often greater than 95% of all macromolecular species present in a purified preparation prior to admixture with other formulation ingredients. In other cases, the purified preparation may be essentially homogeneous, wherein other macromolecular species are not detectable by conventional techniques.
[0107] As used herein, the term "recognizes and specifically binds" or "antibody binding" or "specific binding" means the contact between the antigen binding domain of an antibody, antibody fragment, CAR, TCR, engineered TCR, BCR, MHC, immunoglobulin-like molecule, scFv, CDR or other antigen presentation molecule and an antigen, epitope, or peptide with a binding affinity (KD) of less than 10~5 M. In some aspects, an antigen binding domain binds to both a complex of both an antigen and an MHC molecule. In some aspects, antigen binding domains bind with affinities of less than about 10~6 M, 10~7 M, and preferably 10"8 M, 10"9 M, 10"10 M, 10"U M, or 10"12 M. In a particular aspects, specific binding refers to the binding of an antigen to an MHC molecule, or the binding of an antigen binding domain of an engineered T-cell receptor to an antigen or antigen-MHC complex.
[0108] As used herein, the term "recombinant protein" refers to a polypeptide which is produced by recombinant DNA techniques, wherein generally, DNA encoding the polypeptide is inserted into a suitable expression vector which is in turn used to transform a host cell to produce the heterologous protein.
[0109] A polynucleotide or polynucleotide region (or a polypeptide or polypeptide region) having a certain percentage (for example, 80%, 85%, 90%, or 95%) of "sequence identity" to another sequence means that, when aligned, that percentage of bases (or amino acids) are the same in comparing the two sequences. The alignment and the percent homology or sequence identity can be determined using software programs known in the art, for example those described in Current Protocols in Molecular Biology (Ausubel et al., eds. 1987) Supplement 30, section 7.7.18, Table 7.7.1. Preferably, default parameters are used for alignment. A preferred alignment program is BLAST, using default parameters. In particular, preferred programs are BLASTN and BLASTP, using the following default parameters: Genetic code = standard; filter = none; strand = both; cutoff = 60; expect = 10; Matrix = BLOSUM62;
Descriptions = 50 sequences; sort by = HIGH SCORE; Databases = non-redundant, GenBank + EMBL + DDBJ + PDB + GenBank CDS translations + SwissProtein + SPupdate + PIR. Details of these programs can be found at the following Internet address:
ncbi.nlm.nih.gov/cgi-bin/BLAST. [0110] As used herein, the term "signal peptide" or "signal polypeptide" intends an amino acid sequence usually present at the N-terminal end of newly synthesized secretory or membrane polypeptides or proteins. It acts to direct the polypeptide across or into a cell membrane and is then subsequently removed. Examples of such are well known in the art. Non-limiting examples are those described in U.S. Patent Nos. 8,853,381 and 5,958,736.
[0111] The terms "subject," "host," "individual," and "patient" are as used interchangeably herein to refer to human and veterinary subjects, for example, humans, animals, non-human primates, dogs, cats, sheep, mice, horses, and cows. In some embodiments, the subject is a human. In some aspects, the subject is suffering from a disease or condition to be treated by one of the methods disclosed herein.
[0112] The term "suicide gene" refers to a gene encoding a factor that is capable of inducing death in a cell that expresses it. A suicide gene provides a strategy to regulate cell persistence by providing a mechanism for specific depletion of cells expressing the suicide gene. Once activated, the suicide gene kills the cell through, for example, apoptosis or cell- mediated cytotoxicity. Non limiting examples of suicide genes include (1) iCasp9 which is activated by administration of API 903 to cause apoptosis, (2) CD20 which is activated by administration of CD-20 specific antibody rituximab causing depletion through antibody- dependent cellular cytotoxicity, and (3) herpesvirus thymidine kinase which is activated by ganciclovir.
[0113] As used herein, the term "T-cell," refers to a type of lymphocyte that matures in the thymus. T cells play an important role in cell-mediated immunity and are distinguished from other lymphocytes, such as B cells, by the presence of a T-cell receptor (TCR) on the cell surface. T-cells may either be isolated or obtained from a commercially available source. "T cell" includes all types of immune cells expressing CD3 including T-helper cells (CD4+ cells), cytotoxic T-cells (CD8+ cells), natural killer T-cells, naive T cells (CCR7+,
CD45RA+), regulatory memory T-cell, regulatory memory T-cells, central memory T-cell (CCR7+, CD45RA-), effector memory T-cells (CCR7-, CD45RA-), T-regulatory cells (Treg) and gamma-delta T cells. Natural killer T cells (NKT) co-express NK cell markers and a semi-invariant T cell receptor (TCR). They are implicated in the regulation of immune responses associated with a broad range of diseases. Non-limiting examples of commercially available T-cell lines include lines BCL2 (AAA) Jurkat (ATCC® CRL-2902™), BCL2 (S70A) Jurkat (ATCC® CRL-2900™), BCL2 (S87A) Jurkat (ATCC® CRL-2901™), BCL2 Jurkat (ATCC® CRL-2899™), Neo Jurkat (ATCC® CRL-2898™), TALL- 104 cytotoxic human T cell line (ATCC # CRL-11386). Further examples include but are not limited to mature T-cell lines, e.g., such as Deglis, EBT-8, HPB-MLp-W, HUT 78, HUT 102, Karpas 384, Ki 225, My-La, Se-Ax, SKW-3, SMZ-1 and T34; and immature T- cell lines, e.g., ALL- SIL, Bel3, CCRF-CEM, CML-T1, D D-41, DU.528, EU-9, HD-Mar, HPB-ALL, H-SB2, HT-1, JK-T1, Jurkat, Karpas 45, KE-37, KOPT-K1, K-Tl, L-KAW, Loucy, MAT, MOLT-1, MOLT 3, MOLT-4, MOLT 13, MOLT- 16, MT-1, MT-ALL, P12/Ichikawa, Peer, PER0117, PER-255, PF-382, PFI-285, RPMI-8402, ST-4, SUP-T1 to T14, TALL-1, TALL-101, TALL- 103/2, TALL-104, TALL-105, TALL-106, TALL-107, TALL-197, TK-6, TLBR-1, -2, -3, and -4, CCRF-HSB-2 (CCL-120.1), J.RT3-T3.5 (ATCC TIB-153), J45.01 (ATCC CRL- 1990), J.CaMl .6 (ATCC CRL-2063), RS4; 11 (ATCC CRL-1873), CCRF-CEM (ATCC CRM-CCL-119); and cutaneous T-cell lymphoma lines, e.g., HuT78 (ATCC CRM-TIB-161), MJ[G11] (ATCC CRL-8294), HuT102 (ATCC TIB- 162). Null leukemia cell lines, including but not limited to REH, NALL-1, KM-3, L92-221, are a another commercially available source of immune cells, as are cell lines derived from other leukemias and lymphomas, such as K562 erythroleukemia, THP-1 monocytic leukemia, U937 lymphoma, HEL
erythroleukemia, HL60 leukemia, HMC-1 leukemia, KG-1 leukemia, U266 myeloma. Non- limiting exemplary sources for such commercially available cell lines include the American Type Culture Collection, or ATCC, (http://www.atcc.org/) and the German Collection of Microorganisms and Cell Cultures (https://www.dsmz.de/).
[0114] As used herein, the term "T-cell receptor" or "TCR" refers to a cell surface molecule found on T-cells that functions to recognize and bind antigens presented by antigen presenting molecules. Generally, a TCR is a heterodimer of an alpha chain (TRA) and a beta chain (TRB). Some TCRs are comprised of alternative gamma (TRG) and delta (TRD) chains. T-cells expressing this version of a TCR are known as γδ T-cells. TCRs are part of the immunoglobulin superfamily. Accordingly, like an antibody, the TCR comprises three hypervariable CDR regions per chain. There is also an additional area of hypervari ability on the beta-chain (HV4). The TCR heterodimer is generally present in an octomeric complex that further comprises three dimeric signaling modules Οϋ3γ/ε, CD35/8, and CD247 ζ/ζ or ζ/η. Nonlimiting exemplary amino acid sequence of the human TCR-alpha chain:
METLLGV SL VILWLQL ARVNS QQ GEEDPQ AL S IQEGEN ATMNC S YKTSINNLQWYRQNSGRGLVHLILIRSNEREKHSGRLRVTLDTSKKSSSLLITASRAA DTASYFCAPVLSGGGADGLTFGKGTHLIIQPYIQNPDPAVYQLRDSKSSDKSVCLFTD FDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPE D
TFFP SPE S S CD VKLVEK SFETDT LNFQNLS VIGFRILLLK V AGFNLLMTLRLW S S . Nonlimiting exemplary amino acid sequence of the human TCR-beta chain:
DSAVYLCASSLLRVYEQYFGPGTRLTVTEDLKNVFPPEVAVFEP PEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQP.
[0115] The term "modified TCR" refers to a TCR that has been genetically engineered, and/or a transgenic TCR, and/or a recombinant TCR. Nonlimiting examples of modified TCRs include single-chain VaVP TCRs (scTv), full-length TCRs produced through use of a T cell display system, and TCRs wherein the CDR regions have been engineered to recognize a specific antigen, peptide, fragment, and/or MHC molecule. Methods of developing and engineering modified TCRs are known in the art. For example, see Stone, J.D. et al. Methods in Enzymology 503 : 189-222 (2012), PCT Application WO2014018863 Al .
[0116] Type-1 T Regulatory (TR1) cells are a subset of CD4+ T cells that have regulatory properties and are able to suppress antigen-specific immune responses in vitro and in vivo. These TR1 cells are defined by their unique profile of cytokine production and make high levels of IL-10 and TGF-beta, but no IL-4 or IL-2. The IL-10 and TGF-beta produced by these cells mediate the inhibition of primary naive T cells in vitro. There is also evidence that TR cells exist in vivo, and the presence of high IL-10-producing CD4(+) T cells in patients with severe combined immunodeficiency who have received allogeneic stem-cell transplants have been documented. TR1 cells are involved in the regulation of peripheral tolerance and they could potentially be used as a cellular therapy to modulate immune responses in vivo. See, for example, Levings, M. et al. J. Allergy Clin. Immunol. 106(1 Pt2): S 109-12 (2000).
[0117] TRI cells are defined by their ability to produce high levels of IL-10 and TGF-beta. Trl cells specific for a variety of antigens arise in vivo, but may also differentiate from naive CD4+ T cells in the presence of IL-10 in vitro. TR1 cells have a low proliferative capacity, which can be overcome by IL-15. TR1 cells suppress naive and memory T helper type 1 or 2 responses via production of IL-10 and TGF-beta. Further characterization of TR1 cells at the molecular level will define their mechanisms of action and clarify their relationship with other subsets of Tr cells. The use of TR1 cells to identify novel targets for the development of new therapeutic agents, and as a cellular therapy to modulate peripheral tolerance, can be foreseen. See, for example, Roncarolo, M. et al. Immunol. Rev. 182:68-79 (2001). [0118] As used herein, "treating" or "treatment" of a disease or condition in a subject refers to (1) preventing the symptoms or disease or condition from occurring in a subject that is predisposed or does not yet display symptoms of the disease; (2) inhibiting the disease or condition or arresting its development; or (3) ameliorating or causing regression of the disease or condition or the symptoms of the disease or condition. As understood in the art, "treatment" is an approach for obtaining beneficial or desired results, including clinical results. For the purposes of the present technology, beneficial or desired results can include one or more, but are not limited to, alleviation or amelioration of one or more symptoms, diminishment of extent of a condition (including a disease), stabilized (i.e., not worsening) state of a condition (including disease), delay or slowing of condition (including disease), progression, amelioration or palliation of the condition (including disease), states and remission (whether partial or total), whether detectable or undetectable.
[0119] When the disease or condition is associated with the immune response, the clinical endpoints will vary by the specific tissue targeted or affected by the immune response. The following are non-limiting examples of clinical endpoints for successful treatment: reduction in expression of pro-inflammatory cytokines in the inflamed tissue (or systemically), increase in the expression of anti-inflammatory cytokines in the inflamed tissue (or systemically), reduction in infiltration of lymphocytes to the inflamed tissue, decreased numbers of circulating or localized pathogenic and/or cytotoxic cells, decreased numbers of auto-reactive pathogenic cells, expansion of regulatory cells, reduced pain, reduced swelling, reduced inflammation, reduced or stabilized organ damage, and/or increased or stabilized function of the inflamed tissue.
[0120] When the disease is an adverse cardiovascular event or cardiovascular disease, disorder, or damage, e.g., atherosclerosis, the clinical endpoints for successful treatment include but are not limited to an incremental improvement or a partial reduction in an adverse symptom, disorder, illness, disease or complication caused by or associated with an adverse cardiovascular event or cardiovascular disease or an inhibition, decrease, reduction, suppression, prevention, limit or control of worsening or progression of one or more adverse symptoms, disorders, illnesses, diseases or complications caused by or associated with an adverse cardiovascular event or cardiovascular disease over a short or long duration (hours, days, weeks, months, etc.).
[0121] A beneficial or desired result of treatment also includes reducing or eliminating the need, dosage frequency or amount of additional therapeutics such as another drug or other agent used for treating a subject having or at risk of having an adverse cardiovascular event or cardiovascular disease. For example, reducing an amount of an adjunct therapy, for example, a reduction or decrease of a treatment for an adverse cardiovascular event or cardiovascular disease.
[0122] The term "unit dose" or "dosage" refers to physically discrete units suitable for use in a subject, each unit containing a predetermined quantity of the composition calculated to produce the desired responses in association with its administration, i.e., the appropriate route and regimen. The quantity to be administered, both according to number of treatments and unit dose, depends on the result and/or protection desired. Precise amounts of the
composition also depend on the judgment of the practitioner and are peculiar to each individual. Factors affecting dose include physical and clinical state of the subject, route of administration, intended goal of treatment (alleviation of symptoms versus cure), and potency, stability, and toxicity of the particular composition. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically or prophylactically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described herein.
[0123] As used herein, the term "vector" refers to a nucleic acid construct deigned for transfer between different hosts, including but not limited to a plasmid, a virus, a cosmid, a phage, a BAC, a YAC, etc. A "viral vector" is defined as a recombinantly produced virus or viral particle that comprises a polynucleotide to be delivered into a host cell, either in vivo, ex vivo or in vitro. In some embodiments, plasmid vectors may be prepared from commercially available vectors. In other embodiments, viral vectors may be produced from baculoviruses, retroviruses, adenoviruses, AAVs, etc. according to techniques known in the art. In one embodiment, the viral vector is a lentiviral vector. Examples of viral vectors include retroviral vectors, adenovirus vectors, adeno-associated virus vectors, alphavirus vectors and the like. Infectious tobacco mosaic virus (TMV)-based vectors can be used to manufacturer proteins and have been reported to express Griffithsin in tobacco leaves (O'Keefe et al.
(2009) Proc. Nat. Acad. Sci. USA 106(15): 6099-6104). Alphavirus vectors, such as Semliki Forest virus-based vectors and Sindbis virus-based vectors, have also been developed for use in gene therapy and immunotherapy. See, Schlesinger & Dubensky (1999) Curr. Opin. Biotechnol. 5:434-439 and Ying et al. (1999) Nat. Med. 5(7):823-827. In aspects where gene transfer is mediated by a retroviral vector, a vector construct refers to the polynucleotide comprising the retroviral genome or part thereof, and a gene of interest such as a polynucleotide encoding a CAR. Further details as to modern methods of vectors for use in gene transfer may be found in, for example, Kotterman et al. (2015) Viral Vectors for Gene Therapy: Translational and Clinical Outlook Annual Review of Biomedical Engineering 17. Vectors that contain both a promoter and a cloning site into which a polynucleotide can be operatively linked are well known in the art. Such vectors are capable of transcribing RNA in vitro or in vivo, and are commercially available from sources such as Agilent Technologies (Santa Clara, Calif.) and Promega Biotech (Madison, Wis.).
[0124] Other objects, features and advantages of the present disclosure will become apparent from the following detailed description. Additional definitions are also provided therein. It should be understood, however, that the detailed description and the specific examples, while indicating specific embodiments of the disclosure, are given by way of illustration only, since various changes and modifications within the spirit and scope of the disclosure will become apparent to those skilled in the art from this detailed description.
DESCRIPTIVE EMBODIMENTS
Polynucleotides and Engineered T-cell Receptors
[0125] The present disclosure provides polypeptides encoding an engineered T-cell receptor comprising, consisting essentially of, or yet further consisting of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T- cell receptor is a modified TCR. In other aspects, the engineered T-cell receptor is a CAR. In some aspects, the polynucleotide is the complement of a polynucleotide encoding an engineered T-cell receptor. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the athero-relevant antigen is bound to the MHC molecule. In some aspects, the engineered T- cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
[0126] Also provided herein is a polynucleotide encoding an engineered T-cell receptor comprising, consisting of, or alternatively consisting essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T- cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the athero-relevant antigen is bound to the MHC molecule. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the athero- relevant antigen and the MHC molecule. Also provided herein are the expression product(s) of the polynucleotide encoding an engineered T-cell receptor.
[0127] Extracellular Antigen Binding Domain. In certain aspects, the present disclosure provides an engineered T-cell receptor that comprises, consists, or alternatively consists essentially of an antigen binding domain that specifically recognizes and binds, binds, or is specific to an athero-relevant antigen bound to an MHC molecule. In some aspects, the MHC binds to the athero-relevant antigen with high affinity, optionally an affinity less than 1000 nM. In some aspects, the athero-relevant antigen binds to the MHC with high affinity, optionally an affinity less than 1000 nM.
[0128] In some aspects, the affinity of the interaction between the athero-relevant antigen and the MHC molecule is characterized by a dissociation constant (KD) which is less than about 0.1 nM, less than than about 1 nM, less than about 5 nM, less than about 10 nM, less than about 15 nM, less than about 20 nM, less than about 50 nM, less than about 100 nM, less than about 150 nM, less than about 200 nM, less than about 250 nM, less than about 300 nM, less than about 350 nM, less than about 400 nM, less than about 450 nM, less than about 500 nM, less than about 550 nM, less than about 600 nM, less than about 650 nM, less than about 700 nM, less than about 750 nM, less than about 800 nM, less than about 850 nM, less than about 900 nM, less than about 950 nM, less than about 1000 nM, less than about 1100 nM, less than about 1200 nM, less than about 1300 nM, less than about 1400 nM, less than about 1500 nM, less than about 2000 nM, less than about 2500 nM, less than about 3000 nM, less than about 3500 nM, less than about 4000 nM, less than about 4500 nM, less than about 4800 nM, or less than about 5000 nM {i.e., 5 μΜ). In some aspects, the affinity of the interaction between the antigen and the MHC molecule ranges from: about 1 nM to about 10 nM, about 1 nM to about 15 nM, about 1 nM to about 50 nM, about 1 nM to about 100 nM, about 1 nM to about 200 nM, about 1 nM to about 300 nM, about 1 nM to about 400 nM, about 1 nM to about 500 nM, about 1 nM to about 600 nM, about 1 nM to about 700 nM, about 1 nM to about 800 nM, about 1 nM to about 900 nM, about 1 nm to about 1000 nM, about 1 nM to about 1100 nM, about 1 nM to about 1200 nM, about 1 nM to about 1300 nM, about 1 nM to about 1400 nM, about 1 nM to about 1500 nM, about 1 nM to about 2 μΜ, about 1 nM to about 3 μΜ, about 1 nM to about 4 μΜ , about 1 nM to about 5 μΜ , about 10 nM to about 15 nM, about 10 nM to about 50 nM, about 10 nM to about 100 nM, about 10 nM to about 200 nM, about 10 nM to about 300 nM, about 10 nM to about 400 nM, about 10 nM to about 500 nM, about 10 nM to about 600 nM, about 10 nM to about 700 nM, about 10 nM to about 800 nM, about 10 nM to about 900 nM, about 10 nm to about 1000 nM, about 10 nM to about 1100 nM, about 10 nM to about 1200 nM, about 10 nM to about 1300 nM, about 10 nM to about 1400 nM, about 10 nM to about 1500 nM, about 10 nM to about 2 μΜ, about 10 nM to about 3 μΜ, about 10 nM to about 4 μΜ , about 10 nM to about 5 μΜ, about 50 nM to about 100 nM, about 50 nM to about 200 nM, about 50 nM to about 300 nM, about 50 nM to about 400 nM, about 50 nM to about 500 nM, about 50 nM to about 600 nM, about 50 nM to about 700 nM, about 50 nM to about 800 nM, about 50 nM to about 900 nM, about 50 nm to about 1000 nM, about 50 nM to about 1100 nM, about 50 nM to about 1200 nM, about 50 nM to about 1300 nM, about 50 nM to about 1400 nM, about 50 nM to about 1500 nM, about 50 nM to about 2 μΜ, about 50 nM to about 3 μΜ, about 50 nM to about 4 μΜ , about 50 nM to about 5 μΜ, about 100 nM to about 200 nM, about 100 nM to about 300 nM, about 100 nM to about 400 nM, about 100 nM to about 500 nM, about 100 nM to about 600 nM, about 100 nM to about 700 nM, about 100 nM to about 800 nM, about 100 nM to about 900 nM, about 100 nm to about 1000 nM, about 100 nM to about 1100 nM, about 100 nM to about 1200 nM, about 100 nM to about 1300 nM, about 100 nM to about 1400 nM, about 100 nM to about 1500 nM, about 100 nM to about 2 μΜ, about 100 nM to about 3 μΜ, about 100 nM to about 4 μΜ, about 100 nM to about 5 μΜ, about 200 nM to about 300 nM, about 200 nM to about 400 nM, about 200 nM to about 500 nM, about 200 nM to about 600 nM, about 200 nM to about 700 nM, about 200 nM to about 800 nM, about 200 nM to about 900 nM, about 200 nm to about 1000 nM, about 500 nM to about 1100 nM, about 500 nM to about 1200 nM, about 500 nM to about 1300 nM, about 500 nM to about 1400 nM, about 500 nM to about 1500 nM, about 500 nM to about 2 μΜ, about 500 nM to about 3 μΜ, about 500 nM to about 4 μΜ , about 500 nM to about 5 μΜ. In a preferred embodiment, the MHC's affinity for the antigen is less than about 1000 nM. [0129] In some embodiments, the athero-relevant antigen comprises all or part of an epitope derived from an antigen involved in an adverse cardiovascular event, or
cardiovascular or liver disease, disorder, or damage including but not limited to: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
[0130] In some embodiments, the antigen comprises, consists, or alternatively consists essentially of all or part of an epitope derived from ApoBlOO. A non-limiting example of an ApoBlOO polypeptide sequence from which peptides, sub-sequences, portions, homologues, variants, derivatives and T cell epitopes may be derived is as follows:
MDPPRPALLALLALPALLLLLLAGARAEEEMLENVSLVCPKDATRFKHLRKYTYNY
EAESSSGVPGTADSRSATRINCKVELEVPQLCSFILKTSQCTLKEVYGF PEGKALLK
KTKNSEEFAAAMSRYELKLAIPEGKQVFLYPEKDEPTYILNIKRGIISALLVPPETEEA
KQVLFLDTVYGNCSTHFTVKTRKGNVATEISTERDLGQCDRFKPIRTGISPLALIKGM
TRPLSTLISSSQSCQYTLDAKRKHVAEAICKEQHLFLPFSYK KYGMVAQVTQTLKL
EDTPKINSRFF GEGTKKMGL AFE S TK S T SPPKQ AE A VLKTLQELKKLTISEQNIQRAN
LF KLVTELRGLSDEAVTSLLPQLIEVSSPITLQALVQCGQPQCSTHILQWLKRVHAN
PLLIDVVTYLVALIPEPSAQQLREIF MARDQRSRATLYALSHAVNNYHKTNPTGTQ
ELLDIANYLMEQIQDDCTGDEDYTYLILRVIG MGQTMEQLTPELKSSILKCVQSTKP
SLMIQKAAIQALRKMEPKDKDQEVLLQTFLDDASPGDKRLAAYLMLMRSPSQADIN
KIVQILPWEQ EQVK FVASHIANILNSEELDIQDLKKLVKEALKESQLPTVMDFRKF
SRNYQLYKSVSLPSLDPASAKIEGNLIFDPNNYLPKESMLKTTLTAFGFASADLIEIGL
EGKGFEPTLEALFGKQGFFPDSVNf ALYWVNGQVPDGVSKVLVDHFGYTKDDKHE
QDMVNGFMLSVEKLIKDLKSKEVPEARAYLRILGEELGFASLHDLQLLGKLLLMGAR
TLQGIPQMIGEVIRKGSK DFFLHYIFMENAFELPTGAGLQLQISSSGVIAPGAKAGV
KLEVA MQAELVAKPSVSVEFVT MGIIIPDFARSGVQMNTNFFHESGLEAHVALK
AGKLKFIIPSPKRPVKLLSGGNTLHLVSTTKTEVIPPLIE RQSWSVCKQVFPGLNYCT
SGAYSNASSTDSASYYPLTGDTRLELELRPTGEIEQYSVSATYELQREDRALVDTLKF
VTQAEGAKQTEATMTFKYNRQSMTLSSEVQIPDFDVDLGTILRV DESTEGKTSYRL
TLDIQ KKITEVALMGHLSCDTKEERKIKGVISIPRLQAEARSEILAHWSPAKLLLQM
D S S AT A YGS T VSKRV AWH YDEEKIEFEWNTGTNVDTKKMT S FP VDL SD YPK SLH
MYA RLLDHRVPQTDMTFRHVGSKLIVAMSSWLQKASGSLPYTQTLQDHLNSLKE
F LQ MGLPDFHIPE LFLKSDGRVKYTL KNSLKIEIPLPFGGKSSRDLKMLETVRT PALHFKSVGFHLPSREFQVPTFTIPKLYQLQVPLLGVLDLSTNVYS LYNWSASYSG GNTSTDHFSLRARYHMKADSVVDLLSYNVQGSGETTYDHKNTFTLSCDGSLRHKFL DSNIKFSHVEKLGN PVSKGLLIFDASSSWGPQMSASVHLDSKKKQHLFVKEVKIDG QFRVSSFYAKGTYGLSCQRDPNTGRLNGESNLRFNSSYLQGTNQITGRYEDGTLSLT STSDLQSGIIKNTASLKYENYELTLKSDTNGKYKNFATS KMDMTFSKQNALLRSEY QADYESLRFFSLLSGSLNSHGLELNADILGTDKINSGAHKATLRIGQDGISTSATT LK C SLL VLE ELN AELGL S GASMKLTTNGRFREFINAKF SLDGKAALTELSLGS AYQ AMI LGVDSKNIF FKVSQEGLKLS DMMGSYAEMKFDHTNSLNIAGLSLDFSSKLDNIYS SDKFYKQTVNLQLQPYSLVTTLNSDLKYNALDLTNNGKLRLEPLKLHVAG LKGAY QN EIKHIYAIS S AALS AS YKADT VAKVQGVEF SHRLNTDIAGLAS AIDMSTNYNSD SLHFSNVFRSVMAPFTMTIDAHTNGNGKLALWGEHTGQLYSKFLLKAEPLAFTFSH DYKGSTSHHLVSRKSISAALEHKVSALLTPAEQTGTWKLKTQFNN EYSQDLDAYN TKDKIGVELTGRTLADLTLLDSPIKVPLLLSEPF IIDALEMRDAVEKPQEFTIVAFVK YDKNQDVHSINLPFFETLQEYFER RQTIIVVLENVQRNLKHINIDQFVRKYRAALGK LPQQANDYLNSFNWERQVSHAKEKLTALTKKYRITE DIQIALDDAKINF EKLSQL QTYMIQFDQYIKDSYDLHDLKIAIANIIDEIIEKLKSLDEHYHIRVmVKTIHDLHLFIE NIDF KSGSSTASWIQNVDTKYQIRIQIQEKLQQLKRHIQNIDIQHLAGKLKQHIEAID VRVLLDQLGTTISFERINDVLEHVKHFVINLIGDFEVAEKINAFRAKVHELIERYEVD QQIQVLMDKLVELAHQYKLKETIQKLSNVLQQVKIKDYFEKLVGFIDDAVKKL EL SFKTFIEDV KFLDMLIKKLKSFDYHQFVDETNDKIREVTQRLNGEIQALELPQKAEA LKLFLEETKATVAVYLESLQDTKITLIINWLQEALSSASLAHMKAKFRETLEDTRDR MYQMDIQQELQRYLSLVGQVYSTLVTYISDWWTLAAKNLTDFAEQYSIQDWAKRM KALVEQGFTVPEIKTILGTMPAFEVSLQALQKATFQTPDFIVPLTDLRIPSVQINFKDL KNIKIPSRFSTPEFTILNTFHIPSFTIDFVEMKVKIIRTIDQMLNSELQWPVPDIYLRDLK VEDIPLARITLPDFRLPEIAIPEFIIPTL L DFQVPDLHIPEFQLPHISHTIEVPTFGKLYS ILKIQ SPLF TLD AN ADIGNGTT S A E AGI A ASIT AKGE SKLE VLNFDF Q AN AQL S PKI NPLALKES VKF S SKYLRTEHGSEMLFFGNAIEGKSNTVASLHTEKNTLELSNGVIVKI NNQLTLD SNTK YFHKLNIPKLDF S SQ ADLRNEIKTLLKAGHIAWTS SGKGSWKW AC PRFSDEGTHESQISFTIEGPLTSFGLSNKINSKHLRVNQNLVYESGSLNFSKLEIQSQVD SQHVGHSVLTAKGMALFGEGKAEFTGRHDAHLNGKVIGTLKNSLFFSAQPFEITAST NNEGNLKVRFPLRLTGKIDFLNNYALFLSPSAQQASWQVSARFNQYKYNQNFSAGN NENFMEAHVGINGEANLDFLNIPLTIPEMRLPYTIITTPPLKDFSLWEKTGLKEFLKTT KQSFDLSVKAQYKKNKHRHSITNPLAVLCEFISQSIKSFDRHFEKNRNNALDFVTKSY NETKIKFDKYKAEKSHDELPRTFQIPGYTVPVVNVEVSPFTIEMSAFGYVFPKAVSMP SFSILGSDVRVPSYTLILPSLELPVLHVPR LKLSLPDFKELCTISHIFIPAMGNITYDFS
FK S S VITLNTN AELFNQ SD I V AHLL S S S S S VID ALQ YKLEGTTRLTRKRGLKLATALSL
S KF VEGSHNSTVSLTTK MEVS VATTTKAQIPILRMNFKQELNGNTKSKPTVS S SM
EFKYDFNS SMLYST AKGAVDHKLSLESLTS YF SIES STKGDVKGS VLSREYSGTIASE
ANTYLNSKSTRSSVKLQGTSKroDIWNLEVKE FAGEATLQRIYSLWEHSTK HLQL
EGLFFTNGEHTSKATLELSPWQMSALVQVHASQPSSFHDFPDLGQEVALNANTKNQ
KIRWK EVRIHSGSFQSQVELSNDQEKAHLDIAGSLEGHLRFLKNIILPVYDKSLWDF
LKLDVTTSIGRRQHLRVSTAFVYTK PNGYSFSIPVKVLADKFIIPGLKL DLNSVLV
MPTFHVPF TDLQ VP S CKLDFREIQI YKKLRT S SF AL LP TLPE VKFPE VD VLTK YS QPE
DSLIPFFEITVPESQLTVSQFTLPKSVSDGIAALDLNAVA KIADFELPTIIVPEQTIEIPS
IKF S VP AGIVIP SFQ ALT ARFEVD SP VYNATW S ASLK K AD YVET VLD STC S ST VQFL
EYELNVLGTHKIEDGTLASKTKGTFAHRDFSAEYEEDGKYEGLQEWEGKAHLNIKS
PAFTDLHLRYQKDKKGISTSAASPAVGTVGMDMDEDDDFSKW FYYSPQSSPDKKL
TIFKTELRVRESDEETQIKVNWEEEAASGLLTSLKDNVPKATGVLYDYV KYHWEH
TGLTLREVSSKLRRNLQNNAEWVYQGAIRQIDDIDVRFQKAASGTTGTYQEWKDKA
Q LYQELLTQEGQASFQGLKDNVFDGLVRVTQEFHMKVKHLIDSLIDFLNFPRFQFP
GKPGIYTREELCTMFIREVGTVLSQVYSKVHNGSEILFSYFQDLVITLPFELRKHKLID
VISMYRELLKDLSKEAQEVFKAIQSLKTTEVLR LQDLLQFIFQLIEDNIKQLKEMKF
TYLINYIQDEINTIFSDYIPYVFKLLKENLCL LHKF EFIQ ELQEASQELQQIHQYF
ALREEYFDPSIVGWTVKYYELEEKIVSLIKNLLVALKDFHSEYIVSAS FTSQLSSQVE
QFLHRNIQEYLSILTDPDGKGKEKIAELSATAQEIIKSQAIATKKIISDYHQQFRYKLQ
DF SDQL SD Y YEKF I AE SKRLIDL S IQN YHTFLI YITELLKKLQ S TT VMNP YMKL APGEL
TIIL.
[0131] Athero-relevant antigens can be based upon or derived from an ApoBlOO amino acid sequence. For example, an athero-relevant antigen can comprise an amino acid sequence having 60% or more (e.g., 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, 100%) sequence identity with a region of ApoBlOO. Thus, as disclosed herein, in particular embodiments, the an athero-relevant antigens or equivalents thereof include those having at least partial sequence identity to one or more ApoBlOO peptides, subsequences, portions, homologues, variants or derivatives thereof set forth as any one of the peptides set forth in in Table 1. The percent identity of such sequences can be as little as 60%, or can be greater (e.g., 60%, 65%, 70%, 75%, 75% 80%, 85%, 90%, 95%, 96%, 97%, 98%), 99%), etc.). The percent identity can extend over the entire sequence length or a portion of the sequence. In particular aspects, the length of the sequence sharing the percent identity is 2, 3, 4, 5 or more contiguous amino acids, e.g., 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, etc.
contiguous amino acids.
[0132] In some embodiments, the athero-relevant antigen comprises, consists, or alternatively consists essentially of the ApoB 100-derived peptides listed in the following Table 1, or an equivalent of each thereof:
Table 1: Peptides
Figure imgf000054_0001
3563.0030 FLI YITELLKKLQ S T 4531
3563.0016 GKLYSILKIQSPLFT 2756
3563.0001 PALLALLALPALLLL 6
3563.0003 QELLDIANYLMEQIQ 461
3563.0002 LLIDVVTYLVALIPE 406
3563.0029 IDLSIQNYHTFLIYI 4521
P101 FGKQGFFPDSV KALY
P102 TLYALSHAVNSYFDVD
P103 LYYKEDKTSLSASAAS
[0133] In some embodiments, the athero-relevant antigen comprises, consists, or alternatively consists essentially of the amino acid sequence SLFFSAQPFEITAST,
IKHIYAISSAALSAS, or an equivalent of each thereof.
[0134] The length of the athero-relevant antigen disclosed herein may vary based on the particular MHC allele and/or the specific antigen recognition domain (e.g., TCR, scFv, etc.). Thus, the length of the antigen peptides according to some embodiments described herein may vary from, for example, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 11, at least 12, at least 13, at least 14, at least 15, at least 16, at least 17, at least 18, at least 19, at least 20, between 20 - 25, between 20-30, between 30-40 amino acids, or up to 50 amino acids in length. According to some embodiments, the antigen includes a core of at least at least 5 amino acids, at least 6, at least 7, at least 8, at least 9 and more. According to some embodiments of the invention, the length of the autoantigenic peptide does not exceed about 100 amino acids, does not exceed about 50 amino acids, does not exceed about 30 amino acids, or does not exceed 20 amino acids. According to some embodiments of the invention, the length of the autoantigenic peptide includes at least 5 and no more than 35 amino acids.
[0135] In some embodiments, antigens or equivalents thereof may further comprise independently at least 2, or alternatively at least 3, or alternatively at least 4, or alternatively at least 5, or at least 6, or alternatively at least 7, or alternatively at least 8, or alternatively at least 9 or alternatively at least 10 amino acids at the amino and/or carboxyl terminus of the polypeptide. In some aspects, the antigens listed in Table 1 or equivalents thereof further comprise independently at least 2, or alternatively at least 3, or alternatively at least 4, or alternatively at least 5, or at least 6, or alternatively at least 7, or alternatively at least 8, or alternatively at least 9 or alternatively at least 10 amino acids at the amino and/or carboxyl terminus of the polypeptide.
[0136] There are also provided athero-relevant antigen peptides or equivalents thereof that exhibit sequence identity to a reference ApoBlOO peptide, sub-sequence or portion, or modification thereof set forth as any one of the peptides in Table 1. In one embodiment, an athero-relevant antigen, or a sub-sequence, portion, homologue, variant or derivative thereof comprises, consists or consists essentially of a sequence at least 60% or more (e.g., 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, etc.) identical to a reference ApoBlOO protein or peptide, or sub-sequence, portion, homologue, variant or derivative thereof as set forth as any one of the peptides set forth in in Table 1.
[0137] In another embodiment, athero-relevant antigens, or equivalents thereof, comprise, consist of, or consist essentially of include or consist of an ApoBlOO peptide, wherein the athero-relevant antigen or equivalent thereof has one or more modifications, such as an amino acid addition to, deletion of, or substitution of any amino acid residue in any peptide set forth as any one of the peptides set forth in in Table 1. In particular aspects, a modified sequence is at least 80% or more, e.g., 80-85%, 85-90%, 90-95%, 95-100% identical, to a ApoBlOO peptide, or sub-sequence, portion, homologue or derivative thereof set forth as any one of the peptides set forth in in Table 1 or has 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100, or more, additions to, deletions of, or substitutions.
[0138] Provided herein are antigen binding domains that recognize and/or bind modified and variant forms of athero-relevant antigens including but not limited to ApoBlOO peptides and equivalents thereof. Such forms of athero-relevant antigens (referred to as
"modifications" or "variants") intend an ApoBlOO peptide or equivalent thereof that deviates from a reference sequence. Such modifications may have greater or less activity or function than a reference ApoBlOO peptide, sub-sequence or portion thereof, such as ability to elicit, stimulate, induce, promote, increase or enhance T-cell response or immune or inflammatory response. Athero-antigens or equivalents include sequences having substantially the same, greater or less relative activity or function as a T-cell epitope than a reference epitope set forth in in Table 1, for example, an ability to elicit, stimulate, induce, promote, increase or enhance an immune response in vitro or in vivo.
[0139] Non-limiting examples of modifications include one or more amino acid
substitutions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25- 30, 30-50, 50-100, or more residues), additions and insertions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100, or more residues) and deletions (e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 20-25, 25-30, 30-50, 50-100) of a reference antigen. Additional modifications to the antigens and peptides contemplated herein include but are not limited to acetylation, amidation, azido group conjugated to the primary epsilon amino group on an inserted lysine or as 5-azidopentanoic acid on the N-terminus, biotinylation, carrier proteins and MAP peptides (e.g., KLH or BSA conjugated peptides), MAP peptides, modifications to increase cell penetration, conjugation to 5-azidopentanoic acid, azidogroup conjugated to lysine or propargylglycine can be conjugated to the peptide for reactivity with azido groups, counterions, cholesterol conjugation, C-terminal inserted cysteine, cyclization with disulfide bonds or amide bonds, conjugation of DOTA, DOPA and DTPA to the termini, Caprylic acid (C8), Capric acid (CIO), Laurie acid, (C12), Myristic acid (C14), Palmitic acid (C16), Stearic acid (C18), fluorochromes (e.g., FITC, 5,6 FAM, Rhodamine B), fluorescence/quencher pairs for FRET analysis (e.g., Abz/Dnp and EDANS/Dabcyl), formylation, methylation, phosphorylation of tyrosine, serine or threonine, conjugated to resin, DTT can be added if peptides contain several cysteines or other amino acids that are easily oxidized, sulfation of tyrosine,
Tyr(S03H2), and unnatural amino acids: D-amino acids, Aib, Abu, Ahx, Orn, pGlu, Nle, DAB, Cit, Hyp, Tyr(3-N02), or Met sulfoxide or sulfone.
[0140] In some embodiments, athero-relevant antigens or equivalents thereof can be a part of or contained within a larger molecule, such as another peptide sequence, or a fusion, heterologous domain, or chimera. In particular embodiments, an addition is a chimeric fusion sequence or heterologous domain (i.e. an amino acid sequence having one or more molecules not normally present in a reference endogenous sequence covalently attached to the sequence).
[0141] In some embodiments, the athero-relevant antigen is an MHC-restricted antigen. In some embodiments, the antigen binding domain specifically binds to both the antigen and the MHC molecule. In certain embodiments, the antigen binding domain specifically binds a region spanning the athero-relevant antigen and MHC bound to the athero-relevant antigen (i.e. the antigen-MHC complex). In some embodiments, the MHC molecule comprises, consists, or alternatively consists essentially of all or part of an MHC class I molecule (e.g., HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, or CD1 molecule). In other
embodiments, the MHC molecule comprises, consists of, or alternatively consists essentially of an MHC class II molecule (e.g., HLA-DM, HLA-DO, HLA-DP, HLA-DQ, and HLA-DR). In some embodiments, the MHC molecule is a classical MHC molecule. In other
embodiments, the MHC molecule is a non-classical MHC molecule. In some aspects, the extracellular antigen binding domain specifically binds and recognizes an antigen bound to a specific MHC allele or mutation. Nonlimiting examples of specific peptide-MHC allele complexes are provided in Tables .
[0142] In some embodiments, the MHC class II molecule comprises all or part of an HLA- DR, HLA-DQ, or HLA-DP molecule. In particular embodiments, the MHC molecule is selected from the group of: DRB1*01:01, DRB1*01:02, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:03, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*10:01, DRB1*11:01, DRB1*11:04, DRB1*12:01, DRB1*13:01, DRB1*13:02, DRB1*14:01, DRB1*15:01, DRB3*01:01, DRB3*02:02, DRB4*01:01, DRB5*01:01, DPB1*04:01, DPB1*05:01, or DQB1*06:02 or an equivalent of each thereof. In additional embodiments, the MHC molecule is selected from the group of: DPB1*02:01, DPB1*03:01, DPB1*04:02, DPB1*14:01, DQB1*02:01, DQB1*03:01, DQB1*06:02, DRB1*01:01, DRB1*04:01, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*09:01, DRB1*1101, DRB1*12:01, DRB1*13:02, DRB1*15:01, DRB3*01:01, DRB3*02:02, DRB4*01:01 or DRB5*01:01 or an equivalent of each thereof.
[0143] In particular embodiments, the athero-relevant antigen comprises, consists, or consists essentially any one of the peptides set forth in Table 1, or an equivalent of each thereof, and binds to one or more of the MHC molecules set forth in Table 4, or an equivalent of each thereof. In some embodiments, the athero-relevant antigen comprises all or part of the sequence SLFFSAQPFEITAST or an equivalent thereof and binds to either DRB 1*0101, DRB 1*0701, or an equivalent of each thereof.
[0144] In some embodiments, the antigen binding domain comprises, consists, or consists essentially of Fab, variable regions of a TCR, BCR, or Ig, or a fragment of an scFv (e.g., a VH chain or VL chain). An scFv region can comprise the variable regions of the heavy (VH) and light chains (VL) of immunoglobulins, connected with a short linker peptide. The linker peptide may be from 1 to 50 amino acids, for instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids. In some embodiments, the linker is glycine rich, although it may also contain serine or threonine. [0145] In some embodiments, the heavy chain variable region of the Ig comprises, or consists essentially thereof, or consists of those disclosed herein or an equivalent of each thereof and/or comprises one or more CDR regions comprising those disclosed herein or an equivalent of each thereof. In some embodiments, the light chain variable region of the Ig comprises, or consists essentially thereof, or consists of those disclosed herein or an equivalent of each thereof and/or comprises one or more CDR regions comprising those disclosed herein or an equivalent of each thereof.
[0146] Transmembrane Domain. The transmembrane domain may be derived either from a natural or from a synthetic source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein. Transmembrane regions of particular use in this disclosure may be derived from CD 8 ( M_001768, M_170299), CD28
( M_001243077, M_001243078, M_006139), CD3 ( M_000732, M_000733,
M_000073), CD45 ( M_001267798, M_002838, NM 080921, NM_080922), CD4 ( M_000616, M_001195014, M_001195015, M_001195016, M_001195017), CD 5 ( M_014207, M_001346456), phosphatidate cytidylyltransferase 1 (CDS, M_001263), CD9 ( M_001769, M_001330312), CD16 ( M_000569), CD22 ( M_024916), CD33 ( M_001082618, M_001177608, M_001772), CD37 ( M_001040031, NM_001774), CD64 ( M_000566), CD80 ( M_005191), CD86 ( M_176892, M_001206924,
M_001206925, M_006889, M_175862), CD134 (NM_176892), CD137 ( M_001561), CD 154 ( M_000074), or TCR, or an equivalent of each thereof. Preferably, the
transmembrane domain is a CD3, CD8, or a CD28 transmembrane domain. Alternatively the transmembrane domain may be synthetic, in which case it will comprise predominantly hydrophobic residues such as leucine and valine. Preferably a triplet of phenylalanine, tryptophan and valine will be found at each end of a synthetic transmembrane domain.
Optionally, a short oligo- or polypeptide linker, preferably between 2 and 10 amino acids in length may form the linkage between the transmembrane domain and the cytoplasmic signaling domain of the engineered t-cell receptor. A glycine-serine doublet provides a particularly suitable linker.
[0147] Intracellular Signaling Domain. The intracellular signaling domain (or cytoplasmic domain) of the engineered T-cell receptor is responsible for activation of at least one of the traditional effector functions of an immune cell in which an engineered T-cell receptor has been introduced. In some aspects, the intracellular signaling domain comprises, consists, or consists essentially of the intracellular signaling domain of a co-stimulatory molecule. The intracellular signaling domain refers to a portion of a protein which transmits the effector function signal and directs the immune cell to perform its specific function. An entire signaling domain or a portion thereof may be used so long as the portion is sufficient to transmit the effector function signal. Cytoplasmic sequences of the T-cell receptor (TCR) and co-receptors, as well as derivatives or variants thereof, can function as intracellular signaling domains for use in a CAR or modified TCR. Intracellular signaling domains of particular use in this disclosure may be derived from FcR (e.g., M 000566), TCR, CD3 ( M_000732, M_000733, M_000073), phosphatidate cytidylyltransferase 1 (CDS,
M_001263), CD22 (NM_024916), CD79a ( M_021601, M_001783), CD79b
( M_000626), CD66d ( M_001277163, M_001815). In preferred embodiments, the intracellular signaling domain of the engineered t-cell receptor can comprise the signaling domain of CD28, 4-1BB, CD3 zeta, CD27 ( M_001242), ICOS, or OX40. In some embodiments, the intracellular signaling domain is derived from a protein of the same species as the subject. In other embodiments, the intracellular signaling domain is derived from a protein of a different cell (e.g., macrophage, B cell) or a different species than the subject.
[0148] Signals transmitted through a TCR may be insufficient for full activation of a T-cell. Thus, a second co-stimulatory signal may also be required. The intracellular region of at least one co-stimulatory signaling molecule, including but not limited CD27 ( M_001242), CD28, 4- IBB, OX40, CD30 ( M_001243), CD40 ( M_001250), programmed cell death protein 1 (PD- 1, M 005018), ICOS, lymphocyte function-associated antigen- 1 (LFA-1, M_001114380), CD2 ( M_001767), CD7 (NM_006137), CD27 (NM_001242), CD276 ( M_001024736), or a ligand that specifically binds with CD83, may also be included in the cytoplasmic domain of the engineered T-cell receptor. The engineered T-cell receptor of the present disclosure can comprise one or more co-stimulatory domain. For instance, a CAR may comprise one, two, or more co-stimulatory domains. In some embodiments, the costimulatory domain can be derived from the costimulatory domain of CD28, 4- IBB, CD3 zeta, CD27, ICOS, or OX40. In some embodiments, the costimulatory domain is derived from a protein of the same species as the subject. In other embodiments, the costimulatory domain is derived from a protein of a different species than the subject.
[0149] In some embodiments, the polynucleotide can further comprise a detectable marker or purification marker and/or a polynucleotide encoding a detectable marker or a purification marker, each conjugated to the polynucleotide. [0150] Flexible spacer. The engineered T-cell receptor may optionally further comprise a spacer domain of up to 300 amino acids, preferably 5 to 100 amino acids, more preferably 25 to 50 amino acids. For example, the spacer may be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50 amino acids. A spacer domain may comprise, for example, a portion of a human Fc domain, a CH3 domain, or the hinge region of any immunoglobulin, such as IgA, IgD, IgE, IgG, or IgM, or variants thereof. Additional spacers include, but are not limited to, CD4, CD8, and CD28 hinge regions.
Vectors
[0151] In some embodiments, present disclosure provides vectors comprising, consisting, or alternatively consisting essential of a polynucleotide according to any of the embodiments described herein. In some embodiments, the polynucleotide is operatively linked to a promoter. In some aspects, the vector is from the group of: a plasmid, a retroviral vector, a lentiviral vector, an adenoviral vector, or an adeno-associated viral vector. In some aspects, the vector is an expression vector. In some aspects, the vector is useful for integration in genomic DNA, replication, viral particle production, and/or infection or transduction with high efficiency. In certain embodiments, the disclosed vectors comprise an element that enhances or induces a regulatory T-cell phenotype. In other embodiments, the disclosed vectors comprise an element that reduces or inhibits an effector T-cell phenotype.
[0152] In some embodiments, the isolated nucleic acid sequence is comprised in a vector. In certain embodiments, the vector is a plasmid. In other embodiments, the vector is a viral vector. In specific embodiments, the vector is a lentiviral vector.
[0153] In one aspect, the term "vector" intends a recombinant vector that retains the ability to infect and transduce non-dividing and/or slowly-dividing cells and integrate into the target cell's genome. In several aspects, the vector is derived from or based on a wild-type virus. In further aspects, the vector is derived from or based on a wild-type lentivirus. Examples of such, include without limitation, human immunodeficiency virus (HIV), equine infectious anemia virus (EIAV), simian immunodeficiency virus (SIV) and feline immunodeficiency virus (FIV). Alternatively, it is contemplated that other retrovirus can be used as a basis for a vector backbone such murine leukemia virus (MLV). It will be evident that a viral vector according to the disclosure need not be confined to the components of a particular virus. The viral vector may comprise components derived from two or more different viruses, and may also comprise synthetic components. Vector components can be manipulated to obtain desired characteristics, such as target cell specificity.
[0154] The recombinant vectors of this disclosure may be derived from primates and non- primates. Examples of primate lentiviruses include the human immunodeficiency virus (HIV), the causative agent of human acquired immunodeficiency syndrome (AIDS), and the simian immunodeficiency virus (SIV). The non-primate lentiviral group includes the prototype "slow virus" visna/maedi virus (VMV), as well as the related caprine arthritis- encephalitis virus (CAEV), equine infectious anemia virus (EIAV) and the more recently described feline immunodeficiency virus (FIV) and bovine immunodeficiency virus (BIV). Recombinant lentiviral vectors are known in the art, e.g., see US Patent Nos. 6,924,123; 7,056,699; 7,07,993; 7,419,829 and 7,442,551.
[0155] Retroviral vectors for use in this disclosure include, but are not limited to pLenti series versions 4, 6, and 6.2 (Invitrogen); "ViraPower" system (Lentigen Corp.), pHIV-7- GFP, "Lenti-X", pLVX, (Clontech), pLKO. l-puro (Sigma-Aldrich), pLemiR (Open
Biosystems), and pLV (Charite Medical School, Institute of Virology (CBF), Berlin,
Germany).
[0156] In order to confirm the presence of the recombinant DNA sequence in the host cell, a variety of assays can be performed. Such assays include, for example, Southern and Northern blotting, RT-PCR and PCR; biochemical assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELlSAs and Western blots) or by assays described herein to identify agents falling within the scope of the disclosure.
[0157] The disclosed vectors can further comprise a regulatory element such as an enhancer element. Nonlimiting examples of enhancers include, for example, WPRE, the human cytomegalovirus (HCMV) immediate early (IE) enhancer, the enhancer of the Moloney Murine Sarcoma Virus (MMSV), the U3 region of Rous Sarcoma Virus (RSV), the U3 region of Spleen Focus Forming Virus (SFFV), and the HCMV IE enhancer.
[0158] The disclosed vectors can further comprise a polynucleotide encoding all or part of forkhead box P3 ("FoxP3," NM_001114377, NM_014009), or an equivalent thereof. FoxP3 may be operatively linked to a regulatory control element such as a promoter or an internal ribosome entry site (IRES). In some embodiments, FoxP3 is fused to a detectable marker such as GFP. In some embodiments, the ubiquitin binding sites in FoxP3 are mutated to reduce degradation and/or stabilize the protein. In some embodiments, the STUB1 gene (NM_005861, M_001293197, or an equivalent thereof) is included in the vector to reduce degradation and/or stabilize the protein. A nonlimiting example of the nucleotide sequence of FoxP3 is: GCACACACTC ATCGAAAAAA ATTTGGATTA TTAGAAGAGA
GAGGTCTGCG GCTTCCACAC CGTACAGCGT GGTTTTTCTT CTCGGTATAA AAGCAAAGTT GTTTTTGATA CGTGACAGTT TCCCACAAGC CAGGCTGATC CTTTTCTGTC AGTCCACTTC ACCAAGCCTG CCCTTGGACA AGGACCCGAT GCCCAACCCC AGGCCTGGCA AGCCCTCGGC CCCTTCCTTG GCCCTTGGCC CATCCCCAGG AGCCTCGCCC AGC TGGAGGG CTGCACCCAA AGCCTCAGAC CTGCTGGGGG CCCGGGGCCC AGGGGG A AC C TTCCAGGGCC GAGATCTTCG AGGCGGGGCC CATGCCTCCT CTTCTTCCTT GAACCCCATG CCACCATCGC AGCTGCAGCT CTCAACGGTG GATGCCCACG CCCGGACCCC TGTGCTGCAG GTGCACCCCC TGGAGAGCCC AGCCATGATC AGCCTCACAC CACCCACCAC CGCCACTGGG GTCTTCTCCC TCAAGGCCCG GCCTGGCCTC CCACCTGGGA TCAACGTGGC CAGCCTGGAA TGGGTGTCCA GGGAGCCGGC ACTGCTCTGC ACCTTCCCAA ATCCCAGTGC ACCCAGGAAG GACAGCACCC TTTCGGCTGT GCCCCAGAGC TCCTACCCAC TGCTGGCAAA TGGTGTCTGC AAGTGGCCCG GATGTGAGAA GGTCTTCGAA GAGCCAGAGG ACTTCCTCAA GCACTGCCAG GCGGACCATC TTCTGGATGA GAAGGGCAGG GCACAATGTC TCCTCCAGAG AGAGATGGTA CAGTCTCTGG AGCAGCAGCT GGTGC TGGAG AAGGAGAAGC TGAGTGCCAT GCAGGCCCAC CTGGCTGGGA AAATGGCACT GACCAAGGCT TCATCTGTGG CAAGGGCTCC TGCTGCATCG TAGCTGCTGG CAGCCAAGGC CCTGTCGTCC CAGCCTGGTC TGGCCCCCGG GAGGCCCCTG ACAGCCTGTT TGCTGTCCGG AGGCACCTGT GGGGTAGCCA TGGAAACAGC ACATTCCCAG AGTTCCTCCA CAACATGGAC TACTTCAAGT TCCACAACAT GCGACCCCCT TTCACCTACG CCACGCTCAT CCGCTGGGCC ATCCTGGAGG CTCCAGAGAA GCAGCGGACA CTCAATGAGA TCTACCACTG GTTCACACGC ATGTTTGCCT TCTTCAGAAA CCATCCTGCC ACCTGGAAGA ACGCCATCCG CCACAACCTG AGTCTGC AC A AGTGCTTTGT GCGGGTGGAG AGCGAGAAGG GGGCTGTGTG GACCGTGGAT GAGCTGGAGT TCCGCAAGAA ACGGAGCCAG AGGCCCAGCA GGTGTTCCAA CCCTACACCT GGCCCCTGAC CTCAAGATCA AGGAAAGGAG GATGGACGAA CAGGGGCCAA ACTGGTGGGA GGCAGAGGTG GTGGGGGCAG GGATGATAGG CCCTGGATGT GCCCACAGGG ACCAAGAAGT GAGGTTTCCA CTGTCTTGCC TGCCAGGGCC CCTGTTCCCC CGCTGGCAGC CACCCCCTCC CCCATCATAT CCTTTGCCCC AAGGCTGCTC AGAGGGGCCC CGGTCCTGGC CCCAGCCCCC ACCTCCGCCC CAGACACACC CCCCAGTCGA GCCCTGCAGC CAAACAGAGC CTTCACAACC AGCCACACAG AGCCTGCCTC AGCTGCTCGC ACAGATTACT TCAGGGCTGG AAAAGTCACA CAGACACACA AAATGTCACA ATCCTGTCCC TCACTCAACA CAAACCCCAA AACACAGAGA GCCTGCCTCA GTACACTCAA ACAACCTCAA AGCTGCATCA TCACACAATC ACACACAAGC ACAGCCCTGA CAACCCACAC ACCCCAAGGC ACGCACCCAC AGCCAGCCTC AGGGCCCACA GGGGCACTGT CAACACAGGG GTGTGCCCAG AGGCCTACAC AGAAGCAGCG TCAGTACCCT CAGGATCTGA GGTCCCAACA CGTGCTCGCT CACACACACG GCCTGTTAGA ATTCACCTGT GTATCTCACG CATATGCACA CGCACAGCCC CCCAGTGGGT CTCTTGAGTC CCGTGCAGAC ACACACAGCC ACACACACTG CCTTGCCAAA AATACCCCGT GTCTCCCCTG CCACTCACCT CACTCCCATT CCCTGAGCCC TGATCCATGC CTCAGCTTAG ACTGCAGAGG AACTACTCAT TTATTTGGGA TCCAAGGCCC CCAACCCACA GTACCGTCCC CAATAAACTG CAGCCGAGCT CCCCACAAAA AAAAAAAAAAAA.
[0159] The disclosed vectors can further comprise a polynucleotide encoding all or part of IL-10 ( M 000572) or an equivalent thereof. IL-10 may be operatively linked to a regulatory control element such as a promoter or an internal ribosome entry site (IRES). In some embodiments, IL-10 is fused to a detectable marker such as GFP. In some embodiments, the IL-10 is activation inducible. For example, expression of IL-10 may be under the control of a promoter activated by an inflammatory response (e.g., mxl promoter activated by interferon). A nonlimiting example of the nucleotide sequence of IL-10 is: ACACATCAGG
GGCTTGCTCT TGCAAAACCA AACCACAAGA CAGACTTGCA AAAGAAGGCA TGCACAGCTC AGCACTGCTC TGTTGCCTGG TCCTCCTGAC TGGGGTGAGG GCCAGCCCAG GCCAGGGCAC CCAGTCTGAG AACAGCTGCA CCCACTTCCC AGGCAACCTG CCTAACATGC TTCGAGATCT CCGAGATGCC TTCAGCAGAG TGAAGACTTT CTTTCAAATG AAGGATCAGC TGGACAACTT GTTGTTAAAG GAGTCCTTGC TGGAGGACTT TAAGGGTTAC CTGGGTTGCC AAGCCTTGTC TGAGATGATC CAGTTTTACC TGGAGGAGGT GATGCCCCAA GCTGAGAACC AAGACCCAGA CATCAAGGCG CATGTGAACT CCCTGGGGGA GAACCTGAAG ACCCTCAGGC TGAGGCTACG GCGCTGTCAT CGATTTCTTC CCTGTGAAAA CAAGAGCAAG GCCGTGGAGC AGGTGAAGAA TGCCTTTAAT AAGCTCCAAG AGAAAGGCAT CTACAAAGCC ATGAGTGAGT TTGACATCTT CATCAACTAC ATAGAAGCCT ACATGACAAT GAAGATACGA AACTGAGACA TCAGGGTGGC GACTCTATAG ACTCTAGGAC ATAAATTAGA GGTCTCCAAA ATCGGATCTG GGGCTCTGGG ATAGCTGACC CAGCCCCTTG AGAAACCTTA TTGTACCTCT CTTATAGAAT ATTTATTACC TCTGATACCT CAACCCCCAT TTCTATTTAT TTACTGAGCT TCTCTGTGAA CGATTTAGAA AGAAGCCCAA TATTATAATT TTTTTCAATA TTTATTATTT TCACCTGTTT TTAAGCTGTT TCCATAGGGT GACACACTAT GGTATTTGAG TGTTTTAAGA TAAATTATAA GTTACATAAG GGAGGAAAAA AAATGTTCTT TGGGG AGC C A ACAGAAGCTT CCATTCCAAG CCTGACCACG CTTTCTAGCT GTTGAGCTGT TTTCCCTGAC CTCCCTCTAA TTTATCTTGT CTCTGGGCTT GGGGCTTCCT AACTGCTACA AATACTCTTA GGAAGAGAAA CCAGGGAGCC CCTTTGATGA TTAATTCACC TTCCAGTGTC TCGGAGGGAT TCCCCTAACC TCATTCCCCA ACCACTTCAT TCTTGAAAGC TGTGGCCAGC TTGTTATTTA TAACAACCTA AATTTGGTTC TAGGCCGGGC GCGGTGGCTC ACGCCTGTAA TCCCAGCACT TTGGGAGGCT GAGGCGGGTG GATCACTTGA GGTCAGGAGT TCCTAACCAG CCTGGTCAAC ATGGTGAAAC CCCGTCTCTA CTAAAAATAC AAAAATTAGC CGGGCATGGT GGCGCGCACC TGTAATCCCA GCTACTTGGG AGGCTGAGGC AAGAGAATTG CTTGAACCCA GGAGATGGAA GTTGCAGTGA GCTGATATCA TGCCCCTGTA CTCCAGCCTG GGTGACAGAG CAAGACTCTG TCTCAAAAAA TAAAAATAAA AATAAATTTG GTTCTAATAG AACTCAGTTT TAACTAGAAT TTATTCAATT CCTCTGGGAA TGTTACATTG TTTGTCTGTC TTCATAGCAG ATTTTAATTT TGAATAAATA AATGTATCTT ATTCACATC.
[0160] The disclosed vectors can further comprise a suicide gene to induce cell death in cells comprising and/or expressing the vector. In some aspects, the suicide gene is operatively linked to a promoter. In some aspects, the promoter is inducible (e.g., tetracycline-inducible). In some aspects, the suicide gene is triggered following adoptive cell treatment (Buddee et al., PLoS One, (2013)). Alternatively, the suicide gene may function to downregulate expression of the engineered T-cell receptor following binding to the target antigen (WO 2016/011210). Non-limiting examples of suicide genes include caspase-9 (NM_001229, NM_001278054, NM_032996, or its equivalent) and thymidine kinase (NM_003258 or its equivalent).
Cells, Populations, and Animals
[0161] Aspects of the present disclosure relate to cells comprising, consisting, or alternatively consisting essentially of a polynucleotide, engineered T-cell receptor, or vector according to any of the embodiments disclosed herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T- cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In one aspect, the cells express the polynucleotide or vector according to any of the embodiments disclosed herein. In some aspects, the cells comprise two or more polynucleotides encoding distinct engineered T-cell receptors. In some aspects, the cells comprise two or more vectors encoding distinct engineered T-cell receptors. The cells comprising two or more vectors or polynucleotides may express engineered T-cell receptors that bind a plurality of antigens (e.g., the cells comprise a plurality of engineered T-cell receptors have distinct antigen specificities).
[0162] In some aspects, the cell is an isolated cell. In a particular aspect, the cell is isolated or purified from a subject's peripheral blood mononuclear cells and in other aspects it is a cultured cell from a cell population that optionally is commercially available. The cell is of any appropriate species for the subject being treating, e.g., mammalian, canine, feline, murine or human. In some aspects, the cell is a leukocyte. The leukocyte may be murine, canine, feline, simian, or human. In further aspects, the cell is a T-cell. The T-cell may be regulatory T-cell, a regulatory memory T-cell, a central memory T-cell, a naive T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell, preferably a regulatory T-cell. In other aspects, the cell is an K cell that is isolated or a cultured cell from a cell population that optionally is commercially available. The cell is of any appropriate species for the subject being treating, e.g., mammalian, canine, feline, murine or human.
[0163] In some aspects, the cell comprises and/or expresses an engineered T-cell receptor on the cell surface. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds an antigen that binds an MHC molecule, wherein the antigen binds to the MHC molecule with high affinity, and/or wherein the antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T- cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some
embodiments, the polynucleotide or vector encodes the engineered T cell receptor.
[0164] In one aspect, the cell further comprises the athero-relevant antigen-MHC complex bound to the extracellular antigen binding domain.
[0165] Also provided herein is a population of a cell according to any of the embodiments described herein. In one aspect, the population is substantially homogenous. Substantially homogenous intends a plurality of cells of greater than 50%, 60%>, 70%, 80%>, or 95% purity or homogeneity. In some aspects, the population is a heterogenous mixture of two or more cells comprising and/or expressing distinct engineered T-cell receptors with distinct antigen specificities.
[0166] In certain embodiments, provided herein is a non-human animal comprising, consisting, or alternatively consisting essentially of the polynucleotide or vector of any one of the embodiments described herein.
Compositions and Kits
[0167] Additional aspects of the invention relate to compositions comprising, consisting of, or alternatively consisting essentially of a carrier and one or more of the products disclosed herein: a polynucleotide, vector, engineered T-cell receptor, cell, modified cell, isolated cell, or population comprising an engineered T-cell receptor according to any of the embodiments disclosed herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero- relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some embodiments, the carrier is a pharmaceutically acceptable carrier.
[0168] In some aspects, the composition comprises a pharmaceutically or physiologically acceptable carrier, diluent, or excipient. Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives. Compositions of the present disclosure may be formulated for oral, intravenous, intranasal, intramuscular, intrathecal, topical, enteral, and/or parenteral administration. In particular embodiments, the compositions of the present disclosure are formulated for intravenous administration. In one embodiment, the
compositions are administered systemically. In some embodiments, the addition of one or more antimicrobial agents such as chlorobutanol, ascorbic acid, parabens, thermerosal, or the like can be used to prevent the growth of microorganisms. It may also be preferable to include agents that alter the tonicity such as sugars or salts. For compositions comprising cells or modified cells, solutions can be prepared in suitable diluents such as saline, phosphate-buffered saline, hydrogel, nutrient carrier, albumin, recombinant albumin,
Dulbecco's Modified Eagle Medium, glucose, water, ethanol, glycerol, liquid polyethylene glycol(s), various oils, and/or mixtures thereof, and other diluents known to those skilled in the art. [0169] Administration of the cells or compositions can be effected in one dose, continuously or intermittently throughout the course of treatment. Methods of determining the most effective means and dosage of administration are known to those of skill in the art and will vary with the composition used for therapy, the purpose of the therapy and the subject being treated. In some aspects, a matrix and or catheter may be used. Preferably, the administration is in such an amount as will be therapeutically effective and immune modifying. Single or multiple administrations can be carried out with the dose level and pattern being selected by the treating physician. Suitable dosage formulations and methods of administering the agents are known in the art.
[0170] In some cases, it will be desirable to have multiple administrations of a composition, about, at least about, or at most about 3, 4, 5, 6, 7, 8, 9, 10 or more administrations. The administrations will normally range from 1, 2, 3, 4, 5, 6, or 7 days to annual intervals, more usually from one to two week intervals. Periodic boosters at intervals of every other day, twice a week, weekly, biweekly, monthly, or 0.1, 0.2, 0.3, 0.4, 0.5, 1, 2, 3,4 or 5 years, usually two years, will be desirable to maintain the condition of the immune system. The administration(s) may be followed by assays for autoreactive immune responses,
inflammatory cytokine production, cytotoxic cells, and T cell activity.
[0171] The carrier may be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid poly(ethylene glycol), and the like), suitable mixtures thereof, and vegetable oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion, and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.
[0172] In a further aspect, the cells, populations, vectors, and polynucleotides of the disclosure can be administered in combination with other traditional therapies. These include, but are not limited to, the administration of immunosuppressive or modulating therapies or treatments and therapies to ameliorate the symptoms of and/or treat
cardiovascular disease. Non-limiting examples of immunosuppressive agents or therapies include anti-inflammatory drugs such as sulfasalazine, corticosteroids such as prednisone, and immune system suppressors such as azathioprine and mercaptopurine. Additional classes of immune modulating therapies or treatments include but are not limited to a calcineurin inhibitor, a chemokine receptor inhibitor, a glucocorticoid, an mTOR inhibitor, an anti- metabolic compound, a phosphodiesterase-5 inhibitor, an antibody, or a leukocyte function antigen-3/Fc fusion protein. Therapies or treatments to ameliorate the symptoms of and/or treat cardiovascular disease include but are not limited to cholesterol medications such as statins, anti-platelet medications such as aspirin, angiotensin-converting enzyme inhibitors, calcium channel blockers, diuretics, and invasive procedures such as angioplasty, stent placement, endarterectomy, fibinolytic therapy, and/or bypass surgery.
[0173] The cells and populations of cell are administered to the host using methods known in the art and described, for example, in International Application No. PCT/US2011/064191. This administration of the cells or compositions of the invention can be performed to generate an animal model of the relevant disease, disorder, or condition for experimental assays and screens.
[0174] Also provided herein are kits comprising, consisting of, or alternatively consisting essentially of a composition as described herein and instructions for use. Additional reagents and/or instructions can further be provided as necessary.
Methods of Producing Modified Cells
[0175] Also provided herein is a method of producing a modified cell, comprising, consisting, or alternatively consisting essentially of: (i) introducing a polynucleotide or vector according to any of the embodiments described herein into a cell or a population of cells, and optionally culturing the cell or population of cells under conditions that favor expression of the polynucleotide or the vector; (ii) and further optionally selecting a cell or enriching a cell or a subpopulation of cells that have been successfully modified with the polynucleotide or vector of step (i). In some embodiments, the cells are selected from or isolated from a group consisting of leukocytes, T-cells and NK-cells. In certain embodiments, the T-cells are regulatory T-cells, naive T-cells, central memory T-cells, regulatory memory T-cells, effector memory T-cells, CD4+ T-cells, or a CD8+ T-cells. In some aspects, the cell is isolated from a subject. The subject may be a murine, canine, feline, simian, or a human.
[0176] In certain embodiments, step (i) comprises CRISPR mediated gene editing to introduce the polynucleotide into the genome of the target cell. Methods of using CRISPR to perform gene editing are known in the art. In some embodiments, the polynucleotide or vector is introduced to the target cell via a viral particle comprising, consisting of, or alternatively consisting essentially of a polynucleotide or vector according to the
embodiments described herein.
[0177] In some embodiments, cells expressing the disclosed engineered T-cell receptors may be further modified to express one or more of: FoxP3, IL-10, a detectable or selectable marker, a suicide gene, and/or an equivalent of each thereof as described herein. In some embodiments, one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene may be encoded on one or more vectors introduced to the cell or subpopulation of modified cells. Optionally, each gene may be operatively linked to an expression control element such as a promoter. In some embodiments, one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene are encoded on the same vector. In other embodiments, one or one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene are encoded on separate vectors. In yet another embodiment, one or more of FoxP3, IL-10, the detectable or selectable marker, and/or a suicide gene is encoded on the same vector that encodes an engineered T-cell receptor according to any of the embodiments described herein.
[0178] In certain embodiments, FoxP3 expression is induced by contacting the cell or subpopulation of modified cells with an effective amount of transforming growth factor beta 1-4 ("TGFp," e.g., TGFpl : P 000651; available from Peprotech rhTGFpl cat# 100-21, 100-21C) and/or IL-10 (available from Peprotech rhIL-10 cat# 200-10), thereby inducing FoxP3 expression in the cell or subpopulation of modified cells. In some aspects, the culture conditions comprise about 1 to about 10 ng/mL, or alternatively about 5 to about 20 ng/mL, or alternatively about 5 to about 30 ng/mL, or alternatively about 5 to about 40 ng/mL, or alternatively about 5 to about 50 ng/mL, or alternatively about 5 to about 100 ng/mL, or alternatively about 5 to about 250 ng/mL, or alternatively about 5 to about 500 ng/mL, or alternatively about 25 to about 75 ng/mL, or alternatively about 50 to about 100 ng/mL, or alternatively about 100 to about 500 ng/mL, or or alternatively about 100 ng/mL to about 1 μg/mL, or alternatively about 1 μg/mL to about 10 μg/mL, or alternatively about 10 μg/mL to about 50 μg/mL, or alternatively about 50 μg/mL to about 100 μg/mL, or alternatively about 100 μg/mL to about 500 μg/mL, or alternatively about 100 μg/mL to about 1000 μg/mL of TGFP and/or IL-10. In particular aspects, the culture conditions comprise about 10 ng/mL, or alternatively about 15 ng/mL, or alternatively about 20 ng/mL, or alternatively about 25 ng/mL, or alternatively about 30 ng/mL, or alternatively about 40 ng/mL, or alternatively about 50 ng/ml, or alternatively about 100 ng/mL, or alternatively about 200 ng/mL, or alternatively about 250 ng/mL, or alternatively about 300 ng/mL, or alternatively about 400 ng/mL, or alternatively about 500 ng/mL, or alternatively about 1 μg/mL of TGFP and/or IL- 10. Preferably, TGFP and/or IL-10 is about 5 to about 100 ng/mL.
[0179] In certain embodiments, the cell or subpopulation of modified cells is contacted with an effective amount of anti -interferon γ antibody (e.g., ThermoFisher cat# 16-7311- 81)(Skurkovich, S. et al. J. of Immune Based Therapies, Vaccines, and Antimicrobials, 4: 1-8 (2015)) anti IL-5 antibody (e.g., mepolizumab (GlaxoSmithKline)) (Mukhergee, M. et al. World Allergy Organ J. 7(1): 32 (2014)), anti-T F antibody or inhibitor (e.g., infliximab, adalimumab, certolizumab pegol, golimumab, etenercept, or bupropion), and/or anti-IL-7 antibody (e.g., R&D Systems Human IL-7 antibody cat# MAB207). In some aspects, the antibodies are activation-induced.
Sources of Isolated Cells
[0180] Prior to expansion and genetic modification of the cells disclosed herein, cells may be obtained from a subject - for instance, in embodiments involving autologous therapy - or a commercially available culture, that are available from the American Type Culture
Collection (ATCC), for example.
[0181] Cells can be obtained from a number of sources in a subject, including peripheral blood mononuclear cells (PBMC), bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
[0182] Methods of isolating relevant cells are well known in the art and can be readily adapted to the present application. Isolation methods for use in relation to this disclosure include, but are not limited to Life Technologies Dynabeads® system; STEMcell
Technologies EasySep™, RoboSep™, RosetteSep™, SepMate™; Miltenyi Biotec MACS™ cell separation kits, fluorescence activated cell sorting (FACS), and other commercially available cell separation and isolation kits. Particular subpopulations of immune cells may be isolated through the use of beads or other binding agents available in such kits specific to unique cell surface markers. For example, MACS™ CD4+ and CD8+ MicroBeads or complement depletion may be used to isolate CD4+ and CD8+ T-cells.
[0183] Alternatively, cells may be obtained through commercially available cell lines, including but not limited to BCL2 (AAA) Jurkat (ATCC® CRL-2902™), BCL2 (S70A) Jurkat (ATCC® CRL-2900™), BCL2 (S87A) Jurkat (ATCC® CRL-2901™), BCL2 Jurkat (ATCC® CRL-2899™), Neo Jurkat (ATCC® CRL-2898™), NK-92 (ATCC® CRL- 2407™), NK-92MI (ATCC® CRL-2408™).
[0184] In some aspects, appropriate cells may be derived from stem cells or lymphoid progenitors including iPS cells, ES cells, hematopoietic stem cells, common lymphoid progenitors (CLPs), DN1, DN2, DN3, DN4, or DP cells.
[0185] In one aspect, the cells are autologous to the subject being treated. In another aspect, the cells are allogeneic to the subject being treated.
Packaging vector and cell lines
[0186] Polypeptides encoding engineered T-cell receptors can be packaged into a lentiviral or retroviral packaging system by using a packaging vector and cell lines. The packaging plasmid includes, but is not limited to retroviral vector, lentiviral vector, adenoviral vector, and adeno-associated viral vector. The packaging vector contains elements and sequences that facilitate the delivery of genetic materials into cells. For example, the retroviral constructs are packaging plasmids comprising at least one retroviral helper DNA sequence derived from a replication-incompetent retroviral genome encoding in trans all virion proteins required to package a replication incompetent retroviral vector, and for producing virion proteins capable of packaging the replication-incompetent retroviral vector at high titer, without the production of replication-competent helper virus. The retroviral DNA sequence lacks the region encoding the native enhancer and/or promoter of the viral 5' LTR of the virus, and lacks both the psi function sequence responsible for packaging helper genome and the 3' LTR, but encodes a foreign polyadenylation site, for example the SV40
polyadenylation site, and a foreign enhancer and/or promoter which directs efficient transcription in a cell type where virus production is desired. The retrovirus is a leukemia virus such as a Moloney Murine Leukemia Virus (MMLV), the Human Immunodeficiency Virus (HIV), or the Gibbon Ape Leukemia virus (GALV). The foreign enhancer and promoter may be the human cytomegalovirus (HCMV) immediate early (IE) enhancer and promoter, the enhancer and promoter (U3 region) of the Moloney Murine Sarcoma Virus (MMSV), the U3 region of Rous Sarcoma Virus (RSV), the U3 region of Spleen Focus Forming Virus (SFFV), or the HCMV IE enhancer joined to the native Moloney Murine Leukemia Virus (MMLV) promoter. The retroviral packaging plasmid may consist of two retroviral helper DNA sequences encoded by plasmid based expression vectors, for example where a first helper sequence contains a cDNA encoding the gag and pol proteins of ecotropic MMLV or GALV and a second helper sequence contains a cDNA encoding the env protein. The Env gene, which determines the host range, may be derived from the genes encoding xenotropic, amphotropic, ecotropic, polytropic (mink focus forming) or 10A1 murine leukemia virus env proteins, or the Gibbon Ape Leukemia Virus (GALV env protein, the Human Immunodeficiency Virus env (gpl60) protein, the Vesicular Stomatitus Virus (VSV) G protein, the Human T cell leukemia (HTLV) type I and II env gene products, chimeric envelope gene derived from combinations of one or more of the aforementioned env genes or chimeric envelope genes encoding the cytoplasmic and transmembrane of the aforementioned env gene products and a monoclonal antibody directed against a specific surface molecule on a desired target cell.
Activation and Expansion of T Cells
[0187] Whether prior to or after genetic modification of the T cells to express a desirable engineered T-cell receptor, the cells can be activated and expanded using generally known methods such as those described in U.S. Patent Nos. 6,352,694; 6,534,055; 6,905,680;
6,692,964; 5,858,358; 6,887,466; 6,905,681 ; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7, 175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041. Stimulation with the antigen and/or MHC ex vivo can activate and expand the selected engineered T-cell receptor expressing cell subpopulation.
[0188] Methods of activating relevant cells are well known in the art and can be readily adapted to the present application; an exemplary method is described in the examples below. Isolation methods for use in relation to this disclosure include, but are not limited to Life Technologies Dynabeads® system activation and expansion kits; BD Biosciences
Phosflow™ activation kits, Miltenyi Biotec MACS™ activation/expansion kits, and other commercially available cell kits specific to activation moieties of the relevant cell. Particular subpopulations of immune cells may be activated or expanded through the use of beads or other agents available in such kits. For example, a-CD3/a-CD28 Dynabeads® may be used to activate and expand a population of isolated T-cells.
Methods of Use
[0189] The polynucleotides, cells, vectors, populations, and modified cells of the present disclosure may be used to induce an anti-inflammatory response in a cell, tissue, or subject, mediate an immune response in a cell, tissue, or subject or mediate an inflammatory response in a cell tissue, or subject in vitro, ex vivo, or in vivo. The polynucleotides, cells, vectors, populations, and modified cells of the present invention may be administered either alone or in combination with diluents, known anti-cancer therapeutics, and/or with other components such as cytokines or other cell populations that are immunostimulatory to a subject in need thereof. The cell, tissue, or subject may be canine, equine, murine, rat, simian, feline, or human.
[0190] Method aspects of the present disclosure relate to methods for inducing an antiinflammatory response, mediating an immune response, or mediating an inflammatory response in a subject in need thereof, the method comprising, consisting of, or alternatively consisting essentially of administering to a subject in need thereof an effective amount of the polynucleotides, vectors, cells, modified cells, compositions, or populations disclosed herein. In some aspects, the response is characterized by suppression of pathogenic T-cells. In certain aspects, the response is characterized by increased or decreased expression of one or more pro-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more pro-inflammatory cytokines comprise IL-Ιβ, T F-a, IFN-γ, IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL-21, IL-23, IL-27, and/or TGF-β. In additional aspects, the response is characterized by increased or decreased expression of one or more antiinflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more anti-inflammatory cytokines comprise TGF-β, IL-IRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL- 35, and/or INF-a. In further aspects, the cell, modified cell, or population is autologous to the subject. The subject may be canine, equine, murine, rat, simian, feline, or human.
[0191] Additional method aspects of the present disclosure relate to methods for enhancing the activity of a regulatory T-cell, the methods comprising, consisting of, or alternatively consisting essentially of administering an effective amount of the polynucleotides, vectors, cells, modified cells, compositions, or populations disclosed herein. In some aspects, the enhanced activity of the regulatory T-cell is characterized by increased expression of IL-10. The subject may be canine, equine, murine, rat, simian, feline, or human.
[0192] In one aspect, the present disclosure provides a prophylactic method of protecting a subject against an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage, the method comprising, consisting of, or alternatively consisting essentially of administering to a subject an effective amount of the polynucleotides, vectors, engineered T-cell receptors, cells, modified cells, compositions, or populations disclosed herein. Engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero- relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In additional aspects, the method reduces the chance that a subject will experience an adverse symptom of the adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis. In some aspects, the method reduces the chance that a subject will develop adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis. In some aspects, the subject is at high risk for developing an adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis. In further aspects, the method comprises plaque regression. The subject may be canine, equine, murine, rat, simian, feline, or human.
[0193] Also provided are methods for treating an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage in a subject in need thereof, the methods comprising, consisting of, or alternatively consisting essentially of administering to a subject in need thereof an effective amount of the polynucleotides, vectors, engineered T-cell receptors, cells, modified cells, compositions, or populations disclosed herein. Engineered T- cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some
embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. In some aspects, the adverse cardiovascular event or cardiovascular disease, disorder, or damage is from the group of: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma. In additional aspects, the method reduces the chance that a subject will experience an adverse symptom of the adverse cardiovascular event, cardiovascular disease or liver disease, disorder or damage, including atherosclerosis. In further aspects, the method comprises plaque regression. The subject may be canine, equine, murine, rat, simian, feline, or human.
[0194] In some aspects, provided herein is a method of treating a disease or condition involving an inflammatory response or related to inflammation in a subject in need thereof, comprising, consisting of, or alternatively consisting essentially of administering to a subject in need thereof an effective amount of the polynucleotides, vectors, engineered T-cell receptors, cells, modified cells, compositions, or populations disclosed herein. Engineered T- cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the antigen is bound to an MHC molecule. In some aspects, the engineered T-cell receptors described herein may comprise, consist of, or alternatively consist essentially of: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero-relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO. In some aspects, the athero-relevant antigen induces a specific cytokine response, optionally an IL-17, ΠΤΝΓγ, and/or IL-5 response. In some aspects, the engineered T-cell receptor is a modified T-cell receptor. In other aspects, the engineered T-cell receptor is a chimeric antigen receptor (CAR). In certain aspects, the extracellular antigen binding domain binds both the antigen and the MHC molecule. In some
embodiments, the polynucleotide or vector encodes the engineered T cell receptor. In some embodiments, the cell or modified cell expresses the polynucleotide or vector and/or comprises an engineered T cell receptor on a surface of the cell or modified cell. The subject may be canine, equine, murine, rat, simian, feline, or human.
[0195] In some aspects, the cell, modified cell, or population for use in any of the herein disclosed methods is autologous to the subject being treated and/or to whom the cell, modified cell, or population is administered. In other aspects, the cell, modified cell, or population is allogenic to the subject.
[0196] In additional embodiments, the methods described herein further comprise a combination therapy comprising, consisting, or consisting essentially of administration of an effective amount of one or more therapeutic compounds. These include, but are not limited to, the immunosuppressive or modulating therapies or treatments and therapies to ameliorate the symptoms of and/or treat cardiovascular disease. Non-limiting examples of
immunosuppressive agents or therapies include anti-inflammatory drugs such as
sulfasalazine, corticosteroids such as prednisone, and immune system suppressors such as azathioprine and mercaptopurine. Additional classes of immune modulating therapies or treatments include but are not limited to a calcineurin inhibitor, a chemokine receptor inhibitor, a glucocorticoid, an mTOR inhibitor, an anti-metabolic compound, a
phosphodiesterase-5 inhibitor, an antibody, or a leukocyte function antigen-3/Fc fusion protein. Therapies or treatments to ameliorate the symptoms of and/or treat cardiovascular disease include but are not limited to cholesterol medications such as statins, anti-platelet medications such as aspirin, angiotensin-converting enzyme inhibitors, calcium channel blockers, and diuretics. In some embodiments, the subject has been treated with one or more surgical interventions such as angioplasty, stent placement, endarterectomy, fibinolytic therapy, and/or bypass surgery.
[0197] In some embodiments, the endogenous T-cells and/or other lymphocytes of the patient are depleted prior to administration of an effective amount of the polynucleotides, vectors, cells, modified cells, compositions, or populations disclosed herein. [0198] Methods of the present disclosure may be practiced by any mode of administration or delivery, or by any route, systemic, regional and local administration or delivery. Exemplary administration and delivery routes include intravenous (i.v.), intraperitoneal (i.p.), intrarterial, intramuscular, mucosal, inhalation, respiration, intranasal, intubation, parenteral,
subcutaneous, intra-pleural, topical, dermal, intradermal, transdermal, transmucosal, intracranial, intra-spinal, rectal, oral (alimentary), intrapulmonary, intrapulmonary instillation, buccal, sublingual, intravascular, intrathecal, intracavity, iontophoretic, intraocular, ophthalmic, optical, intraglandular, intraorgan, or intralymphatic. Administration may be systemic. Pharmaceutical compositions of the present invention may be administered in a manner appropriate to the disease, condition, or symptom to be treated or prevented. The quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient's disease, although appropriate dosages may be determined by clinical trials.
[0199] The following examples are illustrative of procedures which can be used in various instances in carrying the disclosure into effect.
EXAMPLES
Example 1: Development of Adoptive Cell Therapy
[0200] ApoBlOO is an apolipoprotein of about 4500 amino acids long and has been shown to be a component involved in the development of atherosclerosis. ApoBlOO has previously been suggested as being an autoantigen relevant to atherosclerosis. Regions of this apolipoprotein that activate T-cells through TCRs to induce inflammatory responses in atherosclerosis were recently identified. 30 peptides that could potentially be used in human patients were identified and screened for binding to 26 HLA alleles by competition assay and peptides were found that bound HLA alleles at 10 nM or better (see Tables 2 and 3 below).
Table 2: ApoBlOO Peptide Binding to Class II HLA Alleles
Figure imgf000079_0001
3563.0020 RGLKLATALSLSNKF 3391 5 4 13 22
3563.0010 HFSNVFRSVMAPFTM 1891 6 3 12 21
3563.0018 SLFFSAQPFEITAST 3036 5 6 10 21
3563.0005 TLTAFGFASADLIEI 676 4 6 10 20
3563.0008 VGSKLIVAMSSWLQK 1226 5 4 1 1 20
3563.0014 HVKHFVINLIGDFEV 2316 5 4 1 1 20
3563.0009 IKHIYAISSAALSAS 1836 4 2 13 19
3563.0022 YKKLRTSSFALNLPT 3771 6 1 12 19
3563.0028 KI V SLIKNLL V ALKD 4406 5 3 1 1 19
3563.0007 VEFVTNMGIIIPDFA 881 3 5 10 18
3563.0017 LEVLNFDFQANAQLS 2801 3 4 1 1 18
3563.0025 KFTYLINYIQDEINT 4321 2 5 1 1 18
3563.0015 LIINWLQEALSSASL 2491 1 4 12 17
3563.0023 ILFSYFQDLVITLPF 4241 4 3 10 17
3563.0012 LSQLQTYMIQFDQYI 2171 3 4 9 16
3563.0021 EGHLRFLKNIILPVY 3666 3 2 1 1 16
3563.0024 QEVFKAIQSLKTTEV 4281 4 1 1 1 16
3563.0026 DEINTIFSDYIPYVF 4331 3 5 8 16
3563.0013 LHDLKIAIANIIDEI 2191 0 5 10 15
3563.0030 FLIYITELLKKLQST 4531 5 0 8 13
3563.0016 GKLYSILKIQSPLFT 2756 1 1 10 12
3563.0001 PALLALLALPALLLL 6 0 4 7 1 1
3563.0003 QELLDIANYLMEQIQ 461 1 4 6 1 1
3563.0002 LLIDVVTYLVALIPE 406 1 2 3 6
3563.0029 IDLSIQNYHTFLIYI 4521 0 1 3 4
P101 FGKQGFFPDSVNKALY
P102 TLYALSHAVNSYFDVD
P103 LYYKEDKTSLSASAAS Table 3: Peptide-HLA Affinity (IC50)
Figure imgf000081_0001
[0201] Atherosclerosis is an inflammation-related disease characterized by monocytes entering the subendothelial space of the aterrial wall where they differentiate into macrophages and foam cells (Lusis, Nature 407: 233 (2000); Glass & Witztum, Cell 104: 503 (2001); and Galkina & Ley, Annu. Rev. Immunol. 27: 165 (2009); Li & Glass, Nat. Med. 8: 1235 (2002)). Foam cell formation is induced by oxidized low density lipoprotein (oxLDL) and leads to production of pro-inflammatory factors and plaque formation.
Ultimately, plaque can rupture, resulting in serious negative clinical consequences like myocardial infarction or stroke. oxLDL-induced foam cell formation is promoted by scavenger receptors such as CD36 and SR-A, which allow uncontrolled accumulation of modified LDL cholesterol in foam cells (Libby et al., Am. J. Med. 104: 14S (1998); and Kunjathoor et al., J. Biol. Chem. 277: 49982 (2002)). [0202] Chimeric antigen receptors (CARs) and modified T-cell receptors offer two distinct approaches to alter immune cell specificity. The primary structural difference between these two receptors is based on their origin. CARs are typically derived from the small chain variable fragments (scFv) of antibody molecules. In contrast, modified TCRs are typically derived from sequenced, disease-relevant T cell receptors. Generally, CARs recognize surface bound antigens expressed by targeted cells without regard to MHC presentation, while modified TCRs recognize peptides presented by MHC molecules, similar to
endogenous TCRs that recognize cognate antigen-MHC complexes. Because modified TCRs bind to antigen-MHC complexes, they can be used to target both extracellular and
intracellular proteins. Both approaches are described in this example.
[0203] The adoptive cell therapy described herein relates to regulatory T-cells that are isolated from an atherosclerotic patient and transduced with factors that direct regulatory T- cell specificity to an ApoB peptide:MHC complex to maintain and promote regulatory T- cell function. Next, the cells are intravenously transfused back into the diseased patient or subject to provide a first in class therapy to slow and/or halt the progression of atherosclerosis.
[0204] Identify T-cell epitopes directed toward disease-relevant antigens. To identify peptide/MHC targets for the therapies described herein, T-cell epitopes appropriate for modulating the immune response with adoptive cell therapy and MHC haplotypes that can present the epitopes are identified (e.g., through epitope screen and next generation sequencing). Briefly, samples comprising peripheral blood mononuclear cells (PBMCs) are obtained from the venous blood of human subjects suffering from the disease or condition of interest (e.g., atherosclerosis). These samples are compared to control samples from healthy donors with no personal or family history of heart disease. The MHC haplotypes of the samples are identified by next-generation sequencing. Peptides comprising epitopes derived from autoantigen targets or other disease-relevant antigen targets are synthesized (e.g., fragments of ApoB 100). In some embodiments, the peptides are predicted to bind specific subtypes and/or alleles of MHC molecules, e.g., those identified to be associated with disease. Next, the PBMCs are stimulated with the synthesized peptides in culture for about two weeks or an appropriate period to measure response. Following the stimulation, inflammatory cytokines (e.g., IFNy or IL-5) are measured in the samples to detect a specific peptide-MHC immune response. Complexes of peptides with MHC molecules are chosen if the affinity of the binding of the peptide to the MHC is less than about 1000 nM or, in some embodiments, if the peptide elicits a cytokine response despite restriction to a particular MHC allele (e.g., binds promiscuously to a panel or several MHC alleles). In some embodiments, donors of the HLADRB 1 *0101 or HLADRB 1 *0701 genotype are specifically identified. Tetramers/dextramers can be used to identify and characterize ApoB specific CD4+ T cells and sort based on Treg, Thl and Thl7 markers.
[0205] Development of modified TCRs. Once disease relevant peptide/MHC complexes are identified, the corresponding TCR construct (CAR or transgenic TCR) is developed. In one approach, the variable regions of the T-cell receptor that recognizes the peptide-MHC are sequenced. First, peptide specific T-cells (e.g., CD4+ T-cells) are expanded in culture. Next, T-cells that produce inflammatory cytokines upon stimulation with peptide are selected and sequenced to determine the amino acid sequence of the variable regions of their T-cell receptor (TCR). HLA:peptide mulitmers (tetramers, dextramers) may be developed to enable cell-tracking and purification. In certain embodiments, the TCR of the present invention may target one or more of the MHC alleles listed in Table 4.
Table 4
MHC Alleles
DRB1 *01 :01
DRB1 *03 :01
DRB1 *04:01
DRB1 *07:01
DRB1 *08:02
DRB1 *09:01
DRB1 * 11 :01
DRB1 * 12:01
DRB1 * 13 :02
DRB1 * 15:01
DRB3 *01 :01
DRB3 *02:02
DRB4 *01 :01
DRB5 *01 :01
DPB1 *01 :01
DPB1 *02:01
DPB1 *03 :01 DPB 1 *04:01
DPB 1 *05 :01
DPB1 * 14:01
DQB1 *02:01
DQB1 *03 :01
DQB1 *03 :01
DQB1 *04:02
DQB1 *05:01
DQB1 *06:02
[0206] Developing scFv specific for selected peptide:MHC complexes. An alternative approach to TCR sequencing is to generate specific single-chain variable fragments (scFv) for specific peptide-MHC complexes. scFv is a fusion protein of the variable regions of immunoglobulin heavy and light chains, connected by linker peptide. scFv can be created from subcloned heavy and light chains derived from a monoclonal antibody or hybridoma, or by phage display. Peptide-MHC complexes identified in the epitope screen are selected for monoclonal antibody development or scFv development. For example, in atherosclerosis, the following combinations are targeted for development:
Table 5
Antibody development for ApoBrMHC
P 18(SLFFS AQPFEIT AST) :DRB 1 *0101
P18(SLFFSAQPFEITAST):DRB1 *0701
[0207] The selection criteria for optimal scFv or antibodies includes clones that produce soluble recombinant IgGl for in vitro blocking assays. If a suitable rodent model for a disease or condition exists, labeled recombinant IgG produced is tested to determine cellular localization and efficacy in high-multi-dose PoC experiments. Tetramers are developed for cell selection and purification. Once suitable a scFv is identified, the amino acid sequence is determined.
[0208] Develop construct and vector for generation of a-plastic, peptide-specific regulatory T-cells. Methods of cloning a polynucleotide encoding the modified TCR variable regions or the scFv sequenced above are known in the art. The additional components of an engineered T-cell receptor are also cloned into the polynucleotide, as applicable (e.g., transmembrane domain, intracellular signaling domain). The polynucleotide is then cloned into a vector. A lentiviral vector can be used as a vector backbone and to allow transduction of cells with high efficiency. Suitable alternative vectors are described herein.
[0209] The vector can further comprise a FoxP3 transcription factor to promote and maintain Treg function. In some aspects, the FoxP3 can be mutated to deactivate STUB1 or ubiquitin binding domains. In some aspects, additional gain of function mutations can be included. The vector can further comprise GFP or another detectable marker. Alternatively, the FoxP3 can be fused to GFP or another detectable marker to allow screening for FoxP3 positive cells.
[0210] Optionally, the vector can further comprise a selection marker, killing marker, and/or a suicide gene (e.g., caspase 9) to attenuate the life of a cell transduced with the vector. Such marker or gene can be inducible (e.g., rapamycin or doxycycline inducible). Additionally, the vector can comprise activation-inducible IL-10.
[0211] The vector is then introduced (e.g., via transduction, CRISPR, transfection) into enriched regulatory T-cells of a subject. Methods of enriching regulatory T-cells are known in the art and described herein. Alternatively, the vector is introduced into NK cells, CD4+ T-cells, CD8+ T-cells, regulatory memory T-cell, regulatory memory T-cells, central memory T-cell, naive T-cells, effector T-cells, or cytotoxic T-cells.
[0212] In vitro co-culture to measure downregulation of pathogenic T cell response.
The expression of the engineered T-cell receptor is measured in the modified cells. Next, the cells are stimulated with the peptide-MHC to measure IL-10 production in vitro. Cell plasticity is assayed in inflammatory cell culture conditions (e.g., in the presence of inflammatory cytokines and/or with co-expression of transcription factors). Suitable modified cells or populations of modified cells are expanded.
[0213] Develop and test efficacy and safety in animal model. A mouse model is used to determine whether cells comprising the engineered T-cell receptor can modulate the immune response in an appropriate disease model. For example, in atherosclerosis, such models may include apoE-/- model and the LDLR-/- (Getz, G. et al. Arterioscler Throm. Vase. Biol. 32(5): 1104-1115). These mice may be crossed with mice carrying humanized alleles of MHC molecules. Additional models in various species are known in the art (see, e.g., Camacho, P. et al. Am. J. Cardiovasc. Dis. 6(3): 70-80 (2016)). [0214] The peptide-MHC affinity is measured for the model. If the affinity is within an acceptable range (up to 1,000 nM), an engineered T-cell receptor is developed as described above. The CD4+ T-cell responses are characterized and compared to those measured in the human subjects.
[0215] Mice comprising the engineered T-cell receptor are crossed to mice with MHC alleles of interest. For example, in atherosclerosis, CAR transgenic mice may be crossed to DRB1 *0101 and DRB1 *0701. The CD4 T-cell responses are characterized and compared to those measured in the human cells. Finally, T-regulatory cells comprising the engineered T- cells are administered to the mice via any appropriate method. Treatment parameters are measured including decreased expression of pro-inflammatory cytokines, increased expression of anti-inflammatory cytokines, suppression of cytotoxic cells, expansion in vivo of regulatory T-cells, reduced inflammation in tissue, and/or amelioration of disease-specific symptoms.
[0216] Adoptive cell therapy. Once the rodent model demonstrates efficacy and safety of the adoptive cell therapy with the engineered T-cell receptor to the same or analogous athero- relevant peptide-MHC, adoptive cell therapy is performed in humans or other mammals. PBMC samples are obtained from healthy donors and patients with cardiovascular disease. ApoBlOO peptides are synthesized with measured affinity to a panel of HLA class II alleles.
[0217] The peptides can optionally be modified. An addition can be the covalent or non- covalent attachment of any type of molecule to the sequence. Specific examples of additions include glycosylation, acetylation, phosphorylation, amidation, formylation, ubiquitination, and derivatization by protecting/blocking groups and any of numerous chemical
modifications. Preferably, the peptides are phosphorylated or MDA modified.
[0218] An epitope screen is performed in healthy and disease patients and their respective HLA restriction for positively scoring peptide epitopes is determined. Patient-specific CAR or modified T-cells are generated and administered to the patients. The mode of
administering the modified cells will vary by condition and target tissue. Administration may occur by any suitable method described herein. The success of the therapy is measured by a reduction in clinical symptoms of the disease or condition, decrease in inflammation, decrease in expression of pro-inflammatory cytokines, increased expression of antiinflammatory cytokines, reduction or suppression of cytotoxic T-cells, expansion of regulatory T-cells, reduction in the infiltration of B and T-cells into the target tissue, or arresting or suppressing the development of clinical symptoms. In the case of cardiovascular disease such as atherosclerosis, success is also measured by regression of plaque formation or by any of the clinical endpoints described herein.
Equivalents
[0219] It should be understood that although the present disclosure has been specifically disclosed by certain embodiments and optional features, modification, improvement and variation of the disclosures embodied disclosed herein may be resorted to by those skilled in the art, and that such modifications, improvements and variations are considered to be within the scope of this disclosure. The materials, methods, and examples provided here are representative of certain embodiments, are exemplary, and are not intended as limitations on the scope of the disclosure.
[0220] The disclosure has been described broadly and generically herein. Each of the narrower species and subgeneric groupings falling within the generic disclosure also form part of the disclosure. This includes the generic description of the disclosure with a proviso or negative limitation removing any subject matter from the genus, regardless of whether or not the excised material is specifically recited herein.
[0221] In addition, where features or aspects of the disclosure are described in terms of Markush groups, those skilled in the art will recognize that the disclosure is also thereby described in terms of any individual member or subgroup of members of the Markush group.
[0222] The use of the term "or" in the claims is used to mean "and/or" unless explicitly indicated to refer to alternatives only or the alternatives are mutually exclusive, although the disclosure supports a definition that refers to only alternatives and "and/or."
[0223] As used in this specification and claim(s), the words "comprising" (and any form of comprising, such as "comprise" and "comprises"), "having" (and any form of having, such as "have" and "has"), "including" (and any form of including, such as "includes" and "include") or "containing" (and any form of containing, such as "contains" and "contain") are inclusive or open-ended and do not exclude additional, unrecited elements or method steps.

Claims

WHAT IS CLAIMED IS:
1. A polynucleotide encoding an engineered T-cell receptor comprising: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the antigen is bound to an MHC molecule.
2. A polynucleotide encoding an engineered T-cell receptor comprising: (a) an extracellular antigen binding domain, (b) a transmembrane domain, and (c) an intracellular signaling domain, wherein the extracellular antigen binding domain binds to an athero- relevant antigen, and wherein the athero-relevant antigen is derived from ApoBlOO.
3. The polynucleotide of claim 1 or 2, wherein the athero-relevant antigen comprises the amino acid sequence of any one of the peptides set forth in Table 1 or an equivalent of each thereof.
4. The polynucleotide of any one of claims 1-3, wherein the athero-relevant antigen comprises the amino acid sequence SLFFSAQPFEITAST or an equivalent of thereof.
5. The polynucleotide of any one of claims 1-3, wherein the athero-relevant antigen comprises the amino acid sequence IKHIYAISSAALSAS or an equivalent thereof.
6. The polynucleotide of any one of claims 1-5, wherein the athero-relevant antigen is bound to an MHC molecule, and optionally wherein the athero-relevant antigen is MHC restricted.
7. The polynucleotide of claim 6, wherein the athero-relevant antigen binds the MHC molecule with an affinity less than 1000 nM.
8. The polynucleotide of claim 7, wherein the athero-relevant antigen binds the MHC molecule with an affinity in a range from a group of ranges from: about 1 nM to about 10 nM, about 1 nM to about 100 nM, about 10 nM to about 100 nM, about 1 nM to about 500 nM, or about 50 nM to about 1000 nM.
9. The polynucleotide of any one of claims 1-8, wherein the extracellular antigen binding domain binds both the athero-relevant antigen and the MHC molecule.
10. The polynucleotide of claim 3, wherein the athero-relevant antigen binds any one of the MHC molecules set forth in Table 4 or an equivalent of each thereof.
11. The polynucleotide of any one of claims 1-10, wherein the MHC molecule bound to the athero-relevant antigen comprises an MHC class I molecule or an MHC class II molecule.
12. The polynucleotide of claim 11, wherein the MHC molecule comprises all or part of an MHC class I molecule.
13. The polynucleotide of claim 12, wherein the MHC class I molecule comprises all or part of an HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, or CD1 molecule.
14. The polynucleotide of claim 11, wherein the MHC molecule comprises all or part of an MHC class II molecule.
15. The polynucleotide of claim 14, wherein the MHC class II molecule comprises all or part of an HLA-DR, HLA-DQ, or HLA-DP molecule.
16. The polynucleotide of claim 4, wherein the athero-relevant antigen is bound to an MHC class II molecule comprising all or part of DRB1*01:01 orDRBl*07:01 or an equivalent of each thereof.
17. The polynucleotide of claim 15, wherein the MHC class II molecule is selected from the group of: DRB1*01:01, DRB1*01:02, DRB1*03:01, DRB1*04:01, DRB1*04:02, DRB1*04:03, DRB1*04:04, DRB1*04:05, DRB1*07:01, DRB1*09:01, DRB1*10:01, DRB1*11:01, DRB1*11:04, DRB1*12:01, DRB1*13:01, DRB1*13:02, DRB1*14:01, DRB1*15:01, DRB3*01:01, DRB3*02:02, DRB4*01:01, DRB5*01:01, DPB1*04:01, DPB1*05:01, or DQB1*06:02.
18. The polynucleotide of claim 5, wherein the athero-relevant antigen is bound to an MHC class II molecule selected from the group of: DPB1*02:01, DPB1*03:01, DPB1*04:02, DPB1*14:01, DQB1*02:01, DQB1*03:01, DQB1*06:02, DRB1*01:01, DRB1*04:01, DRB1*04:05, DRB1*07:01, DRB1*08:02, DRB1*09:01, DRB1*1101, DRB1*12:01, DRB1*13:02, DRB1*15:01, DRB3*01:01, DRB3*02:02, DRB4*01:01, or DRB5*01:01.
19. The polynucleotide of any one of claims 1-18, wherein the engineered T-cell receptor is a modified T-cell receptor.
20. The polynucleotide of any one of claims 1-18, wherein the engineered T-cell receptor is a chimeric antigen receptor (CAR).
21. The polynucleotide of claim 20, wherein the transmembrane domain comprises all or part of the transmembrane domain of CD3, CD8a, CD28, or 4-1BB.
22. The polynucleotide of claim 20 or 21, wherein the intracellular signaling domain comprises an intracellular signaling domain of a costimulatory molecule.
23. The polynucleotide of claim 22, wherein the costimulatory molecule comprises CD28, 4- IBB, CD3 zeta, CD27, ICOS, or OX40.
24. The polynucleotide of claim 22 or 23, wherein the intracellular signaling domain further comprises an intracellular signaling domain of a costimulatory molecule.
25. The polynucleotide of claim 24, wherein the costimulatory molecule comprises CD28, 4- IBB, CD3 zeta, CD27, ICOS, or OX40.
26. The polynucleotide of any one of claims 1-25, wherein the polynucleotide further comprises a polynucleotide encoding a flexible spacer.
27. The polynucleotide of claim 26, wherein polynucleotide encoding the flexible spacer encodes a hinge polypeptide.
28. The polynucleotide of any one of claims 1-27, further comprising a detectable marker or a purification marker and/or a polynucleotide encoding a detectable marker or a
purification marker.
29. A vector comprising the polynucleotide of any one of claims 1-28, optionally operatively linked to a promoter.
30. The vector of claim 29, further comprising an enhancer.
31. The vector of claim 29 or 30, further comprising a polynucleotide encoding FoxP3.
32. The vector of any one of claims 29-31, further comprising a polynucleotide encoding IL-10.
33. The vector of claim 32, wherein the IL-10 is activation-inducible.
34. The vector of any one of claims 29-33, further comprising a suicide gene.
35. The vector of any one of claims 29-34, further comprising a polynucleotide encoding a ubiquitin binding domain and/or STUB1.
36. The vector of any one of claims 29-35, wherein the vector is from the group of: a plasmid, a retroviral vector, a lentiviral vector, an adenoviral vector, or an adeno-associated viral vector.
37. A cell comprising the polynucleotide of any one of claims 1-28 or the vector of any one of claims 29-36, optionally wherein the cell is an isolated cell.
38. A cell expressing the polynucleotide of any one of claims 1-28 or the vector of any one of claims 29-36, optionally wherein the cell is an isolated cell.
39. The cell of claim 37 or 38, wherein the cell is a leukocyte, that is optionally a murine leukocyte cell, a canine leukocyte, a feline leukocyte, a simian leukocyte or a human leukocyte.
40. The cell of claim 37 or 38, wherein the cell is a T-cell, that is optionally a murine T- cell, a canine T-cell, a feline T-cell, a simian T-cell or a human T-cell.
41. The cell of claim 40, wherein the T-cell is a regulatory T-cell, a regulatory memory T- cell, central memory T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell.
42. The cell of claim 41, wherein the T-cell is a regulatory T-cell.
43. The cell of claim 37 or 38, wherein the cell is a natural killer (NK) cell.
44. The cell of any one of claims 37-43, wherein the cell was isolated from peripheral blood mononuclear cells (PBMCs).
45. The cell of any one of claims 37-44, wherein the extracellular antigen binding domain is bound to an athero-relevant antigen-MHC complex.
46. A population of the cell of any of claims 37-45, that is optionally substantially homogenous.
47. A non-human animal comprising one or more of: the polynucleotide of any one of claims 1-28, and/or the vector of any one of claims 29-36, and/or the cell of any one of claims 37-45, and/or the population of claim 46.
48. A composition comprising a carrier and one or more of: the polynucleotide of any one of claims 1-28, and/or the vector of any one of claims 29-36, and/or the cell of any one of claims 37-45, and/or the population of claim 46.
49. The composition of claim 48, wherein the carrier is a pharmaceutically acceptable carrier.
50. A kit comprising the composition of claim 48 or 49 and instructions for use.
51. A method of producing a modified cell, comprising: (i) introducing the polynucleotide of any one of claims 1-28 or the vector of any one of claims 29-36 into a cell or a population of cells, and optionally culturing the cell or population of cells under conditions that favor expression of the polynucleotide of any one of claim 1-28 or the vector of any one of claims 29-36;
(ii) selecting a cell or enriching a cell or a subpopulation of cells that have been successfully modified with the polynucleotide or vector of step (i).
52. The method of claim 51, wherein the cell is isolated from a subject, and wherein the subject is a murine, a canine, a feline, a simian or a human.
53. The method of claim 51 or 52, wherein step (i) comprises CRISPR mediated gene editing.
54. The method of claim 51 or 52, wherein the polynucleotide of any one of claims 1-28 or the vector of any one of claims 29-36, is introduced into the cell or the population of cells by a method comprising infecting the cell or the population of cells with a viral particle comprising the polynucleotide of any one of claims 1-28 or the vector of any one of claims 29-36.
55. The method of any one of claims 51-54, wherein the modified cell is a leukocyte that is optionally a murine leukocyte cell, a canine leukocyte, a feline leukocyte, a simian leukocyte or a human leukocyte.
56. The method of any one of claims 51-54, wherein the modified cell is a T-cell, a murine T-cell, a canine T-cell, a feline T-cell, a simian T-cell or a human T-cell.
57. The method of claim 56, wherein the T-cell is a regulatory T-cell, a regulatory memory T-cell, central memory T-cell, an effector memory T-cell, a CD4+ T-cell, or a CD8+ T-cell.
58. The method of claim 57, wherein the T-cell is a regulatory T-cell.
59. The method of any one of claims 51-54, wherein the modified cell is an K cell.
60. The method of any one of claims 51-59, further comprising inducing a regulatory T- cell phenotype in the cell or subpopulation of modified cells by inducing FoxP3 expression.
61. The method of claim 60, wherein FoxP3 expression is induced by contacting the cell or subpopulation of modified cells with an effective amount of TGFp and/or IL-10, thereby inducing FoxP3 expression in the cell or subpopulation of modified cells.
62. The method of claim 60, wherein FoxP3 expression is induced by introducing a polynucleotide encoding FoxP3 to the cell or subpopulation of modified cells.
63. The method of claim 62, wherein the polynucleotide encoding FoxP3 further comprises one or more mutations in a ubiquitin binding domain and/or a STUBl domain.
64. The method of any one of claims 51-63, further comprising introducing a
polynucleotide encoding IL-10 to the cell or subpopulation of modified cells.
65. The method of claim 64, wherein the polynucleotide encoding IL-10 is activation- inducible.
66. The method of any one of claims 51-65, further comprising introducing a
polynucleotide encoding an inducible suicide gene to the cell or subpopulation of modified cells.
67. The method of any one of claims 62, 64, or 66, wherein the polynucleotide encoding one or more of FoxP3, IL-10, or a suicide gene, is introduced into the cell or the population of cells by a method comprising one or more of transduction, transfection, or CRISPR- mediated gene editing.
68. The method of any one of claims 51-67, further comprising contacting the cell or subpopulation of modified cells with soluble anti-IFNy antibody and/or anti-IL-5 antibody.
69. The method of any one of claims 51-68, further comprising growing or expanding the cell or subpopulation of modified cells in vitro or ex vivo.
70. A modified cell produced by the method of any one of claims 51-69.
71. A population of modified cells produced by the method of any one of claims 51-69.
72. A method of inducing an anti-inflammatory response in a cell or tissue, mediating an immune response in a cell or tissue, or mediating an inflammatory response in a cell or tissue, comprising administering an effective amount of the polynucleotide of any one of claims 1- 28, the vector of any one of claims 29-36, the cell of any one of claims 37-45, the modified cell of claim 70, or the population of claim 46 or 71.
73. A method of inducing an anti-inflammatory response, mediating an immune response, or mediating an inflammatory response in a subject in need thereof, comprising administering an effective amount of the cell of any one of claims 37-45, the modified cell of claim 70, or the population of claim 46 or 71.
74. The method of claim 72 or 73, wherein the response is characterized by suppression of pathogenic T-cells.
75. The method of any one of claims 72-74, wherein the method comprises decreased expression of one or more pro-inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more pro-inflammatory cytokines comprise IL-Ιβ, T F-a, IFN-γ, IL-8, IL-6, IL-12, IL-15, IL-16, IL-17, IL-18, GM-CSF, IL-21, IL-23, IL-27, and/or TGF-β.
76. The method of any one of claims 72-75, wherein the method comprises increased expression of one or more anti -inflammatory cytokines in the cell, tissue, or subject, and optionally wherein the one or more anti -inflammatory cytokines comprise TGF-β, IL-IRa, IL-4, IL-6, IL-10, IL-11, IL-13, IL-35, and/or INF-a.
77. A method of enhancing the activity of a regulatory T-cell, comprising administering an effective amount of the polynucleotide of any one of claims 1-28, the vector of any one of claims 29-36, the cell of any one of claims 37-45, the modified cell of claim 70, or the population of claim 46 or 71.
78. The method of claim 77, wherein the enhanced activity of the regulatory T-cell is characterized by increased expression of IL-10.
79. The method of claim 73, wherein the cell, modified cell, or population is autologous to the subject.
80. A method of protecting a subject against an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage, comprising administering an effective amount of the cell of any one of claims 37-45, the modified cell of claim 70, or the population of claim 46 or 71.
81. A method of treating an adverse cardiovascular event and/or cardiovascular or liver disease, disorder, or damage in a subject in need thereof, comprising administering an effective amount of the cell of any one of claims 37-45, the modified cell of claim 70, or the population of claim 46 or 71.
82. The method of claim 80 or 81, wherein the adverse cardiovascular event or cardiovascular disease, disorder, or damage is from the group of: coronary artery disease, peripheral artery disease, cerebrovascular disease, renal artery disease, stroke, myocardial infarction, ischemic heart failure, transient ischemic attack, atherosclerosis, or brain trauma.
83. The method of claim 82, wherein the adverse cardiovascular event or cardiovascular disease, disorder, or damage comprises atherosclerosis.
84. A method of treating a disease or condition involving an inflammatory response or related to inflammation in a subject in need thereof, comprising administering an effective amount of the cell of any one of claims 37-45, the modified cell of claim 70, or the population of claim 46 or 71.
85. The method of any one of claims 80-84, wherein the method comprises inducing plaque regression.
86. The method of any one of claims 80-85, wherein the cell, modified cell, or population is autologous to the subject being treated.
87. The method of any one of claims 80-86, further comprising administration of an effective amount of one or more immunosuppressive therapeutic compounds and/or a statin.
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