WO2022140665A1 - Compositions and methods for tcr reprogramming using fusion proteins - Google Patents

Compositions and methods for tcr reprogramming using fusion proteins Download PDF

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Publication number
WO2022140665A1
WO2022140665A1 PCT/US2021/065069 US2021065069W WO2022140665A1 WO 2022140665 A1 WO2022140665 A1 WO 2022140665A1 US 2021065069 W US2021065069 W US 2021065069W WO 2022140665 A1 WO2022140665 A1 WO 2022140665A1
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Prior art keywords
tcr
cell
domain
nucleic acid
acid molecule
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PCT/US2021/065069
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English (en)
French (fr)
Inventor
Robert Tighe
Pooja Arora
Robert Hofmeister
Dario Gutierrez
Derrick Mccarthy
Michelle FLEURY
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TCR2 Therapeutics Inc
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TCR2 Therapeutics Inc
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Priority to AU2021410788A priority Critical patent/AU2021410788A1/en
Priority to EP21912227.2A priority patent/EP4267733A4/en
Priority to CA3203180A priority patent/CA3203180A1/en
Priority to JP2023538969A priority patent/JP2024501831A/ja
Priority to CN202180094454.8A priority patent/CN117222738A/zh
Priority to US18/269,214 priority patent/US20240117002A1/en
Publication of WO2022140665A1 publication Critical patent/WO2022140665A1/en
Anticipated expiration legal-status Critical
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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/10—Cellular immunotherapy characterised by the cell type used
    • A61K40/11—T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/32—T-cell receptors [TCR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/30—Cellular immunotherapy characterised by the recombinant expression of specific molecules in the cells of the immune system
    • A61K40/33—Antibodies; T-cell engagers
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4231—Cytokines
    • A61K40/4232—Tumor necrosis factors [TNF] or CD70
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K40/00—Cellular immunotherapy
    • A61K40/40—Cellular immunotherapy characterised by antigens that are targeted or presented by cells of the immune system
    • A61K40/41—Vertebrate antigens
    • A61K40/42—Cancer antigens
    • A61K40/4254—Adhesion molecules, e.g. NRCAM, EpCAM or cadherins
    • A61K40/4255—Mesothelin [MSLN]
    • 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
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/54—Interleukins [IL]
    • C07K14/5443—IL-15
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70521—CD28, CD152
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
    • C07K14/7155—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons for interleukins [IL]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IG], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IG], 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
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C12N5/0602—Vertebrate cells
    • C12N5/0634—Cells from the blood or the immune system
    • C12N5/0636—T lymphocytes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/31—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterized by the route of administration
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/38—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K40/00
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K40/00 characterised by the cancer treated
    • A61K2239/55—Lung
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/02—Fusion polypeptide containing a localisation/targetting motif containing a signal sequence
    • 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
    • C07K2319/50—Fusion polypeptide containing protease site
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2510/00—Genetically modified cells

Definitions

  • cancer immunotherapy Most patients with late-stage solid tumors are incurable with standard therapy. In addition, traditional treatment options often have serious side effects. Numerous attempts have been made to engage a patient’s immune system for rejecting cancerous cells, an approach collectively referred to as cancer immunotherapy. However, several obstacles make it rather difficult to achieve clinical effectiveness. Although hundreds of so- called tumor antigens have been identified, these are often derived from self and thus can direct the cancer immunotherapy against healthy tissue or are poorly immunogenic. Furthermore, cancer cells use multiple mechanisms to render themselves invisible or hostile to the initiation and propagation of an immune attack by cancer immunotherapies.
  • Human T cell therapies rely on enriched or modified human T cells to target and kill cancer cells in a patient.
  • methods have been developed to engineer T cells to express constructs which direct T cells to a particular target cancer cell.
  • CARs Chimeric antigen receptors
  • TCRs engineered T cell receptors
  • successful patient therapy with engineered T cells may require the T cells to be capable of strong activation, expansion, persistence over time, effective tumor targeting, and, in case of relapsing disease, enabling a ‘memory’ response.
  • nucleic acids expressing fusion proteins of TCR subunits, including CD3 epsilon, CD3gamma, CD3 delta, TCR gamma, TCR delta, TCR alpha and TCR beta chains with binding domains specific for cell surface antigens that have the potential to overcome limitations of existing approaches.
  • Said nucleic acid molecules can express a second protein that comprises IE-15, or a fragment thereof, or IL-15-Ra, or a fragment thereof.
  • said IL-15-Ra fusion protein comprises the extracellular domain of PD-1 fused to the intracellular domain of CD28, with the intracellular domain of IL- 15-Ra fused to the C-terminus of the intracellular domain of CD28.
  • Said recombinant nucleic acids can be expressed in a T cell.
  • these IL-15 and/or IL-15-Ra proteins when expressed in combination with the TCR fusion proteins described above, they can confer increased persistence, prolonged activity, and increased efficacy on the T cells for treating the malignancies described herein.
  • These modified T cells may have the ability to kill target cells more efficiently than CARs but release comparable or lower levels of pro-inflammatory cytokines.
  • These modified T cells and methods of their use may represent an advantage for these cells relative to CARs because elevated levels of these cytokines have been associated with dose-limiting toxicities for adoptive CAR T therapies.
  • modified T cells comprising T-cell receptor (TCR) fusion protein (TFP) and an IL- 15 or IL-15Ra polypeptide, methods of producing the modified T cells, and methods of use thereof for the treatment of diseases.
  • TCR T-cell receptor
  • TFP T-cell receptor fusion protein
  • IL- 15 or IL-15Ra polypeptide T-cell receptor fusion protein
  • a recombinant nucleic acid molecule comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises a TCR subunit comprising at least a portion of a TCR extracellular domain, and a TCR transmembrane domain, and an antigen binding domain; and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • IL- 15 interleukin- 15
  • the TFP further comprise a TCR intracellular signaling domain.
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker.
  • the first linker comprises a protease cleavage site.
  • the protease cleavage site is a 2A cleavage site.
  • the IL- 15 polypeptide is secreted when expressed in a T cell.
  • the IL-15 polypeptide comprises a sequence of SEQ ID NO: 375.
  • the second nucleic acid sequence further encodes an IL- 15 receptor (IL-15R) subunit or a fragment thereof.
  • the IL-15R subunit is IL-15R alpha (IL-15Ra).
  • IL-15 and IL-15Ra are operatively linked by a second linker.
  • the second linker is not a cleavable linker.
  • the second linker comprises a sequence comprising (G4S) n , wherein G is glycine, S is serine, and n is an integer from 1 to 10. In some embodiments, n is an integer from 1 to 4. In some embodiments, n is 3. In some embodiments, the second linker comprises a sequence of SEQ ID NO: 378. In some embodiments, the second linker comprises a sequence of SEQ ID NO: 405.
  • the second nucleic acid sequence encodes a fusion protein comprising the IL- 15 polypeptide linked to the IL-15Ra subunit.
  • the IL- 15 polypeptide is linked to N- terminus of the IL-15Ra subunit.
  • the fusion protein comprises amino acids 30-162 of IL-15.
  • the fusion protein comprises amino acids 31-267 of IL-15Ra.
  • the fusion protein further comprises a sushi domain.
  • the fusion protein comprises a sequence of SEQ ID NO: 389.
  • the fusion protein is expressed on cell surface when expressed in a T cell. In some embodiments, the fusion protein is secreted when expressed in a T cell.
  • the recombinant nucleic acid molecule further comprises a third nucleic acid sequence encoding a PD-1 polypeptide which is operably linked via its C-terminus to the N-terminus of an intracellular domain of a costimulatory polypeptide.
  • the recombinant nucleic acid molecule further comprises a third nucleic acid sequence encoding an anti -PD-1 antibody, or antigen binding fragment thereof, which is operably linked via its C-terminus to the N-terminus of an intracellular domain of a costimulatory polypeptide.
  • the PD-1 polypeptide or anti -PD-1 antibody is linked to the intracellular domain of the costimulatory polypeptide via the transmembrane domain of PD-1.
  • the costimulatory poly-peptide is selected from the group consisting of 0X40, CD2, CD27, CDS, ICAM-1, ICOS (CD278), 4-1BB (CD137), GITR, CD28, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD160, CD226, FcyRI, FcyRII, and FcyRIII.
  • the recombinant nucleic acid molecule comprises a sequence of SEQ ID NO: 377, SEQ ID NO: 380, or SEQ ID NO: 381.
  • a recombinant nucleic acid molecule comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises a TCR subunit comprising at least a portion of a TCR extracellular domain, and a TCR transmembrane domain, and an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • IL-15Ra interleukin- 15 receptor alpha
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker.
  • the first linker comprises a protease cleavage site.
  • the protease cleavage site is a 2A cleavage site.
  • the second nucleic acid sequence further encodes PD-1 or a fragment thereof. In some embodiments, the second nucleic acid sequence encodes the extracellular domain of PD-1. In some embodiments, the second nucleic acid sequence encodes the extracellular and transmembrane domain of PD- 1. In some embodiments, the second nucleic acid sequence further encodes CD28 or a fragment thereof. In some embodiments, the second nucleic acid sequence encodes the intracellular domain of CD28. In some embodiments, the second nucleic acid sequence encodes a fusion protein comprising the PD-1 extracellular domain and transmembrane domain linked to the CD28 intracellular domain linked to IL-15Ra. In some embodiments, the CD28 intracellular domain is linked to the intracellular domain of IL-15Ra. In some embodiments, the second nucleic acid sequence comprises a sequence of SEQ ID NO: 390.
  • the recombinant nucleic acid molecule further comprises a third nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof.
  • IL-15 interleukin- 15
  • the IL- 15 polypeptide or a fragment thereof is secreted when expressed in a T cell.
  • the recombinant nucleic acid molecule comprises a sequence of SEQ ID NO: 361, SEQ ID NO: 376, SEQ ID NO: 377, or SEQ ID NO: 381.
  • the TFP functionally interacts with an endogenous TCR complex when expressed in a T cell.
  • the TCR intracellular do-main comprises a stimulatory domain from an intracellular signaling domain of CD3 gamma, CD3 delta, or CD3 epsilon.
  • the TCR intracellular domain comprises an intracellular domain from TCR alpha, TCR beta, TCR gamma, or TCR delta.
  • the antigen binding domain is connected to the TCR extracellular domain by a third linker sequence.
  • the third linker is 120 amino acids in length or less.
  • the third linker sequence comprises (G4S) n , wherein G is glycine, S is serine, and n is an integer from 1 to 10. In some embodiments, n is an integer from 1 to 4.
  • At least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from the same TCR subunit. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR alpha. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR beta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR gamma.
  • At least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR delta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 epsilon. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 delta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 gamma.
  • all three of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from the same TCR subunit.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 epsilon.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 delta.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 gamma.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR alpha.
  • the constant domain of TCR alpha is murine.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR beta.
  • the constant domain of TCR beta is murine.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR gamma.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR delta.
  • the antigen binding domain is a camelid antibody or binding fragment thereof. In some embodiments, the antigen binding domain is a murine antibody or binding fragment thereof. In some embodiments, the antigen binding domain is a human or humanized antibody or binding fragment thereof. In some embodiments, the antigen binding domain is a single-chain variable fragment (scFv) or a single domain antibody (sdAb) domain. In some embodiments, the antigen binding domain is a single domain antibody (sdAb). In some embodiments, the sdAb is a VHH.
  • the antigen binding do-main is selected from the group consisting of an anti-CD19 binding domain, an anti-B-cell maturation antigen (BCMA) binding domain, and an anti-mesothelin (MSLN) binding domain, an anti-CD20 binding domain, an anti-CD70 binding domain, anti-MUC16 binding domain, an anti-Nectin-4 binding domain, an anti-GPC3 binding domain, and an anti-TROP-2 binding domain.
  • BCMA anti-B-cell maturation antigen
  • MSLN anti-mesothelin
  • a T cell expressing the TFP inhibits tumor growth when expressed in a T cell.
  • recombinant nucleic acid molecule described herein further comprise a leader sequence.
  • the recombinant nucleic acid molecule is selected from the group consisting of a DNA and an RNA.
  • the recombinant nucleic acid molecule is an mRNA.
  • the recombinant nucleic acid molecule is a circRNA.
  • the recombinant nucleic acid molecule comprises a nucleotide analog.
  • the nucleotide analog is selected from the group consisting of 2’-O-methyl, 2’-O-methoxyethyl (2’-O-MOE), 2’-O-aminopropyl, 2’-deoxy, 2’- deoxy-2’ -fluoro, 2 ’-0 -aminopropyl (2’-O-AP), 2'-O-dimethylaminoethyl (2’-O-DMAOE), 2 -0- dimethylaminopropyl (2’-O-DMAP), 2’-O-dimethylaminoethyloxyethyl (2’-O-DMAEOE), 2’-O-N- methylacetamido (2’-0-NMA) modified, a locked recombinant nucleic acid molecule (LNA), an ethylene recombinant nucleic acid molecule (ENA), a peptide recombinant nucleic acid molecule (PNA), a I ’
  • LNA
  • recombinant nucleic acid molecule described herein further comprise a promoter.
  • the recombinant nucleic acid molecule is an in vitro transcribed nucleic acid.
  • the recombinant nucleic acid molecule further comprises a sequence encoding a poly(A) tail.
  • the recombinant nucleic acid molecule further comprises a 3’UTR sequence.
  • a vector comprising the recombinant nucleic acid molecule disclosed herein.
  • a cell comprising the recombinant nucleic acid molecule disclosed herein, the polypeptide disclosed herein, or the vector disclosed herein.
  • the cell is a T cell.
  • the T cell is a human T cell.
  • the T cell is a CD8+ or CD4+ T cell.
  • the T cell is a human ot
  • the T cell is a human y5 T cell.
  • the cell is a human NKT cell.
  • the cell is an allogeneic cell or an autologous cell.
  • a cell comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises a TCR subunit comprising at least a portion of a TCR extracellular domain, and a TCR transmembrane domain, and an antigen binding domain; and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • IL-15 interleukin- 15
  • the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid molecule. In some embodiments, the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid molecules. In some embodiments, the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker. In some embodiments, the first linker comprises a protease cleavage site. In some embodiments, the protease cleavage site is a 2A cleavage site.
  • the TFP further comprise a TCR intracellular signaling domain.
  • the IL-15 polypeptide is secreted when expressed in a T cell.
  • the IL-15 polypeptide comprises a sequence of SEQ ID NO: 375.
  • the second nucleic acid sequence further encodes an IL- 15 receptor (IL-15R) subunit or a fragment thereof.
  • the IL-15R subunit is IL-15R alpha (IL-15Ra).
  • IL-15 and IL-15Ra are operatively linked by a second linker.
  • the second linker is not a cleavable linker.
  • the second linker comprises a sequence comprising (G4S) n , wherein G is glycine, S is serine, and n is an integer from 1 to 10. In some embodiments, n is an integer from 1 to 4. In some embodiments, n is 3. In some embodiments, the second linker comprises a sequence of SEQ ID NO: 378. In some embodiments, the second linker comprises a sequence of SEQ ID NO: 405.
  • the second nucleic acid sequence encodes a fusion protein comprising the IL- 15 polypeptide linked to the IL-15Ra subunit.
  • the fusion protein comprises amino acids 30-162 of IL-15.
  • the fusion protein comprises amino acids 31-267 of IL-15Ra.
  • the fusion protein further comprises a sushi domain.
  • the fusion protein comprises a sequence of SEQ ID NO: 389.
  • the fusion protein is expressed on cell surface when expressed in a T cell. In some embodiments, the fusion protein is secreted when expressed in a T cell.
  • the cell further comprises a third nucleic acid sequence encoding a PD-1 polypeptide which is operably linked via its C-terminus to the N-terminus of an intracellular domain of a costimulatory polypeptide.
  • the cell further comprises a third nucleic acid sequence encoding an anti-PD-1 antibody, or antigen binding fragment thereof, which is operably linked via its C- terminus to the N-terminus of an intracellular domain of a costimulatory polypeptide.
  • the third nucleic acid sequence is included in the same nucleic acid molecule as the first and second nucleic acid sequences.
  • the PD-1 polypeptide or anti-PD-1 antibody is linked to the intracellular domain of the costimulatory polypeptide via the transmembrane do-main of PD-1.
  • the costimulatory polypeptide is chosen from a group comprising 0X40, CD2, CD27, CDS, ICAM-1, ICOS (CD278), 4-1BB (CD137), GITR, CD28, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD 160, CD226, FcyRI, FcyRII, and FcyRIII.
  • a cell comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises a TCR subunit comprising at least a portion of a TCR extracellular domain, and a TCR transmembrane domain, and an antigen binding domain; and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • IL-15Ra interleukin- 15 receptor alpha
  • the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid molecule. In some embodiments, the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid molecules. In some embodiments, the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker. In some embodiments, the first linker comprises a protease cleavage site. In some embodiments, the protease cleavage site is a 2A cleavage site.
  • the second nucleic acid sequence further encodes PD-1 or a fragment thereof. In some embodiments, the second nucleic acid sequence encodes the extracellular domain of PD-1. In some embodiments, the second nucleic acid sequence encodes the extracellular and trans-membrane domain of PD- 1. In some embodiments, the second nucleic acid sequence further encodes CD28 or a fragment thereof. In some embodiments, the second nucleic acid sequence encodes the intracellular domain of CD28. In some embodiments, the second nucleic acid sequence encodes a fusion protein comprising the PD-1 extracellular domain and transmembrane domain linked to the CD28 intracellular domain linked to IL-15Ra. In some embodiments, the CD28 intracellular domain is linked to the intracellular domain of IL-15Ra. In some embodiments, the second nucleic acid sequence comprises a sequence of SEQ ID NO: 390.
  • the cell further comprises a third nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • the IL- 15 polypeptide or a fragment thereof is secreted when expressed in a T cell.
  • the cell secretes the IL- 15 polypeptide in response to a T cell activation agent.
  • IL- 15 signaling is increased in response to a T cell activation agent.
  • the T cell activation agent comprises anti-CD3 antibody or a fragment thereof, anti-CD28 antibody or a fragment thereof, a cytokine, an antigen that binds the antigen binding domain of the TFP, or any combinations thereof.
  • the cell has enhanced survival rate compared with a cell not expressing the IL-15 or IL-15Ra polypeptide.
  • the cell has enhanced effector function compared with a cell not expressing the IL-15 or IL-15Ra polypeptide.
  • the cell has enhanced cytotoxicity compared with a cell not expressing the IL-15 or IL-15Ra polypeptide.
  • the TFP functionally interacts with an endogenous TCR complex when expressed in a T cell.
  • the TCR intracellular domain comprises a stimulatory domain from an intracellular signaling domain of CD3 gamma, CD3 delta, or CD3 epsilon.
  • the TCR intracellular domain comprises an intracellular domain from TCR alpha, TCR beta, TCR gamma, or TCR delta.
  • the antigen binding domain is connected to the TCR extracellular domain by a third linker sequence.
  • the third linker is 120 amino acids in length or less.
  • the third linker sequence comprises (G4S) n , wherein G is glycine, S is serine, and n is an integer from 1 to 10. In some embodiments, n is an integer from 1 to 4.
  • At least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from the same TCR subunit. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR alpha. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR beta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR gamma.
  • At least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from TCR delta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 epsilon. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 delta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 gamma.
  • all three of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from the same TCR subunit.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 epsilon.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 delta.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from CD3 gamma.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR alpha.
  • the constant domain of TCR alpha is murine.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR beta.
  • the constant domain of TCR beta is murine.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR gamma.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain comprise or consist of the constant domain of TCR delta.
  • the antigen binding domain is a camelid antibody or binding fragment thereof. In some embodiments, the antigen binding domain is a murine antibody or binding fragment thereof. In some embodiments, the antigen binding domain is a human or humanized antibody or binding fragment thereof. In some embodiments, the antigen binding domain is a single-chain variable fragment (scFv) or a single domain antibody (sdAb) domain. In some embodiments, the antigen binding domain is a single domain antibody (sdAb). In some embodiments, the sdAb is a VHH.
  • the antigen binding domain is selected from the group consisting of an anti-CD19 binding domain, an anti-B-cell maturation antigen (BCMA) binding do-main, and an anti-mesothelin (MSLN) binding domain, an anti-CD20 binding domain, an anti-CD70 binding domain, anti-MUC16 binding domain, an anti-Nectin-4 binding domain, an anti-GPC3 binding domain, and an anti-TROP-2 binding domain.
  • BCMA anti-B-cell maturation antigen
  • MSLN anti-mesothelin
  • the longevity of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL-15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • the persistence of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • the cytotoxicity of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • the cytokine production of the cell is increased com-pared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • the cell retains a naive and/or central memory phenotype.
  • the cell has not differentiated into a terminal effector cell.
  • proliferation of the cell is increased compared to a cell that does not comprise
  • IL-15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • expression of an exhaustion marker of the cell is decreased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 is operatively linked to IL-15Ra.
  • the expression of the exhaustion marker of the cell is decreased for at least about 5%.
  • the exhaustion marker is PD-1, TIM-3 or LAG-3 .
  • tumor infiltration of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or
  • IL-15Ra interleukin- 15 receptor alpha
  • IL- 15 is operatively linked to IL-15Ra.
  • the tumor infiltration of the cell is increased for at least about 2-fold.
  • expression of TCF-1 of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 is operatively linked to IL-15Ra.
  • the expression of TCF-1 of the cell is increased for at least about 5%.
  • a population of cells comprising the cell disclosed herein.
  • the population of cells has an increased proportion of cells having a central memory phenotype relative to a population of cells that do not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • the population of cells has an increased proportion of cells having a naive phenotype relative to a population of cells that do not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • the population of cells has a reduced proportion of cells having a terminal effector phenotype relative to a population of cells that do not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • the population of cells has an increased proportion of cells expressing TCF-1.
  • the cell is any one of the cells disclosed herein.
  • the cell is any one of the cells disclosed herein.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • IL- 15 is operatively linked to IL-15Ra.
  • the cell is any one of the cells as described herein.
  • the cell is any one of the cells as described herein.
  • IL- 15 is operatively linked to IL-15Ra.
  • the cell is any one of the cells as described herein.
  • the cell is any one of the cells as described herein.
  • IL- 15 is operatively linked to IL-15Ra.
  • the cell is any one of the cells as described herein.
  • TCR T cell receptor
  • the cell is any one of the cells as described herein.
  • the cell is any one of the cells as described herein.
  • IL- 15 is operatively linked to IL-15Ra.
  • the cell is any one of the cells as described herein.
  • provided herein is a pharmaceutical composition
  • a pharmaceutical composition comprising the cell or cells disclosed herein and a pharmaceutically acceptable carrier.
  • a method of treating a disease or a condition in a subject in need thereof comprising administering to the subject a therapeutically effective amount of the pharmaceutical composition disclosed herein.
  • the disease or the condition is a cancer or a disease or a condition associated with expression of CD19, B-cell maturation antigen (BCMA), mesothelin (MSLN), CD20, CD70, MUC16, Trop-2, Nectin-4, or GPC3.
  • BCMA B-cell maturation antigen
  • MSLN mesothelin
  • CD20 CD70
  • MUC16 Trop-2
  • Nectin-4 GPC3.
  • the cancer is a hematologic cancer selected from the group consisting of B-cell acute lymphoid leukemia (B-ALL), T cell acute lymphoid leukemia (T-ALL), acute lymphoblastic leukemia (ALL), chronic myelogenous leukemia (CML), chronic lymphocytic leukemia (CLL), B cell prolymphocytic leukemia, blastic plasmacytoid dendritic cell neoplasm, Burkitt’s lymphoma, diffuse large B cell lymphoma, follicular lymphoma, hairy cell leukemia, small cell-follicular lymphoma, large cell- follicular lymphoma, malignant lymphoproliferative conditions, MALT lymphoma, mantle cell lymphoma, Marginal zone lymphoma, multiple myeloma, myelodysplasia, myelodysplastic syndrome, non-Hodgkin’s lymphoma, plasmablastic lymphom
  • Figure 1 shows a schematic illustration of the constructs described in Example 1.
  • Figure 2 is a series of graphs showing expansion of T cells having the TFP constructs shown generated according to the methods described in Example 2.
  • Figure 3 is a series of plots showing the proportion of T cells having the TFP constructs shown generated according to the methods described in Example 2 having cell surface expression of IL-15-Ra, PD-1 and VHH after 10 days of expansion.
  • Figure 4 is a series of plots showing the memory phenotype of T cells having the TFP constructs shown generated according to the methods described in Example 2 after 10 days of expansion.
  • FIG. 5 is a schematic illustration of the experiment described in Example 3.
  • Figures 6A-6C are a series of graphs showing the results of a CSFE assay of T cells having the TFP constructs shown in the assay described in Example 3.
  • Figure 6A and Figure 6B show the in vitro persistence assays at day 7.
  • Figure 6C shows the in vitro persistence assay at day 21.
  • Figures 7A-7C are a series of graphs showing expansion of T cells having the TFP constructs shown in the assay described in Example 3.
  • Figure 7A shows expansion of T cells without stimulation.
  • Figure 7B shows expansion of T cells with sub-optimal TCR stimulation.
  • Figure 7C shows expansion of T cells at day 21 at various conditions (e.g., no stimulation, sub-optimal CD3/28 transactivation, or optimal CD3/28 dynabeads).
  • Figure 8 is a schematic illustration of the experiment described in Example 4.
  • Figure 9 is a series of graphs showing expansion of T cells having the TFP constructs shown in the assay described in Example 4.
  • Figure 10 is a series of graphs showing the results of a CSFE assay of T cells having the TFP constructs shown at day 7 of the assay described in Example 4.
  • Figure 11A and Figure 11B are a series of graphs showing the number of VHH+ (11A) and CD3+ (1 IB) T cells having the TFP constructs shown at days 7, 14, and 21 of the assay described in Example 4.
  • Figure 12 is a series of graphs showing the number of VHH+ T cells having the TFP constructs shown at days 7, 14, and 21 of the assay described in Example 4 relative to the number of VHH+ T cells expressing the MSLN TFP alone.
  • Figure 13A and Figure 13B are a series of graphs showing the memory phenotype of T cells having the TFP constructs shown at days 7 and 21 of the assay described in Example 4.
  • Figure 13A shows the memory phenotype at day 7.
  • Figure 13B shows the memory phenotype at day 21.
  • Figure 14A and Figure 14B are a series of graphs showing target lysis by T cells having the TFP constructs shown at days 8, 15, and 22 of the assay described in Example 4.
  • Figure 15 is a series of graphs showing cytokine secretion by T cells having the TFP constructs shown at day 3 of the assay described in Example 4.
  • Figure 16 is a series of graphs showing in vivo efficacy of T cells having the TFP constructs shown at reducing tumor volume in the murine xenograft model described in Example 5.
  • Figure 17 shows schematic illustrations of the constructs described in Example 8.
  • Figure 18A-18D is a series of graphs showing T cell expansion, transduction efficiency and memory phenotype after transduction with TRuC constructs.
  • Figure 18A shows T cell expansion.
  • Figure 18B shows representative co-expression of CD70 TRuC and mbIL-15fu proteins.
  • Figure 18C shows transduction summary of 3 donors and Figure 18D shows the CD4+/CD8+ ratio for successfully transduced T cells (TRuC+).
  • Figure 19A-19C is a series of graphs showing the T cell differentiation phenotypes of transduced cells.
  • Figure 19A shows characterization of T cell differentiation phenotype by flow cytometry for a representative donor.
  • Figure 19B and Figure 19C show proportions for each T cell differentiation phenotype in TRuC+/CD4+ and TRuC+/CD8+ cells, respectively.
  • Figure 20A-20E is a series of graphs showing cytotoxicity and cytokine production in a co-culture assay using TRuC-T cells.
  • Figure 20A shows 24 hour cytotoxicity against CD70 Hlgh target cell 786-0.
  • Figure 20B shows cytokine production against CD70 Hlgh target cell 786-0.
  • Figure 20C shows 24 hour cytotoxicity against CD70 Moderate target cell ACHN.
  • Figure 20D shows 24 hour cytokine production against CD70 Moderate target cell ACHN.
  • Figure 20E shows 24 hour cytotoxicity against CD70 Negatlve target cell K562.
  • Figure 21A-21C is a series of graphs showing results of a set of persistence and expansion assays.
  • Figure 21A shows T cell persistence in the absence of stimulation.
  • Figure 21B shows T cell expansion after a single round of stimulation with CD70 Hlgh target cells 786-0.
  • Figure 21C shows T cell expansion after repeated stimulation with CD70 Hlgh target cell 786-0.
  • Figure 22A-22J is a series of graphs showing results of in vivo efficacy studies in a mouse tumor model.
  • Figure 22A shows anti-tumor activity of T cells measured by BLI and
  • Figure 22B shows tumor volume as measured by caliper.
  • Figure 22C shows flow cytometry data for T cell accumulation in tumor and blood samples of a representative mouse.
  • Figure 22D shows percentage of human CD45+ cells in tumor.
  • Figure 22E shows percentage of human CD45+ cells in blood.
  • Figure 22F shows number of human CD45+ cells per tumor.
  • Figure 22G shows the number of human CD45+ cells per pL of blood.
  • Figure 22H shows the ratio of CD4+/CD8+ in TRuC+ cells in tumor.
  • Figure 221 shows the ratio of CD4+/CD8+ in TRuC+ cells in blood.
  • Figure 22 J shows the ratio of CD4+/CD8+ in TRuC+ cells of the initial infusion.
  • Figure 23A-23H is a series of graphs showing results of in vivo efficacy studies in a mouse tumor model.
  • Figure 23A shows tumor volume as measured by caliper.
  • Figure 23B shows percentage of human CD45+ cells in tumor.
  • Figure 23C shows percentage of human CD45+ cells in blood.
  • Figure 23D shows number of human CD45+ cells per tumor.
  • Figure 23E shows the number of human CD45+ cells per pL of blood.
  • Figure 23F shows the ratio of CD4+/CD8+ in TRuC+ cells in tumor.
  • Figure 23G shows the ratio of CD4+/CD8+ in TRuC+ cells in blood.
  • Figure 23H shows the ratio of CD4+/CD8+ in TRuC+ cells of the initial infusion.
  • Figures 24A-24D show graphs of quantification of T cell expansion (Figure 24A), CD4/CD8 ratios ( Figure 24B), and transduction efficiency (Round 1 - Figure 24C; Round 2 - Figure 24D) for T cells transduced with various TFP and/or IL- 15 constructs.
  • Figure 25 shows surface expression of the indicated construct in transduced T cells as determined by flow cytometry.
  • Figure 26 shows surface expression of the indicated construct in transduced T cells as determined by flow cytometry.
  • Figures 27A-27F show quantification of the differentiation state (Temra in Figure 27A, Naive in Figure 27B, Tcm in Figure 27C and Tem in Figure 27D) of CD4+ and CD8+ T cells transduced with the noted construct on day 10 post expansion.
  • Figure 27E and 27F show the slight decrease in Temra and slight increase in Tcm phenotypes in IL- 15 expressing transduced T cells, respectively.
  • Figures 28A-28C show quantification of IL-15 production by transduced T cells across three donors ( Figure 28A, 28B, and 28C each being from separate donors). The dotted line indicates the limit of detection for the assay.
  • Figures 29A and 29B show the results of a cytotoxicity assay wherein transduced T cells were cocultured with MSTO-MSLN cells (Figure 29A) or MSTO-MSLN-PDL1 cells ( Figure 29B).
  • Figures 30A-30D show the results of a cytokine response assay in MSTO-MSLN (Figure 30A and Figure 30C) or MSTO-MSLN-PDL1 (Figure 30B and Figure 30D) cells as measured by IFNy ( Figure 30A and Figure 30B) and IL-2 ( Figure 30C and Figure 30D).
  • Figures 31A-31D show cell number quantifications as determined by CD45+ ( Figure 31A and Figure 31 C) or VHH+ ( Figure 31B and Figure 31D) by FACs in a repeated stimulation assay conducted using transduced T cells and MSTO-MSLN cells ( Figure 31 A and Figure 31B) or MSTO-MSLN-PDL1 cells ( Figure 31C and Figure 31D).
  • Figure 32 shows cytokine release data from a repeated stimulation assay.
  • Figure 33 shows the differentiation state of transduced T cells from a repeated stimulation assay.
  • Flow cytometry plots are representative images from Day 4.
  • Figure 34A and Figure 34B show PD1 expression from a repeated stimulation assay conducted in MSTO-MSLN ( Figure 34A) or MSTO-MSLN-PDL1 ( Figure 34B) cells.
  • Figure 35A and Figure 35B show data from an antigen independent expansion (persistence) assay.
  • Figure 35A shows cell counts overtime and
  • Figure 35B shows the cell counts on the final day of the experiment (Day 10).
  • Figure 36A and Figure 36B show data from an antigen independent expansion (persistence) assay.
  • Figure 36A shows percent VHH+ cells in culture over time
  • Figure 36B shows percent VHH+ cells in culture on the final day of the experiment (Day 10).
  • Figure 37 shows quantifications of memory phenotypes of transduced T cells from an antigen independent expansion (persistence) assay.
  • Figure 38A and Figure 38B show data from an antigen independent expansion assay wherein PDL1- Fc was used to coat the bottom of the assay plate.
  • Figure 38A shows cell counts over time and Figure 38B shows cell counts on Day 10.
  • Figure 39A and Figure 39B show cell count data from an antigen independent expansion assay when exogenous cytokines IL-2 ( Figure 39A) or IL- 15 ( Figure 39B) were added.
  • Figures 40A-40D show data from an antigen independent expansion assay when exogenous cytokines IL-2 ( Figure 40A and Figure 40B) and 11-15 ( Figure 40C and Figure 40D) were added.
  • Figure 41 shows a schematic and related data proposing a hypothesis for the decreased expansion of T cells co-expressing IL- 15 in the presence of exogenous cytokines in an antigen independent expansion assay.
  • Figure 42 shows flow cytometry plots of CD 122 surface expression from transduced T cells on Day 4 of an antigen independent expansion assay.
  • Figure 43 shows tumor volume quantification over time in an in vivo efficacy study.
  • Figure 44 shows tumor volume quantification over time in an in vivo efficacy study split by treatment.
  • Figure 45 shows data from an in vivo efficacy study at Day 65 and post re-challenge (Day 65).
  • Figure 46 shows tumor volume quantifications over time after re-challenge (Day 65) split by treatment.
  • Figure 47 shows quantification of TCF7 across experimental conditions for transduced T cells derived from a single donor.
  • Figure 48 shows quantification of TCF7 across experimental conditions for transduced T cells derived from a second donor.
  • Figure 49 shows flow cytometry plots for CD8+ TCF7 (TCF-1) versus T-bet across experimental conditions and for transduced T cells derived from a single donor.
  • Figure 50 shows flow cytometry plots for CD8+ TCF7 (TCF-1) versus T-bet across experimental conditions and for transduced T cells derived from a second donor.
  • Figure 51 shows flow cytometry plots for CD8- TCF7 (TCF-1) versus T-bet across experimental conditions and for transduced T cells derived from a single donor.
  • Figure 52 shows flow cytometry plots for CD8+ TCF7 (TCF-1) versus T-bet across experimental conditions and for transduced T cells derived from a second donor.
  • Figure 53 shows flow cytometry plots for CD8+ TCF7 (TCF-1) versus Granzyme B across experimental conditions and for transduced T cells derived from a single donor.
  • Figure 54 shows flow cytometry plots for CD8+ TCF7 (TCF-1) versus Granzyme B across experimental conditions and for transduced T cells derived from a second donor.
  • Figure 55 shows flow cytometry plots for CD8- TCF7 (TCF-1) versus Granzyme B across experimental conditions and for transduced T cells derived from a single donor.
  • Figure 56 shows flow cytometry plots for CD8- TCF7 (TCF-1) versus Granzyme B across experimental conditions and for transduced T cells derived from a second donor.
  • Figure 57 shows data from an in vivo efficacy study. Tumors harvested from mice treated with transduced T cells were evaluated for CD45 expression and cell count.
  • Figure 58 shows data from an in vivo efficacy study. Flow cytometry plots showing the surface expression of VHH in tumor tissues of mice treated with transduced T cells are shown.
  • Figure 59 shows data from an in vivo efficacy study wherein Ki67 expression was assessed in tumor tissue as a measure of transduced T cell proliferation.
  • Figure 60 shows data from an in vivo efficacy study wherein Ki67 expression was assessed in tumor tissue as a measure of transduced CD8+ or CD4+ transduced T cell proliferation.
  • Figure 61 shows data from an in vivo efficacy study wherein CD4+ and CD8+ cell populations were measured by flow cytometry, quantified and plotted as a ratio in a histogram.
  • Figure 62 shows flow cytometry plots of inhibitory marker (PD-1 and LAG-3) expression in tumor tissue collected from mice treated with transduced T cells.
  • Figure 63 shows flow cytometry plots of inhibitory marker (PD-1 and TIGIT) expression in tumor tissue collected from mice treated with transduced T cells.
  • Figures 64A-64D show in vitro data for transduced T cells.
  • Figure 64A shows T cell expansion over a 10 day period.
  • Figure 64B shows flow cytometry plots measuring the surface presence of TC-210 and IL15Ra in transduced T cells.
  • Figure 64C shows flow cytometry plots for assessing memory phenotype by measuring CD45Ra and CCR7 surface expression in transduced T cells.
  • Figure 64D shows quantification of memory phenotypes in CD4+ or CD8+ transduced T cells.
  • Figures 65A-65C show data collected from in vitro studies of transduced T cells.
  • Figure 65A shows cytotoxicity and cytokine production after 24hr co-culture with MSTO-MSLN cells.
  • Figure 65B shows flow cytometry plots of surface expression of CD27 and TCF-1 after a 96hr activation assay.
  • Figure 65C shows flow cytometry plots of surface expression of TCF-1 and Granzyme B after a 96hr activation assay.
  • Figure 66 shows results of a persistence assay of transduced T cells grown under cytokine free culture conditions or cytokine (IL-2 or IL-15) supplemented culture conditions.
  • Figure 67 shows the results of a repetitive stimulation assay using transduced T cells.
  • Figure 68 shows data from an in vivo efficacy study of transduced T cells.
  • Figure 69 shows data from tumor and blood samples collected during an in vivo efficacy study of transduced T cells.
  • a recombinant nucleic acid molecule comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP TFP fusion protein
  • the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nu
  • a recombinant nucleic acid comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP TFP fusion protein
  • the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a
  • a cell comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP TFP fusion protein
  • the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleuk
  • a cell comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) wherein the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked, and a second nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • TCR T cell receptor
  • TFP T cell receptor
  • IL- 15 interleukin- 15 polypeptide or a fragment thereof in the cell
  • the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • IL-15Ra interleukin- 15 receptor alpha
  • the TFP comprises (a) a TCR subunit comprising (i) at least a portion of a TCR extracellular domain, and (ii) a TCR transmembrane domain, and (b) an antigen binding domain and wherein the TCR subunit and the antigen binding domain are operatively linked.
  • vectors comprising recombinant nucleic acid molecules described herein.
  • cells comprising the recombinant nucleic acid molecules described herein, the polypeptides described herein, or the vectors described herein.
  • a population of cells comprising the cells described herein.
  • a pharmaceutical composition comprising the cells described herein and a pharmaceutically acceptable carrier.
  • an element means one element or more than one element.
  • “about” can mean plus or minus less than 1 or 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, or greater than 30 percent, depending upon the situation and known or knowable by one skilled in the art.
  • subject or “subjects” or “individuals” may include, but are not limited to, mammals such as humans or non-human mammals, e.g., domesticated, agricultural or wild, animals, as well as birds, and aquatic animals.
  • “Patients” are subjects suffering from or at risk of developing a disease, disorder or condition or otherwise in need of the compositions and methods provided herein.
  • treating refers to any indicia of success in the treatment or amelioration of the disease or condition. Treating can include, for example, reducing, delaying or alleviating the severity of one or more symptoms of the disease or condition, or it can include reducing the frequency with which symptoms of a disease, defect, disorder, or adverse condition, and the like, are experienced by a patient.
  • treat or prevent is sometimes used herein to refer to a method that results in some level of treatment or amelioration of the disease or condition and contemplates a range of results directed to that end, including but not restricted to prevention of the condition entirely.
  • preventing refers to the prevention of the disease or condition, e.g. , tumor formation, in the patient. For example, if an individual at risk of developing a tumor or other form of cancer is treated with the methods of the present disclosure and does not later develop the tumor or other form of cancer, then the disease has been prevented, at least over a period of time, in that individual.
  • the disease or condition e.g. , tumor formation
  • a “therapeutically effective amount” is the amount of a composition or an active component thereof sufficient to provide a beneficial effect or to otherwise reduce a detrimental non-beneficial event to the individual to whom the composition is administered.
  • therapeutically effective dose herein is meant a dose that produces one or more desired or desirable (e.g. , beneficial) effects for which it is administered, such administration occurring one or more times over a given period of time. The exact dose will depend on the purpose of the treatment, and will be ascertainable by one skilled in the art using known techniques (see, e.g., Lieberman, Pharmaceutical Dosage Forms (vols. 1-3, 1992); Lloyd, The Art, Science and Technology of Pharmaceutical Compounding (1999); and Pickar, Dosage Calculations (1999))
  • a “T cell receptor (TCR) fusion protein” or “TFP” includes a recombinant polypeptide derived from the various polypeptides comprising the TCR that is generally capable of i) binding to a surface antigen on target cells and ii) interacting with other polypeptide components of the intact TCR complex, typically when co-located in or on the surface of a T cell.
  • TCR T cell receptor
  • TRuC TRuC
  • stimulation refers to a primary response induced by binding of a stimulatory domain or stimulatory molecule (e.g., a TCR/CD3 complex) with its cognate ligand thereby mediating a signal transduction event, such as, but not limited to, signal transduction via the TCR/CD3 complex.
  • a stimulatory domain or stimulatory molecule e.g., a TCR/CD3 complex
  • Stimulation can mediate altered expression of certain molecules, and/or reorganization of cytoskeletal structures, and the like.
  • the term “stimulatory molecule” or “stimulatory domain” refers to a molecule or portion thereof expressed by a T cell that provides the primary cytoplasmic signaling sequence(s) that regulate primary activation of the TCR complex in a stimulatory way for at least some aspect of the T cell signaling pathway.
  • the primary signal is initiated by, for instance, binding of a TCR/CD3 complex with an MHC molecule loaded with peptide, and which leads to mediation of a T cell response, including, but not limited to, proliferation, activation, differentiation, and the like.
  • a primary cytoplasmic signaling sequence (also referred to as a “primary signaling domain”) that acts in a stimulatory manner may contain a signaling motif which is known as immunoreceptor tyrosine-based activation motif or “IT AM”.
  • ITAM immunoreceptor tyrosine-based activation motif
  • Examples of an ITAM containing primary cytoplasmic signaling sequence that is of particular use in the invention includes, but is not limited to, those derived from TCR zeta, FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, CD278 (also known as “ICOS”) and CD66d.
  • the term “antigen presenting cell” or “APC” refers to an immune system cell such as an accessory cell (e.g., a B-cell, a dendritic cell, and the like) that displays a foreign antigen complexed with major histocompatibility complexes (MHC’s) on its surface.
  • T cells may recognize these complexes using their T cell receptors (TCRs).
  • TCRs T cell receptors
  • MHC Major histocompatibility complex
  • TCRs as part of peptide: MHC complex.
  • the MHC molecule may be an MHC class I or II molecule.
  • the complex may be on the surface of an antigen presenting cell, such as a dendritic cell or a B cell, or any other cell, including cancer cells, or it may be immobilized by, for example, coating on to a bead or plate.
  • HLA human leukocyte antigen system
  • MHC major histocompatibility complex
  • HLA class I antigens A, B & C
  • HLA class II antigens DP, DQ, & DR
  • HLA alleles A, B and C present peptides derived mainly from intracellular proteins, e.g., proteins expressed within the cell.
  • T cells undergo a positive selection step to ensure recognition of self MHCs followed by a negative step to remove T cells that bind too strongly to MHC which present selfantigens.
  • a positive selection step to ensure recognition of self MHCs
  • a negative step to remove T cells that bind too strongly to MHC which present selfantigens.
  • certain T cells and the TCRs they express will only recognize peptides presented by certain types of MHC molecules - i.e., those encoded by particular HLA alleles. This is known as HLA restriction.
  • HLA-A*0201 One HLA allele of interest is HLA-A*0201, which is expressed in the vast majority (>50%) of the Caucasian population. Accordingly, TCRs which bind WT1 peptides presented by MHC encoded by HLA- A*0201 (i.e., are HLA-A*0201 restricted) are advantageous since an immunotherapy making use of such TCRs will be suitable for treating a large proportion of the Caucasian population.
  • HLA-A alleles of interest are HLA-A*0101, HLA-A*2402, and HLA-A*0301.
  • intracellular signaling domain refers to an intracellular portion of a molecule.
  • the intracellular signaling domain generates a signal that promotes an immune effector function of the TFP containing cell, e.g, a modified T-T cell.
  • immune effector function e.g., in a modified T-T cell, include cytolytic activity and T helper cell activity, including the secretion of cytokines.
  • the intracellular signaling domain can comprise a primary intracellular signaling domain.
  • Exemplary primary intracellular signaling domains include those derived from the molecules responsible for primary stimulation, or antigen dependent simulation.
  • the intracellular signaling domain can comprise a costimulatory intracellular domain.
  • Exemplary costimulatory intracellular signaling domains include those derived from molecules responsible for costimulatory signals, or antigen independent stimulation.
  • a primary intracellular signaling domain can comprise an ITAM (“immunoreceptor tyrosine-based activation motif’).
  • ITAM containing primary cytoplasmic signaling sequences include, but are not limited to, those derived from CD3 zeta, FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, and CD66d DAP10 and DAP12.
  • costimulatory molecule refers to the cognate binding partner on a T cell that specifically binds with a costimulatory ligand, thereby mediating a costimulatory response by the T cell, such as, but not limited to, proliferation.
  • Costimulatory molecules are cell surface molecules other than antigen receptors or their ligands that are required for an efficient immune response.
  • Costimulatory molecules include but are not limited to an MHC class 1 molecule, BTLA and a Toll ligand receptor, as well as 0X40, CD2, CD27, CD28, CDS, ICAM-1, LFA-1 (CDl la/CD18) and 4-1BB (CD137).
  • a costimulatory intracellular signaling domain can be the intracellular portion of a costimulatory molecule.
  • 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, CD 160, B7-H3, and a ligand that specifically binds with CD83, and the like.
  • the intracellular signaling domain can comprise the entire intracellular portion, or the entire native intracellular signaling domain, of the molecule from which it is derived, or a functional fragment thereof.
  • 4- IBB refers to a member of the TNFR superfamily with an amino acid sequence provided as GenBank Acc. No.
  • AAA62478.2 or the equivalent residues from a non-human species, e.g., mouse, rodent, monkey, ape and the like; and a “4-1BB costimulatory domain” is defined as amino acid residues 214-255 of GenBank Acc. No. AAA62478.2, or the equivalent residues from a non-human species, e.g., mouse, rodent, monkey, ape and the like.
  • antibody refers to a protein, or polypeptide sequences 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 antigen binding domain, i.e., an 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 such as sdAb (either VL or VH), camelid VHH domains, and multi-specific antibodies formed from antibody fragments.
  • scFv refers to a fusion protein comprising at least one antibody fragment comprising a variable region of a light chain and at least one antibody fragment comprising a variable region of a heavy chain, wherein the light and heavy chain variable regions are contiguously linked via a short flexible polypeptide linker, and capable of being expressed as a single polypeptide chain, and wherein the scFv retains the specificity of the intact antibody from which it is derived.
  • “Heavy chain variable region” or “VH” with regard to an antibody refers to the fragment of the heavy chain that contains three CDRs interposed between flanking stretches known as framework regions, these framework regions are generally more highly conserved than the CDRs and form a scaffold to support the CDRs.
  • a camelid “VHH” domain is a heavy chain comprising a single variable antibody domain.
  • a scFv may have the VL and VH variable regions in either order, e.g., with respect to the N-terminal and C-terminal ends of the polypeptide, the scFv may comprise VL-linker-Vn or may comprise Vn-linker-VL.
  • the linker may comprise SEQ ID NO: 401.
  • the portion of the TFP composition of the disclosure comprising an antibody or antibody fragment thereof may exist in a variety of forms where the antigen binding domain is expressed as part of a contiguous polypeptide chain including, for example, a single domain antibody fragment (sdAb), a single chain antibody (scFv) derived from a murine, humanized or human antibody (Harlow et al., 1999, In: Using Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory Press, N.Y.; Harlow et al., 1989, In: Antibodies: A Laboratory Manual, Cold Spring Harbor, N.Y.; Houston et al., 1988, Proc. Natl. Acad. Sci.
  • sdAb single domain antibody fragment
  • scFv single chain antibody
  • the antigen binding domain of a TFP composition of the disclosure comprises an antibody fragment.
  • the TFP comprises an antibody fragment that comprises a scFv or a sdAb.
  • recombinant antibody refers to an antibody that is generated using recombinant DNA technology, such as, for example, an antibody expressed by a bacteriophage or yeast expression system.
  • the term should also be construed to mean an antibody which has been generated by the synthesis of a DNA molecule encoding the antibody and which DNA molecule expresses an antibody protein, or an amino acid sequence specifying the antibody, wherein the DNA or amino acid sequence has been obtained using recombinant DNA or amino acid sequence technology which is available and well known in the art.
  • antigen refers to a molecule that is capable of being bound specifically by an antibody, or otherwise provokes an immune response. This immune response may involve either antibody production, or the activation of specific immunologically-competent cells, or both.
  • 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.
  • 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.
  • CD 19 refers to the Cluster of Differentiation 19 protein, which is an antigenic determinant detectable on B cell leukemia precursor cells, other malignant B cells and most cells of the normal B cell lineage.
  • BCMA refers to the B-cell maturation antigen also known as tumor necrosis factor receptor superfamily member 17 (TNFRSF17) and Cluster of Differentiation 269 protein (CD269) is a protein that in humans is encoded by the TNFRSF17 gene.
  • TNFRSF17 is a cell surface receptor of the TNF receptor superfamily which recognizes B-cell activating factor (BAFF) (see, e.g., Laabi et al., EMBO 11 (11): 3897-904 (1992). This receptor is expressed in mature B lymphocytes and may be important for B-cell development and autoimmune response.
  • BAFF B-cell activating factor
  • CD 16 refers to a cluster of differentiation molecule found on the surface of natural killer cells, neutrophil polymorphonuclear leukocytes, monocytes and macrophages. CD16 has been identified as Fc receptors FcyRIIIa (CD16a) and FcyRIIIb (CD16b), which participate in signal transduction. CD 16 is a molecule of the immunoglobulin superfamily (IgSF) involved in antibody-dependent cellular cytotoxicity (ADCC).
  • IgSF immunoglobulin superfamily
  • NKG2D refers to a transmembrane protein belonging to the CD94/NKG2 family of C-type lectin-like receptors. In humans, NKG2D is expressed by NK cells, y5 T cells and CD8+ ot
  • MSLN Mesothelin
  • Tyrosine-protein kinase transmembrane receptor R0R1 also known as neurotrophic tyrosine kinase, receptor-related 1 (NTRKR1) is a member of the receptor tyrosine kinase-like orphan receptor (ROR) family. It plays a role in metastasis of cancer.
  • MUC16 also known as “mucin 16, cell-surface associated” or “ovarian cancer-related tumor marker CA125” is a membrane-tethered mucin that contains an extracellular domain at its amino terminus, a large tandem repeat domain, and a transmembrane domain with a short cytoplasmic domain. Products of this gene have been used as a marker for different cancers, with higher expression levels associated with poorer outcomes.
  • CD22 also known as sialic acid binding Ig-like lectin 2, SIGLEC-2, T cell surface antigen leu- 14, and B cell receptor CD22, is a protein that mediates B cell/B cell interactions, and is thought to be involved in the localization of B cells in lymphoid tissues, and is associated with diseases including refractory hematologic cancer and hairy cell leukemia.
  • M971 fully human anti-CD22 monoclonal antibody
  • Programmed cell death protein 1 also known as “PD-1” and CD279 (cluster of differentiation 279), is a protein on the surface of cells that has a role in regulating the immune system’s response to the cells of the human body by down-regulating the immune system and promoting self-tolerance by suppressing T cell inflammatory activity. This prevents autoimmune diseases, but it can also prevent the immune system from killing cancer cells.
  • PD-1 is an immune checkpoint and guards against autoimmunity through two mechanisms. First, it promotes apoptosis (programmed cell death) of antigen-specific T-cells in lymph nodes. Second, it reduces apoptosis in regulatory T cells (anti-inflammatory, suppressive T cells).
  • PD-1 is a cell surface receptor that belongs to the immunoglobulin superfamily and is expressed on T cells and pro-B cells. PD-1 binds two ligands, PD-L1 and PD-L2.
  • P-L1 Programmed death-ligand 1
  • PD-L1 is a 40kDa type 1 transmembrane protein that has been speculated to play a major role in suppressing the adaptive arm of immune system during particular events such as pregnancy, tissue allografts, autoimmune disease and other disease states such as hepatitis.
  • the adaptive immune system reacts to antigens that are associated with immune system activation by exogenous or endogenous danger signals.
  • clonal expansion of antigen-specific CD8+ T cells and/or CD4+ helper cells is propagated.
  • the binding of PD-L1 to the inhibitory checkpoint molecule PD-1 transmits an inhibitory signal based on interaction with phosphatases (SHP-1 or SHP-2) via Immunoreceptor Tyrosine- Based Switch Motif (ITSM) motif.
  • SHP-1 or SHP-2 phosphatases
  • IRS Immunoreceptor Tyrosine- Based Switch Motif
  • the “CD79a” and “CD79J3” genes encode proteins that make up the B lymphocyte antigen receptor, a multimeric complex that includes the antigen-specific component, surface immunoglobulin (Ig).
  • Ig surface immunoglobulin
  • Surface Ig non-covalently associates with two other proteins, Ig -alpha and Ig-beta (encoded by CD79a and its paralog CD79J3, respectively) which are necessary for expression and function of the B-cell antigen receptor.
  • Functional disruption of this complex can lead to, e.g., human B-cell chronic lymphocytic leukemias.
  • B cell activating factor is a cytokine that belongs to the tumor necrosis factor (TNF) ligand family. This cytokine is a ligand for receptors TNFRSF13B/TACI, TNFRSF17/BCMA, and TNFRSF13C/BAFF-R. This cytokine is expressed in B cell lineage cells, and acts as a potent B cell activator. It has been also shown to play an important role in the proliferation and differentiation of B cells.
  • TNF tumor necrosis factor
  • IL-15 refers to a pleiotropic cytokine that play important roles in maintenance and homeostatic expansion of various immune cells.
  • IL- 15 plays a critical role in the development of the NK lineage, and in survival, expansion, and function of NK cells.
  • Local secretion of pleiotropic cytokines such as IL- 15 in tumor microenvironment (TME) contributes to enhanced anti -tumor immunity.
  • IL- 15 is also involved in lymphocyte homeostasis as lymphocytes depend upon IL- 15 for survival or expansion.
  • IL-15 also plays multiple roles in peripheral innate and adaptive immune cell functions.
  • IL-15 is trans-presented by antigen presenting cells and has a crucial role in the induction of central memory T cell subset and enhanced cytolytic effectors. It aids in T cell survival by reducing activation induced cell death (AICD).
  • Human IL- 15 precursor protein has two known isoforms based on the length of signal peptide.
  • IL- 15 also referred to as IL-15-S48AA or IL-15LSP for “long signal peptide” has a 48 amino acid signal peptide and propeptide while IL-15-S21AA or IL-15SSP (for “short signal peptide”), which is expressed from an alternatively spliced mRNA has a 21 amino acid signal peptide and propeptide.
  • IL-15SSP has been shown not to be secreted, but rather stored intracellularly in the cytoplasm.
  • IL-15 signal peptide comprises amino acids 1-29 of IL-15 protein sequence. In some embodiments, IL-15 signal peptide comprises a sequence of SEQ ID NO: 374. In some embodiments, IL-15 comprises amino acids 30-162 of IL-15 protein sequence. In some embodiments, IL-15 comprises a sequence of SEQ ID NO: 375.
  • SEQ ID NO: 385 (IL-15 protein sequence) MRISKPHLRSISIQCYLCLLLNSHFLTEAGIHVFILGCFSAGLPKTEANWVNVISDLKKIEDLIQSMHID ATLYTESDVHPSCKVTAMKCFLLELQVISLESGDASIHDTVENLIILANNSLSSNGNVTESGCKECEEL EEKNIKEFLQSFVHIVQMFINTS
  • IL-15R refers to a receptor complex that IL-15 binds to and signals through.
  • IL-15R is composed of three subunits, IL-15 receptor alpha chain (“IL-15Ra” or CD215), IL- 2 receptor beta chain (“IL-2R[3” or CD 122) and IL-2 receptor gamma/the common gamma chain (“IL-2Ry/yc” or CD132).
  • Human IL-15Ra precursor protein has a 30 amino acid signal peptide, a 175 amino acid extracellular domain, a 23 amino acid single membrane -spanning transmembrane stretch, and a 39 amino acid cytoplasmic (or intracellular) domain and contains N- and O-linked glycosylation sites.
  • IL-15Ra contains a Sushi domain (amino acid 31-95) which is essential for IL-15 binding.
  • IL-15Ra also exists as a soluble form (sIL-15Ra).
  • sIL-15Ra is constitutively generated from the transmembrane receptor through a defined proteolytic cleavage, and this process can be enhanced by certain chemical agents, such as PMA.
  • the human sIL-15Ra may could prolong the half-life of IL- 15 or potentiate IL- 15 signaling through IL- 15 binding and IL-2R[3/yc heterodimer.
  • IL-15R shares subunits with IL-2Rthat contain the cytoplasmic motifs required for signal transduction, IL- 15 signaling has separate biological effects in vivo apart from many biological activities overlapping with IL-2 signaling due to IL-15Ra subunit that is unique to IL-15R, availability and concentration of IL-15, the kinetics and affinity of IL- 15 -IL- 15 Ra binding.
  • IL-15 binds to IL-15Ra specifically with high affinity, which then associates with a complex composed of IL-2RJ3 and IL-2Ry/yc subunits, expressed on the same cell (“cis-presentation”) or on a different cell (“transpresentation”).
  • the interaction between IL-15 and IL-15Ra is independent of the complex composed of IL- 2RP and IL-2Ry/yc subunits.
  • IL- 15 binding to the IL-2Rp/yc heterodimeric receptor induces JAK1 activation that phosphorylates STAT3 via the beta chain, and JAK3 activation that phosphorylates STAT5 via the gamma chain.
  • the IL-15/IL-15R interaction modulates not only T-cell development and homeostasis, but also in memory CD8+ T-cell and NK cell development, maintenance, expansion and activities.
  • IL-15Ra cytoplasmic (or intracellular) domain comprises amino acids 229-267 of IL-I5Ra protein. In some embodiments, IL-15Ra cytoplasmic (or intracellular) domain comprises a sequence of SEQ ID NO: 372. In some embodiments, IL-15Ra Sushi domain comprises amino acids 31-95 of IL-15Ra protein. In some embodiments, IL-15Ra Sushi domain comprises a sequence of SEQ ID NO: 382. In some embodiments, IL-15Ra comprises the transmembrane domain and the cytoplasmic (intracellular) domain of IL-15Ra protein. In some embodiments, IL-15Ra comprises amino acids 96-267 of IL-15Ra protein.
  • IL-15Ra comprises a sequence of SEQ ID NO: 383. In some embodiments, sIL-15Ra comprises amino acids 21-205 of IL-15Ra protein. In some embodiments, sIL-15Ra comprises a sequence of SEQ ID NO: 379. In some embodiments, IL-15Ra comprises a sequence of SEQ ID NO: 403.
  • SEQ ID NO: 386 (IL-15Ra protein sequence)
  • anti-tumor effect refers to a biological effect which can be manifested by various means, including but not limited to, e.g. , a decrease in tumor volume, a decrease in the number of tumor cells, a decrease in the number of metastases, an increase in life expectancy, decrease in tumor cell proliferation, decrease in tumor cell survival, or amelioration of various physiological symptoms associated with the cancerous condition.
  • An “anti-tumor effect” can also be manifested by the ability of the peptides, polynucleotides, cells and antibodies of the present disclosure in prevention of the occurrence of tumor in the first place.
  • autologous refers to any material derived from the same individual to whom it is later to be re-introduced into the individual.
  • allogeneic or, alternatively, “allogenic,” refers to any material derived from a different animal of the same species or different patient as the individual to whom the material is introduced. Two or more individuals are said to be allogeneic to one another when the genes at one or more loci are not identical. In some aspects, allogeneic material from individuals of the same species may be sufficiently unlike genetically to interact antigenically.
  • xenogeneic refers to a graft derived from an animal of a different species.
  • cancer refers to a disease characterized by the rapid and uncontrolled growth of aberrant cells. Cancer cells can spread locally or through the bloodstream and lymphatic system to other parts of the body. Examples of various cancers are described herein and include but are not limited to, breast cancer, prostate cancer, ovarian cancer, cervical cancer, skin cancer, pancreatic cancer, colorectal cancer, renal cancer, liver cancer, brain cancer, lymphoma, leukemia, lung cancer and the like.
  • the term “encoding” refers to the inherent property of specific sequences of nucleotides in a polynucleotide, such as a gene, a cDNA, or an mRNA, to serve as templates for synthesis of other polymers and macromolecules in biological processes having either a defined sequence of nucleotides (e.g., rRNA, tRNA and mRNA) or a defined sequence of amino acids and the biological properties resulting therefrom.
  • a gene, cDNA, or RNA encodes a protein if transcription and translation of mRNA corresponding to that gene produces the protein in a cell or other biological system.
  • Both the coding strand the nucleotide sequence of which is identical to the mRNA sequence and is usually provided in sequence listings, and the non-coding strand, used as the template for transcription of a gene or cDNA, can be referred to as encoding the protein or other product of that gene or cDNA.
  • nucleotide sequence encoding an amino acid sequence includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence.
  • the phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some versions contain one or more introns.
  • effective amount or therapeutically effective amount are used interchangeably herein, and refer to an amount of a compound, formulation, material, or composition, as described herein effective to achieve a particular biological or therapeutic result.
  • endogenous refers to any material from or produced inside an organism, cell, tissue or system.
  • exogenous refers to any material introduced from or produced outside an organism, cell, tissue or system.
  • expression refers to the transcription and/or translation of a particular nucleotide sequence driven by a promoter.
  • a functional disruption refers to a physical or biochemical change to a specific (e.g., target) nucleic acid (e.g., gene, RNA transcript, of protein encoded thereby) that prevents its normal expression and/or behavior in the cell.
  • a functional disruption refers to a modification of the gene via a gene editing method.
  • a functional disruption prevents expression of a target gene (e.g., an endogenous gene).
  • transfer vector refers to a composition of matter which comprises an isolated nucleic acid and which can be used to deliver the isolated nucleic acid to the interior of a cell.
  • Numerous vectors are known in the art including, but not limited to, linear polynucleotides, polynucleotides associated with ionic or amphiphilic compounds, plasmids, and viruses.
  • the term “transfer vector” includes an autonomously replicating plasmid or a virus.
  • the term should also be construed to further include non-plasmid and non-viral compounds which facilitate transfer of nucleic acid into cells, such as, for example, a polylysine compound, liposome, and the like.
  • Examples of viral transfer vectors include, but are not limited to, adenoviral vectors, adeno-associated virus vectors, retroviral vectors, lentiviral vectors, and the like.
  • expression vector refers to a vector comprising a recombinant polynucleotide comprising expression control sequences operatively linked to a nucleotide sequence to be expressed.
  • An expression vector comprises sufficient cis-acting elements for expression; other elements for expression can be supplied by the host cell or in an in vitro expression system.
  • Expression vectors include all those known in the art, including cosmids, plasmids (e.g, naked or contained in liposomes) and viruses (e.g., lentiviruses, retroviruses, adenoviruses, and adeno-associated viruses) that incorporate the recombinant polynucleotide.
  • lentivirus refers to a genus of the Retroviridae family. Lentiviruses are unique among the retroviruses in being able to infect non-dividing cells; they can deliver a significant amount of genetic information into the DNA of the host cell, so they are one of the most efficient methods of a gene delivery vector. HIV, SIV, and FIV are all examples of lentiviruses.
  • lentiviral vector refers to a vector derived from at least a portion of a lentivirus genome, including especially a self-inactivating lentiviral vector as provided in Milone et al., Mol. Ther. 17(8): 1453- 1464 (2009).
  • Other examples of lentivirus vectors that may be used in the clinic include but are not limited to, e.g., the LENTIVECTORTM gene delivery technology from Oxford BioMedica, the LENTIMAXTM vector system from Lentigen, and the like. Nonclinical types of lentiviral vectors are also available and would be known to one skilled in the art.
  • homologous refers to the subunit sequence identity between two polymeric molecules, e.g., between two nucleic acid molecules, such as, two DNA molecules or two RNA molecules, or between two polypeptide molecules.
  • a subunit position in both of the two molecules is occupied by the same monomeric subunit; e.g., if a position in each of two DNA molecules is occupied by adenine, then they are homologous or identical at that position.
  • the homology between two sequences is a direct function of the number of matching or homologous positions; e.g. , if half (e.g.
  • positions in two sequences are homologous, the two sequences are 50% homologous; if 90% of the positions (e.g., 9 of 10), are matched or homologous, the two sequences are 90% homologous.
  • “Humanized” forms of non-human (e.g., murine) antibodies are chimeric immunoglobulins, immunoglobulin chains or fragments thereof (such as Fv, Fab, Fab’, F(ab’)2 or other antigen-binding subsequences of antibodies) which contain minimal sequence derived from non-human immunoglobulin.
  • humanized antibodies and antibody fragments thereof are human immunoglobulins (recipient antibody or antibody fragment) in which residues from a complementary-determining region (CDR) of the recipient are replaced by residues from a CDR of a non-human species (donor antibody) such as mouse, rat or rabbit having the desired specificity, affinity, and capacity.
  • Fv framework region (FR) residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • a humanized antibody/antibody fragment can comprise residues which are found neither in the recipient antibody nor in the imported CDR or framework sequences. These modifications can further refine and optimize antibody or antibody fragment performance.
  • the humanized antibody or antibody fragment thereof will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the CDR regions correspond to those of a non-human immunoglobulin and all or a significant portion of the FR regions are those of a human immunoglobulin sequence.
  • the humanized antibody or antibody fragment can also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Human or “fully human” refers to an immunoglobulin, such as an antibody or antibody fragment, where the whole molecule is of human origin or consists of an amino acid sequence identical to a human form of the antibody or immunoglobulin.
  • isolated means altered or removed from the natural state.
  • a nucleic acid or a peptide naturally present in a living animal is not “isolated,” but the same nucleic acid or peptide partially or completely separated from the coexisting materials of its natural state is “isolated.”
  • An isolated nucleic acid or protein can exist in substantially purified form, or can exist in a non-native environment such as, for example, a host cell.
  • A refers to adenosine
  • C refers to cytosine
  • G refers to guanosine
  • T refers to thymidine
  • U refers to uridine.
  • conservative sequence modifications refers to amino acid modifications that do not significantly affect or alter the binding characteristics of the antibody or antibody fragment containing the amino acid sequence. Such conservative modifications include amino acid substitutions, additions and deletions. Modifications can be introduced into an antibody or antibody fragment of the present disclosure by standard techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis. Conservative amino acid substitutions are ones in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art.
  • amino acids with basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid, glutamic acid
  • uncharged polar side chains e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine, tryptophan
  • nonpolar side chains e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine
  • beta-branched side chains e.g., threonine, valine, isoleucine
  • aromatic side chains e.g., tyrosine, phenylalanine, tryptophan, histidine.
  • one or more amino acid residues within a TFP of the present disclosure can be replaced with other amino acid residues from the same side chain family and the altered TFP can be tested using the functional assays described herein.
  • operably linked refers to functional linkage between a regulatory sequence and a heterologous nucleic acid sequence resulting in expression of the latter.
  • a first nucleic acid sequence is operably linked with a second nucleic acid sequence when the first nucleic acid sequence is placed in a functional relationship with the second nucleic acid sequence.
  • a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence.
  • Operably linked DNA sequences can be contiguous with each other and, e.g., where necessary to join two protein coding regions, are in the same reading frame.
  • nucleic acid or “polynucleotide” refers to deoxyribonucleic acids (DNA) or ribonucleic acids (RNA) and polymers thereof in either single- or double -stranded form. Unless specifically limited, the term encompasses nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides.
  • nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions), alleles, orthologs, SNPs, and complementary sequences as well as the sequence explicitly indicated.
  • degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res.
  • peptide refers to a compound comprised of amino acid residues covalently linked by peptide bonds.
  • a protein or peptide must contain at least two amino acids, and no limitation is placed on the maximum number of amino acids that can comprise a protein’s or peptide’s sequence.
  • Polypeptides include any peptide or protein comprising two or more amino acids joined to each other by peptide bonds.
  • the term refers to both short chains, which also commonly are referred to in the art as peptides, oligopeptides and oligomers, for example, and to longer chains, which generally are referred to in the art as proteins, of which there are many types.
  • Polypeptides include, for example, biologically active fragments, substantially homologous polypeptides, oligopeptides, homodimers, heterodimers, variants of polypeptides, modified polypeptides, derivatives, analogs, fusion proteins, among others.
  • a polypeptide includes a natural peptide, a recombinant peptide, or a combination thereof.
  • promoter refers to a DNA sequence recognized by the transcription machinery of the cell, or introduced synthetic machinery, required to initiate the specific transcription of a polynucleotide sequence.
  • promoter/regulatory sequence refers to a nucleic acid sequence which is required for expression of a gene product operably linked to the promoter/regulatory sequence. In some instances, this sequence may be the core promoter sequence and in other instances, this sequence may also include an enhancer sequence and other regulatory elements which are required for expression of the gene product.
  • the promoter/regulatory sequence may, for example, be one which expresses the gene product in a tissue specific manner.
  • constitutive promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell under most or all physiological conditions of the cell.
  • inducible promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide which encodes or specifies a gene product, causes the gene product to be produced in a cell substantially only when an inducer which corresponds to the promoter is present in the cell.
  • tissue-specific promoter refers to a nucleotide sequence which, when operably linked with a polynucleotide encodes or specified by a gene, causes the gene product to be produced in a cell substantially only if the cell is a cell of the tissue type corresponding to the promoter.
  • linker and “flexible polypeptide linker” as used in the context of a scFv refers to a peptide linker that consists of amino acids such as glycine and/or serine residues used alone or in combination, to link variable heavy and variable light chain regions together.
  • the flexible polypeptide linkers include, but are not limited to, (Gly4Ser)4 or (Gly4Ser)3.
  • the linkers include multiple repeats of (Gly2Ser), (GlySer) or (Gly ⁇ Scr). Also included within the scope of the present disclosure are linkers described in WO2012/138475 (incorporated herein by reference).
  • a 5’ cap (also termed an RNA cap, an RNA 7-methylguanosine cap or an RNA m7G cap) is a modified guanine nucleotide that has been added to the “front” or 5 ’ end of a eukaryotic messenger RNA shortly after the start of transcription.
  • the 5’ cap consists of a terminal group which is linked to the first transcribed nucleotide. Its presence is critical for recognition by the ribosome and protection from Rnases. Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other.
  • RNA polymerase Shortly after the start of transcription, the 5’ end of the mRNA being synthesized is bound by a capsynthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the chemical reactions that are required for mRNA capping. Synthesis proceeds as a multi-step biochemical reaction.
  • the capping moiety can be modified to modulate functionality of mRNA such as its stability or efficiency of translation.
  • RNA preferably mRNA, which has been synthesized in vitro.
  • the in vitro transcribed RNA is generated from an in vitro transcription vector.
  • the in vitro transcription vector comprises a template that is used to generate the in vitro transcribed RNA.
  • a “poly(A)” is a series of adenosines attached by polyadenylation to the mRNA. In the preferred embodiment of a construct for transient expression, the polyA is between 50 and 5000, preferably greater than 64, more preferably greater than 100, most preferably greater than 300 or 400.
  • Poly(A) sequences can be modified chemically or enzymatically to modulate mRNA functionality such as localization, stability or efficiency of translation.
  • polyadenylation refers to the covalent linkage of a polyadenylyl moiety, or its modified variant, to a messenger RNA molecule. In eukaryotic organisms, most messenger RNA (mRNA) molecules are polyadenylated at the 3’ end.
  • the 3’ poly(A) tail is a long sequence of adenine nucleotides (often several hundred) added to the pre-mRNA through the action of an enzyme, polyadenylate polymerase.
  • the poly(A) tail is added onto transcripts that contain a specific sequence, the polyadenylation signal.
  • the poly(A) tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases.
  • Polyadenylation is also important fortranscription termination, export of the mRNA from the nucleus, and translation. Polyadenylation occurs in the nucleus immediately after transcription of DNA into RNA, but additionally can also occur later in the cytoplasm. After transcription has been terminated, the mRNA chain is cleaved through the action of an endonuclease complex associated with RNA polymerase. The cleavage site is usually characterized by the presence of the base sequence AAUAAA near the cleavage site.
  • transient refers to expression of a non-integrated transgene for a period of hours, days or weeks, wherein the period of time of expression is less than the period of time for expression of the gene if integrated into the genome or contained within a stable plasmid replicon in the host cell.
  • signal transduction pathway refers to the biochemical relationship between a variety of signal transduction molecules that play a role in the transmission of a signal from one portion of a cell to another portion of a cell.
  • cell surface receptor includes molecules and complexes of molecules capable of receiving a signal and transmitting signal across the membrane of a cell.
  • subject is intended to include living organisms in which an immune response can be elicited (e.g., mammals, human).
  • a “substantially purified” cell refers to a cell that is essentially free of other cell types.
  • a substantially purified cell also refers to a cell which has been separated from other cell types with which it is normally associated in its naturally occurring state.
  • a population of substantially purified cells refers to a homogenous population of cells. In other instances, this term refers simply to cell that have been separated from the cells with which they are naturally associated in their natural state.
  • the cells are cultured in vitro. In other aspects, the cells are not cultured in vitro.
  • terapéutica as used herein means a treatment.
  • a therapeutic effect is obtained by reduction, suppression, remission, or eradication of a disease state.
  • prophylaxis means the prevention of or protective treatment for a disease or disease state.
  • tumor antigen or “hyperproliferative disorder antigen” or “antigen associated with a hyperproliferative disorder” refers to antigens that are common to specific hyperproliferative disorders.
  • the hyperproliferative disorder antigens of the present disclosure are derived from, cancers including but not limited to primary or metastatic melanoma, thymoma, lymphoma, sarcoma, lung cancer, liver cancer, NHL, leukemias, uterine cancer, cervical cancer, bladder cancer, kidney cancer and adenocarcinomas such as breast cancer, prostate cancer, ovarian cancer, pancreatic cancer, and the like.
  • transfected or “transformed” or “transduced” refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell.
  • a “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid.
  • the cell includes the primary subject cell and its progeny.
  • the term “specifically binds,” refers to an antibody, an antibody fragment or a specific ligand, which recognizes and binds a cognate binding partner (e.g., CD 19) present in a sample, but which does not necessarily and substantially recognize or bind other molecules in the sample.
  • a cognate binding partner e.g., CD 19
  • the term “meganuclease” refers to an endonuclease that binds double-stranded DNA at a recognition sequence that is greater than 12 base pairs.
  • the recognition sequence for a meganuclease of the present disclosure is 22 base pairs.
  • a meganuclease can be an endonuclease that is derived from I-Crel and can refer to an engineered variant of I-Crel that has been modified relative to natural I-Crel with respect to, for example, DNA-binding specificity, DNA cleavage activity, DNA-binding affinity, or dimerization properties. Methods for producing such modified variants of I-Crel are known in the art (e.g.
  • a meganuclease as used herein binds to double-stranded DNA as a heterodimer or as a “single-chain meganuclease” in which a pair of DNA-binding domains are joined into a single polypeptide using a peptide linker.
  • the term “homing endonuclease” is synonymous with the term “meganuclease.”
  • Meganucleases of the present disclosure are substantially non-toxic when expressed in cells, particularly in human T cells, such that cells can be transfected and maintained at 37°C without observing deleterious effects on cell viability or significant reductions in meganuclease cleavage activity when measured using the methods described herein.
  • single-chain meganuclease refers to a polypeptide comprising a pair of nuclease subunits joined by a linker.
  • a single-chain meganuclease has the organization: N-terminal subunit - Linker - C-terminal subunit.
  • the two meganuclease subunits will generally be non-identical in amino acid sequence and will recognize non-identical DNA sequences.
  • single-chain meganucleases typically cleave pseudo-palindromic or non-palindromic recognition sequences.
  • a single-chain meganuclease may be referred to as a “single-chain heterodimer” or “single-chain heterodimeric meganuclease” although it is not, in fact, dimeric.
  • the term “meganuclease” can refer to a dimeric or singlechain meganuclease.
  • TALEN refers to an endonuclease comprising a DNA-binding domain comprising 16-22 TAL domain repeats fused to any portion of the Fokl nuclease domain.
  • the term “Compact TALEN” refers to an endonuclease comprising a DNA-binding domain with 16-22 TAL domain repeats fused in any orientation to any catalytically active portion of nuclease domain of the I-Tevl homing endonuclease.
  • CRISPR refers to a caspase-based endonuclease comprising a caspase, such as Cas9, and a guide RNA that directs DNA cleavage of the caspase by hybridizing to a recognition site in the genomic DNA.
  • megaTAL refers to a single-chain nuclease comprising a transcription activator-like effector (TALE) DNA binding domain with an engineered, sequence-specific homing endonuclease.
  • TALE transcription activator-like effector
  • T cell receptor and “T cell receptor complex” are used interchangeably to refer to a molecule found on the surface of T cells that is, in general, responsible for recognizing antigens.
  • the TCR comprises a heterodimer consisting of a TCR alpha and TCR beta chain in 95% of T cells, whereas 5% of T cells have TCRs consisting of TCR gamma and TCR delta chains.
  • the TCR further comprises one or more of CD3a, CD3y, and CD38.
  • the TCR comprises CD3a.
  • the TCR comprises CD3y.
  • the TCR comprises CD35.
  • the TCR comprises CD3 ⁇ .
  • the constant domain of human TCR alpha has a sequence of SEQ ID NO: 142.
  • the constant domain of human TCR alpha has an IgC domain having a sequence of SEQ ID NO: 143, a transmembrane domain having a sequence of SEQ ID NO: 144, and an intracellular domain having a sequence of SS.
  • the constant domain of murine TCR alpha has a sequence of SEQ ID NO: 147.
  • the constant domain of murine TCR alpha has a transmembrane domain having a sequence of SEQ ID NO: 144, and an intracellular domain having a sequence of SS.
  • the constant domain of human TCR beta has a sequence of SEQ ID NO: 148.
  • the constant domain of human TCR beta has an IgC domain having a sequence of SEQ ID NO: 149, a transmembrane domain having a sequence of SEQ ID NO: 150, and an intracellular domain having a sequence of SEQ ID NO: 151.
  • the constant domain of murine TCR beta has a sequence of SEQ ID NO: 152.
  • the constant domain of murine TCR beta has a transmembrane domain having a sequence of SEQ ID NO: 152, and an intracellular domain having a sequence of SEQ ID NO: 153.
  • the constant domain of human TCR delta has a sequence of SEQ ID NO: 243.
  • the constant domain of human TCR delta has an IgC domain having a sequence of SEQ ID NO: 265, a transmembrane domain having a sequence of SEQ ID NO: 158, and an intracellular domain having a sequence of L.
  • the constant domain of human TCR gamma has a sequence of SEQ ID NO: 21.
  • the constant domain of human TCR gamma has an IgC domain having a sequence of SEQ ID NO: 155, a transmembrane domain having a sequence of SEQ ID NO: 156, and an intracellular domain having a sequence of SEQ ID NO: 157.
  • human CD3 epsilon has a sequence of SEQ ID NO: 364. In some embodiments, human CD3 epsilon has an extracellular domain having a sequence of SEQ ID NO: 126, a transmembrane domain having a sequence of SEQ ID NO: 127, and an intracellular domain, e.g., an intracellular signaling domain, having a sequence of SEQ ID NO: 128. In some embodiments, human CD3 delta has a sequence of SEQ ID NO: 136. In some embodiments, human CD3 delta has an extracellular domain having a sequence of SEQ ID NO: 138, a transmembrane domain having a sequence of SEQ ID NO:
  • an intracellular domain e.g., an intracellular signaling domain, having a sequence of SEQ ID NO:
  • human CD3 gamma has a sequence of SEQ ID NO: 130. In some embodiments, human CD3 gamma has an extracellular domain having a sequence of SEQ ID NO: 132, a transmembrane domain having a sequence of SEQ ID NO: 133, and an intracellular domain, e.g., an intracellular signaling domain, having a sequence of SEQ ID NO: 134.
  • Ranges throughout this disclosure, various aspects of the present disclosure can be presented in a range format. It should be understood that the description in range format is merely for convenience and brevity and should not be construed as an inflexible limitation on the scope of the present disclosure. Accordingly, the description of a range should be considered to have specifically disclosed all the possible subranges as well as individual numerical values within that range. For example, description of a range such as from 1 to 6 should be considered to have specifically disclosed subranges such as from 1 to 3, from 1 to 4, from 1 to 5, from 2 to 4, from 2 to 6, from 3 to 6 etc., as well as individual numbers within that range, for example, 1, 2, 2.7, 3, 4, 5, 5.3, and 6.
  • a range such as 95-99% identity includes something with 95%, 96%, 97%, 98% or 99% identity, and includes subranges such as 96-99%, 96-98%, 96- 97%, 97-99%, 97-98% and 98-99% identity. This applies regardless of the breadth of the range.
  • compositions of matter and methods of use for the treatment of a disease such as cancer using modified T cells comprising a T cell receptors (TCR) fusion protein (TFP) in combination with an IL-15 and/or IL-15Ra polypeptide.
  • TCR T cell receptors
  • TFP T cell receptors
  • IL-15 and/or IL-15-Ra proteins when expressed in combination with the TCR fusion proteins, they can confer increased persistence, prolonged activity, and increased efficacy on the T cells for treating the malignancies described herein.
  • a “T cell receptor (TCR) fusion protein” or “TFP” includes a recombinant polypeptide derived from the various polypeptides comprising the TCR that is generally capable of i) binding to a surface antigen on target cells and ii) interacting with other polypeptide components of the intact TCR complex, typically when co-located in or on the surface of a T cell.
  • TFPs provide substantial benefits as compared to Chimeric Antigen Receptors.
  • CAR Chimeric Antigen Receptor
  • a CAR refers to a recombinant polypeptide comprising an extracellular antigen binding domain in the form of, e.g., a single domain antibody or scFv, a transmembrane domain, and cytoplasmic signaling domains (also referred to herein as “intracellular signaling domains”) comprising a functional signaling domain derived from a stimulatory molecule as defined below.
  • the central intracellular signaling domain of a CAR is derived from the CD3 zeta chain that is normally found associated with the TCR complex.
  • the CD3 zeta signaling domain can be fused with one or more functional signaling domains derived from at least one co-stimulatory molecule such as 4-1BB (i.e., CD137), CD27 and/or CD28.
  • T cell receptor (TCR) fusion proteins T cell receptor (TCR) [0239]
  • TFP T cell receptor
  • TFP T cell receptor
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises a binding domain, e.g., an antibody or antibody fragment, a ligand, or a ligand binding protein, wherein the sequence of the binding domain is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to a tumor associated antigen (TAA) wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • TAA tumor associated antigen
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to CD 19, e.g. , human CD 19, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to mesothelin, e.g. , human mesothelin, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to MUC16, e.g., human MUC16, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to CD20, e.g. , human CD20, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to CD70, e.g., human CD70, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to CD79B, e.g., human CD79B, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to HER2, e.g., human HER2, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to PSMA, e.g. , human PSMA, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to BCMA, e.g., human BCMA, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to ROR1, e.g., human ROR1, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to CD22, e.g., human CD22, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to GPC3, e.g., human GPC3, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to Nectin-4, e.g., human Nectin-4, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the present disclosure encompasses recombinant DNA constructs encoding TFPs, wherein the TFP comprises an antibody fragment that binds specifically to Trop-2, e.g., human Trop-2, wherein the sequence of the antibody fragment is contiguous with and in the same reading frame as a nucleic acid sequence encoding a TCR subunit or portion thereof.
  • the TFPs provided herein are able to associate with one or more endogenous (or alternatively, one or more exogenous, or a combination of endogenous and exogenous) TCR subunits in order to form a functional TCR complex.
  • the TFP of the present disclosure comprises a target-specific binding element otherwise referred to as an antigen binding domain.
  • the choice of moiety depends upon the type and number of target antigen that define the surface of a target cell.
  • the antigen binding domain may be chosen to recognize a target antigen that acts as a cell surface marker on target cells associated with a particular disease state.
  • examples of cell surface markers that may act as target antigens for the antigen binding domain in a TFP of the present disclosure include those associated with viral, bacterial and parasitic infections; autoimmune diseases; and cancerous diseases (e.g., malignant diseases).
  • the TFP -mediated T cell response can be directed to an antigen of interest by way of engineering an antigen-binding domain into the TFP that specifically binds a desired antigen.
  • the antigen binding domain can be any domain that binds to the antigen including but not limited to a monoclonal antibody, a polyclonal antibody, a recombinant antibody, a human antibody, a humanized antibody, and a functional fragment thereof, including but not limited to a single-domain antibody such as a heavy chain variable domain (VH), a light chain variable domain (V L ) and a variable domain (VHH) of a camelid derived nanobody, and to an alternative scaffold known in the art to function as antigen binding domain, such as a recombinant fibronectin domain, anticalin, D ARPIN and the like.
  • VH heavy chain variable domain
  • V L light chain variable domain
  • VHH variable domain
  • a natural or synthetic ligand specifically recognizing and binding the target antigen can be used as antigen binding domain for the TFP.
  • the antigen-binding domain comprises a murine, humanized or human antibody or an antibody fragment, or a murine antibody or antibody fragment.
  • the murine, humanized or human anti-TAA binding domain comprises one or more (e.g.
  • LC CDR1 light chain complementary determining region 1
  • LC CDR2 light chain complementary determining region 2
  • LC CDR3 light chain complementary determining region 3
  • HC CDR1 heavy chain complementary determining region 1
  • HC CDR2 heavy chain complementary determining region 2
  • HC CDR3 heavy chain complementary determining region 3
  • a murine, humanized or human anti-TAA binding domain comprising one or more, e.g., all three, LC CDRs and one or more, e.g., all three, HC CDRs.
  • the murine, humanized or human anti-CD19 binding domain comprises one or more (e.g., all three) heavy chain complementary determining region 1 (HC CDR1), heavy chain complementary determining region 2 (HC CDR2), and heavy chain complementary determining region 3 (HC CDR3) of a murine, humanized or human anti-TAA binding domain described herein, e.g., the murine, humanized or human anti-TAA binding domain has two variable heavy chain regions, each comprising a HC CDR1, a HC CDR2 and a HC CDR3 described herein.
  • the murine, humanized or human anti-TAA binding domain comprises a humanized or human light chain variable region described herein and/or a murine, humanized or human heavy chain variable region described herein.
  • the murine, humanized or human anti-TAA binding domain comprises a murine, humanized or human heavy chain variable region described herein, e.g., at least two murine, humanized or human heavy chain variable regions described herein.
  • the anti-TAA binding domain is a scFv comprising a light chain and a heavy chain of an amino acid sequence provided herein.
  • the anti-TAA binding domain (e.g., a scFv) comprises: a light chain variable region comprising an amino acid sequence having at least one, two or three modifications (e.g., substitutions) but not more than 30, 20 or 10 modifications (e.g., substitutions) of an amino acid sequence of a light chain variable region provided herein, or a sequence with 95-99% identity with an amino acid sequence provided herein; and/or a heavy chain variable region comprising an amino acid sequence having at least one, two or three modifications (e.g., substitutions) but not more than 30, 20 or 10 modifications (e.g., substitutions) of an amino acid sequence of a heavy chain variable region provided herein, or a sequence with 95-99% identity to an amino acid sequence provided herein.
  • a light chain variable region comprising an amino acid sequence having at least one, two or three modifications (e.g., substitutions) but not more than 30, 20 or 10 modifications (e.g., substitutions) of an amino acid sequence of a heavy chain variable region provided here
  • the murine, humanized or human anti-TAA binding domain is a scFv, and a light chain variable region comprising an amino acid sequence described herein, is attached to a heavy chain variable region comprising an amino acid sequence described herein, via a linker, e.g., a linker described herein.
  • the murine, humanized, or human anti-TAA binding domain includes a (Gly4-Ser) n linker, wherein n is 1, 2, 3, 4, 5, or 6, preferably 3 or 4.
  • the light chain variable region and heavy chain variable region of a scFv can be, e.g.
  • the linker sequence comprises a long linker (LL) sequence.
  • the linker sequence comprises a short linker (SL) sequence.
  • the antigen-binding domain comprises an anti-CD19 murine, humanized or human antibody or an antibody fragment, or a murine antibody or antibody fragment having a light chain CDR1 of SEQ ID NO: 73, a CDR2 of SEQ ID NO: 75, and a CDR3 of SEQ ID NO: 77 and a heavy chain CDR1 of SEQ ID NO:79, a CDR2 of SEQ ID NO:81, and a CDR3 of SEQ ID NO:83.
  • the anti-CD19 antibody is a murine scFv.
  • the anti-CD-19 antibody comprises a VL of SEQ ID NO: 85 and a VH of SEQ ID NO: 87
  • the antigen-binding domain comprises an anti-mesothelin murine, humanized or human single domain antibody or an antibody fragment having a CDR1 of SEQ ID NO:60, a CDR2 of SEQ ID NO: 61, and a CDR3 of SEQ ID NO: 62 or a CDR1 of SEQ ID NO: 63, a CDR2 of SEQ ID NO: 64, and a CDR3 of SEQ ID NO: 65 or a CDR1 of SEQ ID NO: 66, a CDR2 of SEQ ID NO: 67, and a CDR3 of SEQ ID NO:68.
  • the anti-mesothelin antibody has a variable domain of SEQ ID NO:69, SEQ ID NO:70, or SEQ ID NO:71.
  • the antigen-binding domain comprises an anti-CD70 murine, humanized or human single domain antibody or an antibody fragment having a CDR1 of SEQ ID NO: 88, a CDR2 of SEQ ID NO:89, and a CDR3 of SEQ ID NO:90, or a CDR1 of SEQ ID NO:92, a CDR2 of SEQ ID NO:93, and a CDR3 of SEQ ID NO: 94, or a CDR1 of SEQ ID NO: 96, a CDR2 of SEQ ID NO: 97, and a CDR3 of SEQ ID NO:98, or a CDR1 of SEQ ID NO: 100, a CDR2 of SEQ ID NO: 101, and a CDR3 of SEQ ID NO: 102, or a CDR1 of SEQ ID NO: 104, a CDR2 of SEQ ID NO: 105, and a CDR3 of SEQ ID NO: 106, or a CDR1
  • the antigen-binding domain comprises an anti-CD70 murine, humanized or human single domain antibody or antibody fragment have a CDR1 of SEQ ID NO: 392, a CDR2 of SEQ ID NO: 393, a CDR3 of SEQ ID NO: 394, or a CDR1 of SEQ ID NO: 396, a CDR2 of SEQ ID NO: 397, a CDR3 of SEQ ID NO: 398.
  • the antigen binding domain comprises CDR sequences selected from the group consisting of SEQ ID NO: 392-394 and 396-398.
  • the antigen binding domain comprises SEQ ID Nos: 392-394 and 396-398.
  • the antigen-binding domain comprises an anti-CD70 heavy chain variable domain region comprising SEQ ID NO: 392 as CDR1, a SEQ ID NO: 393 as CDR2, and SEQ ID NO: 394 as CDR3.
  • the antigen binding domain comprises an anti- CD70 light chain variable domain region comprising SEQ ID NO: 396 as CDR1, SEQ ID NO: 397 as CDR2, and SEQ ID NO: 398 as CDR3.
  • the antigen binding domain comprises an anti-CD70 heavy chain variable domain region comprising SEQ ID NO: 392 as CDR1, SEQ ID NO: 393 as CDR2, and SEQ ID NO: 394 as CDR3 and a light chain variable domain region comprising SEQ ID NO: 396 as CDR1, SEQ ID NO: 397 as CDR2, and SEQ ID NO: 398 as CDR3.
  • the antigen binding domain comprises SEQ ID NO: 395.
  • the antigen binding domain comprises SEQ ID NO: 399.
  • the antigen binding domain comprises SEQ ID NO: 395 and SEQ ID NO: 399.
  • the antigen binding domain comprises a linker sequence.
  • the antigen binding domain linker sequence comprises SEQ ID NO: 401. In some embodiments, the antigen binding domain comprises SEQ ID Nos: 399, 401, and 395. In some embodiments, the antigen binding domain comprises SEQ ID Nos: 399, 401, and 395 when read in 5’ to 3’ order.
  • a non-human antibody is humanized, where specific sequences or regions of the antibody are modified to increase similarity to an antibody naturally produced in a human or fragment thereof.
  • the antigen binding domain is humanized.
  • a humanized antibody can be produced using a variety of techniques known in the art, including but not limited to, CDR-grafting (see, e.g., European Patent No. EP 239,400; International Publication No. WO 91/09967; and U.S. Pat. Nos. 5,225,539, 5,530,101, and 5,585,089, each of which is incorporated herein in its entirety by reference), veneering or resurfacing (see, e.g. , European Patent Nos.
  • a humanized antibody or antibody fragment has one or more amino acid residues remaining in it from a source which is nonhuman. These nonhuman amino acid residues are often referred to as “import” residues, which are typically taken from an “import” variable domain.
  • humanized antibodies or antibody fragments comprise one or more CDRs from nonhuman immunoglobulin molecules and framework regions wherein the amino acid residues comprising the framework are derived completely or mostly from human germline.
  • Multiple techniques for humanization of antibodies or antibody fragments are well-known in the art and can essentially be performed following the method of Winter and co-workers (Jones et al., Nature, 321:522-525 (1986); Riechmann et al., Nature, 332:323-327 (1988); Verhoeyen et al., Science, 239: 1534- 1536 (1988)), by substituting rodent CDRs or CDR sequences for the corresponding sequences of a human antibody, i.e., CDR-grafting (EP 239,400; PCT Publication No.
  • WO 91/09967 and U.S. Pat. Nos. 4,816,567; 6,331,415; 5,225,539; 5,530,101; 5,585,089; 6,548,640, the contents of which are incorporated herein by reference in their entirety).
  • Humanized antibodies and antibody fragments substantially less than an intact human variable domain has been substituted by the corresponding sequence from a nonhuman species.
  • Humanized antibodies are often human antibodies in which some CDR residues and possibly some framework (FR) residues are substituted by residues from analogous sites in rodent antibodies.
  • Another method uses a particular framework derived from the consensus sequence of all human antibodies of a particular subgroup of light or heavy chains.
  • the same framework may be used for several different humanized antibodies (see, e.g., Nicholson et al., Mol. Immun. 34 (16-17): 1157-1165 (1997); Carter et al., Proc. Natl. Acad. Sci. USA, 89:4285 (1992); Presta et al., J. Immuno , 151:2623 (1993), the contents of which are incorporated herein by reference herein in their entirety).
  • the framework region e.g. , all four framework regions, of the heavy chain variable region are derived from a VH4-4-59 germline sequence.
  • the framework region can comprise, one, two, three, four or five modifications, e.g., substitutions, e.g., from the amino acid at the corresponding murine sequence.
  • the framework region e.g., all four framework regions of the light chain variable region are derived from a VK3- 1.25 germline sequence.
  • the framework region can comprise, one, two, three, four or five modifications, e.g., substitutions, e.g., from the amino acid at the corresponding murine sequence.
  • the portion of a TFP composition of the present disclosure that comprises an antibody fragment is humanized with retention of high affinity for the target antigen and other favorable biological properties.
  • humanized antibodies and antibody fragments are prepared by a process of analysis of the parental sequences and various conceptual humanized products using three-dimensional models of the parental and humanized sequences.
  • Three-dimensional immunoglobulin models are commonly available and are familiar to those skilled in the art.
  • Computer programs are available which illustrate and display probable three-dimensional conformational structures of selected candidate immunoglobulin sequences. Inspection of these displays permits analysis of the likely role of the residues in the functioning of the candidate immunoglobulin sequence, e.g., the analysis of residues that influence the ability of the candidate immunoglobulin to bind the target antigen.
  • FR residues can be selected and combined from the recipient and import sequences so that the desired antibody or antibody fragment characteristic, such as increased affinity for the target antigen, is achieved.
  • the CDR residues are directly and most substantially involved in influencing antigen binding.
  • a humanized antibody or antibody fragment may retain a similar antigenic specificity as the original antibody, e.g. , in the present disclosure, the ability to bind human a tumor associated antigen (TAA).
  • a humanized antibody or antibody fragment may have improved affinity and/or specificity of binding to, e.g., human CD 19, human BCMA, or another tumor associated antigen.
  • the binding domain is characterized by particular functional features or properties of an antibody or antibody fragment.
  • the portion of a TFP composition of the present disclosure that comprises an antigen binding domain specifically binds human CD19.
  • the antigen binding domain has the same or a similar binding specificity to human CD 19 as the FMC63 scFv described in Nicholson et al., Mol. Immun. 34 (16-17): 1157-1165 (1997).
  • the present disclosure relates to an antigen binding domain comprising an antibody or antibody fragment, wherein the antibody binding domain specifically binds to a CD 19 or BCMA protein or fragment thereof, wherein the antibody or antibody fragment comprises a variable light chain and/or a variable heavy chain that includes an amino acid sequence provided herein.
  • the scFv is contiguous with and in the same reading frame as a leader sequence.
  • the anti -tumor-associated antigen binding domain is a fragment, e.g., a single chain variable fragment (scFv).
  • the anti-TAA binding domain is a Fv, a Fab, a (Fab’)2, or a bi- functional (e.g., bi-specific) hybrid antibody (e.g., Lanzavecchia et al., Eur. J. Immunol. 17, 105 (1987)).
  • the antibodies and fragments thereof of the present disclosure binds a CD 19 protein with wild-type or enhanced affinity.
  • the anti-TAA binding domain comprises a single domain antibody (sdAb or VHH).
  • a target antigen e.g., CD 19, BCMA or any target antigen described elsewhere herein for targets of fusion moiety binding domains
  • the method comprising providing by way of addition, deletion, substitution or insertion of one or more amino acids in the amino
  • VH domains and scFvs can be prepared according to method known in the art (see, for example, Bird et al., (1988) Science 242:423-426 and Huston et al., (1988) Proc. Natl. Acad. Set. USA 85:5879-5883).
  • scFv molecules can be produced by linking VH and VL regions together using flexible polypeptide linkers.
  • the scFv molecules comprise a linker (e.g., a Ser-Gly linker) with an optimized length and/or amino acid composition. The linker length can greatly affect how the variable regions of a scFv fold and interact.
  • the linker sequence comprises a linker sequence.
  • linker orientation and size see, e.g., Hollinger et al., 1993 Proc Natl Acad. Sci. U.S.A. 90:6444-6448, U.S. Patent Application Publication Nos. 2005/0100543, 2005/0175606, 2007/0014794, and PCT publication Nos. W02006/020258 and W02007/024715, each of which is incorporated herein by reference.
  • An scFv can comprise a linker of about 10, 11, 12, 13, 14, 15 or greater than 15 residues between its VL and VH regions.
  • the linker sequence may comprise any naturally occurring amino acid.
  • the linker sequence comprises amino acids glycine and serine.
  • the linker sequence comprises sets of glycine and serine repeats such as (Gly4Ser) n , where n is a positive integer equal to or greater than 1.
  • the linker can be (Gly4Ser)4 or (Gly4Ser)3. Variation in the linker length may retain or enhance activity, giving rise to superior efficacy in activity studies.
  • a tumor associated antigen binding domain e.g., scFv molecules (e.g., soluble scFv)
  • scFv molecules e.g., soluble scFv
  • biophysical properties e.g., thermal stability
  • the humanized or human scFv has a thermal stability that is greater than about 0.
  • the improved thermal stability of the anti-TAA binding domain e.g., scFv is subsequently conferred to the entire TAA-TFP construct, leading to improved therapeutic properties of the anti-TAA TFP construct.
  • the thermal stability of the binding domain e.g. , scFv or sdAb, can be improved by at least about 2 °C or 3 °C as compared to a conventional antibody.
  • the binding domain has a 1 °C improved thermal stability as compared to a conventional antibody.
  • the binding domain has a 2 °C improved thermal stability as compared to a conventional antibody.
  • the scFv has a 4 °C, 5 °C, 6 °C, 7 °C, 8 °C, 9 °C, 10 °C, 11 °C, 12 °C, 13 °C, 14 °C, or 15 °C improved thermal stability as compared to a conventional antibody. Comparisons can be made, for example, between the scFv molecules disclosed herein and scFv molecules or Fab fragments of an antibody from which the scFv VH and VL were derived. Thermal stability can be measured using methods known in the art. For example, in one embodiment, TM can be measured. Methods for measuring TM and other methods of determining protein stability are described in more detail below.
  • the binding domain e.g., a scFv or sdAb, comprises at least one mutation arising from the humanization process such that the mutated scFv confers improved stability to the anti-TAA TFP construct.
  • the anti-TAA binding domain e.g., scFv or sdAb
  • the anti-TAA binding domain comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 mutations arising from the humanization process such that the mutated scFv or sdAb confers improved stability to the TAA-TFP construct.
  • the antigen binding domain of the TFP comprises an amino acid sequence that is homologous to an antigen binding domain amino acid sequence described herein, and the antigen binding domain retains the desired functional properties of the anti-tumor-associated antigen antibody fragments described herein.
  • the TFP composition of the present disclosure comprises an antibody fragment.
  • that antibody fragment comprises a scFv.
  • the antigen binding domain of the TFP is engineered by modifying one or more amino acids within one or both variable regions (e.g. , VH and/or VL), for example within one or more CDR regions and/or within one or more framework regions.
  • the TFP composition of the present disclosure comprises an antibody fragment.
  • that antibody fragment comprises a scFv.
  • the antibody or antibody fragment of the present disclosure may further be modified such that they vary in amino acid sequence (e.g., from wild-type), but not in desired activity.
  • additional nucleotide substitutions leading to amino acid substitutions at “non-essential” amino acid residues may be made to the protein.
  • a nonessential amino acid residue in a molecule may be replaced with another amino acid residue from the same side chain family.
  • a string of amino acids can be replaced with a structurally similar string that differs in order and/or composition of side chain family members, e.g., a conservative substitution, in which an amino acid residue is replaced with an amino acid residue having a similar side chain, may be made.
  • Families of amino acid residues having similar side chains have been defined in the art, including basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta-branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine).
  • basic side chains e.g., lysine, arginine, histidine
  • acidic side chains e.g., aspartic acid
  • Percent identity in the context of two or more nucleic acids or polypeptide sequences refers to two or more sequences that are the same. Two sequences are “substantially identical” if two sequences have a specified percentage of amino acid residues or nucleotides that are the same (e.g., 60% identity, optionally 70%, 71% , 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity over a specified region, or, when not specified, over the entire sequence), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection.
  • the identity exists over a region that is at least about 50 nucleotides (or 10 amino acids) in length, or more preferably over a region that is 100 to 500 or 1000 or more nucleotides (or 20, 50, 200 or more amino acids) in length.
  • sequence comparison typically one sequence acts as a reference sequence, to which test sequences are compared.
  • test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated.
  • sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters. Methods of alignment of sequences for comparison are well known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman, (1970) Adv. Appl. Math.
  • BLAST and BLAST 2.0 algorithms Two examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., (1977) Nuc. Acids Res. 25:3389-3402; and Altschul et al., (1990) J. Mol. Biol. 215:403-410, respectively.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information.
  • the present disclosure contemplates modifications of the starting antibody or fragment (e.g., scFv) amino acid sequence that generate functionally equivalent molecules.
  • the VH or VL of a binding domain, e.g., scFv, comprised in the TFP can be modified to retain at least about 70%, 71%.
  • the present disclosure contemplates modifications of the entire TFP construct, e.g., modifications in one or more amino acid sequences of the various domains of the TFP construct in order to generate functionally equivalent molecules.
  • the TFP construct can be modified to retain at least about 70%, 71%. 72%.
  • the extracellular domain may be derived either from a natural or from a recombinant source. Where the source is natural, the domain may be derived from any protein, but in particular a membrane-bound or transmembrane protein. In one aspect the extracellular domain is capable of associating with the transmembrane domain.
  • An extracellular domain of particular use in this present disclosure may include at least the extracellular region(s) of e.g.
  • the extracellular domain is a TCR extracellular domain.
  • the TCR extracellular domain comprises an extracellular domain or portion thereof of a protein selected from the group consisting of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, a CD3 delta TCR subunit, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR extracellular domain comprises an extracellular domain or portion thereof of a TCR alpha chain, a TCR beta chain, a TCR delta chain, or a TCR gamma chain.
  • the TCR extracellular domain comprises an IgC domain of a TCR alpha chain, a TCR beta chain, a TCR delta chain, or a TCR gamma chain.
  • the extracellular domain comprises, or comprises at least 5, 6, 7, 8, 9, 10, 11,
  • the extracellular domain comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding the extracellular domain of a TCR alpha chain, a TCR beta chain, a TCR delta chain, or a TCR gamma chain.
  • the extracellular domain comprises a sequence encoding the extracellular domain of a TCR alpha chain, a TCR beta chain, a TCR delta chain, or a TCR gamma chain having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more amino acids at the N- or C-terminus or at both the N- and C- terminus.
  • the extracellular domain comprises, or comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40,
  • the extracellular domain comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding an IgC domain of TCR alpha, a TCR beta, a TCR delta, or a TCR gamma.
  • the extracellular domain comprises a sequence encoding an IgC domain of TCR alpha, TCR beta, TCR delta, or TCR gamma having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more amino acids at the N- or C-terminus or at both the N- and C-terminus.
  • the extracellular domain comprises, or comprises at least 5, 6, 7, 8, 9, 10, 11,
  • the extracellular domain comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding the extracellular domain of a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit.
  • the extracellular domain comprises a sequence encoding the extracellular domain of a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more amino acids at the N- or C-terminus or at both the N- and C-terminus.
  • the extracellular domain can be a TCR extracellular domain.
  • the TCR extracellular domain can be derived from a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit or a CD3 delta TCR subunit.
  • the extracellular domain can be a full-length TCR extracellular domain or fragment (e.g., functional fragment) thereof.
  • the extracellular domain can comprise a variable domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the extracellular domain can comprise a variable domain and a constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain. In some cases, the extracellular domain may not comprise a variable domain.
  • the extracellular domain can comprise a constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the extracellular domain can comprise a full-length constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the extracellular domain can comprise a fragment (e.g., functional fragment) of the full-length constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the extracellular domain can comprise at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of the constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain described herein can be derived from various species.
  • the TCR chain can be a murine or human TCR chain.
  • the extracellular domain can comprise a constant domain of a murine TCR alpha chain, a murine TCR beta chain, a human TCR gamma chain or a human TCR delta chain.
  • a TFP sequence contains an extracellular domain and a transmembrane domain encoded by a single genomic sequence.
  • a TFP can be designed to comprise a transmembrane domain that is heterologous to the extracellular domain of the TFP.
  • a transmembrane domain can include one or more additional amino acids adjacent to the transmembrane region, e.g.
  • one or more amino acid associated with the extracellular region of the protein from which the transmembrane was derived e.g., at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more amino acids of the extracellular region
  • one or more additional amino acids associated with the intracellular region of the protein from which the transmembrane protein is derived e.g., 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, or more amino acids of the intracellular region.
  • the transmembrane domain can include at least 30, 35, 40, 45, 50, 55, 60 or more amino acids of the extracellular region.
  • the transmembrane domain can include at least 30, 35, 40, 45, 50, 55, 60 or more amino acids of the intracellular region.
  • the transmembrane domain is one that is associated with one of the other domains of the TFP is used.
  • the transmembrane domain can be selected or modified by amino acid substitution to avoid binding of such domains to the transmembrane domains of the same or different surface membrane proteins, e.g., to minimize interactions with other members of the receptor complex.
  • the transmembrane domain is capable of homodimerization with another TFP on the TFP-T cell surface.
  • the amino acid sequence of the transmembrane domain may be modified or substituted so as to minimize interactions with the binding domains of the native binding partner present in the same TFP.
  • the transmembrane domain may be derived either from a natural or from a recombinant source. Where the source is natural, the domain may be derived from any membrane-bound or transmembrane protein. In one aspect the transmembrane domain is capable of signaling to the intracellular domain(s) whenever the TFP has bound to a target.
  • the TCR-integrating subunit comprises a transmembrane domain comprising a transmembrane domain of a protein selected from the group consisting of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a TCR zeta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, a CD3 delta TCR subunit, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD28, CD37, CD64, CD80, CD86, CD134, CD137, CD154, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the transmembrane domain comprises, or comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more consecutive amino acid residues of the transmembrane domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit.
  • the transmembrane domain comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding the transmembrane domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit.
  • the transmembrane domain comprises a sequence encoding the transmembrane domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more amino acids at the N- or C-terminus or at both the N- and C-terminus.
  • the transmembrane domain can be attached to the extracellular region of the TFP, e.g. , the antigen binding domain of the TFP, via a hinge, e.g. , a hinge from a human protein.
  • a hinge e.g. , a hinge from a human protein.
  • the hinge can be a human immunoglobulin (Ig) hinge, e.g., an IgG4 hinge, or a CD8a hinge.
  • a short oligo- or polypeptide linker may form the linkage between the binding element and the TCR extracellular domain of the TFP.
  • a glycine-serine doublet provides a particularly suitable linker.
  • the linker may be at least about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, or more in length.
  • the linker comprises the amino acid sequence of GGGGSGGGGS or a sequence (GGGGS)x or (G4S) n , wherein X or n is 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more.
  • X or n is an integer from 1 to 10.
  • X or n is an integer from 1 to 4. In some embodiments, X or n is 2. In some embodiments, X or n is 4. In some embodiments, the linker is encoded by a nucleotide sequence of GGTGGCGGAGGTTCTGGAGGTGGAGGTTCC.
  • a linker sequence may comprise SEQ ID NO: 387. In some embodiments, the linker sequence may comprise SEQ ID NO: 388. In some embodiments, the linker sequence may comprise SEQ ID NO: 378. In some embodiments, the linker sequence may comprise SEQ ID NO: 405. In some embodiments, the linker sequence may comprise SEQ ID NO: 23. In some embodiments, the linker sequence may comprise SEQ ID NO: 365. In some embodiments, the linker sequence may comprise SEQ ID NO: 401.
  • the cytoplasmic domain of the TFP can include an intracellular domain.
  • the intracellular domain is from CD3 gamma, CD3 delta, CD3 epsilon, TCR alpha, TCR beta, TCR gamma, or TCR delta.
  • the intracellular domain comprises a signaling domain, if the TFP contains CD3 gamma, delta or epsilon polypeptides; TCR alpha, TCR beta, TCR gamma, and TCR delta subunits generally have short (e.g., 1-19 amino acids in length) intracellular domains and are generally lacking in a signaling domain.
  • An intracellular signaling domain is generally responsible for activation of at least one of the normal effector functions of the immune cell in which the TFP has been introduced. While the intracellular domains of TCR alpha, TCR beta, TCR gamma, and TCR delta do not have signaling domains, they are able to recruit proteins having a primary intracellular signaling domain described herein, e.g., CD3 zeta, which functions as an intracellular signaling domain.
  • effector function refers to a specialized function of a cell. Effector function of a T cell, for example, may be cytolytic activity or helper activity including the secretion of cytokines.
  • intracellular signaling domain refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function. While usually the entire intracellular signaling domain can be employed, in many cases it is not necessary to use the entire chain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion may be used in place of the intact chain as long as it transduces the effector function signal.
  • intracellular signaling domain is thus meant to include any truncated portion of the intracellular signaling domain sufficient to transduce the effector function signal.
  • intracellular domains for use in the TFP of the present disclosure include the cytoplasmic sequences of the T cell receptor (TCR) and co-receptors that are able to act in concert to initiate signal transduction following antigen receptor engagement, as well as any derivative or variant of these sequences and any recombinant sequence that has the same functional capability.
  • the intracellular domain comprises the intracellular domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit.
  • the intracellular domain comprises, or comprises at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, or 19 or more consecutive amino acid residues of the intracellular domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, or a TCR delta chain.
  • the intracellular domain comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding the intracellular domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, or a TCR delta chain.
  • the transmembrane domain comprises a sequence encoding the intracellular domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, or a TCR delta chain having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more amino acids at the N- or C-terminus or at both the N- and C-terminus.
  • the intracellular domain comprises, or comprises at least 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, or 62 or more consecutive amino acid residues of the intracellular domain of a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit.
  • the intracellular domain comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding the intracellular domain of a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit.
  • the intracellular domain comprises a sequence encoding the intracellular domain of a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, or a CD3 delta TCR subunit having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more amino acids at the N- or C-terminus or at both the N- and C-terminus.
  • naive T cell activation can be said to be mediated by two distinct classes of cytoplasmic signaling sequences: those that initiate antigen-dependent primary activation through the TCR (primary intracellular signaling domains) and those that act in an antigenindependent manner to provide a secondary or costimulatory signal (secondary cytoplasmic domain, e.g. , a costimulatory domain).
  • primary intracellular signaling domains those that initiate antigen-dependent primary activation through the TCR
  • secondary cytoplasmic domain e.g. , a costimulatory domain
  • a primary signaling domain regulates primary activation of the TCR complex either in a stimulatory way, or in an inhibitory way.
  • Primary intracellular signaling domains that act in a stimulatory manner may contain signaling motifs which are known as immunoreceptor tyrosine-based activation motifs (ITAMs).
  • ITAMs containing primary intracellular signaling domains include those of CD3 zeta, FcR gamma, FcR beta, CD3 gamma, CD3 delta, CD3 epsilon, CD5, CD22, CD79a, CD79b, and CD66d.
  • a TFP of the present disclosure comprises an intracellular signaling domain, e.g., a primary signaling domain of CD3-epsilon.
  • a primary signaling domain comprises a modified ITAM domain, e.g. , a mutated ITAM domain which has altered (e.g., increased or decreased) activity as compared to the native ITAM domain.
  • a primary signaling domain comprises a modified ITAM-containing primary intracellular signaling domain, e.g., an optimized and/or truncated ITAM-containing primary intracellular signaling domain.
  • a primary signaling domain comprises one, two, three, four or more ITAM motifs.
  • the intracellular signaling domain of the TFP can comprise a CD3 signaling domain, e. g; CD3 epsilon, CD3 delta, CD3 gamma, or CD3 zeta, by itself or it can be combined with any other desired intracellular signaling domain(s) useful in the context of a TFP of the present disclosure.
  • the intracellular signaling domain of the TFP can comprise a CD3 epsilon chain portion and a costimulatory signaling domain.
  • the costimulatory signaling domain refers to a portion of the TFP comprising the intracellular domain of a costimulatory molecule.
  • a costimulatory molecule is a cell surface molecule other than an antigen receptor or its ligands that is required for an efficient response of lymphocytes to an antigen.
  • examples of such molecules include CD27, CD28, 4-1BB (CD137), 0X40, CD30, CD40, PD-1, ICOS, lymphocyte function-associated antigen-1 (LFA-1), CD2, CD7, LIGHT, NKG2C, B7-H3, and a ligand that specifically binds with CD83, and the like.
  • CD27 costimulation has been demonstrated to enhance expansion, effector function, and survival of human TFP-T cells in vitro and augments human T cell persistence and antitumor activity in vivo (Song et al., Blood. 2012; 119(3):696-706).
  • the intracellular signaling sequences within the cytoplasmic portion of the TFP of the present disclosure may be linked to each other in a random or specified order.
  • a short oligo- or polypeptide linker for example, between 2 and 10 amino acids (e.g., , 3, 4, 5, 6, 7, 8, 9, or 10 amino acids) in length may form the linkage between intracellular signaling sequences.
  • a glycine -serine doublet can be used as a suitable linker.
  • a single amino acid e.g., an alanine, a glycine, can be used as a suitable linker.
  • the TFPs described herein may comprise a TCR extracellular domain, a TCR transmembrane domain, and a TCR intracellular domain, wherein at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain are from the same TCR subunit.
  • at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from TCR alpha.
  • at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from TCR beta.
  • At least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from TCR gamma. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from TCR delta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from CD3 epsilon. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from CD3 delta. In some embodiments, at least two of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from CD3 gamma.
  • the TFPs described herein may comprise a TCR extracellular domain, a TCR transmembrane domain, and a TCR intracellular domain, wherein all three of the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from the same TCR subunit.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from CD3 epsilon.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from CD3 delta.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain can be from CD3 gamma.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain may comprise the constant domain of TCR alpha.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain may comprise the constant domain of TCR beta.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain may comprise the constant domain of TCR gamma.
  • the TCR extracellular domain, the TCR transmembrane domain, and the TCR intracellular domain may comprise the constant domain of TCR delta.
  • the constant domain of TCR alpha or the constant domain of TCR beta may be murine.
  • the TFP -expressing cell described herein can further comprise a second TFP, e.g. , a second TFP that includes a different antigen binding domain, e.g., to the same target (e.g., MSLN) or a different target (e.g., CD70, CD19, or MUC16).
  • the antigen binding domains of the different TFPs can be such that the antigen binding domains do not interact with one another.
  • a cell expressing a first and second TFP can have an antigen binding domain of the first TFP, e.g. , as a fragment, e.g. , a scFv, that does not form an association with the antigen binding domain of the second TFP, e.g. , the antigen binding domain of the second TFP is a VHH.
  • the TFP-expressing cells described herein can further express another agent, for example, an agent that can enhance longevity or activity of TFP-expressing cells described herein.
  • the agent is a cytokine such as a pleiotropic cytokine that plays important roles in maintenance and homeostatic expansion of immune cells.
  • local secretion of a pleiotropic cytokine in tumor microenvironment (TME) can contribute to enhanced anti-tumor immunity.
  • the agent activates a cytokine signaling.
  • the agent activates interleukin- 15 (IL-15) signaling.
  • the agent comprises interleukin- 15 (IL-15) and/or interleukin- 15 receptor (IL-15R).
  • the IL-15R is an IL-15R alpha (IL-15Ra) subunit.
  • the present disclosure provides compositions and methods to enhance TFP-T cell persistence by engineering constitutive IL- 15 signaling.
  • the increased TFP persistence can lead to enhanced duration of response (DOR) in patients.
  • IL-15 may have a crucial role in the maintenance of naive and central memory CD8+ T cells and enhancing their survival by reducing activation induced cell death (AICD).
  • IL-15 expressing TFP-T cells in some cases, can show increased in vitro and in vivo persistence.
  • IL- 15 or variants thereof can be a T cell intrinsic enhancement so that they can be used for TFPs targeting various tumor types.
  • various constructs containing the IL-15 or IL-15R alpha or fragment thereof can be referred to as enhancements.
  • the T cells engineered with a TFP can show high transduction efficiency and co-expression.
  • T cells engineered with anti-mesothelin TFP and IL- 15 enhancements described herein can show high transduction efficiency and co -expression.
  • T cells engineered with anti-CD70 TFP and IL-15 enhancements described herein can show high transduction efficiency and co-expression.
  • a cell e.g., a TFP-T cell or transduced T cell
  • a cell described herein can express a IL- 15 polypeptide or fragment thereof or a IL-15R subunit or fragment thereof constitutively.
  • the present disclosure encompasses recombinant nucleic acid molecules encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof.
  • the IL- 15 polypeptide or a fragment thereof comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61,
  • the IL- 15 polypeptide or a fragment thereof comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding IL-15.
  • the IL- 15 polypeptide or a fragment thereof comprises a sequence encoding IL-15 having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25 or more amino acids at the N- or C-terminus or at both the N- and C-terminus.
  • the IL- 15 polypeptide or a fragment thereof may comprise an IL- 15 signal peptide.
  • the IL- 15 polypeptide or a fragment thereof may comprise amino acids 1-29 of IL-15.
  • the IL- 15 polypeptide or a fragment thereof may comprise amino acids 1-29 of SEQ ID NO: 385.
  • the IL-15 polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 374. In some embodiments, the IL-15 polypeptide or a fragment thereof may comprise amino acids 30-162 of IL-15. In some embodiments, the IL- 15 polypeptide or a fragment thereof may comprise amino acids 30-162 of SEQ ID NO: 385. In some embodiments, the IL- 15 polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 375. In some embodiments, the IL-15 polypeptide or a fragment thereof may comprise amino acids 1-162 of SEQ ID NO: 385.
  • the IL-15 polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 374 and a sequence of SEQ ID NO: 375. In some embodiments, the IL-15 polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 380. In some embodiments, IL-15 polypeptide is secreted when expressed in a cell, such as a T cell.
  • the present disclosure further encompasses recombinant nucleic acid molecules encoding an interleukin- 15 receptor (IL-15R) subunit polypeptide or a fragment thereof.
  • IL-15R subunit may be IL-15 receptor alpha chain (“IL-15Ra” or CD215), IL-2 receptor beta chain (“IL-2R[3” or CD122) and IL-2 receptor gamma/the common gamma chain (“IL-2Ry/yc” or CD132).
  • the IL-15R subunit is an IL-15Ra or a fragment thereof.
  • the IL-15Ra polypeptide or a fragment thereof comprises 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59,
  • the IL- 15Ra polypeptide or a fragment thereof comprises a sequence having at least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or more sequence identity to a sequence encoding IL-15Ra.
  • the IL-15Ra polypeptide or a fragment thereof comprises a sequence encoding IL-15Ra having a truncation of at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or more amino acids at the N- or C- termin
  • the IL-15Ra polypeptide or a fragment thereof may comprise IL-15Ra signal peptide. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 1- 30 of IL-15Ra. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 1-30 of SEQ ID NO: 386. In some embodiments, the IL-15Ra polypeptide or a fragment thereof does not comprise IL-15Ra signal peptide. In some embodiments, the IL-15Ra polypeptide or a fragment thereof does not comprise amino acids 1-30 of IL-15Ra. In some embodiments, the IL-15Ra polypeptide or a fragment thereof does not comprise amino acids 1-30 of SEQ ID NO: 386.
  • the IL-15Ra polypeptide or a fragment thereof may comprise IL-15Ra Sushi domain. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 31- 95 of IL-15Ra. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 31-95 of SEQ ID NO: 386. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 382.
  • the IL-15Ra polypeptide or a fragment thereof may comprise an intracellular domain of IL-15Ra. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 229-267 of IL-15Ra. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 229-267 of a sequence of SEQ ID NO: 386. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 372.
  • the IL-15Ra polypeptide or a fragment thereof may comprise IL-15Ra Sushi domain, transmembrane domain, and intracellular domain. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 31 -267 of IL- 15Ra. In some embodiments, the IL- 15Ra polypeptide or a fragment thereof may comprise amino acids 31-267 of SEQ ID NO: 386. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 382. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 383.
  • the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 96-267 of SEQ ID NO: 386. In some embodiments, the IL-15Ra polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 382 and a sequence of SEQ ID NO: 383. In some embodiments, IL- 15Ra comprises a sequence of SEQ ID NO: 403.
  • the IL-15Ra polypeptide or a fragment thereof may be a soluble IL-15Ra (sIL- 15Ra).
  • the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 21- 205 of IL-15Ra.
  • the IL-15Ra polypeptide or a fragment thereof may comprise amino acids 21-205 of a sequence of SEQ ID NO: 386.
  • the IL-15Ra polypeptide or a fragment thereof may comprise a sequence of SEQ ID NO: 379.
  • the present disclosure encompasses recombinant nucleic acid molecules encoding a fusion protein comprising an IL- 15 polypeptide linked to an IL-15R subunit.
  • IL- 15 and IL-15R subunit are operatively linked by a linker.
  • the IL-15R subunit is IL-15R alpha (IL- 15Ra).
  • IL-15 polypeptide may be linked to N-terminus of IL-15Ra subunit.
  • IL-15 polypeptide may be linked to C-terminus of IL-15Ra subunit.
  • IL-15 and IL-15Ra are operatively linked by a linker.
  • the linker is not a cleavable linker.
  • the linker may comprise a sequence comprising (G4S) n , wherein G is glycine, S is serine, and n is an integer from 1 to 10. In some embodiments, n is an integer from 1 to 4. In some embodiments, n is 3. In some embodiments, the linker comprises a sequence of SEQ ID NO: 378. In some embodiments, the linker comprises a sequence of SEQ ID NO: 405.
  • the fusion protein may comprise amino acids 30-162 of IL-15. In some embodiments, the fusion protein may comprise amino acids 30-162 of a sequence of SEQ ID NO: 385. In some embodiments, the fusion protein may comprise a sequence of SEQ ID NO: 375. In some embodiments, the fusion protein does not comprise IL- 15 signal peptide. In some embodiments, the fusion protein does not comprise amino acids 1-29 of IL-15. In some embodiments, the fusion protein does not comprise amino acids 1-29 of a sequence of SEQ ID NO: 385. In some embodiments, the fusion protein does not comprise a sequence of SEQ ID NO: 374.
  • the fusion protein may comprise a Sushi domain. In some embodiments, the fusion protein may comprise amino acids 31-95 of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 31-95 of a sequence of SEQ ID NO: 386. In some embodiments, the fusion protein may comprise a sequence of SEQ ID NO: 382.
  • the fusion protein may comprise the intracellular domain of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 229-267 of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 229-267 of a sequence of SEQ ID NO: 386. In some embodiments, the fusion protein may comprise a sequence of SEQ ID NO: 372.
  • the fusion protein may comprise a soluble IL-15Ra (sIL-15Ra). In some embodiments, the fusion protein may comprise amino acids 21-205 of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 21-205 of a sequence of SEQ ID NO: 386. In some embodiments, the fusion protein may comprise a sequence of SEQ ID NO: 379.
  • the fusion protein may comprise the transmembrane domain and the intracellular domain of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 96-267 of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 96-267 of a sequence of SEQ ID NO: 386. In some embodiments, the fusion protein may comprise a sequence of SEQ ID NO: 383. [0312] In some embodiments, the fusion protein may comprise the Sushi domain, the transmembrane domain, and the intracellular domain of IL-15Ra. In some embodiments, the fusion protein may comprise amino acids 31-267 of IL-15Ra.
  • the fusion protein may comprise amino acids 31-267 of a sequence of SEQ ID NO: 386. In some embodiments, the fusion protein may comprise a sequence of SEQ ID NO: 382 and a sequence of SEQ ID NO: 383. In some embodiments, IL-15Ra comprises a sequence of SEQ ID NO: 403.
  • the fusion protein further comprises an epitope tag.
  • An epitope tag as described herein can be a peptide epitope tag or a protein epitope tag. Examples of a peptide epitope tag includes, but are not limited to, 6X His (also known as His-tag or hexahistidine tag), FLAG (e.g, 3X FLAG), HA, Myc, and V5.
  • a protein epitope tag examples include, but are not limited to, green fluorescent protein (GFP), glutathione-S-transferase (GST), [3-galactosidase (P-GAL), Luciferase, Maltose Binding Protein (MBP), Red Fluorescence Protein (RFP), and Vesicular Stomatitis Virus Glycoprotein (VSV-G).
  • GFP green fluorescent protein
  • GST glutathione-S-transferase
  • P-GAL [3-galactosidase
  • Luciferase Luciferase
  • MBP Maltose Binding Protein
  • RFP Red Fluorescence Protein
  • VSV-G Vesicular Stomatitis Virus Glycoprotein
  • the fusion protein further comprises a FLAG tag.
  • the fusion protein further comprises a 3X FLAG tag.
  • the fusion protein further comprises a sequence of SEQ ID NO: 384.
  • the fusion protein comprises a sequence of SEQ ID NO: 377. In some embodiments, the fusion protein comprises a sequence of SEQ ID NO: 381. In some embodiments, the fusion protein is expressed on cell surface when expressed in a T cell. In some embodiments, the fusion protein is secreted when expressed in a T cell.
  • cells expressing TFPs, an IL-15 polypeptide or a fragment thereof, an IL-15Ra polypeptide or a fragment thereof, and/or a fusion protein comprising an IL- 15 polypeptide and an IL-15Ra polypeptide described herein can yet further express another agent that can enhance the activity of a modified T cell expressing TFPs.
  • the agent that can enhance the activity of a modified T cell can be a PD-1 polypeptide.
  • the PD-1 polypeptide may be operably linked to the N-terminus of an intracellular domain of a costimulatory polypeptide via the C-terminus of the PD-1 polypeptide.
  • the agent that can enhance the activity of a modified T cell expressing TFPs can be an anti -PD-1 antibody, or antigen binding fragment thereof.
  • the anti -PD-1 antibody or antigen binding fragment thereof may be operably linked to the N- terminus of an intracellular domain of a costimulatory polypeptide via the C-terminus of the anti -PD-1 antibody, or antigen binding fragment thereof.
  • the PD-1 polypeptide or anti-PD-1 antibody is linked to the intracellular domain of the costimulatory polypeptide via the transmembrane domain of PD-1.
  • the costimulatory polypeptide is selected from the group consisting of 0X40, CD2, CD27, CDS, ICAM-1, ICOS (CD278), 4-1BB (CD137), GITR, CD28, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD 160, CD226, FcyRI, FcyRII, and FcyRIII.
  • the agent that can enhance the activity of a modified T cell expressing TFPs can be linked to an IL-15Ra polypeptide or a fragment thereof.
  • the agent can be an agent that can inhibit an inhibitory molecule that can decrease the ability of a T cell expressing a TFP to mount an immune effector response.
  • the agent which inhibits an inhibitory molecule comprises a first polypeptide, e.g., an inhibitory molecule, associated with a second polypeptide that provides a positive signal to the cell, e.g., an intracellular signaling domain described herein.
  • the agent may comprise a first polypeptide, e.g., of an inhibitory molecule such as PD-1, LAG3, CTLA4, CD160, BTLA, LAIR1, TIM3, 2B4, and TIGIT, or a fragment of any of these (e.g., at least a portion of an extracellular domain of any of these), and a second polypeptide which is an intracellular signaling domain described herein (e.g., comprising a costimulatory domain (e.g., 4-1BB, CD27, or CD28, as described herein)) and/or a primary signaling domain (e.g., IL-15Ra described herein).
  • the agent may be PD-1 or a fragment thereof.
  • the agent may comprise the extracellular domain of PD-1.
  • the agent may comprise the extracellular domain and transmembrane domain of PD-1.
  • the agent may further comprise CD28 or a fragment thereof.
  • the agent may comprise the intracellular domain of CD28.
  • the agent may comprise a fusion protein comprising the PD-1 extracellular domain and transmembrane domain linked to the CD28 intracellular domain linked to IL-15Ra.
  • the CD28 intracellular domain is linked to the intracellular domain of IL- 15 Ra.
  • the PD-1 or a fragment thereof may comprise a sequence of SEQ ID NO: 366. In some embodiments, the PD-1 or a fragment thereof may comprise a sequence of SEQ ID NO: 367. In some embodiments, the PD-1 or a fragment thereof may comprise a sequence of SEQ ID NO: 368. In some embodiments, the PD-1 or a fragment thereof may comprise a sequence of SEQ ID NO: 369. In some embodiments, the transmembrane domain of PD-1 may comprise a sequence of SEQ ID NO: 370. In some embodiments, the intracellular domain of CD28 may comprise a sequence of SEQ ID NO: 371 .
  • the intracellular domain of IL-15Ra comprises amino acids 229-267 of IL-15Ra. In some embodiments, the intracellular domain of IL-15Ra comprises amino acids 229-267 of a sequence of SEQ ID NO: 386. In some embodiments, the fusion protein comprises a sequence of SEQ ID NO: 372. In some embodiments, the fusion protein comprises a sequence of SEQ ID NO: 376.
  • the agent that can enhance the activity of a modified T cell expressing TFPs can be linked to a fusion protein comprising an IL-15 polypeptide and an IL-15Ra polypeptide.
  • the agent may be PD-1 or a fragment thereof.
  • the agent may comprise the extracellular domain of PD- 1.
  • the agent may comprise the extracellular domain and transmembrane domain of PD-1.
  • the agent may further comprise CD28 or a fragment thereof.
  • the agent may comprise the intracellular domain of CD28.
  • the agent may comprise a fusion protein comprising the PD-1 extracellular domain and transmembrane domain linked to the CD28 intracellular domain linked to the fusion protein comprising an IL- 15 polypeptide and an IL-15Ra polypeptide.
  • the CD28 intracellular domain is linked to the intracellular domain of IL-15Ra.
  • the intracellular domain of IL-15Ra is linked to the IL- 15 polypeptide by a linker described herein.
  • the linker comprises a cleavage site.
  • the cleavage site can be a self-cleaving peptide such as a T2A, P2A, E2A or F2A cleavage site.
  • the cleavage site can comprise a sequence of SEQ ID NO: 373. In some embodiments, the cleavage site may comprise SEQ ID NO: 23. In some embodiments, the cleavage site may comprise SEQ ID NO: 365. [0319] In some embodiments, the fusion protein may comprise a PD-1 or a fragment thereof comprising a sequence of SEQ ID NO: 366. In some embodiments, the fusion protein may comprise a PD-1 or a fragment thereof comprising a sequence of SEQ ID NO: 367. In some embodiments, the fusion protein may comprise a PD-1 or a fragment thereof comprising a sequence of SEQ ID NO: 368.
  • the fusion protein may comprise a PD-1 or a fragment thereof comprising a sequence of SEQ ID NO: 369. In some embodiments, the fusion protein may comprise a PD-1 or a fragment thereof comprising a transmembrane domain of PD-1 comprising a sequence of SEQ ID NO: 370. In some embodiments, the fusion protein may comprise a CD28 or a fragment comprising the intracellular domain of CD28 comprising a sequence of SEQ ID NO: 371. In some embodiments, the intracellular domain of IL-15Ra comprises amino acids 229-267 of IL-15Ra. In some embodiments, the intracellular domain of IL-15Ra comprises amino acids 229-267 of a sequence of SEQ ID NO: 386.
  • the fusion protein comprises a sequence of SEQ ID NO: 372.
  • the IL-15 polypeptide comprises IL-15 signal peptide.
  • the IL- 15 polypeptide comprises amino acids 1-29 of IL-15.
  • the IL- 15 polypeptide comprises amino acids 1-29 of a sequence of SEQ ID NO: 385.
  • the IL-15 polypeptide comprises a sequence of SEQ ID NO: 374.
  • the IL-15 polypeptide comprises amino acids 30-162 of IL-15.
  • the IL- 15 polypeptide comprises amino acids 30-162 of a sequence of SEQ ID NO: 385.
  • the IL-15 polypeptide comprises a sequence of SEQ ID NO: 375.
  • the fusion protein comprises a sequence of SEQ ID NO: 361.
  • the cells expressing TFP, IL-15, and/or IL-15Ra described herein can further express another agent, e.g., an agent which enhances the activity of a modified T cell.
  • the agent can be an agent which inhibits an inhibitory molecule.
  • Inhibitory molecules, e. g , PD- 1 can, in some embodiments, decrease the ability of a modified T cell to mount an immune effector response. Examples of inhibitory molecules include PD-1, PD-L1, CTLA4, TIM3, LAG3, VISTA, BTLA, TIGIT, LAIR1, CD 160, 2B4 and TGFR beta.
  • the agent which inhibits an inhibitory molecule comprises a first polypeptide, e.g., an inhibitory molecule, associated with a second polypeptide that provides a positive signal to the cell, e.g., an intracellular signaling domain described herein.
  • the agent comprises a first polypeptide, e.g., of an inhibitory molecule such as PD-1, LAG3, CTLA4, CD160, BTLA, LAIR1, TIM3, 2B4 and TIGIT, or a fragment of any of these (e.g., at least a portion of an extracellular domain of any of these), and a second polypeptide which is an intracellular signaling domain described herein (e.g., comprising a costimulatory domain (e.g., 4-1BB, CD27 or CD28, e.g., as described herein) and/or a primary signaling domain (e.g., a CD3 zeta signaling domain described herein).
  • an inhibitory molecule such as PD-1, LAG3, CTLA4, CD160, BTLA, LAIR1, TIM3, 2B4 and TIGIT
  • a fragment of any of these e.g., at least a portion of an extracellular domain of any of these
  • a second polypeptide which is an intra
  • the agent comprises a first polypeptide of PD-1 or a fragment thereof (e.g., at least a portion of an extracellular domain of PD-1), and a second polypeptide of an intracellular signaling domain described herein (e.g., a CD28 signaling domain described herein and/or a CD3 zeta signaling domain described herein).
  • PD-1 is an inhibitory member of the CD28 family of receptors that also includes CD28, CTLA-4, ICOS, and BTLA.
  • PD- 1 is expressed on activated B cells, T cells and myeloid cells (Agata et al., 1996, Int. Immunol 8:765-75).
  • PD-L1 Two ligands for PD-1, PD-L1 and PD-L2, have been shown to downregulate T cell activation upon binding to PD- 1 (Freeman et al., 2000 J. Exp. Med. 192: 1027-34; Latchman et al., 2001 Nat. Immunol. 2:261-8; Carter et al., 2002 Eur. J. Immunol. 32:634-43).
  • PD-L1 is abundant in human cancers (Dong et al., 2003 J. Mol. Med.
  • the agent comprises the extracellular domain (ECD) of an inhibitory molecule, e.g., Programmed Death 1 (PD-1) can be fused to a transmembrane domain and optionally an intracellular signaling domain such as 4 IBB and CD3 zeta (also referred to herein as a PD-1 TFP).
  • PD-1 TFP when used in combinations with an anti-TAA TFP described herein, improves the persistence of the T cell.
  • the TFP is a PD-1 TFP comprising the extracellular domain of PD-1.
  • TFPs containing an antibody or antibody fragment such as a scFv that specifically binds to the Programmed Death-Ligand 1 (PD-L1) or Programmed Death-Ligand 2 (PD-L2).
  • the present disclosure provides a population of TFP-expressing T cells, e.g., TFP-T cells.
  • the population of TFP-expressing T cells comprises a mixture of cells expressing different TFPs.
  • the population of TFP-T cells can include a first cell expressing a TFP having a binding domain described herein, and a second cell expressing a TFP having a different anti-TAA binding domain, e.g., a binding domain described herein that differs from the binding domain in the TFP expressed by the first cell.
  • the population of TFP-expressing cells can include a first cell expressing a TFP that includes a first binding domain binding domain, e.g., as described herein, and a second cell expressing a TFP that includes an antigen binding domain to a target other than the binding domain of the first cell (e.g. , another tumor-associated antigen).
  • a first cell expressing a TFP that includes a first binding domain binding domain, e.g., as described herein
  • a second cell expressing a TFP that includes an antigen binding domain to a target other than the binding domain of the first cell (e.g. , another tumor-associated antigen).
  • the present disclosure provides a population of cells wherein at least one cell in the population expresses a TFP having a domain described herein, and a second cell expressing another agent, e.g., an agent which enhances the activity of a modified T cell.
  • the agent can be an agent which inhibits an inhibitory molecule.
  • Inhibitory molecules e.g., can, in some embodiments, decrease the ability of a modified T cell to mount an immune effector response.
  • inhibitory molecules include PD-1, PD-L1, PD-L2, CTLA4, TIM3, LAG3, VISTA, BTLA, TIGIT, LAIR1, CD 160, 2B4 and TGFRbeta.
  • the agent that inhibits an inhibitory molecule comprises a first polypeptide, e.g., an inhibitory molecule, associated with a second polypeptide that provides a positive signal to the cell, e.g., an intracellular signaling domain described herein.
  • recombinant nucleic acid molecules comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) described herein and a second nucleic acid sequence encoding an Interleukin- 15 (IL- 15) polypeptide or a fragment thereof.
  • recombinant nucleic acid molecules comprising a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) and a second nucleic acid sequence encoding an Interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • nucleic acid molecules a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) and a second nucleic acid sequence encoding a fusion protein comprising an IL- 15 polypeptide or a fragment thereof linked to an IL- 15Ra polypeptide or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • nucleic acid molecules a first nucleic acid sequence encoding a T cell receptor (TCR) fusion protein (TFP) and a second nucleic acid sequence encoding a fusion protein comprising a fusion protein comprising an IL-15Ra polypeptide or a fragment thereof linked to PD-1 or a fragment thereof and/or CD28 or a fragment thereof.
  • TCR T cell receptor
  • TFP T cell receptor fusion protein
  • TFP T cell receptor
  • TFP T cell receptor
  • TCR subunit comprising at least a portion of a TCR extracellular domain.
  • the TCR subunit can further comprise a transmembrane domain.
  • the TCR subunit can further comprise an intracellular domain of TCR gamma, TCR delta, TCR alpha or TCR beta or an intracellular domain comprising a stimulatory domain from an intracellular signaling domain of CD3 epsilon, CD3 gamma, CD3 delta.
  • the TFP can further comprise an antibody (e.g., a human, humanized, or murine antibody) comprising an antigen binding domain.
  • the recombinant nucleic acid molecule can further comprise a sequence encoding a TCR constant domain, wherein the TCR constant domain is a TCR alpha constant domain, a TCR beta constant domain, a TCR alpha constant domain and a TCR beta constant domain, a TCR gamma constant domain, a TCR delta constant domain, or a TCR gamma constant domain and a TCR delta constant domain.
  • the TCR subunit and the antibody can be operatively linked.
  • the TFP can functionally incorporate into a TCR complex (e.g., an endogenous TCR complex) when expressed in a T cell.
  • the constant domain can comprise a constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the constant domain can comprise a full-length constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the constant domain can comprise a fragment (e.g., functional fragment) of the full-length constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the constant domain can comprise at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of the constant domain of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the sequence encoding the TCR constant domain can further encode the transmembrane domain and/or intracellular region of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the sequence encoding the TCR constant domain can encode a full-length constant region of a TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the constant region of a TCR chain can comprise a constant domain, a transmembrane domain, and an intracellular region.
  • the constant region of a TCR chain can also exclude the transmembrane domain and the intracellular region of the TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain.
  • the TCR alpha chain, a TCR beta chain, a TCR gamma chain or a TCR delta chain described herein can be derived from various species.
  • the TCR chain can be a murine or human TCR chain.
  • the constant domain can comprise a constant domain of a murine or human TCR alpha chain, TCR beta chain, TCR gamma chain or TCR delta chain.
  • the constant domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the constant domain can comprise a truncated version of a constant domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:243 or SEQ ID NO:265.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:243 or SEQ ID NO:265.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:243 or SEQ ID NO:265.
  • the constant domain can comprise a sequence or fragment thereof of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:243 or SEQ ID NO:265.
  • the constant domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or deletions of the sequence of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO: 207, SEQ ID NO: 209, SEQ ID NO: 243 or SEQ ID NO: 265.
  • the constant domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:243 or SEQ ID NO:265.
  • the constant domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, or SEQ ID NO: 22, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, SEQ ID NO: 155, SEQ ID NO:207, SEQ ID NO:209, SEQ ID NO:243 or SEQ ID NO:265.
  • the murine TCR alpha constant domain can comprise positions 2-137 of SEQ ID NO: 146.
  • the murine TCR alpha constant domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the constant domain can comprise a truncated version of a constant domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of positions 2-137 of SEQ ID NO: 146.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of positions 2-137 of SEQ ID NO: 146.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of positions 2-137 of SEQ ID NO: 146.
  • the constant domain can comprise a sequence or fragment thereof of positions 2-137 of SEQ ID NO: 146.
  • the constant domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or deletions of the sequence of positions 2-137 of SEQ ID NO: 146.
  • the constant domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of positions 2-137 of SEQ ID NO: 146.
  • the constant domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of positions 2-137 of SEQ ID NO: 146.
  • the murine TCR beta constant domain can comprise positions 2-173 of SEQ ID NO: 152.
  • the murine TCR beta constant domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the constant domain can comprise a truncated version of a constant domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of positions 2-173 of SEQ ID NO: 152.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of positions 2-173 of SEQ ID NO: 152.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of positions 2-173 of SEQ ID NO: 152.
  • the constant domain can comprise a sequence or fragment thereof of positions 22-173 of SEQ ID NO: 152.
  • the constant domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or deletions of the sequence of positions 2-173 of SEQ ID NO: 152.
  • the constant domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of positions 2-173 of SEQ ID NO: 152.
  • the constant domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of positions 2-173 of SEQ ID NO: 152.
  • the TCR constant domain is a TCR delta constant domain.
  • the TCR delta constant domain can comprise SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:243 or SEQ ID NO:265, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modification.
  • the TCR delta constant domain can comprise SEQ ID NO:243.
  • the TCR delta constant domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the constant domain can comprise a truncated version of a constant domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of SEQ ID NO:243.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of SEQ ID NO:243.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of SEQ ID NO:243.
  • the constant domain can comprise a sequence or fragment thereof of SEQ ID NO:243.
  • the constant domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or deletions of the sequence of SEQ ID NO:243.
  • the constant domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of SEQ ID NO:243.
  • the constant domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of SEQ ID NO:243.
  • the TCR delta constant domain can comprise SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:243 or SEQ ID NO:265, functional fragments thereof, or amino acid sequences thereof having at least one but not more than 20 modifications.
  • the sequence encoding a TCR delta constant domain further encodes a TCR delta variable domain, thereby encoding a full TCR delta domain.
  • the full TCR delta domain can be delta 2 or delta 1.
  • the full TCR delta constant domain can comprise SEQ ID NO:256, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the full TCR delta domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the delta domain can comprise a truncated version of a delta domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of SEQ ID NO:256.
  • the delta domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of SEQ ID NO:256.
  • the delta domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of SEQ ID NO:256.
  • the delta domain can comprise a sequence or fragment thereof of SEQ ID NO:256.
  • the delta domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or deletions of the sequence of SEQ ID NO:256.
  • the delta domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of SEQ ID NO:256.
  • the delta domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of SEQ ID NO:256.
  • the TCR gamma constant domain can comprise SEQ ID NO:21.
  • the TCR gamma constant domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the constant domain can comprise a truncated version of a constant domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of SEQ ID NO:21.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of SEQ ID NO:21.
  • the constant domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of SEQ ID NO:21.
  • the constant domain can comprise a sequence or fragment thereof of SEQ ID NO:21.
  • the constant domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or deletions of the sequence of SEQ ID NO:21.
  • the constant domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of SEQ ID NO:21.
  • the constant domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of SEQ ID NO:243.
  • the TCR gamma constant domain can comprise SEQ ID NO:21 or SEQ ID NO: 155, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the sequence encoding the TCR gamma constant domain further encodes a TCR gamma variable domain, thereby encoding a full TCR gamma domain.
  • the full TCR gamma domain can be gamma 9 or gamma 4.
  • the full TCR gamma domain can comprise SEQ ID NO:255, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the full TCR gamma domain can comprise truncations, additions, or substitutions of a sequence of a constant domain described herein.
  • the gamma domain can comprise a truncated version of a gamma domain described herein having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid residues of SEQ ID NO:255.
  • the gamma domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more additional amino acid residues of SEQ ID NO:255.
  • the gamma domain can comprise a sequence having at least about 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, 100, 150 or more amino acid substitutions of SEQ ID NO:255.
  • the gamma domain can comprise a sequence or fragment thereof of SEQ ID NO:255.
  • the gamma domain can comprise at least 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more modifications, mutations or gamma of the sequence of SEQ ID NO:255.
  • the gamma domain can comprise at most 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2 or 1 modification, mutations or deletions of the sequence of SEQ ID NO:255.
  • the gamma domain can comprise a sequence having a sequence identity of at least about 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 99% or 100% to the sequence of SEQ ID NO:255.
  • TCR beta chain (Homo sapiens):
  • the murine TCR beta chain constant region canonical sequence is:
  • TCR alpha constant region (Mus musculus) (or [mm]TRAC(82- 137)):
  • ATYPSSDVPCDATLTEKSFETDMNLNFQNLSVMGLRILLLKVAGFNLLMTLRLWSS (SEQ ID NO: 17).
  • the murine TCR alpha chain constant (mTRAC) region canonical sequence is:
  • TCR beta constant region (Mus musculus) (or [mm]TRBCl(123-173)):
  • the murine TCR beta chain constant region canonical sequence is:
  • TCR beta chain (Homo sapiens):
  • TCR delta constant region version 1 (Homo sapiens):
  • TCR gamma constant region Homo sapiens (or [hs]TRGC(l-173)):
  • the TCR constant domain is a TCR delta constant domain.
  • the sequence encoding the TCR delta constant domain can further encode a second antigen binding domain or ligand binding domain that is operatively linked to the sequence encoding the TCR delta constant domain.
  • the second antigen binding domain or ligand binding domain can be the same or different as the antigen binding domain or ligand binding domain of the TFP.
  • the TCR constant domain is a TCR gamma constant domain.
  • the sequence encoding the TCR gamma constant domain can further encode a second antigen binding domain or ligand binding domain that is operatively linked to the sequence encoding the TCR gamma constant domain.
  • the second antigen binding domain or ligand binding domain can be the same or different as the antigen binding domain or ligand binding domain of the TFP.
  • the recombinant nucleic acid comprises a sequence encoding a TCR gamma constant domain and a TCR delta constant domain.
  • the TCR gamma constant domain can comprise SEQ ID NO:21 or SEQ ID NO: 155, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the sequence encoding the TCR gamma constant domain can further encode a TCR gamma variable domain, thereby encoding a full TCR gamma domain.
  • the TCR gamma domain can be gamma 9 or gamma 4.
  • the full TCR gamma domain comprises SEQ ID NO:255, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR delta constant domain can comprise SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:243 or SEQ ID NO:265, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the sequence encoding the TCR delta constant domain can further encode a TCR delta variable domain, thereby encoding a full TCR delta domain.
  • the TCR delta domain can be delta 2 or delta 1.
  • the full TCR delta domain can comprise SEQ ID NO:256, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR constant domain incorporates into a functional TCR complex when expressed in a T cell.
  • the TCR constant domain incorporates into a same functional TCR complex as the functional TCR complex that incorporates the TFP when expressed in a T cell.
  • the sequence encoding the TFP and the sequence encoding the TCR constant domain are contained within a same nucleic acid molecule.
  • the sequence encoding the TFP and the sequence encoding the TCR constant domain are contained within different nucleic acid molecules.
  • the sequence can further encode a cleavage site (e.g., a protease cleavage site) between the encoded TFP and the TCR constant domain.
  • the cleavage site can be a protease cleavage site.
  • the cleavage site can be a self-cleaving peptide such as a T2A, P2A, E2A or F2A cleavage site.
  • the cleavage site can comprise a sequence of SEQ ID NO: 23.
  • T2A cleavage site EGRGSLLTCGDVEENPGP (SEQ ID NO: 23).
  • the TCR subunit of the TFP and the constant domain can comprise a sequence derived from a same TCR chain or a different TCR chain.
  • the TCR subunit of the TFP and the constant domain are derived from different TCR chains.
  • the TCR subunit can comprise (1) at least a portion of a TCR extracellular domain, (2) a transmembrane domain, and (3) an intracellular domain, where the TCR extracellular domain, the transmembrane domain and the intracellular domain are derived from a TCR alpha chain, and the constant domain can comprise a constant domain of a TCR beta chain.
  • the TCR subunit can comprise (1) at least a portion of a TCR extracellular domain, (2) a transmembrane domain, and (3) an intracellular domain, where the TCR extracellular domain, the transmembrane domain and the intracellular domain are derived from a TCR beta chain, and the constant domain can comprise a constant domain of a TCR alpha chain.
  • the TCR subunit can comprise (1) at least a portion of a TCR extracellular domain, (2) a transmembrane domain, and (3) an intracellular domain, where the TCR extracellular domain, the transmembrane domain and the intracellular domain are derived from a TCR gamma chain, and the constant domain can comprise a constant domain of a TCR delta chain.
  • the TCR subunit can comprise (1) at least a portion of a TCR extracellular domain, (2) a transmembrane domain, and (3) an intracellular domain, where the TCR extracellular domain, the transmembrane domain and the intracellular domain are derived from a TCR delta chain, and the constant domain can comprise a constant domain of a TCR gamma chain.
  • the TCR subunit and the antibody domain, the antigen domain or the binding ligand or fragment thereof are operatively linked by a linker sequence.
  • the transmembrane domain is a TCR transmembrane domain from CD3 epsilon, CD3 gamma, CD3 delta, TCR gamma, TCR delta, TCR alpha or TCR beta.
  • the intracellular domain is derived from only CD3 epsilon, only CD3 gamma, only CD3 delta, only TCR gamma, only TCR delta, only TCR alpha or only TCR beta.
  • the TCR subunit comprises (i) at least a portion of a TCR extracellular domain, (ii) a TCR transmembrane domain, and (iii) a TCR intracellular domain, wherein at least two or all of (i), (ii), and (iii) are from the same TCR subunit.
  • the TCR extracellular domain comprises an extracellular domain or portion thereof of a protein selected from the group consisting of a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, a CD3 delta TCR subunit, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR subunit comprises a transmembrane domain comprising a transmembrane domain of a protein selected from the group consisting of a TCR alpha chain, a TCR beta chain, a TCR zeta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, a CD3 delta TCR subunit, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD28, CD37, CD64, CD80, CD86, CD134, CD137, CD154, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR subunit comprises a TCR intracellular domain of TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, or a fragment thereof.
  • the TCR subunit comprises an intracellular domain comprising a stimulatory domain of a protein selected from an intracellular signaling domain of CD3 epsilon, CD3 gamma or CD3 delta, or an amino acid sequence having at least one modification thereto.
  • the TCR subunit can comprise (i) at least a portion of a TCR extracellular domain, (ii) a TCR transmembrane domain, and (iii) a TCR intracellular domain of a TCR gamma chain or a TCR delta chain.
  • the TCR extracellular domain can comprise the extracellular portion of a constant domain of a TCR gamma chain or a TCR delta chain, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR subunit comprising (i) at least a portion of a TCR extracellular domain, (ii) a TCR transmembrane domain, and (iii) a TCR intracellular domain is or comprises a delta constant domain, or a fragment thereof, e.g. , a delta constant domain described herein.
  • the delta constant domain can have the sequence of SEQ ID NO:20, SEQ ID NO:22, SEQ ID NO:243 or SEQ ID NO:265, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR subunit comprising (i) at least a portion of a TCR extracellular domain, (ii) a TCR transmembrane domain, and (iii) a TCR intracellular domain is or comprises a gamma constant domain, e.g., a gamma constant domain described herein.
  • the gamma constant domain can have the sequence of SEQ ID NO:21 or SEQ ID NO: 155, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the extracellular domain of the TFP may not comprise the variable domain of a gamma chain or a delta chain.
  • the TCR subunit of the TFP can comprise the extracellular, transmembrane and intracellular domain of CD3 epsilon, CD3 gamma, or CD3 delta.
  • recombinant nucleic acid comprises a TFP comprising the extracellular, transmembrane and intracellular domain of CD3 epsilon, CD3 gamma, or CD3 delta and the constant domains of TCR beta and TCR alpha.
  • recombinant nucleic acid comprises a TFP comprising the extracellular, transmembrane and intracellular domain of CD3 epsilon and the constant domains of TCR gamma and TCR delta.
  • recombinant nucleic acid comprises a TFP comprising the extracellular, transmembrane and intracellular domain of CD3 epsilon and full length TCF gamma and full length TCR delta.
  • the TCR subunit of the TFP comprises CD3 epsilon.
  • the TCR subunit of CD3 epsilon can comprise the sequence of SEQ ID NO:364 functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR subunit comprising at least a portion of a murine TCR alpha or murine TCR beta extracellular domain and a murine TCR alpha or murine TCR beta transmembrane domain is or comprises a TCR alpha constant domain or a TCR beta constant domain.
  • the TCR subunit can comprise an intracellular domain of murine TCR alpha or murine TCR beta.
  • the TCR constant domain can be a TCR alpha constant domain, e.g., a TCR alpha constant domain described herein.
  • the TCR alpha constant domain can comprise SEQ ID NO: 17, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, or SEQ ID NO: 207, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the sequence encoding the TCR alpha constant domain can further encode a second antigen binding domain or ligand binding domain that is operatively linked to the sequence encoding the TCR alpha constant domain.
  • the second antigen binding domain or ligand binding domain can be the same or different as the antigen binding domain or ligand binding domain of the TFP.
  • the TCR alpha constant domain can comprise a murine TCR alpha constant domain.
  • the murine TCR alpha constant domain can comprise amino acids 2-137 of the murine TCR alpha constant domain.
  • the murine TCR alpha constant domain can comprise amino acids 2-137 of SEQ ID NO: 146.
  • the murine TCR alpha constant domain can comprise a sequence of SEQ ID NO:207.
  • the murine TCR alpha constant domain can comprise amino acids 82-137 of SEQ ID NO: 146.
  • the murine TCR alpha constant domain comprises a sequence of SEQ ID NO: 17.
  • the TCR constant domain can be a TCR beta constant domain, e.g., a TCR beta constant domain described herein.
  • the TCR beta constant domain can comprise SEQ ID NO: 18, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, or SEQ ID NO:209, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the sequence encoding the TCR beta constant domain can further encode a second antigen binding domain or ligand binding domain that is operatively linked to the sequence encoding the TCR beta constant domain.
  • the second antigen binding domain or ligand binding domain can be the same or different as the antigen binding domain or ligand binding domain of the TFP.
  • TCR beta constant domain can comprise a murine TCR beta constant domain.
  • the murine TCR beta constant domain can comprise amino acids 2-173 of the murine TCR beta constant domain.
  • the murine TCR beta constant domain can comprise amino acids 2-173 of SEQ ID NO: 152.
  • the murine TCR beta constant domain can comprise SEQ ID NO:209.
  • the TCR beta constant domain can comprise amino acids 123-173 of SEQ ID NO: 152.
  • the TCR beta constant domain can comprise SEQ ID NO: 18
  • the recombinant nucleic acid can comprise sequence encoding a TCR alpha constant domain and a TCR beta constant domain.
  • the TCR alpha constant domain can comprise SEQ ID NO: 17, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 146, or SEQ ID NO:207, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR beta constant domain can comprise SEQ ID NO: 18, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 152, or SEQ ID NO:209, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the intracellular signaling domain can be CD3 epsilon, CD3 gamma, or CD3 delta.
  • the intracellular signaling domain can be CD3 epsilon.
  • the sequence encoding the TCR constant domain can comprise from 5’ to 3’, a first leader sequence, an antigen binding domain sequence, a linker, a TRAC gene sequence, a cleavable linker sequence, a second leader sequence, and a TRBC gene sequence.
  • the sequence encoding the TCR constant domain can comprise, from 5’ to 3’, a first leader sequence, an antigen binding domain sequence, a linker, a TRAC gene sequence, a cleavable linker sequence, a second leader sequence, and a TRBC gene sequence.
  • the sequence encoding the TCR constant domain can comprise, from 5’ to 3’, a first leader sequence, a TRAC gene sequence, a cleavable linker sequence, a second leader sequence, an antigen binding domain sequence, a linker, and a TRBC gene sequence.
  • the sequence encoding the TCR constant domain can comprise, from 5’ to 3’, a first leader sequence, an antigen binding domain sequence, a linker, a TRAC gene sequence, a cleavable linker sequence, a second leader sequence, an antigen binding domain sequence, a linker, and a TRBC gene sequence.
  • the sequence encoding the TCR constant domain can comprise, from 5’-3’, a first leader sequence, a TRAC gene sequence, a first cleavable linker sequence, a second leader sequence, a TRBC gene sequence, a second cleavable linker sequence, a third leader sequence, an antigen binding domain sequence, a linker sequence, and a CD 3 epsilon gene sequence.
  • the at least one but not more than 20 modifications thereto of a sequence described herein can comprise a modification of an amino acid that mediates cell signaling or a modification of an amino acid that is phosphorylated in response to a ligand binding to the TFP.
  • the TCR subunit comprises an intracellular domain comprising a stimulatory domain of a protein selected from a functional signaling domain of 4-1BB and/or a functional signaling domain of CD3 zeta, or an amino acid sequence having at least one modification thereto.
  • the recombinant nucleic acid further comprises a sequence encoding a costimulatory domain.
  • the costimulatory domain comprises a functional signaling domain of a protein selected from the group consisting of 0X40, CD2, CD27, CD28, CDS, ICAM-1, LFA-1 (CD1 la/CD18), ICOS (CD278), and 4-1BB (CD137), and amino acid sequences thereof having at least one but not more than 20 modifications thereto.
  • the TCR subunit comprises an immunoreceptor tyrosine-based activation motif (ITAM) of a TCR subunit that comprises an ITAM or portion thereof of a protein selected from the group consisting of CD3 zeta TCR subunit, CD3 epsilon TCR subunit, CD3 gamma TCR subunit, CD3 delta TCR subunit, TCR zeta chain, Fc epsilon receptor 1 chain, Fc epsilon receptor 2 chain, Fc gamma receptor 1 chain, Fc gamma receptor 2a chain, Fc gamma receptor 2b 1 chain, Fc gamma receptor 2b2 chain, Fc gamma receptor 3a chain, Fc gamma receptor 3b chain, Fc beta receptor 1 chain, TYROBP (DAP12), CD5, CD16a, CD 16b, CD22, CD23, CD32, CD64, CD79a, CD79b, CD89, CD278, CD66
  • ITAM immunorecept
  • the ITAM replaces an ITAM of CD3 gamma, CD3 delta, or CD3 epsilon.
  • the ITAM is selected from the group consisting of CD3 zeta TCR subunit, CD3 epsilon TCR subunit, CD3 gamma TCR subunit, and CD3 delta TCR subunit and replaces a different ITAM selected from the group consisting of CD3 zeta TCR subunit, CD3 epsilon TCR subunit, CD3 gamma TCR subunit, and CD3 delta TCR subunit.
  • the TFP, the TCR gamma constant domain, the TCR delta constant domain, and any combination thereof is capable of functionally interacting with an endogenous TCR complex and/or at least one endogenous TCR polypeptide.
  • the TCR constant domain is a TCR gamma constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of TCR delta, CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof
  • the TCR constant domain is a TCR delta constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of TCR gamma, CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof
  • the TCR constant domain is a TCR gamma constant domain and a TCR delta constant domain and the TFP functionally integrates into a TCR complex comprising
  • the at least one but not more than 20 modifications thereto comprise a modification of an amino acid that mediates cell signaling or a modification of an amino acid that is phosphorylated in response to a ligand binding to the TFP.
  • the antibody or antigen binding domain can be an antibody fragment.
  • the antibody or antigen binding domain can be murine, human or humanized.
  • the murine, human or humanized antibody is an antibody fragment.
  • the antibody fragment is a scFv, a single domain antibody domain, a VH domain or a VL domain.
  • murine, human or humanized antibody comprising an antigen binding domain is selected from a group consisting of an anti-CD19 binding domain, anti-B-cell maturation antigen (BCMA) binding domain, anti-mesothelin (MSLN) binding domain, anti-CD22 binding domain, anti-PD-1 binding domain, anti-BAFF or BAFF receptor binding domain, and anti-ROR-1 binding domain.
  • An antigen binding domain described herein can be selected from a group consisting of an anti-CD19 binding domain, an anti-B-cell maturation antigen (BCMA) binding domain, an anti-mesothelin (MSLN) binding domain, an anti-CD20 binding domain, an anti-CD70 binding domain, an anti-79b binding domain, an anti-HER2 binding domain, an anti-PMSA binding domain, an anti-MUC16 binding domain, an anti-CD22 binding domain, an anti-PD-Ll binding domain, an anti BAFF or BAFF receptor binding domain, an anti- Nectin-4 binding domain, an anti-TROP-2 binding domain, an anti-GPC3 binding domain, and anti-ROR-1 binding domain.
  • BCMA anti-B-cell maturation antigen
  • MSLN anti-mesothelin
  • the nucleic acid is selected from the group consisting of a DNA and an RNA. In some instances, the nucleic acid is an mRNA. In some instances, the recombinant nucleic acid comprises a nucleic acid analog, wherein the nucleic acid analog is not in an encoding sequence of the recombinant nucleic acid.
  • the nucleic analog is selected from the group consisting of 2’-O-methyl, 2’-O- methoxyethyl (2’-O-MOE), 2’-O-aminopropyl, 2’-deoxy, T-deoxy-2’-fluoro, 2’-O-aminopropyl (2’-O-AP), 2'-O-dimethylaminoethyl (2’-O-DMAOE), 2’-O-dimethylaminopropyl (2’-O-DMAP), T-O- dimethylaminoethyloxyethyl (2’-O-DMAEOE), 2’-O-N-methylacetamido (2’-0-NMA) modified, a locked nucleic acid (LNA), an ethylene nucleic acid (ENA), a peptide nucleic acid (PNA), a l’,5’- anhydrohexitol nucleic acid (HNA), a morpholino, a
  • the recombinant nucleic acid further comprises a leader sequence. In some instances, the recombinant nucleic acid further comprises a promoter sequence. In some instances, the recombinant nucleic acid further comprises a sequence encoding a poly(A) tail. In some instances, the recombinant nucleic acid further comprises a 3’UTR sequence. In some instances, the nucleic acid is an isolated nucleic acid or a non-naturally occurring nucleic acid. In some instances, the nucleic acid is an in vitro transcribed nucleic acid. [0375] In some instances, the recombinant nucleic acid further comprises a sequence encoding a TCR alpha transmembrane domain.
  • the recombinant nucleic acid further comprises a sequence encoding a TCR beta transmembrane domain. In some instances, the recombinant nucleic acid further comprises a sequence encoding a TCR alpha transmembrane domain and a sequence encoding a TCR beta transmembrane domain.
  • the TCR subunit comprises an immunoreceptor tyrosine-based activation motif (ITAM) of a TCR subunit that comprises an ITAM or portion thereof of a protein selected from the group consisting of CD3 zeta TCR subunit, CD3 epsilon TCR subunit, CD3 gamma TCR subunit, CD3 delta TCR subunit, TCR zeta chain, Fc epsilon receptor 1 chain, Fc epsilon receptor 2 chain, Fc gamma receptor 1 chain, Fc gamma receptor 2a chain, Fc gamma receptor 2b 1 chain, Fc gamma receptor 2b2 chain, Fc gamma receptor 3a chain, Fc gamma receptor 3b chain, Fc beta receptor 1 chain, TYROBP (DAP12), CD5, CD16a, CD 16b, CD22, CD23, CD32, CD64, CD79a, CD79b, CD89, CD278, CD66
  • ITAM immunorecept
  • the ITAM replaces an ITAM of CD3 gamma, CD3 delta, or CD3 epsilon.
  • the ITAM is selected from the group consisting of CD3 zeta TCR subunit, CD3 epsilon TCR subunit, CD3 gamma TCR subunit, and CD3 delta TCR subunit and replaces a different ITAM selected from the group consisting of CD3 zeta TCR subunit, CD3 epsilon TCR subunit, CD3 gamma TCR subunit, and CD3 delta TCR subunit.
  • the TFP, the TCR gamma constant domain, the TCR delta constant domain, the TCR alpha constant domain, the TCR beta constant domain, and any combination thereof is capable of functionally interacting with an endogenous TCR complex and/or at least one endogenous TCR polypeptide.
  • the TCR constant domain is a TCR gamma constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of TCR beta, CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof;
  • the TCR constant domain is a TCR delta constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of TCR alpha, CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof;
  • the TCR constant domain is a TCR gamma constant domain and a TCR delta constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof;
  • the TCR constant domain is a TCR alpha constant domain and the TFP functionally integrates into a TCR complex comprising
  • the at least one but not more than 20 modifications thereto comprise a modification of an amino acid that mediates cell signaling or a modification of an amino acid that is phosphorylated in response to a ligand binding to the TFP.
  • the murine, human or humanized antibody is an antibody fragment.
  • the antibody fragment is a scFv, a single domain antibody domain (sdAb), a VH domain or a VL domain.
  • murine, human or humanized antibody comprising an antigen binding domain is selected from a group consisting of an anti-CD19 binding domain, anti-B-cell maturation antigen (BCMA) binding domain, anti-mesothelin (MSLN) binding domain, anti-CD22 binding domain, anti-PD-1 binding domain, anti PD-L1 binding domain, anti IL13Ra2 binding domain, anti-BAFF or BAFFR binding domain, and anti-ROR-1 binding domain.
  • BCMA anti-B-cell maturation antigen
  • MSLN anti-mesothelin
  • the antigen domain comprises a ligand.
  • the ligand binds to the receptor of a cell.
  • the ligand binds to the polypeptide expressed on a surface of a cell.
  • the receptor or polypeptide expressed on a surface of a cell comprises a stress response receptor or polypeptide.
  • the receptor or polypeptide expressed on a surface of a cell is an MHC class I-related glycoprotein.
  • the MHC class I-related glycoprotein is selected from the group consisting of MICA, MICB, RAET1E, RAET1G, ULBP1, ULBP2, ULBP3, ULBP4 and combinations thereof.
  • the antigen domain comprises a monomer, a dimer, atrimer, a tetramer, a pentamer, a hexamer, a heptamer, an octomer, a nonamer, or a decamer.
  • the antigen domain comprises a monomer or a dimer of the ligand or fragment thereof.
  • the ligand or fragment thereof is a monomer, a dimer, a trimer, a tetramer, a pentamer, a hexamer, a heptamer, an octomer, a nonamer, or a decamer.
  • the ligand or fragment thereof is a monomer or a dimer. In some instances, the antigen domain does not comprise an antibody or fragment thereof. In some instances, the antigen domain does not comprise a variable region. In some instances, the antigen domain does not comprise a CDR. In some instances, the ligand or fragment thereof is a Natural Killer Group 2D (NKG2D) ligand or a fragment thereof.
  • NVG2D Natural Killer Group 2D
  • the TCR subunit and the antibody domain, the antigen domain or the binding ligand or fragment thereof are operatively linked by a linker sequence.
  • the transmembrane domain is a TCR transmembrane domain from CD3 epsilon, CD3 gamma, CD3 delta, TCR alpha, TCR beta, TCR delta, or TCR gamma.
  • the intracellular domain is derived from only CD3 epsilon, only CD3 gamma, only CD3 delta, only TCR alpha, only TCR beta, only TCR delta, or only TCR gamma.
  • the TCR subunit comprises (i) at least a portion of a TCR extracellular domain, (ii) a TCR transmembrane domain, and (iii) a TCR intracellular domain, wherein at least two of (i), (ii), and (iii) are from the same TCR subunit.
  • the TCR extracellular domain comprises an extracellular domain or portion thereof of a protein selected from the group consisting of a TCR alpha chain, a TCR beta chain, a TCR delta chain, a TCR gamma chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, a CD3 delta TCR subunit, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TCR subunit comprises a transmembrane domain comprising a transmembrane domain of a protein selected from the group consisting of a TCR alpha chain, a TCR beta chain, a TCR delta chain, a TCR gamma chain, a TCR zeta chain, a CD3 epsilon TCR subunit, a CD3 gamma TCR subunit, a CD3 delta TCR subunit, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD28, CD37, CD64, CD80, CD86, CD134, CD137, CD154, functional fragments thereof, and amino acid sequences thereof having at least one but not more than 20 modifications.
  • the TFP, the TCR gamma constant domain, the TCR delta constant domain, the TCR alpha constant domain, the TCR beta constant domain, and any combination thereof is capable of functionally interacting with an endogenous TCR complex and/or at least one endogenous TCR polypeptide.
  • the TCR constant domain is a TCR gamma constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of TCR beta, CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof;
  • the TCR constant domain is a TCR delta constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of TCR gamma, CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof;
  • the TCR constant domain is a TCR gamma constant domain and a TCR delta constant domain and the TFP functionally integrates into a TCR complex comprising an endogenous subunit of CD3 epsilon, CD3 gamma, CD3 delta, or a combination thereof;
  • the TCR constant domain is a TCR alpha constant domain and the TFP functionally integrates into a TCR complex
  • the at least one but not more than 20 modifications thereto comprise a modification of an amino acid that mediates cell signaling or a modification of an amino acid that is phosphorylated in response to a ligand binding to the TFP.
  • the murine, human or humanized antibody is an antibody fragment.
  • the antibody fragment is a scFv, a single domain antibody domain, a VH domain or a VL domain.
  • murine, human or humanized antibody comprising an antigen binding domain is selected from a group consisting of an anti-CD19 binding domain, anti-CD20 binding domain, anti-mesothelin binding domain, anti-PMSA binding domain, anti-CD70 binding domain, anti-CD79b binding domain, anti-MUC16 binding domain, anti-anti-B-cell maturation antigen (BCMA) binding domain, anti-mesothelin (MSLN) binding domain, anti-IL13Ra2 binding domain, anti-CD22 binding domain, anti-BAFF or anti-BAFFR binding domain, anti-PD-1 binding domain, anti-PD-Ll binding domain, and anti-ROR-1 binding domain.
  • a sequence encoding the antigen binding domain or ligand binding domain is operatively linked to a sequence encoding a delta constant domain.
  • the intracellular domain is an intracellular domain of TCR gamma.
  • a sequence encoding the antigen binding domain or ligand binding domain is operatively linked to a sequence encoding a gamma constant domain.
  • the intracellular domain is an intracellular domain of TCR delta.
  • a sequence encoding the antigen binding domain or ligand binding domain is operatively linked to both a sequence encoding a TCR delta constant domain or fragment thereof and a TCR gamma constant domain or fragment thereof.
  • the intracellular signaling domain is CD3 epsilon, CD3 gamma, or CD3 delta. In some embodiments, the intracellular signaling domain is CD3 epsilon. In some embodiments, the recombinant nucleic acid further comprises at least one leader sequence and at least one linker. In some embodiments, the recombinant nucleic acid further comprises a portion of a TCR alpha constant domain, a portion of a TCR beta domain, or both.
  • the sequence comprises, from 5’ to 3’, a first leader sequence, an antigen binding domain sequence, a linker, a TRDC gene sequence, a cleavable linker sequence, a second leader sequence, and a TRGC gene sequence. In some embodiments, the sequence comprises, from 5’-3’, a first leader sequence, a TRDC gene sequence, a cleavable linker sequence, a second leader sequence, an antigen binding domain sequence, a linker sequence, and a TRGC gene sequence.
  • the sequence comprises, from 5’-3’, a first leader sequence, an antigen binding domain sequence, a first linker sequence, a TRDC gene sequence, a cleavable linker, a second leader sequence, a second antigen binding domain sequence, a second linker sequence, and a TRGC gene sequence.
  • the sequence comprises, from 5’-3’, a first leader sequence, a TRDC gene sequence, a first cleavable linker sequence, a second leader sequence, a TRGC gene sequence, a second cleavable linker sequence, a third leader sequence, an antigen binding domain sequence, a linker sequence, and a CD3 epsilon gene sequence.
  • the sequence comprises, from 5’-3’, a first leader sequence, a first antigen binding domain sequence, a first linker sequence, a TRDC gene sequence or fragment thereof, a TRAC gene sequence or fragment thereof, a cleavable linker sequence, a second leader sequence, a second antigen binding domain sequence, a second linker sequence, a TRGC gene sequence or fragment thereof, and a TRBC gene sequence or fragment thereof.
  • the binding ligand is capable of binding an Fc domain of the antibody.
  • the binding ligand is capable of selectively binding an IgGl antibody.
  • the binding ligand is capable of specifically binding an IgG4 antibody.
  • the antibody or fragment thereof binds to a cell surface antigen. In some embodiments, the antibody or fragment thereof is murine, human or humanized. In some embodiments, the antibody or fragment thereof binds to a cell surface antigen on the surface of a tumor cell. In some embodiments, the binding ligand comprises a monomer, a dimer, a trimer, a tetramer, a pentamer, a hexamer, a heptamer, an octomer, a nonamer, or a decamer. In some embodiments, the binding ligand does not comprise an antibody or fragment thereof. In some embodiments, the binding ligand comprises a CD 16 polypeptide or fragment thereof.
  • the binding ligand comprises a CD16-binding polypeptide. In some embodiments, the binding ligand is human or humanized. In some embodiments, the recombinant nucleic acid further comprises a nucleic acid sequence encoding an antibody or fragment thereof capable of being bound by the binding ligand. In some embodiments, the antibody or fragment thereof is capable of being secreted from a cell.
  • Recombinant Nucleic Acid Encoding IL-15 and/or IL-15Ra Disclosed herein are recombinant nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof. Any recombinant nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein may further comprise a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL-15Ra polypeptide or a fragment thereof.
  • Any recombinant nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein may further comprise a second nucleic acid sequence encoding an IL-15Ra polypeptide or a fragment thereof.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid molecules.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid molecule.
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL-15Ra polypeptide or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid molecules.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL-15Ra polypeptide or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid molecule.
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker.
  • the first linker may be a cleavable linker.
  • the first linker may comprise a protease cleavage site.
  • the cleavage site can be a self-cleaving peptide, for example, a 2A cleavage site such as a T2A, P2A, E2A or F2A cleavage site.
  • the protease cleavage site is a T2A cleavage site.
  • the cleavage site can comprise a sequence of SEQ ID NO: 365, when expressed.
  • the first linker comprises a sequence of SEQ ID NO: 365, when expressed.
  • the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof may comprise a sequence encoding IL- 15 signal peptide.
  • IL- 15 signal peptide comprises amino acids 1-29 of SEQ ID NO: 385, when expressed.
  • IL-15 signal peptide comprises a sequence of SEQ ID NO: 374, when expressed.
  • the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof may comprise a sequence encoding amino acids 30-162 of SEQ ID NO: 385.
  • the nucleic acid sequence encoding the IL-15 polypeptide, or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 375. In some embodiments, the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof may comprise a sequence encoding amino acids 1-162 of SEQ ID NO: 385. In some embodiments, the nucleic acid sequence encoding the IL-15 polypeptide, or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 374 and a sequence of SEQ ID NO: 375. In some embodiments, the IL-15 polypeptide or a fragment thereof is secreted when expressed in a T cell. In some embodiments, the IL- 15 polypeptide comprises a sequence of SEQ ID NO: 375, when expressed.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof and an IL-15R subunit or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid molecules.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof and an IL-15R subunit or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid molecule.
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker described herein.
  • An IL-15R subunit may be an IL-15R alpha (IL-15Ra), an IL-2R beta (IL-2[3), or an IL-2R gamma/the common gamma chain (IL-2Ry/yc).
  • the IL-15R subunit is IL-15R alpha (IL-15Ra).
  • IL- 15 and IL-15R subunit are operatively linked by a second linker.
  • IL- 15 and IL-15Ra are operatively linked by a second linker.
  • the second linker is not a cleavable linker.
  • the second linker may comprise a sequence comprising (G 4 S) n, wherein G is glycine, S is serine, and n is an integer from 1 to 10. In some embodiments, n is an integer from 1 to 4. In some embodiments, n is 3. In some embodiments, the second linker comprises a sequence of SEQ ID NO: 378. In some embodiments, the second linker comprises a sequence of SEQ ID NO: 405.
  • the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding the intracellular domain of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 229-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL- 15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 229-267 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 372.
  • the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding IL-15Ra Sushi domain. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 31-95 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL- 15 Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 31-95 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 382.
  • the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding the transmembrane domain and the intracellular domain of IL- 15Ra. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 96-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 96-267 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 383.
  • the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding the Sushi domain, the transmembrane domain, and the intracellular domain of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 31-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 31-267 of SEQ ID NO: 386.
  • the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 382 and a sequence of SEQ ID NO: 383.
  • IL-15Ra comprises a sequence of SEQ ID NO: 403.
  • the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding a soluble IL-15Ra (sIL-15Ra). In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 21-205 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding amino acids 21-205 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the IL-15Ra polypeptide or a fragment thereof may comprise a sequence encoding a sequence of SEQ ID NO: 379.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding a fusion protein comprising an IL- 15 polypeptide linked to an IL-15Ra subunit, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid molecules.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding a fusion protein comprising an IL- 15 polypeptide linked to an IL-15Ra subunit, wherein the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid molecule.
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker described herein.
  • IL-15 polypeptide may be linked to N-terminus of IL-15Ra subunit.
  • IL-15 polypeptide may be linked to C-terminus of IL-15Ra subunit.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 1-29 of IL- 15.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 1-29 of SEQ ID NO: 385.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 374.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 30-162 of IL-15.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 30-162 of SEQ ID NO: 385. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 375. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 1-162 of IL-15. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 1-162 of SEQ ID NO: 385. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 374 and a sequence encoding a sequence of SEQ ID NO: 375.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding the intracellular domain of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 229-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 229-267 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 372.
  • the nucleic acid sequence encoding the fusion protein may further comprise a sequence encoding IL-15Ra Sushi domain. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 31-95 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 31-95 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 382.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding the transmembrane domain and the intracellular domain of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 96-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 96-267 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 383.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding the Sushi domain, the transmembrane domain, and the intracellular domain of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 31-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 31-267 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 382 and a sequence of SEQ ID NO: 383. In some embodiments, IL-15Ra comprises a sequence of SEQ ID NO: 403.
  • the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a soluble IL-15Ra (sIL-15Ra). In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 21-205 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding amino acids 21-205 of SEQ ID NO: 386. In some embodiments, the nucleic acid sequence encoding the fusion protein may comprise a sequence encoding a sequence of SEQ ID NO: 379.
  • the nucleic acid sequence encoding the fusion protein may further comprise a sequence encoding an epitope tag.
  • An epitope tag as described herein can be a peptide epitope tag or a protein epitope tag. Examples of a peptide epitope tag includes, but are not limited to, 6X His (also known as His-tag or hexahistidine tag), FLAG (e.g. , 3X FLAG), HA, Myc, and V5.
  • a protein epitope tag examples include, but are not limited to, green fluorescent protein (GFP), glutathione-S-transferase (GST), [3-galactosidase ([3- GAL), Luciferase, Maltose Binding Protein (MBP), Red Fluorescence Protein (RFP), and Vesicular Stomatitis Virus Glycoprotein (VSV-G).
  • GFP green fluorescent protein
  • GST glutathione-S-transferase
  • [3-galactosidase [3- GAL) Luciferase, Maltose Binding Protein (MBP), Red Fluorescence Protein (RFP), and Vesicular Stomatitis Virus Glycoprotein (VSV-G).
  • the nucleic acid sequence encoding the fusion protein further comprises a sequence encoding a FLAG tag.
  • the nucleic acid sequence encoding the fusion protein further comprises a sequence encoding a 3X FLAG tag.
  • the fusion protein is expressed on cell surface when expressed from the recombinant nucleic acid molecule described herein in a T cell. In some embodiments, the fusion protein is secreted when expressed from the recombinant nucleic acid molecule described herein in a T cell.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein, a second nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof, and a third nucleic acid sequence encoding an agent that can enhance the activity of a modified T cell expressing the TFP.
  • the third nucleic acid sequence is included in a separate nucleic acid sequence.
  • the third nucleic acid sequence is included in the same nucleic acid molecule as the first nucleic acid sequence or the second nucleic acid sequence, or the first and the second nucleic acid sequences.
  • the agent that can enhance the activity of a modified T cell can be a PD-1 polypeptide.
  • the PD-1 polypeptide may be operably linked to the N-terminus of an intracellular domain of a costimulatory polypeptide via the C-terminus of the PD-1 polypeptide.
  • the agent that can enhance the activity of a modified T cell can be an anti -PD-1 antibody, or antigen binding fragment thereof.
  • the anti -PD-1 antibody or antigen binding fragment thereof may be operably linked to the N-terminus of an intracellular domain of a costimulatory polypeptide via the C-terminus of the anti-PD-1 antibody, or antigen binding fragment thereof.
  • the PD-1 polypeptide or anti- PD-1 antibody is linked to the intracellular domain of the costimulatory polypeptide via the transmembrane domain of PD-1.
  • the costimulatory polypeptide is selected from the group consisting of 0X40, CD2, CD27, CDS, ICAM-1, ICOS (CD278), 4-1BB (CD137), GITR, CD28, CD30, CD40, BAFFR, HVEM, CD7, LIGHT, NKG2C, SLAMF7, NKp80, CD 160, CD226, FcyRI, FcyRII, and FcyRIII.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein and a second nucleic acid sequence encoding an IL- 15Ra polypeptide or a fragment thereof, wherein the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker described herein, and wherein the second nucleic acid sequence further encodes an agent that can enhance the activity of a modified T cell expressing the TFP.
  • the agent can be an agent that can inhibit an inhibitory molecule that can decrease the ability of a T cell expressing a TFP to mount an immune effector response.
  • the agent which inhibits an inhibitory molecule comprises a first polypeptide, e.g., an inhibitory molecule, associated with a second polypeptide that provides a positive signal to the cell, e.g., an intracellular signaling domain described herein.
  • the agent may comprise a first polypeptide, e.g., of an inhibitory molecule such as PD-1, LAG3, CTLA4, CD160, BTLA, LAIR1, TIM3, 2B4, and TIGIT, or a fragment of any of these (e.g., at least a portion of an extracellular domain of any of these), and a second polypeptide which is an intracellular signaling domain described herein (e.g., comprising a costimulatory domain (e.g., 4-1BB, CD27, or CD28, as described herein)) and/or a primary signaling domain (e.g., IL-15Ra described herein).
  • a first polypeptide e.g., of an inhibitory molecule such as PD-1, LAG3, CTLA4, CD160, BTLA, LAIR1, TIM3, 2B4, and TIGIT, or a fragment of any of these (e.g., at least a portion of an extracellular domain of any of these)
  • the second nucleic acid sequence further comprises a sequence encoding PD-1 or a fragment thereof. In some embodiments, the second nucleic acid sequence comprises a sequence encoding the extracellular domain of PD-1. In some embodiments, the second nucleic acid sequence comprises a sequence encoding the extracellular domain and transmembrane domain of PD-1. In some embodiments, the second nucleic acid sequence may further comprise a sequence encoding CD28 or a fragment thereof. In some embodiments, the second nucleic acid sequence comprises a sequence encoding the intracellular domain of CD28.
  • the second nucleic acid sequence comprises a sequence encoding a fusion protein comprising the PD-1 extracellular domain and transmembrane domain linked to the CD28 intracellular domain linked to IL-15Ra.
  • the CD28 intracellular domain is linked to the intracellular domain of IL- 15Ra.
  • the intracellular domain of IL-15Ra comprises amino acids 229-267 of IL- 15Ra.
  • the intracellular domain of IL-15Ra comprises amino acids 229-267 of SEQ ID NO: 386.
  • the intracellular domain of IL-15Ra comprises a sequence of SEQ ID NO: 372.
  • the second nucleic acid sequence encoding PD-1, or a fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 366. In some embodiments, the second nucleic acid sequence encoding PD-1, or a fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 367. In some embodiments, the second nucleic acid sequence encoding PD-1, or a fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 368.
  • the second nucleic acid sequence encoding PD-1, or a fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 369.
  • the nucleic acid sequence encoding the transmembrane domain of PD-1 may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 370.
  • the nucleic acid sequence encoding the intracellular domain of CD28 may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 371.
  • the intracellular domain of IL-15Ra comprises amino acids 229-267 of IL-15Ra.
  • the nucleic acid encoding the intracellular domain of IL-15Ra comprises a nucleic acid encoding amino acids 229-267 of SEQ ID NO: 386. In some embodiments, the nucleic acid encoding the intracellular domain of IL- 15Ra comprises a nucleic acid encoding a sequence of SEQ ID NO: 372.
  • nucleic acid molecules comprising a first nucleic acid sequence encoding a TFP described herein, a second nucleic acid sequence encoding an IL-15Ra polypeptide or a fragment thereof and an agent that can enhance the activity of a modified T cell expressing the TFP described herein, and a third nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof.
  • the first nucleic acid sequence and the second nucleic acid sequence are included in two separate nucleic acid sequences.
  • the first nucleic acid sequence and the second nucleic acid sequence are included in a single nucleic acid sequence.
  • the first nucleic acid sequence and the second nucleic acid sequence are operatively linked by a first linker described herein.
  • the third nucleic acid sequence is included in a separate nucleic acid sequence.
  • the third nucleic acid sequence is included in the same nucleic acid molecule as the first nucleic acid sequence or the second nucleic acid sequence, or the first and the second nucleic acid sequences.
  • the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding amino acids 1-29 of IL-15.
  • the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding amino acids 1-29 of SEQ ID NO: 385. In some embodiments, the third nucleic acid sequence encoding the IL-15 polypeptide may comprise a sequence encoding a sequence of SEQ ID NO: 374. In some embodiments, the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding amino acids 30-162 of IL-15. In some embodiments, the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding amino acids 30-162 of SEQ ID NO: 385.
  • the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding a sequence of SEQ ID NO: 375.
  • the IL-15 polypeptide is secreted when expressed in a T cell.
  • the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding amino acids 1-162 of IL-15.
  • the third nucleic acid sequence encoding the IL- 15 polypeptide may comprise a sequence encoding amino acids 1-162 of SEQ ID NO: 385.
  • the third nucleic acid sequence encoding the IL-15 polypeptide may comprise a sequence encoding a sequence of SEQ ID NO: 374 and a sequence of SEQ ID NO: 375.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding a PD-1 polypeptide or a fragment thereof, a nucleic acid sequence encoding CD28 polypeptide or a fragment thereof, a nucleic acid sequence encoding an IL-15Ra or a fragment thereof described herein, and a nucleic acid sequence encoding an IL-15 polypeptide, or a fragment thereof described herein.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding anti-MSLN antibody. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 363. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 signal peptide. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 366. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 N-Loop. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 367.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 IgV. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 368. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 Stalk. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 369.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 transmembrane domain. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 370. In some embodiments, the nucleic acid sequence encoding the CD28 polypeptide or a fragment thereof comprises a sequence encoding CD28 intracellular domain. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 371.
  • the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof comprise a sequence encoding amino acids 229-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 372. In some embodiments, the nucleic acid sequence encoding IL-15 polypeptide or fragment thereof comprise a sequence encoding amino acids 1-29 of IL-15. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 374.
  • the nucleic acid sequence encoding IL-15 polypeptide or fragment thereof may comprise a sequence encoding amino acids 30-162 of IL-15.
  • the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 375.
  • the nucleic acid sequence encoding the TFP and the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof are operatively linked by a T2A linker.
  • the T2A linker may comprise a sequence of SEQ ID NO: 365.
  • the nucleic acid sequence encoding the IL-15Ra or a fragment thereof and the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof are operatively linked by a P2A linker.
  • the P2A linker may comprise a sequence of SEQ ID NO: 373.
  • the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding a PD-1 polypeptide or a fragment thereof, a nucleic acid sequence encoding CD28 polypeptide or a fragment thereof, a nucleic acid sequence encoding an IL-15Ra, and a nucleic acid sequence encoding an IL-15 polypeptide, or a fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 361.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding a PD-1 polypeptide or a fragment thereof, a nucleic acid sequence encoding CD28 polypeptide or a fragment thereof, and a nucleic acid sequence encoding an IL-15Ra or a fragment thereof described herein.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding anti-MSLN antibody. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 363. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 signal peptide.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 366. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 N-Loop. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 367. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 IgV.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 368. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 Stalk. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 369. In some embodiments, the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a sequence encoding PD-1 transmembrane domain.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 370.
  • the nucleic acid sequence encoding the CD28 polypeptide or a fragment thereof comprises a sequence encoding CD28 intracellular domain.
  • the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 371.
  • the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof comprise a sequence encoding amino acids 229-267 of IL-15Ra.
  • the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 372.
  • the nucleic acid sequence encoding the TFP and the nucleic acid sequence encoding the PD-1 polypeptide, or a fragment thereof are operatively linked by a T2A linker.
  • the T2A linker may comprise a sequence of SEQ ID NO: 365.
  • the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding a PD-1 polypeptide or a fragment thereof, a nucleic acid sequence encoding CD28 polypeptide or a fragment thereof, and a nucleic acid sequence encoding an IL-15Ra may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 376.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding an IL- 15 polypeptide, or a fragment thereof described herein, and a nucleic acid sequence encoding an IL-15Ra or a fragment thereof described herein.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding anti-MSLN antibody. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 363. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a sequence encoding amino acids 1- 29 of IL-15.
  • the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 374. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a sequence encoding amino acids 30-162 of IL-15. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 375. In some embodiments, the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof comprise a sequence encoding amino acids 21-205 of IL- 15 Ra.
  • the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 379.
  • the nucleic acid sequence encoding the TFP and the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof are operatively linked by a T2A linker.
  • the T2A linker may comprise a sequence of SEQ ID NO: 365.
  • the nucleic acid sequence encoding the IL- 15 polypeptide or a fragment thereof and the nucleic acid sequence encoding the IL-15Ra or a fragment thereof are operatively linked by a non-cleavable linker.
  • the non-cleavable linker may comprise a sequence of SEQ ID NO: 378.
  • the non-cleavable linker comprises a sequence of SEQ ID NO: 405.
  • the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof, and a nucleic acid sequence encoding an IL-15Ra may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 377.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein and a nucleic acid sequence encoding an IL- 15 polypeptide, or a fragment thereof described herein.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding anti-MSLN antibody.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 363. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a sequence encoding amino acids 1-29 of IL-15.
  • the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 374. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a sequence encoding amino acids 30-162 of IL-15. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 375. In some embodiments, the nucleic acid sequence encoding the TFP and the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof are operatively linked by a T2A linker.
  • the T2A linker may comprise a sequence of SEQ ID NO: 365.
  • the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a TFP described herein and a nucleic acid sequence encoding an IL- 15 polypeptide, or a fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 380.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding an IL- 15 polypeptide, or a fragment thereof described herein, and a nucleic acid sequence encoding an IL-15Ra or a fragment thereof described herein.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding anti-MSLN antibody. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 363. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a sequence encoding amino acids 1- 29 of IL-15.
  • the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 374. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a sequence encoding amino acids 30-162 of IL-15. In some embodiments, the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 375. In some embodiments, the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof comprise a sequence encoding amino acids 31-95 of IL-15Ra.
  • the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 382. In some embodiments, the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof comprise a sequence encoding amino acids 96-267 of IL-15Ra. In some embodiments, the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 383. In some embodiments, the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding SEQ ID NO: 403.
  • the nucleic acid sequence encoding the TFP and the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof are operatively linked by a T2A linker.
  • the T2A linker may comprise a sequence of SEQ ID NO: 365.
  • the nucleic acid sequence encoding the IL-15 polypeptide or a fragment thereof and the nucleic acid sequence encoding the IL-15Ra or a fragment thereof are operatively linked by a non-cleavable linker.
  • the non-cleavable linker may comprise a sequence of SEQ ID NO: 378.
  • the non-cleavable linker may comprise a sequence of SEQ ID NO: 405.
  • the recombinant nucleic acid molecule may further comprise a sequence encoding a 3X FLAG tag.
  • the 3X FLAG comprises a sequence of SEQ ID NO: 384.
  • the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof, and a nucleic acid sequence encoding an IL-15Ra may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 381.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein and a nucleic acid sequence encoding an anti-CD70 antibody or a fragment thereof (CD70 CD3e).
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding an anti-CD70 antibody or a fragment thereof.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 399. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 395. In some embodiments, a linker sequence may be used in the antibody sequence region. In some embodiments, the linker sequence may comprise a sequence encoding SEQ ID NO: 401. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364. In some embodiments, the nucleic acid sequence encoding the anti-CD70 antibody or a fragment thereof and the nucleic acid sequence encoding the CD3s or a fragment thereof are operatively linked by a linker. In some embodiments, the linker may comprise a sequence of SEQ ID NO: 387.
  • the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a CD70 CD3e TFP as described herein may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 400.
  • nucleic acid molecules comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding an anti-CD70 antibody or a fragment thereof, a nucleic acid sequence encoding an IL- 15 polypeptide, or a fragment thereof, and a nucleic acid sequence encoding an IL-15Ra or a fragment thereof (CD70 + mbIL-15Ra).
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CSF2RA signal peptide.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 362. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a sequence encoding an anti-CD70 antibody or a fragment thereof. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 399. In some embodiments, the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 395. In some embodiments, a linker sequence may be used in the antibody sequence region.
  • the linker sequence may comprise a sequence encoding SEQ ID NO: 401.
  • the nucleic acid sequence encoding a TFP may comprise a sequence encoding CD3s.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364.
  • the nucleic acid sequence encoding a TFP may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 364.
  • the nucleic acid sequence encoding the anti-CD70 antibody or a fragment thereof and the nucleic acid sequence encoding the CD3s or a fragment thereof are operatively linked by a linker.
  • the linker may comprise a sequence of SEQ ID NO: 387.
  • the recombinant nucleic acid molecule may comprise a nucleic acid sequence encoding an IL- 15 polypeptide or fragment thereof.
  • the nucleic acid sequence encoding IL- 15 polypeptide or fragment thereof comprises a nucleic acid sequence encoding a sequence of SEQ ID NO: 385.
  • the recombinant nucleic acid molecule may comprise a nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof.
  • the nucleic acid sequence encoding IL-15Ra polypeptide or fragment thereof may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 403.
  • the nucleic acid sequence encoding the TFP and the nucleic acid sequence encoding the IL- 15 polypeptide, or a fragment thereof are operatively linked by a T2A linker.
  • the T2A linker may comprise a sequence of SEQ ID NO: 365.
  • the nucleic acid sequence encoding the IL-15 polypeptide or a fragment thereof and the nucleic acid sequence encoding the IL-15Ra or a fragment thereof are operatively linked by a non-cleavable linker.
  • the non-cleavable linker may comprise a sequence of SEQ ID NO: 378. In some embodiments, the non-cleavable linker comprises a sequence of SEQ ID NO: 405. In some embodiments, the recombinant nucleic acid molecule comprising a nucleic acid sequence encoding a TFP described herein, a nucleic acid sequence encoding an IL- 15 polypeptide or a fragment thereof, and a nucleic acid sequence encoding an IL-15Ra may comprise a nucleic acid sequence encoding a sequence of SEQ ID NO: 402. In some embodiments, the recombinant nucleic acid molecule may comprise a sequence encoding SEQ ID NO: 404.
  • recombinant nucleic acid molecules described herein further comprise a leader sequence.
  • the recombinant nucleic acid molecule is selected from the group consisting of a DNA and an RNA.
  • the recombinant nucleic acid molecule is an mRNA.
  • the recombinant nucleic acid molecule is a circRNA.
  • the recombinant nucleic acid molecule comprises a nucleic acid analog.
  • the nucleic acid analog is not in an encoding sequence of the recombinant nucleic acid.
  • the nucleic analog is selected from the group consisting of 2’-O-methyl, 2’-O-methoxyethyl (2’-O-MOE), 2’-O-aminopropyl, 2’-deoxy, T- deoxy-2’ -fluoro, 2 ’-0 -aminopropyl (2’-O-AP), 2'-O-dimethylaminoethyl (2’-O-DMAOE), 2 -O- dimethylaminopropyl (2’-O-DMAP), T-O-dimethylaminoethyloxyethyl (2’-O-DMAEOE), 2’-O-N- methylacetamido (2’-0-NMA) modified, a locked nucleic acid (LNA), an ethylene nucleic acid (ENA), a peptide nucleic acid (PNA), a l’,5’- anhydrohexitol nucleic acid (HNA), a morph
  • the recombinant nucleic acid molecule further comprises a leader sequence. In some embodiments, the recombinant nucleic acid molecule further comprises a promoter sequence. In some embodiments, the recombinant nucleic acid molecule further comprises a sequence encoding a poly(A) tail. In some embodiments, the recombinant nucleic acid molecule further comprises a 3’UTR sequence. In some embodiments, the recombinant nucleic acid molecule is an isolated nucleic acid or a non-naturally occurring nucleic acid. In some embodiments, the nucleic acid is an in vitro transcribed nucleic acid.
  • vectors comprising the recombinant nucleic acid molecules disclosed herein.
  • the vector is selected from the group consisting of a DNA, a RNA, a plasmid, a lentivirus vector, adenoviral vector, an adeno-associated viral vector (AAV), a Rous sarcoma viral (RSV) vector, or a retrovirus vector.
  • the vector is an AAV6 vector.
  • the vector further comprises a promoter.
  • the vector is an in vitro transcribed vector.
  • nucleic acid sequences coding for the desired molecules can be obtained using recombinant methods known in the art, such as, for example by screening libraries from cells expressing the gene, by deriving the gene from a vector known to include the same, or by isolating directly from cells and tissues containing the same, using standard techniques.
  • the gene of interest can be produced synthetically, rather than cloned.
  • the present disclosure also provides vectors in which a DNA of the present disclosure is inserted.
  • Vectors derived from retroviruses such as the lentivirus are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene and its propagation in daughter cells.
  • Lentiviral vectors have the added advantage over vectors derived from onco-retroviruses such as murine leukemia viruses in that they can transduce non-proliferating cells, such as hepatocytes. They also have the added advantage of low immunogenicity.
  • the vector comprising the nucleic acid encoding the desired TFP, IL- 15 polypeptide, and/or IL-15Ra polypeptide of the present disclosure is an adenoviral vector (A5/35).
  • the expression of nucleic acids encoding TFPs, IL-15 polypeptide, and/or IL-15Ra polypeptide can be accomplished using of transposons such as sleeping beauty, crisper, CAS9, and zinc finger nucleases. See below June et al. 2009 Nature Reviews Immunology 9.10: 704-716, is incorporated herein by reference.
  • the expression constructs of the present disclosure may also be used for nucleic acid immunization and gene therapy, using standard gene delivery protocols.
  • the present disclosure provides a gene therapy vector.
  • the nucleic acid can be cloned into a number of types of vectors.
  • the nucleic acid can be cloned into a vector including, but not limited to a plasmid, a phagemid, a phage derivative, an animal virus, and a cosmid.
  • Vectors of particular interest include expression vectors, replication vectors, probe generation vectors, and sequencing vectors.
  • the expression vector may be provided to a cell in the form of a viral vector.
  • Viral vector technology is well known in the art and is described, for example, in Sambrook et al., 2012, Molecular Cloning: A Laboratory Manual, volumes 1-4, Cold Spring Harbor Press, NY), and in other virology and molecular biology manuals.
  • Viruses, which are useful as vectors include, but are not limited to, retroviruses, adenoviruses, adeno-associated viruses, herpes viruses, and lentiviruses.
  • a suitable vector contains an origin of replication functional in at least one organism, a promoter sequence, convenient restriction endonuclease sites, and one or more selectable markers, (e g., WO 01/96584; WO 01/29058; and U.S. Pat. No. 6,326,193).
  • retroviruses provide a convenient platform for gene delivery systems.
  • a selected gene can be inserted into a vector and packaged in retroviral particles using techniques known in the art.
  • the recombinant virus can then be isolated and delivered to cells of the subject either in vivo or ex vivo.
  • retroviral systems are known in the art.
  • adenovirus vectors are used.
  • a number of adenovirus vectors are known in the art.
  • lentivirus vectors are used.
  • Additional promoter elements e.g., enhancers, regulate the frequency of transcriptional initiation.
  • these are located in the region 30-110 bp upstream of the start site, although a number of promoters have been shown to contain functional elements downstream of the start site as well.
  • the spacing between promoter elements frequently is flexible, so that promoter function is preserved when elements are inverted or moved relative to one another.
  • tk thymidine kinase
  • the spacing between promoter elements can be increased to 50 bp apart before activity begins to decline.
  • individual elements can function either cooperatively or independently to activate transcription.
  • a promoter that is capable of expressing a TFP transgene, IL- 15 transgene, and/or IL- 15Ra transgene in a mammalian T cell is the EFla promoter.
  • the native EFla promoter drives expression of the alpha subunit of the elongation factor- 1 complex, which is responsible for the enzymatic delivery of aminoacyl tRNAs to the ribosome.
  • the EFla promoter has been extensively used in mammalian expression plasmids and has been shown to be effective in driving TFP, IL-15, and/or IL-15Ra expression from transgenes cloned into a lentiviral vector (see, e.g., Milone et al., Mol. Ther. 17(8): 1453-1464 (2009)).
  • Another example of a promoter is the immediate early cytomegalovirus (CMV) promoter sequence. This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto.
  • CMV immediate early cytomegalovirus
  • constitutive promoter sequences may also be used, including, but not limited to the simian virus 40 (SV40) early promoter, mouse mammary tumor virus (MMTV), human immunodeficiency virus (HIV) long terminal repeat (LTR) promoter, MoMuLV promoter, an avian leukemia virus promoter, an Epstein-Barr virus immediate early promoter, a Rous sarcoma virus promoter, as well as human gene promoters such as, but not limited to, the actin promoter, the myosin promoter, the elongation factor- la promoter, the hemoglobin promoter, and the creatine kinase promoter. Further, the present disclosure should not be limited to the use of constitutive promoters.
  • inducible promoters are also contemplated as part of the present disclosure.
  • the use of an inducible promoter provides a molecular switch capable of turning on expression of the polynucleotide sequence which it is operatively linked when such expression is desired or turning off the expression when expression is not desired.
  • inducible promoters include, but are not limited to a metallothionine promoter, a glucocorticoid promoter, a progesterone promoter, and a tetracycline-regulated promoter.
  • the expression vector to be introduced into a cell can also contain either a selectable marker gene or a reporter gene or both to facilitate identification and selection of expressing cells from the population of cells sought to be transfected or infected through viral vectors.
  • the selectable marker may be carried on a separate piece of DNA and used in a co-transfection procedure. Both selectable markers and reporter genes may be flanked with appropriate regulatory sequences to enable expression in the host cells.
  • Useful selectable markers include, for example, antibiotic -resistance genes, such as neo and the like.
  • Reporter genes are used for identifying potentially transfected cells and for evaluating the functionality of regulatory sequences.
  • a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells.
  • Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al., 2000 FEBS Letters 479: 79-82). Suitable expression systems are well known and may be prepared using known techniques or obtained commercially. In general, the construct with the minimal 5 ’ flanking region showing the highest level of expression of reporter gene is identified as the promoter. Such promoter regions may be linked to a reporter gene and used to evaluate agents for the ability to modulate promoter-driven transcription.
  • the vector can be readily introduced into a host cell, e.g., mammalian, bacterial, yeast, or insect cell by any method in the art.
  • the expression vector can be transferred into a host cell by physical, chemical, or biological means.
  • Physical methods for introducing a polynucleotide into a host cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and/or exogenous nucleic acids are well-known in the art. See, for example, Sambrook et al., 2012, Molecular Cloning: A Laboratory Manual, volumes 1-4, Cold Spring Harbor Press, NY). A preferred method for the introduction of a polynucleotide into a host cell is calcium phosphate transfection
  • Biological methods for introducing a polynucleotide of interest into a host cell include the use of DNA and RNA vectors.
  • Viral vectors, and especially retroviral vectors have become the most widely used method for inserting genes into mammalian, e.g., human cells.
  • Other viral vectors can be derived from lentivirus, poxviruses, herpes simplex virus I, adenoviruses and adeno-associated viruses, and the like (see, e.g., U.S. Pat. Nos. 5,350,674 and 5,585,362.
  • Chemical means for introducing a polynucleotide into a host cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil- in-water emulsions, micelles, mixed micelles, and liposomes.
  • An exemplary colloidal system for use as a delivery vehicle in vitro and in vivo is a liposome (e.g., an artificial membrane vesicle).
  • Other methods of state-of-the-art targeted delivery of nucleic acids are available, such as delivery of polynucleotides with targeted nanoparticles or other suitable sub-micron sized delivery system.
  • an exemplary delivery vehicle is a liposome.
  • lipid formulations is contemplated for the introduction of the nucleic acids into a host cell (in vitro, ex vivo or in vivo).
  • the nucleic acid may be associated with a lipid.
  • the nucleic acid associated with a lipid may be encapsulated in the aqueous interior of a liposome, interspersed within the lipid bilayer of a liposome, attached to a liposome via a linking molecule that is associated with both the liposome and the oligonucleotide, entrapped in a liposome, complexed with a liposome, dispersed in a solution containing a lipid, mixed with a lipid, combined with a lipid, contained as a suspension in a lipid, contained or complexed with a micelle, or otherwise associated with a lipid.
  • Lipid, lipid/DNA or lipid/expression vector associated compositions are not limited to any particular structure in solution.
  • Lipids are fatty substances which may be naturally occurring or synthetic lipids.
  • lipids include the fatty droplets that naturally occur in the cytoplasm as well as the class of compounds which contain long-chain aliphatic hydrocarbons and their derivatives, such as fatty acids, alcohols, amines, amino alcohols, and aldehydes.
  • Lipids suitable for use can be obtained from commercial sources. For example, dimyristyl phosphatidylcholine (“DMPC”) can be obtained from Sigma, St.
  • DCP dicetyl phosphate
  • Choi cholesterol
  • DMPG dimyristyl phosphatidylglycerol
  • Stock solutions of lipids in chloroform or chloroform/methanol can be stored at about -20 °C. Chloroform is used as the only solvent since it is more readily evaporated than methanol.
  • Liposome is a generic term encompassing a variety of single and multilamellar lipid vehicles formed by the generation of enclosed lipid bilayers or aggregates. Liposomes can be characterized as having vesicular structures with a phospholipid bilayer membrane and an inner aqueous medium. Multilamellar liposomes have multiple lipid layers separated by aqueous medium. They form spontaneously when phospholipids are suspended in an excess of aqueous solution. The lipid components undergo selfrearrangement before the formation of closed structures and entrap water and dissolved solutes between the lipid bilayers (Ghosh et al., 1991 Glycobiology 5: 505-10).
  • compositions that have different structures in solution than the normal vesicular structure are also encompassed.
  • the lipids may assume a micellar structure or merely exist as nonuniform aggregates of lipid molecules.
  • lipofectamine -nucleic acid complexes are also contemplated.
  • assays include, for example, “molecular biological” assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR; “biochemical” assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELISAs and western blots) or by assays described herein to identify agents falling within the scope of the present disclosure.
  • moleukin assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR
  • biochemical assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological means (ELISAs and western blots) or by assays described herein to identify agents falling within the scope of the present disclosure.
  • the present disclosure further provides a vector comprising a nucleic acid molecule encoding a TFP described herein, an IL-15 polypeptide or a fragment described herein, and/or IL-15Ra polypeptide or a fragment described herein.
  • a vector encoding a TFP described herein, an IL- 15 polypeptide or a fragment described herein, and/or IL-15Ra polypeptide or a fragment described herein can be directly transduced into a cell, e.g., a T cell.
  • the vector is a cloning or expression vector, e.g., a vector including, but not limited to, one or more plasmids (e.g., expression plasmids, cloning vectors, minicircles, minivectors, double minute chromosomes), retroviral and lentiviral vector constructs.
  • the vector is capable of expressing the TFP construct, an IL-15 construct, and/or an IL-15Ra construct in mammalian T cells.
  • the mammalian T cell is a human T cell.
  • RNA construct a TFP encoding RNA construct, a TFP encoding RNA construct, a TFP encoding RNA construct, a
  • IL- 15 encoding RNA construct and/or IL-15Ra encoding RNA construct that can be directly transfected into a cell.
  • a method for generating mRNA for use in transfection can involve in vitro transcription (IVT) of a template with specially designed primers, followed by polyA addition, to produce a construct containing 3 ’ and 5’ untranslated sequence (“UTR”), a 5’ cap and/or Internal Ribosome Entry Site (IRES), the nucleic acid to be expressed, and a polyA tail, typically 50-2000 bases in length.
  • RNA so produced can efficiently transfect different kinds of cells.
  • the template includes sequences for the TFP, IL-15 polypeptide or a fragment thereof, and/or IL-15Ra polypeptide or a fragment thereof described herein.
  • the anti-TAA TFP, IL- 15 polypeptide or a fragment thereof, and/or IL-15Ra polypeptide or a fragment thereof described herein is encoded by a messenger RNA (mRNA).
  • mRNA messenger RNA
  • the mRNA encoding the anti-TAA TFP, IL-15 polypeptide or a fragment thereof, or IL-15Ra polypeptide and/or a fragment thereof described herein is introduced into a T cell for production of a T cell expressing the TFP, IL- 15 polypeptide or a fragment thereof, and/or IL-15Ra polypeptide or a fragment thereof described herein.
  • the in vitro transcribed RNA encoding a TFP, IL-15 polypeptide or a fragment thereof, or IL-15Ra polypeptide or a fragment thereof described herein can be introduced to a cell as a form of transient transfection.
  • the RNA is produced by in vitro transcription using a polymerase chain reaction (PCR)-generated template.
  • DNA of interest from any source can be directly converted by PCR into a template for in vitro mRNA synthesis using appropriate primers and RNA polymerase.
  • the source of the DNA can be, for example, genomic DNA, plasmid DNA, phage DNA, cDNA, synthetic DNA sequence or any other appropriate source of DNA.
  • the desired template for in vitro transcription is a TFP of the present disclosure.
  • the DNA to be used for PCR contains an open reading frame.
  • the DNA can be from a naturally occurring DNA sequence from the genome of an organism.
  • the nucleic acid can include some or all of the 5’ and/or 3’ untranslated regions (UTRs).
  • the nucleic acid can include exons and introns.
  • the DNA to be used for PCR is a human nucleic acid sequence.
  • the DNA to be used for PCR is a human nucleic acid sequence including the 5’ and 3’ UTRs.
  • the DNA can alternatively be an artificial DNA sequence that is not normally expressed in a naturally occurring organism.
  • An exemplary artificial DNA sequence is one that contains portions of genes that are ligated together to form an open reading frame that encodes a fusion protein.
  • the portions of DNA that are ligated together can be from a single organism or from more than one organism.
  • PCR is used to generate a template for in vitro transcription of mRNA which is used for transfection. Methods for performing PCR are well known in the art. Primers for use in PCR are designed to have regions that are substantially complementary to regions of the DNA to be used as a template for the PCR. “Substantially complementary,” as used herein, refers to sequences of nucleotides where a majority or all of the bases in the primer sequence are complementary, or one or more bases are non-complementary, or mismatched.
  • the primers can be designed to be substantially complementary to any portion of the DNA template.
  • the primers can be designed to amplify the portion of a nucleic acid that is normally transcribed in cells (the open reading frame), including 5 ’ and 3 ’ UTRs.
  • the primers can also be designed to amplify a portion of a nucleic acid that encodes a particular domain of interest.
  • the primers are designed to amplify the coding region of a human cDNA, including all or portions of the 5’ and 3’ UTRs.
  • Primers useful for PCR can be generated by synthetic methods that are well known in the art.
  • “Forward primers” are primers that contain a region of nucleotides that are substantially complementary to nucleotides on the DNA template that are upstream of the DNA sequence that is to be amplified.
  • Upstream is used herein to refer to a location 5, to the DNA sequence to be amplified relative to the coding strand.
  • “Reverse primers” are primers that contain a region of nucleotides that are substantially complementary to a double -stranded DNA template that are downstream of the DNA sequence that is to be amplified.
  • Downstream is used herein to refer to a location 3’ to the DNA sequence to be amplified relative to the coding strand.
  • Any DNA polymerase useful for PCR can be used in the methods disclosed herein.
  • the reagents and polymerase are commercially available from a number of sources.
  • the RNA preferably has 5’ and 3’ UTRs.
  • the 5’ UTR is between one and 3000 nucleotides in length.
  • the length of 5 ’ and 3 ’ UTR sequences to be added to the coding region can be altered by different methods, including, but not limited to, designing primers for PCR that anneal to different regions of the UTRs. Using this approach, one of ordinary skill in the art can modify the 5’ and 3’ UTR lengths required to achieve optimal translation efficiency following transfection of the transcribed RNA.
  • the 5’ and 3’ UTRs can be the naturally occurring, endogenous 5’ and 3’ UTRs for the nucleic acid of interest.
  • UTR sequences that are not endogenous to the nucleic acid of interest can be added by incorporating the UTR sequences into the forward and reverse primers or by any other modifications of the template.
  • the use of UTR sequences that are not endogenous to the nucleic acid of interest can be useful for modifying the stability and/or translation efficiency of the RNA. For example, it is known that AU-rich elements in 3’UTR sequences can decrease the stability of mRNA. Therefore, 3’ UTRs can be selected or designed to increase the stability of the transcribed RNA based on properties of UTRs that are well known in the art.
  • the 5’ UTR can contain the Kozak sequence of the endogenous nucleic acid.
  • a consensus Kozak sequence can be redesigned by adding the 5’ UTR sequence.
  • Kozak sequences can increase the efficiency of translation of some RNA transcripts but do not appear to be required for all RNAs to enable efficient translation. The requirement for Kozak sequences for many mRNAs is known in the art.
  • the 5’ UTR can be 5 ’UTR of an RNA virus whose RNA genome is stable in cells.
  • various nucleotide analogues can be used in the 3’ or 5’ UTR to impede exonuclease degradation of the mRNA.
  • a promoter of transcription should be attached to the DNA template upstream of the sequence to be transcribed.
  • the RNA polymerase promoter becomes incorporated into the PCR product upstream of the open reading frame that is to be transcribed.
  • the promoter is a T7 polymerase promoter, as described elsewhere herein.
  • Other useful promoters include, but are not limited to, T3 and SP6 RNA polymerase promoters.
  • the mRNA has both a cap on the 5’ end and a 3’ poly(A) tail which determine ribosome binding, initiation of translation and stability mRNA in the cell.
  • RNA polymerase produces a long concatemeric product which is not suitable for expression in eukaryotic cells.
  • the transcription of plasmid DNA linearized at the end of the 3’ UTR results in normal sized mRNA which is not effective in eukaryotic transfection even if it is polyadenylated after transcription.
  • phage T7 RNA polymerase can extend the 3’ end of the transcript beyond the last base of the template (Schenbom and Mierendorf, Nuc Acids Res., 13:6223-36 (1985); Nacheva and Berzal-Herranz, Eur. J. Biochem., 270: 1485-65 (2003).
  • the polyA/T segment of the transcriptional DNA template can be produced during PCR by using a reverse primer containing a poly-T tail, such as 100 T tail (size can be 50-5000 T), or after PCR by any other method, including, but not limited to, DNA ligation or in vitro recombination.
  • Poly(A) tails also provide stability to RNAs and reduce their degradation. Generally, the length of a poly(A) tail positively correlates with the stability of the transcribed RNA. In one embodiment, the poly(A) tail is between 100 and 5000 adenosines.
  • Poly(A) tails of RNAs can be further extended following in vitro transcription with the use of a poly(A) polymerase, such as E. coli polyA polymerase (E-PAP).
  • E-PAP E. coli polyA polymerase
  • increasing the length of a poly(A) tail from 100 nucleotides to between 300 and 400 nucleotides results in about a two-fold increase in the translation efficiency of the RNA.
  • the attachment of different chemical groups to the 3’ end can increase mRNA stability. Such attachment can contain modified/artificial nucleotides, aptamers and other compounds.
  • ATP analogs can be incorporated into the poly(A) tail using poly(A) polymerase. ATP analogs can further increase the stability of the RNA.
  • RNAs produced by the methods disclosed herein include a 5’ cap.
  • the 5’ cap is provided using techniques known in the art and described herein (Cougot, et al., Trends in Biochem. Set., 29:436-444 (2001); Stepinski, et al., RNA, 7: 1468-95 (2001); Elango, et al., Biochim. Biophys. Res. Commun., 330:958-966 (2005)).
  • RNAs produced by the methods disclosed herein can also contain an internal ribosome entry site (IRES) sequence.
  • IRES sequence may be any viral, chromosomal or artificially designed sequence which initiates cap-independent ribosome binding to mRNA and facilitates the initiation of translation. Any solutes suitable for cell electroporation, which can contain factors facilitating cellular permeability and viability such as sugars, peptides, lipids, proteins, antioxidants, and surfactants can be included.
  • RNA can be introduced into target cells using any of a number of different methods, for instance, commercially available methods which include, but are not limited to, electroporation (Amaxa Nucleofector®-II (Amaxa Biosystems, Cologne, Germany)), ECM 830 (BTX) (Harvard Instruments, Boston, Mass.) or the Gene Pulser® II (BioRad, Denver, Colo.), Multiporator® (Eppendorf, Hamburg Germany), cationic liposome mediated transfection using lipofection, polymer encapsulation, peptide mediated transfection, or biolistic particle delivery systems such as “gene guns” (see, for example, Nishikawa, et al. Hum Gene Ther., 12(8):861-70 (2001).
  • cells comprising the recombinant nucleic acid disclosed herein, the polypeptide disclosed herein, or the vectors disclosed herein.
  • cells comprising the recombinant nucleic acid disclosed herein, the polypeptide disclosed herein, or the vectors disclosed herein; wherein cells comprising the sequence encoding a TFP disclosed herein, an IL-15 polypeptide or a fragment disclosed herein, and/or an IL-15Ra polypeptide or a fragment disclosed herein.
  • the modified cells described herein can be engineered cells expressing an anti-mesothelin TFP and IL- 15 enhancements described herein.
  • the engineered cells can show high transduction efficiency and co-expression.
  • the anti-mesothelin TFP-T cells expressing the IL- 15 enhancement can be highly cytotoxic and produce cytokines in response to mesothelin-expressing tumor cells.
  • the TFP-T cells expressing the IL-15 enhancements described herein can have a favorable phenotype enriched for CD8+ TCSM/TCM cells and show enhanced sternness following activation.
  • the IL- 15 enhancements described herein can autonomously increase TFP-T cell persistence in vitro and in vivo in the absence of external activating stimuli.
  • the TFP-T cells bearing IL- 15 enhancements can show increased expansion and/or persistence in vivo (e.g., protecting mice from tumor rechallenge as shown in Examples).
  • the IL- 15 enhancements described herein can have the potential to increase TFP-T cells persistence in cancer patients for improved efficacy against solid tumors.
  • the cell is a T cell.
  • the T cell is a human T cell.
  • the T cell is a CD8+ or CD4+ T cell.
  • the T cell is a human ot
  • the T cell is a human y5 T cell.
  • the cell is a human NKT cell.
  • the cell is an allogeneic cell or an autologous cell.
  • the T cell is modified to comprise a functional disruption of the TCR.
  • the modified T cells are y5 T cells and do not comprise a functional disruption of an endogenous TCR.
  • the y5 T cells are V51+ V52- y8 T cells. In some embodiments, the y5 T cells are V ⁇ 51- V52+ y8 T cells. In some embodiments, the y5 T cells are V51- ⁇ ! 82- y8 T cells.
  • cells comprising the recombinant nucleic acid disclosed herein, the polypeptide disclosed herein, or the vectors disclosed herein wherein cells comprising the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the IL-15 polypeptide or a fragment thereof is secreted when expressed in a cell.
  • cells disclosed herein may secrete IL-15 polypeptide expressed from the recombinant nucleic acid molecules disclosed herein in response to a cell activation agent.
  • IL- 15 signaling is increased in response to a cell activation agent.
  • the cell activation agent comprises a T cell activation agent.
  • a T cell activation agent as described herein, may include, but is not limited to, an anti-CD3 antibody or a fragment thereof, an anti-CD28 antibody or a fragment thereof, a cytokine, an antigen that binds the antigen binding domain of the TFP described herein, or any combinations thereof.
  • cells comprising the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein may have enhanced survival rate, enhanced effector function, and/or enhanced cytotoxicity compared to cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the cell has enhanced survival rate compared to a cell that does not have IL- 15 signaling.
  • the cell has enhanced survival rate compared to a cell that does not express the IL- 15 polypeptide or a fragment thereof and/or IL-15Ra polypeptide or a fragment thereof. In some embodiments, the cell has enhanced effector function compared to a cell that does not have IL-15 signaling. In some embodiments, the cell has enhanced effector function compared to a cell that does not express the IL- 15 polypeptide or a fragment thereof and/or IL-15Ra polypeptide or a fragment thereof. In some embodiments, the cell has enhanced cytotoxicity compared to a cell that does not have IL-15 signaling. In some embodiments, the cell has enhanced cytotoxicity compared to a cell that does not express the IL- 15 polypeptide or a fragment thereof and/or IL-15Ra polypeptide or a fragment thereof.
  • cells comprising the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein may have increased longevity compared to cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the longevity of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • cells comprising the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein may have increased persistence compared to cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the persistence of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • cells comprising the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein may have increased cytotoxicity compared to cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the cytotoxicity of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • cells comprising the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein may have increased cytokine production compared to cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the cytokine production of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • cells disclosed herein retains naive and/or central memory phenotypes. In some embodiments, cells disclosed herein have not differentiated into terminal effector cells.
  • a population of cells comprising any of the cell described herein.
  • a population of cells comprising any of the cell described herein, wherein the population of cells has an increased proportion of cells having a central memory phenotype relative to a population of cells that do not comprise the sequence encoding TFP disclosed herein, IL-15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the population of cells has an increased proportion of cells having a central memory phenotype relative to a population of cells that do not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • population of cells comprising any of the cell described herein, wherein the population of cells has an increased proportion of cells having a naive phenotype relative to a population of cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the population of cells has an increased proportion of cells having a naive phenotype relative to a population of cells that do not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • population of cells comprising any of the cell described herein, wherein the population of cells has a reduced proportion of cells having a terminal effector phenotype relative to a population of cells that do not comprise the sequence encoding TFP disclosed herein, IL- 15 polypeptide or a fragment disclosed herein, and/or IL-15Ra polypeptide or a fragment disclosed herein.
  • the population of cells has a reduced proportion of cells having a terminal effector phenotype relative to a population of cells that do not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • modified T cells comprising the recombinant nucleic acid disclosed herein, or the vectors disclosed herein; wherein the modified T cell comprises a functional disruption of an endogenous TCR.
  • modified T cells comprising the sequence encoding the TFP of the nucleic acid disclosed herein or a TFP encoded by the sequence of the nucleic acid disclosed herein, wherein the modified T cell comprises a functional disruption of an endogenous TCR.
  • modified allogenic T cells comprising the sequence encoding the TFP disclosed herein or a TFP encoded by the sequence of the nucleic acid disclosed herein.
  • the T cell further comprises a heterologous sequence encoding a TCR constant domain, wherein the TCR constant domain is a TCR alpha constant domain, a TCR beta constant domain, a TCR alpha constant domain and a TCR beta constant domain, a TCR gamma constant domain, a TCR delta constant domain or a TCR gamma constant domain and a TCR delta constant domain.
  • the TCR constant domain is a TCR alpha constant domain, a TCR beta constant domain, a TCR alpha constant domain and a TCR beta constant domain, a TCR gamma constant domain, a TCR delta constant domain or a TCR gamma constant domain and a TCR delta constant domain.
  • the endogenous TCR that is functionally disrupted is an endogenous TCR alpha chain, an endogenous TCR beta constant domain, an endogenous TCR alpha constant domain and an endogenous TCR beta constant domain, an endogenous TCR gamma chain, an endogenous TCR delta chain, or an endogenous TCR gamma chain and an endogenous TCR delta chain.
  • the endogenous TCR that is functionally disrupted has reduced binding to MHC -peptide complex compared to that of an unmodified control T cell.
  • the functional disruption is a disruption of a gene encoding the endogenous TCR.
  • the disruption of a gene encoding the endogenous TCR is a removal of a sequence of the gene encoding the endogenous TCR from the genome of a T cell.
  • the T cell is a human T cell.
  • the T cell is a CD8+ or CD4+ T cell.
  • the T cell is an allogenic T cell.
  • the modified T cells further comprise a nucleic acid encoding an inhibitory molecule that comprises a first polypeptide comprising at least a portion of an inhibitory molecule, associated with a second polypeptide comprising a positive signal from an intracellular signaling domain.
  • the inhibitory molecule comprises the first polypeptide comprising at least a portion of PD-1 and the second polypeptide comprising a costimulatory domain and primary signaling domain.
  • a T cell expressing the TFP descried herein can inhibit tumor growth when expressed in a T cell.
  • proliferation of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • the proliferation of the cell can be increased for at least about 5%.
  • IL-15 is operatively linked to IL-15Ra.
  • the activity or persistence of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15 polypeptide or a fragment thereof as described herein is increased.
  • IL- 15 is operatively linked to IL-15Ra.
  • the activity or persistence of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%, at least 2000%, at least 300
  • the activity or persistence of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold, at least 600 fold,
  • the activity or persistence of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased.
  • the activity or persistence of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%, at least 2000%, at least
  • the activity or persistence of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold, at least 600 fold
  • the proliferation of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased.
  • IL- 15 is operatively linked to IL- 15Ra.
  • the proliferation of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%, at least 2000%, at least 3000%,
  • the proliferation of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold, at least 600 fold, at least
  • the proliferation of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased.
  • the proliferation of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%, at least 2000%, at least 3000%
  • the proliferation of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold, at least 600 fold, at
  • expression of an exhaustion marker of the cell is decreased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL-15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • expression of the exhaustion marker of the cell can be decreased for at least about 5% .
  • the exhaustion marker can be PD-1, TIM-3 or LAG-3 .
  • IL- 15 is operatively linked to IL-15Ra.
  • the expression of one or more exhaustion markers in the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15 polypeptide or a fragment thereof as described herein is decreased.
  • IL- 15 is operatively linked to IL-15Ra.
  • the expression of one or more exhaustion markers in the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is decreased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.9%, or 100% as compared with the cells expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein, but do not express a recombinant nucleic acid molecule comprising a sequence encoding an IL- 15 poly
  • the expression of one or more exhaustion markers in the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is decreased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold
  • the expression of one or more exhaustion markers in the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is decreased.
  • the expression of one or more exhaustion markers in the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is decreased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98%, at least 99%, at least 99.5%, at least 99.9%, or 100% as compared with the cells expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein, but do not express a recombinant nucleic acid molecule comprising a sequence encoding an IL-15R
  • the expression of one or more exhaustion markers in the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is decreased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550
  • expression of TCF-1 of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • the TCF-1 + T cell population is increased in a population of the cells expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein.
  • IL-15 is operatively linked to IL-15Ra.
  • the TCF-1+ T cell population is increased in a population of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%,
  • the TCF-1+ T cell population is increased in a population of the cells expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least
  • the TCF-1+ T cell population is increased in a population of the cells expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein.
  • the TCF-1+ T cell population is increased in a population of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%
  • the TCF-1+ T cell population is increased in a population of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least
  • tumor infiltration of the cell is increased compared to a cell that does not comprise (i) a nucleic acid sequence encoding an interleukin- 15 (IL- 15) polypeptide or a fragment thereof or (ii) a nucleic acid sequence encoding an interleukin- 15 receptor alpha (IL-15Ra) polypeptide or a fragment thereof.
  • IL- 15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • the tumor infiltration of the cell can be increased for at least about 2-fold.
  • IL- 15 is operatively linked to IL-15Ra.
  • the tumor infiltration of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased.
  • IL- 15 is operatively linked to IL-15Ra.
  • the tumor infiltration of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%, at least 2000%, at least 300
  • the tumor infdtration of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL- 15 polypeptide or a fragment thereof as described herein is increased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold, at least
  • the tumor infdtration of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased.
  • the tumor infiltration of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased by at least 5%, at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 35%, at least 40%, at least 45%, at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 100%, at least 150%, at least 200%, at least 250%, at least 300%, at least 350%, at least 400%, at least 450%, at least 500%, at least 550%, at least 600%, at least 650%, at least 700%, at least 750%, at least 800%, at least 850%, at least 900%, at least 950%, at least 1000%, at least 2000%, at least
  • the tumor infiltration of the cell expressing a recombinant nucleic acid molecule comprising a sequence encoding TFP as described herein and a sequence encoding an IL-15Ra polypeptide or a fragment thereof as described herein is increased by at least 2 fold, at least 3 fold, at least 4 fold, at least 5 fold, at least 6 fold, at least 7 fold, at least 8 fold, at least 9 fold, at least 10 fold, at least 15 fold, at least 20 fold, at least 25 fold, at least 30 fold, at least 35 fold, at least 40 fold, at least 45 fold, at least 50 fold, at least 55 fold, at least 60 fold, at least 65 fold, at least 70 fold, at least 75 fold, at least 80 fold, at least 85 fold, at least 90 fold, at least 95 fold, at least 100 fold, at least 150 fold, at least 200 fold, at least 250 fold, at least 300 fold, at least 350 fold, at least 400 fold, at least 450 fold, at least 500 fold, at least 550 fold, at least 600 fold
  • a source of T cells is obtained from a subject.
  • the term “subject” is intended to include living organisms in which an immune response can be elicited (e.g., mammals). Examples of subjects include humans, dogs, cats, mice, rats, and transgenic species thereof.
  • T cells can be obtained from a number of sources, including 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 aspects of the present disclosure, any number of T cell lines available in the art, may be used.
  • T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled artisan, such as FicollTM separation.
  • cells from the circulating blood of an individual are obtained by apheresis.
  • the apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets.
  • the cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps.
  • the cells are washed with phosphate buffered saline (PBS).
  • PBS phosphate buffered saline
  • the wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations. Initial activation steps in the absence of calcium can lead to magnified activation.
  • a washing step may be accomplished by methods known to those in the art, such as by using a semi-automated “flow-through” centrifuge (for example, the Cobe® 2991 cell processor, the Baxter Oncology CytoMateTM, or the Haemonetics® Cell Saver® 5) according to the manufacturer’s instructions.
  • a semi-automated “flow-through” centrifuge for example, the Cobe® 2991 cell processor, the Baxter Oncology CytoMateTM, or the Haemonetics® Cell Saver® 5
  • the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca-free, Mg-free PBS, PlasmaLyte A, or other saline solution with or without buffer.
  • buffers such as, for example, Ca-free, Mg-free PBS, PlasmaLyte A, or other saline solution with or without buffer.
  • the undesirable components of the apheresis sample may be removed, and the cells directly resuspended in culture media.
  • T cells are isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLL® gradient or by counterflow centrifugal elutriation.
  • a specific subpopulation of T cells such as CD3+, CD28+, CD4+, CD8+, CD45RA+, and CD45RO+ T cells, can be further isolated by positive or negative selection techniques.
  • T cells are isolated by incubation with anti-CD3/anti-CD28 (e.g., 3x28)-conjugated beads, such as DYNABEADS® M-450 CD3/CD28 T, for a time period sufficient for positive selection of the desired T cells.
  • the time period is about 30 minutes.
  • the time period ranges from 30 minutes to 36 hours or longer and all integer values there between.
  • the time period is at least 1, 2, 3, 4, 5, or 6 hours.
  • the time period is 10 to 24 hours.
  • the incubation time period is 24 hours.
  • TIL tumor infiltrating lymphocytes
  • subpopulations of T cells can be preferentially selected for or against at culture initiation or at other desired time points.
  • multiple rounds of selection can also be used in the context of this present disclosure. In certain aspects, it may be desirable to perform the selection procedure and use the “unselected” cells in the activation and expansion process. “Unselected” cells can also be subjected to further rounds of selection.
  • Enrichment of a T cell population by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells.
  • One method is cell sorting and/or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected.
  • a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CD1 lb, CD16, HLA-DR, and CD8.
  • it may be desirable to enrich for or positively select for regulatory T cells which typically express CD4+, CD25+, CD62Lhi, GITR+, and FoxP3+.
  • T regulatory cells are depleted by anti-C25 conjugated beads or other similar method of selection.
  • a T cell population can be selected that expresses one or more of IFN-y TNF- alpha, IL-17A, IL-2, IL-3, IL-4, GM-CSF, IL-10, IL-13, granzyme B, and perforin, or other appropriate molecules, e.g., other cytokines.
  • Methods for screening for cell expression can be determined, e.g., by the methods described in PCT Publication No.: WO 2013/126712.
  • the concentration of cells and surface can be varied.
  • it may be desirable to significantly decrease the volume in which beads and cells are mixed together e.g., increase the concentration of cells, to ensure maximum contact of cells and beads.
  • a concentration of 2 billion cells/mL is used.
  • a concentration of 1 billion cells/mL is used.
  • greater than 100 million cells/mL is used.
  • a concentration of cells of 10, 15, 20, 25, 30, 35, 40, 45, or 50 million cells/mL is used.
  • a concentration of cells from 75, 80, 85, 90, 95, or 100 million cells/mL is used.
  • concentrations of 125 or 150 million cells/mL can be used.
  • Using high concentrations can result in increased cell yield, cell activation, and cell expansion.
  • use of high cell concentrations allows more efficient capture of cells that may weakly express target antigens of interest, such as CD28-negative T cells, or from samples where there are many tumor cells present (e.g., leukemic blood, tumor tissue, etc.). Such populations of cells may have therapeutic value and would be desirable to obtain.
  • using high concentration of cells allows more efficient selection of CD8+ T cells that normally have weaker CD28 expression.
  • the concentration of cells used is 5xlO 6 /mL. In other aspects, the concentration used can be from about I x I OVmL to lxlO 6 /mL, and any integer value in between. In other aspects, the cells may be incubated on a rotator for varying lengths of time at varying speeds at either 2-10 °C or at room temperature.
  • T cells for stimulation can also be frozen after a washing step.
  • the freeze and subsequent thaw step provides a more uniform product by removing granulocytes and to some extent monocytes in the cell population.
  • the cells may be suspended in a freezing solution.
  • one method involves using PBS containing 20% DMSO and 8% human serum albumin, or culture media containing 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin and 7.5% DMSO, or 31.25% Plasmalyte-A, 31.25% Dextrose 5%, 0.45% NaCl, 10% Dextran 40 and 5% Dextrose, 20% Human Serum Albumin, and 7.5% DMSO or other suitable cell freezing media containing for example, Hespan and PlasmaLyte A, the cells then are frozen to -80 °C at a rate of 1 per minute and stored in the vapor phase of a liquid nitrogen storage tank.
  • cryopreserved cells are thawed and washed as described herein and allowed to rest for one hour at room temperature prior to activation using the methods of the present disclosure.
  • a blood sample or an apheresis product is taken from a generally healthy subject.
  • a blood sample or an apheresis is taken from a generally healthy subject who is at risk of developing a disease, but who has not yet developed a disease, and the cells of interest are isolated and frozen for later use.
  • the T cells may be expanded, frozen, and used at a later time.
  • samples are collected from a patient shortly after diagnosis of a particular disease as described herein but prior to any treatments.
  • the cells are isolated from a blood sample or an apheresis from a subject prior to any number of relevant treatment modalities, including but not limited to treatment with agents such as natalizumab, efalizumab, antiviral agents, chemotherapy, radiation, immunosuppressive agents such as cyclosporin, azathioprine, methotrexate, and mycophenolate, antibodies, or other immunoablative agents such as alemtuzumab, anti-CD3 antibodies, cytoxan, fludarabine, cyclosporin, tacrolimus, rapamycin, mycophenolic acid, steroids, romidepsin, and irradiation.
  • agents such as natalizumab, efalizumab, antiviral agents, chemotherapy, radiation, immunosuppressive agents such as cyclosporin, azathioprine, methotrexate, and mycophenolate, antibodies, or other immunoablative agents such as alemtuzumab, anti-CD3
  • T cells are obtained from a patient directly following treatment that leaves the subject with functional T cells.
  • the quality of T cells obtained may be optimal or improved for their ability to expand ex vivo.
  • these cells may be in a preferred state for enhanced engraftment and in vivo expansion.
  • mobilization for example, mobilization with GM-CSF
  • conditioning regimens can be used to create a condition in a subject wherein repopulation, recirculation, regeneration, and/or expansion of particular cell types is favored, especially during a defined window of time following therapy.
  • Illustrative cell types include T cells, B cells, dendritic cells, and other cells of the immune system. Activation and Expansion of T Cells
  • T cells may be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and 7,572,631.
  • the T cells of the present disclosure may be expanded by contact with a surface having attached thereto an agent that stimulates a CD3/TCR complex associated signal and a ligand that stimulates a costimulatory molecule on the surface of the T cells.
  • T cell populations may be stimulated as described herein, such as by contact with an anti-CD3 antibody, or antigen-binding fragment thereof, or an anti-CD2 antibody immobilized on a surface, or by contact with a protein kinase C activator (e.g., bryostatin) in conjunction with a calcium ionophore.
  • a ligand that binds the accessory molecule is used for co-stimulation of an accessory molecule on the surface of the T cells.
  • a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells.
  • an anti-CD3 antibody and an anti-CD28 antibody include 9.3, B- T3, XR-CD28 (Diaclone, Besancon, France) can be used as can other methods commonly known in the art (Berg et al., Transplant Proc. 30(8):3975-3977, 1998; Haanen et al., J. Exp. Med. 190(9): 13191328, 1999; Garland et al., J.
  • T cells are activated by incubation with anti-CD3/anti-CD28-conjugated beads, such as DYNABEADS® or Trans-Act® beads, for a time period sufficient for activation of the T cells.
  • the time period is at least 1, 2, 3, 4, 5, or 6 hours.
  • the time period is 10 to 24 hours, e.g., 24 hours.
  • T cells are activated by stimulation with an anti-CD3 antibody and an anti-CD28 antibody in combination with cytokines that bind the common gamma-chain (e.g., IL-2, IL-7, IL-12, IL-15, IL-21, and others).
  • T cells are activated by stimulation with an anti-CD3 antibody and an anti-CD28 antibody in combination with 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500, 600, 700, 800, 900, or 100 U/mL of IL-2, IL-7, and/or IL-15.
  • the cells are activated for 24 hours.
  • the cells after transduction, are expanded in the presence of anti-CD3 antibody, anti-CD28 antibody in combination with the same cytokines.
  • cells activated in the presence of an anti-CD3 antibody and an anti-CD28 antibody in combination with cytokines that bind the common gamma-chain are expanded in the presence of the same cytokines in the absence of the anti-CD3 antibody and anti-CD28 antibody after transduction.
  • the cells after transduction, the cells are expanded in the presence of anti-CD3 antibody, anti-CD28 antibody in combination with the same cytokines up to a first washing step, when the cells are sub-cultured in media that includes the cytokines but does not include the anti-CD3 antibody and anti-CD28 antibody.
  • the cells are subcultured every 1, 2, 3, 4, 5, or 6 days.
  • cells are expanded for 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 days.
  • T cells may be stimulated with zoledronic acid (Zometa), alendronic acid (Fosamax) or other related bisphosphonate drugs at concentrations of 0.1, 0.25, 0.5, 1.0, 2.0, 3.0, 4.0, 5.0, 7.5, 10, or 100 pM in the presence of feeder cells (irradiated cancer cells, PBMCs, artificial antigen presenting cells).
  • Zometa zoledronic acid
  • Fosamax alendronic acid
  • 5.0, 7.5, 10 pM
  • feeder cells irradiated cancer cells, PBMCs, artificial antigen presenting cells.
  • T cells may be stimulated with isopentyl pyrophosphate (IPP), (E)-4-Hydroxy-3 -methyl -but-2- enyl pyrophosphate (HMBPP or HMB-PP) or other structurutally related compounds at concentrations of 0.1, 0.25, 0.5, 1.0, 2.0, 3.0, 4.0, 5.0, 7.5, 10, or 100 pM in the presence of feeder cells (irradiated cancer cells, PBMCs, artificial antigen presenting cells).
  • IPP isopentyl pyrophosphate
  • HMBPP or HMB-PP HMB-4-Hydroxy-3 -methyl -but-2- enyl pyrophosphate
  • HMBPP or HMB-PP structurutally related compounds at concentrations of 0.1, 0.25, 0.5, 1.0, 2.0, 3.0, 4.0, 5.0, 7.5, 10, or 100 pM in the presence of feeder cells (irradiated cancer cells, PBMCs, artificial
  • the expansion of T cells may be stimulated with synthetic phosphoantigens (e.g., bromohydrin pyrophosphate; BrHPP), 2M3B1 PP, or 2-methyl-3- butenyl-1 -pyrophosphate in the presence of IL-2 for one-to-two weeks.
  • the expansion of T cells may be stimulated with immobilized anti-TCRyd (e.g., pan TCRY6) in the presence of IL-2, e.g., for approximately 14 days.
  • the expansion of T cells may be stimulated with culture of immobilized anti-CD3 antibodies (e.g., OKT3) in the presence of IL-2.
  • the aforementioned culture is maintained for about seven days prior to subculture in soluble anti-CD3, and IL-2.
  • T cells that have been exposed to varied stimulation times may exhibit different characteristics.
  • typical blood or apheresed peripheral blood mononuclear cell products have a helper T cell population (TH, CD4+) that is greater than the cytotoxic or suppressor T cell population (TC, CD8+).
  • TH, CD4+ helper T cell population
  • TC cytotoxic or suppressor T cell population
  • Ex vivo expansion of T cells by stimulating CD3 and CD28 receptors produces a population of T cells that prior to about days 8-9 consists predominately of TH cells, while after about days 8-9, the population of T cells comprises an increasingly greater population of TC cells.
  • infusing a subject with a T cell population comprising predominately of TH cells may be advantageous.
  • an antigen-specific subset of TC cells may be beneficial to expand this subset to a greater degree.
  • anti-CD19, anti-BCMA, anti-CD22, anti-RORl, anti-PD-1, or anti-BAFF, anti-MUC16, anti- mesothelin, anti-HER2, anti-PMSA, anti-CD20, anti-CD70, anti-GPC3, anti-Nectin-4, anti-Trop2, or antiCD79b TFP is constructed, various assays can be used to evaluate the activity of the molecule, such as but not limited to, the ability to expand T cells following antigen stimulation, sustain T cell expansion in the absence of re-stimulation, and anti -cancer activities in appropriate in vitro and animal models.
  • TFP expression in primary T cells can be used to detect the presence of monomers and dimers (see, e.g., Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)).
  • T cells (1: 1 mixture of CD4 + and CD8 + T cells) expressing the TFPs are expanded in vitro for more than 10 days followed by lysis and SDS-PAGE under reducing conditions. TFPs are detected by western blotting using an antibody to a TCR chain. The same T cell subsets are used for SDS-PAGE analysis under non-reducing conditions to permit evaluation of covalent dimer formation.
  • In vitro expansion of TFP + T cells following antigen stimulation can be measured by flow cytometry.
  • a mixture of CD4 + and CD8 + T cells are stimulated with alphaCD3/alphaCD28 and APCs followed by transduction with lentiviral vectors expressing GFP under the control of the promoters to be analyzed.
  • promoters include the CMV IE gene, EF-1 alpha, ubiquitin C, or phosphoglycerokinase (PGK) promoters.
  • GFP fluorescence is evaluated on day 6 of culture in the CD4+ and/or CD8+ T cell subsets by flow cytometry (see, e.g, Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)).
  • a mixture of CD4+ and CD8+ T cells are stimulated with alphaCD3/alphaCD28 coated magnetic beads on day 0 and transduced with TFP on day 1 using a bicistronic lentiviral vector expressing TFP along with eGFP using a 2A ribosomal skipping sequence.
  • Cultures are re-stimulated with either TAA+ K562 cells (K562-TAA), wild-type K562 cells (K562 wild type) or K562 cells expressing hCD32 and 4-1BBL in the presence of anti- CD3 and anti-CD28 antibody (K562-BBL-3/28) following washing.
  • Exogenous IL-2 is added to the cultures every other day at 100 lU/mL.
  • GFP+ T cells are enumerated by flow cytometry using bead-based counting (see, e.g., Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)).
  • Sustained TFP+ T cell expansion in the absence of re -stimulation can also be measured (see, e.g., Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)). Briefly, mean T cell volume (fl) is measured on day 8 of culture using a Coulter Multisizer III particle counter following stimulation with alphaCD3/alphaCD28 coated magnetic beads on day 0, and transduction with the indicated TFP on day 1. [0500] Animal models can also be used to measure a TFP-T activity.
  • xenograft model using, e.g., human CD19-specific TFP+ T cells to treat a primary human pre-B ALL in immunodeficient mice can be used (see, e.g., Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)).
  • mice are randomized as to treatment groups. Different numbers of engineered T cells are coinjected at a 1: 1 ratio into NOD/SCID/y-/- mice bearing B-ALL. The number of copies of each vector in spleen DNA from mice is evaluated at various times following T cell injection. Animals are assessed for leukemia at weekly intervals.
  • Peripheral blood CD 19+ B-ALL blast cell counts are measured in mice that are injected with alphaCD 19 -zeta TFP+ T cells or mock-transduced T cells. Survival curves for the groups are compared using the log-rank test.
  • absolute peripheral blood CD4+ and CD8+ T cell counts 4 weeks following T cell injection in NOD/SCID/y-/- mice can also be analyzed. Mice are injected with leukemic cells and 3 weeks later are injected with T cells engineered to express TFP by a bicistronic lentiviral vector that encodes the TFP linked to eGFP. T cells are normalized to 45-50% input GFP+ T cells by mixing with mock-transduced cells prior to injection and confirmed by flow cytometry. Animals are assessed for leukemia at 1-week intervals. Survival curves for the TFP+ T cell groups are compared using the log-rank test.
  • Dose dependent TFP treatment response can be evaluated (see, e.g. , Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)).
  • peripheral blood is obtained 35-70 days after establishing leukemia in mice injected on day 21 with TFP T cells, an equivalent number of mock-transduced T cells, or no T cells. Mice from each group are randomly bled for determination of peripheral blood CD 19+ ALL blast counts and then killed on days 35 and 49. The remaining animals are evaluated on days 57 and 70.
  • Assessment of cell proliferation and cytokine production has been previously described, e.g., at Milone et al., Molecular Therapy 17(8): 1453-1464 (2009).
  • TFP-mediated proliferation is performed in microtiter plates by mixing washed T cells with K562 cells expressing the tumor associated antigen (TAA, e.g., CD19) CD19 (K19) or CD32 and CD137 (KT32-BBL) for a final T cell:K562 ratio of 2: 1.
  • K562 cells are irradiated with gamma-radiation prior to use.
  • Anti-CD3 (clone OKT3) and anti-CD28 (clone 9.3) monoclonal antibodies are added to cultures with KT32-BBL cells to serve as a positive control for stimulating T cell proliferation since these signals support long-term CD8+ T cell expansion ex vivo.
  • T cells are enumerated in cultures using CountBrightTM fluorescent beads (Invitrogen) and flow cytometry as described by the manufacturer.
  • TFP+ T cells are identified by GFP expression using T cells that are engineered with eGFP-2A linked TFP -expressing lentiviral vectors.
  • the TFP+ T cells are detected with biotinylated recombinant CD19 protein and a secondary avidin-PE conjugate.
  • CD4+ and CD8+ expression on T cells are also simultaneously detected with specific monoclonal antibodies (BD Biosciences).
  • Cytokine measurements are performed on supernatants collected 24 hours following restimulation using the human TH1/TH2 cytokine cytometric bead array kit (BD Biosciences) according the manufacturer’s instructions. Fluorescence is assessed using a FACScaliburTM flow cytometer (BD Biosciences), and data are analyzed according to the manufacturer’s instructions.
  • Cytotoxicity can be assessed by a standard 51 Cr-release assay (see, e.g. , Milone et al., Molecular Therapy 17(8): 1453-1464 (2009)).
  • Target cells K562 lines and primary pro-B-ALL cells
  • 51 Cr as NaCrCfi. New England Nuclear
  • Effector T cells are mixed with target cells in the wells in complete RPMI at varying ratios of effector cell: target cell (E:T).
  • Imaging technologies can be used to evaluate specific trafficking and proliferation of TFPs in tumorbearing animal models. Such assays have been described, e.g., in Barrett et al., Human Gene Therapy T. 1575-1586 (2011).
  • NOD/SCID/yc-/- (NSG) mice are injected IV with Nalm-6 cells (ATCC® CRL- 3273TM) followed 7 days later with T cells 4 hour after electroporation with the TFP constructs.
  • the T cells are stably transfected with a lentiviral construct to express firefly luciferase, and mice are imaged for bioluminescence.
  • therapeutic efficacy and specificity of a single injection of TFP+ T cells in Nalm-6 xenograft model can be measured as the following: NSG mice are injected with Nalm-6 transduced to stably express firefly luciferase, followed by a single tail-vein injection of T cells electroporated with a TAA- TFP 7 days later. Animals are imaged at various time points post injection. For example, photon-density heat maps of firefly luciferase positive leukemia in representative mice at day 5 (2 days before treatment) and day 8 (24 hours post TFP+ PBLs) can be generated.
  • compositions comprising: (a) the cells of the disclosure; and (b) a pharmaceutically acceptable carrier.
  • pharmaceutical compositions comprising: (a) the modified T cells of the disclosure; and (b) a pharmaceutically acceptable carrier.
  • Such compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives.
  • Compositions of the present disclosure are in one aspect formulated for intravenous administration.
  • compositions of the present disclosure may be administered in a manner appropriate to the disease to be treated (or prevented).
  • the quantity and frequency of administration will be determined by such factors as the condition of the patient, and the type and severity of the patient’s disease, although appropriate dosages may be determined by clinical trials.
  • the pharmaceutical composition is substantially free of, e.g., there are no detectable levels of a contaminant, e.g., selected from the group consisting of endotoxin, mycoplasma, replication competent lentivirus (RCL), p24, VSV-G nucleic acid, HIV gag, residual anti-CD3/anti-CD28 coated beads, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture media components, vector packaging cell or plasmid components, a bacterium and a fungus.
  • a contaminant e.g., selected from the group consisting of endotoxin, mycoplasma, replication competent lentivirus (RCL), p24, VSV-G nucleic acid, HIV gag, residual anti-CD3/anti-CD28 coated beads, mouse antibodies, pooled human serum, bovine serum albumin, bovine serum, culture media components, vector packaging cell or plasmid components, a bacterium and a fungus.
  • the bacterium is at least one selected from the group consisting of Alcaligenes faecalis, Candida albicans, Escherichia coli, Haemophilus influenza, Neisseria meningitides, Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumonia, and Streptococcus pyogenes group A.
  • an immunologically effective amount When “an immunologically effective amount,” “an anti-tumor effective amount,” “a tumor-inhibiting effective amount,” or “therapeutic amount” is indicated, the precise amount of the compositions of the present disclosure to be administered can be determined by a physician with consideration of individual differences in age, weight, tumor size, extent of infection or metastasis, and condition of the patient (subject). It can generally be stated that a pharmaceutical composition comprising the T cells described herein may be administered at a dosage of 10 4 to 10 9 cells/kg body weight, in some instances 10 5 to 10 6 cells/kg body weight, including all integer values within those ranges. T cell compositions may also be administered multiple times at these dosages. The cells can be administered by using infusion techniques that are commonly known in immunotherapy (see, e.g., Rosenberg et al., New Eng. J. Med. 319: 1676, 1988).
  • T cells can be activated from blood draws of from 10 cc to 400 cc.
  • T cells are activated from blood draws of 20 cc, 30 cc, 40 cc, 50 cc, 60 cc, 70 cc, 80 cc, 90 cc, or 100 cc.
  • compositions described herein may be administered to a patient trans arterially, subcutaneously, intradermally, intratumorally, intranodally, intramedullary, intramuscularly, by intravenous (i.v.) injection, or intraperitoneally.
  • the T cell compositions of the present disclosure are administered to a patient by intradermal or subcutaneous injection.
  • the T cell compositions of the present disclosure are administered by i.v. injection.
  • the compositions of T cells may be injected directly into a tumor, lymph node, or site of infection.
  • subjects may undergo leukapheresis, wherein leukocytes are collected, enriched, or depleted ex vivo to select and/or isolate the cells of interest, e.g., T cells.
  • T cell isolates may be expanded by methods known in the art and treated such that one or more TFP constructs of the present disclosure may be introduced, thereby creating a modified T-T cell of the present disclosure.
  • Subjects in need thereof may subsequently undergo standard treatment with high dose chemotherapy followed by peripheral blood stem cell transplantation.
  • subjects receive an infusion of the expanded modified T cells of the present disclosure.
  • expanded cells are administered before or following surgery.
  • the dosage of the above treatments to be administered to a patient will vary with the precise nature of the condition being treated and the recipient of the treatment.
  • the scaling of dosages for human administration can be performed according to art-accepted practices.
  • the dose for alemtuzumab will generally be in the range 1 to about 100 mg for an adult patient, usually administered daily for a period between 1 and 30 days.
  • the preferred daily dose is 1 to 10 mg per day although in some instances larger doses of up to 40 mg per day may be used (described in U.S. Pat. No. 6,120,766).
  • the TFP is introduced into T cells, e.g., using in vitro transcription, and the subject (e.g, human) receives an initial administration of TFP T cells of the present disclosure, and one or more subsequent administrations of the TFP T cells of the present disclosure, wherein the one or more subsequent administrations are administered less than 15 days, e.g., 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, or 2 days after the previous administration.
  • more than one administration of the TFP T cells of the present disclosure are administered to the subject (e.g., human) per week, e.g., 1, 3, or 4 administrations of the TFP T cells of the present disclosure are administered per week.
  • the subject receives more than one administration of the TFP T cells per week (e.g., 2, 3 or 4 administrations per week) (also referred to herein as a cycle), followed by a week of no TFP T cells administrations, and then one or more additional administration of the TFP T cells (e.g. , more than one administration of the TFP T cells per week) is administered to the subject.
  • the subject receives more than one cycle of TFP T cells, and the time between each cycle is less than 10, 9, 8, 7, 6, 5, 4, or 3 days.
  • the TFP T cells are administered every other day for 3 administrations per week.
  • the TFP T cells of the present disclosure are administered for at least two, three, four, five, six, seven, eight or more weeks.
  • CD 19 TFP T cells are generated using lentiviral viral vectors, such as lentivirus. TFP-T cells generated that way will have stable TFP expression.
  • TFP T cells transiently express TFP vectors for 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 days after transduction.
  • Transient expression of TFPs can be affected by RNA TFP vector delivery.
  • the TFP RNA is transduced into the T cell by electroporation.
  • a potential issue that can arise in patients being treated using transiently expressing TFP T cells is anaphylaxis after multiple treatments.
  • anaphylactic response might be caused by a patient developing humoral anti-TFP response, i.e., anti-TFP antibodies having an anti-IgE isotype. It is thought that a patient’s antibody producing cells undergo a class switch from IgG isotype (that does not cause anaphylaxis) to IgE isotype when there is a ten to fourteen day break in exposure to antigen.
  • TFP T cell infusion breaks should not last more than ten to fourteen days.
  • a method of producing the modified T cell of the disclosure comprising (a) disrupting an endogenous TCR gene encoding a TCR alpha chain, a TCR beta chain, a TCR gamma chain, a TCR delta chain, or any combination thereof; thereby producing a T cell containing a functional disruption of an endogenous TCR gene; and (b) transducing the T cell containing a functional disruption of an endogenous TCR gene with the recombinant nucleic acid of the disclosure, or the vectors disclosed herein.
  • disrupting comprises transducing the T cell with a nuclease protein or a nucleic acid sequence encoding a nuclease protein that targets the endogenous gene encoding a TCR alpha chain, a TCR beta chain, or a TCR alpha chain and a TCR beta chain.
  • the method comprising transducing a T cell containing a functional disruption of an endogenous TCR gene with the recombinant nucleic acid disclosed herein, or the vectors disclosed herein.
  • the T cell containing a functional disruption of an endogenous TCR gene is a T cell containing a functional disruption of an endogenous TCR gene encoding a TCR alpha chain, a TCR beta chain, or a TCR alpha chain and a TCR beta chain.
  • the T cell is a human T cell.
  • the T cell containing a functional disruption of an endogenous TCR gene has reduced binding to MHC-peptide complex compared to that of an unmodified control T cell.
  • the nuclease is a meganuclease, a zinc -finger nuclease (ZFN), a transcription activator-like effector nuclease (TALEN), a CRISPR/Cas nuclease, CRISPR/Cas nickase, or a megaTAL nuclease.
  • the sequence comprised by the recombinant nucleic acid or the vector is inserted into the endogenous TCR subunit gene at the cleavage site, and wherein the insertion of the sequence into the endogenous TCR subunit gene functionally disrupts the endogenous TCR subunit.
  • the nuclease is a meganuclease.
  • the meganuclease comprises a first subunit and a second subunit, wherein the first subunit binds to a first recognition half-site of the recognition sequence, and wherein the second subunit binds to a second recognition half-site of the recognition sequence.
  • the meganuclease is a single-chain meganuclease comprising a linker, wherein the linker covalently joins the first subunit and the second subunit.
  • the modified T cells disclosed herein are engineered using a gene editing technique such as clustered regularly interspaced short palindromic repeats (CRISPR®, see, e.g., US Patent No. 8,697,359), transcription activator-like effector (TALE) nucleases (TALENs, see, e.g., U.S. Patent No. 9,393,257), meganucleases (endodeoxyribonucleases having large recognition sites comprising doublestranded DNA sequences of 12 to 40 base pairs), zinc finger nuclease (ZFN, see, e.g., Umov et al., Nat. Rev.
  • CRISPR® clustered regularly interspaced short palindromic repeats
  • TALE transcription activator-like effector
  • TALENs transcription activator-like effector
  • meganucleases endodeoxyribonucleases having large recognition sites comprising doublestranded DNA sequences of 12 to 40 base pairs
  • ZFN zinc finger nu
  • a chimeric construct may be engineered to combine desirable characteristics of each subunit, such as conformation or signaling capabilities. See also Sander & Joung, Nat. Biotech. (2014) v32, 347-55; and June et al., 2009 Nature Reviews Immunol. 9.10: 704-716, each incorporated herein by reference.
  • one or more of the extracellular domain, the transmembrane domain, or the cytoplasmic domain of a TFP subunit are engineered to have aspects of more than one natural TCR subunit domain (e.g., are chimeric).
  • the endogenous TCR gene encoding a TCR alpha chain, a TCR beta chain, or a TCR alpha chain and a TCR beta chain can be inactivated in the modified cell (e.g., modified T cell) described herein.
  • the inactivation can include disruption of genomic gene locus, gene silencing, inhibition or reduction of transcription, or inhibition or reduction of translation.
  • the endogenous TCR gene can be silenced, for example, by inhibitory nucleic acids such as siRNA and shRNA.
  • the translation of the endogenous TCR gene can be inhibited by inhibitory nucleic acids such as microRNA.
  • gene editing techniques are employed to disrupt an endogenous TCR gene.
  • mentioned endogenous TCR gene encodes a TCR alpha chain, a TCR beta chain, or a TCR alpha chain and a TCR beta chain.
  • gene editing techniques pave the way for multiplex genomic editing, which allows simultaneous disruption of multiple genomic loci in endogenous TCR gene.
  • multiplex genomic editing techniques are applied to generate gene-disrupted T cells that are deficient in the expression of endogenous TCR, and/or human leukocyte antigens (HLAs), and/or programmed cell death protein 1 (PD- 1), and/or other genes.
  • HLAs human leukocyte antigens
  • PD- 1 programmed cell death protein 1
  • DSB may then be repaired by either non-homologous end joining (NHEJ) or -when donor DNA is present- homologous recombination (HR), an event that introduces the homologous sequence from a donor DNA fragment.
  • NHEJ non-homologous end joining
  • HR homologous recombination
  • nickase nucleases generate single-stranded DNA breaks (SSB).
  • DSBs may be repaired by single strand DNA incorporation (ssDI) or single strand template repair (ssTR), an event that introduces the homologous sequence from a donor DNA.
  • ssDI single strand DNA incorporation
  • ssTR single strand template repair
  • Genome DNA can be performed using site-specific, rare-cutting endonucleases that are engineered to recognize DNA sequences in the locus of interest.
  • Methods for producing engineered, site-specific endonucleases are known in the art.
  • ZFNs zinc-finger nucleases
  • ZFNs are chimeric proteins comprising a zinc finger DNA-binding domain fused to the nuclease domain of the Fokl restriction enzyme.
  • the zinc finger domain can be redesigned through rational or experimental means to produce a protein that binds to a pre -determined DNA sequence -18 base pairs in length.
  • TAL-effector nucleases can be generated to cleave specific sites in genomic DNA.
  • a TALEN comprises an engineered, site-specific DNA-binding domain fused to the Fokl nuclease domain (reviewed in Mak et al. (2013), Curr Opin Struct Biol. 23:93-9).
  • the DNA binding domain comprises a tandem array of TAL- effector domains, each of which specifically recognizes a single DNA base pair.
  • Compact TALENs have an alternative endonuclease architecture that avoids the need for dimerization (Beurdeley et al. (2013), Nat Commun. 4: 1762).
  • a Compact TALEN comprises an engineered, site-specific TAL-effector DNA-binding domain fused to the nuclease domain from the I-TevI homing endonuclease. Unlike Fokl, I-TevI does not need to dimerize to produce a double-strand DNA break so a Compact TALEN is functional as a monomer.
  • Engineered endonucleases based on the CRISPR/Cas9 system are also known in the art (Ran et al. (2013), Nat Protoc. 8:2281-2308; Mali et al. (2013), Nat Methods 10:957-63).
  • the CRISPR gene-editing technology is composed of an endonuclease protein whose DNA-targeting specificity and cutting activity can be programmed by a short guide RNA or a duplex crRNA/TracrRNA.
  • a CRISPR endonuclease comprises two components: (1) a caspase effector nuclease, typically microbial Cas9; and (2) a short “guide RNA” or an RNA duplex comprising an 18 to 20 nucleotide targeting sequence that directs the nuclease to a location of interest in the genome.
  • a caspase effector nuclease typically microbial Cas9
  • a short “guide RNA” or an RNA duplex comprising an 18 to 20 nucleotide targeting sequence that directs the nuclease to a location of interest in the genome.
  • CRISPR systems There are two classes of CRISPR systems known in the art (Adli (2016) Nat. Commun. 9: 1911), each containing multiple CRISPR types. Class 1 contains type I and type III CRISPR systems that are commonly found in Archaea. And, Class II contains type II, IV, V, and VI CRISPR systems. Although the most widely used CRISPR/Cas system is the type II CRISPR-Cas9 system, CRISPR/Cas systems have been repurposed by researchers for genome editing. More than 10 different CRISPR/Cas proteins have been remodeled within last few years (Adli (2016) Nat. Commun. 9: 1911). Among these, such as Casl2a (Cpfl) proteins from Acid- aminococcus sp (AsCpfl) and Lachnospiraceae bacterium (LbCpfl), are particularly interesting.
  • Cpfl Casl2a
  • AsCpfl Acid- aminococcus sp
  • LbCpfl Lachnospir
  • Homing endonucleases are a group of naturally-occurring nucleases that recognize 15-40 base-pair cleavage sites commonly found in the genomes of plants and fungi. They are frequently associated with parasitic DNA elements, such as group 1 self-splicing introns and inteins. They naturally promote homologous recombination or gene insertion at specific locations in the host genome by producing a double - stranded break in the chromosome, which recruits the cellular DNA-repair machinery (Stoddard (2006), Q. Rev. Biophys. 38: 49-95).
  • meganucleases are monomeric proteins with innate nuclease activity that are derived from bacterial homing endonucleases and engineered for a unique target site (Gersbach (2016), Molecular Therapy. 24: 430-446).
  • meganuclease is engineered I-Crel homing endonuclease. In other embodiments, meganuclease is engineered I-Scel homing endonuclease.
  • chimeric proteins comprising fusions of meganucleases, ZFNs, and TALENs have been engineered to generate novel monomeric enzymes that take advantage of the binding affinity of ZFNs and TALENs and the cleavage specificity of meganucleases (Gersbach (2016), Molecular Therapy 24: 430-446).
  • a megaTAL is a single chimeric protein, which is the combination of the easy-to-tailor DNA binding domains from TALENs with the high cleavage efficiency of meganucleases.
  • the nucleases and in the case of the CRISPR/ Cas9 system, a gRNA, may need to be efficiently delivered to the cells of interest. Delivery methods such as physical, chemical, and viral methods are also know in the art (Mali (2013). Indian J. Hum. Genet. 19: 3-8.). In some instances, physical delivery methods can be selected from the methods but not limited to electroporation, microinjection, or use of ballistic particles. On the other hand, chemical delivery methods require use of complex molecules such calcium phosphate, lipid, or protein. In some embodiments, viral delivery methods are applied for gene editing techniques using viruses such as but not limited to adenovirus, lentivirus, and retrovirus.
  • viruses such as but not limited to adenovirus, lentivirus, and retrovirus.
  • the endogenous TCR gene (e.g. , a TRAC locus or a TRBC locus) encoding a TCR alpha chain, a TCR beta chain, or a TCR alpha chain and a TCR beta chain can be inactivated by CRISPR/Cas9 system.
  • the gRNA used to inactivate (e.g., disrupt) the TRAC locus can comprise a sequence of SEQ ID: 406.
  • the gRNA used to disrupt the TRBC locus can comprise a sequence of SEQ ID: 197.
  • CTCGACCAGCTTGACATCAC (SEQ ID NO: 406).
  • ACACTGGTGTGCCTGGCCAC (SEQ ID NO: 197).
  • a method of treating a disease or a condition in a subject in need thereof comprising administering to the subject a therapeutically effective amount of the pharmaceutical compositions described herein.
  • methods of treating a disease or a condition in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a pharmaceutical composition comprising (a) a cell produced according to the methods disclosed herein; and (b) a pharmaceutically acceptable carrier.
  • the disease or the condition is a cancer or a disease or a condition associated with expression of CD 19, B-cell maturation antigen (BCMA), mesothelin (MSLN), CD20, CD70, MUC16, Trop-2, Nectin-4, or GPC3.
  • the cancer is a hematologic cancer.
  • B-cell acute lymphoid leukemia B-ALL
  • T-ALL T cell acute lymphoid leukemia
  • ALL acute lymphoblastic leukemia
  • CML chronic myelogenous leukemia
  • CLL chronic lymphocytic leukemia
  • B-ALL B-cell acute lymphoid leukemia
  • T-ALL T cell acute lymphoid leukemia
  • ALL acute lymphoblastic leukemia
  • CML chronic myelogenous leukemia
  • CLL chronic lymphocytic leukemia
  • B cell prolymphocytic leukemia blastic plasmacytoid dendritic cell neoplasm
  • Burkitt s lymphoma
  • diffuse large B cell lymphoma follicular lymphoma
  • hairy cell leukemia small cell-follicular lymphoma
  • large cell- follicular lymphoma malignant lymphoproliferative conditions
  • MALT lymphoma mantle cell lymphoma
  • IL-15 interleukin- 15
  • IL-15Ra interleukin- 15 receptor alpha
  • a pharmaceutical composition comprising (a) a modified T cell produced according to the methods disclosed herein; and (b) a pharmaceutically acceptable carrier.
  • the modified T cell is an autologous T cell.
  • the T cell is an allogeneic T cell.
  • less cytokines are released in the subject compared a subject administered an effective amount of an unmodified control T cell.
  • less cytokines are released in the subject compared a subject administered an effective amount of a modified T cell comprising the recombinant nucleic acid disclosed herein, or the vector disclosed herein.
  • the method comprises administering the pharmaceutical composition in combination with an agent that increases the efficacy of the pharmaceutical composition. In some instances, the method comprises administering the pharmaceutical composition in combination with an agent that ameliorates one or more side effects associated with the pharmaceutical composition.
  • the cancer is a solid cancer, a lymphoma or a leukemia.
  • the cancer is selected from the group consisting of renal cell carcinoma, breast cancer, lung cancer, ovarian cancer, prostate cancer, colon cancer, cervical cancer, brain cancer, liver cancer, pancreatic cancer, kidney and stomach cancer.
  • the present disclosure includes a type of cellular therapy where T cells are genetically modified to express a TFP and an IL- 15 and/or IL-15Raand the modified T cell is infused to a recipient in need thereof.
  • the infused cell is able to kill tumor cells in the recipient.
  • modified T cells are able to replicate in vivo resulting in long-term persistence that can lead to sustained tumor control.
  • the T cells administered to the patient, or their progeny persist in the patient for at least four months, five months, six months, seven months, eight months, nine months, ten months, eleven months, twelve months, thirteen months, fourteen month, fifteen months, sixteen months, seventeen months, eighteen months, nineteen months, twenty months, twenty-one months, twenty-two months, twenty-three months, two years, three years, four years, or five years after administration of the T cell to the patient.
  • the present disclosure also includes a type of cellular therapy where T cells are modified, e.g. , by in vitro transcribed RNA, to transiently express a TFP and an IL- 15 and/or IL-15Ra and the modified T cell is infused to a recipient in need thereof.
  • the infused cell is able to kill tumor cells in the recipient.
  • the T cells administered to the patient is present for less than one month, e.g., three weeks, two weeks, or one week, after administration of the T cell to the patient.
  • the anti-tumor immunity response elicited by the modified T cells may be an active or a passive immune response, or alternatively may be due to a direct vs indirect immune response.
  • the human modified T cells of the disclosure may be a type of vaccine for ex vivo immunization and/or in vivo therapy in a mammal.
  • the mammal is a human.
  • cells are isolated from a mammal (e.g. , a human) and genetically modified (e.g., transduced or transfected in vitro) with a vector disclosed herein.
  • the modified T cell can be administered to a mammalian recipient to provide a therapeutic benefit.
  • the mammalian recipient may be a human and the modified cell can be autologous with respect to the recipient.
  • the cells can be allogeneic, syngeneic or xenogeneic with respect to the recipient.
  • ex vivo culture and expansion of T cells comprises: (1) collecting CD34+ hematopoietic stem and progenitor cells from a mammal from peripheral blood harvest or bone marrow explants; and (2) expanding such cells ex vivo.
  • other factors such as flt3-U, IL-1, IL-3 and c-kit ligand, can be used for culturing and expansion of the cells.
  • compositions and methods for in vivo immunization to elicit an immune response directed against an antigen in a patient In addition to using a cell-based vaccine in terms of ex vivo immunization, the present disclosure also provides compositions and methods for in vivo immunization to elicit an immune response directed against an antigen in a patient.
  • the cells activated and expanded as described herein may be utilized in the treatment and prevention of diseases that arise in individuals who are immunocompromised.
  • modified T cells of the present disclosure may be administered either alone, or as a pharmaceutical composition in combination with diluents and/or with other components such as IL-2 or other cytokines or cell populations.
  • a modified T cell described herein may be used in combination with other known agents and therapies.
  • Administered “in combination”, as used herein, means that two (or more) different treatments are delivered to the subject during the course of the subject’s affliction with the disorder, e.g., the two or more treatments are delivered after the subject has been diagnosed with the disorder and before the disorder has been cured or eliminated or treatment has ceased for other reasons.
  • the delivery of one treatment is still occurring when the delivery of the second begins, so that there is overlap in terms of administration. This is sometimes referred to herein as “simultaneous” or “concurrent delivery”.
  • the delivery of one treatment ends before the delivery of the other treatment begins.
  • the treatment is more effective because of combined administration.
  • the second treatment is more effective, e.g., an equivalent effect is seen with less of the second treatment, or the second treatment reduces symptoms to a greater extent, than would be seen if the second treatment were administered in the absence of the first treatment or the analogous situation is seen with the first treatment.
  • delivery is such that the reduction in a symptom, or other parameter related to the disorder is greater than what would be observed with one treatment delivered in the absence of the other.
  • the effect of the two treatments can be partially additive, wholly additive, or greater than additive.
  • the delivery can be such that an effect of the first treatment delivered is still detectable when the second is delivered.
  • the “at least one additional therapeutic agent” includes a modified T cell. Also provided are T cells that express multiple TFPs, which bind to the same or different target antigens, or same or different epitopes on the same target antigen.
  • a modified T cell described herein and the at least one additional therapeutic agent can be administered simultaneously, in the same or in separate compositions, or sequentially.
  • the modified T cell described herein can be administered first, and the additional agent can be administered second, or the order of administration can be reversed.
  • a modified T cell described herein may be used in a treatment regimen in combination with surgery, chemotherapy, radiation, immunosuppressive agents, such as cyclosporin, azathioprine, methotrexate, mycophenolate, and tacrolimus, antibodies, or other immunoablative agents such as alemtuzumab, anti-CD3 antibodies or other antibody therapies, cytoxin, fludarabine, cyclosporin, tacrolimus, rapamycin, mycophenolic acid, steroids, romidepsin, cytokines, and irradiation, peptide vaccine, such as that described in Izumoto et al., 2008 J. Neurosurg. 108:963-971.
  • immunosuppressive agents such as cyclosporin, azathioprine, methotrexate, mycophenolate, and tacrolimus
  • antibodies or other immunoablative agents such as alemtuzumab, anti-CD3 antibodies or other antibody therapies, cytoxin, fludarabine
  • the subject can be administered an agent which reduces or ameliorates a side effect associated with the administration of a modified T cell.
  • Side effects associated with the administration of a modified T cell include but are not limited to cytokine release syndrome (CRS), and hemophagocytic lymphohistiocytosis (HLH), also termed Macrophage Activation Syndrome (MAS).
  • CRS cytokine release syndrome
  • HHL hemophagocytic lymphohistiocytosis
  • MAS Macrophage Activation Syndrome
  • Symptoms of CRS include high fevers, nausea, transient hypotension, hypoxia, and the like.
  • the methods disclosed herein can comprise administering a modified T cell described herein to a subject and further administering an agent to manage elevated levels of a soluble factor resulting from treatment with a modified T cell.
  • the soluble factor elevated in the subject is one or more of IFN-y, TNFa, IL-2 and IL-6. Therefore, an agent administered to treat this side effect can be an agent that neutralizes one or more of these soluble factors.
  • agents include, but are not limited to a steroid, an inhibitor of TNFa, and an inhibitor of IL-6.
  • An example of a TNFa inhibitor is entanercept.
  • An example of an IL-6 inhibitor is tocilizumab (toe).
  • the subject can be administered an agent which enhances the activity of a modified T cell.
  • the agent can be an agent which inhibits an inhibitory molecule.
  • Inhibitory molecules e.g., Programmed Death 1 (PD-1)
  • PD-1 can, in some embodiments, decrease the ability of a modified T cell to mount an immune effector response.
  • inhibitory molecules include PD-1, PD-L1, CTLA4, TIM3, LAG3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4 and TGFR beta.
  • Inhibition of an inhibitory molecule, e.g. , by inhibition at the DNA, RNA or protein level, can optimize a modified T cell performance.
  • an inhibitory nucleic acid e.g., an inhibitory nucleic acid, e.g., a dsRNA, e.g., an siRNA or shRNA
  • an inhibitory nucleic acid e.g., an inhibitory nucleic acid, e.g., a dsRNA, e.g., an siRNA or shRNA
  • the inhibitor is a shRNA.
  • the inhibitory molecule is inhibited within a modified T cell.
  • a dsRNA molecule that inhibits expression of the inhibitory molecule is linked to the nucleic acid that encodes a component, e.g., all of the components, of the TFP.
  • the inhibitor of an inhibitory signal can be, e.g., an antibody or antibody fragment that binds to an inhibitory molecule.
  • the agent can be an antibody or antibody fragment that binds to PD-1, PD-L1, PD-L2 or CTLA4 (e.g., ipilimumab (also referred to as MDX-010 and MDX-101 and marketed as Yervoy®; Bristol-Myers Squibb; tremelimumab (IgG2 monoclonal antibody available from Pfizer, formerly known as ticilimumab, CP -675, 206)).
  • the agent is an antibody or antibody fragment that binds to TIM3.
  • the agent is an antibody or antibody fragment that binds to LAG3.
  • the agent which enhances the activity of a modified T cell can be, e.g., a fusion protein comprising a first domain and a second domain, wherein the first domain is an inhibitory molecule, or fragment thereof, and the second domain is a polypeptide that is associated with a positive signal, e.g. , a polypeptide comprising an intracellular signaling domain as described herein.
  • the polypeptide that is associated with a positive signal can include a costimulatory domain of CD28, CD27, ICOS, e.g., an intracellular signaling domain of CD28, CD27 and/or ICOS, and/or a primary signaling domain, e.g., of CD3 zeta, e.g., described herein.
  • the fusion protein is expressed by the same cell that expressed the TFP. In another embodiment, the fusion protein is expressed by a cell, e.g., a T cell that does not express an anti-TAA TFP.
  • TFP constructs can be generated as previously described.
  • An anti-MSLN or CD 19 binder can be linked to a CD3 or TCR DNA fragment by either a DNA sequence encoding a short linker (SL): AAAGGGGSGGGGSGGGGSLE (SEQ ID NO: 387) or a long linker (LL): AAAIEVMYPPPYLGGGGSGGGGSGGGGSLE (SEQ ID NO: 388) into pLRPO or p510 vector.
  • the TFP used is TC-210 (e.g., an anti-MSLN MHle VHH antibody linked to CD3 epsilon) having the sequence of SEQ ID NO: 195.
  • the TFP used is TC-110 (e.g., an anti-CD19 FMC63 scFv antibody linked to CD3 epsilon) having the sequence of SEQ ID NO: 196.
  • a TCR complex contains the CD3-epsilon polypeptide, the CD3-gamma poly peptide, the CD3-delta polypeptide, and the TCR alpha chain polypeptide and the TCR beta chain polypeptide or the TCR delta chain polypeptide and the TCR gamma chain polypeptide.
  • TCR alpha, TCR beta, TCR gamma, and TCR delta recruit the CD3 zeta polypeptide.
  • the human CD3-epsilon polypeptide canonical sequence is Uniprot Accession No. P07766.
  • the human CD3-gamma polypeptide canonical sequence is Uniprot Accession No. P09693.
  • the human CD3-delta polypeptide canonical sequence is Uniprot Accession No. P043234.
  • the human CD3-zeta polypeptide canonical sequence is Uniprot Accession No. P20963.
  • the human TCR alpha chain canonical sequence is Uniprot Accession No. Q6ISU1.
  • the murine TCR alpha chain canonical sequence is Uniprot Accession No. A0A075B662.
  • the human TCR beta chain constant region canonical sequence is Uniprot Accession No. P01850.
  • the murine TCR beta chain constant region canonical sequence is Uniprot Accession No. P01852.
  • the human CD3 -epsilon polypeptide canonical sequence is: MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQHNDKNIG GDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCENCMEMDVMSVATI
  • VIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERPPPVPNPDYEPIRKGQRDLYS GLNQRRI (SEQ ID NO: 124).
  • the mature human CD3 -epsilon polypeptide sequence is:
  • the signal peptide of human CD3a is: MQSGTHWRVLGLCLLSVGVWGQ (SEQ ID NO: 125).
  • the transmembrane domain of human CD3s is: VMSVATIVIVDICITGGLLLLVYYWS (SEQ ID NO: 127).
  • the human CD3 -gamma polypeptide canonical sequence is:
  • the mature human CD3 -gamma polypeptide sequence is:
  • the signal peptide of human CD3y is: MEQGKGLAVLILAIILLQGTLA (SEQ ID NO: 131).
  • the transmembrane domain of human CD3y is: GFLFAEIVSIFVLAVGVYFIA (SEQ ID NO: 133).
  • the intracellular domain of human CD3y is:
  • GQDGVRQSRASDKQTLLPNDQLYQPLKDREDDQYSHLQGNQLRRN (SEQ ID NO: 134).
  • the human CD3 -delta polypeptide canonical sequence is:
  • the mature human CD3 -delta polypeptide sequence is:
  • the signal peptide of human CD35 is: MEHSTFLSGLVLATLLSQVSP (SEQ ID NO: 137).
  • the transmembrane domain of human CD35 is: GUVTDVIATLLLALGVFCFA (SEQ ID NO: 139).
  • the intracellular domain of human CD35 is:
  • the human CD3-zeta polypeptide canonical sequence is:
  • the human TCR alpha chain constant region canonical sequence is:
  • KSDFACANAFNNSIIPEDTFFPSPESSCDVKLVEKSFETDTNLNFQNLSVIGFRILLLKVAGFNLLMTLR LWSS (SEQ ID NO: 142).
  • the human TCR alpha chain human IgC sequence is:
  • the transmembrane domain of the human TCR alpha chain is:
  • VIGFRILLLKVAGFNLLMTLRLW (SEQ ID NO: 144).
  • the intracellular domain of the human TCR alpha chain is: SS (SEQ ID NO: 145)
  • the murine TCR alpha chain constant (mTRAC) region canonical sequence is:
  • the transmembrane domain of the murine TCR alpha chain is: MGLRILLLKVAGFNLLMTLRLW (SEQ ID NO: 147).
  • the intracellular domain of the murine TCR alpha chain is: SS (SEQ ID NO: 145)
  • the human TCR beta chain constant region (mTRBC) canonical sequence is:
  • the human TCR beta chain human IgC sequence is:
  • EDLNKVFPP EVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQP ALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRADCGF
  • the transmembrane domain of the human TCR beta chain is: ILLGKATLYAVLVSALVLMAM (SEQ ID NO: 150).
  • the intracellular domain of the human TCR beta chain is: VKRKDF (SEQ ID NO: 151)
  • the murine TCR beta chain constant region canonical sequence is:
  • the transmembrane domain of the murine TCR beta chain is:
  • ILYEILLGKATLYAVLVSTLVVMAMVK (SEQ ID NO: 153).
  • the intracellular domain of the murine TCR beta chain is: KRKNS (SEQ ID NO: 154)
  • the human TCR gamma chain constant region canonical sequence is:
  • the human TCR gamma human IgC sequence is:
  • the transmembrane domain of the human TCR gamma chain is: YYMYLLLLLKSVVYFAIITCCLL (SEQ ID NO: 156).
  • the intracellular domain of the human TCR gamma chain is: RRTAFCCNGEKS (SEQ ID NO: 157)
  • the human TCR delta chain C region canonical sequence is:
  • the human TCR delta human IgC sequence is:
  • the transmembrane domain of the human TCR delta chain is:
  • LGLRMLFAKTVAVNFLLTAKLFF (SEQ ID NO: 158).
  • the intracellular domain of the human TCR delta chain is: L
  • TFP constructs are in a vector that further contains a sequence encoding an IL- 15 peptide or an IL15-Ra peptide.
  • the IL- 15 may be encoded in the same open reading frame and separated by a self-cleaving peptide (e.g., a P2A or a T2A self-cleaving peptide).
  • the IL-15 peptide comprises a secreted IL-15.
  • the secreted IL-15 can have the sequence of SEQ ID NO: 375.
  • the IL-15 peptide is an IL-15-IL15Ra fusion.
  • IL-15Ra comprises the sequence of SEQ ID NO: 383 or SEQ ID NO: 386.
  • the IL-15-IL15Ra fusion comprises a linker followed by a sushi domain linking IL-15 and IL-15Ra.
  • the IL-15-IL15Ra fusion comprises the sequence of SEQ ID NO: 389.
  • IL-15Ra peptide comprises the extracellular and transmembrane domain of PD-1. The extracellular and transmembrane domain of PD-1 can be fused to the intracellular domain of CD28.
  • the IL-15Ra peptide can further comprise the intracellular domain of IL-15Ra fused to the C-terminus of CD28 (e.g., intracellular domain of CD28).
  • the PD-l-CD28-IL-15Ra fusion comprises the sequence of SEQ ID NO: 390.
  • the vector further contains a sequence encoding a PD-1-CD28 fusion protein.
  • the fusion protein can have the transmembrane domain of PD-1.
  • the PD-1-CD28 fusion protein comprises the sequence of SEQ ID NO: 391. A schematic of the constructs used in this study is shown in Figure 1.

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