WO2024019961A1 - Cd2 recruiting chimeric antigen receptors and fusion proteins - Google Patents

Cd2 recruiting chimeric antigen receptors and fusion proteins Download PDF

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Publication number
WO2024019961A1
WO2024019961A1 PCT/US2023/027881 US2023027881W WO2024019961A1 WO 2024019961 A1 WO2024019961 A1 WO 2024019961A1 US 2023027881 W US2023027881 W US 2023027881W WO 2024019961 A1 WO2024019961 A1 WO 2024019961A1
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domain
cell
composition
car
cancer
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PCT/US2023/027881
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French (fr)
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Matthew SIEGEL
Michael Bethune
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Cargo Therapeutics, Inc.
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Publication of WO2024019961A1 publication Critical patent/WO2024019961A1/en

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    • 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
    • A61P37/02—Immunomodulators
    • A61P37/04—Immunostimulants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K35/00—Medicinal preparations containing materials or reaction products thereof with undetermined constitution
    • A61K35/12—Materials from mammals; Compositions comprising non-specified tissues or cells; Compositions comprising non-embryonic stem cells; Genetically modified cells
    • A61K35/14—Blood; Artificial blood
    • A61K35/17—Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A61K39/001102—Receptors, cell surface antigens or cell surface determinants
    • A61K39/001111—Immunoglobulin superfamily
    • A61K39/001113—CD22, BL-CAM, siglec-2 or sialic acid- binding Ig-related lectin 2
    • 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
    • A61K39/463—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
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A61K39/464411—Immunoglobulin superfamily
    • A61K39/464412—CD19 or B4
    • 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
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A61K39/464429—Molecules with a "CD" designation not provided for elsewhere
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • 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
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • C07K16/2806—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily against CD2
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/33—Fusion polypeptide fusions for targeting to specific cell types, e.g. tissue specific targeting, targeting of a bacterial subspecies

Definitions

  • Immunotherapeutic CAR-T cell (chimeric antigen receptor T cell) therapies have been used for the treatment of diseases such as B-cell lymphoma or for patients who have relapsed after receiving chemotherapy. While approximately 50% of patients receiving existing CAR-T therapeutics achieve complete responses, a significant subset of patients experience relapse and/or disease progression.
  • engineered chimeric antigen receptor fusion proteins are engineered to express one or more chimeric antigen receptors, CD2 recruiting chimeric antigen receptors, anti-CD2 fusion proteins, and methods of use thereof for the treatment of diseases.
  • An aspect of the disclosure may be a composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising: (a) an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain.
  • the first antigen binding domain binds to endogenous CD2.
  • the endogenous CD2 is not an endogenous CD2 molecule expressed by the target cell.
  • the CAR when the CAR is expressed in a T cell, the first antigen binding domain binds to endogenous CD2 of the T cell.
  • the CAR is expressed in a cell.
  • a further aspect of the disclosure is a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising a first antigen binding domain, wherein the first antigen binding domain binds to a receptor expressed by the same T cell expressing the CAR; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain.
  • the extracellular domain further comprises a second antigen binding domain that binds to an antigen of a target cell.
  • the T cell binds to the target cell with higher avidity compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • the T cell in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • the T cell in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • a further aspect of the disclosure is comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain, wherein the T cell binds to the target cell with higher avidity compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • CAR chimeric antigen receptor
  • a further aspect of the disclosure is a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain and/or increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • CAR comprises: (a) an extracellular domain comprising (i) a first antigen binding domain that
  • a further aspect of the disclosure is a composition
  • a composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising: (a) an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain, wherein the second antigen binding domain binds to : glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2,
  • the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3s, CD35, CD22, CD79a, CD79b, CD665, Toll-like receptors 1-10 (TLR1), (TLR2), (TLR3), (TLR4), (TLR5), (TLR6), (TLR7), (TLR8), (TLR9), (TLR10), Caspase recruitment domain-containing protein 11 (CARD11), CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278/inducible T cell co-stimulator (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • CD3 CD137
  • CD28 CD28
  • ICOS FcyRI,
  • the second antigen binding domain is linked to the first antigen binding domain by a linker sequence, wherein the linker sequence is at least 10 or 15 amino acids in length, at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length, or from 10 to 45 or from 15 to 30 amino acids in length.
  • the first antigen binding domain is N-terminal to the second antigen binding domain.
  • the second antigen binding domain is an antibody domain or binding fragment thereof.
  • the first antigen binding domain is not an antibody domain or binding fragment thereof.
  • the first antigen binding domain is from CD58.
  • the first antigen binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2.
  • a further aspect of the disclosure is a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises: (a) an extracellular domain comprising an antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c)an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises: (a) an extracellular domain comprising an anti-CD2 binding domain that binds to CD2; and (b) a transmembrane domain; wherein (i) the transmembrane domain of the anti- CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or ii) the anti-CD2
  • the first and second multimerization domains are leucine zipper domains. In some embodiments, the first multimerization domain is within the extracellular domain of the anti-CD2 fusion protein and second multimerization domain is within the extracellular domain of the CAR. In some embodiments, when the CAR and the anti-CD2 fusion protein are expressed in a cell a complex comprising the CAR, the anti-CD2 fusion protein and CD2 is formed. In some embodiments, wherein the transmembrane domain of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR.
  • the transmembrane domain of the anti-CD2 fusion protein is from the alpha or beta chain of the T-cell receptor, CD3y, CD33, CD3s, CD3 , CD35, CD4, CD5, CD8a, CD9, CD16, CD22, CD27, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD152, CD154, and/or PD-1.
  • the transmembrane domain of the anti-CD2 fusion protein is from CD8a or CD28.
  • the transmembrane domain of the CAR is from the alpha or beta chain of the T-cell receptor, CD3y, CD33, CD3s, CD3 ⁇ , CD35, CD4, CD5, CD8a, CD9, CD16, CD22, CD27, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD152, CD154, and/or PD-1.
  • the transmembrane domain of the CAR is from CD8a or CD28.
  • the anti-CD2 fusion protein lacks an intracellular signaling domain.
  • the antigen binding domain is an antibody domain or binding fragment thereof.
  • the antigen binding domain is an scFv or a single domain antibody domain (sdAb). In some embodiments, the scFv is a FMC63 domain. In some embodiments, the anti-CD2 binding domain is not an antibody domain or binding fragment thereof. In some embodiments, the anti-CD2 binding domain is from CD58. In some embodiments, the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2, wherein the anti-CD2 binding domain binds to endogenous CD2. In some embodiments, when the anti-CD2 fusion protein is expressed in a T cell, the anti-CD2 binding domain binds to endogenous CD2 of the T cell.
  • the cell is a T cell, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain of the CAR compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain.
  • the T cell exhibits increased CD2 signaling compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain.
  • the antigen binding domain binds to glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostate- specific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, me
  • CEA
  • the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • CD3 CD137
  • CD28 CD28
  • ICOS FcyRI, FcRy, FcR, CD3y, CD38, CD3E, CD35, CD22, CD79a, CD79b
  • the extracellular domain of the anti-CD2 fusion protein comprises a hinge domain wherein the anti-CD2 binding domain is linked to the hinge domain or the transmembrane domain of the anti-CD2 fusion protein by a linker sequence, wherein the linker sequence is at least 10 or 15 amino acids in length, at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length, or from 10 to 45 or from 15 to 30 amino acids in length.
  • the intracellular signaling domain of the CAR comprises a CD2 intracellular signaling domain.
  • the cell is a population of at least lxl0 A 5 cells.
  • a further aspect of the disclosure is a pharmaceutical composition
  • a pharmaceutical composition comprising the composition of any of the disclosed embodiments and a pharmaceutically acceptable excipient or carrier.
  • a further aspect of the disclosure is a method of treating a disease or condition in a subject in need thereof comprising administering a therapeutically effective amount of the pharmaceutical composition to a subject, wherein the disease or condition is cancer, wherein the cancer is lymphoma or leukemia.
  • the cancer is a solid tumor cancer.
  • the solid tumor cancer is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA
  • UCS
  • FIG. 1A shows an exemplary anti-CD19 or anti-CD22 CAR construct with an extracellular domain having an scFv that binds CD 19 or CD22 and a CD58 domain.
  • FIG. IB shows a T cell expressing an anti-CD19 CAR with an extracellular domain having a CD58 domain that binds to endogenous CD2 (left) and in complex with a B cell (right).
  • FIG. 2A shows an exemplary CAR with an extracellular domain containing an scFv that binds CD 19 (FMC63) and a CD58 domain bound to endogenous CD2. Tethering of the CD58 domain recruits endogenous CD2.
  • FIG. 2B shows an exemplary CAR with an extracellular domain containing an scFv that binds CD19 (FMC63) and an anti-CD2 fusion protein with a transmembrane domain or multimerization domain that interacts with the transmembrane domain or multimerization domain of the CAR resulting in proxy receptor recruitment of endogenous CD2.
  • the depicted anti-CD2 fusion protein is bound to endogenous CD2.
  • FIG. 3A shows exemplary IL-2 secretion data from T cells transduced with retrovirus to express an anti-CD19-CD28-CD3z CAR with or without the N-terminal extracellular domain of CD58 attached.
  • CAR T cells were incubated with wild type (WT) B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IL-2 secretion by ELISA.
  • WT wild type B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IL-2 secretion by ELISA.
  • FIG. 3B shows exemplary IFN-y secretion data from T cells transduced with retrovirus to express an anti-CD19-CD28-CD3z CAR with or without the N-terminal extracellular domain of CD58 attached.
  • CAR T cells were incubated with wild type (WT) B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IFN-y secretion by ELISA.
  • WT wild type B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IFN-y secretion by ELISA.
  • the present disclosure encompasses recombinant polynucleic acids encoding chimeric antigen receptors and variants thereof, wherein the CAR comprises an anti-CD2 binding domain and a second antigen binding domain.
  • the anti-CD2 binding domain comprises a CD58 extracellular domain capable of recruiting endogenous CD2.
  • the endogenous CD2 is expressed in the same cell as the CAR.
  • the present disclosure also provides recombinant polynucleic acids encoding CARs and an antiCD fusion protein.
  • the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell.
  • the first and second multimerization domains are leucine zipper domains.
  • ‘Percent (%) amino acid sequence identity” or “homology” with respect to the nucleic acid or amino acid sequences identified herein is defined as the percentage of nucleic acid or amino acid residues in a candidate sequence that are identical with the amino acid residues in the polypeptide being compared, after aligning the sequences considering any conservative substitutions as part of the sequence identity.
  • ‘Percent (%) identity” with respect to the nucleic acid or amino acid sequences identified herein is defined as the percentage of nucleic acid or amino acid residues in a candidate sequence that are identical with the amino acid residues in the polypeptide being compared, after aligning the sequences considering any conservative substitutions as part of the sequence identity.
  • a “therapeutically effective amount” or “therapeutically effective number” of an agent is an amount or number sufficient to provide a therapeutic benefit in the treatment or management of a disease or disorder, or to delay or minimize one or more symptoms associated with the disease or disorder.
  • a therapeutically effective amount of an agent means an amount of therapeutic agent, alone or in combination with other therapeutic agents, which provides a therapeutic benefit in the treatment or management of the cancer.
  • the term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the disease or disorder, or enhances the therapeutic efficacy of another therapeutic agent.
  • an “effective amount” is an amount sufficient to contribute to the treatment, prevention, or reduction of a symptom or symptoms of a disease, which could also be referred to as a “therapeutically effective amount.”
  • a “reduction” of a symptom means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s).
  • the exact amount of a composition including a “therapeutically effective amount” will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques.
  • binding domain refers to a protein, or polypeptide sequence, which specifically binds to a target.
  • the target is a polypeptide.
  • the target is CD2.
  • the target is cell-surface bound CD2.
  • the binding domain is not an antibody or fragment thereof.
  • antibody refers to a protein, or polypeptide sequence, derived from an immunoglobulin molecule, which specifically binds to an antigen.
  • Antibodies can be intact immunoglobulins of polyclonal or monoclonal origin, or fragments thereof and can be derived from natural or from recombinant sources.
  • antibody fragment refers to at least one portion of an antibody, or recombinant variants thereof, that contains the antigenic determining variable region of an intact antibody that is sufficient to confer recognition and specific binding of the antibody fragment to a target, such as an antigen and its defined epitope.
  • antibody fragments include, but are not limited to, Fab, Fab’, F(ab’)2, and Fv fragments, single-chain (sc)Fv (“scFv”) antibody fragments, linear antibodies, single domain antibodies (abbreviated “sdAb”) (either VL or VH), camelid VHH domains, and multi-specific antibodies formed from antibody fragments.
  • sdAb single domain antibodies
  • the TFP composition of the disclosure does not comprise an antibody or antibody fragment.
  • antigens can be derived from recombinant or genomic DNA.
  • any DNA which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein.
  • an antigen need not be encoded solely by a full-length nucleotide sequence of a gene.
  • an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be generated synthesized or can be derived from a biological sample, or might be macromolecule besides a polypeptide.
  • a biological sample can include, but is not limited to a tissue sample, a tumor sample, a cell or a fluid with other biological components.
  • the recombinant polypeptide, and/or recombinant nucleic acids encoding the recombinant polypeptides may include any of a variety of proteins of interest.
  • the recombinant polypeptide comprises a protein of interest that is engineered.
  • engineered is meant the protein of interest does not have a native/wild- type counterpart, e.g., by virtue of the protein of interest including one or more heterologous domains, an engineered or synthetic domain (e.g., an engineered extracellular binding domain in the case of cell surface molecule (e.g., a cell surface receptor), etc.), and/or the like.
  • the protein of interest is an engineered cell surface receptor.
  • Non-limiting examples of engineered cell surface receptors include chimeric receptors (e.g., chimeric antigen receptors (CARs)), engineered T cell receptors (TCRs) (e.g., having altered (or “engineered”) specificity and/or affinity for an antigen as compared to a counterpart wild-type TCR, having one or more polypeptides covalently or non-covalently bound (e.g., fused) to one another, and/or the like), anti-CD2 fusion proteins and the like.
  • CARs chimeric antigen receptors
  • TCRs engineered T cell receptors
  • An immune receptor such as chimeric antigen receptors (CARs) and T-cell receptors (TCRs) in general comprise an extracellular antigen binding domain, a transmembrane domain, and a cytoplasmic signaling domain that activates the T cell cytotoxic response.
  • the CAR frequently also has a spacer domain between the antigen binding domain and the transmembrane domain, which often includes a hinge domain.
  • the cytoplasmic signaling domain can further comprise one or more co-stimulatory regions, as described herein.
  • the protein of interest is an engineered cell surface receptor, and the engineered cell surface receptor is a chimeric antigen receptor (CAR) or anti-CD2 fusion protein.
  • the CARs and anti-CD2 fusion proteins provided herein contain an anti-CD2 binding domain that can recruit CD2, such as endogenous CD2. Recruitment of CD2 can lead to CD2 intracellular signaling, such as endogenous CD2 intracellular signaling.
  • CAR structures are often abbreviated to list the target antigen (or the antigen binding domain or agent); optionally the spacer domain; optionally the transmembrane domain; and the co-stimulatory and stimulatory domains of the cytoplasmic signaling domain.
  • a CAR having an anti-CD19 scFv antigen binding domain, a CD8a transmembrane domain (which may include the extracellular hinge region), a 4- IBB co stimulatory domain, and a CD3 ⁇ activating domain can be indicated as CD19-8tm-41BBz.
  • the domains are commonly used they are often abbreviated even further, such that a CAR having a CD28 transmembrane domain, a 4- IBB domain, and a CD3 activating domain could be abbreviated as CD19-28tm-28BBz.
  • CD19-28BBz omitting designation of the transmembrane domain
  • antigen binding domain rather than only its specificity, e.g., m971 rather than CD22 or FMC63 rather than CD19, indicating that the antigen binding domain is the m971 scFv or FMC63 scFv, respectively.
  • the protein of interest, or nucleic acid encoding the protein of interest is a CAR comprising an antigen binding domain and an anti-CD2 binding domain and/or an anti-CD2 fusion protein comprising an anti-CD2 binding domain.
  • a CAR comprises an antigen binding domain and an anti-CD2 binding domain and the anti-CD2 binding domain of the CAR directly recruits CD2 to the CAR.
  • CAR comprises an antigen binding domain and an anti- CD2 fusion protein comprises an anti-CD2 binding domain and the anti-CD2 binding domain of the anti- CD2 fusion protein binds to CD2 and the CAR binds to the anti-CD2 fusion protein via a multimerization domain (e.g., the transmembrane domains or the extracellular domains), thereby indirectly recruiting CD2 to the CAR via the anti-CD2 fusion protein.
  • the anti-CD2 fusion protein can comprise a multimerization domain that multimerizes with a multimerization domain of the CAR.
  • the anti-CD2 fusion protein can comprise a first multimerization domain and the CAR can comprise a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell.
  • An aspect of the disclosure may be a recombinant polynucleic acid encoding a CAR comprising: (a) an extracellular domain comprising a first antigen-binding domain that is an anti-CD2 binding domain, and a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain as shown in FIG. 1A and/or FIG. IB.
  • An aspect of the disclosure may be a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises: (a) an extracellular domain comprising an antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises: (a) an extracellular domain comprising an anti-CD2 binding domain that binds to CD2; and (b) a transmembrane domain; wherein (i) the transmembrane domain of the anti- CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or (ii) the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain
  • an anti-CD2 fusion protein may be tethered to a CAR as in FIG. 2A and/or FIG. 2B.
  • the anti-CD2 fusion protein may comprise a first multimerization domain and the CAR may comprise a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell.
  • the first multimerization domain and the second multimerization domain forma homodimer.
  • the first multimerization domain and the second multimerization domain forma heterodimer.
  • the first multimerization domain can be a transmembrane domain and the second multimerization domain can be a transmembrane domain.
  • the first multimerization domain can be an extracellular domain and the second multimerization domain can be an extracellular domain.
  • the transmembrane domain of an anti-CD2 fusion protein may multimerize with the transmembrane domain of the CAR.
  • the extracellular domain of an anti-CD2 fusion protein may multimerize with the extracellular domain of the CAR.
  • the first multimerization domain can be a CD28 transmembrane and/or hinge domain and the second multimerization domain can be a CD28 transmembrane and/or hinge domain.
  • the first multimerization domain can be a CD8 alpha transmembrane and/or hinge domain and the second multimerization domain can be a CD8 beta transmembrane and/or hinge domain.
  • the first multimerization domain can be a CD8 beta transmembrane and/or hinge domain and the second multimerization domain can be a CD8 alpha transmembrane and/or hinge domain.
  • the multimerization domains may comprise a leucine zipper.
  • the CAR may have an anti-CD2 binding domain.
  • the anti-CD2 binding domain may be from CD58.
  • the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2.
  • a CAR construct has at least about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity to any one of the sequences depicted in Table 1. In some embodiments, a CAR construct has 100% sequence identity to one or more of the sequences depicted in Table 1.
  • an anti-CD2 fusion protein construct has at least about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity to any one of the sequences depicted in Table 2. In some embodiments, an anti-CD2 fusion protein construct has 100% sequence identity to one or more of the sequences depicted in Table 2.
  • the cell in which the CAR or anti-CD2 fusion protein with an anti-CD2 binding domain is expressed is an immune cell. In some embodiments, the cell in which the CAR or anti- CD2 fusion protein is expressed is a T cell. In some embodiments, the cell in which the CAR or anti-CD2 fusion protein is expressed is a CD8+ T cell. In some embodiments, the cell in which the CAR or anti- CD2 fusion protein is expressed is a CD4+ T cell.
  • the cell in which the CAR or anti-CD2 fusion protein is expressed is a B-cell, neutrophil, eosinophil, basophil, mast cell, monocyte, macrophage, dendritic cell, and/or natural killer cell.
  • the CAR or anti-CD2 fusion protein comprises a signal peptide sequence.
  • the CAR or anti-CD2 fusion protein comprises a signal peptide sequence located on the N-terminus of the CAR or anti-CD2 fusion protein.
  • the CAR or anti-CD2 fusion protein comprises a signal peptide sequence from CD8, CSF2RA, HGH or TCR
  • the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MALPVTALLLPLALLLHAARP.
  • the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MLLLVTSLLLCELPHPAFLLIP.
  • the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MATGSRTSLLLAFGLLCLPWLQEGSA. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MGTSLLCWMALCLLGADHAD.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises the anti- CD2 binding domain.
  • the anti-CD2 binding domain of the CAR is an N-terminal domain of the CAR that binds to CD2.
  • the anti-CD2 binding domain of the anti- CD2 fusion protein is an N-terminal domain of the CAR that binds to CD2.
  • the extracellular domain of the CAR comprises a domain that binds to CD2 that is located N-terminal to an antigen binding domain of the CAR.
  • the extracellular domain of the CAR or antiCD fusion protein comprises a domain from CD58 that binds to CD2. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 that binds to endogenous CD2. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 that binds to CD2 on the same cell in which the CAR or anti-CD2 fusion protein is expressed.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 that binds to CD2.
  • the CAR or anti-CD2 fusion protein comprises a CD58 N-terminal domain.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises an N-terminal domain from CD58 that binds to CD2.
  • Such a CAR may further include a spacer domain between the CD58 N-terminal domain and the antigen-binding portion.
  • Such an anti-CD2 fusion protein may further include a spacer domain between the CD58 N-terminal domain and the transmembrane domain.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises an extracellular domain (ECD) from CD58 that binds to CD2.
  • ECD extracellular domain
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to a CD58 N-terminal domain.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVL.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 85, 90, 95, 97, 98, or 99% sequence identity to
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with 100% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVL.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to a CD58 extracellular domain (ECD).
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVLESLPSPTLTCALTNGSIEVQCMIPEHYNSHRGLIMY SWDCPMEQCKRNSTSIYFKMENDLPQKIQCTLSNPLFNTTSSIILTTCIPSSGHSRHR.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 85, 90, 95, 97, 98, or 99% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVLESLPSPTLTCALTNGSIEVQCMIPEHYNSHRGLIMY SWDCPMEQCKRNSTSIYFKMENDLPQKIQCTLSNPLFNTTSSIILTTCIPSSGHSRHR.
  • the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with 100% sequence identity to
  • the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein binds to CD2 with low affinity.
  • the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein can bind to CD2 with a KA of less than or equal to about 200 nM, 300 nM, 400 nM, 500 nM, IpM, 5 pM, 10 pM, 15pM, 20pM, 25pM, 30pM, 35pM, 40pM, 45pM, and/or 50pM.
  • the anti- CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to or associate with CD2 with a KA of less than or equal to about 10 A 5 M' 1 .
  • the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to CD2 with a KA of less than or equal to about 10 A 6 M’ 1 , 10 A 7 M’ 1 , 10 A 8 M’ 1 , 10 A 9 M’ 1 , 10 A l 0 M’ 1 , 10 A l 1 M’ 1 , 10 A 12 M’ 1 , or 10 A 13 M’ 1 .
  • the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein can bind to CD2 with a KD of greater than or equal to about 200 nM, 300 nM, 400 nM, 500 nM, IpM, 5 pM, 10 pM, 15pM, 20pM, 25 pM, 30pM, 35pM, 40pM, 45pM, 50pM, or greater than 50pM.
  • the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to or associate with CD2 with a KD of greater than or equal to about 10 A 5 M' 1 .
  • the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to CD2 with a KD of greater than or equal to about 10 A 6 M’ 1 , 10 A 7 M’ 1 , 10 A 8 M’ 1 , 10 A 9 M’ 1 , 10 A 10 M’ 1 , 10 A l 1 M’ 1 , 10 A 12 M’ 1 , or 10 A l 3 M' 1 .
  • binding affinity of the anti-CD2 binding domain to CD2 can be readily determined using conventional techniques, e.g., by competitive ELISA (enzyme-linked immunosorbent assay), equilibrium dialysis, by using surface plasmon resonance (SPR) technology (e.g., the BIAcore 2000 instrument, using general procedures outlined by the manufacturer); by radioimmunoassay; or the like.
  • binding of the antigen binding domain of the CAR to the antigen may provide enough avidity to cluster endogenous CD2.
  • binding of the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein to CD2 clusters endogenous CD2.
  • clustering of endogenous CD2 may increase signaling in the cell in which the CAR or anti- CD2 fusion protein with the anti-CD2 binding domain is expressed.
  • the increased signaling may be 1-fold, 2-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1000-fold, 10000-fold, or more than 10000-fold greater than a cell in which the CAR or anti-CD2 fusion protein is not expressed.
  • a cell expressing a CAR or anti-CD2 fusion protein with an anti-CD2 binding domain exhibits increased target cell killing compared to the target cell killing of a cell which does not express the CAR or anti-CD2 fusion protein.
  • the increased killing may be 1-fold, 2-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1000-fold, 10000-fold, or more than 10000-fold greater than the target cell killing of a cell in which the CAR or anti-CD2 fusion protein is not expressed.
  • the target cell is a cancer cell.
  • the cancer is from a hematological cancer.
  • the cancer cell is from a solid tumor cancer.
  • the cancer is a cell of a lymphoma, leukemia, lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromine
  • the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a hinge domain by a linker. In some embodiments, the anti-CD2 binding domain of an anti- CD2 fusion protein provided herein is operatively linked to a transmembrane domain by a linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a transmembrane domain by a linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a (G4S)n linker, where n is an integer of from 1 to 10.
  • the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a (G4S)3 linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a (G4S)6 linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a linker according to the sequence GGGGSGGGGSGGGGS.
  • the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a linker according to the sequence GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a linker according to the sequence GSTSGSGKPGSGEGSTKG.
  • the extracellular domain of a CAR provided herein can further comprises an antigen binding domain in addition to an anti-CD2 binding domain.
  • the antigen binding domain of the CAR is C-terminal to the anti-CD2 binding domain.
  • the antigen binding domain of the CAR is N-terminal to the anti-CD2 binding domain.
  • an anti-CD2 fusion protein provided herein comprises an anti-CD2 binding domain and lacks an antigen binding domain.
  • the antigen binding domain of the CAR is linked to the anti-CD2 binding domain by a first linker. In some embodiments, the antigen binding domain of a CAR provided herein is linked to a hinge domain by a second linker. In some embodiments, the antigen binding domain of a CAR provided herein is operatively linked to a transmembrane domain by a second linker. In some embodiments, the antigen binding domain of a CAR provided herein provided herein is directly linked to a transmembrane domain by a second linker.
  • the antigen binding domains provided herein include, but are not limited to, protein domains, antibody domains, ligands, extracellular domains of receptors and the like.
  • the antigen binding domain comprises an antigen-binding portion of an antibody (e.g., a single chain antibody domain or an scFv) that binds to an antigen of interest.
  • Functional fragments of any of the antibodies herein are also contemplated.
  • the terms “antigen-binding portion of an antibody,” “antigen-binding fragment,” “antigen binding domain,” “antibody fragment,” or a “functional fragment of an antibody” can refer to one or more fragments of an antibody that retain the ability to specifically bind to an antigen.
  • Representative antigen-binding fragments include a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, a dsFv, a variable heavy domain, a variable light domain, a variable NAR domain, bi-specific scFv, a bi-specific Fab2, a trispecific Fab3, an AVIMER®, a minibody, a diabody, a triabody, a maxibody, a camelid, a VHH, a minibody, an intrabody, fusion proteins comprising an antibody portion ( e.g a domain antibody), and a single chain binding polypeptide.
  • Native antibodies and native immunoglobulins can be heterotetrameric glycoproteins of about 150,000 Daltons, composed of two identical light chains and two identical heavy chains. Antibodies can further refer to camelid antibodies, which can be not tetrameric.
  • Each light chain can be typically linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages can vary among the heavy chains of different immunoglobulin isotypes.
  • Each heavy and light chain can have regularly spaced intrachain disulfide bridges.
  • Each heavy chain can have at one end a variable domain (“VH”) followed by a number of constant domains (“CH”).
  • Each light chain can have a variable domain at one end (“VL”) and a constant domain (“CL”) at its other end; the constant domain of the light chain can be aligned with the first constant domain of the heavy chain, and the light-chain variable domain can be aligned with the variable domain of the heavy chain.
  • Particular amino acid residues can form an interface between the light- and heavy -chain variable domains.
  • F(ab’)2” and “Fab”’ moieties can be produced by treating an Ig with a protease such as pepsin and papain, and include antibody fragments generated by digesting immunoglobulin near the disulfide bonds existing between the hinge regions in each of the two heavy chains.
  • a protease such as pepsin and papain
  • papain can cleave IgG upstream of the disulfide bonds existing between the hinge regions in each of the two heavy chains to generate two homologous antibody fragments in which a light chain composed of VL and CL (light chain constant region), and a heavy chain fragment composed of VH and Ciiyi (gi) region in the constant region of the heavy chain) are connected at their C terminal regions through a disulfide bond.
  • Each of these two homologous antibody fragments can be called Fab’.
  • Pepsin can also cleave IgG downstream of the disulfide bonds existing between the hinge regions in each of the two heavy chains to generate an antibody fragment slightly larger than the fragment in which the two above-mentioned Fab' are connected at the hinge region.
  • This antibody fragment can be called F(ab’)2.
  • the Fab fragment can also contain the constant domain of the light chain and the first constant domain (CHI) of the heavy chain.
  • Fab' fragments can differ from Fab fragments by the addition of a few residues at the carboxyl terminus of the heavy chain CHI domain including one or more cysteine(s) from the antibody hinge region.
  • Fab'-SH can be a Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group.
  • F(ab')2 antibody fragments can be produced, for example, as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments can also be employed.
  • a “Fv” as used herein can refer to an antibody fragment which contains a complete antigenrecognition and antigen-binding site.
  • This region can consist of a dimer of one heavy chain and one light chain variable domain in tight, non-covalent or covalent association (disulfide linked Fvs have been described, see, e.g., Reiter el al. (1996) Nature Biotechnology 14:1239-1245).
  • the three CDRs of each variable domain can interact to define an antigen-binding site on the surface of the VH-VL dimer.
  • a combination of one or more of the CDRs can from each of the VH and VL chains confer antigen-binding specificity to the antibody.
  • the CDRH3 and CDRL3 can be sufficient to confer antigen-binding specificity to an antibody when transferred to VH and VL chains of a recipient antibody or antigen-binding fragment thereof and this combination of CDRs can be tested for binding, specificity, affinity, etc. using, for example, techniques described herein.
  • a single variable domain or half of an Fv comprising only three CDRs specific for an antigen
  • VL and VH Fv fragments
  • VL and VH Fv fragments
  • scFv single chain Fv
  • scFvs single chain Fv
  • Osbourn et al. (1998) Nat. Biotechnol. 16:778).
  • scFvs can be encompassed within the term “antigen-binding portion” of an antibody.
  • VH and VL sequences of specific scFv can be linked to an Fc region cDNA or genomic sequences in order to generate expression vectors encoding complete Ig (e.g., IgG) molecules or other isotypes.
  • VH and VL can also be used in the generation of Fab, Fv, or other fragments of Igs using either protein chemistry or recombinant DNA technology.
  • Single-chain Fv or “scFv” antibody fragments can include the VH and VL domains of an antibody, wherein these domains can be present in a single polypeptide chain.
  • the Fv polypeptide can further include a polypeptide linker between the VH and VL domains which enables the sFv to form the desired structure for antigen binding.
  • a “dsFv” can be a Fv fragment obtained, for example, by introducing a Cys residue into a suitable site in each of a heavy chain variable region and a light chain variable region, and then stabilizing the heavy chain variable region and the light chain variable region by a disulfide bond.
  • the site in each chain, into which the Cys residue can be introduced, can be determined based on a conformation predicted by molecular modeling.
  • a conformation can be predicted from the amino acid sequences of the heavy chain variable region and light chain variable region of the above-described antibody, and DNA encoding each of the heavy chain variable region and the light chain variable region, into which a mutation has been introduced based on such prediction, can be then constructed.
  • the DNA construct can be incorporated then into a suitable vector and prepared from a transformant obtained by transformation with the aforementioned vector.
  • Diabodies can be single chain antibodies. Diabodies can be bivalent, bispecific antibodies in which VH and VL domains can be expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites (see e.g., Holliger, P., etal., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993); and Poljak, R. I, etal, Structure, 2:1121-1123 (1994)).
  • the antigen binding domain can be any molecule that binds to the selected antigen with sufficient affinity and specificity, and is often an antibody or an antibody derivative, such as an scFv, single domain antibody (sdAb), Fab' fragment, (Fab')2 fragment, nanobody, diabody, or the like.
  • the antigen binding domain can be a receptor or a receptor fragment that binds specifically to the target antigen.
  • the antigen binding domain can be attached to the rest of the receptor directly (covalently) or indirectly (for example, through the noncovalent binding of two or more binding partners).
  • Antibody derivatives are molecules that resemble antibodies in their mechanism of ligand binding, and include, for example, nanobodies, duobodies, diabodies, triabodies, minibodies, F(ab')2 fragments, Fab fragments, single chain variable fragments (scFv), single domain antibodies (sdAb), and functional fragments thereof. See for example, D.L. Porter et al., N Engl J Med ( 2011) 365(8):725-33 (scFv); E.L. Smith et al, Mol Ther (2016)26(6): 1447-56 (scFv); S.R. Bamhashemi et al., Iran J Basic Med Sci (2016) 21(5):455-64 (CD19 nanobody); F.
  • Antibody derivatives can also be prepared from therapeutic antibodies, for example without limitation, by preparing a nanobody, duobody, diabody, triabody, minibody, F(ab')2 fragment, Fab fragment, single chain variable fragment (scFv), or single domain antibody (sdAb) based on a therapeutic antibody.
  • Antibody derivatives can also be designed using phage display techniques (see, e.g., E. Romao et al., Curr Pharm Des (2016) 22(43):6500-18).
  • the antigen binding domain may include binding domains for multiple antigens, which may be the same or different.
  • the antigen binding domain can comprise a bispecific (Fab')2, specific for two antigens, or for two epitopes on the same antigen.
  • Multispecific antigen binding domains can increase the sensitivity of the CAR, for example by allowing the CAR to recognize and react to multiple antigens, he antigen binding domain can alternatively be expressed independently from the rest of the CAR, and bind to it through non-covalent interactions.
  • the extracellular portion of the CAR can comprise one member of a specific binding pair, which binds to the independent antigen binding domain (without interfering with antigen binding by the antigen binding domain).
  • the CAR extracellular domain can comprise streptavidin, while the independent antigen binding domain is biotinylated.
  • the CAR extracellular domain can comprise an antibody or antibody derivative that is specific for the independent antigen binding domain. This division into independent antigen binding domain and CAR enables one to change the antigen specificity of the receptor without transducing a new receptor. See, e.g., N.G. Minutolo et al, Front Oncol (2019) 9: 176.
  • the anti-CD2 fusion protein does not comprise a single chain antibody domain or an scFv.
  • the antigen binding domain comprises an antigen-binding portion from a single domain antibody (sdAb).
  • the antigen binding domain comprises a single chain variable fragment (scFv).
  • the antigen binding domain comprises an antigen-binding portion of a monoclonal antibody, a chimeric antibody, a humanized antibody, a fully human antibody, or the like.
  • the antigen binding domain comprises an antigen-binding portion from an antibody approved by the United States Food and Drug Administration and/or the European Medicines Agency (EMA) for use as a therapeutic antibody or an scFv version thereof.
  • the antigen binding domain can comprise an antigen-binding portion from an antibody or an scFv version thereof selected from the group consisting of Adecatumumab, Ascrinvacumab, Cixutumumab, Conatumumab, Daratumumab, Drozitumab, Duligotumab, Durvalumab, Dusigitumab, Enfortumab, Enoticumab, Figitumumab, Ganitumab, Glembatumumab, Intetumumab, Ipilimumab, Iratumumab, Icrucumab, Lexatumumab, Lucatumumab, Mapatumumab, Namatumab, Ne
  • the antigen binding domain targets CD19.
  • the antigen binding domain comprises an scFv with a variable light chain domain (VL) having a light chain CDR1 (LCDR1), LCDR2 and LCDR3 of RASQDISKYLN, SRLHSGV and GNTLPYTFG, respectively.
  • VL variable light chain domain
  • the antigen binding domain comprises an scFv with a variable light chain domain (VL) having at least about 80% sequence identity to DIQMTQTTSSLSASLGDRVTISCRASQDISKYLNWYQQKPDGTVKLLIYHTSRLHSGVPSRFSGS GSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIT.
  • VH variable heavy chain domain
  • HCDR1 heavy chain CDR1
  • VIWGSETTYYNSALKS and YAMDYWG respectively.
  • the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having at least about 80% sequence identity to EVKLQESGPGLVAPSQSLSVTCTVSGVSLPDYGVSWIRQPPRKGLEWLGVIWGSETTYYNSALK SRLTIIKDNSKSQVFLKMNSLQTDDTAIYYCAKHYYYGGSYAMDYWGQGTSVTVSS.
  • VH variable heavy chain domain
  • the antigen binding domain comprises an scFv with at least about 80% sequence identity to
  • the antigen binding domain comprises an scFv with at least about 80% sequence identity to
  • the antigen binding domain targets CD22.
  • the antigen binding domain comprises an scFv with a variable light chain domain (VL) having a light chain CDR1 (LCDR1), LCDR2 and LCDR3 of QTIWSY. AAS and QQSYSIPOT. respectively.
  • the antigen binding domain comprises an scFv with a variable light chain domain (VL) having at least about 80% sequence identity to DIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRFSGR GSGTDFTLTISSLOAEDFATYYCOQSYSIPOTFGOGTKLEI.
  • the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having a heavy chain CDR1 (HCDR1), HCDR2 and HCDR3 of GDSVSSNSAA. TYYRSKWYN and ARE VT GDLED AFDI. respectively.
  • the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having at least about 80% sequence identity to
  • the antigen binding domain comprises an scFv with at least about 80% sequence identity to
  • the antigen binding domain comprises an scFv with at least about 80% sequence identity to
  • the antigen binding domain comprises an scFv with at least about 85, 90, 95, 97, 98, or 99% sequence identity to OVOLOQSGPGLVKPSOTLSLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDY AVSVKSRITINPDTSKNOFSLQLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSSGG GGSDIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRF SGRGSGTDFTLTISSLOAEDFATYYCOOSYSIPOTFGOGTKLEIK.
  • the antigen binding domain comprises an scFv with 100% sequence identity OVOLOQSGPGLVKPSOTLSLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDY AVSVKSRITINPDTSKNOFSLOLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSSGG GGSDIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRF SGRGSGTDFTLTISSLOAEDFATYYCOQSYSIPOTFGOGTKLEIK.
  • the protein of interest, or nucleic acid encoding the protein of interest is a CAR including one or more linker sequences between the various domains.
  • a “variable region linking sequence” is an amino acid sequence that connects a heavy chain variable region to a light chain variable region and provides a spacer function compatible with interaction of the two sub-binding domains so that the resulting polypeptide retains a specific binding affinity to the same target molecule as an antibody that includes the same light and heavy chain variable regions.
  • a non-limiting example of a variable region linking sequence is a serine-glycine linker, such as a serine-glycine linker that includes the amino acid sequence GGGGSGGGGSGGGGS (G4S)3.
  • a linker separates one or more heavy or light chain variable domains, hinge domains, transmembrane domains, co-stimulatory domains, and/or primary signaling domains.
  • the CAR includes one, two, three, four, or five or more linkers.
  • the length of a linker is about 1 to about 25 amino acids, about 5 to about 20 amino acids, or about 10 to about 20 amino acids, or any intervening length of amino acids.
  • the linker is 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, or more amino acids long.
  • an antibody or an antigen-binding fragment thereof includes an isolated antibody or antigen-binding fragment thereof, a purified antibody or antigen-binding fragment thereof, a recombinant antibody or antigen-binding fragment thereof, a modified antibody or antigen-binding fragment thereof, or a synthetic antibody or antigen-binding fragment thereof.
  • Antibodies and antigenbinding fragments herein can be partly or wholly synthetically produced.
  • An antibody or antigen-binding fragment can be a polypeptide or protein having a binding domain which can be, or can be homologous to, an antigen binding domain.
  • an antibody or an antigen-binding fragment thereof can be produced in an appropriate in vivo animal model and then isolated and/or purified.
  • Antibodies useful in the present disclosure can encompass monoclonal antibodies, polyclonal antibodies, chimeric antibodies, bispecific antibodies, multispecific antibodies, heteroconjugate antibodies, humanized antibodies, human antibodies, deimmunized antibodies, mutants thereof, fusions thereof, immunoconjugates thereof, antigen-binding fragments thereof, and/or any other modified configuration of the immunoglobulin molecule that includes an antigen recognition site of the required specificity, including glycosylation variants of antibodies, amino acid sequence variants of antibodies, and covalently modified antibodies.
  • a multispecific antibody can be trispecific (e.g., an anti-tumor antigen, CD2, and CD3).
  • a multispecific antibody can be bispecific (e.g., an anti-tumor antigen and CD2).
  • Bispecific antibodies can be antibodies that have binding specificities for at least two different antigens and can be prepared using the antibodies disclosed herein. Exemplary methods for making bispecific antibodies are described (see, e.g., Suresh et al, 1986, Methods in Enzymology 121:210).
  • bispecific antibodies can be based on the co-expression of two immunoglobulin heavy chain-light chain pairs, with the two heavy chains having different specificities (Millstein and Cuello, 1983, Nature, 305, 537- 539).
  • Bispecific antibodies can be composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm.
  • This asymmetric structure, with an immunoglobulin light chain in only one half of the bispecific molecule, can facilitate separation of the desired bispecific compound from unwanted immunoglobulin chain combinations.
  • the CAR or anti-CD2 fusion protein comprises an extracellular binding domain that specifically binds a molecule on the surface of a target cell.
  • the target cell may be any cell type of interest.
  • the target cell may be a genetically and/or phenotypically normal cell.
  • the target cell is a genetically and/or phenotypically abnormal cell.
  • Abnormal cells of interest include, but are not limited to, cancer cells, cells in the tumor microenvironment (e.g., tumor stromal cells) such as cancer-associated fibroblasts (CAFs), myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs), tumor endothelial cells (TECs), and the like.
  • cancer cell is meant a cell exhibiting a neoplastic cellular phenotype, which may be characterized by one or more of the following exemplary characteristics: abnormal cell growth, abnormal cellular proliferation, loss of density dependent growth inhibition, anchorage-independent growth potential, ability to promote tumor growth and/or development in an immunocompromised non-human animal model, and/or any appropriate indicator of cellular transformation.
  • Cancer cell may be used interchangeably herein with “tumor cell”, “malignant cell” or “cancerous cell”, and encompasses cancer cells of a solid tumor, a semi-solid tumor, a hematological malignancy (e.g., a leukemia cell, a lymphoma cell, a myeloma cell, etc.), a primary tumor, a metastatic tumor, and the like.
  • the protein of interest is a TCR that recognizes an antigenic peptide complexed with a major histocompatibility complex (MHC) molecule displayed on the surface of a cancer cell.
  • MHC major histocompatibility complex
  • the target cell is a cancer cell
  • the CAR or anti-CD2 fusion protein specifically binds to a tumor antigen on the surface of the cancer cell.
  • the antigen binding domain binds to an antigen selected from the group consisting of glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostate- specific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-
  • an antigen selected from the
  • tumor antigens to which the cell surface molecule may specifically bind include 5T4, AXL receptor tyrosine kinase (AXL), B-cell maturation antigen (BCMA), c-MET, C4.4a, carbonic anhydrase 6 (CA6), carbonic anhydrase 9 (CA9), Cadherin-6, CD 19, CD20, CD22, CD25, CD27L, CD30, CD33, CD37, CD44v6, CD56, CD70, CD74, CD79b, CD123, CD138, carcinoembryonic antigen (CEA), cKit, Cripto protein, CS1, delta-like canonical Notch ligand 3 (DLL3), endothelin receptor type B (EDNRB), ephrin A4 (EFNA4), epidermal growth factor receptor (EGFR), EGFRvlll, ectonucleotide pyrophosphatase/phosphodiesterase 3 (ENPP3), EPH receptor
  • the antigen binding domain of the CAR or anti-CD2 fusion protein may bind to or associate with the antigen with an affinity (KA) of, for example, greater than or equal to about 10 A 5 M' 1 .
  • the extracellular binding domain of the CAR or anti-CD2 fusion protein binds to an antigen with a KA greater than or equal to about 10 A 6 M’ 1 , 10 A 7 M’ 1 , 10 A 8 M’ 1 , 10 A 9 M’ 1 , 10 A l 0 M’ 1 , 10 A l 1 M’ 1 , 10 A 12 M’ 1 , or 10 A 13 M' 1 .
  • the extracellular binding domain of the CAR or anti- CD2 fusion protein binds to an antigen with a KD of less than or equal to about 10 A 5 M’ 1 , 10 A 6 M’ 1 , 10 A 7 M’ 1 , 10 A 8 M’ 1 , 10 A 9 M’ 1 , 10 A 10 M’ 1 , 10 A l 1 M’ 1 , 10 A 12 M’ 1 , or 10 A 13 M’ 1 .
  • the binding affinity of the extracellular binding domain for the target antigen can be readily determined using conventional techniques, e.g., by competitive ELISA (enzyme-linked immunosorbent assay), equilibrium dialysis, by using surface plasmon resonance (SPR) technology (e.g., the BIAcore 2000 instrument, using general procedures outlined by the manufacturer); by radioimmunoassay; or the like.
  • competitive ELISA enzyme-linked immunosorbent assay
  • equilibrium dialysis by using surface plasmon resonance (SPR) technology (e.g., the BIAcore 2000 instrument, using general procedures outlined by the manufacturer); by radioimmunoassay; or the like.
  • SPR surface plasmon resonance
  • the target antigen of the antigen binding domain is CD19, CD20, or CD22. In an embodiment, the target antigen of the antigen binding domain is CD 19. In an embodiment, the target antigen of the antigen binding domain is CD22. In some embodiments, the CAR lacks a CD2 binding domain and is expressed with an anti-CD2 fusion protein.
  • the antigen binding domain of a CAR provided herein is directly linked to a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein is linked to a hinge domain by a second linker. In some embodiments, the antigen binding domain of a CAR provided herein is operatively linked to a transmembrane domain by a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein provided herein is directly linked to a transmembrane domain by a hinge domain. [0084] In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain.
  • the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a hinge domain by a linker. In some embodiments, the anti- CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein is operatively linked to a transmembrane domain by a hinge domain. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain.
  • the antigen binding domain of a CAR provided herein is directly linked to a transmembrane domain by a hinge domain.
  • the hinge domain of a CAR or anti-CD2 fusion protein provided herein is from CD28.
  • the hinge domain of a CAR or anti-CD2 fusion protein provided herein has the sequence IEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKP.
  • the hinge domain of a CAR or anti-CD2 fusion protein provided herein is from CD8.
  • the hinge domain of a CAR or anti-CD2 fusion protein provided herein has the sequence TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIY.
  • a hinge or spacer domain is a portion of an immunoglobulin, including, but not limited to, one or more heavy chain constant regions, e.g., CH2 and CH3.
  • the spacer domain may include the amino acid sequence of a naturally occurring immunoglobulin hinge region or an altered immunoglobulin hinge region.
  • the spacer domain includes the CH2 and/or CH3 of IgG 1, lgG4, or IgD.
  • Illustrative spacer domains suitable for use in the CARs or anti-CD2 fusion proteins described herein include the hinge region derived from the extracellular regions of type 1 membrane proteins such as CD8a and CD28, which may be wild-type hinge regions from these molecules or variants thereof.
  • the hinge domain includes a CD8a or CD28 hinge region.
  • the hinge is a PD-1 hinge or CD152 hinge.
  • the CAR or anti-CD2 fusion protein further includes an extracellular spacer domain, which may include a hinge domain.
  • the hinge domain is generally a flexible polypeptide connector region disposed between the targeting moiety and the transmembrane domain.
  • Exemplary hinge domain sequences include those from IgG subclasses (such as IgGl and IgG4), IgD, CD28, and CD8 domains.
  • the hinge domain provides structural flexibility to flanking polypeptide regions.
  • the hinge domain may consist of natural or synthetic polypeptides.
  • hinge domains may improve the function of the CAR or anti-CD2 fusion protein by promoting optimal positioning of the antigen binding domain and/or anti-CD2 binding domain in relationship to the portion of the antigen or CD2 recognized by it.
  • a hinge domain may not be required for optimal CAR activity or anti-CD2 fusion protein.
  • a hinge domain comprising a short sequence of amino acids promotes CAR or anti-CD2 fusion protein activity by facilitating antigen-binding by, for example, relieving steric constraints that could otherwise alter antibody binding kinetics.
  • the hinge domain is linked downstream of the antigen-binding domain of a CAR and upstream of the transmembrane domain of a CAR. In some embodiments, the hinge domain is linked downstream of the anti-CD2 binding domain of an anti-CD2 fusion protein and upstream of the transmembrane domain of an anti-CD2 fusion protein.
  • Non-limiting examples of suitable hinge domains include those derived from CD8a, CD28, CTLA4, CD4, PD1, IgGl, PGK, or IgG4.
  • the hinge domain can include regions derived from a human CD8a (also known as CD8a) molecule, a CD28 molecule, and any other receptors that provide a similar function in providing flexibility to flanking regions.
  • the CAR disclosed herein includes a hinge domain derived from a CD8a hinge domain.
  • the CAR disclosed herein includes a hinge domain derived from a CD28 or CD2 hinge domain.
  • the hinge domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to a CD8a, CD28, CTLA4, CD4, PD1, IgGl, PGK, or IgG4 hinge domain.
  • the spacer domain further comprises a linker including one or more intervening amino acid residues that are positioned between the antigen binding domain and the extracellular hinge domain.
  • the linker is positioned downstream from the antigen binding domain and upstream from the hinge domain.
  • there are no particular limitations to the length and/or amino acid composition of the linker there are no particular limitations to the length and/or amino acid composition of the linker.
  • any arbitrary single-chain peptide comprising about one to about 300 amino acid residues (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acid residues) can be used as a linker.
  • the linker includes at least about 5, 6, 7, 8, 9, 10, 11, 12, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids. In some embodiments, the linker includes no more than about 300, 250, 200, 150, 140, 130, 120, 110, 100, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, or 30 amino acid residues. In some embodiments, the length and amino acid composition of the extracellular spacer can be optimized to vary the orientation and/or proximity of the antigen binding domain and the extracellular hinge domain to one another to achieve a desired activity of the CAR or anti-CD2 fusion protein.
  • the orientation and/or proximity of the antigen binding domain and the extracellular hinge domain to one another can be varied and/or optimized as a “tuning” tool or effect to enhance or reduce the efficacy of the CAR or anti-CD2 fusion protein. In some embodiments, the orientation and/or proximity of the antigen binding domain and the hinge domain to one another can be varied and/or optimized to create a partially functional version of the CAR or anti-CD2 fusion protein.
  • the extracellular spacer domain includes an amino acid sequence corresponding to an IgG4 hinge domain and an IgG4 CH2-CH3 domain.
  • the spacer domain can be a synthetic polypeptide spacer, such as a spacer having a random sequence, a (gly-gly-ser)n (“GGSn”) sequence, or a variation thereof such as (SGG)n, (GGGS)n, (SGGG)n, (GSGGG)n, and the like, where n can range from about 1 to about 15.
  • the synthetic polypeptide spacer domain can also include a naturally occurring sequence, such as a hinge domain derived from CD8a, IgG, and the like.
  • the “transmembrane domain” is the portion of the CAR or anti-CD2 fusion protein that fuses the extracellular binding portion and intracellular signaling domain and anchors the CAR or anti-CD2 fusion protein to the plasma membrane of the cell (e.g., immune effector cell).
  • the transmembrane domain serves to link the extracellular domain (antigen binding domain and spacer domain) of the receptor with the cytoplasmic domain.
  • any transmembrane domain capable of working in a CAR can be used in the receptors and methods of the disclosure.
  • the CAR or anti-CD2 fusion protein comprises a transmembrane domain from a polypeptide selected from the group consisting of: CD4, CD8a, CD28, CD 154, and PD-1; and one or more intracellular costimulatory signaling domains from a polypeptide selected from the group consisting of: 4-1BB, CD28, CD134, and CD137; and an intracellular signaling domain from a polypeptide selected from the group consisting of: FcyRI, FcRy, FcR, CD3y, CD38, CD3s, CD3 ⁇ , CD35, CD22, CD79a, CD79, and CD665.
  • Such a CAR may further include a spacer domain between the antigenbinding portion and the transmembrane domain, e.g., a CD8a hinge.
  • the CAR or anti-CD2 fusion protein comprises a transmembrane domain from CD28.
  • the CAR or anti-CD2 fusion protein comprises a transmembrane domain with the sequence FWVLVVVGGVLACYSLLVTVAFIIFWV.
  • the CAR or anti-CD2 fusion protein comprises a transmembrane domain from CD8.
  • the CAR or anti-CD2 fusion protein comprises a transmembrane domain with the sequence IWAPLAGTCGVLLLSLVITLYC.
  • the transmembrane domain may be derived either from a natural, synthetic, semi-synthetic, or recombinant source.
  • the TM domain is derived from (e.g., includes at least the transmembrane region(s) or a functional portion thereof) of the alpha or beta chain of the T-cell receptor, CD3y, CD38, CD3E, CD35, CD3 ⁇ , CD4, CD5, CD8a, CD9, CD16, CD22, CD27, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD152, CD154, and/or PD-1.
  • the transmembrane domain may include, for example without limitation, all or part of the transmembrane domain of the CD3 chain), CD28, CD2, CD4, 0X40, 4-1BB (CD137), ICOS (CD278), ILRB (CD122), IL-2RG (CD132), CTLA-4, PD-1, or CD40, or a sequence derived from such a transmembrane domain.
  • the cytoplasmic signaling domain in general comprises a domain that transduces the event of ligand binding into an intracellular signal that activates the T cell.
  • the CD3z intracellular domain/activating domain is frequently used, although others such as MyD88 can be used.
  • the transmembrane domain is the transmembrane domain from CD3eta, CD2, CD8, or CD28. In an embodiment, the transmembrane domain is derived from the transmembrane domain from CD2 or CD28. In some embodiments, the transmembrane domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to a CD3 , CD28, CD2, CD4, 0X40, 4-1BB (CD137), FcERIy, ICOS (CD278), ILRB (CD122), IL-2RG (CD132), or CD40 transmembrane domain.
  • the protein of interest, or nucleic acid encoding the protein of interest is a CAR or anti-CD2 fusion protein that comprises a transmembrane domain derived from CD8a or CD28.
  • a CAR or anti-CD2 fusion protein includes a transmembrane domain derived from CD8a or CD28 and a short polypeptide linker, e.g., between 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids in length, that links the transmembrane domain and the intracellular signaling domain of the CAR or anti-CD2 fusion protein.
  • a glycine-serine linker may be employed as such a linker, for example.
  • the transmembrane of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR.
  • the transmembrane domain of the anti-CD2 fusion protein may be from CD8, CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), DAP10, LAT, KD2C, SLP76, TRIM, or ZAP70.
  • the cytoplasmic or intracellular signaling domain in general, comprises an activating domain having an immunoreceptor tyrosine-based activation motif (IT AM), which when phosphorylated activates the T cell reaction to an antigen. Phosphorylation occurs as a result of antigen binding.
  • IT AM immunoreceptor tyrosine-based activation motif
  • the “intracellular signaling” domain of a CAR can refer to the part of a CAR that participates in transducing the signal from CAR binding to a target molecule/antigen into the interior of the immune effector cell to elicit effector cell function, e.g., activation, cytokine production, proliferation and/or cytotoxic activity, including the release of cytotoxic factors to the CAR-bound target cell, or other cellular responses elicited with target molecule/antigen binding to the extracellular CAR domain.
  • the term “intracellular signaling domain” can refer to the portion(s) or domain(s) of a protein which transduce the effector function signal and that direct the cell to perform a specialized function.
  • intracellular signaling domain is meant to include any truncated portion of an intracellular signaling domain sufficient for transducing effector function signal.
  • the anti-CD2 fusion protein lacks an intracellular domain. In some embodiments, the anti-CD2 fusion protein comprises and intracellular domain that lacks an intracellular signaling domain. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from 4-1BB (CD137). In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL.
  • the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD3 ⁇ .
  • the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence RVKFSRSADAPAYKQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNEL QKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR.
  • the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence
  • the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD3 and an intracellular signaling domain from 4- 1BB (CD 137).
  • the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD2. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence KRKKQRSRRNDEELETRAHRVATEERGRKPHQIPASTPQNPAT. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence PATSQHPPPPPGHRSQAPSHRPPPPGHRVQH.
  • the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD3 epsilon. In some embodiments, the CAR or anti- CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence RPPPVPNPDYEPIRKGQRDLYSGLNQRRI. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising a truncated CD3 epsilon intracellular domain. [0102] Signals generated through the T cell receptor (TCR) alone may be insufficient for full activation of the T cell and a secondary or costimulatory signal may also be required.
  • TCR T cell receptor
  • T cell activation can be mediated by two distinct classes of intracellular signaling domains: primary signaling domains that initiate antigen-dependent primary activation through the TCR (e.g., a TCR/CD3 complex) and costimulatory signaling domains that act in an antigen- independent manner to provide a secondary or costimulatory signal.
  • primary signaling domains that initiate antigen-dependent primary activation through the TCR
  • costimulatory signaling domains that act in an antigen- independent manner to provide a secondary or costimulatory signal.
  • the protein of interest is a CAR or anti-CD2 fusion protein
  • the CAR or anti-CD2 fusion protein may include an intracellular signaling domain that includes one or more costimulatory signaling domains and a primary signaling domain.
  • Primary signaling domains can regulate primary activation of the TCR complex either in a stimulatory manner, or in an inhibitory manner.
  • Primary signaling domains that act in a stimulatory manner may contain signaling motifs which are known as immunoreceptor tyrosine-based activation motifs (or “IT AMs”).
  • ITAM-containing primary signaling domains suitable for use in a CAR or anti-CD2 fusion protein include those derived from FcyRI, FcRy, FcR, CD3y, CD35, CD3E, CD3 ⁇ , CD35, CD22, CD79a, CD79b, and CD665.
  • a CAR or anti-CD2 fusion protein includes a CD3 ⁇ primary signaling domain and one or more costimulatory signaling domains. In certain embodiments, a CAR or anti-CD2 fusion protein includes a 4-1BB costimulatory signaling domain. The intracellular primary signaling and costimulatory signaling domains are operably linked to the carboxyl terminus of the transmembrane domain. In certain embodiments, a CAR or anti- CD2 fusion protein lacks a CD2 intracellular signaling domain.
  • the CAR or anti-CD2 fusion protein includes one or more costimulatory signaling domains to enhance the efficacy and expansion of T cells expressing the CAR.
  • costimulatory molecules suitable for use in CARs or anti-CD2 fusion proteins contemplated in particular embodiments include TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD28, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • the costimulatory signaling domain has at least about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to a costimulatory signaling domain from TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD28, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • a CAR or anti-CD2 fusion protein includes one or more costimulatory signaling domains selected from the group consisting of CD2, 4-1BB, CD28, CD137, and CD 134, and a CD3 primary signaling domain.
  • a costimulatory molecule can be represented in the following protein families: TNF receptor proteins, Immunoglobulin-like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SLAM proteins), and activating NK cell receptors.
  • the CAR or anti-CD2 fusion protein comprises two or more intracellular signaling domains.
  • the CAR or anti-CD2 fusion protein may comprise a first signaling domain and a second signaling domain or fragments thereof independently selected from a i5n3z intracellular signaling domain, a CD28 intracellular signaling domain, a 4-1BB intracellular signaling domain, an OX-40 intracellular signaling domain, an inducible co-stimulator (ICOS) intracellular signaling domain, a CD27 intracellular signaling domain, and a MyD88/CD40 intracellular signaling domain.
  • a CAR may include a first intracellular signaling domain or fragment thereof that is a CD3 ⁇ intracellular signaling domain and a second intracellular signaling domain or fragment thereof that is a CD28 intracellular signaling domain.
  • a CAR or anti-CD2 fusion protein may include a first intracellular signaling domain or fragment thereof that is a CD3 ⁇ intracellular signaling domain and a second intracellular signaling domain or fragment thereof that is a 4- IBB intracellular signaling domain.
  • a CAR or anti-CD2 fusion protein may include a first intracellular signaling domain or fragment thereof that is a CD3 intracellular signaling domain, a second intracellular signaling domain or fragment thereof that is a 4- IBB intracellular signaling domain, and a third intracellular signaling domain or fragment thereof that is a CD3 epsilon intracellular signaling domain.
  • CARs and anti-CD2 fusion proteins of the disclosure may comprise a CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3e, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70 cytoplasmic signaling domain.
  • CD137 CD137
  • CD28 CD28
  • ICOS FcyRI, FcRy, FcR, CD3y, CD38, CD3e, CD35, CD22, CD79a, CD79b,
  • the cytoplasmic signaling domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to an CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4- 1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70 cytoplasmic signaling domain.
  • CD137 CD137
  • CD28 CD28
  • ICOS FcyRI, FcR
  • CARs of the disclosure may comprise a CD2 co-stimulatory domain, and one or more additional co-stimulatory domains to increase cytokine production or sensitivity, reduce or prevent anergy, and/or to increase proliferation and cytotoxic activity.
  • additional co-stimulatory domains can be derived from co-stimulatory proteins such as B7-1 (CD80), B7-2 (CD86), CTLA-4, PD-1, CD278, CD122, CD132, B7- H2, B7-H3, PD-L1, PD-L2, B7-H4, PDCD6, BTLA, 41BB (CD137), FcERTy, CD40L, 4- 1BBL, GITR, BAFF, GITR-L, BAFF-R, HVEM, CD27, LIGHT, CD27L, 0X40, OX40L, CD30, CD30L, TAC1, CD40, CD244, CD84, BLAME, CD229, CRACC, CD2F-10, NTB-A, CD48
  • the cytoplasmic signaling domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to an B7-1 (CD80), B7-2 (CD86), CTLA- 4, PD-1, CD278, CD122, CD132, B7- H2, B7-H3, PD-L1, PD-L2, B7-H4, PDCD6, BTLA, 41BB (CD137), FcERTy, CD40L, 4- 1BBL, GITR, BAFF, GITR-L, BAFF-R, HVEM, CD27, LIGHT, CD27L, 0X40, OX40L, CD30, CD30L, TAC1, CD40, CD244, CD84, BLAME, CD229, CRACC, CD2F-10, NTB-A, CD48, SLAM (CD150), CD58, ikaros, CD53, integrin a4, CD82, integrin a4
  • An aspect of the disclosure may be a transgenic T cell receptor for use with a CAR in a CAR-T therapy.
  • a TCR can be found on the surface of a cell or in soluble form. Generally, a TCR is found on the surface of T cells (or T lymphocytes) where it is generally responsible for recognizing antigens bound to major histocompatibility complex (MHC) molecules.
  • MHC major histocompatibility complex
  • a TCR can be an intact or full-length TCR, including a TCR in the a0 form or y8 form.
  • a TCR is a dimeric TCR (dTCR).
  • a TCR is a single-chain TCR (scTCR).
  • the TCR is an antigen-binding portion that is less than a full-length TCR but that binds to a specific peptide bound in an MHC molecule, such as binds to an MHC -peptide complex.
  • an antigen-binding portion or fragment of a TCR can contain only a portion of the structural domains of a full-length or intact TCR, but yet is able to bind the peptide epitope, such as MHC -peptide complex, to which the full TCR binds.
  • an antigen-binding portion contains the variable domains of a TCR, such as variable a chain and variable p chain of a TCR, sufficient to form a binding site for binding to a specific MHC -peptide complex.
  • the variable chains of a TCR contain complementarity determining regions involved in recognition of the peptide, MHC and/or MHC -peptide complex.
  • a TCR can contain a constant domain, a transmembrane domain and/or a short cytoplasmic tail.
  • each chain of the TCR can possess one N-terminal immunoglobulin variable domain, one immunoglobulin constant domain, a transmembrane region, and a short cytoplasmic tail at the C-terminal end.
  • a TCR is associated with invariant proteins of the CD3 complex involved in mediating signal transduction.
  • a TCR contains one or more constant domain.
  • the extracellular portion of a given TCR chain e.g., a chain or chain
  • the extracellular portion of the TCR formed by the two chains contains two membrane-proximal constant domains, and two membrane-distal variable domains, which variable domains each contain CDRs.
  • the constant domain of the TCR can contain short connecting sequences in which a cysteine residue forms a disulfide bond, thereby linking the two chains of the TCR.
  • a TCR can have an additional cysteine residue in each of the a and b chains, such that the TCR contains two disulfide bonds in the constant domains.
  • a TCR is a dimeric TCR (dTCR).
  • the dTCR can contain a first polypeptide wherein a sequence corresponding to a TCRa chain variable region sequence is fused to the N terminus of a sequence corresponding to a TCRa chain constant region extracellular sequence, and a second polypeptide wherein a sequence corresponding to a TCRp chain variable region sequence is fused to the N terminus a sequence corresponding to a TCRP chain constant region extracellular sequence, the first and second polypeptides being linked by a disulfide bond.
  • the bond can correspond to the native interchain disulfide bond present in native dimeric TCRab forms.
  • the interchain disulfide bonds are not present in a native TCR.
  • one or more cysteines can be incorporated into the constant region extracellular sequences of dTCR polypeptide pair.
  • a dTCR can have both a native and one or more non-native disulfide bonds.
  • a dTCR can contain a transmembrane sequence to anchor to the membrane.
  • a dTCR can contain a TCRa chain containing a variable a domain, a constant a domain and a first dimerization motif attached to the C-terminus of the constant a domain, and a TCR b chain comprising a variable b domain, a constant b domain and a first dimerization motif attached to the C-terminus of the constant b domain, wherein the first and second dimerization motifs easily interact to form a covalent bond between an amino acid in the first dimerization motif and an amino acid in the second dimerization motif linking the TCR a chain and TCR b chain together.
  • a TCR or antigen binding portion thereof is one that has been modified or engineered.
  • the antigen binding domain of a TCR can be multispecific.
  • a TCR or antigen-binding portion thereof can be a recombinantly produced natural protein or a mutated form thereof in which one or more property, such as a binding characteristic, has been altered.
  • directed evolution methods are used to generate TCRs with altered properties, such as with higher affinity for a specific MHC -peptide complex.
  • directed evolution is achieved by display methods including, but not limited to, yeast display.
  • display approaches can involve engineering, or modifying, a known, parent or reference TCR.
  • a wild-type TCR can be used as a template for producing mutagenized TCRs in which in one or more residues of the CDRs are mutated, and mutants with a desired altered property, such as higher affinity for a desired target antigen, can be selected.
  • peptides suitable for use in generating TCRs or antigen-binding portions can be determined based on the presence of an HLA- restricted motif in a target polypeptide of interest.
  • peptides are identified using computer prediction models known to those of skill in the art.
  • a TCR can be generated from a known TCR sequence(s), such as sequences of Va and/or nb chains, for which a substantially full-length coding sequence is readily available. Methods for obtaining full-length TCR sequences, including V chain sequences, from cell sources are well known.
  • nucleic acids encoding the TCR can be obtained from a variety of sources, such as by polymerase chain reaction (PCR) amplification of TCR-encoding nucleic acids within or isolated from a given cell or cells, or synthesis of publicly available TCR DNA sequences.
  • PCR polymerase chain reaction
  • a TCR is obtained from a biological source, such as from a T cell (e.g., cytotoxic T cell), T-cell hybridomas or other publicly available source.
  • the T-cells can be obtained from in vivo isolated cells, e.g., from a human subject.
  • the TCR is a thymically selected TCR.
  • the TCR is a neoepitope-restricted TCR.
  • the T-cells can be a cultured T-cell hybridoma or clone.
  • the TCR or antigen binding portion thereof can be synthetically generated from knowledge of the sequence of the TCR.
  • a TCR is generated from the TCR identified or selected from screening a library of candidate TCRs against a target polypeptide antigen, or target T cell epitope thereof.
  • TCR libraries can be generated by amplification of the repertoire of Va and Vb from T cells isolated from a subject, including cells present in PBMCs, spleen or other lymphoid organs. In some cases, T cells can be amplified from tumor-infiltrating lymphocytes (TILs). In some embodiments, TCR libraries can be generated from CD4+ or CD8+ cells. In some embodiments, the TCRs can be amplified from a T cell source of a normal of healthy subject, i. e. normal TCR libraries.
  • the TCRs can be amplified from a T cell source of a diseased subject, i.e., diseased TCR libraries.
  • degenerate primers are used to amplify the gene repertoire of Va and Va, such as by RT-PCR in samples, such as T cells, obtained from humans.
  • scTv libraries can be assembled from naive Va and nb libraries in which the amplified products are cloned or assembled to be separated by a linker.
  • the libraries can be HLA allele specific.
  • TCR libraries can be generated by mutagenesis or diversification of a parent or scaffold TCR molecule.
  • the TCRs are subjected to directed evolution, such as by mutagenesis, e.g., of the a or b chain. In some embodiments, particular residues within CDRs of the TCR can be altered. In some embodiments, selected TCRs can be modified by affinity maturation. In some embodiments, antigen-specific T cells can be selected, such as by screening to assess CTL activity against the peptide. In some aspects, TCRs, e.g., present on the antigen-specific T cells, may be selected, such as by binding activity, e.g., particular affinity or avidity for the antigen.
  • a TCR of the present disclosure binds to a tumor specific antigen or tumor- associated antigen.
  • CD2 signaling in a T cell expressing a transgenic TCR or in bulk tumor infiltrating lymphocytes (TILs) grown ex vivo can be enhanced by several methods.
  • the TILs can then be given back to a patient.
  • the T cells can be transduced with a co-receptor that enhances CD2 signaling (in addition to expressing the transgenic TCR).
  • the co-receptor comprising an extracellular ligand binding domain, a transmembrane domain, and a CD2 signaling domain can be transcribed in a virus or other vector and can provide CD2 signaling in trans even when the target tumor cells express low, absent, or mutated CD58.
  • the extracellular portion of the co-receptor can comprise an scFv recognizing an antigen expressed by the tumor cells or a ligand for a common receptor expressed on the target tumor cell of interest.
  • Another way to enhance CD2 signaling in a CAR T cell, a transgenic TCR T cell, or bulk TILs can comprise transducing the T cells to constitutively express a secreted molecule capable of crosslinking the cell’s native CD2 through use of one or more anti-CD2 scFvs, antibodies, Fabs, DARPINs, ligands, or other binders/antigen binding domains.
  • the secreted molecule can be expressed under an activation switch.
  • the secreted molecule can be membrane bound and can consist of two scFv’s connected by a linker: one scFv that binds CD2 on the T cell (activating its native CD2 signaling) and the other scFv or ligand recognizing a protein or target expressed on tumor cells such that CD2 is crosslinked and activated when the T cell encounters tumor cells.
  • nucleic acids comprising a sequence encoding the CAR and/or anti-CD2 fusion proteins provided herein.
  • nucleic acid and “polynucleotide” are used interchangeably herein, and refer to both RNA and DNA molecules, including nucleic acid molecules comprising cDNA, genomic DNA, and/or synthetic DNA, and DNA or RNA molecules containing nucleic acid analogs.
  • the nucleic acid can comprise one or more bases and/or linkages that do not occur naturally in DNA or RNA, such as phosphoramidite linkages, 2'-modified ribose or deoxyribose, morpholino phosphoramidites, peptidenucleic acid links, locked nucleic acid links, xanthine, 7-methylguanine, inosine, dihydro uracil, 5- methylcytosine, 5- hydroxymethylcytosine, and others. See, e.g., C.I.E. Smith et al., Ann Rev Pharmacol Toxicol (2019) 59:605-30, incorporated herein by reference.
  • a nucleic acid can be double-stranded or single-stranded (for example, a sense strand or an antisense strand).
  • a nucleic acid may contain unconventional or modified nucleotides.
  • polynucleotide sequence and “nucleic acid sequence” as used herein interchangeably refer to the sequence of a nucleic acid molecule.
  • Nucleic acids of the disclosure can encode a CAR, a transgenic TCR and/or, an anti-CD2 fusion protein.
  • nucleic acids of the disclosure can encode both an anti-CD2 fusion protein and a CAR (which can be a CD2 recruiting CAR).
  • nucleic acids of the disclosure can encode both an anti-CD2 fusion protein and a transgenic TCR.
  • nucleic acids of the disclosure can encode both a CAR and a transgenic TCR.
  • the recombinant nucleic acid is operably linked to a heterologous nucleic acid sequence, such as, for example a structural gene that encodes a protein of interest or a regulatory sequence (e.g., a promoter sequence).
  • the recombinant nucleic acid is further defined as an expression cassette or a vector.
  • the vector is a lentiviral vector, an adeno virus vector, an adeno-associated virus vector, or a retroviral vector.
  • Some embodiments disclosed herein relate to vectors or expression cassettes including a recombinant nucleic acid molecule as disclosed herein.
  • An expression cassette is a construct of genetic material that contains coding sequences and enough regulatory information to direct proper transcription and/or translation of the coding sequences in a recipient cell, in vivo and/or ex vivo.
  • the expression cassette may be inserted into a vector for targeting to a desired host cell.
  • the term expression cassette may be used interchangeably with the term “expression construct.”
  • the nucleic acid molecules described above can be contained within a vector that is capable of directing their expression in, for example, a cell that has been transduced with the vector.
  • Suitable vectors for use in eukaryotic cells are known in the art and are commercially available or readily prepared by a skilled artisan. Additional vectors can also be found, for example, in Ausubel, F. M., et al, Current Protocols in Molecular Biology, (Current Protocol, 1994) and Sambrook et al, “ Molecular Cloning: A Laboratory Manual,” 2nd Ed. (1989).
  • the CARs, the TCRs, and/or anti-CD2 fusion proteins of the present disclosure can be expressed from vectors, generally expression vectors.
  • the vectors are useful for autonomous replication in a host cell or may be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome (e.g., non-episomal mammalian vectors).
  • Expression vectors are capable of directing the expression of coding sequences to which they are operably linked.
  • expression vectors of utility in recombinant DNA techniques are often in the form of plasmids (vectors).
  • other forms of expression vectors such as viral vectors (e.g., replication defective retroviruses, adenoviruses, and adeno-associated viruses) are also included.
  • DNA vectors can be introduced into eukaryotic cells via conventional transformation or transfection techniques. Suitable methods for transforming or transfecting host cells can be found in Sambrook et al. ( 1 89) Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.) and other standard molecular biology laboratory manuals.
  • Vectors suitable for use include the pMSXND expression vector for use in mammalian cells.
  • nucleic acid inserts which encode the subject CAR and/or anti-CD2 fusion protein in such vectors, can be operably linked to a promoter, which is selected based on, for example, the cell type in which expression is sought.
  • Viral vectors that can be used in the disclosure include, for example, retroviral, adenoviral, and adeno-associated vectors, herpes virus, simian virus 40 (SV40), and bovine papilloma virus vectors (see, for example, Gluzman (Ed.), Eukaryotic Viral Vectors, CSH Laboratory Press, Cold Spring Harbor, N.Y.).
  • the expression vector can be a viral vector.
  • viral vector is widely used to refer either to a nucleic acid molecule that includes virus-derived nucleic acid elements that typically facilitate transfer of the nucleic acid molecule or integration into the genome of a cell, or to a viral particle that mediates nucleic acid transfer. Viral particles typically include viral components, and sometimes also host cell components, in addition to nucleic acid(s).
  • Retroviral vectors used herein contain structural and functional genetic elements, or portions thereof, that are primarily derived from a retrovirus.
  • Retroviral lentivirus vectors contain structural and functional genetic elements, or portions thereof including LTRs, that are primarily derived from a lentivirus (a sub-type of retrovirus).
  • Viral vectors that can be used in the disclosure include, for example, retrovirus vectors (including lentivirus vectors), adenovirus vectors, and adeno-associated virus vectors, herpes virus, simian virus 40 (SV40), and bovine papilloma virus vectors (see, for example, Gluzman (Ed.), Eukaryotic Viral Vectors, CSH Laboratory Press, Cold Spring Harbor, N.Y.).
  • the nucleic acid molecules are delivered by viral or non-viral delivery vehicles known in the art.
  • the nucleic acid molecule can be stably integrated in the host genome, or can be episomally replicating, or present in the recombinant host cell as a mini-circle expression vector for stable or transient expression.
  • the nucleic acid molecule is maintained and replicated in the recombinant host cell as an episomal unit.
  • the nucleic acid molecule is stably integrated into the genome of the recombinant cell.
  • Stable integration can also be accomplished using classical random genomic recombination techniques or with more precise genome editing techniques such as using guide RNA-directed CRISPR/Cas9, DNA-guided endonuclease genome editing NgAgo (Natronobacterium gregoryi Argonaute), or TALENs genome editing (transcription activator-like effector nucleases).
  • the nucleic acid molecule is present in the recombinant host cell as a mini circle expression vector for stable or transient expression.
  • the nucleic acid molecules can be encapsulated in a viral capsid or a lipid nanoparticle.
  • endonuclease polypeptide(s) can be delivered by viral or non- viral delivery vehicles known in the art, such as electroporation or lipid nanoparticles.
  • introduction of nucleic acids into cells may be achieved using viral transduction methods.
  • adeno-associated virus AAV is a non-enveloped virus that can be engineered to deliver nucleic acids to target cells via viral transduction.
  • AAV serotypes have been described, and all of the known serotypes can infect cells from multiple diverse tissue types.
  • AAV is capable of transducing a wide range of species and tissues in vivo with no evidence of toxicity, and it generates relatively mild innate and adaptive immune responses.
  • Lentiviral systems are also useful for nucleic acid delivery and gene therapy via viral transduction.
  • Lentiviral vectors offer several attractive properties as gene-delivery vehicles, including: (i) sustained gene delivery through stable vector integration into the host cell genome; (ii) the ability to infect both dividing and non-dividing cells; (iii) broad tissue tropisms, including important gene- and cell-therapy - target cell types; (iv) no expression of viral proteins after vector transduction; (v) the ability to deliver complex genetic elements, such as polycistronic or intron-containing sequences; (vi) a potentially safer integration site profile (e.g., by targeting a site for integration that has little or no oncogenic potential); and (vii) a relatively easy system for vector manipulation and production.
  • Engineered cells that contain and express a nucleic acid that encodes a CAR, a transgenic TCR and/or an anti-CD2 fusion protein are also an aspect of the disclosure.
  • An engineered cell of the disclosure is a transduced cell, i.e., a cell into which a nucleic acid molecule, for example a nucleic acid molecule encoding a CAR and/or an anti-CD2 fusion protein, has been introduced by means of recombinant DNA techniques. The progeny of such a cell are also considered within the scope of the disclosure.
  • Engineered cells of the disclosure are useful for aiding in the treatment of hyperproliferative diseases and disorders such as cancer.
  • the engineered cells of the disclosure can exhibit improved functional properties, as compared to CAR-T cells lacking the features of the disclosure.
  • an engineered cell of the disclosure having a CAR that comprises a CD58 extracellular domain, a transgenic TCR, and/or an anti-CD2 fusion protein can exhibit improved efficacy against target cells that downregulate expression of or do not substantially express CD58; improved efficacy against target cells that downregulate the selected antigen, or express a mutated form of the selected antigen; and/or exhibit improved selectivity for the target cell.
  • the engineered cell can express a molecule (either secreted or surface expressed) that can crosslink native CD2 in response to a tumor specific antigen in the tumor microenvironment.
  • Improved efficacy against target cells that downregulate expression of or do not substantially express CD58 can be determined by laboratory experiments comparing engineered cells of the disclosure with conventional CAR-T cells, using target cells that express a reduced level of CD58 or a non-functional mutated form of CD58, where improved efficacy can be any demonstration of superior ability to kill or inhibit the target cells. Similar experiments can determine improved efficacy against target cells with down-regulated expression of the selected target antigen. Improved selectivity can be demonstrated by measuring the reduction of on-target off-tumor activity, either in vivo or in a suitable in vitro model.
  • host cells can be genetically engineered (e.g., transduced, transformed, or transfected) with, for example, a vector construct of the present disclosure that can be, for example, a viral vector or a vector for homologous recombination that includes nucleic acid sequences homologous to a portion of the genome of the host cell, or can be an expression vector for the expression of the polypeptides of interest.
  • a vector construct of the present disclosure can be, for example, a viral vector or a vector for homologous recombination that includes nucleic acid sequences homologous to a portion of the genome of the host cell, or can be an expression vector for the expression of the polypeptides of interest.
  • Host cells can be either untransformed cells or cells that have already been transfected with at least one nucleic acid molecule.
  • the host cell is an immune cell, a stem cell, a mammalian cell, a primate cell, or a human cell.
  • the host cell is autologous or allogeneic. In some embodiments, the host cell is a T cell, a CD8-positive T cell, a CD4-positive T cell, a regulatory T cell, a cytotoxic T cell, or a tumor infdtrating lymphocyte.
  • Host cells can be transduced with a nucleic acid encoding a CD2 recruiting CAR and/or an antiCD fusion protein, or with one or more nucleic acids encoding a CAR and/or a transgenic TCR plus an anti-CD2 fusion protein.
  • a host cell can be transduced with a nucleic acid encoding a CAR and/or an anti-CD2 fusion protein, and an additional nucleic acid encoding a transgenic TCR.
  • the host cell is transduced with a bicistronic nucleic acid encoding a CAR and an anti-CD2 fusion protein.
  • the host cell is transduced with a bicistronic nucleic acid encoding a CAR and a transgenic TCR. In an embodiment, the host cell is transduced with a tricistronic nucleic acid encoding a CAR, a transgenic TCR and an anti-CD2 fusion protein. In some embodiments, the host cell is further transduced with an additional nucleic acid encoding one or more additional therapeutic agents such as, for example, but not limited to, an antibody, an antibody fragment thereof, or a protein therapeutic capable of stimulating CD2. In some embodiments, a vaccine, an oncoloytic virus, a checkpoint inhibitor, a T cell agonist antibody, chemotherapy, and/or a bispecific antibody can be combined with CAR T cells or other adoptively transferred T cells.
  • the recombinant cell is an animal cell.
  • the animal cell is a mammalian cell.
  • the animal cell is a mouse cell.
  • the animal cell is a human cell.
  • the recombinant cell is an immune system cell, e.g., a lymphocyte (for example without limitation, a T cell, natural killer cell or NK cell, natural killer T cell or NKT cell, a B cell, a plasma cell, tumor-infdtrating lymphocyte (TIL)), a monocyte or macrophage, or a dendritic cell.
  • a lymphocyte for example without limitation, a T cell, natural killer cell or NK cell, natural killer T cell or NKT cell, a B cell, a plasma cell, tumor-infdtrating lymphocyte (TIL)), a monocyte or macrophage, or a dendritic cell.
  • TIL tumor-infdtrating lymphocyte
  • the immune system cell is selected from the group consisting of B cells, T cells, monocytes, dendritic cells, and epithelial cells.
  • the immune system cell is a T lymphocyte.
  • the immune cell can also be a precursor cell, i.e., a cell that is capable of differentiating into an immune cell.
  • Techniques for transforming a wide variety of the above-mentioned host cells and species are known in the art and described in the technical and scientific literature.
  • the nucleic acid molecule is introduced into a host cell by a transduction procedure, electroporation procedure, or a biolistic procedure.
  • cell cultures including at least one recombinant cell as disclosed herein are also within the scope of this application.
  • Methods and systems suitable for generating and maintaining cell cultures are known in the art.
  • An aspect of the disclosure may be a method for making an engineered cell, by transducing the cell with a nucleic acid that encodes a CD2 recruiting CAR and/or an anti-CD2 fusion protein of the disclosure, in such a manner that the nucleic acid is expressed.
  • some embodiments of the disclosure relate to a cell culture including at least one recombinant cell as disclosed herein, and a culture medium.
  • the culture medium can be any one of suitable culture media for the cell cultures described herein.
  • the recombinant cell expresses a CAR and/or anti-CD2 fusion protein described herein.
  • An aspect of the disclosure may be an antibody or an antigen binding fragment thereof for use with a CAR and/or an anti-CD2 fusion protein in a CAR-T therapy.
  • the antibody or the antigen binding fragment thereof is multispecific.
  • a multispecific antibody is bispecific.
  • the antibody or the antigen binding fragment thereof is bispecific (e.g., a tumor specific antigen or tumor-associated antigen and CD2).
  • a multispecific antibody is trispecific.
  • the antibody or the antigen binding fragment thereof is trispecific (e.g., a tumor specific antigen or tumor-associated antigen, CD2, and CD3).
  • a cell of the present disclosure is produced by transfecting the cell with a viral vector encoding the recombinant polypeptide.
  • the protein of interest of the recombinant polypeptide is a CAR and the cell is a T cell, such that provided are methods of producing a CAR T cell in which cell surface expression of the CAR is regulatable.
  • cell surface expression or “expressed on the surface of the cell” is meant the cell surface molecule - when no longer associated with the protein localization tag (e.g., ER localization tag, Golgi localization tag, or the like) has been trafficked to the cell membrane such that - in the case of a cell surface receptor (e.g., a CAR, TCR, etc.) - the extracellular binding domain is displayed on the cell surface, the transmembrane portion passes through the cell membrane, and the one or more intracellular signaling domains are disposed adjacent to the intracellular side of the cell membrane.
  • protein localization tag e.g., ER localization tag, Golgi localization tag, or the like
  • a cell surface receptor e.g., a CAR, TCR, etc.
  • the intracellular signaling domain of the cell surface receptor participates in transducing the signal from the binding into the interior of the cell (e.g., an effector cell, such as a T cell, to elicit effector cell function).
  • an effector cell such as a T cell
  • the methods of producing a CAR T cell include activating a population of T cells (e.g., T cells obtained from an individual to whom a CAR T cell therapy will be administered), stimulating the population of T cells to proliferate, and transducing the T cell with a viral vector encoding the CAR.
  • the T cells are transduced with a retroviral vector, e.g., a gamma retroviral vector or a lentiviral vector, encoding the CAR. In some embodiments, the T cells are transduced with a lentiviral vector encoding the CAR.
  • a retroviral vector e.g., a gamma retroviral vector or a lentiviral vector
  • the T cells are transduced with a lentiviral vector encoding the CAR.
  • Cells of the present disclosure may be autologous/autogeneic (“self’) or non- autologous (“nonself,” e.g., allogeneic, syngeneic or xenogeneic).
  • autologous refers to cells derived from the same individual to which they are subsequently administered.
  • Allogeneic refers to cells of the same species that differ genetically from the cell in comparison.
  • Syngeneic refers to cells of a different individual that are genetically identical to the cell in comparison.
  • the cells are T cells obtained from a mammal.
  • the mammal is a primate.
  • the primate is a human.
  • T cells may be obtained from a number of sources including, but not limited to, peripheral blOOd, peripheral blOOd mononuclear cells, bone marrow, lymph node tissue, cord blOOd, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors.
  • T cells can be obtained from a unit of blOOd collected from an individual using any number of known techniques such as sedimentation, e.g., FICOLLTM separation.
  • an isolated or purified population of T cells is used.
  • TCTL and TH lymphocytes are purified from PBMCs.
  • the TCTL and TH lymphocytes are sorted into naive (TN), memory (TMEM), stem cell memory (TSCM), central memory (TCM), effector memory (TEM), and effector (TEFF) T cell subpopulations either before or after activation, expansion, and/or genetic modification.
  • Suitable approaches for such sorting include, e.g., magnetic-activated cell sorting (MACS), where TN are CD45RA+ CD62L+ CD95-; TSCM are CD45RA+ CD62L+ CD95+; TCM are CD45RO+ CD62L+ CD95+; and TEM are CD45RO+ CD62L- CD95+.
  • MCS magnetic-activated cell sorting
  • TN are CD45RA+ CD62L+ CD95-
  • TSCM are CD45RA+ CD62L+ CD95+
  • TCM are CD45RO+ CD62L+ CD95+
  • TEM are CD45RO+ CD62L- CD95+.
  • a specific subpopulation of T cells expressing one or more of the following markers: CD3, CD4, CD8, CD28, CD45RA, CD45RO, CD62, CD127, and HLA-DR can be further isolated by positive or negative selection techniques.
  • a specific subpopulation of T cells, expressing one or more of the markers selected from the group consisting of CD62L, CCR7, CD28, CD27, CD122, CD127, CD197; or CD38 or CD62L, CD127, CD 197, and CD38 is further isolated by positive or negative selection techniques.
  • the manufactured T cell compositions do not express one or more of the following markers: CD57, CD244, CD 160, PD-1, CTLA4, TIM3, and LAG3.
  • the manufactured T cell compositions do not substantially express one or more of the following markers: CD57, CD244, CD 160, PD-1, CTLA4, TIM3, and LAG3.
  • the T cells may be subjected to one or more rounds of stimulation, activation and/or expansion.
  • T cells can be activated and expanded generally using methods as described, for example, in U.S. Patents 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; and 6,867,041, each of which is incorporated herein by reference in its entirety for all purposes.
  • T cells are activated and expanded for about 1 to 21 days, e.g., about 5 to 21 days. In some embodiments, T cells are activated and expanded for about 1 day to about 4 days, about 1 day to about 3 days, about 1 day to about 2 days, about 2 days to about 3 days, about 2 days to about 4 days, about 3 days to about 4 days, or about 1 day, about 2 days, about 3 days, or about 4 days prior to introduction of a nucleic acid (e.g., expression vector) encoding the polypeptide into the T cells.
  • a nucleic acid e.g., expression vector
  • T cells are activated and expanded for about 6 hours, about 12 hours, about 18 hours or about 24 hours prior to introduction of a nucleic acid (e.g., expression vector) encoding the cell surface receptor the into the T cells.
  • T cells are activated at the same time that a nucleic acid (e.g., an expression vector) encoding the cell surface receptor is introduced into the T cells.
  • conditions appropriate for T cell culture include an appropriate media (e.g., Minimal Essential Media or RPMI Media 1640 or, X-vivo 15, (Lonza)) and one or more factors necessary for proliferation and viability including, but not limited to serum (e.g., fetal bovine or human serum), interleukin-2 (IL-2), insulin, ILN-g, IL- 4, IL-7, IL-21, GM-CSL, IL-10, IL-12, IL-15, TGLp, and TNE-a or any other additives suitable for the growth of cells known to the skilled artisan.
  • serum e.g., fetal bovine or human serum
  • IL-2 interleukin-2
  • insulin ILN-g, IL- 4, IL-7, IL-21, GM-CSL, IL-10, IL-12, IL-15, TGLp, and TNE-a or any other additives suitable for the growth of cells known to the skilled artisan.
  • Lurther illustrative examples of cell culture media include, but are not limited to, RPMI 1640, Clicks, AEVI-V, DMEM, MEM, a- MEM, L-12, X-Vivo 15, and/or X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and/or an amount of cytokine(s) sufficient for the growth and expansion of T cells.
  • the nucleic acid (e.g., an expression vector) encoding the cell surface receptor is introduced into the cell (e.g., a T cell) by microinjection, transfection, lipofection, heatshock, electroporation, transduction, gene gun, microinjection, DEAE- dextran-mediated transfer, and the like.
  • the nucleic acid (e.g., expression vector) encoding the cell surface receptor is introduced into the cell (e.g., a T cell) by AAV transduction.
  • the AAV vector may comprise ITRs from AAV2, and a serotype from any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, or AAV 10.
  • the AAV vector comprises ITRs from AAV2 and a serotype from AAV6.
  • the nucleic acid (e.g., expression vector) encoding the cell surface receptor is introduced into the cell (e.g., a T cell) by lentiviral transduction.
  • the lentiviral vector backbone may be derived from HIV-1, HIV-2, visna-maedi virus (VMV) virus, caprine arthritis-encephalitis virus (CAEV), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FI V), bovine immune deficiency virus (BIV), or simian immunodeficiency virus (SIV).
  • the lentiviral vector may be integration competent or an integrase deficient lentiviral vector (TDLV).
  • IDLV vectors including an HIV-based vector backbone i.e., HIV cis-acting sequence elements
  • viruses that include any of the recombinant polypeptides, nucleic acids, and/or expression vectors of the present disclosure.
  • compositions are also provided.
  • the pharmaceutical compositions may include any of the cells of the present disclosure, and a pharmaceutically acceptable carrier.
  • the pharmaceutical compositions generally include a therapeutically effective amount of the cells.
  • therapeutically effective amount is meant a number of cells sufficient to produce a desired result, e.g., an amount sufficient to effect beneficial or desired therapeutic (including preventative) results, such as a reduction in a symptom of a disease (e.g., cancer) or disorder associated, e.g., with the target cell or a population thereof (e.g., cancer cells), as compared to a control.
  • An effective amount can be administered in one or more administrations.
  • the cells of the present disclosure can be incorporated into a variety of formulations for therapeutic administration. More particularly, the cells of the present disclosure can be formulated into pharmaceutical compositions by combination with appropriate, pharmaceutically acceptable excipients or diluents.
  • Formulations of the cells suitable for administration to a patient are generally sterile and may further be free of detectable pyrogens or other contaminants contraindicated for administration to a patient according to a selected route of administration.
  • the cells may be formulated for parenteral (e.g., intravenous, intra-arterial, intraosseous, intramuscular, intracerebral, intracerebroventricular, intrathecal, subcutaneous, etc.) administration, or any other suitable route of administration.
  • parenteral e.g., intravenous, intra-arterial, intraosseous, intramuscular, intracerebral, intracerebroventricular, intrathecal, subcutaneous, etc.
  • compositions that include the cells of the present disclosure may be prepared by mixing the cells having the desired degree of purity with optional physiologically acceptable carriers, excipients, stabilizers, surfactants, buffers and/or tonicity agents.
  • Acceptable carriers, excipients and/or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid, glutathione, cysteine, methionine and citric acid; preservatives (such as ethanol, benzyl alcohol, phenol, m-cresol, p-chlor-m- cresol, methyl or propyl parabens, benzalkonium chloride, or combinations thereof); amino acids such as arginine, glycine, ornithine, lysine, histidine, glutamic acid, aspartic acid, isoleucine, leucine, alanine, phenylalanine, tyrosine
  • An aqueous formulation of the recombinant polypeptides, proteases, nucleic acids, expression vectors, and/or cells may be prepared in a pH-buffered solution, e.g., at pH ranging from about 4.0 to about 7.0, or from about 5.0 to about 6.0, or alternatively about 5.5.
  • buffers that are suitable for a pH within this range include phosphate-, histidine-, citrate-, succinate-, acetate-buffers and other organic acid buffers.
  • the buffer concentration can be from about 1 mM to about 100 mM, or from about 5 mM to about 50 mM, depending, e.g., on the buffer and the desired tonicity of the formulation.
  • a tonicity agent may be included in the formulation to modulate the tonicity of the formulation.
  • Example tonicity agents include sodium chloride, potassium chloride, glycerin and any component from the group of amino acids, sugars as well as combinations thereof.
  • the aqueous formulation is isotonic, although hypertonic or hypotonic solutions may be suitable.
  • the term “isotonic” denotes a solution having the same tonicity as some other solution with which it is compared, such as physiological salt solution or serum.
  • Tonicity agents may be used in an amount of about 5 mM to about 350 mM, e.g., in an amount of 100 mM to 350 mM.
  • a surfactant may also be added to the formulation to reduce aggregation and/or minimize the formation of particulates in the formulation and/or reduce adsorption.
  • Example surfactants include polyoxyethylensorbitan fatty acid esters (Tween), polyoxyethylene alkyl ethers (Brij), alkylphenylpolyoxyethylene ethers (Triton-X), polyoxyethylene- polyoxypropylene copolymer (Poloxamer, Pluronic), and sodium dodecyl sulfate (SDS).
  • suitable polyoxyethylenesorbitan- fatty acid esters are polysorbate 20, (sold under the trademark Tween 20TM) and polysorbate 80 (sold under the trademark Tween 80TM).
  • Suitable polyethylene-polypropylene copolymers are those sold under the names Pluronic® F68 or Poloxamer 188TM.
  • suitable Polyoxyethylene alkyl ethers are those sold under the trademark BrijTM.
  • Example concentrations of surfactant may range from about 0.001% to about 1% w/v.
  • the pharmaceutical composition includes cells of the present disclosure, and one or more of the above-identified agents (e.g., a surfactant, a buffer, a stabilizer, a tonicity agent) and is essentially free of one or more preservatives, such as ethanol, benzyl alcohol, phenol, m-cresol, p- chlor-m-cresol, methyl or propyl parabens, benzalkonium chloride, and combinations thereof.
  • a preservative is included in the formulation, e.g., at concentrations ranging from about 0.001 to about 2% (w/v).
  • a pharmaceutical composition that includes a therapeutically effective amount of cells (e.g., T cells, such as CAR T cells) of the present disclosure.
  • a “therapeutically effective amount” of such cells may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the cells to elicit a desired response in the individual.
  • a therapeutically effective amount is also one in which any toxic or detrimental effects of the cells are outweighed by the therapeutically beneficial effects.
  • the term “therapeutically effective amount” includes an amount that is effective to “treat” an individual, e.g., a patient.
  • a pharmaceutical composition of the present disclosure includes from 1x10 A 6 to 5xl0 A 10 of the cells of the present disclosure.
  • Engineered cells of the disclosure may be used to aid in the therapy of a hyperproliferative disorder, for example a cancer.
  • Administration of engineered cells (or nucleic acids for generating engineered cells in situ), alone or in combination with other agents (e.g., an antibody or an antigen binding fragment thereof, or a molecule (administered, secreted, or surface expressed) that can crosslink native CD2 in response to a tumor specific antigen in the tumor microenvironment) aids in the treatment or therapy by reducing the number and/or severity of symptoms experienced by a subject, increasing overall or long term survival, killing pathological cells such as tumor cells or other hyperproliferative cells, reducing the tumor burden, inhibiting the growth of tumor cells or other hyperproliferative cells, inhibiting the spread or proliferation of tumor cells or other hyperproliferative cells, and the like.
  • a vaccine, an oncoloytic virus, a checkpoint inhibitor, a T cell agonist antibody, chemotherapy, and/or a bispecific antibody can be
  • Hyperproliferative disorders include cancers and hyperplasia characterized by the unregulated overgrowth of cells. Hyperproliferative disorders frequently display loss of genetic regulatory mechanisms, and may express native proteins inappropriately (including expression of proteins from other cell types or developmental stages, expression of mutated proteins, and expression of proteins at levels higher or lower than normal).
  • B-cell hyperproliferative disorders include B-cell leukemias and lymphomas such as, but not limited to, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), B-cell prolymphocytic leukemia, precursor B lymphoblastic leukemia, hairy cell leukemia, diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, marginal zone lymphoma, mantle cell lymphoma, Burkitt’s lymphoma, MALT lymphoma, Waldenstrom’s macroglobulinemia, and/or other disorders characterized by the overgrowth of B-lineage cells.
  • ALL acute lymphoblastic leukemia
  • CLL chronic lymphocytic leukemia
  • B-cell prolymphocytic leukemia precursor B lymphoblastic leukemia
  • hairy cell leukemia hairy cell leukemia
  • DLBCL diffuse large B-cell lymphoma
  • follicular lymphoma marginal
  • Hyperproliferative disorders include diseases such as, but not limited to, bladder cancer, including upper tract tumors and urothelial carcinoma of the prostate; bone cancer, including chondrosarcoma, Ewing's sarcoma, and osteosarcoma; breast cancer, including noninvasive, invasive, phyllodes tumor, Paget's disease, and breast cancer during pregnancy; central nervous system cancers, adult low-grade infiltrative supratentorial astrocytoma/oligodendroglioma, adult intracranial ependymoma, anaplastic astrocytoma/anaplastic oligodendroglioma/glioblastoma multiforme, limited (1-3) metastatic lesions, multiple (>3) metastatic lesions, carcinomatous lymphomatous meningitis, non-immunosuppressed primary CNS lymphoma, and metastatic spine tumors; cervical cancer; colon cancer, rectal cancer, anal carcinoma; esophageal cancer; gastric (
  • the method comprises administering a CAR- T cell of the disclosure.
  • therapeutic agents described herein e.g., engineered CAR-T cells with chimeric polypeptides and/or a transgenic TCR, can be used in methods of treating individuals who have, who are suspected of having, or who may be at high risk for developing a cancer.
  • the cancer under expresses CD58, or expresses a mutated form of CD58 that can no longer ligate CD2.
  • the cancer is a leukemia. In these instances, the leukemia can generally be of any type of leukemia. In some embodiments, the cancer is a lymphoma.
  • the cancer is acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), B-cell prolymphocytic leukemia, precursor B lymphoblastic leukemia, hairy cell leukemia, diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, marginal zone lymphoma, mantle cell lymphoma, Burkitt’s lymphoma, MALT lymphoma, Waldenstrom’s macroglobulinemia, or another disorder characterized by the overgrowth of B-lineage cells.
  • ALL acute lymphoblastic leukemia
  • CLL chronic lymphocytic leukemia
  • B-cell prolymphocytic leukemia precursor B lymphoblastic leukemia
  • hairy cell leukemia hairy cell leukemia
  • DLBCL diffuse large B-cell lymphoma
  • follicular lymphoma marginal zone lymphoma
  • mantle cell lymphoma mantle cell lymphoma
  • Burkitt
  • the tumor is a solid tumor cancer.
  • the solid tumor cell is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, or esophageal cancer.
  • the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell.
  • the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), stomach adenocarcinoma (STAD), cholangiocarcinoma (CHOL), adenoid cystic carcinoma (ACC), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), DLBC, lung adenocarcinoma (LUAD), head-neck squamous cell carcinoma (HNSC), pancreatic adenocarcinom
  • UCS
  • the administered first therapeutic agent inhibits tumor growth or metastasis of the cancer in the subject.
  • the cancer includes a metastatic cancer cell, a multiply drug resistant cancer cell, or a recurrent cancer cell.
  • the administered first therapeutic agent confers increased production of interferon gamma (IFNy) and/or interleukin-2 (IL-2) in the subject.
  • the cancer has reduced expression of CD58.
  • the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM), or skin cutaneous melanoma (SKCM).
  • UCS uterine carcinosarcoma
  • LGG brain lower grade glioma
  • THYM thymoma
  • TGCT testicular germ cell tumors
  • GBM glioblastoma multiforme
  • SKCM skin cutaneous melanoma
  • an effective amount of the engineered cells described herein is determined based on the intended goal, for example tumor regression.
  • the amount of a therapeutic agent disclosed herein to be administered may be greater than where administration of the therapeutic agent is for prevention of cancer.
  • One of ordinary skill in the art will be able to determine the amount of a therapeutic agent to be administered and the frequency of administration in view of this disclosure.
  • the quantity to be administered both according to number of treatments and dose, also depends on the individual to be treated, the state of the individual, and the protection desired. Precise amounts of the therapeutic agent also depend on the judgment of the practitioner and can be peculiar to each individual. Frequency of administration could range from 1-2 days, to 2-6 hours, to 6-10 hours, to 1- 2 weeks or longer depending on the judgment of the practitioner.
  • the therapeutic agents will be an aqueous composition that includes the engineered cells described herein.
  • Aqueous compositions of the present disclosure contain an effective amount of a therapeutic agent disclosed herein in a pharmaceutically acceptable carrier or aqueous medium.
  • the “pharmaceutical preparation” or “pharmaceutical composition” of the disclosure can include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the recombinant cells disclosed herein, its use in the manufacture of the pharmaceutical compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.
  • preparations should meet sterility, pyrogenicity, general safety, and purity standards as required by the FDA Center for Biologies.
  • the engineered cells described herein can be used to cure established tumors, inhibit tumor growth or metastasis of cancer in the treated subject relative to the tumor growth or metastasis in subjects who have not been administered one of the therapeutic compositions disclosed herein.
  • the engineered cells can be used to stimulate immune responses against the tumor via inducing the production of interferon gamma (IFNy) and/or interleukin-2 (IL-2), and other pro-inflammatory cytokines.
  • IFNy interferon gamma
  • IL-2 interleukin-2
  • interferon gamma IFNy
  • interleukin-2 IL-2
  • the production of interferon gamma (IFNy) and/or interleukin-2 (IL-2) can be stimulated to produce up to about 20 fold, such as any of about 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 11 fold, 12 fold, 13 fold, 14 fold, 15 fold 16 fold, 17 fold, 18 fold, 19 fold, or 20 fold or higher compared to the production of interferon gamma (IFNy) and/or interleukin-2 (IL-2) in subjects who have not been administered one of the therapeutic compositions disclosed herein.
  • IFNy interferon gamma
  • IL-2 interleukin-2
  • engineered cells can be administered in combination with one or more additional therapeutic agents such as, for example, chemotherapeutics or anti-cancer agents or anti-cancer therapies, antibodies or antigen binding fragments thereof, or a molecule (administered, secreted, or surface expressed) that can crosslink native CD2 in response to a tumor specific antigen in the tumor microenvironment.
  • Administration “in combination with” one or more additional therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order.
  • the one or more additional therapeutic agents, chemotherapeutics, anti-cancer agents, or anti-cancer therapies is selected from the group consisting of chemotherapy, radiotherapy, immunotherapy, hormonal therapy, toxin therapy, and surgery.
  • “Chemotherapy” and “anti-cancer agent” are used interchangeably herein.
  • Various classes of anti-cancer agents can be used.
  • Non-limiting examples include alkylating agents, antimetabolites, anthracyclines, plant alkaloids, topoisomerase inhibitors, podophyllotoxin, antibodies (e.g., monoclonal or polyclonal), checkpoint inhibitors, immunomodulators, cytokines, nanoparticles, radiation therapy, tyrosine kinase inhibitors (for example, imatinib mesylate), hormone treatments, soluble receptors and/or other antineoplastics.
  • alkylating agents include alkylating agents, antimetabolites, anthracyclines, plant alkaloids, topoisomerase inhibitors, podophyllotoxin, antibodies (e.g., monoclonal or polyclonal), checkpoint inhibitors, immunomodulators, cytokines, nanoparticles, radiation therapy, tyrosine
  • a therapeutic agent is a secreted, surface expressed, or administered molecule that is capable of crosslinking cell’s native CD2 in response to a tumor specific antigen expressed in the tumor microenvironment.
  • T cells can be transduced to constitutively express a secreted molecule capable of crosslinking the cell’s native CD2 through use of one or more anti-CD2 scFv’s, antibodies, Fabs, DARPINs, ligands, or other binders/antigen binding domains.
  • the secreted molecule can be expressed under an activation switch.
  • the secreted molecule can be membrane bound and can consist of two scFv’s connected by a linker: one scFv that binds CD2 on the T cell (activating its native CD2 signaling) and the other scFv or ligand recognizing a protein or target expressed on tumor cells such that CD2 is crosslinked and activated when the T cell encounters tumor cells.
  • Topoisomerase inhibitors are also another class of anti-cancer agents that can be used herein. Topoisomerases are essential enzymes that maintain the topology of DNA. Inhibition of type I or type II topoisomerases interferes with both transcription and replication of DNA by upsetting proper DNA supercoiling. Some type I topoisomerase inhibitors include camptothecins: irinotecan and topotecan. Examples of type II inhibitors include amsacrine, etoposide, etoposide phosphate, and teniposide. These are semisynthetic derivatives of epipodophyllotoxins, alkaloids naturally occurring in the root of American Mayapple ( Podophyllum peltatum).
  • Antineoplastics include the immunosuppressant dactinomycin, doxorubicin, epirubicin, bleomycin, mechlorethamine, cyclophosphamide, chlorambucil, ifosfamide.
  • the antineoplastic compounds generally work by chemically modifying a cell's DNA.
  • Alkylating agents can alkylate many nucleophilic functional groups under conditions present in cells. Cisplatin and carboplatin, and oxaliplatin are alkylating agents. They impair cell function by forming covalent bonds with the amino, carboxyl, sulfhydryl, and phosphate groups in biologically important molecules.
  • Vinca alkaloids bind to specific sites on tubulin, inhibiting the assembly of tubulin into microtubules (M phase of the cell cycle).
  • the vinca alkaloids include vincristine, vinblastine, vinorelbine, and vindesine.
  • Anti-metabolites resemble purines (azathioprine, mercaptopurine) or pyrimidine and prevent these substances from becoming incorporated into DNA during the “S” phase of the cell cycle, stopping normal development and division. Anti-metabolites also affect RNA synthesis.
  • Taxanes as a group includes paclitaxel and docetaxel.
  • Paclitaxel is a natural product, originally known as Taxol and first derived from the bark of the Pacific Yew tree.
  • Docetaxel is a semi-synthetic analogue of paclitaxel. Taxanes enhance stability of microtubules, preventing the separation of chromosomes during anaphase.
  • Podophyllotoxin is a plant-derived compound which has been reported to help with digestion as well as used to produce two other cytostatic drugs, etoposide and teniposide. They prevent the cell from entering the G1 phase (the start of DNA replication) and the replication of DNA (the S phase).
  • the anti-cancer agents can be selected from remicade, docetaxel, celecoxib, melphalan, dexamethasone (Decadron®), steroids, gemcitabine, cisplatinum, temozolomide, etoposide, cyclophosphamide, temodar, carboplatin, procarbazine, gliadel, tamoxifen, topotecan, methotrexate, gefitinib (Iressa®), taxol, taxotere, fluorouracil, leucovorin, irinotecan, xeloda, CPT-11, interferon alpha, pegylated interferon alpha (e.g., PEG INTRON-A), capecitabine, cisplatin, thiotepa, fludarabine, carboplatin, liposomal daunorubicin, cytarabine, doxe
  • the anti-cancer agent can be selected from bortezomib, cyclophosphamide, dexamethasone, doxorubicin, interferon-alpha, lenalidomide, melphalan, pegylated interferon-a, prednisone, thalidomide, or vincristine.
  • the methods of treatment as described herein further include administration of a compound that inhibits one or more immune checkpoint molecules.
  • the one or more immune checkpoint molecules include one or more of CTLA4, PD-1, PD-L1, A2AR, B7-H3, B7- H4, TIM3 , and combinations of any thereof.
  • the compound that inhibits the one or more immune checkpoint molecules includes an antagonistic antibody.
  • the antagonistic antibody is ipilimumab, nivolumab, pembrolizumab, durvalumab, atezolizumab, tremelimumab, or avelumab.
  • the one or more anti-cancer therapy is radiation therapy.
  • the radiation therapy can include the administration of radiation to kill cancerous cells. Radiation interacts with molecules in the cell such as DNA to induce cell death. Radiation can also damage the cellular and nuclear membranes and other organelles. Depending on the radiation type, the mechanism of DNA damage may vary as does the relative biologic effectiveness. For example, heavy particles (protons and neutrons) damage DNA directly and have a greater relative biologic effectiveness. Electromagnetic radiation results in indirect ionization acting through short-lived, hydroxyl free radicals produced primarily by the ionization of cellular water.
  • Radioactive nuclei that decay and emit alpha particles, or beta particles along with a gamma ray.
  • Radiation also contemplated herein includes, for example, the directed delivery of radioisotopes to cancer cells.
  • Other forms of DNA damaging factors are also contemplated herein such as microwaves and UV irradiation.
  • Radiation may be given in a single dose or in a series of small doses in a dose- fractionated schedule.
  • the amount of radiation contemplated herein ranges from about 1 to about 100 Gy, including, for example, about 5 to about 80, about 10 to about 50 Gy, or about 10 Gy.
  • the total dose may be applied in a fractioned regime.
  • the regime may include fractionated individual doses of 2 Gy.
  • Dosage ranges for radioisotopes vary widely, and depends on the half-life of the isotope and the strength and type of radiation emitted.
  • the isotope may be conjugated to a targeting agent, such as a therapeutic antibody, which carries the agent to the target tissue (e.g., tumor tissue).
  • Surgery described herein includes resection in which all or part of a cancerous tissue is physically removed, exercised, and/or destroyed.
  • Tumor resection refers to physical removal of at least part of a tumor.
  • treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically controlled surgery (Mohs surgery). Removal of precancers or normal tissues is also contemplated herein.
  • the methods of the disclosure further include administering to the individual a second therapeutic agent, such as an anti-cancer agent, a chemotherapeutic, or anticancer therapy.
  • a second therapeutic agent such as an anti-cancer agent, a chemotherapeutic, or anticancer therapy.
  • the second anti-cancer agent or anti-cancer therapy is selected from the group consisting of chemotherapy, radiotherapy, immunotherapy, hormonal therapy, toxin therapy, and surgery.
  • the first therapeutic agent and the second anti-cancer agent or therapy are administered concomitantly.
  • the first therapeutic agent and the second anticancer agent or therapy are administered sequentially.
  • the first therapeutic agent is administered before the second anti-cancer agent or therapy.
  • the first therapeutic agent or therapy is administered before and/or after the second anti-cancer agent or therapy. In some embodiments, the first therapeutic agent and the second anti-cancer agent or therapy are administered in rotation. In some embodiments, the first therapeutic agent is administered at the same time as the second anti-cancer agent or therapy. In some embodiments, the first therapeutic agent and the second anti-cancer agent or therapy are administered together in a single formulation.
  • kits that include any of the nucleic acids and/or expression vectors of the present disclosure, and instructions for introducing the nucleic acid or expression vector into a cell.
  • the expression vector when the expression vector encodes a recombinant polypeptide that does not comprise the protease (trans configuration), the expression vector further encodes the protease.
  • the expression vector is configured to express the recombinant polypeptide and the protease from the same promoter.
  • the expression vector may be a bicistronic expression vector for expression of separate recombinant polypeptides and protease molecules under the same promoter in the cell.
  • kits of the present disclosure may further include any other reagents useful for regulatable signaling of the cell surface receptor, such as transfection/transduction reagents useful for introducing the nucleic acid or expression vector into cells of interest, e.g., immune cells (e.g., T cells) or other cells of interest.
  • transfection/transduction reagents useful for introducing the nucleic acid or expression vector into cells of interest, e.g., immune cells (e.g., T cells) or other cells of interest.
  • kits may be present in separate containers, or multiple components may be present in a single container.
  • a suitable container includes a single tube (e.g., vial), one or more wells of a plate (e.g., a 96-well plate, a 384-well plate, etc.), or the like.
  • the instructions of the kits may be recorded on a suitable recording medium.
  • the instructions may be printed on a substrate, such as paper or plastic, etc.
  • the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or sub packaging), etc.
  • the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g., portable flash drive, DVD, CD-ROM, diskette, etc.
  • the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g., via the internet, are provided.
  • An example of this embodiment is a kit that includes a web address where the instructions can be viewed and/or from which the instructions can be downloaded.
  • the means for obtaining the instructions is recorded on a suitable substrate.
  • a composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising:
  • an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell;
  • composition of embodiment 1, wherein the first antigen binding domain binds to endogenous CD2.
  • composition comprising a cell comprising the composition of any one of embodiments 1-3.
  • composition of embodiment 4, wherein the cell is a T cell.
  • composition comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises:
  • composition of embodiment 6, wherein the extracellular domain further comprises a second antigen binding domain that binds to an antigen of a target cell.
  • composition of embodiment 8 or 10 wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • a composition comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises:
  • an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell;
  • an intracellular domain comprising an intracellular signaling domain, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain and/or increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
  • the composition of any one of embodiments 1-11, wherein the first antigen binding domain binds to an endogenous receptor expressed by the same T cell expressing the CAR.
  • the composition of embodiment 14 or 15, wherein the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • CD137 CD137
  • CD28 CD28
  • ICOS FcyRI, FcRy, Fc
  • the composition of embodiment 17, wherein the linker sequence is at least 10 or 15 amino acids in length.
  • the composition of embodiment 17, wherein the linker sequence is at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length.
  • the composition of embodiment 17, wherein the linker sequence is from 10 to 45 or from 15 to 30 amino acids in length.
  • the composition of any one of embodiments 1-5 and 7-20, wherein to the first antigen binding domain is N terminal to the second antigen binding domain.
  • the composition of any one of embodiments 1-21, wherein the second antigen binding domain is an antibody domain or binding fragment thereof.
  • composition of embodiment 22, wherein the second antigen binding domain is an scFv or a single domain antibody domain (sdAb).
  • the composition of any one of embodiments 1-24, wherein the first antigen binding domain is from CD58.
  • a composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises:
  • an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises:
  • transmembrane domain of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or
  • the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell.
  • composition of any one of embodiments 30-32 wherein when the CAR and the anti-CD2 fusion protein are expressed in a cell, a complex comprising the CAR, the anti-CD2 fusion protein and CD2 is formed.
  • composition of any one of embodiments 30-35, wherein the transmembrane domain of the antiCD fusion protein is from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • CD137 CD137
  • CD28 CD28
  • ICOS FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD
  • composition of any one of embodiments 30-36, wherein the transmembrane domain of the CAR is from CD28.
  • the composition of any one of embodiments 30-37, wherein the anti-CD2 fusion protein lacks an intracellular signaling domain.
  • sdAb single domain antibody domain
  • the composition of any one of embodiments 30-41, wherein the anti-CD2 binding domain is from CD58.
  • composition of any one of embodiments 30-42, wherein the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2.
  • composition of any one of embodiments 30-46, wherein the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70.
  • CD3 , 4-1BB CD137
  • CD28 CD28
  • ICOS FcyRI, FcRy, FcR, CD3y, CD38, CD3E, CD35, CD22, CD79a,
  • composition of any one of embodiments 30-47, wherein the extracellular domain of the anti-CD2 fusion protein comprises a hinge domain.
  • the composition of embodiment 48, wherein the anti-CD2 binding domain is linked to the hinge domain or the transmembrane domain of the anti-CD2 fusion protein by a linker sequence.
  • the composition of embodiment 49, wherein the linker sequence is at least 10 or 15 amino acids in length.
  • the composition of embodiment 49, wherein the linker sequence is at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length.
  • the composition of embodiment 49, wherein the linker sequence is from 10 to 45 or from 15 to 30 amino acids in length.
  • the composition of any one of embodiments 30-52, wherein the intracellular signaling domain of the CAR comprises a CD2 intracellular signaling domain.
  • a composition comprising a cell comprising the composition of any one of embodiments 30-53.
  • composition of embodiment 55 or 56 wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain.
  • a pharmaceutical composition comprising the composition of any one of embodiments 1-58, and a pharmaceutically acceptable excipient or carrier.
  • a method of treating a disease or condition in a subject in need thereof comprising administering a therapeutically effective amount of the pharmaceutical composition of embodiment 59 to the subject.
  • the method of embodiment 60, wherein the disease or condition is cancer.
  • the method of embodiment 61, wherein the cancer is lymphoma or leukemia.
  • the method of embodiment 63, wherein the cancer is a solid tumor cancer.
  • the method of embodiment 63, wherein the cancer is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblast
  • Exemplary CAR constructs include the constructs listed in Table 1.
  • Exemplary anti-CD2 fusion protein constructs include the constructs listed in Table 2.
  • CARs chimeric antigen receptors
  • Genes encoding scFvs are synthesized as either gene fragments (gBlock, IDT DNA) or geneencoding plasmids synthesized by GeneArt (Life Technologies), and then cloned into a MSGV1 retroviral expression vectors using restriction cloning (Roche) or In-fusion cloning (Takara).
  • CARs having CD 19- BBz or CD22-BBz are constructed having a CD8a hinge domain and CD8a transmembrane domain.
  • CARs having CD19-28z are constructed having a CD28 hinge and transmembrane domain.
  • CARs having CD2 signaling domains are constructed having a CD8a hinge and transmembrane domain.
  • Retroviral supernatant is produced via transient transfection of the 293 GP packaging cell line as previously described. Briefly, 70% confluent cells are co-transfected via Lipofectamine® 2000 (Life Technologies) in 150 mm Poly-D-Lysine culture dishes with the plasmids encoding the CARs and the RD114 envelope protein. Media is replaced at 24 and 48 hours post transfection. Viral supernatant is harvested 48 and 72 hours post transfection and centrifuged to remove cell debris and stored at -80°C until use.
  • Primary human T cells are isolated from healthy donors using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies), using buffy coats obtained from the Stanford Bl OOd Center and processed according to the manufacturer’s protocol using Lymphoprep® density gradient medium and SepMate-50 tubes. Isolated T cells are cryopreserved in CryoStor CS10 cryopreservation medium (Stem Cell Technologies).
  • T cells are thawed and activated with Human T-Expander CD3/CD28 Dynabeads (Gibco) at a 3 : 1 beadsxell ratio in AIM-V media supplemented with 5% FBS, 10 mM HEPES, 2 mM L-glutamine, 100 U/mL penicillin, and 100 pg/mL streptomycin (Gibco) and with 100 lU/ml of recombinant IL-2 (Preprotech).
  • T cells are transduced with retroviral vector on days 2 and 3 post activation and anti-CD3/CD28 beads are removed on day 5.
  • Car T-cells are maintained at 0.3-1 c 106 cells per mL in T cell medium with IL-2. CAR expression is assessed by Flow Cytometry after incubation with soluble, recombinant, human CD 19 or CD22 labelled with Dylight650. CAR-T cells are used for in vitro assays or transferred into mice on day 10 post activation.
  • Cytokine release is assayed by co-incubating CAR+ T cells and tumor cells in complete RPMI- 1640 in triplicates. At 24 hours, culture media is collected, and cytokines are measured using IFNy and IL-2 MAbs (BioLegend).
  • GPF-positive tumor cells are plated in triplicates in 96- well flat-bottom plates and co-incubated with CAR-positive T-cells or an equivalent number of control
  • T cells were transduced with retrovirus to express an anti-CD19-CD28-CD3z CAR with or without the N-terminal extracellular domain of CD58 attached.
  • CAR T cells were incubated with wild type (WT) B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IL-2 (FIG. 3A) and IFN-y secretion (FIG. 3B) by ELISA.
  • CD19-28z CAR T cells have reduced cytokine secretion when incubated with CD58 knockout NALM6 cells relative to WT NALM6 cells.
  • CD19-28z CAR T cells with CD58 attached have comparable levels of cytokine secretion against CD58 knockout NALM6 and WT NALM6.
  • CAR T cells with or without appended CD58 domain are incubated with wild type or CD58 knockout target cells.
  • CAR T cells without appended CD58 may not kill CD58 knockout target cells as efficiently as wild type target cells.
  • CAR T cells with appended CD58 may kill wild type and CD58 knockout target cells to a similar extent.

Abstract

The present application provides engineered chimeric antigen receptor fusions, cells engineered to express one or more chimeric antigen receptors, CD2 recruiting chimeric antigen receptors, and anti-CD2 fusion protein construct compositions, uses thereof for the treatment of diseases, conditions and/or disorders, and uses thereof for manufacturing T cell populations.

Description

CD2 RECRUITING CHIMERIC ANTIGEN RECEPTORS AND FUSION PROTEINS
CROSS-REFERENCE
[0001] This application claims the benefit of U.S. Provisional Application No. 63/390,116, filed on July 18, 2022, which is incorporated herein by reference in its entirety.
BACKGROUND
[0002] Immunotherapeutic CAR-T cell (chimeric antigen receptor T cell) therapies have been used for the treatment of diseases such as B-cell lymphoma or for patients who have relapsed after receiving chemotherapy. While approximately 50% of patients receiving existing CAR-T therapeutics achieve complete responses, a significant subset of patients experience relapse and/or disease progression.
[0003] Therefore, an urgent medical need exists for novel CAR-T constructs to treat patients who fail to obtain remission using existing CAR-T therapies.
SUMMARY
[0004] Provided herein are engineered chimeric antigen receptor fusion proteins, cells engineered to express one or more chimeric antigen receptors, CD2 recruiting chimeric antigen receptors, anti-CD2 fusion proteins, and methods of use thereof for the treatment of diseases.
[0005] An aspect of the disclosure may be a composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising: (a) an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain. In some embodiments, the first antigen binding domain binds to endogenous CD2. In some embodiments, the endogenous CD2 is not an endogenous CD2 molecule expressed by the target cell. In some embodiments, when the CAR is expressed in a T cell, the first antigen binding domain binds to endogenous CD2 of the T cell. In some embodiments, the CAR is expressed in a cell.
[0006] A further aspect of the disclosure is a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising a first antigen binding domain, wherein the first antigen binding domain binds to a receptor expressed by the same T cell expressing the CAR; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain. In some embodiments, the extracellular domain further comprises a second antigen binding domain that binds to an antigen of a target cell. In some embodiments, the T cell binds to the target cell with higher avidity compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain. In some embodiments, in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain. In some embodiments, in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
[0007] A further aspect of the disclosure is comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain, wherein the T cell binds to the target cell with higher avidity compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain. [0008] A further aspect of the disclosure is a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain and/or increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
[0009] A further aspect of the disclosure is a composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising: (a) an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain, wherein the second antigen binding domain binds to : glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostatespecific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothelin, MART-1, gplOO (Pmel 17), tyrosinase, Human tyrosinase related protein 1 (TRP-1), Human tyrosinase related protein 2 (TRP-2), melanoma antigen-encoding gene 1 and 3 (MAGE-1), (MAGE-3), B melanoma antigen (BAGE), GAGE-1, GAGE-2, pl5, carcinoembryonic antigen (CEA), p53, Ras, human epidermal growth factor receptor 2 (HER-2), BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS CD 19, CD20, CD22, R0R1, and/or GD2. In some embodiments the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3s, CD35, CD22, CD79a, CD79b, CD665, Toll-like receptors 1-10 (TLR1), (TLR2), (TLR3), (TLR4), (TLR5), (TLR6), (TLR7), (TLR8), (TLR9), (TLR10), Caspase recruitment domain-containing protein 11 (CARD11), CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278/inducible T cell co-stimulator (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. In some embodiments, wherein the second antigen binding domain is linked to the first antigen binding domain by a linker sequence, wherein the linker sequence is at least 10 or 15 amino acids in length, at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length, or from 10 to 45 or from 15 to 30 amino acids in length. In some embodiments, the first antigen binding domain is N-terminal to the second antigen binding domain. In some embodiments, the second antigen binding domain is an antibody domain or binding fragment thereof. In some embodiments, the first antigen binding domain is not an antibody domain or binding fragment thereof. In some embodiments, the first antigen binding domain is from CD58. In some embodiments, the first antigen binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2. [0010] A further aspect of the disclosure is a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises: (a) an extracellular domain comprising an antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c)an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises: (a) an extracellular domain comprising an anti-CD2 binding domain that binds to CD2; and (b) a transmembrane domain; wherein (i) the transmembrane domain of the anti- CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or ii) the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell. In some embodiments, the first and second multimerization domains are leucine zipper domains. In some embodiments, the first multimerization domain is within the extracellular domain of the anti-CD2 fusion protein and second multimerization domain is within the extracellular domain of the CAR. In some embodiments, when the CAR and the anti-CD2 fusion protein are expressed in a cell a complex comprising the CAR, the anti-CD2 fusion protein and CD2 is formed. In some embodiments, wherein the transmembrane domain of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR. In some embodiments, the transmembrane domain of the anti-CD2 fusion protein is from the alpha or beta chain of the T-cell receptor, CD3y, CD33, CD3s, CD3 , CD35, CD4, CD5, CD8a, CD9, CD16, CD22, CD27, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD152, CD154, and/or PD-1. In some embodiments, the transmembrane domain of the anti-CD2 fusion protein is from CD8a or CD28. In some embodiments, the transmembrane domain of the CAR is from the alpha or beta chain of the T-cell receptor, CD3y, CD33, CD3s, CD3^, CD35, CD4, CD5, CD8a, CD9, CD16, CD22, CD27, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD152, CD154, and/or PD-1. In some embodiments, the transmembrane domain of the CAR is from CD8a or CD28. In some embodiments, the anti-CD2 fusion protein lacks an intracellular signaling domain. In some embodiments, the antigen binding domain is an antibody domain or binding fragment thereof. In some embodiments, the antigen binding domain is an scFv or a single domain antibody domain (sdAb). In some embodiments, the scFv is a FMC63 domain. In some embodiments, the anti-CD2 binding domain is not an antibody domain or binding fragment thereof. In some embodiments, the anti-CD2 binding domain is from CD58. In some embodiments, the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2, wherein the anti-CD2 binding domain binds to endogenous CD2. In some embodiments, when the anti-CD2 fusion protein is expressed in a T cell, the anti-CD2 binding domain binds to endogenous CD2 of the T cell. In some embodiments, the cell is a T cell, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain of the CAR compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain. In some embodiments, wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain. In some embodiments, the antigen binding domain binds to glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostate- specific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothelin, MART-1, gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE- 3, BAGE, GAGE-1, GAGE-2, pl5, CEA, p53, Ras, HER-2, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS, CD19, CD20, CD22, R0R1, and/or GD2. In some embodiments, the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. In some embodiments the extracellular domain of the anti-CD2 fusion protein comprises a hinge domain wherein the anti-CD2 binding domain is linked to the hinge domain or the transmembrane domain of the anti-CD2 fusion protein by a linker sequence, wherein the linker sequence is at least 10 or 15 amino acids in length, at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length, or from 10 to 45 or from 15 to 30 amino acids in length. In some embodiments, the intracellular signaling domain of the CAR comprises a CD2 intracellular signaling domain. In some embodiments, the cell is a population of at least lxl0A5 cells.
[0011] A further aspect of the disclosure is a pharmaceutical composition comprising the composition of any of the disclosed embodiments and a pharmaceutically acceptable excipient or carrier.
[0012] A further aspect of the disclosure is a method of treating a disease or condition in a subject in need thereof comprising administering a therapeutically effective amount of the pharmaceutical composition to a subject, wherein the disease or condition is cancer, wherein the cancer is lymphoma or leukemia. In some embodiments, the cancer is a solid tumor cancer. In some embodiments, the solid tumor cancer is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), stomach adenocarcinoma (STAD), cholangiocarcinoma (CHOL), adenoid cystic carcinoma (ACC), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), DLBC, lung adenocarcinoma (LUAD), head-neck squamous cell carcinoma (HNSC), pancreatic adenocarcinoma (PAAD), breast cancer (BRCA), mesothelioma (MESO), colon and rectal adenocarcinoma (COAD), rectum adenocarcinoma (READ), esophageal carcinoma (ESCA), ovarian cancer (OV), lung squamous cell carcinoma (LUSC), bladder urothelial carcinoma (BLCA), sarcoma (SARC), or uterine corpus endometrial carcinoma (UCEC).
INCORPORATION BY REFERENCE
[0013] All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent, or patent application was specifically and individually indicated to be incorporated by reference.
BRIEF DESCRIPTION OF THE DRAWINGS
[0014] The novel features of the disclosure are set forth with particularity in the appended claims. A better understanding of the features and advantages of the present disclosure will be obtained by reference to the following detailed description that sets forth illustrative embodiments, in which the principles of the disclosure are utilized, and the accompanying drawings of which:
[0015] FIG. 1A shows an exemplary anti-CD19 or anti-CD22 CAR construct with an extracellular domain having an scFv that binds CD 19 or CD22 and a CD58 domain.
[0016] FIG. IB shows a T cell expressing an anti-CD19 CAR with an extracellular domain having a CD58 domain that binds to endogenous CD2 (left) and in complex with a B cell (right).
[0017] FIG. 2A shows an exemplary CAR with an extracellular domain containing an scFv that binds CD 19 (FMC63) and a CD58 domain bound to endogenous CD2. Tethering of the CD58 domain recruits endogenous CD2.
[0018] FIG. 2B shows an exemplary CAR with an extracellular domain containing an scFv that binds CD19 (FMC63) and an anti-CD2 fusion protein with a transmembrane domain or multimerization domain that interacts with the transmembrane domain or multimerization domain of the CAR resulting in proxy receptor recruitment of endogenous CD2. The depicted anti-CD2 fusion protein is bound to endogenous CD2.
[0019] FIG. 3A shows exemplary IL-2 secretion data from T cells transduced with retrovirus to express an anti-CD19-CD28-CD3z CAR with or without the N-terminal extracellular domain of CD58 attached. CAR T cells were incubated with wild type (WT) B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IL-2 secretion by ELISA.
[0020] FIG. 3B shows exemplary IFN-y secretion data from T cells transduced with retrovirus to express an anti-CD19-CD28-CD3z CAR with or without the N-terminal extracellular domain of CD58 attached. CAR T cells were incubated with wild type (WT) B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IFN-y secretion by ELISA.
DETAILED DESCRIPTION OF THE DISCLOSURE
[0021] The present disclosure encompasses recombinant polynucleic acids encoding chimeric antigen receptors and variants thereof, wherein the CAR comprises an anti-CD2 binding domain and a second antigen binding domain. In some embodiments the anti-CD2 binding domain comprises a CD58 extracellular domain capable of recruiting endogenous CD2. In some embodiments, the endogenous CD2 is expressed in the same cell as the CAR. [0022] The present disclosure also provides recombinant polynucleic acids encoding CARs and an antiCD fusion protein. In some embodiments, the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell. In some embodiments, the first and second multimerization domains are leucine zipper domains. [0023] Before the recombinant polypeptides, methods and other aspects of the present disclosure are described in greater detail, it is to be understood that the recombinant polypeptides, methods and other aspects of the present disclosure are not limited to particular exemplary embodiments described herein, as such may, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular exemplary embodiments only, and is not intended to be limiting, since the scope of the recombinant polypeptides, methods and other aspects will be limited only by the appended claims. [0024] The singular form “a”, “an”, and “the” include plural references unless the context clearly dictates otherwise. For example, the term “a cell” includes one or more cells, including mixtures thereof. “A and/or B” is used herein to include all of the following alternatives: “A”, “B”, “A or B”, and “A and B.”
[0025] Where a range of values is provided, it is understood that each intervening value, to the tenth of the unit of the lower limit unless the context clearly dictates otherwise, between the upper and lower limit of that range and any other stated or intervening value in that stated range, is encompassed within the disclosure. The upper and lower limits of these smaller ranges may independently be included in the smaller ranges, and are also encompassed within the disclosure, subject to any specifically excluded limit in the stated range. Where the stated range includes one or both of the limits, ranges excluding either or both of those included limits are also included in the disclosure.
[0026] Certain ranges are presented herein with numerical values being preceded by the term “about.” The term “about” is used herein to provide literal support for the exact number that it precedes, as well as a number that is near to or approximately the number that the term precedes. In determining whether a number is near to or approximately a specifically recited number, the near or approximating unrecited number may be a number which, in the context in which it is presented, provides the substantial equivalent of the specifically recited number.
[0027] ‘ ‘Percent (%) amino acid sequence identity” or “homology” with respect to the nucleic acid or amino acid sequences identified herein is defined as the percentage of nucleic acid or amino acid residues in a candidate sequence that are identical with the amino acid residues in the polypeptide being compared, after aligning the sequences considering any conservative substitutions as part of the sequence identity. [0028] ‘ ‘Percent (%) identity” with respect to the nucleic acid or amino acid sequences identified herein is defined as the percentage of nucleic acid or amino acid residues in a candidate sequence that are identical with the amino acid residues in the polypeptide being compared, after aligning the sequences considering any conservative substitutions as part of the sequence identity.
[0029] All ranges disclosed herein also encompass any and all possible sub-ranges and combinations of sub-ranges thereof. Any listed range can be recognized as sufficiently describing and enabling the same range being broken down into at least equal halves, thirds, quarters, fifths, tenths, and so forth. As a nonlimiting example, each range discussed herein can be readily broken down into a lower third, middle third and upper third, and the like. As will also be understood by one skilled in the art all language such as “up to,” “at least,” “greater than,” “less than,” and the like include the number recited and refer to ranges which can be subsequently broken down into sub-ranges as discussed above. Finally, as will be understood by one skilled in the art, a range includes each individual member. Thus, for example, a group having 1-3 articles refers to groups having 1, 2, or 3 articles. Similarly, a group having 1-5 articles refers to groups having 1, 2, 3, 4, or 5 articles, and so forth.
[0030] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the recombinant polypeptides, methods and other aspects belong. Although any recombinant polypeptides, methods and other aspects similar or equivalent to those described herein can also be used in the practice or testing of the recombinant polypeptides, methods and other aspects, representative illustrative recombinant polypeptides, methods and other aspects are now described.
[0031] As used herein, a “therapeutically effective amount” or “therapeutically effective number” of an agent is an amount or number sufficient to provide a therapeutic benefit in the treatment or management of a disease or disorder, or to delay or minimize one or more symptoms associated with the disease or disorder. A therapeutically effective amount of an agent means an amount of therapeutic agent, alone or in combination with other therapeutic agents, which provides a therapeutic benefit in the treatment or management of the cancer. The term “therapeutically effective amount” can encompass an amount that improves overall therapy, reduces or avoids symptoms or causes of the disease or disorder, or enhances the therapeutic efficacy of another therapeutic agent. An example of an “effective amount” is an amount sufficient to contribute to the treatment, prevention, or reduction of a symptom or symptoms of a disease, which could also be referred to as a “therapeutically effective amount.” A “reduction” of a symptom means decreasing of the severity or frequency of the symptom(s), or elimination of the symptom(s). The exact amount of a composition including a “therapeutically effective amount” will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques.
[0032] The term “binding domain”, as used herein, refers to a protein, or polypeptide sequence, which specifically binds to a target. In some embodiments, the target is a polypeptide. In some embodiments, the target is CD2. In some embodiments, the target is cell-surface bound CD2. In some embodiments, the binding domain is not an antibody or fragment thereof.
[0033] The term “antibody,” as used herein, refers to a protein, or polypeptide sequence, derived from an immunoglobulin molecule, which specifically binds to an antigen. Antibodies can be intact immunoglobulins of polyclonal or monoclonal origin, or fragments thereof and can be derived from natural or from recombinant sources.
[0034] The terms “antibody fragment” refer to at least one portion of an antibody, or recombinant variants thereof, that contains the antigenic determining variable region of an intact antibody that is sufficient to confer recognition and specific binding of the antibody fragment to a target, such as an antigen and its defined epitope. Examples of antibody fragments include, but are not limited to, Fab, Fab’, F(ab’)2, and Fv fragments, single-chain (sc)Fv (“scFv”) antibody fragments, linear antibodies, single domain antibodies (abbreviated “sdAb”) (either VL or VH), camelid VHH domains, and multi-specific antibodies formed from antibody fragments. The TFP composition of the disclosure does not comprise an antibody or antibody fragment.
[0035] The skilled artisan will understand that any macromolecule, including virtually all proteins or peptides, can serve as an antigen. Furthermore, antigens can be derived from recombinant or genomic DNA. A skilled artisan will understand that any DNA, which comprises a nucleotide sequences or a partial nucleotide sequence encoding a protein that elicits an immune response therefore encodes an “antigen” as that term is used herein. Furthermore, one skilled in the art will understand that an antigen need not be encoded solely by a full-length nucleotide sequence of a gene. It is readily apparent that the present disclosure includes, but is not limited to, the use of partial nucleotide sequences of more than one gene and that these nucleotide sequences are arranged in various combinations to encode polypeptides that elicit the desired immune response. Moreover, a skilled artisan will understand that an antigen need not be encoded by a “gene” at all. It is readily apparent that an antigen can be generated synthesized or can be derived from a biological sample, or might be macromolecule besides a polypeptide. Such a biological sample can include, but is not limited to a tissue sample, a tumor sample, a cell or a fluid with other biological components. [0036] It is appreciated that certain features of the recombinant polypeptides, and/or recombinant nucleic acids encoding the recombinant polypeptides, methods and other aspects, which are, for clarity, described in the context of separate embodiments, may also be provided in combination in a single embodiment. Conversely, various features of the recombinant polypeptides, and/or recombinant nucleic acids encoding the recombinant polypeptides, methods and other aspects, which are, for brevity, described in the context of a single embodiment, may also be provided separately or in any suitable sub-combination. All combinations of the embodiments are specifically embraced by the present disclosure and are disclosed herein just as if each and every combination was individually and explicitly disclosed, to the extent that such combinations embrace operable processes and/or compositions. In addition, all sub-combinations listed in the embodiments describing such variables are also specifically embraced by the present recombinant polypeptides, methods and other aspects and are disclosed herein just as if each and every such sub-combination was individually and explicitly disclosed herein.
[0037] The recombinant polypeptide, and/or recombinant nucleic acids encoding the recombinant polypeptides, may include any of a variety of proteins of interest. In certain embodiments, the recombinant polypeptide comprises a protein of interest that is engineered. By “engineered” is meant the protein of interest does not have a native/wild- type counterpart, e.g., by virtue of the protein of interest including one or more heterologous domains, an engineered or synthetic domain (e.g., an engineered extracellular binding domain in the case of cell surface molecule (e.g., a cell surface receptor), etc.), and/or the like. In certain embodiments, the protein of interest is an engineered cell surface receptor. Non-limiting examples of engineered cell surface receptors include chimeric receptors (e.g., chimeric antigen receptors (CARs)), engineered T cell receptors (TCRs) (e.g., having altered (or “engineered”) specificity and/or affinity for an antigen as compared to a counterpart wild-type TCR, having one or more polypeptides covalently or non-covalently bound (e.g., fused) to one another, and/or the like), anti-CD2 fusion proteins and the like.
CD2 Recruiting CARs and anti-CD2 Fusion Proteins
[0038] An immune receptor, such as chimeric antigen receptors (CARs) and T-cell receptors (TCRs) in general comprise an extracellular antigen binding domain, a transmembrane domain, and a cytoplasmic signaling domain that activates the T cell cytotoxic response. The CAR frequently also has a spacer domain between the antigen binding domain and the transmembrane domain, which often includes a hinge domain. The cytoplasmic signaling domain can further comprise one or more co-stimulatory regions, as described herein. According to some embodiments, the protein of interest is an engineered cell surface receptor, and the engineered cell surface receptor is a chimeric antigen receptor (CAR) or anti-CD2 fusion protein. The CARs and anti-CD2 fusion proteins provided herein contain an anti-CD2 binding domain that can recruit CD2, such as endogenous CD2. Recruitment of CD2 can lead to CD2 intracellular signaling, such as endogenous CD2 intracellular signaling. CAR structures are often abbreviated to list the target antigen (or the antigen binding domain or agent); optionally the spacer domain; optionally the transmembrane domain; and the co-stimulatory and stimulatory domains of the cytoplasmic signaling domain. For example, a CAR having an anti-CD19 scFv antigen binding domain, a CD8a transmembrane domain (which may include the extracellular hinge region), a 4- IBB co stimulatory domain, and a CD3^ activating domain can be indicated as CD19-8tm-41BBz. Where the domains are commonly used they are often abbreviated even further, such that a CAR having a CD28 transmembrane domain, a 4- IBB domain, and a CD3 activating domain could be abbreviated as CD19-28tm-28BBz. These are often further abbreviated by omitting designation of the transmembrane domain, e.g., CD19-28BBz. It is also common to indicate a particular antigen binding domain rather than only its specificity, e.g., m971 rather than CD22 or FMC63 rather than CD19, indicating that the antigen binding domain is the m971 scFv or FMC63 scFv, respectively.
[0039] In certain embodiments, the protein of interest, or nucleic acid encoding the protein of interest, is a CAR comprising an antigen binding domain and an anti-CD2 binding domain and/or an anti-CD2 fusion protein comprising an anti-CD2 binding domain. In some embodiments, a CAR comprises an antigen binding domain and an anti-CD2 binding domain and the anti-CD2 binding domain of the CAR directly recruits CD2 to the CAR. In some embodiments, CAR comprises an antigen binding domain and an anti- CD2 fusion protein comprises an anti-CD2 binding domain and the anti-CD2 binding domain of the anti- CD2 fusion protein binds to CD2 and the CAR binds to the anti-CD2 fusion protein via a multimerization domain (e.g., the transmembrane domains or the extracellular domains), thereby indirectly recruiting CD2 to the CAR via the anti-CD2 fusion protein. For example, the anti-CD2 fusion protein can comprise a multimerization domain that multimerizes with a multimerization domain of the CAR. For example, the anti-CD2 fusion protein can comprise a first multimerization domain and the CAR can comprise a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell.
[0040] An aspect of the disclosure may be a recombinant polynucleic acid encoding a CAR comprising: (a) an extracellular domain comprising a first antigen-binding domain that is an anti-CD2 binding domain, and a second antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain as shown in FIG. 1A and/or FIG. IB.
[0041] Chimeric Antigen Receptor with anti-CD2 fusion protein [0042] An aspect of the disclosure may be a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises: (a) an extracellular domain comprising an antigen binding domain that binds to an antigen of a target cell; (b) a transmembrane domain; and (c) an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises: (a) an extracellular domain comprising an anti-CD2 binding domain that binds to CD2; and (b) a transmembrane domain; wherein (i) the transmembrane domain of the anti- CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or (ii) the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell.
[0043] In some embodiments, an anti-CD2 fusion protein may be tethered to a CAR as in FIG. 2A and/or FIG. 2B. In some embodiments, the anti-CD2 fusion protein may comprise a first multimerization domain and the CAR may comprise a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell. In some embodiments, the first multimerization domain and the second multimerization domain forma homodimer. In some embodiments, the first multimerization domain and the second multimerization domain forma heterodimer. In some embodiments, the first multimerization domain can be a transmembrane domain and the second multimerization domain can be a transmembrane domain. In some embodiments, the first multimerization domain can be an extracellular domain and the second multimerization domain can be an extracellular domain. For example, the transmembrane domain of an anti-CD2 fusion protein may multimerize with the transmembrane domain of the CAR. For example, the extracellular domain of an anti-CD2 fusion protein may multimerize with the extracellular domain of the CAR. For example, the first multimerization domain can be a CD28 transmembrane and/or hinge domain and the second multimerization domain can be a CD28 transmembrane and/or hinge domain. For example, the first multimerization domain can be a CD8 alpha transmembrane and/or hinge domain and the second multimerization domain can be a CD8 beta transmembrane and/or hinge domain. For example, the first multimerization domain can be a CD8 beta transmembrane and/or hinge domain and the second multimerization domain can be a CD8 alpha transmembrane and/or hinge domain. In some embodiments, the multimerization domains may comprise a leucine zipper. In some embodiments, the CAR may have an anti-CD2 binding domain. In some embodiments, the anti-CD2 binding domain may be from CD58. In some embodiments, the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2. [0044] In some embodiments, a CAR construct has at least about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity to any one of the sequences depicted in Table 1. In some embodiments, a CAR construct has 100% sequence identity to one or more of the sequences depicted in Table 1. In some embodiments, an anti-CD2 fusion protein construct has at least about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity to any one of the sequences depicted in Table 2. In some embodiments, an anti-CD2 fusion protein construct has 100% sequence identity to one or more of the sequences depicted in Table 2.
[0045] In some embodiments, the cell in which the CAR or anti-CD2 fusion protein with an anti-CD2 binding domain is expressed is an immune cell. In some embodiments, the cell in which the CAR or anti- CD2 fusion protein is expressed is a T cell. In some embodiments, the cell in which the CAR or anti-CD2 fusion protein is expressed is a CD8+ T cell. In some embodiments, the cell in which the CAR or anti- CD2 fusion protein is expressed is a CD4+ T cell. In some embodiments, the cell in which the CAR or anti-CD2 fusion protein is expressed is a B-cell, neutrophil, eosinophil, basophil, mast cell, monocyte, macrophage, dendritic cell, and/or natural killer cell.
Extracellular Domain
[0046] In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence located on the N-terminus of the CAR or anti-CD2 fusion protein. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence from CD8, CSF2RA, HGH or TCR|3. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MALPVTALLLPLALLLHAARP. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MLLLVTSLLLCELPHPAFLLIP. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MATGSRTSLLLAFGLLCLPWLQEGSA. In some embodiments, the CAR or anti-CD2 fusion protein comprises a signal peptide sequence with the sequence MGTSLLCWMALCLLGADHAD.
Anti-CD2 Binding Domain
[0047] Provided herein are CARs and anti-CD2 fusion proteins containing an anti-CD2 binding domain. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises the anti- CD2 binding domain. In some embodiments, the anti-CD2 binding domain of the CAR is an N-terminal domain of the CAR that binds to CD2. In some embodiments, the anti-CD2 binding domain of the anti- CD2 fusion protein is an N-terminal domain of the CAR that binds to CD2. In some embodiments, the extracellular domain of the CAR comprises a domain that binds to CD2 that is located N-terminal to an antigen binding domain of the CAR. In some embodiments, the extracellular domain of the CAR or antiCD fusion protein comprises a domain from CD58 that binds to CD2. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 that binds to endogenous CD2. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 that binds to CD2 on the same cell in which the CAR or anti-CD2 fusion protein is expressed.
[0048] In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 that binds to CD2. In some embodiments, the CAR or anti-CD2 fusion protein comprises a CD58 N-terminal domain. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises an N-terminal domain from CD58 that binds to CD2. Such a CAR may further include a spacer domain between the CD58 N-terminal domain and the antigen-binding portion. Such an anti-CD2 fusion protein may further include a spacer domain between the CD58 N-terminal domain and the transmembrane domain.
[0049] In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises an extracellular domain (ECD) from CD58 that binds to CD2. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to a CD58 N-terminal domain. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVL. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 85, 90, 95, 97, 98, or 99% sequence identity to
FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVL. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with 100% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVL. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to a CD58 extracellular domain (ECD). In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 80% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVLESLPSPTLTCALTNGSIEVQCMIPEHYNSHRGLIMY SWDCPMEQCKRNSTSIYFKMENDLPQKIQCTLSNPLFNTTSSIILTTCIPSSGHSRHR. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with at least about 85, 90, 95, 97, 98, or 99% sequence identity to FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVLESLPSPTLTCALTNGSIEVQCMIPEHYNSHRGLIMY SWDCPMEQCKRNSTSIYFKMENDLPQKIQCTLSNPLFNTTSSIILTTCIPSSGHSRHR. In some embodiments, the extracellular domain of the CAR or anti-CD2 fusion protein comprises a domain from CD58 with 100% sequence identity to
FSQQIYGVVYGNVTFHVPSNVPLKEVLWKKQKDKVAELENSEFRAFSSFKNRVYLDTVSGSLTI YNLTSSDEDEYEMESPNITDTMKFFLYVLESLPSPTLTCALTNGSIEVQCMIPEHYNSHRGLIMY SWDCPMEQCKRNSTSIYFKMENDLPQKIQCTLSNPLFNTTSSIILTTCIPSSGHSRHR.
[0050] In some embodiments, the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein binds to CD2 with low affinity. For example, the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein can bind to CD2 with a KA of less than or equal to about 200 nM, 300 nM, 400 nM, 500 nM, IpM, 5 pM, 10 pM, 15pM, 20pM, 25pM, 30pM, 35pM, 40pM, 45pM, and/or 50pM. For example, the anti- CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to or associate with CD2 with a KA of less than or equal to about 10A5 M'1. For example, the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to CD2 with a KA of less than or equal to about 10A6 M’1, 10A7 M’1, 10A8 M’1, 10A9 M’1, 10Al 0 M’1, 10Al 1 M’1, 10A12 M’1, or 10A13 M’1. For example, the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein can bind to CD2 with a KD of greater than or equal to about 200 nM, 300 nM, 400 nM, 500 nM, IpM, 5 pM, 10 pM, 15pM, 20pM, 25 pM, 30pM, 35pM, 40pM, 45pM, 50pM, or greater than 50pM. For example, the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to or associate with CD2 with a KD of greater than or equal to about 10A5 M'1. For example, the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein may bind to CD2 with a KD of greater than or equal to about 10A6 M’1, 10A7 M’1, 10A8 M’1, 10A9 M’1, 10A10 M’1, 10Al 1 M’1, 10A12 M’1, or 10Al 3 M'1. The binding affinity of the anti-CD2 binding domain to CD2 can be readily determined using conventional techniques, e.g., by competitive ELISA (enzyme-linked immunosorbent assay), equilibrium dialysis, by using surface plasmon resonance (SPR) technology (e.g., the BIAcore 2000 instrument, using general procedures outlined by the manufacturer); by radioimmunoassay; or the like. [0051] In some embodiments, binding of the antigen binding domain of the CAR to the antigen may provide enough avidity to cluster endogenous CD2. In some embodiments, binding of the anti-CD2 binding domain of the CAR or anti-CD2 fusion protein to CD2 clusters endogenous CD2. In some embodiments, clustering of endogenous CD2 may increase signaling in the cell in which the CAR or anti- CD2 fusion protein with the anti-CD2 binding domain is expressed. In some embodiments, the increased signaling may be 1-fold, 2-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1000-fold, 10000-fold, or more than 10000-fold greater than a cell in which the CAR or anti-CD2 fusion protein is not expressed.
[0052] In some embodiments, a cell expressing a CAR or anti-CD2 fusion protein with an anti-CD2 binding domain exhibits increased target cell killing compared to the target cell killing of a cell which does not express the CAR or anti-CD2 fusion protein. In some embodiments the increased killing may be 1-fold, 2-fold, 10-fold, 50-fold, 100-fold, 500-fold, 1000-fold, 10000-fold, or more than 10000-fold greater than the target cell killing of a cell in which the CAR or anti-CD2 fusion protein is not expressed. [0053] In some embodiments, the target cell is a cancer cell. In some embodiments, the cancer is from a hematological cancer. In some embodiments, the cancer cell is from a solid tumor cancer. In some embodiments, the cancer is a cell of a lymphoma, leukemia, lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), stomach adenocarcinoma (STAD), cholangiocarcinoma (CHOL), adenoid cystic carcinoma (ACC), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), DLBC, lung adenocarcinoma (LUAD), head-neck squamous cell carcinoma (HNSC), pancreatic adenocarcinoma (PAAD), breast cancer (BRCA), mesothelioma (MESO), colon and rectal adenocarcinoma (COAD), rectum adenocarcinoma (READ), esophageal carcinoma (ESCA), ovarian cancer (OV), lung squamous cell carcinoma (LUSC), bladder urothelial carcinoma (BLCA), sarcoma (SARC), and/or uterine corpus endometrial carcinoma (UCEC).
[0054] In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a hinge domain by a linker. In some embodiments, the anti-CD2 binding domain of an anti- CD2 fusion protein provided herein is operatively linked to a transmembrane domain by a linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a transmembrane domain by a linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a (G4S)n linker, where n is an integer of from 1 to 10. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a (G4S)3 linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a (G4S)6 linker. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a linker according to the sequence GGGGSGGGGSGGGGS. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a linker according to the sequence GGGGSGGGGSGGGGSGGGGSGGGGSGGGGS. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a transmembrane domain by a linker according to the sequence GSTSGSGKPGSGEGSTKG.
Antigen Binding Domain
[0055] The extracellular domain of a CAR provided herein can further comprises an antigen binding domain in addition to an anti-CD2 binding domain. In some embodiments, the antigen binding domain of the CAR is C-terminal to the anti-CD2 binding domain. In some embodiments, the antigen binding domain of the CAR is N-terminal to the anti-CD2 binding domain. In some embodiments, an anti-CD2 fusion protein provided herein comprises an anti-CD2 binding domain and lacks an antigen binding domain.
[0056] In some embodiments, the antigen binding domain of the CAR is linked to the anti-CD2 binding domain by a first linker. In some embodiments, the antigen binding domain of a CAR provided herein is linked to a hinge domain by a second linker. In some embodiments, the antigen binding domain of a CAR provided herein is operatively linked to a transmembrane domain by a second linker. In some embodiments, the antigen binding domain of a CAR provided herein provided herein is directly linked to a transmembrane domain by a second linker.
[0057] The antigen binding domains provided herein include, but are not limited to, protein domains, antibody domains, ligands, extracellular domains of receptors and the like. In some embodiments, the antigen binding domain comprises an antigen-binding portion of an antibody (e.g., a single chain antibody domain or an scFv) that binds to an antigen of interest. Functional fragments of any of the antibodies herein are also contemplated. The terms “antigen-binding portion of an antibody,” “antigen-binding fragment,” “antigen binding domain,” “antibody fragment,” or a “functional fragment of an antibody” can refer to one or more fragments of an antibody that retain the ability to specifically bind to an antigen. Representative antigen-binding fragments include a Fab, a Fab’, a F(ab’)2, a Fv, a scFv, a dsFv, a variable heavy domain, a variable light domain, a variable NAR domain, bi-specific scFv, a bi-specific Fab2, a trispecific Fab3, an AVIMER®, a minibody, a diabody, a triabody, a maxibody, a camelid, a VHH, a minibody, an intrabody, fusion proteins comprising an antibody portion ( e.g a domain antibody), and a single chain binding polypeptide.
[0058] Native antibodies and native immunoglobulins (Igs) can be heterotetrameric glycoproteins of about 150,000 Daltons, composed of two identical light chains and two identical heavy chains. Antibodies can further refer to camelid antibodies, which can be not tetrameric. Each light chain can be typically linked to a heavy chain by one covalent disulfide bond, while the number of disulfide linkages can vary among the heavy chains of different immunoglobulin isotypes. Each heavy and light chain can have regularly spaced intrachain disulfide bridges. Each heavy chain can have at one end a variable domain (“VH”) followed by a number of constant domains (“CH”). Each light chain can have a variable domain at one end (“VL”) and a constant domain (“CL”) at its other end; the constant domain of the light chain can be aligned with the first constant domain of the heavy chain, and the light-chain variable domain can be aligned with the variable domain of the heavy chain. Particular amino acid residues can form an interface between the light- and heavy -chain variable domains.
[0059] “F(ab’)2” and “Fab”’ moieties can be produced by treating an Ig with a protease such as pepsin and papain, and include antibody fragments generated by digesting immunoglobulin near the disulfide bonds existing between the hinge regions in each of the two heavy chains. For example, papain can cleave IgG upstream of the disulfide bonds existing between the hinge regions in each of the two heavy chains to generate two homologous antibody fragments in which a light chain composed of VL and CL (light chain constant region), and a heavy chain fragment composed of VH and Ciiyi (gi) region in the constant region of the heavy chain) are connected at their C terminal regions through a disulfide bond. Each of these two homologous antibody fragments can be called Fab’. Pepsin can also cleave IgG downstream of the disulfide bonds existing between the hinge regions in each of the two heavy chains to generate an antibody fragment slightly larger than the fragment in which the two above-mentioned Fab' are connected at the hinge region. This antibody fragment can be called F(ab’)2.
[0060] The Fab fragment can also contain the constant domain of the light chain and the first constant domain (CHI) of the heavy chain. Fab' fragments can differ from Fab fragments by the addition of a few residues at the carboxyl terminus of the heavy chain CHI domain including one or more cysteine(s) from the antibody hinge region. Fab'-SH can be a Fab' in which the cysteine residue(s) of the constant domains bear a free thiol group. F(ab')2 antibody fragments can be produced, for example, as pairs of Fab' fragments which have hinge cysteines between them. Other chemical couplings of antibody fragments can also be employed.
[0061] A “Fv” as used herein can refer to an antibody fragment which contains a complete antigenrecognition and antigen-binding site. This region can consist of a dimer of one heavy chain and one light chain variable domain in tight, non-covalent or covalent association (disulfide linked Fvs have been described, see, e.g., Reiter el al. (1996) Nature Biotechnology 14:1239-1245). In this configuration that the three CDRs of each variable domain can interact to define an antigen-binding site on the surface of the VH-VL dimer. Collectively, a combination of one or more of the CDRs can from each of the VH and VL chains confer antigen-binding specificity to the antibody. For example, the CDRH3 and CDRL3 can be sufficient to confer antigen-binding specificity to an antibody when transferred to VH and VL chains of a recipient antibody or antigen-binding fragment thereof and this combination of CDRs can be tested for binding, specificity, affinity, etc. using, for example, techniques described herein. In some cases, even a single variable domain (or half of an Fv comprising only three CDRs specific for an antigen) can have the ability to recognize and bind antigen, although likely at a lower specificity or affinity than when combined with a second variable domain. Furthermore, although the two domains of a Fv fragment (VL and VH) can be coded for by separate genes, they can be joined using recombinant methods, for example by a synthetic linker that enables them to be made as a single protein chain in which the VL and VH regions pair to form monovalent molecules (known as single chain Fv (scFv); Bird et al. (1988) Science 242:423-426; Huston et al. (1988) Proc. Natl. Acad. Sci. USA 85:5879-5883; and Osbourn et al. (1998) Nat. Biotechnol. 16:778). Such scFvs can be encompassed within the term “antigen-binding portion” of an antibody. Any VH and VL sequences of specific scFv can be linked to an Fc region cDNA or genomic sequences in order to generate expression vectors encoding complete Ig (e.g., IgG) molecules or other isotypes. VH and VL can also be used in the generation of Fab, Fv, or other fragments of Igs using either protein chemistry or recombinant DNA technology.
[0062] “Single-chain Fv” or “scFv” antibody fragments can include the VH and VL domains of an antibody, wherein these domains can be present in a single polypeptide chain. In some embodiments, the Fv polypeptide can further include a polypeptide linker between the VH and VL domains which enables the sFv to form the desired structure for antigen binding. For a review of scFvs, see, e.g., Pluckthun in The Pharmacology of Monoclonal Antibodies, Vol. 113, Rosenburg and Moore eds. Springer-Verlag, New York, pp. 269-315 (1994).
[0063] As used herein, a “dsFv” can be a Fv fragment obtained, for example, by introducing a Cys residue into a suitable site in each of a heavy chain variable region and a light chain variable region, and then stabilizing the heavy chain variable region and the light chain variable region by a disulfide bond. The site in each chain, into which the Cys residue can be introduced, can be determined based on a conformation predicted by molecular modeling. In the present disclosure, for example, a conformation can be predicted from the amino acid sequences of the heavy chain variable region and light chain variable region of the above-described antibody, and DNA encoding each of the heavy chain variable region and the light chain variable region, into which a mutation has been introduced based on such prediction, can be then constructed. The DNA construct can be incorporated then into a suitable vector and prepared from a transformant obtained by transformation with the aforementioned vector.
[0064] Diabodies can be single chain antibodies. Diabodies can be bivalent, bispecific antibodies in which VH and VL domains can be expressed on a single polypeptide chain, but using a linker that is too short to allow for pairing between the two domains on the same chain, thereby forcing the domains to pair with complementary domains of another chain and creating two antigen binding sites (see e.g., Holliger, P., etal., Proc. Natl. Acad. Sci. USA, 90:6444-6448 (1993); and Poljak, R. I, etal, Structure, 2:1121-1123 (1994)).
[0065] The antigen binding domain can be any molecule that binds to the selected antigen with sufficient affinity and specificity, and is often an antibody or an antibody derivative, such as an scFv, single domain antibody (sdAb), Fab' fragment, (Fab')2 fragment, nanobody, diabody, or the like. Alternatively, the antigen binding domain can be a receptor or a receptor fragment that binds specifically to the target antigen. The antigen binding domain can be attached to the rest of the receptor directly (covalently) or indirectly (for example, through the noncovalent binding of two or more binding partners). Antibody derivatives are molecules that resemble antibodies in their mechanism of ligand binding, and include, for example, nanobodies, duobodies, diabodies, triabodies, minibodies, F(ab')2 fragments, Fab fragments, single chain variable fragments (scFv), single domain antibodies (sdAb), and functional fragments thereof. See for example, D.L. Porter et al., N Engl J Med ( 2011) 365(8):725-33 (scFv); E.L. Smith et al, Mol Ther (2018)26(6): 1447-56 (scFv); S.R. Bamhashemi et al., Iran J Basic Med Sci (2018) 21(5):455-64 (CD19 nanobody); F. Rahbarizadeh et al Adv Drug Deliv Rev (2019) 141:41-46 (sdAb);S.M. Kipriyanov et al., Int J Cancer (1998) 77(5):763-72 (diabody); F. Le Gall et al., FEBS Lett (1999) 453(1-2): 164-68 (triabody); M.A. Ghetie et al., BlOOd (1994) 83(5): 1329-36 (F(ab')2); and M.A. Ghetie et al., Clin Cancer Res (1999) 5(12):3920-27 (F(ab')2 and Fab'). Antibody derivatives can also be prepared from therapeutic antibodies, for example without limitation, by preparing a nanobody, duobody, diabody, triabody, minibody, F(ab')2 fragment, Fab fragment, single chain variable fragment (scFv), or single domain antibody (sdAb) based on a therapeutic antibody. Antibody derivatives can also be designed using phage display techniques (see, e.g., E. Romao et al., Curr Pharm Des (2016) 22(43):6500-18).
[0066] The antigen binding domain may include binding domains for multiple antigens, which may be the same or different. For example, the antigen binding domain can comprise a bispecific (Fab')2, specific for two antigens, or for two epitopes on the same antigen. Multispecific antigen binding domains can increase the sensitivity of the CAR, for example by allowing the CAR to recognize and react to multiple antigens, he antigen binding domain can alternatively be expressed independently from the rest of the CAR, and bind to it through non-covalent interactions. For example, the extracellular portion of the CAR can comprise one member of a specific binding pair, which binds to the independent antigen binding domain (without interfering with antigen binding by the antigen binding domain). For example, the CAR extracellular domain can comprise streptavidin, while the independent antigen binding domain is biotinylated. Alternatively, the CAR extracellular domain can comprise an antibody or antibody derivative that is specific for the independent antigen binding domain. This division into independent antigen binding domain and CAR enables one to change the antigen specificity of the receptor without transducing a new receptor. See, e.g., N.G. Minutolo et al, Front Oncol (2019) 9: 176.
[0067] In some embodiments, the anti-CD2 fusion protein does not comprise a single chain antibody domain or an scFv. In some embodiments, the antigen binding domain comprises an antigen-binding portion from a single domain antibody (sdAb). In some embodiments, the antigen binding domain comprises a single chain variable fragment (scFv). In some embodiments, the antigen binding domain comprises an antigen-binding portion of a monoclonal antibody, a chimeric antibody, a humanized antibody, a fully human antibody, or the like. In some embodiments, the antigen binding domain comprises an antigen-binding portion from an antibody approved by the United States Food and Drug Administration and/or the European Medicines Agency (EMA) for use as a therapeutic antibody or an scFv version thereof. For example, the antigen binding domain can comprise an antigen-binding portion from an antibody or an scFv version thereof selected from the group consisting of Adecatumumab, Ascrinvacumab, Cixutumumab, Conatumumab, Daratumumab, Drozitumab, Duligotumab, Durvalumab, Dusigitumab, Enfortumab, Enoticumab, Figitumumab, Ganitumab, Glembatumumab, Intetumumab, Ipilimumab, Iratumumab, Icrucumab, Lexatumumab, Lucatumumab, Mapatumumab, Namatumab, Necitumumab, Nesvacumab, Ofatumumab, Olaratumab, Panitumumab, Patritumab, Pritumumab, Radretumab, Ramucirumab, Rilotumumab, Robatumumab, Seribantumab, Tarextumab, Teprotumumab, Tovetumab, Vantictumab, Vesencumab, Votumumab, Zalutumumab, Flanvotumab, Altumomab, Anatumomab, Arcitumomab, Bectumomab, Blinatumomab, Detumomab, Ibritumomab, Minretumomab, Mitumomab, Moxetumomab, Naptumomab, Nofetumomab, Pemtumomab, Pintumomab, Racotumomab, Satumomab, Solitomab, Taplitumomab, Tenatumomab, Tositumomab, Tremelimumab, Abagovomab, Igovomab, Oregovomab, Capromab, Edrecolomab, Nacolomab, Amatuximab, Bavituximab, Brentuximab, Cetuximab, Derlotuximab, Dinutuximab, Ensituximab, Futuximab, Girentuximab, Indatuximab, Isatuximab, Margetuximab, Rituximab, Siltuximab, Ublituximab, Ecromeximab, Abituzumab, Alemtuzumab, Bevacizumab, Bivatuzumab, Brontictuzumab, Cantuzumab, Cantuzumab, Citatuzumab, Clivatuzumab, Dacetuzumab, Demcizumab, Dalotuzumab, Denintuzumab, Elotuzumab, Emactuzumab, Emibetuzumab, Enoblituzumab, Etaracizumab, Farletuzumab, Ficlatuzumab, Gemtuzumab, Imgatuzumab, Inotuzumab, Labetuzumab, Lifastuzumab, Lintuzumab, Lorvotuzumab, Lumretuzumab, Matuzumab, Milatuzumab, Nimotuzumab, Obinutuzumab, Ocaratuzumab, Otlertuzumab, Onartuzumab, Oportuzumab, Parsatuzumab, Pertuzumab, Pinatuzumab, Polatuzumab, Sibrotuzumab, Simtuzumab, Tacatuzumab, Tigatuzumab, Trastuzumab, Tucotuzumab, Vandortuzumab, Vanucizumab, Veltuzumab, Vorsetuzumab, Sofituzumab, Catumaxomab, Ertumaxomab, Depatuxizumab, Ontuxizumab, Blontuvetmab, Tamtuvetmab, or an antigen-binding variant thereof.
[0068] In some embodiments, the antigen binding domain targets CD19. In some embodiments, the antigen binding domain comprises an scFv with a variable light chain domain (VL) having a light chain CDR1 (LCDR1), LCDR2 and LCDR3 of RASQDISKYLN, SRLHSGV and GNTLPYTFG, respectively. In some embodiments, the antigen binding domain comprises an scFv with a variable light chain domain (VL) having at least about 80% sequence identity to DIQMTQTTSSLSASLGDRVTISCRASQDISKYLNWYQQKPDGTVKLLIYHTSRLHSGVPSRFSGS GSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIT. In some embodiments, the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having a heavy chain CDR1 (HCDR1), HCDR2 and HCDR3 of DYGVS, VIWGSETTYYNSALKS and YAMDYWG, respectively. In some embodiments, the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having at least about 80% sequence identity to EVKLQESGPGLVAPSQSLSVTCTVSGVSLPDYGVSWIRQPPRKGLEWLGVIWGSETTYYNSALK SRLTIIKDNSKSQVFLKMNSLQTDDTAIYYCAKHYYYGGSYAMDYWGQGTSVTVSS.
[0069] In some embodiments, the antigen binding domain comprises an scFv with at least about 80% sequence identity to
DIQMTQTTSSLSASLGDRVTISCRASQDISKYLNWYQQKPDGTVKLLIYHTSRLHSGVPSRFSGS GSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEITGGGGSGGGGSGGGGSEVKLQES GPGLVAPSQSLSVTCTVSGVSLPDYGVSWIRQPPRKGLEWLGVIWGSETTYYNSALKSRLTIIKD NSKSQVFLKMNSLQTDDTAIYYCAKHYYYGGSYAMDYWGQGTSVTVSS.
[0070] hi some embodiments, the antigen binding domain comprises an scFv with at least about 80% sequence identity to
EVKLQESGPGLVAPSQSLSVTCTVSGVSLPDYGVSWIRQPPRKGLEWLGVIWGSETTYYNSALK SRLTIIKDNSKSQVFLKMNSLQTDDTAIYYCAKHYYYGGSYAMDYWGQGTSVTVSSGGGGSG GGGSGGGGSDIQMTQTTSSLSASLGDRVTISCRASQDISKYLNWYQQKPDGTVKLLIYHTSRLH SGVPSRFSGSGSGTDYSLTISNLEQEDIATYFCQQGNTLPYTFGGGTKLEIT.
[0071] In some embodiments, the antigen binding domain targets CD22. In some embodiments, the antigen binding domain comprises an scFv with a variable light chain domain (VL) having a light chain CDR1 (LCDR1), LCDR2 and LCDR3 of QTIWSY. AAS and QQSYSIPOT. respectively. In some embodiments, the antigen binding domain comprises an scFv with a variable light chain domain (VL) having at least about 80% sequence identity to DIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRFSGR GSGTDFTLTISSLOAEDFATYYCOQSYSIPOTFGOGTKLEI.
[0072] In some embodiments, the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having a heavy chain CDR1 (HCDR1), HCDR2 and HCDR3 of GDSVSSNSAA. TYYRSKWYN and ARE VT GDLED AFDI. respectively. In some embodiments, the antigen binding domain comprises an scFv with a variable heavy chain domain (VH) having at least about 80% sequence identity to
OVOLOQSGPGLVKPSOTLSLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDY AVSVKSRITINPDTSKNOFSLQLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSS.
[0073] In some embodiments, the antigen binding domain comprises an scFv with at least about 80% sequence identity to
OVOLOQSGPGLVKPSOTLSLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDY AVSVKSRITINPDTSKNOFSLOLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSSGG GGSDIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRF SGRGSGTDFTLTISSLOAEDFATYYCOOSYSIPOTFGOGTKLEIK.
[0074] In some embodiments, the antigen binding domain comprises an scFv with at least about 80% sequence identity to
DIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRFSGR GSGTDFTLTISSLOAEDFATYYCOQSYSIPOTFGOGTKLEIKGGGGSOVOLOOSGPGLVKPSOTL SLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDYAVSVKSRITINPDTSKNOF SLOLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSS. In some embodiments, the antigen binding domain comprises an scFv with at least about 85, 90, 95, 97, 98, or 99% sequence identity to OVOLOQSGPGLVKPSOTLSLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDY AVSVKSRITINPDTSKNOFSLQLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSSGG GGSDIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRF SGRGSGTDFTLTISSLOAEDFATYYCOOSYSIPOTFGOGTKLEIK. In some embodiments, the antigen binding domain comprises an scFv with 100% sequence identity OVOLOQSGPGLVKPSOTLSLTCAISGDSVSSNSAAWNWIROSPSRGLEWLGRTYYRSKWYNDY AVSVKSRITINPDTSKNOFSLOLNSVTPEDTAVYYCAREVTGDLEDAFDIWGOGTMVTVSSGG GGSDIOMTOSPSSLSASVGDRVTITCRASOTIWSYLNWYOORPGKAPNLLIYAASSLQSGVPSRF SGRGSGTDFTLTISSLOAEDFATYYCOQSYSIPOTFGOGTKLEIK.
[0075] In certain embodiments, the protein of interest, or nucleic acid encoding the protein of interest, is a CAR including one or more linker sequences between the various domains. A “variable region linking sequence” is an amino acid sequence that connects a heavy chain variable region to a light chain variable region and provides a spacer function compatible with interaction of the two sub-binding domains so that the resulting polypeptide retains a specific binding affinity to the same target molecule as an antibody that includes the same light and heavy chain variable regions. A non-limiting example of a variable region linking sequence is a serine-glycine linker, such as a serine-glycine linker that includes the amino acid sequence GGGGSGGGGSGGGGS (G4S)3. In certain aspects, a linker separates one or more heavy or light chain variable domains, hinge domains, transmembrane domains, co-stimulatory domains, and/or primary signaling domains. In particular embodiments, the CAR includes one, two, three, four, or five or more linkers. In particular embodiments, the length of a linker is about 1 to about 25 amino acids, about 5 to about 20 amino acids, or about 10 to about 20 amino acids, or any intervening length of amino acids. In some embodiments, the linker is 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, or more amino acids long.
[0076] In some instances, an antibody or an antigen-binding fragment thereof includes an isolated antibody or antigen-binding fragment thereof, a purified antibody or antigen-binding fragment thereof, a recombinant antibody or antigen-binding fragment thereof, a modified antibody or antigen-binding fragment thereof, or a synthetic antibody or antigen-binding fragment thereof. Antibodies and antigenbinding fragments herein can be partly or wholly synthetically produced. An antibody or antigen-binding fragment can be a polypeptide or protein having a binding domain which can be, or can be homologous to, an antigen binding domain. In some instances, an antibody or an antigen-binding fragment thereof can be produced in an appropriate in vivo animal model and then isolated and/or purified.
[0077] Antibodies useful in the present disclosure can encompass monoclonal antibodies, polyclonal antibodies, chimeric antibodies, bispecific antibodies, multispecific antibodies, heteroconjugate antibodies, humanized antibodies, human antibodies, deimmunized antibodies, mutants thereof, fusions thereof, immunoconjugates thereof, antigen-binding fragments thereof, and/or any other modified configuration of the immunoglobulin molecule that includes an antigen recognition site of the required specificity, including glycosylation variants of antibodies, amino acid sequence variants of antibodies, and covalently modified antibodies.
[0078] Any of the antibodies herein can be multispecific. In an embodiment, a multispecific antibody can be trispecific (e.g., an anti-tumor antigen, CD2, and CD3). In another embodiment, a multispecific antibody can be bispecific (e.g., an anti-tumor antigen and CD2). Bispecific antibodies can be antibodies that have binding specificities for at least two different antigens and can be prepared using the antibodies disclosed herein. Exemplary methods for making bispecific antibodies are described (see, e.g., Suresh et al, 1986, Methods in Enzymology 121:210). The recombinant production of bispecific antibodies can be based on the co-expression of two immunoglobulin heavy chain-light chain pairs, with the two heavy chains having different specificities (Millstein and Cuello, 1983, Nature, 305, 537- 539). Bispecific antibodies can be composed of a hybrid immunoglobulin heavy chain with a first binding specificity in one arm, and a hybrid immunoglobulin heavy chain-light chain pair (providing a second binding specificity) in the other arm. This asymmetric structure, with an immunoglobulin light chain in only one half of the bispecific molecule, can facilitate separation of the desired bispecific compound from unwanted immunoglobulin chain combinations.
[0079] According to some embodiments, the CAR or anti-CD2 fusion protein comprises an extracellular binding domain that specifically binds a molecule on the surface of a target cell. The target cell may be any cell type of interest. For example, the target cell may be a genetically and/or phenotypically normal cell. In other embodiments, the target cell is a genetically and/or phenotypically abnormal cell. Abnormal cells of interest include, but are not limited to, cancer cells, cells in the tumor microenvironment (e.g., tumor stromal cells) such as cancer-associated fibroblasts (CAFs), myeloid-derived suppressor cells (MDSCs), tumor-associated macrophages (TAMs), tumor endothelial cells (TECs), and the like. See, e.g., Labanieh et al. (2018) Nature Biomedical Engineering 2:377-391. By “cancer cell” is meant a cell exhibiting a neoplastic cellular phenotype, which may be characterized by one or more of the following exemplary characteristics: abnormal cell growth, abnormal cellular proliferation, loss of density dependent growth inhibition, anchorage-independent growth potential, ability to promote tumor growth and/or development in an immunocompromised non-human animal model, and/or any appropriate indicator of cellular transformation. “Cancer cell” may be used interchangeably herein with “tumor cell”, “malignant cell” or “cancerous cell”, and encompasses cancer cells of a solid tumor, a semi-solid tumor, a hematological malignancy (e.g., a leukemia cell, a lymphoma cell, a myeloma cell, etc.), a primary tumor, a metastatic tumor, and the like. According to some embodiments, the protein of interest is a TCR that recognizes an antigenic peptide complexed with a major histocompatibility complex (MHC) molecule displayed on the surface of a cancer cell. In certain embodiments, when the target cell is a cancer cell, the CAR or anti-CD2 fusion protein specifically binds to a tumor antigen on the surface of the cancer cell.
[0080] In some embodiments, the antigen binding domain binds to an antigen selected from the group consisting of glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostate- specific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothehn, MART-1, gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, pl5, CEA, p53, Ras, HER-2, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE-5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS CD 19, CD20, CD22, ROR1, and GD2. Other nonlimiting examples of tumor antigens to which the cell surface molecule may specifically bind include 5T4, AXL receptor tyrosine kinase (AXL), B-cell maturation antigen (BCMA), c-MET, C4.4a, carbonic anhydrase 6 (CA6), carbonic anhydrase 9 (CA9), Cadherin-6, CD 19, CD20, CD22, CD25, CD27L, CD30, CD33, CD37, CD44v6, CD56, CD70, CD74, CD79b, CD123, CD138, carcinoembryonic antigen (CEA), cKit, Cripto protein, CS1, delta-like canonical Notch ligand 3 (DLL3), endothelin receptor type B (EDNRB), ephrin A4 (EFNA4), epidermal growth factor receptor (EGFR), EGFRvlll, ectonucleotide pyrophosphatase/phosphodiesterase 3 (ENPP3), EPH receptor A2 (EPHA2), fibroblast growth factor receptor 2 (FGFR2), fibroblast growth factor receptor 3 (FGFR3), FMS-like tyrosine kinase 3 (FLT3), folate receptor 1 (F0LR1), glycoprotein non metastatic B (GPNMB), guanylate cyclase 2 C (GUCY2C), human epidermal growth factor receptor 2 (HER2), human epidermal growth factor receptor 3 (HER3), Integrin alpha, lysosomal-associated membrane protein 1 (LAMP-1), Lewis Y, LIV-1, leucine rich repeat containing 15 (LRRC15), mesothelin (MSLN), mucin 1 (MUC1), mucin 16 (MUC16), sodium-dependent phosphate transport protein 2B (NaPi2b), Nectin-4, NMB, N0TCH3, p-cadherin (p-CAD), prostatespecific membrane antigen (PSMA), protein tyrosine kinase 7 (PTK7), solute carrier family 44 member 4 (SLC44A4), SLIT like family member 6 (SLITRK6), STEAP family member 1 (STEAP1), tissue factor (TF), T cell immunoglobulin and mucin protein- 1 (TIM-1), trophoblast cell-surface antigen (TROP-2), and Wilms' tumor 1 (WT1).
[0081] The antigen binding domain of the CAR or anti-CD2 fusion protein may bind to or associate with the antigen with an affinity (KA) of, for example, greater than or equal to about 10A5 M'1. In certain embodiments, the extracellular binding domain of the CAR or anti-CD2 fusion protein binds to an antigen with a KA greater than or equal to about 10A6 M’1, 10A7 M’1, 10A8 M’1, 10A9 M’1, 10Al 0 M’1, 10Al 1 M’1, 10A12 M’1, or 10A13 M'1. In certain embodiments, the extracellular binding domain of the CAR or anti- CD2 fusion protein binds to an antigen with a KD of less than or equal to about 10A5 M’1, 10A6 M’1, 10A7 M’1, 10A8 M’1, 10A9 M’1, 10A10 M’1, 10Al 1 M’1, 10A12 M’1, or 10A13 M’1. The binding affinity of the extracellular binding domain for the target antigen can be readily determined using conventional techniques, e.g., by competitive ELISA (enzyme-linked immunosorbent assay), equilibrium dialysis, by using surface plasmon resonance (SPR) technology (e.g., the BIAcore 2000 instrument, using general procedures outlined by the manufacturer); by radioimmunoassay; or the like.
[0082] In some embodiments, the target antigen of the antigen binding domain is CD19, CD20, or CD22. In an embodiment, the target antigen of the antigen binding domain is CD 19. In an embodiment, the target antigen of the antigen binding domain is CD22. In some embodiments, the CAR lacks a CD2 binding domain and is expressed with an anti-CD2 fusion protein.
Hinge/Spacer Domain
[0083] In some embodiments, the antigen binding domain of a CAR provided herein is directly linked to a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein is linked to a hinge domain by a second linker. In some embodiments, the antigen binding domain of a CAR provided herein is operatively linked to a transmembrane domain by a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein provided herein is directly linked to a transmembrane domain by a hinge domain. [0084] In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is linked to a hinge domain by a linker. In some embodiments, the anti- CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein is operatively linked to a transmembrane domain by a hinge domain. In some embodiments, the anti-CD2 binding domain of an anti-CD2 fusion protein provided herein is directly linked to a hinge domain. In some embodiments, the antigen binding domain of a CAR provided herein is directly linked to a transmembrane domain by a hinge domain. In some embodiments, the hinge domain of a CAR or anti-CD2 fusion protein provided herein is from CD28. In some embodiments, the hinge domain of a CAR or anti-CD2 fusion protein provided herein has the sequence IEVMYPPPYLDNEKSNGTIIHVKGKHLCPSPLFPGPSKP. In some embodiments, the hinge domain of a CAR or anti-CD2 fusion protein provided herein is from CD8. In some embodiments, the hinge domain of a CAR or anti-CD2 fusion protein provided herein has the sequence TTTPAPRPPTPAPTIASQPLSLRPEACRPAAGGAVHTRGLDFACDIY.
[0085] In certain embodiments, a hinge or spacer domain is a portion of an immunoglobulin, including, but not limited to, one or more heavy chain constant regions, e.g., CH2 and CH3. The spacer domain may include the amino acid sequence of a naturally occurring immunoglobulin hinge region or an altered immunoglobulin hinge region. In one embodiment, the spacer domain includes the CH2 and/or CH3 of IgG 1, lgG4, or IgD. Illustrative spacer domains suitable for use in the CARs or anti-CD2 fusion proteins described herein include the hinge region derived from the extracellular regions of type 1 membrane proteins such as CD8a and CD28, which may be wild-type hinge regions from these molecules or variants thereof. In certain aspects, the hinge domain includes a CD8a or CD28 hinge region. In some embodiments, the hinge is a PD-1 hinge or CD152 hinge.
[0086] In some embodiments, the CAR or anti-CD2 fusion protein further includes an extracellular spacer domain, which may include a hinge domain. The hinge domain is generally a flexible polypeptide connector region disposed between the targeting moiety and the transmembrane domain. Exemplary hinge domain sequences include those from IgG subclasses (such as IgGl and IgG4), IgD, CD28, and CD8 domains. In some embodiments, the hinge domain provides structural flexibility to flanking polypeptide regions. The hinge domain may consist of natural or synthetic polypeptides. It will be appreciated by those skilled in the art that hinge domains may improve the function of the CAR or anti-CD2 fusion protein by promoting optimal positioning of the antigen binding domain and/or anti-CD2 binding domain in relationship to the portion of the antigen or CD2 recognized by it. In some embodiments, a hinge domain may not be required for optimal CAR activity or anti-CD2 fusion protein. In some embodiments, a hinge domain comprising a short sequence of amino acids promotes CAR or anti-CD2 fusion protein activity by facilitating antigen-binding by, for example, relieving steric constraints that could otherwise alter antibody binding kinetics. In some embodiments, the hinge domain is linked downstream of the antigen-binding domain of a CAR and upstream of the transmembrane domain of a CAR. In some embodiments, the hinge domain is linked downstream of the anti-CD2 binding domain of an anti-CD2 fusion protein and upstream of the transmembrane domain of an anti-CD2 fusion protein.
[0087] Non-limiting examples of suitable hinge domains include those derived from CD8a, CD28, CTLA4, CD4, PD1, IgGl, PGK, or IgG4. In some embodiments, the hinge domain can include regions derived from a human CD8a (also known as CD8a) molecule, a CD28 molecule, and any other receptors that provide a similar function in providing flexibility to flanking regions. In some embodiments, the CAR disclosed herein includes a hinge domain derived from a CD8a hinge domain. In some embodiments, the CAR disclosed herein includes a hinge domain derived from a CD28 or CD2 hinge domain. In some embodiments, the hinge domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to a CD8a, CD28, CTLA4, CD4, PD1, IgGl, PGK, or IgG4 hinge domain.
[0088] In some embodiments, the spacer domain further comprises a linker including one or more intervening amino acid residues that are positioned between the antigen binding domain and the extracellular hinge domain. In some embodiments, the linker is positioned downstream from the antigen binding domain and upstream from the hinge domain. In principle, there are no particular limitations to the length and/or amino acid composition of the linker. In some embodiments, any arbitrary single-chain peptide comprising about one to about 300 amino acid residues (e.g., 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more amino acid residues) can be used as a linker. In some embodiments, the linker includes at least about 5, 6, 7, 8, 9, 10, 11, 12, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids. In some embodiments, the linker includes no more than about 300, 250, 200, 150, 140, 130, 120, 110, 100, 90, 85, 80, 75, 70, 65, 60, 55, 50, 45, 40, 35, or 30 amino acid residues. In some embodiments, the length and amino acid composition of the extracellular spacer can be optimized to vary the orientation and/or proximity of the antigen binding domain and the extracellular hinge domain to one another to achieve a desired activity of the CAR or anti-CD2 fusion protein. In some embodiments, the orientation and/or proximity of the antigen binding domain and the extracellular hinge domain to one another can be varied and/or optimized as a “tuning” tool or effect to enhance or reduce the efficacy of the CAR or anti-CD2 fusion protein. In some embodiments, the orientation and/or proximity of the antigen binding domain and the hinge domain to one another can be varied and/or optimized to create a partially functional version of the CAR or anti-CD2 fusion protein. In some embodiments, the extracellular spacer domain includes an amino acid sequence corresponding to an IgG4 hinge domain and an IgG4 CH2-CH3 domain.
[0089] Alternatively, the spacer domain can be a synthetic polypeptide spacer, such as a spacer having a random sequence, a (gly-gly-ser)n (“GGSn”) sequence, or a variation thereof such as (SGG)n, (GGGS)n, (SGGG)n, (GSGGG)n, and the like, where n can range from about 1 to about 15. The synthetic polypeptide spacer domain can also include a naturally occurring sequence, such as a hinge domain derived from CD8a, IgG, and the like.
Transmembrane Domain
[0090] The “transmembrane domain” (TM domain) is the portion of the CAR or anti-CD2 fusion protein that fuses the extracellular binding portion and intracellular signaling domain and anchors the CAR or anti-CD2 fusion protein to the plasma membrane of the cell (e.g., immune effector cell). The transmembrane domain serves to link the extracellular domain (antigen binding domain and spacer domain) of the receptor with the cytoplasmic domain. In general, any transmembrane domain capable of working in a CAR can be used in the receptors and methods of the disclosure.
[0091] In some embodiments, the CAR or anti-CD2 fusion protein comprises a transmembrane domain from a polypeptide selected from the group consisting of: CD4, CD8a, CD28, CD 154, and PD-1; and one or more intracellular costimulatory signaling domains from a polypeptide selected from the group consisting of: 4-1BB, CD28, CD134, and CD137; and an intracellular signaling domain from a polypeptide selected from the group consisting of: FcyRI, FcRy, FcR, CD3y, CD38, CD3s, CD3^, CD35, CD22, CD79a, CD79, and CD665. Such a CAR may further include a spacer domain between the antigenbinding portion and the transmembrane domain, e.g., a CD8a hinge. In some embodiments, the CAR or anti-CD2 fusion protein comprises a transmembrane domain from CD28. In some embodiments, the CAR or anti-CD2 fusion protein comprises a transmembrane domain with the sequence FWVLVVVGGVLACYSLLVTVAFIIFWV. In some embodiments, the CAR or anti-CD2 fusion protein comprises a transmembrane domain from CD8. In some embodiments, the CAR or anti-CD2 fusion protein comprises a transmembrane domain with the sequence IWAPLAGTCGVLLLSLVITLYC.
[0092] The transmembrane domain may be derived either from a natural, synthetic, semi-synthetic, or recombinant source. In some embodiments, the TM domain is derived from (e.g., includes at least the transmembrane region(s) or a functional portion thereof) of the alpha or beta chain of the T-cell receptor, CD3y, CD38, CD3E, CD35, CD3^, CD4, CD5, CD8a, CD9, CD16, CD22, CD27, CD28, CD33, CD37, CD45, CD64, CD80, CD86, CD134, CD137, CD152, CD154, and/or PD-1.
[0093] The transmembrane domain may include, for example without limitation, all or part of the transmembrane domain of the CD3 chain), CD28, CD2, CD4, 0X40, 4-1BB (CD137), ICOS (CD278), ILRB (CD122), IL-2RG (CD132), CTLA-4, PD-1, or CD40, or a sequence derived from such a transmembrane domain. The cytoplasmic signaling domain in general comprises a domain that transduces the event of ligand binding into an intracellular signal that activates the T cell. The CD3z intracellular domain/activating domain is frequently used, although others such as MyD88 can be used. In an embodiment, the transmembrane domain is the transmembrane domain from CD3eta, CD2, CD8, or CD28. In an embodiment, the transmembrane domain is derived from the transmembrane domain from CD2 or CD28. In some embodiments, the transmembrane domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to a CD3 , CD28, CD2, CD4, 0X40, 4-1BB (CD137), FcERIy, ICOS (CD278), ILRB (CD122), IL-2RG (CD132), or CD40 transmembrane domain.
[0094] In certain embodiments, the protein of interest, or nucleic acid encoding the protein of interest, is a CAR or anti-CD2 fusion protein that comprises a transmembrane domain derived from CD8a or CD28. According to some embodiments, a CAR or anti-CD2 fusion protein includes a transmembrane domain derived from CD8a or CD28 and a short polypeptide linker, e.g., between 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids in length, that links the transmembrane domain and the intracellular signaling domain of the CAR or anti-CD2 fusion protein. A glycine-serine linker may be employed as such a linker, for example. [0095] In some embodiments, the transmembrane of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR. In some embodiments, the transmembrane domain of the anti-CD2 fusion protein may be from CD8, CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), DAP10, LAT, KD2C, SLP76, TRIM, or ZAP70.
Intracellular Domain
[0096] The cytoplasmic or intracellular signaling domain, in general, comprises an activating domain having an immunoreceptor tyrosine-based activation motif (IT AM), which when phosphorylated activates the T cell reaction to an antigen. Phosphorylation occurs as a result of antigen binding. The “intracellular signaling” domain of a CAR can refer to the part of a CAR that participates in transducing the signal from CAR binding to a target molecule/antigen into the interior of the immune effector cell to elicit effector cell function, e.g., activation, cytokine production, proliferation and/or cytotoxic activity, including the release of cytotoxic factors to the CAR-bound target cell, or other cellular responses elicited with target molecule/antigen binding to the extracellular CAR domain. Accordingly, the term “intracellular signaling domain” can refer to the portion(s) or domain(s) of a protein which transduce the effector function signal and that direct the cell to perform a specialized function. To the extent that a truncated portion of an intracellular signaling domain is used, such truncated portion may be used in place of a full-length intracellular signaling domain as long as it transduces the effector function signal. The term intracellular signaling domain is meant to include any truncated portion of an intracellular signaling domain sufficient for transducing effector function signal.
[0097] In some embodiments, the anti-CD2 fusion protein lacks an intracellular domain. In some embodiments, the anti-CD2 fusion protein comprises and intracellular domain that lacks an intracellular signaling domain. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from 4-1BB (CD137). In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence KRGRKKLLYIFKQPFMRPVQTTQEEDGCSCRFPEEEEGGCEL.
[0098] In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD3^. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence RVKFSRSADAPAYKQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNEL QKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence
RVKFSRSADAPAYQQGQNQLYNELNLGRREEYDVLDKRRGRDPEMGGKPRRKNPQEGLYNEL QKDKMAEAYSEIGMKGERRRGKGHDGLYQGLSTATKDTYDALHMQALPPR.
[0099] In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD3 and an intracellular signaling domain from 4- 1BB (CD 137).
[0100] In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD2. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence KRKKQRSRRNDEELETRAHRVATEERGRKPHQIPASTPQNPAT. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence PATSQHPPPPPGHRSQAPSHRPPPPGHRVQH.
[0101] In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain from CD3 epsilon. In some embodiments, the CAR or anti- CD2 fusion protein comprises an intracellular domain comprising an intracellular signaling domain with the sequence RPPPVPNPDYEPIRKGQRDLYSGLNQRRI. In some embodiments, the CAR or anti-CD2 fusion protein comprises an intracellular domain comprising a truncated CD3 epsilon intracellular domain. [0102] Signals generated through the T cell receptor (TCR) alone may be insufficient for full activation of the T cell and a secondary or costimulatory signal may also be required. Thus, T cell activation can be mediated by two distinct classes of intracellular signaling domains: primary signaling domains that initiate antigen-dependent primary activation through the TCR (e.g., a TCR/CD3 complex) and costimulatory signaling domains that act in an antigen- independent manner to provide a secondary or costimulatory signal. As such, when the protein of interest is a CAR or anti-CD2 fusion protein, the CAR or anti-CD2 fusion protein may include an intracellular signaling domain that includes one or more costimulatory signaling domains and a primary signaling domain.
[0103] Primary signaling domains can regulate primary activation of the TCR complex either in a stimulatory manner, or in an inhibitory manner. Primary signaling domains that act in a stimulatory manner may contain signaling motifs which are known as immunoreceptor tyrosine-based activation motifs (or “IT AMs”). Non-limiting examples of ITAM-containing primary signaling domains suitable for use in a CAR or anti-CD2 fusion protein include those derived from FcyRI, FcRy, FcR, CD3y, CD35, CD3E, CD3^, CD35, CD22, CD79a, CD79b, and CD665. In certain embodiments, a CAR or anti-CD2 fusion protein includes a CD3^ primary signaling domain and one or more costimulatory signaling domains. In certain embodiments, a CAR or anti-CD2 fusion protein includes a 4-1BB costimulatory signaling domain. The intracellular primary signaling and costimulatory signaling domains are operably linked to the carboxyl terminus of the transmembrane domain. In certain embodiments, a CAR or anti- CD2 fusion protein lacks a CD2 intracellular signaling domain.
[0104] In some embodiments, the CAR or anti-CD2 fusion protein includes one or more costimulatory signaling domains to enhance the efficacy and expansion of T cells expressing the CAR. Exemplary costimulatory molecules suitable for use in CARs or anti-CD2 fusion proteins contemplated in particular embodiments include TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD28, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. In some embodiments, the costimulatory signaling domain has at least about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or 100% sequence identity to a costimulatory signaling domain from TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD28, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. In some embodiments, a CAR or anti-CD2 fusion protein includes one or more costimulatory signaling domains selected from the group consisting of CD2, 4-1BB, CD28, CD137, and CD 134, and a CD3 primary signaling domain. A costimulatory molecule can be represented in the following protein families: TNF receptor proteins, Immunoglobulin-like proteins, cytokine receptors, integrins, signaling lymphocytic activation molecules (SLAM proteins), and activating NK cell receptors. Examples of such molecules include CD27, CD28, 4-1BB (CD137), 0X40, GITR, CD30, CD40, ICOS, BAFFR, HVEM, lymphocyte function-associated antigen- 1 (LFA-1), CD2, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD160, B7-H3, and a ligand that specifically binds with CD83, and the like. In certain embodiments, the CAR or anti-CD2 fusion protein comprises two or more intracellular signaling domains. For example, the CAR or anti-CD2 fusion protein may comprise a first signaling domain and a second signaling domain or fragments thereof independently selected from a i5n3z intracellular signaling domain, a CD28 intracellular signaling domain, a 4-1BB intracellular signaling domain, an OX-40 intracellular signaling domain, an inducible co-stimulator (ICOS) intracellular signaling domain, a CD27 intracellular signaling domain, and a MyD88/CD40 intracellular signaling domain. By way of example, a CAR may include a first intracellular signaling domain or fragment thereof that is a CD3^ intracellular signaling domain and a second intracellular signaling domain or fragment thereof that is a CD28 intracellular signaling domain. Also, by way of example, a CAR or anti-CD2 fusion protein may include a first intracellular signaling domain or fragment thereof that is a CD3^ intracellular signaling domain and a second intracellular signaling domain or fragment thereof that is a 4- IBB intracellular signaling domain. Also, by way of example, a CAR or anti-CD2 fusion protein may include a first intracellular signaling domain or fragment thereof that is a CD3 intracellular signaling domain, a second intracellular signaling domain or fragment thereof that is a 4- IBB intracellular signaling domain, and a third intracellular signaling domain or fragment thereof that is a CD3 epsilon intracellular signaling domain.
[0105] CARs and anti-CD2 fusion proteins of the disclosure may comprise a CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3e, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70 cytoplasmic signaling domain. In some embodiments, the cytoplasmic signaling domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to an CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4- 1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70 cytoplasmic signaling domain. CARs of the disclosure may comprise a CD2 co-stimulatory domain, and one or more additional co-stimulatory domains to increase cytokine production or sensitivity, reduce or prevent anergy, and/or to increase proliferation and cytotoxic activity. These additional co-stimulatory domains can be derived from co-stimulatory proteins such as B7-1 (CD80), B7-2 (CD86), CTLA-4, PD-1, CD278, CD122, CD132, B7- H2, B7-H3, PD-L1, PD-L2, B7-H4, PDCD6, BTLA, 41BB (CD137), FcERTy, CD40L, 4- 1BBL, GITR, BAFF, GITR-L, BAFF-R, HVEM, CD27, LIGHT, CD27L, 0X40, OX40L, CD30, CD30L, TAC1, CD40, CD244, CD84, BLAME, CD229, CRACC, CD2F-10, NTB-A, CD48, SLAM (CD150), CD58, ikaros, CD53, integrin a4, CD82, integrin a4bl, CD90, integrin a4b7, CD96, LAG-3, CD160, LMIR, CRTAM, TCL1A, DAP12; TIM-1, Dectin-1, TIM-4, TSLP, EphB6, TSLP-R, and/or HLA-DR. In some embodiments, the cytoplasmic signaling domain has about 70, 75, 80, 85, 90, 92, 93, 94, 95, 96, 97, 98, 99 or about 100% sequence identity to an B7-1 (CD80), B7-2 (CD86), CTLA- 4, PD-1, CD278, CD122, CD132, B7- H2, B7-H3, PD-L1, PD-L2, B7-H4, PDCD6, BTLA, 41BB (CD137), FcERTy, CD40L, 4- 1BBL, GITR, BAFF, GITR-L, BAFF-R, HVEM, CD27, LIGHT, CD27L, 0X40, OX40L, CD30, CD30L, TAC1, CD40, CD244, CD84, BLAME, CD229, CRACC, CD2F-10, NTB-A, CD48, SLAM (CD150), CD58, ikaros, CD53, integrin a4, CD82, integrin a4bl, CD90, integrin a4b7, CD96, LAG-3, CD160, LMIR, CRTAM, TCL1 A, DAP12; TIM- 1, Dectin-1, TIM-4, TSLP, EphB6, TSLP-R, and/or HLA-DR domains.
T Cell Receptors
[0106] An aspect of the disclosure may be a transgenic T cell receptor for use with a CAR in a CAR-T therapy. A TCR can be found on the surface of a cell or in soluble form. Generally, a TCR is found on the surface of T cells (or T lymphocytes) where it is generally responsible for recognizing antigens bound to major histocompatibility complex (MHC) molecules.
[0107] In some embodiments, a TCR can be an intact or full-length TCR, including a TCR in the a0 form or y8 form. In some embodiments, a TCR is a dimeric TCR (dTCR). In some embodiments, a TCR is a single-chain TCR (scTCR). In some embodiments, the TCR is an antigen-binding portion that is less than a full-length TCR but that binds to a specific peptide bound in an MHC molecule, such as binds to an MHC -peptide complex. In some cases, an antigen-binding portion or fragment of a TCR can contain only a portion of the structural domains of a full-length or intact TCR, but yet is able to bind the peptide epitope, such as MHC -peptide complex, to which the full TCR binds. In some cases, an antigen-binding portion contains the variable domains of a TCR, such as variable a chain and variable p chain of a TCR, sufficient to form a binding site for binding to a specific MHC -peptide complex. Generally, the variable chains of a TCR contain complementarity determining regions involved in recognition of the peptide, MHC and/or MHC -peptide complex.
[0108] In some embodiments, a TCR can contain a constant domain, a transmembrane domain and/or a short cytoplasmic tail. In some embodiments, each chain of the TCR can possess one N-terminal immunoglobulin variable domain, one immunoglobulin constant domain, a transmembrane region, and a short cytoplasmic tail at the C-terminal end. In some embodiments, a TCR is associated with invariant proteins of the CD3 complex involved in mediating signal transduction.
[0109] In some embodiments, a TCR contains one or more constant domain. For example, the extracellular portion of a given TCR chain (e.g., a chain or chain) can contain two immunoglobulin-like domains, such as a variable domain (e.g., Va or VP) and a constant domain (e.g., Ca or CP) adjacent to the cell membrane. For example, in some cases, the extracellular portion of the TCR formed by the two chains contains two membrane-proximal constant domains, and two membrane-distal variable domains, which variable domains each contain CDRs. The constant domain of the TCR can contain short connecting sequences in which a cysteine residue forms a disulfide bond, thereby linking the two chains of the TCR. [0110] In some embodiments, a TCR can have an additional cysteine residue in each of the a and b chains, such that the TCR contains two disulfide bonds in the constant domains.
[OHl] In some embodiments, a TCR is a dimeric TCR (dTCR). In some embodiments, the dTCR can contain a first polypeptide wherein a sequence corresponding to a TCRa chain variable region sequence is fused to the N terminus of a sequence corresponding to a TCRa chain constant region extracellular sequence, and a second polypeptide wherein a sequence corresponding to a TCRp chain variable region sequence is fused to the N terminus a sequence corresponding to a TCRP chain constant region extracellular sequence, the first and second polypeptides being linked by a disulfide bond. In some embodiments, the bond can correspond to the native interchain disulfide bond present in native dimeric TCRab forms. In some embodiments, the interchain disulfide bonds are not present in a native TCR. For example, in some embodiments, one or more cysteines can be incorporated into the constant region extracellular sequences of dTCR polypeptide pair. In some embodiments, a dTCR can have both a native and one or more non-native disulfide bonds. In some embodiments, a dTCR can contain a transmembrane sequence to anchor to the membrane. In some embodiments, a dTCR can contain a TCRa chain containing a variable a domain, a constant a domain and a first dimerization motif attached to the C-terminus of the constant a domain, and a TCR b chain comprising a variable b domain, a constant b domain and a first dimerization motif attached to the C-terminus of the constant b domain, wherein the first and second dimerization motifs easily interact to form a covalent bond between an amino acid in the first dimerization motif and an amino acid in the second dimerization motif linking the TCR a chain and TCR b chain together.
[0112] In some embodiments, a TCR or antigen binding portion thereof is one that has been modified or engineered. In some embodiments, the antigen binding domain of a TCR can be multispecific. In some embodiments, a TCR or antigen-binding portion thereof can be a recombinantly produced natural protein or a mutated form thereof in which one or more property, such as a binding characteristic, has been altered. In some embodiments, directed evolution methods are used to generate TCRs with altered properties, such as with higher affinity for a specific MHC -peptide complex. In some embodiments, directed evolution is achieved by display methods including, but not limited to, yeast display. In some embodiments, display approaches can involve engineering, or modifying, a known, parent or reference TCR. For example, in some cases, a wild-type TCR can be used as a template for producing mutagenized TCRs in which in one or more residues of the CDRs are mutated, and mutants with a desired altered property, such as higher affinity for a desired target antigen, can be selected. In some embodiments, peptides suitable for use in generating TCRs or antigen-binding portions can be determined based on the presence of an HLA- restricted motif in a target polypeptide of interest. In some embodiments, peptides are identified using computer prediction models known to those of skill in the art.
[0113] In some embodiments, a TCR can be generated from a known TCR sequence(s), such as sequences of Va and/or nb chains, for which a substantially full-length coding sequence is readily available. Methods for obtaining full-length TCR sequences, including V chain sequences, from cell sources are well known. In some embodiments, nucleic acids encoding the TCR can be obtained from a variety of sources, such as by polymerase chain reaction (PCR) amplification of TCR-encoding nucleic acids within or isolated from a given cell or cells, or synthesis of publicly available TCR DNA sequences.
[0114] In some embodiments, a TCR is obtained from a biological source, such as from a T cell (e.g., cytotoxic T cell), T-cell hybridomas or other publicly available source. In some embodiments, the T-cells can be obtained from in vivo isolated cells, e.g., from a human subject. In some embodiments, the TCR is a thymically selected TCR. In some embodiments, the TCR is a neoepitope-restricted TCR. In some embodiments, the T-cells can be a cultured T-cell hybridoma or clone. In some embodiments, the TCR or antigen binding portion thereof can be synthetically generated from knowledge of the sequence of the TCR.
[0115] In some embodiments, a TCR is generated from the TCR identified or selected from screening a library of candidate TCRs against a target polypeptide antigen, or target T cell epitope thereof. TCR libraries can be generated by amplification of the repertoire of Va and Vb from T cells isolated from a subject, including cells present in PBMCs, spleen or other lymphoid organs. In some cases, T cells can be amplified from tumor-infiltrating lymphocytes (TILs). In some embodiments, TCR libraries can be generated from CD4+ or CD8+ cells. In some embodiments, the TCRs can be amplified from a T cell source of a normal of healthy subject, i. e. normal TCR libraries. In some embodiments, the TCRs can be amplified from a T cell source of a diseased subject, i.e., diseased TCR libraries. In some embodiments, degenerate primers are used to amplify the gene repertoire of Va and Va, such as by RT-PCR in samples, such as T cells, obtained from humans. In some embodiments, scTv libraries can be assembled from naive Va and nb libraries in which the amplified products are cloned or assembled to be separated by a linker. Depending on the source of the subject and cells, the libraries can be HLA allele specific. Alternatively, in some embodiments, TCR libraries can be generated by mutagenesis or diversification of a parent or scaffold TCR molecule. In some aspects, the TCRs are subjected to directed evolution, such as by mutagenesis, e.g., of the a or b chain. In some embodiments, particular residues within CDRs of the TCR can be altered. In some embodiments, selected TCRs can be modified by affinity maturation. In some embodiments, antigen-specific T cells can be selected, such as by screening to assess CTL activity against the peptide. In some aspects, TCRs, e.g., present on the antigen-specific T cells, may be selected, such as by binding activity, e.g., particular affinity or avidity for the antigen.
[0116] In some embodiments, a TCR of the present disclosure binds to a tumor specific antigen or tumor- associated antigen.
[0117] In some embodiments, CD2 signaling in a T cell expressing a transgenic TCR or in bulk tumor infiltrating lymphocytes (TILs) grown ex vivo can be enhanced by several methods. The TILs can then be given back to a patient. For example, the T cells can be transduced with a co-receptor that enhances CD2 signaling (in addition to expressing the transgenic TCR). The co-receptor comprising an extracellular ligand binding domain, a transmembrane domain, and a CD2 signaling domain can be transcribed in a virus or other vector and can provide CD2 signaling in trans even when the target tumor cells express low, absent, or mutated CD58. The extracellular portion of the co-receptor can comprise an scFv recognizing an antigen expressed by the tumor cells or a ligand for a common receptor expressed on the target tumor cell of interest. Another way to enhance CD2 signaling in a CAR T cell, a transgenic TCR T cell, or bulk TILs can comprise transducing the T cells to constitutively express a secreted molecule capable of crosslinking the cell’s native CD2 through use of one or more anti-CD2 scFvs, antibodies, Fabs, DARPINs, ligands, or other binders/antigen binding domains. Alternatively, the secreted molecule can be expressed under an activation switch. The secreted molecule can be membrane bound and can consist of two scFv’s connected by a linker: one scFv that binds CD2 on the T cell (activating its native CD2 signaling) and the other scFv or ligand recognizing a protein or target expressed on tumor cells such that CD2 is crosslinked and activated when the T cell encounters tumor cells.
Nucleic Acids
[0118] Also provided herein are nucleic acids comprising a sequence encoding the CAR and/or anti-CD2 fusion proteins provided herein.
[0119] The terms “nucleic acid “ and “polynucleotide” are used interchangeably herein, and refer to both RNA and DNA molecules, including nucleic acid molecules comprising cDNA, genomic DNA, and/or synthetic DNA, and DNA or RNA molecules containing nucleic acid analogs. The nucleic acid can comprise one or more bases and/or linkages that do not occur naturally in DNA or RNA, such as phosphoramidite linkages, 2'-modified ribose or deoxyribose, morpholino phosphoramidites, peptidenucleic acid links, locked nucleic acid links, xanthine, 7-methylguanine, inosine, dihydro uracil, 5- methylcytosine, 5- hydroxymethylcytosine, and others. See, e.g., C.I.E. Smith et al., Ann Rev Pharmacol Toxicol (2019) 59:605-30, incorporated herein by reference. A nucleic acid can be double-stranded or single-stranded (for example, a sense strand or an antisense strand). A nucleic acid may contain unconventional or modified nucleotides. The terms “polynucleotide sequence” and “nucleic acid sequence” as used herein interchangeably refer to the sequence of a nucleic acid molecule.
[0120] Nucleic acids of the disclosure can encode a CAR, a transgenic TCR and/or, an anti-CD2 fusion protein. In some embodiments, nucleic acids of the disclosure can encode both an anti-CD2 fusion protein and a CAR (which can be a CD2 recruiting CAR). In some embodiments, nucleic acids of the disclosure can encode both an anti-CD2 fusion protein and a transgenic TCR. In some embodiments, nucleic acids of the disclosure can encode both a CAR and a transgenic TCR.
[0121] In some embodiments, the recombinant nucleic acid is operably linked to a heterologous nucleic acid sequence, such as, for example a structural gene that encodes a protein of interest or a regulatory sequence (e.g., a promoter sequence). In some embodiments, the recombinant nucleic acid is further defined as an expression cassette or a vector. In some embodiments, the vector is a lentiviral vector, an adeno virus vector, an adeno-associated virus vector, or a retroviral vector. [0122] Some embodiments disclosed herein relate to vectors or expression cassettes including a recombinant nucleic acid molecule as disclosed herein. An expression cassette is a construct of genetic material that contains coding sequences and enough regulatory information to direct proper transcription and/or translation of the coding sequences in a recipient cell, in vivo and/or ex vivo. The expression cassette may be inserted into a vector for targeting to a desired host cell. As such, the term expression cassette may be used interchangeably with the term “expression construct.”
[0123] Also provided herein are vectors, plasmids or viruses containing one or more of the nucleic acid molecules encoding any of the CARs and anti-CD2 fusion proteins disclosed herein. The nucleic acid molecules described above can be contained within a vector that is capable of directing their expression in, for example, a cell that has been transduced with the vector. Suitable vectors for use in eukaryotic cells are known in the art and are commercially available or readily prepared by a skilled artisan. Additional vectors can also be found, for example, in Ausubel, F. M., et al, Current Protocols in Molecular Biology, (Current Protocol, 1994) and Sambrook et al, “ Molecular Cloning: A Laboratory Manual,” 2nd Ed. (1989).
[0124] Accordingly, in some embodiments, the CARs, the TCRs, and/or anti-CD2 fusion proteins of the present disclosure can be expressed from vectors, generally expression vectors. The vectors are useful for autonomous replication in a host cell or may be integrated into the genome of a host cell upon introduction into the host cell, and thereby are replicated along with the host genome (e.g., non-episomal mammalian vectors). Expression vectors are capable of directing the expression of coding sequences to which they are operably linked. In general, expression vectors of utility in recombinant DNA techniques are often in the form of plasmids (vectors). However, other forms of expression vectors, such as viral vectors (e.g., replication defective retroviruses, adenoviruses, and adeno-associated viruses) are also included.
[0125] DNA vectors can be introduced into eukaryotic cells via conventional transformation or transfection techniques. Suitable methods for transforming or transfecting host cells can be found in Sambrook et al. ( 1 89) Molecular Cloning: A Laboratory Manual (2nd ed., Cold Spring Harbor Laboratory Press, Plainview, N.Y.) and other standard molecular biology laboratory manuals.
[0126] Vectors suitable for use include the pMSXND expression vector for use in mammalian cells. In some embodiments, nucleic acid inserts, which encode the subject CAR and/or anti-CD2 fusion protein in such vectors, can be operably linked to a promoter, which is selected based on, for example, the cell type in which expression is sought. Viral vectors that can be used in the disclosure include, for example, retroviral, adenoviral, and adeno-associated vectors, herpes virus, simian virus 40 (SV40), and bovine papilloma virus vectors (see, for example, Gluzman (Ed.), Eukaryotic Viral Vectors, CSH Laboratory Press, Cold Spring Harbor, N.Y.).
[0127] bi some embodiments, the expression vector can be a viral vector. The term “viral vector” is widely used to refer either to a nucleic acid molecule that includes virus-derived nucleic acid elements that typically facilitate transfer of the nucleic acid molecule or integration into the genome of a cell, or to a viral particle that mediates nucleic acid transfer. Viral particles typically include viral components, and sometimes also host cell components, in addition to nucleic acid(s). Retroviral vectors used herein contain structural and functional genetic elements, or portions thereof, that are primarily derived from a retrovirus. Retroviral lentivirus vectors contain structural and functional genetic elements, or portions thereof including LTRs, that are primarily derived from a lentivirus (a sub-type of retrovirus).
[0128] Viral vectors that can be used in the disclosure include, for example, retrovirus vectors (including lentivirus vectors), adenovirus vectors, and adeno-associated virus vectors, herpes virus, simian virus 40 (SV40), and bovine papilloma virus vectors (see, for example, Gluzman (Ed.), Eukaryotic Viral Vectors, CSH Laboratory Press, Cold Spring Harbor, N.Y.).
[0129] In some embodiments, the nucleic acid molecules are delivered by viral or non-viral delivery vehicles known in the art. For example, the nucleic acid molecule can be stably integrated in the host genome, or can be episomally replicating, or present in the recombinant host cell as a mini-circle expression vector for stable or transient expression. Accordingly, in some embodiments disclosed herein, the nucleic acid molecule is maintained and replicated in the recombinant host cell as an episomal unit. In some embodiments, the nucleic acid molecule is stably integrated into the genome of the recombinant cell. Stable integration can also be accomplished using classical random genomic recombination techniques or with more precise genome editing techniques such as using guide RNA-directed CRISPR/Cas9, DNA-guided endonuclease genome editing NgAgo (Natronobacterium gregoryi Argonaute), or TALENs genome editing (transcription activator-like effector nucleases). In some embodiments, the nucleic acid molecule is present in the recombinant host cell as a mini circle expression vector for stable or transient expression.
[0130] The nucleic acid molecules can be encapsulated in a viral capsid or a lipid nanoparticle. Alternatively, endonuclease polypeptide(s) can be delivered by viral or non- viral delivery vehicles known in the art, such as electroporation or lipid nanoparticles. For example, introduction of nucleic acids into cells may be achieved using viral transduction methods. In a non-limiting example, adeno-associated virus (AAV) is a non-enveloped virus that can be engineered to deliver nucleic acids to target cells via viral transduction. Several AAV serotypes have been described, and all of the known serotypes can infect cells from multiple diverse tissue types. AAV is capable of transducing a wide range of species and tissues in vivo with no evidence of toxicity, and it generates relatively mild innate and adaptive immune responses. [0131] Lentiviral systems are also useful for nucleic acid delivery and gene therapy via viral transduction. Lentiviral vectors offer several attractive properties as gene-delivery vehicles, including: (i) sustained gene delivery through stable vector integration into the host cell genome; (ii) the ability to infect both dividing and non-dividing cells; (iii) broad tissue tropisms, including important gene- and cell-therapy - target cell types; (iv) no expression of viral proteins after vector transduction; (v) the ability to deliver complex genetic elements, such as polycistronic or intron-containing sequences; (vi) a potentially safer integration site profile (e.g., by targeting a site for integration that has little or no oncogenic potential); and (vii) a relatively easy system for vector manipulation and production.
[0132] Engineered cells that contain and express a nucleic acid that encodes a CAR, a transgenic TCR and/or an anti-CD2 fusion protein are also an aspect of the disclosure. An engineered cell of the disclosure is a transduced cell, i.e., a cell into which a nucleic acid molecule, for example a nucleic acid molecule encoding a CAR and/or an anti-CD2 fusion protein, has been introduced by means of recombinant DNA techniques. The progeny of such a cell are also considered within the scope of the disclosure. Engineered cells of the disclosure are useful for aiding in the treatment of hyperproliferative diseases and disorders such as cancer.
[0133] The engineered cells of the disclosure can exhibit improved functional properties, as compared to CAR-T cells lacking the features of the disclosure. For example, an engineered cell of the disclosure having a CAR that comprises a CD58 extracellular domain, a transgenic TCR, and/or an anti-CD2 fusion protein can exhibit improved efficacy against target cells that downregulate expression of or do not substantially express CD58; improved efficacy against target cells that downregulate the selected antigen, or express a mutated form of the selected antigen; and/or exhibit improved selectivity for the target cell. In an embodiment, the engineered cell can express a molecule (either secreted or surface expressed) that can crosslink native CD2 in response to a tumor specific antigen in the tumor microenvironment. Improved efficacy against target cells that downregulate expression of or do not substantially express CD58 can be determined by laboratory experiments comparing engineered cells of the disclosure with conventional CAR-T cells, using target cells that express a reduced level of CD58 or a non-functional mutated form of CD58, where improved efficacy can be any demonstration of superior ability to kill or inhibit the target cells. Similar experiments can determine improved efficacy against target cells with down-regulated expression of the selected target antigen. Improved selectivity can be demonstrated by measuring the reduction of on-target off-tumor activity, either in vivo or in a suitable in vitro model. [0134] In some embodiments, host cells can be genetically engineered (e.g., transduced, transformed, or transfected) with, for example, a vector construct of the present disclosure that can be, for example, a viral vector or a vector for homologous recombination that includes nucleic acid sequences homologous to a portion of the genome of the host cell, or can be an expression vector for the expression of the polypeptides of interest. Host cells can be either untransformed cells or cells that have already been transfected with at least one nucleic acid molecule. In some embodiments, the host cell is an immune cell, a stem cell, a mammalian cell, a primate cell, or a human cell. In some embodiments, the host cell is autologous or allogeneic. In some embodiments, the host cell is a T cell, a CD8-positive T cell, a CD4-positive T cell, a regulatory T cell, a cytotoxic T cell, or a tumor infdtrating lymphocyte.
[0135] Host cells can be transduced with a nucleic acid encoding a CD2 recruiting CAR and/or an antiCD fusion protein, or with one or more nucleic acids encoding a CAR and/or a transgenic TCR plus an anti-CD2 fusion protein. For example, without limitation, a host cell can be transduced with a nucleic acid encoding a CAR and/or an anti-CD2 fusion protein, and an additional nucleic acid encoding a transgenic TCR. In an embodiment, the host cell is transduced with a bicistronic nucleic acid encoding a CAR and an anti-CD2 fusion protein. In an embodiment, the host cell is transduced with a bicistronic nucleic acid encoding a CAR and a transgenic TCR. In an embodiment, the host cell is transduced with a tricistronic nucleic acid encoding a CAR, a transgenic TCR and an anti-CD2 fusion protein. In some embodiments, the host cell is further transduced with an additional nucleic acid encoding one or more additional therapeutic agents such as, for example, but not limited to, an antibody, an antibody fragment thereof, or a protein therapeutic capable of stimulating CD2. In some embodiments, a vaccine, an oncoloytic virus, a checkpoint inhibitor, a T cell agonist antibody, chemotherapy, and/or a bispecific antibody can be combined with CAR T cells or other adoptively transferred T cells.
[0136] In some embodiments, the recombinant cell is an animal cell. In some embodiments, the animal cell is a mammalian cell. In some embodiments, the animal cell is a mouse cell. In some embodiments, the animal cell is a human cell. In some embodiments, the recombinant cell is an immune system cell, e.g., a lymphocyte (for example without limitation, a T cell, natural killer cell or NK cell, natural killer T cell or NKT cell, a B cell, a plasma cell, tumor-infdtrating lymphocyte (TIL)), a monocyte or macrophage, or a dendritic cell. In some embodiments, the immune system cell is selected from the group consisting of B cells, T cells, monocytes, dendritic cells, and epithelial cells. In some embodiments, the immune system cell is a T lymphocyte. The immune cell can also be a precursor cell, i.e., a cell that is capable of differentiating into an immune cell. [0137] Techniques for transforming a wide variety of the above-mentioned host cells and species are known in the art and described in the technical and scientific literature. In some embodiments, the nucleic acid molecule is introduced into a host cell by a transduction procedure, electroporation procedure, or a biolistic procedure. Accordingly, cell cultures including at least one recombinant cell as disclosed herein are also within the scope of this application. Methods and systems suitable for generating and maintaining cell cultures are known in the art. An aspect of the disclosure may be a method for making an engineered cell, by transducing the cell with a nucleic acid that encodes a CD2 recruiting CAR and/or an anti-CD2 fusion protein of the disclosure, in such a manner that the nucleic acid is expressed.
[0138] In a related aspect, some embodiments of the disclosure relate to a cell culture including at least one recombinant cell as disclosed herein, and a culture medium. Generally, the culture medium can be any one of suitable culture media for the cell cultures described herein. In some embodiments, the recombinant cell expresses a CAR and/or anti-CD2 fusion protein described herein.
[0139] An aspect of the disclosure may be an antibody or an antigen binding fragment thereof for use with a CAR and/or an anti-CD2 fusion protein in a CAR-T therapy. In some embodiments, the antibody or the antigen binding fragment thereof is multispecific. In some embodiments, a multispecific antibody is bispecific. In an embodiment, the antibody or the antigen binding fragment thereof is bispecific (e.g., a tumor specific antigen or tumor-associated antigen and CD2). In some embodiments, a multispecific antibody is trispecific. In an embodiment, the antibody or the antigen binding fragment thereof is trispecific (e.g., a tumor specific antigen or tumor-associated antigen, CD2, and CD3).
[0140] In some embodiments, a cell of the present disclosure is produced by transfecting the cell with a viral vector encoding the recombinant polypeptide. In some embodiments, the protein of interest of the recombinant polypeptide is a CAR and the cell is a T cell, such that provided are methods of producing a CAR T cell in which cell surface expression of the CAR is regulatable. By “cell surface expression” or “expressed on the surface of the cell” is meant the cell surface molecule - when no longer associated with the protein localization tag (e.g., ER localization tag, Golgi localization tag, or the like) has been trafficked to the cell membrane such that - in the case of a cell surface receptor (e.g., a CAR, TCR, etc.) - the extracellular binding domain is displayed on the cell surface, the transmembrane portion passes through the cell membrane, and the one or more intracellular signaling domains are disposed adjacent to the intracellular side of the cell membrane. Upon binding of the extracellular binding domain to the target ligand/antigen, the intracellular signaling domain of the cell surface receptor participates in transducing the signal from the binding into the interior of the cell (e.g., an effector cell, such as a T cell, to elicit effector cell function). [0141] In some embodiments, when the protein of interest is a CAR, the methods of producing a CAR T cell include activating a population of T cells (e.g., T cells obtained from an individual to whom a CAR T cell therapy will be administered), stimulating the population of T cells to proliferate, and transducing the T cell with a viral vector encoding the CAR. In certain embodiments, the T cells are transduced with a retroviral vector, e.g., a gamma retroviral vector or a lentiviral vector, encoding the CAR. In some embodiments, the T cells are transduced with a lentiviral vector encoding the CAR.
[0142] Cells of the present disclosure may be autologous/autogeneic (“self’) or non- autologous (“nonself,” e.g., allogeneic, syngeneic or xenogeneic). “Autologous” as used herein, refers to cells derived from the same individual to which they are subsequently administered. “Allogeneic” as used herein refers to cells of the same species that differ genetically from the cell in comparison. “Syngeneic,” as used herein, refers to cells of a different individual that are genetically identical to the cell in comparison. In some embodiments, the cells are T cells obtained from a mammal. In some embodiments, the mammal is a primate. In some embodiments, the primate is a human.
[0143] T cells may be obtained from a number of sources including, but not limited to, peripheral blOOd, peripheral blOOd mononuclear cells, bone marrow, lymph node tissue, cord blOOd, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In certain embodiments, T cells can be obtained from a unit of blOOd collected from an individual using any number of known techniques such as sedimentation, e.g., FICOLL™ separation.
[0144] In some embodiments, an isolated or purified population of T cells is used. In some embodiments, TCTL and TH lymphocytes are purified from PBMCs. In some embodiments, the TCTL and TH lymphocytes are sorted into naive (TN), memory (TMEM), stem cell memory (TSCM), central memory (TCM), effector memory (TEM), and effector (TEFF) T cell subpopulations either before or after activation, expansion, and/or genetic modification. Suitable approaches for such sorting are known and include, e.g., magnetic-activated cell sorting (MACS), where TN are CD45RA+ CD62L+ CD95-; TSCM are CD45RA+ CD62L+ CD95+; TCM are CD45RO+ CD62L+ CD95+; and TEM are CD45RO+ CD62L- CD95+. An exemplary approach for such sorting is described in Wang et al. (2016) BlOOd 127(24):2980- 90.
[0145] A specific subpopulation of T cells expressing one or more of the following markers: CD3, CD4, CD8, CD28, CD45RA, CD45RO, CD62, CD127, and HLA-DR can be further isolated by positive or negative selection techniques. In some embodiments, a specific subpopulation of T cells, expressing one or more of the markers selected from the group consisting of CD62L, CCR7, CD28, CD27, CD122, CD127, CD197; or CD38 or CD62L, CD127, CD 197, and CD38, is further isolated by positive or negative selection techniques. In some embodiments, the manufactured T cell compositions do not express one or more of the following markers: CD57, CD244, CD 160, PD-1, CTLA4, TIM3, and LAG3. In some embodiments, the manufactured T cell compositions do not substantially express one or more of the following markers: CD57, CD244, CD 160, PD-1, CTLA4, TIM3, and LAG3.
[0146] In order to achieve therapeutically effective doses of T cell compositions, the T cells may be subjected to one or more rounds of stimulation, activation and/or expansion. T cells can be activated and expanded generally using methods as described, for example, in U.S. Patents 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; and 6,867,041, each of which is incorporated herein by reference in its entirety for all purposes. In some embodiments, T cells are activated and expanded for about 1 to 21 days, e.g., about 5 to 21 days. In some embodiments, T cells are activated and expanded for about 1 day to about 4 days, about 1 day to about 3 days, about 1 day to about 2 days, about 2 days to about 3 days, about 2 days to about 4 days, about 3 days to about 4 days, or about 1 day, about 2 days, about 3 days, or about 4 days prior to introduction of a nucleic acid (e.g., expression vector) encoding the polypeptide into the T cells.
[0147] In some embodiments, T cells are activated and expanded for about 6 hours, about 12 hours, about 18 hours or about 24 hours prior to introduction of a nucleic acid (e.g., expression vector) encoding the cell surface receptor the into the T cells. In some embodiments, T cells are activated at the same time that a nucleic acid (e.g., an expression vector) encoding the cell surface receptor is introduced into the T cells. [0148] In some embodiments, conditions appropriate for T cell culture include an appropriate media (e.g., Minimal Essential Media or RPMI Media 1640 or, X-vivo 15, (Lonza)) and one or more factors necessary for proliferation and viability including, but not limited to serum (e.g., fetal bovine or human serum), interleukin-2 (IL-2), insulin, ILN-g, IL- 4, IL-7, IL-21, GM-CSL, IL-10, IL-12, IL-15, TGLp, and TNE-a or any other additives suitable for the growth of cells known to the skilled artisan. Lurther illustrative examples of cell culture media include, but are not limited to, RPMI 1640, Clicks, AEVI-V, DMEM, MEM, a- MEM, L-12, X-Vivo 15, and/or X-Vivo 20, Optimizer, with added amino acids, sodium pyruvate, and vitamins, either serum-free or supplemented with an appropriate amount of serum (or plasma) or a defined set of hormones, and/or an amount of cytokine(s) sufficient for the growth and expansion of T cells. In some embodiments, the nucleic acid (e.g., an expression vector) encoding the cell surface receptor is introduced into the cell (e.g., a T cell) by microinjection, transfection, lipofection, heatshock, electroporation, transduction, gene gun, microinjection, DEAE- dextran-mediated transfer, and the like. In some embodiments, the nucleic acid (e.g., expression vector) encoding the cell surface receptor is introduced into the cell (e.g., a T cell) by AAV transduction. The AAV vector may comprise ITRs from AAV2, and a serotype from any one of AAV1, AAV2, AAV3, AAV4, AAV5, AAV6, AAV7, AAV8, AAV9, or AAV 10. In some embodiments, the AAV vector comprises ITRs from AAV2 and a serotype from AAV6. In some embodiments, the nucleic acid (e.g., expression vector) encoding the cell surface receptor is introduced into the cell (e.g., a T cell) by lentiviral transduction. The lentiviral vector backbone may be derived from HIV-1, HIV-2, visna-maedi virus (VMV) virus, caprine arthritis-encephalitis virus (CAEV), equine infectious anemia virus (EIAV), feline immunodeficiency virus (FI V), bovine immune deficiency virus (BIV), or simian immunodeficiency virus (SIV). The lentiviral vector may be integration competent or an integrase deficient lentiviral vector (TDLV). In one embodiment, IDLV vectors including an HIV-based vector backbone (i.e., HIV cis-acting sequence elements) are employed.
[0149] Also provided are viruses that include any of the recombinant polypeptides, nucleic acids, and/or expression vectors of the present disclosure.
Pharmaceutical Compositions
[0150] Pharmaceutical compositions are also provided. The pharmaceutical compositions may include any of the cells of the present disclosure, and a pharmaceutically acceptable carrier. The pharmaceutical compositions generally include a therapeutically effective amount of the cells. By “therapeutically effective amount” is meant a number of cells sufficient to produce a desired result, e.g., an amount sufficient to effect beneficial or desired therapeutic (including preventative) results, such as a reduction in a symptom of a disease (e.g., cancer) or disorder associated, e.g., with the target cell or a population thereof (e.g., cancer cells), as compared to a control. An effective amount can be administered in one or more administrations.
[0151] The cells of the present disclosure can be incorporated into a variety of formulations for therapeutic administration. More particularly, the cells of the present disclosure can be formulated into pharmaceutical compositions by combination with appropriate, pharmaceutically acceptable excipients or diluents.
[0152] Formulations of the cells suitable for administration to a patient (e.g., suitable for human administration) are generally sterile and may further be free of detectable pyrogens or other contaminants contraindicated for administration to a patient according to a selected route of administration.
[0153] The cells may be formulated for parenteral (e.g., intravenous, intra-arterial, intraosseous, intramuscular, intracerebral, intracerebroventricular, intrathecal, subcutaneous, etc.) administration, or any other suitable route of administration.
[0154] Pharmaceutical compositions that include the cells of the present disclosure may be prepared by mixing the cells having the desired degree of purity with optional physiologically acceptable carriers, excipients, stabilizers, surfactants, buffers and/or tonicity agents. Acceptable carriers, excipients and/or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid, glutathione, cysteine, methionine and citric acid; preservatives (such as ethanol, benzyl alcohol, phenol, m-cresol, p-chlor-m- cresol, methyl or propyl parabens, benzalkonium chloride, or combinations thereof); amino acids such as arginine, glycine, ornithine, lysine, histidine, glutamic acid, aspartic acid, isoleucine, leucine, alanine, phenylalanine, tyrosine, tryptophan, methionine, serine, proline and combinations thereof; monosaccharides, disaccharides and other carbohydrates; low molecular weight (less than about 10 residues) polypeptides; proteins, such as gelatin or serum albumin; chelating agents such as EDTA; sugars such as trehalose, sucrose, lactose, glucose, mannose, maltose, galactose, fructose, sorbose, raffinose, glucosamine, N-methylglucosamine, galactosamine, and neuraminic acid; and/or non-ionic surfactants such as Tween, Brij Pluronics, Triton-X, or polyethylene glycol (PEG).
[0155] An aqueous formulation of the recombinant polypeptides, proteases, nucleic acids, expression vectors, and/or cells may be prepared in a pH-buffered solution, e.g., at pH ranging from about 4.0 to about 7.0, or from about 5.0 to about 6.0, or alternatively about 5.5. Examples of buffers that are suitable for a pH within this range include phosphate-, histidine-, citrate-, succinate-, acetate-buffers and other organic acid buffers. The buffer concentration can be from about 1 mM to about 100 mM, or from about 5 mM to about 50 mM, depending, e.g., on the buffer and the desired tonicity of the formulation.
[0156] A tonicity agent may be included in the formulation to modulate the tonicity of the formulation. Example tonicity agents include sodium chloride, potassium chloride, glycerin and any component from the group of amino acids, sugars as well as combinations thereof. In some embodiments, the aqueous formulation is isotonic, although hypertonic or hypotonic solutions may be suitable. The term “isotonic” denotes a solution having the same tonicity as some other solution with which it is compared, such as physiological salt solution or serum. Tonicity agents may be used in an amount of about 5 mM to about 350 mM, e.g., in an amount of 100 mM to 350 mM.
[0157] A surfactant may also be added to the formulation to reduce aggregation and/or minimize the formation of particulates in the formulation and/or reduce adsorption. Example surfactants include polyoxyethylensorbitan fatty acid esters (Tween), polyoxyethylene alkyl ethers (Brij), alkylphenylpolyoxyethylene ethers (Triton-X), polyoxyethylene- polyoxypropylene copolymer (Poloxamer, Pluronic), and sodium dodecyl sulfate (SDS). Examples of suitable polyoxyethylenesorbitan- fatty acid esters are polysorbate 20, (sold under the trademark Tween 20™) and polysorbate 80 (sold under the trademark Tween 80™). Examples of suitable polyethylene-polypropylene copolymers are those sold under the names Pluronic® F68 or Poloxamer 188™. Examples of suitable Polyoxyethylene alkyl ethers are those sold under the trademark Brij™. Example concentrations of surfactant may range from about 0.001% to about 1% w/v.
[0158] In some embodiments, the pharmaceutical composition includes cells of the present disclosure, and one or more of the above-identified agents (e.g., a surfactant, a buffer, a stabilizer, a tonicity agent) and is essentially free of one or more preservatives, such as ethanol, benzyl alcohol, phenol, m-cresol, p- chlor-m-cresol, methyl or propyl parabens, benzalkonium chloride, and combinations thereof. In other embodiments, a preservative is included in the formulation, e.g., at concentrations ranging from about 0.001 to about 2% (w/v).
[0159] In certain aspects, provided is a pharmaceutical composition that includes a therapeutically effective amount of cells (e.g., T cells, such as CAR T cells) of the present disclosure. A “therapeutically effective amount” of such cells may vary according to factors such as the disease state, age, sex, and weight of the individual, and the ability of the cells to elicit a desired response in the individual. A therapeutically effective amount is also one in which any toxic or detrimental effects of the cells are outweighed by the therapeutically beneficial effects. The term “therapeutically effective amount” includes an amount that is effective to “treat” an individual, e.g., a patient. When a therapeutic amount is indicated, the precise amount of the compositions contemplated in particular embodiments, to be administered, can be determined by a physician in view of the specification and with consideration of individual differences in age, weight, tumor size, extent of infection or metastasis, and condition of the patient (individual). In some embodiments, a pharmaceutical composition of the present disclosure includes from 1x10A6 to 5xl0A10 of the cells of the present disclosure.
Methods of Treatment
[0160] Engineered cells of the disclosure may be used to aid in the therapy of a hyperproliferative disorder, for example a cancer. Administration of engineered cells (or nucleic acids for generating engineered cells in situ), alone or in combination with other agents (e.g., an antibody or an antigen binding fragment thereof, or a molecule (administered, secreted, or surface expressed) that can crosslink native CD2 in response to a tumor specific antigen in the tumor microenvironment), aids in the treatment or therapy by reducing the number and/or severity of symptoms experienced by a subject, increasing overall or long term survival, killing pathological cells such as tumor cells or other hyperproliferative cells, reducing the tumor burden, inhibiting the growth of tumor cells or other hyperproliferative cells, inhibiting the spread or proliferation of tumor cells or other hyperproliferative cells, and the like. In some embodiments, a vaccine, an oncoloytic virus, a checkpoint inhibitor, a T cell agonist antibody, chemotherapy, and/or a bispecific antibody can be combined with CAR T cells or other adoptively transferred T cells.
[0161] Hyperproliferative disorders include cancers and hyperplasia characterized by the unregulated overgrowth of cells. Hyperproliferative disorders frequently display loss of genetic regulatory mechanisms, and may express native proteins inappropriately (including expression of proteins from other cell types or developmental stages, expression of mutated proteins, and expression of proteins at levels higher or lower than normal).
[0162] B-cell hyperproliferative disorders include B-cell leukemias and lymphomas such as, but not limited to, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), B-cell prolymphocytic leukemia, precursor B lymphoblastic leukemia, hairy cell leukemia, diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, marginal zone lymphoma, mantle cell lymphoma, Burkitt’s lymphoma, MALT lymphoma, Waldenstrom’s macroglobulinemia, and/or other disorders characterized by the overgrowth of B-lineage cells.
[0163] Hyperproliferative disorders include diseases such as, but not limited to, bladder cancer, including upper tract tumors and urothelial carcinoma of the prostate; bone cancer, including chondrosarcoma, Ewing's sarcoma, and osteosarcoma; breast cancer, including noninvasive, invasive, phyllodes tumor, Paget's disease, and breast cancer during pregnancy; central nervous system cancers, adult low-grade infiltrative supratentorial astrocytoma/oligodendroglioma, adult intracranial ependymoma, anaplastic astrocytoma/anaplastic oligodendroglioma/glioblastoma multiforme, limited (1-3) metastatic lesions, multiple (>3) metastatic lesions, carcinomatous lymphomatous meningitis, non-immunosuppressed primary CNS lymphoma, and metastatic spine tumors; cervical cancer; colon cancer, rectal cancer, anal carcinoma; esophageal cancer; gastric (stomach) cancer; head and neck cancers, including ethmoid sinus tumors, maxillary sinus tumors, salivary gland tumors, cancer of the lip, cancer of the oral cavity, cancer of the oropharynx, cancer of the hypopharynx, occult primary, cancer of the glottic larynx, cancer of the supraglottic larynx, cancer of the nasopharynx, and advanced head and neck cancer; hepatobiliary cancers, including hepatocellular carcinoma, gallbladder cancer, intrahepatic cholangiocarcinoma, and extrahepatic cholangiocarcinoma; Hodgkin disease/lymphoma; kidney cancer; melanoma; multiple myeloma, systemic light chain amyloidosis, Waldenstrom's macroglobulinemia; myelodysplastic syndromes; neuroendocrine tumors, including multiple endocrine neoplasia, type 1, multiple endocrine neoplasia, type 2, carcinoid tumors, islet cell tumors, pheochromocytoma, poorly differentiated/small cell/atypical lung carcinoids; Non-Hodgkin's Lymphomas, including chronic lymphocytic leukemia/ small lymphocytic lymphoma, follicular lymphoma, marginal zone lymphoma, mantle cell lymphoma, diffuse large B-Cell lymphoma, Burkitt's lymphoma, lymphoblastic lymphoma, AIDS-Related B-Cell lymphoma, peripheral T-Cell lymphoma, and mycosis fungoides/Sezary Syndrome; non-melanoma skin cancers, including basal and squamous cell skin cancers, dermato fibrosarcoma protuberans, Merkel cell carcinoma; non-small cell lung cancer (NSCLC), including thymic malignancies; occult primary; ovarian cancer, including epithelial ovarian cancer, borderline epithelial ovarian cancer (Low Malignant Potential), and less common ovarian histologies; pancreatic adenocarcinoma; prostate cancer; small cell lung cancer and lung neuroendocrine tumors; soft tissue sarcoma, including soft-tissue extremity, retroperitoneal, intraabdominal sarcoma, and desmoid; testicular cancer; thymic malignancies, including thyroid carcinoma, nodule evaluation, papillary carcinoma, follicular carcinoma, Hurthle cell neoplasm, medullary carcinoma, and anaplastic carcinoma; uterine neoplasms, including endometrial cancer and/or uterine sarcoma.
[0164] Methods for administering immune cells for therapy are known and may be used in connection with the provided methods and compositions. For example, adoptive T cell therapy methods are described in US 2003/0170238; US 4690915; S.A. Rosenberg, Nat Rev Clin Oncol (2011) 8(10):577-85. See also M. Themeli et al., Nat Biotechnol (2013) 31 (10):928-33 ; and T. Tsukahara et al., Biochem Biophys Res Commun (2013) 438(1): 84-89. In an aspect of the disclosure, the method comprises administering a CAR- T cell of the disclosure.
[0165] In some embodiments, therapeutic agents described herein, e.g., engineered CAR-T cells with chimeric polypeptides and/or a transgenic TCR, can be used in methods of treating individuals who have, who are suspected of having, or who may be at high risk for developing a cancer. In some embodiments, the cancer under expresses CD58, or expresses a mutated form of CD58 that can no longer ligate CD2. In some embodiments, the cancer is a leukemia. In these instances, the leukemia can generally be of any type of leukemia. In some embodiments, the cancer is a lymphoma. In some embodiments, the cancer is acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia (CLL), B-cell prolymphocytic leukemia, precursor B lymphoblastic leukemia, hairy cell leukemia, diffuse large B-cell lymphoma (DLBCL), follicular lymphoma, marginal zone lymphoma, mantle cell lymphoma, Burkitt’s lymphoma, MALT lymphoma, Waldenstrom’s macroglobulinemia, or another disorder characterized by the overgrowth of B-lineage cells.
[0166] In other embodiments, the tumor is a solid tumor cancer. In some embodiments, the solid tumor cell is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, or esophageal cancer. In some embodiments, the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell. In some embodiments, the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), stomach adenocarcinoma (STAD), cholangiocarcinoma (CHOL), adenoid cystic carcinoma (ACC), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), DLBC, lung adenocarcinoma (LUAD), head-neck squamous cell carcinoma (HNSC), pancreatic adenocarcinoma (PAAD), breast cancer (BRCA), mesothelioma (MESO), colon and rectal adenocarcinoma (COAD), rectum adenocarcinoma (READ), esophageal carcinoma (ESCA), ovarian cancer (OV), lung squamous cell carcinoma (LUSC), bladder urothelial carcinoma (BLCA), sarcoma (SARC), or uterine corpus endometrial carcinoma (UCEC). In some embodiments, the administered first therapeutic agent inhibits tumor growth or metastasis of the cancer in the subject. In some embodiments, the cancer includes a metastatic cancer cell, a multiply drug resistant cancer cell, or a recurrent cancer cell. In some embodiments, the administered first therapeutic agent confers increased production of interferon gamma (IFNy) and/or interleukin-2 (IL-2) in the subject. In some embodiments, the cancer has reduced expression of CD58. In some embodiments, the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM), or skin cutaneous melanoma (SKCM).
[0167] An effective amount of the engineered cells described herein is determined based on the intended goal, for example tumor regression. For example, where existing cancer is being treated, the amount of a therapeutic agent disclosed herein to be administered may be greater than where administration of the therapeutic agent is for prevention of cancer. One of ordinary skill in the art will be able to determine the amount of a therapeutic agent to be administered and the frequency of administration in view of this disclosure. The quantity to be administered, both according to number of treatments and dose, also depends on the individual to be treated, the state of the individual, and the protection desired. Precise amounts of the therapeutic agent also depend on the judgment of the practitioner and can be peculiar to each individual. Frequency of administration could range from 1-2 days, to 2-6 hours, to 6-10 hours, to 1- 2 weeks or longer depending on the judgment of the practitioner.
[0168] In certain embodiments of the present disclosure, the therapeutic agents will be an aqueous composition that includes the engineered cells described herein. Aqueous compositions of the present disclosure contain an effective amount of a therapeutic agent disclosed herein in a pharmaceutically acceptable carrier or aqueous medium. Thus, the “pharmaceutical preparation” or “pharmaceutical composition” of the disclosure can include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the recombinant cells disclosed herein, its use in the manufacture of the pharmaceutical compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions. For human administration, preparations should meet sterility, pyrogenicity, general safety, and purity standards as required by the FDA Center for Biologies.
[0169] The engineered cells described herein can be used to cure established tumors, inhibit tumor growth or metastasis of cancer in the treated subject relative to the tumor growth or metastasis in subjects who have not been administered one of the therapeutic compositions disclosed herein. In some embodiments, the engineered cells can be used to stimulate immune responses against the tumor via inducing the production of interferon gamma (IFNy) and/or interleukin-2 (IL-2), and other pro-inflammatory cytokines. The production of interferon gamma (IFNy) and/or interleukin-2 (IL-2) can be stimulated to produce up to about 20 fold, such as any of about 2 fold, 3 fold, 4 fold, 5 fold, 6 fold, 7 fold, 8 fold, 9 fold, 10 fold, 11 fold, 12 fold, 13 fold, 14 fold, 15 fold 16 fold, 17 fold, 18 fold, 19 fold, or 20 fold or higher compared to the production of interferon gamma (IFNy) and/or interleukin-2 (IL-2) in subjects who have not been administered one of the therapeutic compositions disclosed herein.
[0170] As discussed herein, engineered cells can be administered in combination with one or more additional therapeutic agents such as, for example, chemotherapeutics or anti-cancer agents or anti-cancer therapies, antibodies or antigen binding fragments thereof, or a molecule (administered, secreted, or surface expressed) that can crosslink native CD2 in response to a tumor specific antigen in the tumor microenvironment. Administration “in combination with” one or more additional therapeutic agents includes simultaneous (concurrent) and consecutive administration in any order. In some embodiments, the one or more additional therapeutic agents, chemotherapeutics, anti-cancer agents, or anti-cancer therapies is selected from the group consisting of chemotherapy, radiotherapy, immunotherapy, hormonal therapy, toxin therapy, and surgery. “Chemotherapy” and “anti-cancer agent” are used interchangeably herein. Various classes of anti-cancer agents can be used. Non-limiting examples include alkylating agents, antimetabolites, anthracyclines, plant alkaloids, topoisomerase inhibitors, podophyllotoxin, antibodies (e.g., monoclonal or polyclonal), checkpoint inhibitors, immunomodulators, cytokines, nanoparticles, radiation therapy, tyrosine kinase inhibitors (for example, imatinib mesylate), hormone treatments, soluble receptors and/or other antineoplastics. In some embodiments, a therapeutic agent is a secreted, surface expressed, or administered molecule that is capable of crosslinking cell’s native CD2 in response to a tumor specific antigen expressed in the tumor microenvironment. In some embodiments, T cells can be transduced to constitutively express a secreted molecule capable of crosslinking the cell’s native CD2 through use of one or more anti-CD2 scFv’s, antibodies, Fabs, DARPINs, ligands, or other binders/antigen binding domains.
[0171] Alternatively, the secreted molecule can be expressed under an activation switch. The secreted molecule can be membrane bound and can consist of two scFv’s connected by a linker: one scFv that binds CD2 on the T cell (activating its native CD2 signaling) and the other scFv or ligand recognizing a protein or target expressed on tumor cells such that CD2 is crosslinked and activated when the T cell encounters tumor cells.
[0172] Topoisomerase inhibitors are also another class of anti-cancer agents that can be used herein. Topoisomerases are essential enzymes that maintain the topology of DNA. Inhibition of type I or type II topoisomerases interferes with both transcription and replication of DNA by upsetting proper DNA supercoiling. Some type I topoisomerase inhibitors include camptothecins: irinotecan and topotecan. Examples of type II inhibitors include amsacrine, etoposide, etoposide phosphate, and teniposide. These are semisynthetic derivatives of epipodophyllotoxins, alkaloids naturally occurring in the root of American Mayapple ( Podophyllum peltatum).
[0173] Antineoplastics include the immunosuppressant dactinomycin, doxorubicin, epirubicin, bleomycin, mechlorethamine, cyclophosphamide, chlorambucil, ifosfamide. The antineoplastic compounds generally work by chemically modifying a cell's DNA.
[0174] Alkylating agents can alkylate many nucleophilic functional groups under conditions present in cells. Cisplatin and carboplatin, and oxaliplatin are alkylating agents. They impair cell function by forming covalent bonds with the amino, carboxyl, sulfhydryl, and phosphate groups in biologically important molecules.
[0175] Vinca alkaloids bind to specific sites on tubulin, inhibiting the assembly of tubulin into microtubules (M phase of the cell cycle). The vinca alkaloids include vincristine, vinblastine, vinorelbine, and vindesine.
[0176] Anti-metabolites resemble purines (azathioprine, mercaptopurine) or pyrimidine and prevent these substances from becoming incorporated into DNA during the “S” phase of the cell cycle, stopping normal development and division. Anti-metabolites also affect RNA synthesis.
[0177] Plant alkaloids and terpenoids are obtained from plants and block cell division by preventing microtubule function. Since microtubules are vital for cell division, without them, cell division cannot occur. The main examples are vinca alkaloids and taxanes. Taxanes as a group includes paclitaxel and docetaxel. Paclitaxel is a natural product, originally known as Taxol and first derived from the bark of the Pacific Yew tree. Docetaxel is a semi-synthetic analogue of paclitaxel. Taxanes enhance stability of microtubules, preventing the separation of chromosomes during anaphase.
[0178] Podophyllotoxin is a plant-derived compound which has been reported to help with digestion as well as used to produce two other cytostatic drugs, etoposide and teniposide. They prevent the cell from entering the G1 phase (the start of DNA replication) and the replication of DNA (the S phase).
[0179] In some embodiments, the anti-cancer agents can be selected from remicade, docetaxel, celecoxib, melphalan, dexamethasone (Decadron®), steroids, gemcitabine, cisplatinum, temozolomide, etoposide, cyclophosphamide, temodar, carboplatin, procarbazine, gliadel, tamoxifen, topotecan, methotrexate, gefitinib (Iressa®), taxol, taxotere, fluorouracil, leucovorin, irinotecan, xeloda, CPT-11, interferon alpha, pegylated interferon alpha (e.g., PEG INTRON-A), capecitabine, cisplatin, thiotepa, fludarabine, carboplatin, liposomal daunorubicin, cytarabine, doxetaxol, pacilitaxel, vinblastine, IL-2, GM-CSF, dacarbazine, vinorelbine, zoledronic acid, palmitronate, biaxin, busulphan, prednisone, bortezomib (Velcade®), bisphosphonate, arsenic tri oxide, vincristine, doxorubicin (Doxil®), paclitaxel, ganciclovir, adriamycin, estrainustine sodium phosphate (Emcyt®), sulindac, etoposide, and combinations of any thereof.
[0180] In other embodiments, the anti-cancer agent can be selected from bortezomib, cyclophosphamide, dexamethasone, doxorubicin, interferon-alpha, lenalidomide, melphalan, pegylated interferon-a, prednisone, thalidomide, or vincristine.
[0181] In some embodiments, the methods of treatment as described herein further include administration of a compound that inhibits one or more immune checkpoint molecules. In some embodiments, the one or more immune checkpoint molecules include one or more of CTLA4, PD-1, PD-L1, A2AR, B7-H3, B7- H4, TIM3 , and combinations of any thereof. In some embodiments, the compound that inhibits the one or more immune checkpoint molecules includes an antagonistic antibody. In some embodiments, the antagonistic antibody is ipilimumab, nivolumab, pembrolizumab, durvalumab, atezolizumab, tremelimumab, or avelumab.
[0182] In some aspects, the one or more anti-cancer therapy is radiation therapy. In some embodiments, the radiation therapy can include the administration of radiation to kill cancerous cells. Radiation interacts with molecules in the cell such as DNA to induce cell death. Radiation can also damage the cellular and nuclear membranes and other organelles. Depending on the radiation type, the mechanism of DNA damage may vary as does the relative biologic effectiveness. For example, heavy particles (protons and neutrons) damage DNA directly and have a greater relative biologic effectiveness. Electromagnetic radiation results in indirect ionization acting through short-lived, hydroxyl free radicals produced primarily by the ionization of cellular water. Clinical applications of radiation consist of external beam radiation (from an outside source) and brachytherapy (using a source of radiation implanted or inserted into the patient). External beam radiation consists of X-rays and/or gamma rays, while brachytherapy employs radioactive nuclei that decay and emit alpha particles, or beta particles along with a gamma ray. Radiation also contemplated herein includes, for example, the directed delivery of radioisotopes to cancer cells. Other forms of DNA damaging factors are also contemplated herein such as microwaves and UV irradiation.
[0183] Radiation may be given in a single dose or in a series of small doses in a dose- fractionated schedule. The amount of radiation contemplated herein ranges from about 1 to about 100 Gy, including, for example, about 5 to about 80, about 10 to about 50 Gy, or about 10 Gy. The total dose may be applied in a fractioned regime. For example, the regime may include fractionated individual doses of 2 Gy. Dosage ranges for radioisotopes vary widely, and depends on the half-life of the isotope and the strength and type of radiation emitted. When the radiation includes use of radioactive isotopes, the isotope may be conjugated to a targeting agent, such as a therapeutic antibody, which carries the agent to the target tissue (e.g., tumor tissue).
[0184] Surgery described herein includes resection in which all or part of a cancerous tissue is physically removed, exercised, and/or destroyed. Tumor resection refers to physical removal of at least part of a tumor. In addition to tumor resection, treatment by surgery includes laser surgery, cryosurgery, electrosurgery, and microscopically controlled surgery (Mohs surgery). Removal of precancers or normal tissues is also contemplated herein.
[0185] Accordingly, in some embodiments, the methods of the disclosure further include administering to the individual a second therapeutic agent, such as an anti-cancer agent, a chemotherapeutic, or anticancer therapy. In some embodiments, the second anti-cancer agent or anti-cancer therapy is selected from the group consisting of chemotherapy, radiotherapy, immunotherapy, hormonal therapy, toxin therapy, and surgery. In some embodiments, the first therapeutic agent and the second anti-cancer agent or therapy are administered concomitantly. In some embodiments, the first therapeutic agent and the second anticancer agent or therapy are administered sequentially. In some embodiments, the first therapeutic agent is administered before the second anti-cancer agent or therapy. In some embodiments, the first therapeutic agent or therapy is administered before and/or after the second anti-cancer agent or therapy. In some embodiments, the first therapeutic agent and the second anti-cancer agent or therapy are administered in rotation. In some embodiments, the first therapeutic agent is administered at the same time as the second anti-cancer agent or therapy. In some embodiments, the first therapeutic agent and the second anti-cancer agent or therapy are administered together in a single formulation.
Kits
[0186] Also provided by the present disclosure are kits. In certain embodiments, provided are kits that include any of the nucleic acids and/or expression vectors of the present disclosure, and instructions for introducing the nucleic acid or expression vector into a cell. According to some embodiments, when the expression vector encodes a recombinant polypeptide that does not comprise the protease (trans configuration), the expression vector further encodes the protease. In certain embodiments, the expression vector is configured to express the recombinant polypeptide and the protease from the same promoter. For example, the expression vector may be a bicistronic expression vector for expression of separate recombinant polypeptides and protease molecules under the same promoter in the cell.
[0187] The kits of the present disclosure may further include any other reagents useful for regulatable signaling of the cell surface receptor, such as transfection/transduction reagents useful for introducing the nucleic acid or expression vector into cells of interest, e.g., immune cells (e.g., T cells) or other cells of interest.
[0188] Components of the kits may be present in separate containers, or multiple components may be present in a single container. A suitable container includes a single tube (e.g., vial), one or more wells of a plate (e.g., a 96-well plate, a 384-well plate, etc.), or the like.
[0189] The instructions of the kits may be recorded on a suitable recording medium. For example, the instructions may be printed on a substrate, such as paper or plastic, etc. As such, the instructions may be present in the kits as a package insert, in the labeling of the container of the kit or components thereof (i.e., associated with the packaging or sub packaging), etc. In other embodiments, the instructions are present as an electronic storage data file present on a suitable computer readable storage medium, e.g., portable flash drive, DVD, CD-ROM, diskette, etc. In yet other embodiments, the actual instructions are not present in the kit, but means for obtaining the instructions from a remote source, e.g., via the internet, are provided. An example of this embodiment is a kit that includes a web address where the instructions can be viewed and/or from which the instructions can be downloaded. As with the instructions, the means for obtaining the instructions is recorded on a suitable substrate.
[0190] As will be apparent to those of skill in the art upon reading this disclosure, each of the individual embodiments described and illustrated herein has discrete components and features which may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the present methods. Any recited method can be carried out in the order of events recited or in any other order that is logically possible.
[0191] List of Embodiments
1. A composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising:
(a) an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain.
2. The composition of embodiment 1, wherein the first antigen binding domain binds to endogenous CD2.
3. The composition of embodiment 1, wherein when the CAR is expressed in a T cell, the first antigen binding domain binds to endogenous CD2 of the T cell.
4. A composition comprising a cell comprising the composition of any one of embodiments 1-3.
5. The composition of embodiment 4, wherein the cell is a T cell.
6. A composition comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises:
(a) an extracellular domain comprising a first antigen binding domain, wherein the first antigen binding domain binds to a receptor expressed by the same T cell expressing the CAR;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain.
7. The composition of embodiment 6, wherein the extracellular domain further comprises a second antigen binding domain that binds to an antigen of a target cell.
8. The composition of embodiment 7, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
9. The composition of embodiment 8 or 10, wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain. A composition comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises:
(a) an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain and/or increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain. The composition of any one of embodiments 1-10, wherein the first antigen binding domain is an antiCD binding domain. The composition of any one of embodiments 1-11, wherein the first antigen binding domain binds to an endogenous receptor expressed by the same T cell expressing the CAR. The composition of embodiment 2 or 12, wherein the receptor expressed by the same T cell expressing the CAR is a costimulatory receptor. The composition of any one of embodiments 1-5 and 7-13, wherein the second antigen binding domain binds to a tumor antigen, optionally wherein the tumor antigen is selected from the group consisting of: glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostatespecific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothehn, MART-1, gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, pl5, CEA, p53, Ras, HER-2, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE- 5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS CD 19, CD20, CD22, R0R1, and/or GD2. The composition of any one of embodiments 1-5 and 7-13, wherein the second antigen binding domain is an anti-CD22 binding domain. The composition of embodiment 14 or 15, wherein the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. The composition of any one of embodiments 1-5 and 7-16, wherein the second antigen binding domain is linked to the first antigen binding domain by a linker sequence. The composition of embodiment 17, wherein the linker sequence is at least 10 or 15 amino acids in length. The composition of embodiment 17, wherein the linker sequence is at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length. The composition of embodiment 17, wherein the linker sequence is from 10 to 45 or from 15 to 30 amino acids in length. The composition of any one of embodiments 1-5 and 7-20, wherein to the first antigen binding domain is N terminal to the second antigen binding domain. The composition of any one of embodiments 1-21, wherein the second antigen binding domain is an antibody domain or binding fragment thereof. The composition of embodiment 22, wherein the second antigen binding domain is an scFv or a single domain antibody domain (sdAb). The composition of any one of embodiments 1-23, wherein the first antigen binding domain is not an antibody domain or binding fragment thereof. The composition of any one of embodiments 1-24, wherein the first antigen binding domain is from CD58. The composition of embodiment 25, wherein the first antigen binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2. The composition of any one of embodiments 1-26, wherein the extracellular domain comprises a hinge domain. The composition of any one of embodiments 1-27, wherein the intracellular signaling domain comprises a CD2 intracellular signaling domain. The composition of any one of embodiments 3-28, wherein the cell is a population of at least 1x10A5 cells. A composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises:
(a) an extracellular domain comprising an antigen binding domain that binds to an antigen of a target cell;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises:
(a) an extracellular domain comprising an anti-CD2 binding domain that binds to CD2; and
(b) a transmembrane domain; wherein
(i) the transmembrane domain of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or
(ii) the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell. The composition of embodiment 30, wherein the first and second multimerization domains are leucine zipper domains. The composition of embodiment 30 or 31, wherein the first multimerization domain is within the extracellular domain of the anti-CD2 fusion protein and second multimerization domain is within the extracellular domain of the CAR. The composition of any one of embodiments 30-32, wherein when the CAR and the anti-CD2 fusion protein are expressed in a cell, a complex comprising the CAR, the anti-CD2 fusion protein and CD2 is formed. The composition of any one of embodiments 30-33, wherein the transmembrane domain of the anti- CD2 fusion protein multimerizes with the transmembrane domain of the CAR. The composition of any one of embodiments 30-34, wherein the first multimerization domain is the transmembrane domain of the anti-CD2 fusion protein and second multimerization domain is the transmembrane domain of the CAR. The composition of any one of embodiments 30-35, wherein the transmembrane domain of the antiCD fusion protein is from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. The composition of any one of embodiments 30-36, wherein the transmembrane domain of the CAR is from CD28. The composition of any one of embodiments 30-37, wherein the anti-CD2 fusion protein lacks an intracellular signaling domain. The composition of any one of embodiments 30-38, wherein the antigen binding domain is an antibody domain or binding fragment thereof. The composition of any one of embodiments 30-39, wherein the antigen binding domain is an scFv or a single domain antibody domain (sdAb). The composition of any one of embodiments 30-40, wherein the anti-CD2 binding domain is not an antibody domain or binding fragment thereof. The composition of any one of embodiments 30-41, wherein the anti-CD2 binding domain is from CD58. The composition of any one of embodiments 30-42, wherein the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2. The composition of any one of embodiments 30-43, wherein the anti-CD2 binding domain binds to endogenous CD2. The composition of any one of embodiments 30-44, wherein when the anti-CD2 fusion protein is expressed in a T cell, the anti-CD2 binding domain binds to endogenous CD2 of the T cell. The composition of any one of embodiments 30-45, wherein the antigen binding domain binds to glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostate- specific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothehn, MART-1, gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, pl5, CEA, p53, Ras, HER-2, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE- 5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS CD 19, CD20, CD22, R0R1, and/or GD2. The composition of any one of embodiments 30-46, wherein the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. The composition of any one of embodiments 30-47, wherein the extracellular domain of the anti-CD2 fusion protein comprises a hinge domain. The composition of embodiment 48, wherein the anti-CD2 binding domain is linked to the hinge domain or the transmembrane domain of the anti-CD2 fusion protein by a linker sequence. The composition of embodiment 49, wherein the linker sequence is at least 10 or 15 amino acids in length. The composition of embodiment 49, wherein the linker sequence is at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length. The composition of embodiment 49, wherein the linker sequence is from 10 to 45 or from 15 to 30 amino acids in length. The composition of any one of embodiments 30-52, wherein the intracellular signaling domain of the CAR comprises a CD2 intracellular signaling domain. A composition comprising a cell comprising the composition of any one of embodiments 30-53. The composition of embodiment 54, wherein the cell is a T cell. The composition of embodiment 55, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain of the CAR compared to a T cell that lacks antiCD fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain. The composition of embodiment 55 or 56, wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain. The composition of any one of embodiments 54-57, wherein the cell is a population of at least lxlOA5 cells. A pharmaceutical composition comprising the composition of any one of embodiments 1-58, and a pharmaceutically acceptable excipient or carrier. A method of treating a disease or condition in a subject in need thereof comprising administering a therapeutically effective amount of the pharmaceutical composition of embodiment 59 to the subject. The method of embodiment 60, wherein the disease or condition is cancer. The method of embodiment 61, wherein the cancer is lymphoma or leukemia. The method of embodiment 63, wherein the cancer is a solid tumor cancer. The method of embodiment 63, wherein the cancer is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), stomach adenocarcinoma (STAD), cholangiocarcinoma (CHOL), adenoid cystic carcinoma (ACC), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), DLBC, lung adenocarcinoma (LUAD), head-neck squamous cell carcinoma (HNSC), pancreatic adenocarcinoma (PAAD), breast cancer (BRCA), mesothelioma (MESO), colon and rectal adenocarcinoma (COAD), rectum adenocarcinoma (READ), esophageal carcinoma (ESCA), ovarian cancer (OV), lung squamous cell carcinoma (LUSC), bladder urothelial carcinoma (BLCA), sarcoma (SARC), or uterine corpus endometrial carcinoma (UCEC).
EXAMPLES
[0192] The practice of the present disclosure will employ, unless otherwise indicated, conventional techniques of molecular biology, microbiology, cell biology, biochemistry, nucleic acid chemistry, and immunology, which are well known to those skilled in the art. Such techniques are explained fully in the literature cited herein.
[0193] Additional embodiments are disclosed in further detail in the following examples, which are provided by way of illustration and are not in any way intended to limit the scope of this disclosure or the claims.
Example 1 - Exemplary CAR constructs
[0194] Exemplary CAR constructs include the constructs listed in Table 1.
Table 1: Exemplary Tethered CD58 CAR Constructs
Figure imgf000068_0001
Figure imgf000069_0001
Figure imgf000070_0001
Figure imgf000071_0001
Figure imgf000072_0001
Figure imgf000073_0001
Figure imgf000074_0001
Figure imgf000075_0001
Figure imgf000076_0001
Figure imgf000077_0001
Example 2 - Exemplary anti-CD2 fusion protein constructs
[0195] Exemplary anti-CD2 fusion protein constructs include the constructs listed in Table 2.
Table 2: Exemplary Tethered CD58 fusion protein constructs
Figure imgf000077_0002
Figure imgf000078_0001
Example 3: CAR-T cell manufacturing and Activity Testing
1. Synthesis of chimeric antigen receptors (CARs) and chimeric polypeptides [0196] Genes encoding scFvs are synthesized as either gene fragments (gBlock, IDT DNA) or geneencoding plasmids synthesized by GeneArt (Life Technologies), and then cloned into a MSGV1 retroviral expression vectors using restriction cloning (Roche) or In-fusion cloning (Takara). CARs having CD 19- BBz or CD22-BBz are constructed having a CD8a hinge domain and CD8a transmembrane domain. CARs having CD19-28z are constructed having a CD28 hinge and transmembrane domain. CARs having CD2 signaling domains are constructed having a CD8a hinge and transmembrane domain.
Retroviral vector production and T-cell transduction
[0197] Retroviral supernatant is produced via transient transfection of the 293 GP packaging cell line as previously described. Briefly, 70% confluent cells are co-transfected via Lipofectamine® 2000 (Life Technologies) in 150 mm Poly-D-Lysine culture dishes with the plasmids encoding the CARs and the RD114 envelope protein. Media is replaced at 24 and 48 hours post transfection. Viral supernatant is harvested 48 and 72 hours post transfection and centrifuged to remove cell debris and stored at -80°C until use.
[0198] Primary human T cells are isolated from healthy donors using the RosetteSep Human T cell Enrichment kit (Stem Cell Technologies), using buffy coats obtained from the Stanford Bl OOd Center and processed according to the manufacturer’s protocol using Lymphoprep® density gradient medium and SepMate-50 tubes. Isolated T cells are cryopreserved in CryoStor CS10 cryopreservation medium (Stem Cell Technologies). Cryopreserved T cells are thawed and activated with Human T-Expander CD3/CD28 Dynabeads (Gibco) at a 3 : 1 beadsxell ratio in AIM-V media supplemented with 5% FBS, 10 mM HEPES, 2 mM L-glutamine, 100 U/mL penicillin, and 100 pg/mL streptomycin (Gibco) and with 100 lU/ml of recombinant IL-2 (Preprotech). T cells are transduced with retroviral vector on days 2 and 3 post activation and anti-CD3/CD28 beads are removed on day 5. Car T-cells are maintained at 0.3-1 c 106 cells per mL in T cell medium with IL-2. CAR expression is assessed by Flow Cytometry after incubation with soluble, recombinant, human CD 19 or CD22 labelled with Dylight650. CAR-T cells are used for in vitro assays or transferred into mice on day 10 post activation.
ELISA
[0199] Cytokine release is assayed by co-incubating CAR+ T cells and tumor cells in complete RPMI- 1640 in triplicates. At 24 hours, culture media is collected, and cytokines are measured using IFNy and IL-2 MAbs (BioLegend).
IncuCyte® killing assays
[0200] For IncuCyte® incubator killing assays, GPF-positive tumor cells are plated in triplicates in 96- well flat-bottom plates and co-incubated with CAR-positive T-cells or an equivalent number of control
-n- CAR T cells at 1 : 1 effector to target ratios in 200 mLRPMI-1640. Plates are imaged every 2-3 hours using the IncuCyte® ZOOM Live-Cell analysis system (Essen Bioscience) and 4 images per well at lOx zoom are collected at each time point. Total integrated GFP intensity per well is assessed as a quantitative measure of viable, GFP-positive tumor cells. Values are normalized to the starting measurement and plotted over time.
Example 4 - Increased costimulatory signaling with CD2 recruiting CARs
[0201] T cells were transduced with retrovirus to express an anti-CD19-CD28-CD3z CAR with or without the N-terminal extracellular domain of CD58 attached. CAR T cells were incubated with wild type (WT) B-cell acute lymphoblastic leukemia cell line NALM6 or NALM6 with CD58 knocked out. After 24 hours, supernatant was collected from the cultures and tested for IL-2 (FIG. 3A) and IFN-y secretion (FIG. 3B) by ELISA. CD19-28z CAR T cells have reduced cytokine secretion when incubated with CD58 knockout NALM6 cells relative to WT NALM6 cells. CD19-28z CAR T cells with CD58 attached have comparable levels of cytokine secretion against CD58 knockout NALM6 and WT NALM6.
Example 5: Increased target cell killing with CD2 recruiting CARs
[0202] CAR T cells with or without appended CD58 domain are incubated with wild type or CD58 knockout target cells. CAR T cells without appended CD58 may not kill CD58 knockout target cells as efficiently as wild type target cells. However, CAR T cells with appended CD58 may kill wild type and CD58 knockout target cells to a similar extent.
[0203] While preferred embodiments of the present disclosure have been shown and described herein, it will be obvious to those skilled in the art that such embodiments are provided by way of example only. Numerous variations, changes, and substitutions will now occur to those skilled in the art without departing from the disclosure. It should be understood that various alternatives to the embodiments of the disclosure described herein may be employed in practicing the disclosure. It is intended that the following claims define the scope of the disclosure and that methods and structures within the scope of these claims and their equivalents be covered thereby.

Claims

CLAIMS WHAT IS CLAIMED IS:
1. A composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), the CAR comprising:
(a) an extracellular domain comprising (i) a first antigen binding domain that is an anti-CD2 binding domain and (ii) a second antigen binding domain that binds to an antigen of a target cell;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain.
2. The composition of claim 1, wherein the first antigen binding domain binds to endogenous CD2.
3. The composition of claim 1, wherein when the CAR is expressed in a T cell, the first antigen binding domain binds to endogenous CD2 of the T cell.
4. A composition comprising a cell comprising the composition of any one of claims 1-3.
5. The composition of claim 4, wherein the cell is a T cell.
6. A composition comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises:
(a) an extracellular domain comprising a first antigen binding domain, wherein the first antigen binding domain binds to a receptor expressed by the same T cell expressing the CAR;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain.
7. The composition of claim 6, wherein the extracellular domain further comprises a second antigen binding domain that binds to an antigen of a target cell.
8. The composition of claim 7, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
9. The composition of claim 8 or 10, wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain.
10. A composition comprising a T cell comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR), wherein the T cell expresses the CAR, wherein the CAR comprises: (a) an extracellular domain comprising (i) a first antigen binding domain that binds to a receptor expressed by T cells and (ii) a second antigen binding domain that binds to an antigen of a target cell;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain and/or increased CD2 signaling compared to a T cell expressing a CAR that comprises the same transmembrane domain, the same intracellular domain and an extracellular domain comprising the same second antigen binding domain but lacking the first antigen binding domain. The composition of any one of claims 1-10, wherein the first antigen binding domain is an anti-CD2 binding domain. The composition of any one of claims 1-11, wherein the first antigen binding domain binds to an endogenous receptor expressed by the same T cell expressing the CAR. The composition of claim 2 or 12, wherein the receptor expressed by the same T cell expressing the CAR is a costimulatory receptor. The composition of any one of claims 1-5 and 7-13, wherein the second antigen binding domain binds to a tumor antigen, optionally wherein the tumor antigen is selected from the group consisting of: glioma-associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alpha-fetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostatespecific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothehn, MART-1, gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, pl5, CEA, p53, Ras, HER-2, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE- 5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS CD 19, CD20, CD22, ROR1, and/or GD2. The composition of any one of claims 1-5 and 7-13, wherein the second antigen binding domain is an anti-CD22, anti-CD20 or anti-CD19 binding domain. The composition of claim 14 or 15, wherein the intracellular domain comprises an intracellular signaling domain from CD3 , 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD35, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. The composition of any one of claims 1-5 and 7-16, wherein the second antigen binding domain is linked to the first antigen binding domain by a linker sequence. The composition of claim 17, wherein the linker sequence is at least 10 or 15 amino acids in length. The composition of claim 17, wherein the linker sequence is at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length. The composition of claim 17, wherein the linker sequence is from 10 to 45 or from 15 to 30 amino acids in length. The composition of any one of claims 1-5 and 7-20, wherein to the first antigen binding domain is N terminal to the second antigen binding domain. The composition of any one of claims 1-21, wherein the second antigen binding domain is an antibody domain or binding fragment thereof. The composition of claim 22, wherein the second antigen binding domain is an scFv or a single domain antibody domain (sdAb). The composition of any one of claims 1 -23, wherein the first antigen binding domain is not an antibody domain or binding fragment thereof. The composition of any one of claims 1-24, wherein the first antigen binding domain is from CD58. The composition of claim 25, wherein the first antigen binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2. The composition of any one of claims 1-26, wherein the extracellular domain comprises a hinge domain. The composition of any one of claims 1-27, wherein the intracellular signaling domain comprises a CD2 intracellular signaling domain. The composition of any one of claims 3-28, wherein the cell is a population of at least lxl0A5 cells. A composition comprising a recombinant polynucleic acid encoding a chimeric antigen receptor (CAR) and an anti-CD2 fusion protein, wherein the CAR comprises:
(a) an extracellular domain comprising an antigen binding domain that binds to an antigen of a target cell;
(b) a transmembrane domain; and
(c) an intracellular domain comprising an intracellular signaling domain; and wherein the anti-CD2 fusion protein comprises:
(c) an extracellular domain comprising an anti-CD2 binding domain that binds to CD2; and
(d) a transmembrane domain; wherein
(i) the transmembrane domain of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR, and/or
(ii) the anti-CD2 fusion protein comprises a first multimerization domain and the CAR comprises a second multimerization domain, wherein the first and second multimerization domains form a multimer when the CAR and the anti-CD2 fusion protein are expressed in a cell. The composition of claim 30, wherein the first and second multimerization domains are leucine zipper domains. The composition of claim 30 or 31, wherein the first multimerization domain is within the extracellular domain of the anti-CD2 fusion protein and second multimerization domain is within the extracellular domain of the CAR. The composition of any one of claims 30-32, wherein when the CAR and the anti-CD2 fusion protein are expressed in a cell, a complex comprising the CAR, the anti-CD2 fusion protein and CD2 is formed. The composition of any one of claims 30-33, wherein the transmembrane domain of the anti-CD2 fusion protein multimerizes with the transmembrane domain of the CAR. The composition of any one of claims 30-34, wherein the first multimerization domain is the transmembrane domain of the anti-CD2 fusion protein and second multimerization domain is the transmembrane domain of the CAR. The composition of any one of claims 30-35, wherein the transmembrane domain of the anti-CD2 fusion protein is from CD3 , 4-1BB (CD137), CD28, CD8, ICOS, FcyRI, FcRy, FcR, FCER1G, CD3y, CD38, CD3E, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD3O, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. The composition of any one of claims 30-36, wherein the transmembrane domain of the CAR is from CD28. The composition of any one of claims 30-37, wherein the anti-CD2 fusion protein lacks an intracellular signaling domain. The composition of any one of claims 30-38, wherein the antigen binding domain is an antibody domain or binding fragment thereof. The composition of any one of claims 30-39, wherein the antigen binding domain is an scFv or a single domain antibody domain (sdAb). The composition of any one of claims 30-40, wherein the anti-CD2 binding domain is not an antibody domain or binding fragment thereof. The composition of any one of claims 30-41, wherein the anti-CD2 binding domain is from CD58. The composition of any one of claims 30-42, wherein the anti-CD2 binding domain comprises a CD58 extracellular domain or fragment thereof capable of binding CD2, or an N-terminal domain of CD58 capable of binding CD2. The composition of any one of claims 30-43, wherein the anti-CD2 binding domain binds to endogenous CD2. The composition of any one of claims 30-44, wherein when the anti-CD2 fusion protein is expressed in a T cell, the anti-CD2 binding domain binds to endogenous CD2 of the T cell. The composition of any one of claims 30-45, wherein the antigen binding domain binds to glioma- associated antigen, carcinoembryonic antigen (CEA), beta-human chorionic gonadotropin, alphafetoprotein (AFP), lectin-reactive AFP, thyroglobulin, RAGE-1, MN-CA IX, human telomerase reverse transcriptase, RU1, RU2 (AS), intestinal carboxyl esterase, mut HSP70-2, M-CSF, prostatespecific antigen (PSA), PAP, NY-ESO-1, LAGE-la, p53, prostein, PSMA, HER2, survivin and telomerase, prostate-carcinoma tumor antigen-1 (PCTA-1), MAGE, ELF2M, neutrophil elastase, ephrinB2, insulin growth factor (IGF)-I, IGF-II, IGF-I receptor, GD2, GD3, B7-H3, GPC2, LI CAM, EGFR, mesothehn, MART-1, gplOO (Pmel 17), tyrosinase, TRP-1, TRP-2, MAGE-1, MAGE-3, BAGE, GAGE-1, GAGE-2, pl5, CEA, p53, Ras, HER-2, BCR-ABL, E2A-PRL, H4-RET, IGH-IGK, MYL-RAR, EBVA, human papillomavirus (HPV) antigens E6 and E7, TSP-180, MAGE-4, MAGE- 5, MAGE-6, RAGE, pl85erbB2, pl80erbB-3, c-met, nm-23Hl, PSA, TAG-72, CA 19-9, CA 72-4, CAM 17.1, NuMa, K-ras, b-Catemn, CDK4, Mum-1, pl5, pl6, 43-9F, 5T4, 791Tgp72, a-fetoprotein, b-HCG, BCA225, BTAA, CA125, BCAA, CA195, CA242, CA-50, CAM43, CD68/P1, CO-029, FGF-5, G250, Ga733/EpCAM, HTgp-175, M344, MA-50, MG7-Ag, M0V18, NB/70K, NY-CO-1, RCAS1, SDCCAG16, TA-90, TAAL6, TAG72, TLP, TPS CD 19, CD20, CD22, R0R1, and/or GD2. The composition of any one of claims 30-46, wherein the intracellular domain comprises an intracellular signaling domain from CD3^, 4-1BB (CD137), CD28, ICOS, FcyRI, FcRy, FcR, CD3y, CD38, CD3s, CD35, CD22, CD79a, CD79b, CD665, TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, TLR10, CARD11, CD2, CD7, CD27, CD30, CD40, CD54 (ICAM), CD83, CD134 (0X40), CD137 (4-1BB), CD278 (ICOS), DAP10, DAP12, LAT, KD2C, SLP76, TRIM, GYPA and/or ZAP70. The composition of any one of claims 30-47, wherein the extracellular domain of the anti-CD2 fusion protein comprises a hinge domain. The composition of claim 48, wherein the anti-CD2 binding domain is linked to the hinge domain or the transmembrane domain of the anti-CD2 fusion protein by a linker sequence. The composition of claim 49, wherein the linker sequence is at least 10 or 15 amino acids in length. The composition of claim 49, wherein the linker sequence is at most 15, 20, 25, 30, 35, 40 or 45 amino acids in length. The composition of claim 49, wherein the linker sequence is from 10 to 45 or from 15 to 30 amino acids in length. The composition of any one of claims 30-52, wherein the intracellular signaling domain of the CAR comprises a CD2 intracellular signaling domain. A composition comprising a cell comprising the composition of any one of claims 30-53. The composition of claim 54, wherein the cell is a T cell. The composition of claim 55, wherein in the presence of the target cell the T cell exhibits increased signaling through the intracellular domain of the CAR compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain. The composition of claim 55 or 56, wherein in the presence of the target cell the T cell exhibits increased CD2 signaling compared to a T cell that lacks anti-CD2 fusion protein and expresses a CAR that comprises the same transmembrane domain, the same intracellular domain and the same extracellular domain comprising the same antigen binding domain. The composition of any one of claims 54-57, wherein the cell is a population of at least 1 *10A5 cells. A pharmaceutical composition comprising the composition of any one of claims 1-58, and a pharmaceutically acceptable excipient or carrier. A method of treating a disease or condition in a subject in need thereof comprising administering a therapeutically effective amount of the pharmaceutical composition of claim 59 to the subject. The method of claim 60, wherein the disease or condition is cancer. The method of claim 61, wherein the cancer is lymphoma or leukemia. The method of claim 61, wherein the cancer is a solid tumor cancer. The method of claim 63, wherein the cancer is lung cancer, liver cancer, pancreatic cancer, stomach cancer, colon cancer, kidney cancer, brain cancer, head and neck cancer, breast cancer, skin cancer, rectal cancer, uterine cancer, cervical cancer, ovarian cancer, testicular cancer, skin cancer, esophageal cancer, and/or the cancer includes a sarcoma cell, a rhabdoid cancer cell, a neuroblastoma cell, retinoblastoma cell, or a medulloblastoma cell, and/or the cancer is uterine carcinosarcoma (UCS), brain lower grade glioma (LGG), thymoma (THYM), testicular germ cell tumors (TGCT), glioblastoma multiforme (GBM) and skin cutaneous melanoma (SKCM), liver hepatocellular carcinoma (LIHC), uveal melanoma (UVM), kidney chromophobe (KICH), thyroid cancer (THCA), kidney renal clear cell carcinoma (KIRC), kidney renal papillary cell carcinoma (KIRP), stomach adenocarcinoma (STAD), cholangiocarcinoma (CHOL), adenoid cystic carcinoma (ACC), prostate adenocarcinoma (PRAD), pheochromocytoma and paraganglioma (PCPG), DLBC, lung adenocarcinoma (LUAD), head-neck squamous cell carcinoma (HNSC), pancreatic adenocarcinoma (PAAD), breast cancer (BRCA), mesothelioma (MESO), colon and rectal adenocarcinoma (COAD), rectum adenocarcinoma (READ), esophageal carcinoma (ESCA), ovarian cancer (OV), lung squamous cell carcinoma (LUSC), bladder urothelial carcinoma (BLCA), sarcoma (SARC), or uterine corpus endometrial carcinoma (UCEC).
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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20180050065A1 (en) * 2015-03-23 2018-02-22 Ucl Business Plc Chimeric antigen receptor
US20200071397A1 (en) * 2018-05-31 2020-03-05 Washington University Chimeric antigen receptor t cells (car-t) for the treatment of cancer
US20210332101A1 (en) * 2018-11-01 2021-10-28 Gracell Biotechnologies (Shanghai) Co., Ltd. Compositions and methods for t cell engineering

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20180050065A1 (en) * 2015-03-23 2018-02-22 Ucl Business Plc Chimeric antigen receptor
US20200071397A1 (en) * 2018-05-31 2020-03-05 Washington University Chimeric antigen receptor t cells (car-t) for the treatment of cancer
US20210332101A1 (en) * 2018-11-01 2021-10-28 Gracell Biotechnologies (Shanghai) Co., Ltd. Compositions and methods for t cell engineering

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