WO2023141530A2 - Récepteurs fournissant une costimulation ciblée destinée à une thérapie cellulaire adoptive - Google Patents

Récepteurs fournissant une costimulation ciblée destinée à une thérapie cellulaire adoptive Download PDF

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WO2023141530A2
WO2023141530A2 PCT/US2023/060937 US2023060937W WO2023141530A2 WO 2023141530 A2 WO2023141530 A2 WO 2023141530A2 US 2023060937 W US2023060937 W US 2023060937W WO 2023141530 A2 WO2023141530 A2 WO 2023141530A2
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amino acid
sequence
domain
protein
seq
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PCT/US2023/060937
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WO2023141530A3 (fr
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John Bridgeman
Robert Hawkins
Ruben Rodriguez
Gray KUEBERUWA
Milena KALAITSIDOU
Michael Gavin King
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Instil Bio (Uk) Limited
Instil Bio, Inc.
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Priority claimed from US17/807,109 external-priority patent/US11945876B2/en
Application filed by Instil Bio (Uk) Limited, Instil Bio, Inc. filed Critical Instil Bio (Uk) Limited
Priority to AU2023209445A priority Critical patent/AU2023209445A1/en
Publication of WO2023141530A2 publication Critical patent/WO2023141530A2/fr
Publication of WO2023141530A3 publication Critical patent/WO2023141530A3/fr

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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
    • C07K14/715—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons
    • C07K14/7151—Receptors; Cell surface antigens; Cell surface determinants for cytokines; for lymphokines; for interferons for tumor necrosis factor [TNF], for lymphotoxin [LT]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A61K39/464429—Molecules with a "CD" designation not provided for elsewhere
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/46448—Cancer antigens from embryonic or fetal origin
    • A61K39/464482—Carcinoembryonic antigen [CEA]
    • 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
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/70521—CD28, CD152
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70578—NGF-receptor/TNF-receptor superfamily, e.g. CD27, CD30, CD40, CD95
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1025—Acyltransferases (2.3)
    • C12N9/104—Aminoacyltransferases (2.3.2)
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/27—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by targeting or presenting multiple antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/27—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by targeting or presenting multiple antigens
    • A61K2239/28—Expressing multiple CARs, TCRs or antigens
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/20—Immunoglobulins specific features characterized by taxonomic origin
    • C07K2317/24—Immunoglobulins specific features characterized by taxonomic origin containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2317/00—Immunoglobulins specific features
    • C07K2317/60—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments
    • C07K2317/62—Immunoglobulins specific features characterized by non-natural combinations of immunoglobulin fragments comprising only variable region components
    • C07K2317/622—Single chain antibody (scFv)
    • C—CHEMISTRY; METALLURGY
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    • C12N2740/00—Reverse transcribing RNA viruses
    • C12N2740/00011—Details
    • C12N2740/10011—Retroviridae
    • C12N2740/15011—Lentivirus, not HIV, e.g. FIV, SIV
    • C12N2740/15041—Use of virus, viral particle or viral elements as a vector
    • C12N2740/15043—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector

Definitions

  • the present invention relates to variants of a TRAF domain.
  • T-cells may be genetically modified to retarget them towards defined tumor antigens. This can be done via the gene transfer of peptide (p)-major histocompatibility complex (MHC) specific T-cell Receptors (TCRs) or synthetic fusions between tumor specific single chain antibody fragment (scFv) and T-cell signaling domains (e.g. CD3Q, the latter being termed chimeric antigen receptors (CARs).
  • MHC peptide
  • TCRs tumor specific T-cell Receptors
  • scFv tumor specific single chain antibody fragment
  • CD3Q tumor specific single chain antibody fragment
  • TIL and TCR transfer has proven particularly good when targeting melanoma (Rosenberg et al. 2011; Morgan 2006), whereas CAR therapy has shown much promise in the treatment of certain B-cell malignancies (Grupp et al. 2013).
  • Costimulatory signals are useful to achieve robust CAR T cell expansion, function, persistence and antitumor activity.
  • the success of CAR therapy in leukemia has been partly attributed to the incorporation of costimulatory domains (e.g. CD28 or CD137) into the CAR construct, signals from which synergize with the signal provided by CD3( ⁇ to enhance anti -tumor activity.
  • costimulatory domains e.g. CD28 or CD137
  • signal 1 provided by the TCR complex, synergizes with signal 2 provided by costimulatory receptors such as CD28, CD137 or CD134 to permit the cells to undergo clonal expansion, IL2 production and long term survival without the activation induced cell death (AICD) associated with signal 1 alone. Furthermore the involvement of signal 2 enhances the signal generated through signal 1 allowing the cells to respond better to low avidity interactions such as those encountered during anti-tumor responses.
  • costimulatory receptors such as CD28, CD137 or CD134
  • Targeted costimulation will have beneficial effects for non-CAR-based T-cell therapies.
  • incorporating costimulatory domains into a chimeric TCR has been shown to enhance responses of T-cells towards pMHC (Govers 2014).
  • generating chimeric costimulatory receptors which separate the signal 2 generating costimulatory domain onto a separate receptor from the signal 1 generating CD3( ⁇ (or other) moiety which can also reduce the chances of tonic signalling (Fisher et al 2019).
  • TILs tumor infiltrating lymphocytes
  • TIL tumor infiltrating lymphocytes
  • the invention provides novel chimeric costimulatory antigen receptors (CoStARs) that bind to carcinoembryonic antigen (CEA) and cells comprising or expressing the CoStARs which are beneficial for CAR and non-CAR based T-cell therapies alike.
  • CoStARs novel chimeric costimulatory antigen receptors
  • CEA carcinoembryonic antigen
  • the present invention uses cells that express a novel chimeric costimulatory receptor to provide a costimulatory signal to T-cells upon engagement with a defined disease-associated, for example tumor-associated, antigen.
  • a CoStAR of the invention induces signal 2 upon engagement with a defined antigen such as a disease associated or tumor associated antigen.
  • the full length CD28 molecule contains motifs critical to its native function in binding members of the B7 family of receptors; although this is potentially dangerous from the perspective of CARs carrying CD28 and CD3( ⁇ receptors in tandem, wherein ligation of CAR by B7 could trigger T-cell activation, there are beneficial qualities for receptors harbouring signal 2 receptors alone.
  • the invention provides a targeted chimeric costimulatory receptor (CoStAR) which comprises an extracellular binding domain operatively linked to a transmembrane domain, a first signaling domain, and a CD40 signaling domain or a signaling fragment thereof.
  • costimulatory receptors comprising a CD40 signaling domain display novel and improved activity profiles.
  • the inventors have further discovered that variants of TRAF2, TRAF2/3, and TRAF6 binding domains within CD40 modulate signaling.
  • the CD40 signaling domain comprises SEQ ID NO:32, SEQ ID NO:33, or SEQ ID NO:34.
  • the CD40 signaling fragment comprises an SH3 motif (KPTNKAPH, SEQ ID NO:35), TRAF2 motif (PKQE, SEQ ID NO: 36, PVQE, SEQ ID NO: 37, SVQE, SEQ ID NO: 38), TRAF6 motif (QEPQEINFP, SEQ ID NO:39), PKA motif (KKPTNKA, SEQ ID NO:40, SRISVQE, SEQ ID NO:41), or a combination thereof, or is a full length CD40 intracellular domain.
  • one or more of the SH3, TRAF2, TRAF6, or PKA motifs of the CD40 signaling domain is mutated.
  • the first signaling domain of the CoStAR comprises a signaling domain or signaling fragment of a receptor, such as, for example a tumor necrosis factor receptor superfamily (TNFRSF) receptor, including but not limited to CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), DAP10, NTKR, CD357 (GITR), or EphB6.
  • TNFRSF tumor necrosis factor receptor superfamily
  • the CoStAR comprises CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS) , DAP 10, NTKR, CD357 (GITR), or EphB6.
  • the first signaling domain comprises a CD40 signaling domain
  • the CoStAR comprises elements of two CD40 signaling domains.
  • the CoStAR comprises a second signaling domain or signaling fragment of a receptor, such as, for example a tumor necrosis factor receptor superfamily (TNFRSF) receptor, including but not limited to CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
  • the first signaling domain or signaling fragment, the CD40 signaling domain or signaling fragment, and the second signaling domain or signaling fragment can be in any order.
  • Exemplary embodiments include, without limitation, CoStAR which comprise CD28, CD137, and CD40 signaling domains, CD28, CD 134, and CD40 signaling domains, CD28, CD2, and CD40 signaling domains, CD28, GITR, and CD40 signaling domains, CD28, CD29, and CD40 signaling domains, or CD28, CD 150, and CD40 signaling domains.
  • CoStAR which comprise CD28, CD137, and CD40 signaling domains, CD28, CD 134, and CD40 signaling domains, CD28, CD2, and CD40 signaling domains, CD28, GITR, and CD40 signaling domains, CD28, CD29, and CD40 signaling domains, or CD28, CD 150, and CD40 signaling domains.
  • the extracellular antigen-binding domain (e.g., without limitation CEA-binding domain, MSLN-binding domain) of a CoStAR of the invention is operatively linked to the transmembrane domain by a linker and/or a spacer.
  • the linker comprises from about 5 to about 20 amino acids.
  • the linker comprises AAAGSGGSG (SEQ ID NO: 18).
  • a CoStAR of the invention comprises a spacer which operatively links the extracellular binding domain to the transmembrane domain and comprises from about 10 to about 250 amino acids.
  • the spacer comprises an extracellular sequence of CD8 or CD28 or a fragment thereof.
  • the CoStAR comprises a second extracellular binding domain.
  • the second binding domain comprises an extracellular ligand binding domain from CD8 or CD28.
  • the spacer comprises one or more immunoglobulin domains or an immunoglobulin constant region.
  • the spacer comprises one or more immunoglobulin domains or an immunoglobulin constant region such as, without limitation, SEQ ID NO:24.
  • the transmembrane domain of a CoStAR of the invention comprises a transmembrane domain of a TNFRSF protein. In some embodiments, a transmembrane domain of a CoStAR of the invention comprises a transmembrane domain of CD28 or CD8. In some embodiments, a transmembrane domain of a CoStAR of the invention comprises a transmembrane sequence of CD28 or CD8.
  • the CoStARs of the invention are useful to stimulate an immune response against a selected target that expresses a tumor associated antigen (TAA), e.g. without limitation, carcinoembryonic antigen (CEA), mesothelin (MSLN), or other.
  • TAA tumor associated antigen
  • CEA carcinoembryonic antigen
  • MSLN mesothelin
  • the CoStAR comprises an antigen binding fragment of the scFv of SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, or SEQ ID NO: 14, e.g., a fragment comprising one, two, three, four, five, or all six complementary determining regions (CDRs).
  • the CoStAR comprises the scFv of SEQ ID NO:9, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, or SEQ ID NO: 14.
  • the CoStAR comprises an antigen binding fragment of the scFv of SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 1191, e.g., a fragment comprising one, two, three, four, five, or all six CDRs.
  • the CoStAR comprises the scFv of SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, or SEQ ID NO: 191.
  • an extracellular binding domain can comprise, without limit, an scFv, a peptide, an antigen binding portion of an antibody, an antibody heavy-chain variable domain, an antibody light chain variable domain, a single domain antibody, a CEA ligand, or an MSLN ligand.
  • a CoStAR of the invention comprises a CD3( ⁇ signaling domain, for example located at the C-terminus.
  • a CoStAR of the invention comprises an N-terminal signal peptide.
  • N-terminal signal peptides are signal peptides of oncostatin M (OSM), CD8a, CD2, interleukin-2 (IL-2), granulocyte-macrophage colony stimulating factor (GM-CSF), and human IgGK.
  • nucleic acid which encodes a CoStAR of the invention.
  • the nucleic acid may be optimized, for example be codon optimized for expression in a host cell.
  • nucleic acid is codon optimized for expression in a human cell.
  • vector which encodes and is capable of expressing a CoStAR of any embodiment of the present disclosure.
  • a cell which expresses a CoStAR of any embodiment of the present disclosure.
  • the cell expresses two or more CoStARs, for example the cell expresses a CoStAR that binds to CEA or MSLN and a CoStAR that binds to FOLR1 or a CoStAR that binds to CA125, such as but not limited to anti- CEA.CD28.CD40 and anti-CA125.41BB.CD40 or anti-MSLN.CD28.CD40 and anti- CA125.41BB.CD40.
  • the cell expresses a CoStAR which binds to CEA and a CoStAR which binds to PDL1, such as but not limited to anti-CEA.CD28.CD40 and PD1.CD28.CD40 or expresses a CoStAR which binds to MSLN and a CoStAR which binds to PDL1, such as but not limited to anti-MSLN.CD28.CD40 and PD1.CD28.CD40.
  • a cell engineered to express a CoStAR of any embodiment of the present disclosure comprises an alpha-beta T cell, gamma-delta T cell, T regulatory cell, TIL, NKT cell or NK cell.
  • a cell engineered to express a CoStAR of any embodiment of the present disclosure coexpresses a chimeric antigen receptor (CAR) or a T cell receptor (TCR).
  • CAR chimeric antigen receptor
  • TCR T cell receptor
  • Some embodiments provide a method of making the cell which expresses a CoStAR which comprises transducing or transfecting a cell with a vector which encodes and is capable of expressing a CoStAR of any embodiment of the present disclosure.
  • Some embodiments provide a method for preparing a population of cells that express a CoStAR of any embodiment of the present disclosure by transducing or transfecting cells, detecting expression of the CoStAR and enriching, expanding, and/or selecting cells that express the CoStAR.
  • Some embodiments provide a method of treating a disease in a subject by administering a population of cells which express a CoStAR of any embodiment of the present disclosure.
  • the protein will comprise a variant CD40 and/or TRAF 2, 2/3, 6 domain as disclosed herein.
  • a protein comprising an amino acid sequence comprising a sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein: Xi is any amino acid, X2 is any amino acid, X3 is P, X4 is any amino acid, X5 is Q, Xe is C, E, or A, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid.
  • the protein is part of a TRAF domain. In some embodiments, the protein is part of a TRAF2 domain.
  • the protein is part of a TRAF2/3 domain.
  • the sequence comprises: Xi is S or P, X2 is V, H, or Y, X4 is I, Q, V, X7 is T or S, Xs is D, X9 is K, D, or G, X10 is T, S, G, or A, and Xu is D, S, N, or D; or the sequence is at least 60% identical to a).
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42299.
  • the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42377. In some embodiments, the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42378.
  • a protein comprising an amino acid sequence comprising a sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein: Xi is any amino acid, X 2 is any amino acid, X3 is P, S, A, or T, X4 is any amino acid, X5 is Q or E, Xe is E, X7 is any amino acid, X 8 is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid.
  • the protein is part of a TRAF domain. In some embodiments, the protein is part of a TRAF2 domain.
  • the protein is part of a TRAF2/3 domain.
  • the sequence comprises: Xi is P, A, M, T, S, R, V, H, X 2 is F, A, L, I, T, V, G, C, A, F, P, X 4 is K, V, I, H, A, Q, T, E, S, X 7 is C, T, E, D, S, A, X 8 is A, L, G, Y, I, Q, D, E, X 9 is F, H, K, R, P, A, G, Y, E, N, X10 is R, G, E, K, A, S, D, C, C, P, V, and Xu is S, C, D, P, W, T, A, G, E; or the sequence is at least 60% identical to a).
  • the sequence is part of a Traf 2/3 sequence.
  • the protein is of the sequence 08X1X1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42300.
  • the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42379.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42380.
  • a protein comprising an amino acid sequence comprising a sequence of Consensus C, or X1X2X3X4X5X6, wherein: Xi is P, X 2 is any amino acid, X3 is E, X4 is any amino acid, X5 is any amino acid, and Xe is Ac/ Ar.
  • the protein is part of a TRAF domain. In some embodiments, the protein is part of a TRAF6 domain.
  • the sequence comprises: X 2 is Q, P, E, V, T, or S, X4 is I, L M, N, S, T, N, D, X5 is N, D, R, S, G, or Y; or the sequence is at least 60% identical to a).
  • the protein is of the sequence PKQEX1X2X3X4X5X6, SEQ ID NO: 42301.
  • the protein is of the sequence X1X2X3X4X5X6PDDL, SEQ ID NO: 42381.
  • the protein is of the sequence PKQEX1X2X3X4X5X6PDDL, SEQ ID NO: 42382.
  • amino acid sequence comprising: (a) one or more of SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; (b) a sequence that is at least 70% identical to a sequence in a); or (c) a sequence that is at least 80% similar to a).
  • TRAF domain in a CD40 protein comprises one or more of: (a) SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; (b) a sequence that is at least 70% identical to a sequence in a); or (c) a sequence that is at least 80% similar to a).
  • TRAF6 domain sequence comprising: PQEINF, PEEMSW, PPENYE, or PQENS Y.
  • TRAF2/3 domain sequence comprising: PVQET, TQEET, SKEET, AVEET, or PVQET.
  • TRAF2 domain sequence comprising: SVQE, AVEE or PEEE.
  • TRAF 6 or TRAF2/3 domain that comprises: (a) the amino acid sequence of one of SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511,
  • the sequence is within a CD40 protein sequence for the protein, amino acid sequence, or TRAF domain of any one of the embodiments of the present discosure. In some embodiments, the sequence is within a CD40 protein and is located at a corresponding TRAF 2, TRAF2/3, and/or TRAF6 domain within the CD40 protein.
  • a TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X2 is any amino acid, X3 is P, X4 is any amino acid, X5 is Q, Xe is C, E, or A, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42299.
  • the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42377. In some embodiments, the protein is of the sequence 68 ⁇ X1X2X3X4X5X6X7X8X9X10X1 iQPVT, SEQ ID NO: 42378.
  • TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X2 is any amino acid, X3 is P, S, A, or T, X4 is any amino acid, X5 is Q or E, Xe is E, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42300. In some embodiments, the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42379. In some embodiments, the protein is of the sequence GSNTXIX 2 X3X4X 5 X6X7X8X9XIOXUQPVT, SEQ ID NO: 42380.
  • the protein is of the sequence PKQEX1X2X3X4X5X6, SEQ ID NO: 42301.
  • the protein is of the sequence X1X2X3X4X5X6PDDL, SEQ ID NO: 42381.
  • the protein is of the sequence PKQEX1X2X3X4X5X6PDDL, SEQ ID NO: 42382.
  • a CD40 domain that comprises an amino acid sequence of one or more of the following: (a) TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X 2 is any amino acid, X3 is P, X4 is any amino acid, X5 is Q, Xe is C, E, or A, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid, (b) a TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X 2 is any amino acid, X3 is P, S, A, or T, X4 is any amino acid,
  • a chimeric costimulatory antigen receptor which comprises: an extracellular binding domain that binds to carcinoembryonic antigen (CEA), or an extracellular binding domain that binds to mesothelin (MSLN); a transmembrane domain that is linked to the extracellular binding domain, a first signaling domain; and a second signaling domain, wherein the second signaling domain comprises a variant CD40 signaling domain or a signaling fragment thereof, wherein the variant CD40 comprises a sequence of a variant TRAF2/TRAF3 sequence, or a variant TRAF6 sequence, or a variant TRAF2 sequence, wherein the variant CD40 does not comprise SEQ ID NO: 42.
  • the first signaling domain comprises a signaling domain or signaling fragment of CD28 or CD278 (ICOS).
  • the construct is as shown in Fig. 88A.
  • the construct is as shown in Fig. 88B.
  • the construct is as shown in Fig. 88C.
  • the first signaling domain comprises a full-length costimulatory domain.
  • the extracellular binding domain is operatively linked to the transmembrane domain by a linker and/or a spacer.
  • the linker comprises from about 5 to about 20 amino acids. In some embodiments, the linker comprises from about 10 to about 250 amino acids.
  • the transmembrane domain comprises a transmembrane domain from CD28, CD8, ICOS, DAP 10, or NTRK. In some embodiments, the transmembrane domain comprises the transmembrane domain sequence of SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22. In some embodiments, the extracellular binding domain comprises an scFv, a peptide, an antibody heavy-chain variable domain, an antibody light-chain variable domain, or a CEA ligand. [0048] In some embodiments is a nucleic acid which encodes the CoStAR of any one of the embodiments of the present disclosure.
  • nucleic acid of any one of the embodiments of the present disclosure is a vector comprising the nucleic acid of any one of the embodiments of the present disclosure.
  • the cell which expresses the CoStAR of any one of the embodiments of the present disclosure.
  • the cell comprises an alpha-beta T cell, gamma-delta T cell, T regulatory cell, TIL, NKT cell or NK cell.
  • the cell coexpresses a CAR or a TCR.
  • a method of making the cell of any one of the embodiments of the present disclosure which comprises the step of transducing or transfecting a cell with a vector of any one of the embodiments of the present disclosure
  • a method for preparing a population of cells that express a CoStAR of any one the embodiments of the present disclosure which comprises: detecting expression of the CoStAR on the surface of cells transfected or transduced with a vector of alternative 62; and selecting cells which are identified as expressing the CoStAR.
  • In some embodiments is a cell population which is enriched for cell expression a CoStAR of any one of the embodiments of the present disclosure.
  • a method for treating a disease in a subject which comprises the step of administering a cell according to any one of the embodiments of the present disclosure, or a cell population according to any one of the embodiments of the present disclosure, to the subject.
  • the protein comprises the amino acid sequence of one of SEQ ID NOs: 510-519.
  • the protein comprises the sequence of SEQ ID NO: 510.
  • the protein comprises the sequence of SEQ ID NO: 511.
  • the protein comprises the sequence of SEQ ID NO: 512.
  • the protein comprises the sequence of SEQ ID NO: 513.
  • the protein comprises the sequence of SEQ ID NO: 514.
  • the protein comprises the sequence of SEQ ID NO: 515.
  • the protein comprises the sequence of SEQ ID NO: 516.
  • the protein comprises the sequence of SEQ ID NO: 517.
  • the protein comprises the sequence of SEQ ID NO: 518. In some embodiments, the protein comprises the sequence of SEQ ID NO: 519. In some embodiments, the protein comprises any of the constructs as shown in Fig. 92 (CTP188-CTP202).
  • Fig. 1 Structural organisation of single costimulatory and fusion costimulatory domain receptors.
  • a schematic representation of CoStAR receptors set out in the claims is shown.
  • Figs. 2Ai-2E Genomic organisation of potential CoStAR configurations -
  • the CoStAR consists of an antigen binding domain, an optional spacer domain and a costimulatory domain as shown in figure and described in claims.
  • the CoStAR may be expressed: (Figs.
  • FIG. 2Ai- 2 Aii alone from a promoter with the CoStAR consisting of a single (Fig. 2Ai) or fusion (Fig. 2 Aii) costimulatory receptor;
  • Fig. 2B may be expressed with an epitope tag (e.g. His tag, DYKDDDDK (SEQ ID NO:449) etc) at the N or C-terminus to enable direct staining of the CoStAR;
  • FIG. 2C along with a marker gene separated using a 2A cleavage sequence or internal ribosomal entry site (IRES);
  • FIG. 2D along with a marker gene which is expressed from a second promoter;
  • a protein of interest such as a chimeric antigen receptor or T-cell receptor separated using a 2A cleavage sequence or internal ribosomal entry site (IRES);
  • Fig. 2F along with a protein of interest such as a chimeric antigen receptor or T-cell receptor which is expressed from a second promoter.
  • Figs. 3A-3E Functional activity of CoStAR in T-cells in response to LS174T and LoVo tumour presented antigen.
  • Normal donor T-cell populations from donor 1 (Fig. 3A & 3D), donor 2 (Fig. 3B) and donor 3 (Fig. 3C & 3E) were lentivirally engineered to express a CoStAR which targets carcinoembryonic antigen and magnetically sorted to enrich for the transgene using CD34 magnetic selection.
  • T-cells were mixed with wild-type un-engineered CEA+ tumour cells (Non-activating tumour) or CEA+ tumour cells engineered to express a cell surface anchored anti- CD3 single chain antibody fragment (Activating tumour) at the indicated effector to target ratios and IL-2 measured in the supernatant by ELISA.
  • Figs. 4A-4D Effect of CoStAR on T-cell proliferation. 5x10 ⁇ transduced and non transduced T-cells were mixed with 6.25x10 ⁇ wild-type LoVo or LoVo-OKT3 cells in the presence (Fig. 4A) or absence (Fig. 4B) of IL-2 and cell counts made after three days. In another assay under the same cell ratios T-cells from two donors (Fig. 4C and 4D) were loaded with proliferation dye and the number of proliferation cycles the cells had gone through determined by dye dilution after six days using flow cytometry.
  • Fig. 5 - IL-2 activity of CoStAR fusion receptors in primary human T-cells Normal donor CD8+ T-cells from seven donors (except control CoStAR is three donors) were lentivirally transduced with the indicated CEA-targeting CoStARs and IL-2 production assessed after an overnight stimulation in the presence of LoVo-OKT3 cells. The proportion of IL-2 positive cells was determined using intracellular flow staining in both the CD34 negative (CoStAR nontransduced) and CD34+ (CoStAR transduced) populations. Asterisks show significant differences between the transduced and non-transduced populations using paired Wilcoxon signed rank test with * p ⁇ 0.05
  • Figs. 6A-6D Multi parameter analysis of CoStAR activity in primary human T-cells.
  • Normal donor CD8+ T-cells were lentivirally transduced with the indicated CEA-targeting CoStARs and IL-2 production assessed after an overnight stimulation in the presence of LoVo- OKT3 cells.
  • the proportion of IL-2 (seven donors) (Fig. 6A), IFNy (seven donors) (Fig. 6B), BCL- xL (five donors) (Fig. 6C) and CD107a (six donors) (Fig. 6D) positive cells was determined using intracellular flow staining in both the CD34 negative (CoStAR non-transduced) and CD34+ (CoStAR transduced) populations.
  • Control is a non-specific CA125 targeting CoStAR and is from three donors in all instances. Heat maps are averages of all donors with the intensity of colour related to the percentage of cells positive for a particular read out under the defined conditions.
  • Fig. 7 - CD40 enhances IL-2 production from CD28-based CoStARs.
  • Primary human T-cells from three healthy donors were left non-transduced or transduced with either extracellular domain truncated CD28 (Tr CD28), full length CD28 (FL CD28), or CD28.CD40-based CoStARs harbouring a CEA specific scFv (MFE23).
  • Transduced cells were selected using a CD34 marker gene and expanded prior to analysis.
  • T-cells were mixed at an 8: 1 effector to target ratio with 0KT3 expressing CEA+ LoVo cells for 20 hours before analysis of IL-2 production by ELISA.
  • FIG. 8 Effect of signalling domain and target antigen on CoStAR-mediated T-cell expansion.
  • T-cells were transduced with either DYKDDDDK (SEQ ID NO:449) epitope- tagged CD28 or CD28.CD40 based CoStARs harbouring CA125, FolR or CEA specific scFv, or FolR specific binding peptide (C7).
  • T-cells were mixed with OKT3 expressing, CA125+/FolR+/CEA- cell line OVCAR3. The number of transduced cells were counted every 7 days up to 21 days, with fresh OVCAR3 cells added following each count.
  • FIG. 9 Effect of signalling domain and target antigen on CoStAR- mediated T-cell expansion.
  • T-cells were transduced with either DYKDDDDK (SEQ ID NO:449) epitope-tagged CD28 or CD28.CD40 based CoStARs harbouring CA125, FolR or CEA specific scFv, or FolR specific binding peptide (C7).
  • T-cells were mixed with OKT3 expressing CA125+/FolR+/CEA- cell line OVCAR3. The number of transduced cells were counted every 7 days up to 21 days, with fresh OVCAR3 cells added following each count.
  • Figs. 10A-10B - (Fig. 10A and 10B) CD40 based CoStARs enhance costimulation of T-cells in a model of TCR-transfer.
  • Primary human T-cells from three healthy donors were transduced with a CEA specific TCR plus either a DYKDDDK -tagged CD28 or CD28.
  • CD40 based CoStAR harbouring either an MFE (open or closed circles) or CA125 (open squares) specific scFv.
  • T-cells were mixed at a 1 : 1 effectortarget ratio with CEA+/CA125- H508 cells and intracellular cytokine staining performed to determine the number of responding CD4+ or CD8+ T-cells in the TCR+/CoStAR+, TCR+/CoStAR-, TCR-/CoStAR+ and TCR-/CoStAR- populations.
  • a 2-way ANOVA (Tukeys test) was performed to determine significant differences in activity: *p>0.05, ** p>0.01, *** p>0.001, **** p>0.0001.
  • Fig. 11 depicts enrichment and expansion of primary human T-cells transduced to express costimulatory molecules of the invention.
  • MFE23 is a single chain Fv antibody that has a high affinity for carcinoembryonic antigen (CEA).
  • Primary human T-cells were mock transduced or transduced with MFE23 CD28 or MFE23 CD28.CD40 CoStAR, each harboring a CD34 marker gene separated by a 2A cleavage peptide.
  • MACSTM paramagnetic selection reagents Miltenyi Biotech
  • Figs. 12A-12D depict expansion of T-cells transduced with costimulatory molecules of the invention in response to stimulation and exogenous IL-2.
  • Cells were mock transduced or transduced with MFE23.CD28 or MFE23.CD28.CD40 CoStAR and cocultured with LoVo-OKT3 cells at an 8: 1 effectortarget ratio in the presence (200 lU/ml) or absence of exogenous IL-2.
  • days 1, 4, 7, 11 and 18 cells were taken and the number of viable T-cells enumerated by using anti- CD2 reagents on a MACSQuant flow cytometer.
  • Fig. 12A In the absence of stimulation by tumor and IL-2 cells declined in number as would be expected.
  • FIG. 12B In the absence of stimulation but presence of IL-2 there was a more apparent survival of the cells, but no specific growth.
  • FIG. 12C In the presence of tumor, but absence of IL-2 mock cells did not show specific survival.
  • MFE23.CD28 CoStAR mediated an apparent doubling in expansion over the first four days followed by decline.
  • MFE23.CD28.CD40 mediated a greater expansion up to day 7 followed by a steady decline.
  • FIG. 12D Under the same conditions but in the presence of IL-2 both mock and MFE23.CD28 transduced cells demonstrated a 20-fold expansion over 18 days, whereas MFE23.CD28.CD40 cells expanded by over 60-fold.
  • CD28.CD40 based receptors demonstrate superior expansion and survival under conditions of stimulation both in the presence and absence of exogenous IL-2.
  • Figs. 13A-13M depict cytokine production by mock, MFE23.CD28 or MFE23.CD28.CD40 engineered T-cells. Bead array analysis was performed on supernatants obtained from T-cell/tumour cocultures. Engineered T-cells were incubated at a 1 : 1 effectortarget ratio with LoVo-OKT3 cells for 24 hours and supernatant collected. Conditioned supernatant was also collected from an equal number of T-cells alone, or LoVo-OKT3 cells alone. Cytokine production was analysed using a LegendplexTM Human TH1/TH2 cytokine panel (Biolegend). (Fig. 13A) IL-2; (Fig.
  • MFE23.CD28 enhanced production of IL-2, IL-5, IL-17A/17F, IL-10, IL-9 and IL-21 compared to mock.
  • MFE23.CD28.CD40 also enhanced production of TNFa, IL-13 and IL-22.
  • MFE23.CD28.CD40 and further enhanced the production of a number of cytokines greater than that provided by MFE23.CD28 (IL-2, IL-9 and IL-17F), as well as reducing the production of some cytokines below the levels seen with MFE23.CD28 (IL-5 and IL-10).
  • MFE23.CD28 enhanced production of IL-2, IL-5, IL-17A/17F, IL-10, IL-9 and IL-21 compared to mock.
  • MFE23.CD28.CD40 also enhanced production of TNFa, IL-13 and IL-22.
  • MFE23.CD28.CD40 and further enhanced the production of a number of cytokines greater than that provided by MFE23.CD
  • Figs. 14A-14M depict an analysis of chemokines using a LegendplexTM Human Pro inflammatory chemokine panel.
  • Fig. 14A IL-8 (CXCL8);
  • Fig. 14B IP-10 (CSCL10);
  • Fig. 14C Eotaxin (CCL11);
  • Fig. 14D TARC (CCL17);
  • Fig. 14E MCP-1 (CCL2);
  • Fig. 14F RANTES (CCL5);
  • FIG. 14G MIP-la (CCL3)
  • FIG. 14H MIG (CXCL9)
  • Fig. 14 J MIP-3a (CCL20)
  • CXCL1 GROa (CXCL1)
  • Fig. 14L I-TAC (CXCL11)
  • Fig. 14M MEP- ip (CCL4).
  • Chemokines were either very low or undetectable in media from T-cells alone. When cocultured with tumor, chemokine production was enhanced.
  • MFE23.CD28 enhanced production of CXCL5, CXCL10, CXCL11, CCL17 and CCL20 compared to mock.
  • MFE23.CD28.CD40 also enhanced production of CCL2, CXCL1 and CXCL9.
  • MFE23.CD28.CD40 further enhanced the production of a number of cytokines greater than that provided by MFE23.CD28 (CXCL1, CXCL9, CXCL10, CXCL11, CCL17, CCL2, CXCL9, CCL5 and CCL20), as well as reducing the production of some cytokines below the levels seen with MFE23.CD28 (CCL4).
  • Figs. 15A-15H depict functional activity of ovarian CoStAR engineered cells using a CoStAR harbouring a FolR or CA125 reactive scFv (M0V19 & 196-14 respectively).
  • Human folate receptor alpha represents a suitable target for a number of tumours including ovarian, head and neck, renal and lung and CA125 represents an alternative target for ovarian cancer.
  • Primary human T-cells from six healthy donors were engineered with either 196-14. CD28, 196- 14.CD28.CD40, MOV19.CD28 or MOV19.CD28.CD40 receptors, all harbouring a DYKDDDDK epitope tag for detection.
  • Transduced cells were mixed with FolR+/CA125+ OVCAR-OKT3 cells before analysis of effector activity using intracellular staining in the epitope tag positive and negative populations.
  • Specific enhancement of effector activity determined by production of IL-2 (Fig. 15A and 15B), TNFa (Fig. 15C and 15D), CD137 (Fig. 15E and 15F), and BCL-xL (Fig. 15G and 15H) was observed in in CD28 and CD28.CD40 engineered cells in response to both CA125 and FolR, except for specific BCL-xL induction by MOV19.CD28 which was not observed compared to MOV19.CD28.CD40.
  • Figs. 16A-16F depict three TIL populations mock transduced or engineered with MOV19.CD28.CD40 CoStAR and then mixed with patient matched tumor digest.
  • the donor tumors displayed varying levels of FolR on the digest, ranging from negative (Fig. 16A), low expression (Fig. 16B) to high expression (Fig. 16C).
  • Mock and CoStAR negative TIL in the CoStAR engineered populations of TIL matched for the FolR negative digest demonstrated similar levels of CD137 upregulation following tumor coculture which was not enhanced by the presence of CoStAR (Fig. 16D).
  • Figs. 17A-17C depict enhancement of effector functions.
  • a FolR targeting CoStAR enhanced CD137 expression from -20% to -50% (Fig. 17A), TNFa production from 10 % to 15 % (Fig. 17B) and IL-2 production from 2 % to 5 %.( Fig. 17C) in response to FolR+ tumor digest.
  • T-cells from three healthy donors were engineered with MOV19.CD28 or MOV19.CD28.CD40 CoStAR and activated with either immobilised OKT3, providing stimulation in the absence of FolR, or with OvCAR-OKT3, to provide TCR and CoStAR activity.
  • BCL-xL activity was increased from between 10 and 20 % across the three donors following OKT3 stimulation (Fig. 18 A) whereas IL- 2 was increased between 0 and 12% (Fig. 18B) and TNFa increased between 0 and 20% (Fig. 18C).
  • the presence of exogenous soluble FolR did not enhance any of these particular effector functions.
  • OvCAR-OKT3 BCL-XL induction was enhanced by -20 % in CD28 CoStAR but by -35 % in CD28.CD40 CoStAR (Fig. 18D)
  • IL-2 induction was enhanced by - 20% in CD28 CoStAR but 30-50 % in CD28.CD40 CoStAR (Fig.
  • Fig. 19 depicts surface expression of anti-MSLN CoStAR expression on the surface of HD T cells.
  • Transduced and non-transduced (MOCK) cells underwent a rapid expansion protocol (REP) and were assessed for transduction efficiency either via surface detection of the marker gene tCD34 (truncated CD34) or CoStAR molecule using an anti-CD34-APC (black) or anti-MSLN- PE (red) antibody, respectively.
  • the results represent 3 biological replicates.
  • Figs. 20A-20C depict cytokine expression in healthy donor (HD) T cells transduced with anti-MSLN CoStARs and cocultured with OVCAR-3 cell lines.
  • CoStARs comprising combinations of six different anti-MSLN scFvs (SSI, M5, HN1, M912, huYP218, P4) and three different spacer/transmembrane domains (CD28, N-terminal truncated CD28, CD8) were compared.
  • Structural details are provided in Table 8, Table 9, and Table 10.
  • Cytokine concentrations for (Fig. 20A) IL-2 (Fig. 20B) IFNy and (Fig. 20C) TNFa following cocultures with OVCAR-3 or OVCAR3-OKT3 cell lines are shown.
  • Non-treated T cells were used as a control. The results represent 1-3 biological replicates with 3 technical replicates each.
  • Figs. 21A-21C depict cytokine expression in healthy donor (HD) T cells transduced with anti-MSLN CoStARs and cocultured with K562 cell lines.
  • CoStARs comprising combinations of six different anti-MSLN scFvs (SSI, M5, HN1, M912, huYP218, P4) and three different spacer/transmembrane domains (CD28, N-terminal truncated CD28, CD8) were compared.
  • Structural details are provided in Table 8, Table 9, and Table 10.
  • Cytokine concentrations for (Fig. 21A) IL-2 (Fig. 21B) IFNy and (Fig. 21C) TNFa following cocultures with K562-MSNL or K562-MSNL-OKT3 cell lines are shown.
  • Non-treated T cells were used as a control. The results represent 1-3 biological replicates with 3 technical replicates each.
  • Fig. 22 depicts surface expression of MFE23 scFV anti-CEA CoStARs expressed with six different secretion signal peptides (OSM1, CD8, CD2, IL2, GMCSF, hlgGK). Structural details are provided in Table 11. Following expansion, cells were assessed for transduction efficiency either via surface detection of the marker gene truncated CD34 (tCD34) or CoStAR molecule using an anti-CD34-APC (black bars) or using a primary rhCEACAM5-Fc antibody with a secondary anti-IgG-Fc-PE (grey bars) antibody, respectively.
  • tCD34 marker gene truncated CD34
  • CoStAR molecule using an anti-CD34-APC (black bars) or using a primary rhCEACAM5-Fc antibody with a secondary anti-IgG-Fc-PE (grey bars) antibody, respectively.
  • Fig. 23 depicts surface expression of CoStARs comprising six different anti-CEA scFvs (MFE23, MFE23(Q>K), hMFE23, CEA6, BW431/26, hT84.66). Structural details are provided in Table 12. Following expansion, cells were assessed for transduction efficiency either via surface detection of the marker gene truncated CD34 (tCD34) or CoStAR molecule using an anti-CD34- APC (black bars) or using a primary rhCEACAM5-Fc antibody with a secondary anti-IgG-Fc-PE (grey bars) antibody, respectively.
  • tCD34 marker gene truncated CD34
  • CoStAR molecule using an anti-CD34- APC (black bars) or using a primary rhCEACAM5-Fc antibody with a secondary anti-IgG-Fc-PE (grey bars) antibody, respectively.
  • Figs. 24A-24C depict cytokine production by healthy donor (HD) T cells transduced with anti-CEA CoStARs (MFE23, MFE23(Q>K), hMFE23, CEA6, BW431/26, hT84.66) and cocultured with LoVo cell lines. Structural details are provided in Table 12. Cytokine concentrations are shown for (Fig. 24A) IL-2 (Fig. 24B) IFNy and (Fig. 24C) TNFa following cocultures with Lovo or Lovo-OKT3 cell lines. Non-treated T cells were used as a negative control. [0084] Figs.
  • 25A-25C depict cytokine production in healthy donor (HD) T cells transduced with anti-CEA CoStARs (MFE23, MFE23(Q>K), hMFE23, CEA6, BW431/26, hT84.66) and cocultured with K562 cell lines. Cytokine concentrations are shown for (Fig. 25 A) IL-2 (Fig. 25B) IFNy and (Fig. 25C) TNFa following cocultures with K562.CEACAM5 (signal 2) or K562.CEACAM5.OKT3 (signal 1+2) cell lines. Non-treated T cells were used as a negative control.
  • Fig. 26 depicts surface expression of hMFE23 scFV anti-CEA CoStARs expressed with three different spacer/transmembrane domains. Structural details are provided in Table 13. Following expansion, cells were assessed for transduction efficiency via surface detection of the marker gene truncated CD34 (tCD34) using an anti-CD34-APC (black bars) or the CoStAR molecule using a primary rhCEACAM5-Fc antibody with a secondary anti-IgG-Fc-PE antibody (grey bars).
  • Figs. 27A-27C depict cytokine production by the MFE23 scFV anti-CEA spacer variants. Cytokine concentrations for (Fig. 27A) IL-2 (Fig. 27B) IFNy and (Fig. 27C) TNFa following cocultures with Lovo or Lovo.OKT3 cell lines are shown. Non-treated T cells were used as a control.
  • Fig. 28 depicts anti-CEA CoStARs comprising an hMFE23 CEA-binding domain with intracellular signalling domains comprising CD40, CD134, CD137, CD2, ICOS, DAP10 and NTRK1 signaling elements.
  • Fig. 29 depicts surface expression of hMFE23 scFV anti-CEA CoStARs comprising domain combinations depicted in Fig. 28 and detail in Table 14.
  • tCD34 marker gene truncated CD34
  • APC anti-CD34-APC
  • CoStAR molecule using a primary rhCEACAM5-Fc antibody with a secondary anti-IgG-Fc-PE antibody (red circles). The results represent three biological replicates.
  • Fig. 30 depicts T cell phenotypes of CoStAR transfected HD T cells in three separate donors.
  • Cells were sorted using CD34 microbeads and underwent a rapid expansion protocol (REP) for 14 days. Following outgrowth and REP, IxlO 5 cells were assessed for the differentiation subtype using flow cytometry.
  • Tcm central memory T cell
  • Tern effector memory T cell
  • Tn naive T cell
  • Tscm stem cell memory T cell
  • Tte terminal effector T cell. See Table 15 for T cell subtype definitions.
  • FIG. 31A-31C depict cytokine production by hMFE23 scFV anti-CEA CoStAR transduced HD T cells cocultured with K562 cell lines. Cytokine concentrations for (Fig. 31 A) IL-2, (Fig. 3 IB) IFNy, and (Fig. 31C) TNFa are shown following cocultures with K562.CEACAM5 (signal 2) or K562.CEACAM5.OKT3 (signal 1+2) cell lines. Non-treated T cells were used as a control.
  • Figs. 32A-32C depict cytokine expression in HD T cells transduced with hMFE23 scFV anti-MSLN CoStARs and cocultured with K562 cell lines.
  • Frequency of (Fig. 32A) IL-2, (Fig. 32B) IFNy, and (Fig. 32C) TNFa expressing cells is shown following cocultures with K562.CEACAM5 (signal 2) or K562.CEACAM5.OKT3 ( signal 1+2) cell lines.
  • Non-treated T cells were used as a control.
  • Fig. 33 depicts proliferation of HD T cells from transduced with hMFE23 scFV anti- MSLN CoStARs cocultured with K562.CEACAM5.OKT3 (signal 1+2) cell lines.
  • HD T cells were procured from two donors. The figures represent fold expansion of input cells.
  • Fig. 34 depicts proliferation of HD T cells from transduced with hMFE23 scFV anti- MSLN CoStARs cocultured with K562.CEACAM5.OKT3 (signal 1+2) cell lines.
  • HD T cells were procured from two donors. The figures represent fold expansion of input cells on Day 6 post stimulation.
  • Figs. 35A-35B depict TRAF and TRAF-like binding sites and motifs and signalling pathways.
  • Fig. 35A depicts a CoStAR CD40 intracellular domain showing TRAF binding sites and signalling.
  • Fig. 35B depicts a CoStAR comprising an IProx domain.
  • Figs. 36A-36B depict the effect of mutations in CoStAR CD40 intracellular signaling domain on cytokine secretion and long-term survival and proliferation of CD28.CD40 CoStAR transduced T cells cocultured with LoVo.OKT3.
  • Cells of three donors were activated with Dynabeads and transduced with WT CD28.CD40 (CTP194), CD28.CD40 containing TRAF2 binding site mutation SVQE>AVQA (CTP195), TRAF2/TRAF3 binding site mutation PVQET+AVAEA (CTP196), TRAF 6 binding site mutation PQEINF+AQAINF (CTP197), Q263A (CTP199), or mock transduced.
  • CTP194 CD28.CD40 containing TRAF2 binding site mutation SVQE>AVQA
  • CTP196 TRAF2/TRAF3 binding site mutation
  • PVQET+AVAEA CTP196
  • TRAF 6 binding site mutation PQEINF+AQAINF CTP
  • IL-2 was measured in supernatants collected 24 hours after coculture in absence of IL-2 with LoVo or LoVo.OKT3.GFP tumor cells.
  • Fig. 36B Viability and absolute count were assessed after 6-8 days and live T cells were rechallenged for an additional week with fresh LoVo.OKT3.GFP tumor cells. At the end of the long-term coculture, the viability and absolute count were measured, and the fold expansion was calculated. Data shown as mean +/- SEM of n ⁇ 3 donors analysed in triplicates.
  • Figs. 37A-37B depict percentage of TIL (Fig. 37A) and total TIL counts (Fig. 37B) based on CD2+ stain in thawed OC samples at day 1.
  • Fig. 38 depicts growth of non-Td and Td TILs.
  • Cells were counted using CD2 and DRAQ7 staining and acquisition on the Novocyte 3005.
  • Cell counts at the end of REP on day 25 are graphically represented. Shapes corresponding to the each of the 5 ovarian cancer samples are depicted. Filled shapes are Non-Td and open shapes are Td TILs. Statistical analysis was performed using a paired t-test.
  • Figs. 39A-39D depict transduction efficiency and viral integrations per cell of CoStAR modified TILs.
  • Nontransduced (Non-Td) and anti-FOLRl CoStAR transduced (Td) TILs were assessed for the transduction efficiency on day 25 post REP in the CD3+ (Fig. 39A), CD4+ (Fig. 39B) and CD8+ (Fig. 39C) cell populations.
  • the viral copy number (VCN) was assesed to determine viral integrations (Fig. 39D). Shapes corresponding to the each of the 5 ovarian cancer samples are depicted. Filled shapes are non-Td and clear shapes are Td TILs.
  • Fig. 40 depicts CD4 and CD8 populations in post-REP TILs.
  • Nontransduced (Non- Td) and anti-FOLRl CoStAR- transduced (Td) and anti-FOLRl CoStAR+ Td TILs were assessed for the CD4 and CD8 composition on D25 post-REP using flow cytometry.
  • Statistical analysis was performed using a two-way ANOVA with matched Tukey's multiple comparisons post-test.
  • Figs. 41A-41C depict the effect of CoStAR modification on the differentiation status of TILs.
  • Nontransduced (Non-Td), anti-FOLRl CoStAR- transduced (Td) TILs and anti-FOLRl CoStAR+ Td TILs were assessed fortheir differentiation status on D25 post-REP from total T cell (Fig. 41A), CD4+ (Fig. 41B) and CD8+ (Fig. 41C) cell populations.
  • Statistical analysis was performed using a two-way ANOVA with matched Tukey’s multiple comparisons test.
  • Figs. 42A-42B depict effects of CoStAR modification of TILs on co-inhibitory or costimulatory marker expression.
  • Nontransduced (Non-Td), anti-FOLRl CoStAR-transduced (Td) TILs and anti-FOLRl CoStAR+ Td TILs were assessed for the expression of co-inhibitory and co-stumulatory markers in CD4+ (Fig. 42A) and CD8+ (Fig. 42B) cell populations. Shapes corresponding to the each of the 5 ovarian cancer samples are depicted regardless of the filling.
  • Black, dark grey and light grey bars represent Non-Td TILs, anti-FOLRl CoStAR- Td and anti- F0LR1 CoStAR+ Td TILs, respectively.
  • Statistical analysis was performed using a Two-way ANOVA with a matched Tukey's multiple comparisons post-test. *p ⁇ 0.05
  • Figs. 43A-43B depicts effects of CoStAR modification on TCRaP, TCRyS and Treg frequency in TILs.
  • Nontransduced (Non-Td), anti-FOLRl CoStAR- transduced (Td) TILs and anti-FOLRl CoStAR+ Td TILs were assessed for the frequency of TCRaP ( CD3+TCRaP+), and TCRyd (CD3+TCRy6+) in CD3+ cell populations (Fig. 43 A).
  • the frequency of Tregs in the CD4+ subpopulation was also assessed (Fig. 43B). Shapes corresponding to the each of the 5 ovarian cancer samples are depicted regardless of the filling.
  • Figs. 44A-44C depict effects of CoStAR modification of TIL on cytokine production upon mitogenic activation.
  • Nontransduced (Non-Td), anti-FOLRl CoStAR-transduced (Td) TILs and anti-FOLRl CoStAR+ Td TILs were assessed for the producrtion of cytokines upon 4 hour stimulation with PMA (50 ng/mL) /lonomycin (1 pg/mL) in CD3+ (Fig. 44A), CD4+ (Fig. 44B) and CD8+ (Fig. 44C) cell populations. Shapes corresponding to the each of the 5 OC samples are depicted regardless of the filling.
  • Black, dark grey and light grey bars represent Non-Td TILs, anti- FOLRl CoStAR- Td TILs and anti-FOLRl CoStAR+ Td TILs, respectively.
  • Statistical analysis was performed using a two-way ANOVA with matched Tukey's multiple comparisons post-test. * p ⁇ 0.05, *** p ⁇ 0.001.
  • Fig. 45 depicts Expression of FOLR1 on OC digest cells. Cryopreserved autologous tumor digest was thawed and analyzed by flow cytometry to determine the surface expression of FOLR1 of each donor. All 5 donors used in the study are shown. Abbreviations: OC, ovarian cancer, FOLR1, folate receptor alpha; FOLR1 PE, anti-FOLRl antibody conjugated to PE; PE, phycoerythrin.
  • Figs. 46A-46D depict effect of CoStAR modification on cytokine producing cells upon coculture with autologous tumors.
  • Non-Td and anti-FOLRl CoStAR Td TILs were cocultured with autologous tumor digests for 16 hours and intracellular flow cytometry was performed to evaluate the proportion of cells producing cytokines.
  • the frequency of IL-2 positive (Fig. 46A) CD4 and (Fig. 46B) CD8 TILs as well as the frequency of TNFa positive (Fig. 46C) CD4 and (Fig. 46D) CD8 TILs were assessed. Results represent 5 biological replicates with 3 technical replicates each. Statistical analysis was performed using a two-way ANOVA with Tukey’s multiple comparisons test. *P ⁇ 0.05.
  • Figs. 47A-47E depict the effect of CoStAR modification on cytokine secretion upon coculture with autologous tumor digests expressing FOLR1.
  • Non-Td and anti-FOLRl CoStAR transduced (Td) TILs were cocultured with autologous tumor digest for 24 hours, following which supernatants were collected and analyzed for cytokine secretion using an MSD immunoassay.
  • the graphs represent measured concentrations of (Fig. 47A) IL-2, (Fig. 47B) TNFa, (Fig. 47C) IL-13 and (Fig. 47D) fFNy in coculture supernatants.
  • Fig. 47A measured concentrations of (Fig. 47A) IL-2,
  • Fig. 47B TNFa
  • Fig. 47C IL-13
  • Fig. 47D fFNy in coculture supernatants.
  • Fig. 48 depicts assessment of MHC-dependent CoStAR functionality in cocultures with autologous tumor digests.
  • Non-Td and anti-FOLRl CoStAR transduced (Td) TILs were cocultured with autologous tumor digests in the presence of MHC blocking reagents or isotype controls for 24 hours. The supernatants were then analyzed for fFNy cytokine production using the MSD immunoassay. Results represent 3 biological replicates with 3 technical replicates each. Statistical analysis was performed using a two-way ANOVA with Tukey’s multiple comparisons test.
  • Figs. 49A-49B depicts the effect of CoStAR modification in cytokine producing cell frequencies upon coculture with engineered cell lines.
  • Non-Td and anti-FORLl CoStAR transduced (Td) TILs were cocultured with engineered target cell lines for 16 hours and cytokine producing cells were measured using intracellular flow cytometry.
  • Frequency of TNFa positive Fig.
  • Figs. 50A-50D depict the effect of CoStAR modification in cytokine secretion upon coculture with engineered cell lines.
  • Non-Td and anti-FOLRl CoStAR transduced (Td) TILs were cocultured with engineered target cell lines for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted. Cytokine concentrations for (Fig. 50A) IL-2, (Fig. 50B) TNFa, (Fig. 50C) IL-13 and (Fig. 50D) fFNy following cocultures with (left) K-562, and (right) BA/F3 derived cell lines are shown. The results represent 5 biological replicates with 3 technical replicates each. Statistical analysis was performed using a two-way ANOVA with Tukey’s multiple comparisons test. *P ⁇ 0.05, **P ⁇ 0.01, ***p ⁇ 0.001, ****p ⁇ 0.0001.
  • Figs. 51A-51C depict assessment of the impact of CoStAR modification on the cytotoxic capacity of TILs against OKT3 bearing targets.
  • Non-Td and anti- FOLR1 CoStAR transduced (Td) TILs were cocultured with BA/F3 or OVCAR-3 engineered cell lines and the cytotoxicity was assessed using a flow cytometry based (Fig. 51 A) and an xCELLigence-based assay (Fig. 5 IB and 51C), respectively.
  • Fig. 5 IB E:T ratio of 1 :5
  • Fig. 51C E:T ratio of 1 :30.
  • Results represent 5 biological replicates with 3 technical replicates each.
  • Statistical analysis was performed using a two-way ANOVA with Tukey’s multiple comparisons test for flow cytometry data and 1-way ANOVA with Tukey’s multiple comparisons test for xCELLigence data. *P ⁇ 0.05, **P ⁇ 0.01.
  • Figs. 52A-52D depict expansion of NSCLC TILs with >80% viability (Fig. 52A) and ⁇ 100-200 million cells (Fig. 52B), 40-55 % CoStar transduction in CD3+ T cells (Fig. 52C) and >90 % CD3+ T cell purity (Fig. 52D).
  • Fig. 53 depicts expansion of NSCLC TILs with >80% viability. There was no difference in CoStAR transduced and nontransduced populations in terms of viability and cell expansion.
  • Fig. 54 depicts expansion of NSCLC TILs with 50-500 million cells at harvest. There was no differnce in CoStAR transduced and nontransduced populations in terms of viability and cell expansion.
  • Fig. 55 depicts T cell populations of seven patient samples.
  • Fig. 56 depicts CD3 vs CD56 which marks CD3+ as T cells and CD3-CD56+ as NK cells.
  • Fig. 57 depicts quantification of non-transduced and CoStAR transduced T cells.
  • Fig. 58 depicts CoStAR staining on T cell subsets.
  • Fig. 59A depicts the cell count and
  • Fig. 59B depicts the viability of ovarian cancer TILs over 10 days.
  • Fig. 59C depicts the cell count and Fig. 59D depicts the viability following the manufacturing process.
  • Figs. 60A-60D depicts renal cancer TILs demonstrated consistently >50% viability during outgrowth and >90% viability at the end of the manufacturing process, with 100-350 million cells at harvest.
  • Fig. 60A depicts the cell count and
  • Fig. 60B depicts the viability of renal cancer TILs over 10 days.
  • Fig. 60C depicts the cell count and
  • Fig. 60D depicts the viability following the manufacturing process.
  • Fig. 61 depicts an experimental setup as outlined in Example 16, wherein CD40 signaling motif mutant constructs were incorporated into a cell to screen for changes to transcription.
  • Fig. 62A depicts the 23 day experimental approach for manufacturing TRAF variant CoSTARs in T cells, as outlined in Example 17.
  • Fig. 62B depicts the 26 day experimental approach for monitoring the effect of TRAF variant CoSTARs on proliferation in T cells, as outlined in Example 17.
  • Fig. 63A-63C depicts the change in total number of CD2+ T cells expressing TRAF variant CoSTARs with IL-2 treatment. Graphs are given for change in cell numbers from cells collected from donor HD 702C (Fig. 63 A), HD 1004 (Fig. 63B), and HD 2000 (Fig. 63C).
  • Fig. 64A-64C depicts the fold-change in number of CD2+ T cells expressing TRAF variant CoSTARs with IL-2 treatment. Graphs are given for the fold change in cell numbers from cells collected from donor HD 702C (Fig. 64A), HD 1004 (Fig. 64B), and HD 2000 (Fig. 64C).
  • Fig. 65A-65C depicts the change in total number of CD2+ T cells expressing TRAF variant CoSTARs, wherein the T cells did not receive any IL-2 treatment. Graphs are given for change in cell numbers from cells collected from donor HD 702C (Fig. 65A), HD 1004 (Fig. 65B), and HD 2000 (Fig. 65C).
  • Fig. 66A-66C depicts the fold-change in number of CD2+ T cells expressing TRAF variant CoSTARs, wherein the T cells did not receive any IL-2 treatment. Graphs are given for the fold change in cell numbers from cells collected from donor HD 702C (Fig. 66A), HD 1004 (Fig. 66B), and HD 2000 (Fig. 66C).
  • Fig. 67 depicts some embodiments of CD40 TRAF variants of SEQ ID NOS: 510-519. In this figure, the underlined region is CD40, sequences highlighted in grey is the TRAF6 binding domain region, sequences highlighted in light grey is the TRAF2/3 binding domain, and sequences highlighted in grey and surrounded with double brackets is the TRAF2 binding domain.
  • Fig. 68 depicts the transduction levels of constructs into primary T cells collected from donor HD 702C, HD 1004, and HD 2000.
  • Figs. 69A-69F depict the fold change in cell proliferation compared to baseline in primary human donors 702C (Figs. 69A and 69D) 1004 (Figs. 69B and 69E), and 2000 (Figs. 69C and 69F) primary T cells expressing CoStAr constructs with TRAF6 variants, and with either IL- 2 treatment (Figs. 69A-69C) or without IL-2 treatment (Figs. 69D-69F), as outlined in Example 18.
  • Figs. 70A-70F depict the fold change in cell proliferation compared to baseline in primary human donors 702C (Figs. 70A and 70D) 1004 (Figs. 70B and 70E), and 2000 (Figs. 70C and 70F) primary T cells expressing CoStAr constructs with TRAF2/3 variants, and with either IL-2 treatment (Figs. 70A-70C) or without IL-2 treatment (Figs. 70D-70F), as outlined in Example 18.
  • Figs. 71A-71F depict the fold change in cell proliferation compared to baseline in primary human donors 702C (Figs. 71 A and 71D) 1004 (Figs. 71B and 71E), and 2000 (Figs. 71C and 7 IF) primary T cells expressing CoStAr constructs with TRAF2 variants, and with either IL- 2 treatment (Figs. 71A-71C) or without IL-2 treatment (Figs. 71D-71F), as outlined in Example 18.
  • Figs. 72A-72F depict the fold change in cell proliferation compared to baseline in primary human donors 702C (Figs. 72A and 72D) 1004 (Figs. 72B and 72E), and 2000 (Figs. 72C and 72F) primary T cells expressing CoStAr constructs with various TRAF variants, and with either IL-2 treatment (Figs. 72A-72C) or without IL-2 treatment (Figs. 72D-72F), as outlined in Example 18.
  • Figs. 73A-73D depict the combined data of Figs. 69A-69C, 70A-70C, 71A-71C, and 72A-72C, in which the fold change in cell proliferation compared to baseline in primary T cells across three donors is graphed over time.
  • the graphs show cells treated with IL-2, and represent the combined data for cells expressing a TRAF6 (Fig. 73 A), TRAF2/3 (Fig. 73B), TRAF2 (Fig. 73 C), or other TRAF (Fig. 73D) variant.
  • Figs. 74A-74D depict the combined data of Figs.
  • 69A-69C, 70A-70C, 71A-71C, and 72A-72C in which the fold change in cell proliferation compared to baseline in primary T cells across three donors is graphed over time.
  • the graphs show cells that were not given IL-2 treatment, and represent the combined data for cells expressing a TRAF6 (Fig. 74A), TRAF2/3 (Fig. 74B), TRAF2 (Fig. 74C), or other TRAF (Fig. 74D) variant.
  • Figs. 75A-75B depict the combined fold changes in cell proliferation compared to baseline in primary human T cells from 3 donors at Day 21 for cells with IL-2 treatment (Fig. 75A) and without IL-2 treatment (Fig. 75B).
  • Figs. 76A-76C depict non-limiting examples of schematic models for universal costimulatory proteins with TRAF variants.
  • TCR incorporated antigen agnostic receptor comprises modifying components of the TCR complex and associated signaling adaptors.
  • Fig. 76B A constitutive costimulatory receptor comprising transmembrane domains (TMDs) and features that enable inducible or constitutive activation.
  • Fig. 76C An inducible costimulatory receptor capable of induction and activation by extracellular ligand binding.
  • the TRAF variant is part of the CD40 domain (shown as “CD40*”).
  • Figs. 77A-77C depict a non-limiting example protein construct of some embodiments herein.
  • Fig. 77A is a general schematic of the protein comprising a universal CoStAR sequence, further comprising an optional section, a binding domain, a CD28 domain, and a CD40 domain with a TRAF variant.
  • Fig. 77B is a schematic of some embodiments provided herein.
  • Fig. 77C outlines a set of sequences of some embodiments provided herein.
  • Fig. 78 depicts set of sequences of some embodiments provided herein (SEQ ID NOS: 40839-41074). In some embodiments, these sequences are excluded from the consensus sequences or other TRAF variant constructs provided herein (including excluded from those in FIG. 84 and 85).
  • Fig. 79 depicts set of sequences of some embodiments provided herein (SEQ ID NOS: 41075-43474). In some embodiments, these sequences are excluded from the consensus sequences or other TRAF variant constructs provided herein (including excluded from those in FIG. 84 and 85).
  • Fig. 80 depicts a non-limiting example of mutation analysis of CD40 using constructs CTP195, CTP196, and CTP197 to assess the function of signaling motifs, as described in Example 13.
  • Fig. 81 depicts a non-limiting example of mutation analysis of CD40 using constructs CTP195, CTP196, CTP197, CTP198, and CTP199 to assess the function of signaling motifs, as described in Example 13.
  • Fig. 82A depicts the minor consensus sequence generated from the alignments of variants in the TRAF2 domain as shown in Table 1, wherein the highlighted amino acids are conserved across variants.
  • Fig. 82B depicts the major consensus sequence generated from the alignments of variants in the TRAF2 domain as shown in Table 1, wherein the highlighted amino acids are conserved across variants.
  • Fig. 82C depicts the consensus sequence generated from the alignments of variants in the TRAF6 domain as shown in Table 3, wherein the highlighted amino acids are conserved across variants.
  • Fig. 83 depicts non-limiting example sequences of variants in the TRAF2 domain (SEQ ID NOS: 520-679).
  • Fig. 84 depicts non-limiting example sequences of variants in the TRAF2/3 domain (SEQ ID NOS: 680-839).
  • Fig. 85 depicts non-limiting example sequences of variants in the TRAF6 domain (SEQ ID NOS: 840-40839).
  • Figs. 86A-86D illustrate a schematic showing some embodiments of a FOLR1 -alpha CoStAR and/or a fusion protein with a CD40 variant. Some general embodiments are depicted in Fig. 86A.
  • Fig. 86B depicts some embodiments of a FOLRl-alpha CoStAR or a fusion protein.
  • Fig. 86C depicts some embodiments of a CoStAR or a fusion protein.
  • Fig. 86D depicts some embodiments of a CoStAR or a fusion protein.
  • the sequences described the structure in its entirety and no further functional aspects are required to describe the CoStAR or fusion protein.
  • Figs. 87A-87D illustrate a schematic showing some embodiments of an anti- pembrolizumab CoStAR and/or a fusion protein with a CD40 variant. Some general embodiments are depicted in Fig. 87A.
  • Fig. 87B depicts some embodiments of an anti-pembrolizumab CoStAR or a fusion protein.
  • Fig. 87C depicts some embodiments of a CoStAR or a fusion protein.
  • Fig. 87D depicts some embodiments of a CoStAR or a fusion protein.
  • the sequences describe the structure in its entirety and no further functional aspects are required to describe the CoStAR or fusion protein.
  • Figs. 88A-88D illustrate a schematic showing some embodiments of a CEA CoStAR and/or a fusion protein with a CD40 variant. Some general embodiments are depicted in Fig. 88A.
  • Fig. 88B depicts some embodiments of a CEA CoStAR or a fusion protein.
  • Fig. 88C depicts some embodiments of a CoStAR or a fusion protein.
  • Fig. 88D depicts some embodiments of a CoStAR or a fusion protein.
  • the sequences describe the structure in its entirety and no further functional aspects are required to describe the CoStAR or fusion protein.
  • Figs. 89A-89D illustrate a schematic showing some embodiments of a CEA CoStAR and/or a fusion protein with a CD40 variant. Some general embodiments are depicted in Fig. 89A.
  • Fig. 89B depicts some embodiments of a MSLN CoStAR or a fusion protein.
  • Fig. 89C depicts some embodiments of a CoStAR or a fusion protein.
  • Fig. 89D depicts some embodiments of a CoStAR or a fusion protein.
  • the sequences describe the structure in its entirety and no further functional aspects are required to describe the CoStAR or fusion protein.
  • Figs. 90A-90C depict the quantity of cytokines TNF-alpha (Fig. 90A), IFN-gamma (Fig. 90B), and IL-2 (Fig. 90C) present after expression of T cells with CD40 variants, as outlined in Example 19.
  • Figs. 91 A-91B depict the IL-2 production (Fig. 91 A) and fold expansion (Fig. 91B) in cells expressing one of constructs CTP194-CTP200, as outlined in Example 20.
  • Fig. 92 depicts schematics of the protein constructs CTP188-CTP202, as described herein.
  • the disclosure herein relates to sequences that encode variants of TRAF binding domains.
  • these variants can be for TRAF2, TRAF2/3, or TRAF6 domains.
  • the TRAF2 variant will include one or more of the variants or point mutations provided herein.
  • the TRAF2/3 variant will include one or more of the variants or point mutations provided herein.
  • the TRAF6 variant will include one or more of the variants or point mutations provided herein.
  • the TRAF2, TRAF2/3, or TRAF6 variant will be any one or more of those provided herein, including, for example, one or more of SEQ ID Nos: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519.
  • the variant will comprise any one or more of the constructs from Table 2, Table 4, Table 5, or Fig. 67.
  • the variant is not one of the constructs of Fig. 78 (SEQ ID NOS: 40839-41074) or Fig. 79 (SEQ ID NOS: 41075-43474).
  • the variant comprises at least one of the constructs of Fig. 83, Fig. 84, or Fig. 85.
  • the TRAF2, TRAF2/3, or TRAF6 variant will be part of a CD40 protein.
  • the CD40 protein is part of a CoSTAR protein or other fusion construct as provided herein.
  • the TRAF variant is expressed in a T cell as provided herein.
  • the TRAF variant is expressed in a cell as shown in Figs. 76A-76C.
  • the TRAF variant is part of a peptide construct as shown in Figs. 77A-77C, 86A-86D, 87A-87D, 88A-88D, and/or 89A-89D.
  • any of the proteins and/or CoSTARs provided herein can employ a CD40 or TRAF variant instead of a wild-type CD40 or TRAF domain.
  • the sequences of FIG. 78 and 79 are optionally to be excluded from the options of variants of the invention.
  • the sequence is a variant of TRAF2.
  • the sequence is selected from any one of SEQ ID NOS: 520-679.
  • the sequence has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to any one of SEQ ID NOS: 520-679.
  • the sequence is a variant of TRAF2/3.
  • the sequence is selected from any one of SEQ ID NOS: 680-839.
  • the sequence has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to any one of SEQ ID NOS: 680-839.
  • the sequence is a variant of TRAF6.
  • the sequence is selected from any one of SEQ ID NOS: 840-40839.
  • the sequence has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to any one of SEQ ID NOS: 840-40839.
  • the sequence comprises at least 2, 3, and/or 4 variants of TRAF.
  • the sequence comprises a sequence from Table 2, 4, or 5. In some embodiments, the sequence comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to a sequence from Table 2, 4, or 5. In some embodiments, the sequence is selected from any one of SEQ ID NOS: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, and 519.
  • the sequence has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to any one of SEQ ID NOS: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, and 519.
  • Some embodiments of the present disclosure relate to a protein comprising an amino acid sequence comprising a sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11.
  • Xi is any amino acid
  • X2 is any amino acid
  • X3 is P
  • X4 is any amino acid
  • X5 is Q
  • Xe is C
  • E or A
  • X7 is any amino acid
  • Xs is any amino acid
  • X9 is any amino acid
  • X10 is any amino acid
  • Xu is any amino acid.
  • Xi, and X2 are any amino acids
  • X3 is P
  • X4 is any amino acid
  • X5 is Q
  • Xe, X7, Xs, X9, X10, and Xu are any amino acids.
  • any one of Xi-Xu is a naturally occurring amino acid.
  • any one of Xi-Xu is a modified amino acid.
  • X3 and/or X5 is conservatively mutated to another amino acid with similar properties as P and/or Q, respectively.
  • the protein is part of a TRAF domain. In some embodiments, the protein is part of a TRAF2 domain.
  • the protein is part of a TRAF2/3 domain.
  • the sequence comprises: Xi is S or P, X2 is V, H, or Y, X4 is I, Q, V, X7 is T or S, Xs is D, X9 is K, D, or G, X10 is T, S, G, or A, and Xu is D, S, N, or D; or the sequence is at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, and/or at least 100%, identical to (a).
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42299. In some embodiments, the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42377. In some embodiments, the protein is of the sequence GSNTXIX 2 X3X4X 5 X6X 7 X8X9XIOXIIQPVT, SEQ ID NO: 42378.
  • a protein comprising an amino acid sequence comprising a sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein: Xi is any amino acid, X2 is any amino acid, X3 is P, S, A, or T, X4 is any amino acid, X5 is Q or E, Xe is E, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid. In some embodiments, any one of Xi-Xu is a naturally occurring amino acid.
  • any one of Xi-Xu is a modified amino acid.
  • X3 is conservatively mutated to another amino acid with similar properties as P, S, A, and/or T.
  • X5 is conservatively mutated to another amino acid with similar properties as Q and/or E.
  • Xe is conservatively mutated to another amino acid with similar properties as E.
  • the protein is part of a TRAF domain. In some embodiments, the protein is part of a TRAF2 domain. In some embodiments, the protein is part of a TRAF2/3 domain.
  • the sequence comprises: Xi is P, A, M, T, S, R, V, H, X 2 is F, A, L, I, T, V, G, C, A, F, P, X 4 is K, V, I, H, A, Q, T, E, S, X 7 is C, T, E, D, S, A, X 8 is A, L, G, Y, I, Q, D, E, X 9 is F, H, K, R, P, A, G, Y, E, N, X10 is R, G, E, K, A, S, D, C, C, P, V, and Xu is S, C, D, P, W, T, A, G, E; or the sequence is at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, and/or at least 100%, identical to (a).
  • the sequence is part of a Traf 2/3 sequence.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42300.
  • the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42379.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42380.
  • a protein comprising an amino acid sequence comprising a sequence of Consensus C, or X1X2X3X4X5X6, wherein: Xi is P, X2 is any amino acid, X3 is E, X4 is any amino acid, X5 is any amino acid, and Xe is Ac/ Ar.
  • Xi is P, and X2, X3 X4, X5 and Xe are any amino acids.
  • any one of Xi-Xe is a naturally occurring amino acid.
  • any one of Xi-Xe is a modified amino acid.
  • Xi is conservatively mutated to another amino acid with similar properties as P.
  • Xe is an aromatic amino acid.
  • Xe is an acidic amino acid.
  • Xe is conservatively mutated to another amino acid with similar properties as an acidic and/or aromatic amino acid.
  • Xe is selected from Y, H, W, or F amino acids.
  • Xe is selected from D or E amino acids.
  • the protein is part of a TRAF domain. In some embodiments, the protein is part of a TRAF6 domain.
  • the sequence comprises: X2 is Q, P, E, V, T, or S, X4 is I, L M, N, S, T, N, D, X5 is N, D, R, S, G, or Y; or the sequence is at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, and/or at least 100%, identical to (a).
  • the protein is of the sequence PKQEX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42301.
  • the protein is of the sequence X1X2X3X4X5X6PDDL, SEQ ID NO: 42381.
  • the protein is of the sequence PKQEX1X2X3X4X5X6PDDL, SEQ ID NO: 42382.
  • the amino acid sequence comprises: (a) one or more of SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; or (b) a sequence that is at least 60%, , at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, and/or at least 100%, identical to (a).
  • the TRAF domain is in a CD40 protein, wherein the TRAF domain comprises one or more of: (a) SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; or (b) a sequence that is at least 60%, , at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, and/or at least 100%, identical to (a).
  • the TRAF6 domain sequence comprises: PQEINF, PEEMSW, PPENYE, or PQENSY.
  • a TRAF2/3 domain sequence comprising: PVQET, TQEET, SKEET, AVEET, or PVQET.
  • a TRAF2 domain sequence comprising: SVQE, AVEE or PEEE.
  • the TRAF 6 or TRAF2/3 domain comprises: (a) the amino acid sequence of one of SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; or (b) a sequence that is at least 60%, , at least 70%, at least 80%, at least 90%, at least 95%, at least 99%, and/or at least 100%, identical to (a).
  • the sequence is within a CD40 protein sequence for the protein, amino acid sequence, or TRAF domain of any one of the embodiments of the present disclosure. In some embodiments, the sequence is within a CD40 protein and is located at a corresponding TRAF 2, TRAF2/3, and/or TRAF6 domain within the CD40 protein.
  • the TRAF2/TRAF3 domain comprises an amino acid sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X2 is any amino acid, X3 is P, X4 is any amino acid, X5 is Q, Xe is C, E, or A, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42299.
  • the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42377. In some embodiments, the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42378.
  • the TRAF2/TRAF3 domain comprises an amino acid sequence of Consensus B, or. X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X2 is any amino acid, X3 is P, S, A, or T, X4 is any amino acid, X5 is Q or E, Xe is E, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid.
  • the protein is of the sequence GSNTX1X2X3X4X5X6X7X8X9X10X11, SEQ ID NO: 42300. In some embodiments, the protein is of the sequence X1X2X3X4X5X6X7X8X9X10X11QPVT, SEQ ID NO: 42379. In some embodiments, the protein is of the sequence GSNTXIX 2 X3X4X 5 X6X 7 X8X9XIOXIIQPVT, SEQ ID NO: 42380.
  • the TRAF6 domain comprises an amino acid sequence of Consensus C, or X1X2X3X4X5X6, wherein Xi is P, X2 is any amino acid, X3 is E, X4 is any amino acid, X5 is any amino acid, and Xe is Ac/ Ar.
  • the protein is of the sequence PKQEX1X2X3X4X5X6, SEQ ID NO: 42301.
  • the protein is of the sequence X1X2X3X4X5X6PDDL, SEQ ID NO: 42381.
  • the protein is of the sequence PKQEX1X2X3X4X5X6PDDL, SEQ ID NO: 42382.
  • the CD40 domain comprises an amino acid sequence of one or more of the following: (a) TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X2 is any amino acid, X3 is P, X4 is any amino acid, X5 is Q, Xe is C, E, or A, X7 is any amino acid, Xs is any amino acid, X9 is any amino acid, X10 is any amino acid, and Xu is any amino acid, (b) a TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein Xi is any amino acid, X2 is any amino acid, X3 is P, S, A, or T, X4 is any amino acid, X5
  • a chimeric costimulatory antigen receptor which comprises: an extracellular binding domain that binds to a tumor associated antigen; a transmembrane domain that is linked to the extracellular binding domain, a first signaling domain; and a second signaling domain, wherein the second signaling domain comprises a variant CD40 signaling domain or a signaling fragment thereof, wherein the variant CD40 comprises a sequence of a variant TRAF2/TRAF3 sequence, or a variant TRAF6 sequence, or a variant TRAF2 sequence, wherein the variant CD40 does not comprise SEQ ID NO: 42.
  • CoStAR costimulatory antigen receptor
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a chimeric costimulatory antigen receptor which comprises: an extracellular binding domain that binds to carcinoembryonic antigen (CEA), or an extracellular binding domain that binds to mesothelin (MSLN); a transmembrane domain that is linked to the extracellular binding domain, a first signaling domain; and a second signaling domain, wherein the second signaling domain comprises a variant CD40 signaling domain or a signaling fragment thereof, wherein the variant CD40 comprises a sequence of a variant TRAF2/TRAF3 sequence, or a variant TRAF6 sequence, or a variant TRAF2 sequence, wherein the variant CD40 does not comprise SEQ ID NO: 42.
  • the first signaling domain comprises a signaling domain or signaling fragment of CD28 or CD278 (ICOS). In some embodiments, the first signaling domain comprises a full-length costimulatory domain. In some embodiments, the construct is as shown in Fig. 88A. In some embodiments, the construct is as shown in Fig. 88B. In some embodiments, the construct is as shown in Fig. 88C. In some embodiments, any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein, including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs.
  • the extracellular binding domain is operatively linked to the transmembrane domain by a linker and/or a spacer.
  • the linker comprises about 2, 3, 5, 10, 15, 20, 25, 50, 75, 100, 150, 200, 250, 300, 350, or any integer that is between 2 and 350, amino acids.
  • the linker comprises from about 5 to about 20 amino acids.
  • the linker comprises from about 10 to about 250 amino acids.
  • the linker comprises 5 amino acids.
  • the linker comprises 10 amino acids.
  • the linker comprises 20 amino acids.
  • the linker comprises 50 amino acids.
  • the linker comprises 100 amino acids.
  • the linker comprises 250 amino acids.
  • the transmembrane domain comprises a transmembrane domain from CD28, CD8, ICOS, DAP10, or NTRK. In some embodiments, the transmembrane domain comprises a transmembrane domain from CD28. In some embodiments, the transmembrane domain comprises a transmembrane domain from CD8. In some embodiments, the transmembrane domain comprises a transmembrane domain from ICOS. In some embodiments, the transmembrane domain comprises a transmembrane domain from DAP 10. In some embodiments, the transmembrane domain comprises a transmembrane domain from NTRK.
  • the transmembrane domain comprises the transmembrane domain sequence of SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22. In some embodiments, the transmembrane domain comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to any one SEQ ID NOS:20, SEQ ID NO:21, or SEQ ID NO:22. In some embodiments, the extracellular binding domain comprises an scFv, a peptide, an antibody heavy-chain variable domain, an antibody light-chain variable domain, or a CEA ligand.
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7- 14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • nucleic acid which encodes the CD40 TRAF variant construct of any one of the embodiments of the present disclosure.
  • nucleic acid which encodes the CoStAR of any one of the embodiments of the present disclosure.
  • nucleic acid of any one of the embodiments of the present disclosure.
  • the cell which expresses the CD40 TRAF variant construct of any one of the embodiments of the present disclosure.
  • the cell comprises an alpha-beta T cell, gamma-delta T cell, T regulatory cell, TIL, NKT cell or NK cell.
  • the cell co-expresses a CAR or a TCR.
  • the cell which expresses the CoStAR of any one of the embodiments of the present disclosure.
  • the cell comprises an alpha-beta T cell, gamma-delta T cell, T regulatory cell, TIL, NKT cell or NK cell.
  • the cell co-expresses a CAR or a TCR.
  • a method of making the cell of any one of the embodiments of the present disclosure which comprises the step of transducing or transfecting a cell with a vector of any one of the embodiments of the present disclosure
  • [00182] is a method for preparing a population of cells that express a CoStAR of any one the embodiments of the present disclosure, which comprises: detecting expression of the CoStAR on the surface of cells transfected or transduced with a vector of alternative 62; and selecting cells which are identified as expressing the CoStAR.
  • In some embodiments is a cell population which is enriched for cell expression a CoStAR of any one of the embodiments of the present disclosure.
  • a method for treating a disease in a subject which comprises the step of administering a cell according to any one of the embodiments of the present disclosure, or a cell population according to any one of the embodiments of the present disclosure, to the subject.
  • a protein comprising the amino acid sequence of one of SEQ ID NOs: 510-519.
  • the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to any one SEQ ID NOS: SEQ ID NOs: 510-519.
  • the protein comprises the sequence of SEQ ID NO: 510.
  • the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 510.
  • the protein comprises the sequence of SEQ ID NO: 511. In some embodiments, the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 511. In some embodiments, the protein comprises the sequence of SEQ ID NO: 512. In some embodiments, the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 512. In some embodiments, the protein comprises the sequence of SEQ ID NO: 513.
  • the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 513. In some embodiments, the protein comprises the sequence of SEQ ID NO: 514. In some embodiments, the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 514. In some embodiments, the protein comprises the sequence of SEQ ID NO: 515.
  • the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 515. In some embodiments, the protein comprises the sequence of SEQ ID NO: 516. In some embodiments, the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 516. In some embodiments, the protein comprises the sequence of SEQ ID NO: 517.
  • the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 517. In some embodiments, the protein comprises the sequence of SEQ ID NO: 518. In some embodiments, the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 518. In some embodiments, the protein comprises the sequence of SEQ ID NO: 519.
  • the protein comprises a sequence that has about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, about 100%, or any integer that is between about 60 and about 100%, identity to SEQ ID NO: 519.
  • an immune cell comprising an extracellular tumor-associated antigen (TAA) specific binding domain and a transmembrane domain, comprising: a) a CD28 intracellular signalling domain; and b) a CD40 intracellular signalling domain, wherein the CD40 intracellular signalling domain comprises a TRAF variant of any one of the embodiments of the present disclosure.
  • an isolated nucleic acid molecule encoding the chimeric receptor of an immune cell comprising an extracellular tumor-associated antigen (TAA) specific binding domain and a transmembrane domain, wherein the nucleic acid molecule further comprises a TRAF variant of any one of the embodiments of the present disclosure.
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510- 519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a chimeric costimulatory receptor comprising an extracellular ligand binding fragment of a first costimulatory receptor and an intracellular signalling fragment of a second costimulatory receptor fused to a tumour associated antigen specific binding domain linked to a signalling domain, wherein the CoStAR further comprises a TRAF variant of any one of the embodiments of the present disclosure.
  • a CoStAR comprising an antigen specific binding domain, which is selected from: (a) a single chain antibody fragment which binds a tumour, associated antigen including, but not limited to, carcinoembryonic antigen (CEA), 5T4, melanotransferrin (CD228), Her2, EGFR, GPC3, melanoma-associated chondroitin sulphate proteoglycan (MCSP/CSPG4), CD71, folate receptor or CA125; or (b) a single chain antibody fragment which binds a tumour specific peptide (p)-major histocompatibility (MHO) complex; or (c) a tumour specific pMHC complex antigen specific single chain T-cell receptor (scTCR); or (d) a natural antigen binding polypeptide such as, but not limited to, transferrin; or (e) a domain which bind an antibody (e.g.
  • the CoStAr is fused to at least one of: (1) a fusion signalling domain comprising or consisting of full length human CD28, or a variant thereof having at least 60%, 70%, 80%, 90%, 95%, 99%, 100%, or any integer that is between 60 and 100%, sequence identity at the protein level; (2) the intracellular domain from human CD137, such as or a variant thereof having at least 60%, 70%, 80%, 90%, 95%, 99%, 100%, or any integer that is between 60 and 100%, sequence identity at the protein level, (3) the intracellular domain from human CD 134, or a variant thereof having at least 60%, 70%, 80%, 90%, 95%, 99%, 100%, or any integer that is between 60 and 100%, sequence identity at the protein level, (4) the intracellular domain from human CD2, or a variant thereof having at least 60%, 70%, 80%, 90%, 95%, 99%, 100%, or
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510- 519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a chimeric costimulatory antigen receptor which comprises: an extracellular binding domain operatively linked to a transmembrane domain, a CD28 signaling domain and a CD40 signaling domain, wherein the at least one extracellular binding domain comprises the amino acid sequence of SEQ ID NO:42275, wherein the CD28 signaling domain comprises the amino acid sequence of SEQ ID NO: 42276, and wherein the CD40 signaling domain comprises the amino acid sequence of SEQ ID NO: 42277.
  • the CoStAR further comprises at least one TRAF variant of any one of the embodiments of the present disclosure.
  • a protein that comprises: a first portion that comprises the amino acid sequence of SEQ ID NO:42275 that is linked to; a second portion that comprises a transmembrane domain that is linked to; a third portion that comprises the amino acid sequence of SEQ ID NO: 42276 that is linked to; a fourth portion that comprises the amino acid sequence of SEQ ID NO: 42277.
  • the protein further comprises at least one TRAF variant of any one of the embodiments of the present disclosure.
  • a protein that comprises: a first portion that comprises the amino acid sequence of SEQ ID NO: 42275; a second portion that comprises the amino acid sequence of SEQ ID NO: 42278; a third portion that comprises the amino acid sequence of SEQ ID NO: 42276; a fourth portion that comprises the amino acid sequence of SEQ ID NO: 42277; and a fifth portion that comprises SEQ ID NO: 42279, wherein the first portion is linked to the second portion by the fifth portion, wherein the third portion is linked to the second portion, and wherein the fourth portion is linked to the third portion.
  • the protein further comprises at least one TRAF variant of any one of the embodiments of the present disclosure.
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a chimeric costimulatory antigen receptor which comprises: an extracellular binding domain comprising a VH of antibody 196-14 and a VL of antibody 196-14, operatively linked to a transmembrane domain, a CD28 signaling domain and a CD40 signaling domain, wherein the CD28 signaling domain comprises the amino acid sequence of SEQ ID NO: 42276, and wherein the CD40 signaling domain comprises the amino acid sequence of SEQ ID NO: 42277.
  • the CoStAR further comprises at least one TRAF variant of any one of the embodiments of the present disclosure.
  • a cell population enriched for cell expression of a CoStAR comprising: an extracellular binding domain comprising a VH of antibody 196-14 and a VL of antibody 196-14, operatively linked to a transmembrane domain, a CD28 signaling domain and a CD40 signaling domain, wherein the CD28 signaling domain comprises the amino acid sequence of SEQ ID NO: 42276, and wherein the CD40 signaling domain comprises the amino acid sequence of SEQ ID NO: 42277.
  • the CoStAR further comprises at least one TRAF variant of any one of the embodiments of the present disclosure.
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • CoStAR which comprises: an extracellular binding domain operatively linked to a transmembrane domain, a first signaling domain, a CD40 signaling domain or a fragment thereof, and at least one TRAF variant of any one of the embodiments of the present disclosure.
  • the CD40 signaling fragment comprises an SH3 motif (KPTNKAPH, SEQ ID NO: 42280), TRAF2 motif (PKQE, SEQ ID NO: 42281, PVQE, SEQ ID NO: 42282, SVQE, SEQ ID NO: 42283), TRAF 6 motif (QEPQEINFP, SEQ ID NO: 42284), PKA motif (KKPTNKA, SEQ ID NO: 42285, SRISVQE, SEQ ID NO: 42286), or a combination thereof, or is a full length CD40 intracellular domain.
  • SH3 motif KPTNKAPH, SEQ ID NO: 42280
  • TRAF2 motif PQE, SEQ ID NO: 42281, PVQE, SEQ ID NO: 42282, SVQE, SEQ ID NO: 42283
  • TRAF 6 motif QEPQEINFP, SEQ ID NO: 42284
  • PKA motif KKPTNKA, SEQ ID NO: 42285, SRISVQE, SEQ ID NO
  • the first signaling domain comprises a signaling domain or signaling fragment of CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
  • the extracellular binding domain binds to CD70, CD146, FOLRI, carcinoembryonic antigen (CEA), 5T4, mellanotransferrin (CD228), Her2, EGFR, GPC3, melanoma-associated chondroitin sulphate proteoglycan (MCSP/CSPG4), CD71, EPCAM, SM5- 1, folate receptor or CA125, PDL-1, CD155 PD-I, mesothelin, or a tumor specific peptide (p )- major histocompatability (MHC) complex, or a tumor specific pMHC complex antigen specific single chain T-cell receptor (scTCR), or transferrin, or an antibody or antigen binding protein.
  • CEA carcinoembryonic antigen
  • 5T4 mellanotransferrin
  • CD228 Her2, EGFR, GPC3, melanoma-associated chondroitin sulphate proteoglycan
  • MCSP/CSPG4 mel
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a chimeric costimulatory antigen receptor which comprises: an extracellular binding domain specific for a tumor associated antigen (TAA) operatively linked to a transmembrane domain, a CD28 signaling domain, a CD40 signaling domain or a signaling fragment thereof, and at least one TRAF variant of any one of the embodiments of the present disclosure.
  • TAA tumor associated antigen
  • the CoStAR is specific for FOLR1.
  • the CoStAR is specific for PDL1.
  • the CoStAR is specific for CEA.
  • the extracellular binding domain comprises M0V19 scFv.
  • the extracellular binding domain is specific for CD70, CD 146, FOLR1, carcinoembryonic antigen (CEA), 5T4, mellanotransferrin (CD228), Her2, EGFR, GPC3, melanoma-associated chondroitin sulphate proteoglycan (MCSP/CSPG4), CD71, EPCAM, SM5- 1, folate receptor or CA125, PDL-1, CD155 PD-1, mesothelin, or a tumor specific peptide (p)- major histocompatability (MHC) complex, or a tumor specific pMHC complex antigen specific single chain T-cell receptor (scTCR), or transferrin, or an antibody or antigen binding protein.
  • CD70 CD 146, FOLR1, carcinoembryonic antigen (CEA), 5T4, mellanotransferrin (CD228), Her2, EGFR, GPC3, melanoma-associated chondroitin sulphate proteoglycan (MCSP/CS
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present method and/or construct and/or protein.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a fusion protein comprising: at least one TRAF variant of any one of the embodiments of the present disclosure, (a) a binding domain, wherein the binding domain comprises: an L-CDR1 sequence comprising the amino acid sequence of SEQ ID NO: 42287, an L-CDR2 sequence comprising the amino acid sequence of SEQ ID NO: 42288, an L- CDR3 sequence comprising the amino acid sequence of SEQ ID NO: 42289, an H-CDR1 sequence comprising the amino acid sequence of SEQ ID NO: 42290, an H-CDR2 sequence comprising the amino acid sequence of SEQ ID NO: 42291, and an H-CDR3 sequence comprising the amino acid sequence of SEQ ID NO: 173; (b) an amino acid sequence of SEQ ID NO: 42293 linked to the binding domain; (c) an amino acid sequence of SEQ ID NO: 42294 linked to (b); (d) an amino acid sequence of SEQ ID NO: 42295 linked to (c); and (e) an L-CDR1 sequence comprising
  • a fusion protein comprising the amino acid sequence of SEQ ID NO: 42297 or 42298, and at least one TRAF variant of any one of the embodiments of the present disclosure.
  • an engineered protein comprising a clustering domain and a signaling domain comprising a CD40 signaling domain or signaling fragment thereof and at least one TRAF variant of any one of the embodiments of the present disclosure is provided, wherein the clustering domain is capable of oligomerization whereby the signaling domain is activated.
  • the protein comprises a constitutively stimulating antigen agnostic receptor (C-SAAR).
  • the protein comprises at least one of: LZ(cFos)- EGFRTM/JMD- CD28-CD40, LZ(cFos)-CD28TM- CD28-CD40, LZ(cJun)- EGFRTM/JMDCD28-CD40, LZ( cJun)-CD28TM-CD28-CD40, LZ(c/EBP)-EGFRTM/JMD- CD28-CD40, or LZ(c/EBP)-CD28TM- CD28-CD40.
  • the protein further comprises an inducible costimulatory receptor.
  • the protein comprises at least one of: anti-IDl-VHVL(A3 0514-pembro)-CD28TMD-CD28-CD40, or Anti-ID 1-VL- VH(A3 0514-pembro)CD28TMD-CD28-CD40, or Anti-ID2-VH-VL(A3 0523-pembro)- CD28TMD-CD28-CD40, or anti-ID2-VL-Vh(A3 0523-pembro)-CD28TMD-CD28-CD40, or Anti-ID3-Vh-VL(A3063 3-pembro)-CD28TMD-CD28-CD40, or Anti-ID3-VL-VH(A 3063 3- pembro)-CD28TMD-CD28-CD40.
  • the engineered protein comprises a transmembrane domain and the clustering domain oligomerizes when the engineered protein is bound by a ligand.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • the extracellular binding domain is operatively linked to ICOS, wherein ICOS comprises the amino acid sequence of SEQ ID NO: 515, wherein ICOS is linked to a CD40 signaling domain, and wherein the extracellular binding domain comprises: a HCDR1 that is an HCDR1 in SEQ ID NO: 12; a HCDR2 that is an HCDR2 in SEQ ID NO: 12; a HCDR3 that is an HCDR3 in SEQ ID NO: 12; a LCDR1 that is an LCDR1 in SEQ ID NO: 12; a LCDR2 that is an LCDR2 in SEQ ID NO: 12; and a LCDR3 that is an HCDR3 in SEQ ID NO: 12.
  • a fusion protein comprising at least one TRAF variant of any one of the embodiments of the present disclosure, wherein the fusion protein further comprises a HCDR1 that is an HCDR1 in SEQ ID NO: 12; a HCDR2 that is an HCDR2 in SEQ ID NO: 12; a HCDR3 that is an HCDR3 in SEQ ID NO: 12; a LCDR1 that is an LCDR1 in SEQ ID NO: 12; a LCDR2 that is an LCDR2 in SEQ ID NO: 12; and a LCDR3 that is an HCDR3 in SEQ ID NO: 12.
  • the construct is as shown in Fig. 88A. In some embodiments, the construct is as shown in Fig.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • a CoStAR which comprises: an extracellular binding domain that binds to mesothelin (MSLN) and at least one TRAF variant of any one of the embodiments of the present disclosure.
  • the CoStAR further comprises a transmembrane domain; a CD28 signaling domain, wherein the CD28 signaling domain comprises the amino acid sequence of SEQ ID NO: 25; and a CD40 signaling domain, wherein the extracellular binding domain comprises any one of: a HCDR1 that is an HCDR1 in SEQ ID NO: 186, a HCDR2 that is an HCDR2 in SEQ ID NO: 186, a HCDR3 that is an HCDR3 in SEQ ID NO: 186, a LCDR1 that is an LCDR1 in SEQ ID NO: 186, a LCDR2 that is an LCDR2 in SEQ ID NO: 186, and LCDR3 that is an LCDR3 in SEQ ID NO: 186;
  • the fusion protein further comprises a first sequence, comprising any one or more of: a HCDR1 that is an HCDR1 in SEQ ID NO: 186, a HCDR2 that is an HCDR2 in SEQ ID NO: 186, a HCDR3 that is an HCDR3 in SEQ ID NO: 186, a LCDR1 that is an LCDR1 in SEQ ID NO: 186, a LCDR2 that is an LCDR2 in SEQ ID NO: 186, and LCDR3 that is an LCDR3 in SEQ ID NO: 186; a HCDR1 that is an HCDR1 in SEQ ID NO: 187, a HCDR2 that is an HCDR2 in SEQ ID NO: 187, a HCDR3 that is an HCDR3 in SEQ ID NO: 187, a LCDR1 that is an LCDR
  • the fusion protein further comprises a second sequence that is a transmembrane domain, a third sequence that comprises the amino acid sequence of SEQ ID NO: 25; and a fourth sequence that comprises the amino acid sequence of SEQ ID NO: 32, wherein the first sequence is linked to the second sequence, wherein the second sequence is linked to the third sequence, and wherein the third sequence is linked to the fourth sequence.
  • a CoStAR comprising at least one TRAF variant of any one of the embodiments of the present disclosure, wherein the CoStAR is capable of CoStAR-ligand- inducible activation of an immune cell bearing a T cell receptor (TCR) when the TCR is engaged by a target of the TCR, which comprises an extracellular ligand binding domain specific for the inducing ligand, a transmembrane domain, and an intracellular signaling domain.
  • TCR T cell receptor
  • the cell comprises an alpha-beta T cell.
  • the alpha-beta T cell comprises a tumor infiltrating lymphocyte (TIL).
  • TIL tumor infiltrating lymphocyte
  • the CoStAR does not comprise a full length CD28 extracellular domain.
  • the CoStAR comprises a truncated CD28 extracellular domain or a CD8 extracellular domain located between the ligand binding domain and the transmembrane domain.
  • the intracellular signaling domain comprises one or more of CD28, CD40, CD137, 0X40, ICOS, CD2, or DAP10 or signaling fragments thereof.
  • the ligand-binding domain binds to tafasitamab, cetuximab, trastuzumab, and/or pembrolizumab.
  • a method of cell therapy comprising identifying a subject in need thereof and administering the CoStAR, fusion protein, nucleic acid, vector, or cell of any one of the embodiments of the present disclosure.
  • a method for preparing a population of cells enriched for the CoStAR or protein expressing the TRAF variant comprising detecting expression of the CoStAR or protein on the surface of the cells transfected or transduced with a vector of any one of the embodiments of the present disclosure and selecting cells with are identified as expressing the CoStAR or protein.
  • [00199] is a method for treating a disease in a subject in need thereof, the method comprising administering the cell or cell population of any one of the embodiments of the present disclosure to the subject.
  • CD40 is a TNF receptor superfamily member that provides activation signals in antigen-presenting cells such as B cells, macrophages, and dendritic cells. Multimerization of CD40 by its ligand initiates signaling by recruiting TNF receptor-associated factors (TRAFs) to the CD40 cytoplasmic domain. TRAF binding sites are responsible for the intracellular signalling of CD40.
  • TNF receptor-associated factors TRAF binding sites are responsible for the intracellular signalling of CD40.
  • the TRAF domain mediates oligomerization of TRAF proteins as well as their association with upstream receptors or adaptors and downstream effector proteins.
  • the RING domain is best known for its function to mediate protein ubiquitination in a large family of E3 ubiquitinase ligases.
  • TRAFs include nuclear factor kappa beta (NF-KB) and mitogen-activated protein kinases (MAPKs), which are in turn important for induction of genes associated with innate immunity, inflammation, and cell survival.
  • TRAF2 and TRAF3 function as negative regulators in some signaling pathways involved in the survival of B cells and inflammatory responses of innate immune cells.
  • the canonical pathway of NF-KB is induced by TNFa, IL-1, or LPS and uses a large variety of signalling adaptors to engage IKK activity. Phosphorylation of serine residues in the signal responsive region (SRR) of classical IKBS by IKKP leads to IKB ubiquitination and subsequent proteosomal degradation. This results in release of the NF-KB dimer, which can then translocate to the nucleus and induce transcription of target genes.
  • the non-canonical pathway depends on NIK (NF-KB -inducing kinase) induced activation of IKKa. IKKa phosphorylates the plOO NF-KB subunit, which leads to proteosomal processing of plOO to p52. This results in the activation of p52-RelB dimers, which target specific KB elements.
  • costimulatory receptors comprising a CD40 signaling domain display novel and improved activity profiles. It has further been discovered that variants of TRAF2, TRAF2/3, and TRAF6 binding domains within CD40 modulate signaling.
  • the activity profiles can be modulated by selecting an intracellular domain of a receptor protein for joining to the CD40 signaling domain and/or by selecting elements of the CD40 signaling domains to join to the intracellular domain of a receptor protein.
  • CoStARs recombinant costimulatory antigen receptors
  • the CoStAR comprises an extracellular segment of a stimulatory receptor protein.
  • the extracellular segment of the stimulatory receptor protein is capable of binding ligand.
  • the extracellular segment of a stimulatory receptor protein is truncated and does not bind ligand.
  • the extracellular segment of the stimulatory receptor protein operates as an adjustable length spacer allowing the disease- or tumor-associated antigen binding domain to be located away from the surface of the cell in which it is expressed for example to form a more optimal immune synapse.
  • the extracellular segment of a stimulatory receptor protein and the first intracellular segment comprise segments of the same receptor protein.
  • the extracellular segment and the first intracellular segment comprise segments of different receptor proteins.
  • the CoStARs comprise an intervening transmembrane domain between the disease or tumor antigen binding domain and the first intracellular domain. When an extracellular segment of a stimulatory receptor protein is present, the transmembrane domain is intervening between the extracellular segment and the first intracellular signaling domain.
  • any of the CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7-14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C, can be used in the present methods and/or constructs and/or proteins.
  • the sequence options in FIGs. 78 and 79 can be optionally excluded from all of the embodiments provided herein.
  • full length protein or “full length receptor” refers to a receptor protein, such as, for example, a CD28 receptor protein.
  • full length encompasses receptor proteins lacking up to about 5 or up to 10 amino acids, for example 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acids, at the N-terminal of the mature receptor protein once its signal peptide has been cleaved. For instance, while a specific cleavage site of a receptors N-terminal signal peptide may be defined, variability in exact point of cleavage has been observed.
  • full length does not imply presence or absence of amino acids of the receptors N-terminal signal peptide.
  • the term “full length” encompasses mature receptor proteins (e.g. CD28 according to certain aspects of the invention) lacking the N terminal signal peptide lacking up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N-terminal of the mature receptor protein once its signal peptide has been cleaved.
  • a “full length” CD28 receptor or other receptor or tumor antigen binding domain does not include the signal peptide and may lack up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N-terminal of the mature receptor protein (e.g.
  • N terminal residues N, K, I, L and/or V N terminal residues N, K, I, L and/or V. This is shown in the exemplary fusions, e.g. SEQ ID Nos. 4-12 (note that these may lack up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N- terminal of the mature receptor protein as shown in the boxed region).
  • CoStARs have modular form and can be constructed to comprise extracellular, transmembrane and intracellular domains obtained from a one or more proteins, along with the scFv obtained from an antibody that binds to a disease-associated antigen, for example, a tumor associated antigen.
  • a CoStAR comprises a disease- associated, for example a tumor-associated, antigen receptor, such as but not limited to a tumor- associated antigen specific scFv, and a primary costimulatory receptor protein that is capable of binding to its cognate ligand and providing an intracellular signal.
  • the primary costimulatory receptor can be less than a full length protein but is sufficient to bind cognate ligand and transduce a signal.
  • the primary costimulatory receptor domain is full length, such as but not limited to, full length CD28.
  • CoStAR constructs that comprise an antigen binding domain, an optional spacer, an optional costimulatory receptor protein comprising an extracellular ligand binding segment or fragment thereof and intracellular CD40 signaling domain.
  • a CoStAR comprises an antigen binding domain, an optional spacer, an extracellular ligand-binding portion of a costimulatory receptor protein, a transmembrane domain, and an intracellular signaling domain of a selected costimulatory receptor protein and intracellular CD40 signaling domain.
  • the extracellular ligand-binding portion comprises a CD28 truncation, for example, a C-terminal CD28 truncation after amino acids IEV, and is followed by an intracellular signaling domain.
  • the intracellular signaling domain is from CD40.
  • the transmembrane domain separating the extracellular ligand-binding and intracellular signaling domains can be from, with limitation, CD28, CD40.
  • CoStARs can comprise additional costimulatory domains, for example a third, intracellular costimulatory signaling domain and in this respect may be similar to certain chimeric antigen receptors (CARs), which have been classified into first (CD3 ⁇ only), second (one costimulatory domain + CD3Q, or third generation (more than one costimulatory domain + CD3Q.
  • CARs chimeric antigen receptors
  • Costimulatory receptor proteins useful in CoStARs of the invention include, without limitation, CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6, which in their natural form comprise extracellular ligand binding domains and intracellular signal transducing domains.
  • CD2 is characterized as a cell adhesion molecule found on the surface of T cells and is capable of initiating intracellular signals necessary for T cell activation.
  • CD27 is characterized as a type II transmembrane glycoprotein belonging to the TNFR superfamily (TNFRSF) whose expression on B cells is induced by antigen-receptor activation in B cells.
  • CD28 is one of the proteins on T cells and is the receptor for CD80 (B7.1) and CD86 (B7.2) ligands on antigen-presenting cells.
  • CD137 (4-1BB) ligand is found on most leukocytes and on some non-immune cells.
  • 0X40 ligand is expressed on many antigen- presenting cells such as DC2s (dendritic cells), macrophages, and B lymphocytes.
  • the costimulatory receptor protein is full length CD28 as defined herein.
  • CD40 is a member of the tumor necrosis factor receptor (TNFR) superfamily and several isoforms are generated by alternative splicing. Its ligand, CD 154 (also called CD40L) is a protein that is primarily expressed on activated T cells.
  • CD40 isoform 1 protein sequence is set forth in GenBank accession No. NP 001241.1, including signal peptide (amino acids 1-20), transmembrane domain (amino acids 194-215), and cytoplasmic domain (amino acids 216-277)(SEQ ID NO:32).
  • CD40 receptor signaling involves adaptor proteins including but not limited to TNF receptor-associated factors (TRAF), and the CD40 cytoplasmic domain comprises signaling components, including amino acid sequences fitting an SH3 motif (KPTNKAPH) (SEQ ID NO:35), TRAF2 motif (PKQE (SEQ ID NO:36), PVQE (SEQ ID NO: 37), SVQE (SEQ ID NO: 38)), TRAF 6 motif (QEPQEINFP) (SEQ ID NO: 39) and PKA motif (KKPTNKA (SEQ ID NO:40), SRISVQE (SEQ ID NO:41)).
  • the invention further includes engineered signaling domains, such as engineered CD40 signaling domains, comprising TRAF- binding amino acid sequences.
  • Engineered signaling domains that bind to TRAF1, TRAF2, TRAF3, and TRAF5 may comprise the major consensus sequence (P/S/A/T)X(Q/E)E or minor consensus sequence PXQXXD and can be identified in or obtained from, without limitation, TNFR family members such as CD30, 0X40, 41BB, and the EBV oncoprotein LMP1.
  • TNFR family members such as CD30, 0X40, 41BB, and the EBV oncoprotein LMP1.
  • Examples disclosed herein demonstrate operation of CD40 as a costimulatory signaling domain in a CoStAR and further that cytokine and chemokine expression profiles are altered by signaling domain selection.
  • the costimulatory CD40 signaling domain of a CoStAR promotes pro-inflammatory cytokines (e.g., IL-2, TNFa).
  • the costimulatory CD40 signaling domain of a CoStAR reduces immunosuppressive cytokines (e.g., IL-5, IL- 10).
  • Costimulatory activity of a CD40 signaling domain or fragment can be observed in combination with a first receptor signaling domain such as but not limited to CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6, as compared to activity of the first receptor signaling domain without the CD40 signaling domain or fragment.
  • a first receptor signaling domain such as but not limited to CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82
  • the CD40 signaling domains of the invention including signaling fragments comprising particular factor binding sites or wherein particular factor binding sites are mutated, in combination with a costimulatory first signaling domain, are capable of promoting or suppressing relative expression of particular cytokines and/or chemokines as compared to the first signaling domain alone, activity of a costimulatory signaling domain.
  • a costimulatory signaling domain See, e.g., Ahonen, CL et al., The CD40-TRAF6 axis controls affinity maturation and the generation of long-lived plasma cells. Nat Immunol.
  • a CoStAR of the invention comprises substantially all of a CD40 costimulatory domain. In some embodiments, a CoStAR of the invention comprises two or more CD40 costimulatory domains. In some embodiments, a CoStAR of the invention comprises a CD40 costimulatory domain signaling component or fragment or motif.
  • the CD40 signaling fragment or motif comprises, consists, or consists essentially of an SH3 binding sequence (e.g., without limitation, KPTNKAPH (SEQ ID NO:35), PTNKAPHP (SEQ ID NO:443) or PTNKAPH (SEQ ID NO:444)), TRAF2/TRAF3 binding sequence (e g., without limitation, PKQE (SEQ ID NO:506), PKQET (SEQ ID NO:445), PVQE (SEQ ID NO:507), PVQET (SEQ ID NO:446), SVQE (SEQ ID NO:508), SVQET (SEQ ID NO:447)), TRAF6 binding sequence (e.g., without limitation, PQEINF (SEQ ID NO:509), QEPQEINF (SEQ ID NO:448) or QEPQEINFP (SEQ ID NO:39)) or PKA sequence (e.g., without limitation, KKPTNKA (SEQ ID NO:40),
  • a CoStAR of the invention comprises a CD40 costimulatory domain and a CD40 costimulatory domain signaling component or motif.
  • one or more of the SH3, TRAF2/TRAF3, TRAF6, or PKA motifs of the CD40 signaling domain is mutated.
  • the SH3 motif, TRAF2/TRAF3 motif, and TRAF6 motif are sufficient to modulate pro-inflammatory and/or immunosuppressive cytokines.
  • adding tandem copies of those motifs and/or mutating certain motifs amplifies these effects.
  • Table 1 provides non-limiting examples of TRAF2/TRAF3 binding domains.
  • the alignments of Table 1 with the minor and major consensus sequences are as shown in Figs. 82A- 82B, respectively.
  • TRAF2/TRAF3 binding sequences of the invention further include sequences such as P1V2Q3E4 and variants wherein Pi is substituted with S, A, or T, V2 is substituted with Q, K, or E, Q3 is substituted with E, and/or E4 is substituted with A.
  • any one, two, three, or all four of P1V2Q3E4 may be substituted.
  • Non-limiting examples are shown in Table 1 at positions P-2, P-1, P0, Pl.
  • CD40 TRAF2/TRAF3 sequence variants include the following, the amino acids at P-2, P-1, P0, and Pl enclosed by dashes, and the TRAF2/TRAF3 source protein identified.
  • Table 3 provides non-limiting examples of TRAF6 binding sequences. The alignments of Table 3 with the major TRAF6 consensus sequences is as shown in Fig. 82C.
  • Illustrative non-limiting examples of CD40 TRAF6 sequence variants include the following, the amino acids at P-2, P-1, P0, Pl, P2, and P3 enclosed by dashes, and the TRAF6 sequence origin identified.
  • selection of one or more costimulatory domain signaling component or motif is guided by the cell in which the CoStAR is to be expressed and/or a desired costimulatory activity more closely identified with a signaling component or motif, or avoidance of a costimulatory activity more closely identified with a signaling component or motif.
  • a CoStAR signaling domain comprises, in addition to a CD40 costimulatory domain or signaling component or motif thereof, or two or more such domains or components or motifs or combinations thereof, an additional full length costimulatory domain or signaling component thereof from, without limitation, CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6, [00218]
  • the human CD28 protein sequence is set forth in GenBank accession No.
  • NP 006130.1 including signal peptide (amino acids 1-18), extracellular domain (amino acids 19- 152), transmembrane domain (amino acids 153-179) and cytoplasmic domain (amino acids 180- 200).
  • the extracellular domain includes an immunoglobulin type domain (amino acids 21-136) which contains amino acids with compose the antigen binding site and amino acids that form the homodimer interface.
  • the extracellular domain includes several asparagine residues which may be glycosylated, and the intracellular domain comprises serine and tyrosine residues, which may be phosphorylated.
  • NP_001139345.1 including signal peptide (amino acids 1-21), extracellular domain (amino acids 22-182), transmembrane domain (amino acids 183-203), and cytoplasmic domain (amino acids 204-235).
  • the extracellular domain includes an immunoglobulin type domain (amino acids 28-128) which contains amino acids with compose the antigen binding site and amino acids that form the homodimer interface.
  • the extracellular domain includes several asparagine residues which may be glycosylated, and the intracellular domain comprises serine and tyrosine residues, which may be phosphorylated.
  • the human IgG4 constant region sequence is set forth in UniProtKB/Swiss-Prot: accession No. P01861.1, including CHI (amino acids 1-98), hinge (amino acids 99-110), CH2 (amino acids 111-220), CH3 (amino acids 221-327).
  • the CH2 region includes asparagine at amino acid 177, which is the glycosylated and associated with Fc receptor and antibody-dependent cell-mediated cytotoxicity (ADCC).
  • CD137 4-1BB
  • NP_001552.2 the protein sequence of human CD137 (4-1BB), another TNFR superfamily member, is set forth by GenBank accession No. NP_001552.2, including signal peptide (amino acids 1-23), extracellular domain (amino acids 24-186), transmembrane domain (amino acids 187-213), and cytoplasmic domain (amino acids 214-255).
  • binding of CD137L ligand trimers expressed on antigen presenting cells to CD 137 leads to receptor trimerization and activation of signaling cascades involved in T cell reactivity and survival (Li et al., Limited Cross- Linking of 4- IBB by 4- IBB Ligand and the Agonist Monoclonal Antibody Utomilumab .
  • the human CD134 (0X40) protein sequence is set forth by GenBank accession No. NP 003318.1, including signal peptide (amino acids 1-28), extracellular domain (amino acids 29-214), transmembrane domain (amino acids 215-235), and cytoplasmic domain (amino acids 236-277).
  • This receptor has been shown to activate NF-kappaB through its interaction with adaptor proteins TRAF2 and TRAF5 and studies suggest that this receptor promotes expression of apoptosis inhibitors BCL2 and BCL21L1/BCL2-XL.
  • the human T-cell surface antigen CD2 has at least two isoforms.
  • the human CD2 isoforml protein sequence is set forth by NP 001315538.1, including signal peptide (amino acids 1-24), extracellular domain (amino acids 25-235), transmembrane domain (amino acids 236-261), and cytoplasmic domain (amino acids 262-377).
  • the human CD2 isoform2 protein sequence is set forth by NP_001758.2
  • the human CD357 (GITR) isoform-1 protein sequence is set forth by GenBank accession No. NP 004186.1, including signal peptide (amino acids 1-25), extracellular domain (amino acids 26-162), transmembrane domain (amino acids 163-183), and cytoplasmic domain (amino acids 184-241).
  • the human CD29 (betal integrin) protein sequence is set forth by GenBank accession No. NP 596867, including signal peptide (amino acids 1-20), extracellular domain (amino acids 21-728), transmembrane domain (amino acids 729-751), and cytoplasmic domain (amino acids 752-798).
  • the human CD 150 (SLAM) protein sequence has at several isoforms.
  • mCD150 transmembrane form of CD150
  • sCD150 secreted form of CD 150
  • human SLAM isoform b is set forth by GenBank accession No. NP 003028.1, including signal peptide (amino acids 1-20), extracellular domain (amino acids 21- 237), transmembrane domain (amino acids 238-258), and cytoplasmic domain (amino acids 259- 335).
  • Human SLAM isoform a is set forth by GenBank accession No. NP 001317683.1.
  • CD278 or ICOS is a CD28-superfamily costimulatory molecule that is expressed on activated T cells.
  • Human ICOS precursor (199 aa with signal peptide) is set forth by GenBank accession No. NP 036224.1, including signal peptide (amino acids 1-20), an Ig-V-like domain (amino acids 21-140), transmembrane domain (amino acids 141- 161) and intracellular domain (amino acids 162-199).
  • ICOS contains an IProx motif sequence SSSVHDPNGE (SEQ ID NO:466).
  • IProx motif sequence SSSXXXPXGE (SEQ ID NO:467) resembles certain binding sites of TRAF1 (SASFQRPQSE (SEQ ID NO:468)), TRAF2 (SSSFQRPVND (SEQ ID NO:469)), TRAF3 (SSFKKPTGE (SEQ ID NO:470)), and TRAF5 (SSSFKRPDGE (SEQ ID NO:471)).
  • Hematopoietic cell signal transducer also known as DAP 10, KAP10, PIK3AP, and hematopoietic cell signal transducer (GenBank accession No. NP 055081.1) encodes a transmembrane signaling adaptor thought to form part of a receptor complex with the C-type lectin-like receptor NKG2D.
  • the intracellular domain contains a YxxM motif of a phosphatidylinositol 3 -kinase binding site.
  • a CoStAR may be expressed alone under the control of a promoter in a therapeutic population of cells that have therapeutic activity, for example, Tumour Infiltrating Lymphocytes (TILs).
  • TILs Tumour Infiltrating Lymphocytes
  • the CoStAR may be expressed along with a therapeutic transgene such as a chimeric antigen receptor (CAR) and/or T-cell Receptor (TCR), (note that may lack up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N- terminal of the mature receptor protein).
  • CAR chimeric antigen receptor
  • TCR T-cell Receptor
  • the invention also relates to CoStAR constructs, not limited to those having a sequence as shown in any of SEQ ID NOS:42-185, 192- 335, 344-430, including one of these sequences which lacks up to about 5, for example 1, 2, 3, 4, 5, or up to 10 amino acids at the N-terminal of the mature receptor protein).
  • Suitable TCRs and CARs are well known in the literature, for example HLA-A*02-NYESO-1 specific TCRs (Rapoport et al. Nat Med 2015) or anti-CD19scFv.CD3 ⁇ fusion CARs (Kochenderfer et al.
  • the CoStARs described herein may be expressed with any known CAR or TCR thus providing the cell with a regulatable growth switch to allow cell expansion in-vitro or in-vivo, and a conventional activation mechanism in the form of the TCR or CAR for anti-cancer activity.
  • the invention provides a cell for use in adoptive cell therapy comprising a CoStAR as described herein and a TCR and/or CAR that specifically binds to a tumor associated antigen.
  • An exemplary CoStAR comprising CD28 includes an extracellular antigen binding domain and an extracellular, transmembrane and intracellular signaling domain.
  • antigen binding domain refers to an antibody fragment including, but not limited to, a diabody, a Fab, a Fab’, a F(ab’)2, an Fv fragment, a disulfide stabilized Fv fragment (dsFv), a (dsFv)2, a bispecific dsFv (dsFv-dsFv 1 ), a disulfide stabilized diabody (ds diabody), a single-chain antibody molecule (scFv), an scFv dimer (bivalent diabody), a multispecific antibody formed from a portion of an antibody comprising one or more CDRs, a camelized single domain antibody, a nanobody, a domain antibody, a bivalent domain antibody, or any other antibody fragment that binds to an antigen but does not comprise a complete antibody structure.
  • an antigen binding domain is capable of binding to the same antigen to which the parent antibody or a parent antibody fragment (e.g., a parent scFv) binds.
  • an antigen-binding fragment may comprise one or more complementarity determining regions (CDRs) from a particular human antibody grafted to frameworks (FRs) from one or more different human antibodies.
  • An “antigen binding domain” may be referred to as a “ligand binding domain.”
  • the antigen binding domain can be made specific for any disease-associated antigen, including but not limited to tumor-associated antigens (TAAs) and infectious disease-associated antigens.
  • TAAs tumor-associated antigens
  • infectious disease-associated antigens infectious disease-associated antigens.
  • the ligand binding domain is bispecific.
  • TAA Antigens have been identified in most of the human cancers, including Burkitt lymphoma, neuroblastoma, melanoma, osteosarcoma, renal cell carcinoma, breast cancer, prostate cancer, lung carcinoma, and colon cancer.
  • TAA’s include, without limitation, CD 19, CD20, CD22, CD24, CD33, CD38, CD 123, CD228, CD138, BCMA, GPC3, CEA, folate receptor (FRa), mesothelin, CD276, gplOO, 5T4, GD2, EGFR, MUC-1, PSMA, EpCAM, MCSP, SM5-1, MICA, MICB, ULBP and HER-2.
  • TAAs further include neoantigens, peptide/MHC complexes, and HSP/peptide complexes.
  • the antigen binding domain comprises a T-cell receptor or binding fragment thereof that binds to a defined tumor specific peptide-MHC complex.
  • T cell receptor refers to a heterodimeric receptor composed of aP or y6 chains that pair on the surface of a T cell. Each a, P, y, and 6 chain is composed of two Ig- like domains: a variable domain (V) that confers antigen recognition through the complementarity determining regions (CDR), followed by a constant domain (C) that is anchored to cell membrane by a connecting peptide and a transmembrane (TM) region.
  • V variable domain
  • CDR complementarity determining regions
  • C constant domain
  • TM transmembrane
  • Each of the V domains has three CDRs. These CDRs interact with a complex between an antigenic peptide bound to a protein encoded by the major histocompatibility complex (pMHC) (Davis and Bjorkman (1988) Nature, 334, 395-402; Davis et al. (1998) Annu Rev Immunol, 16, 523-544; Murphy (2012), xix, 868 p.).
  • pMHC major histocompatibility complex
  • the antigen binding domain comprises a natural ligand of a tumor expressed protein or tumor-binding fragment thereof.
  • PD1 which binds to PDL1.
  • TfRl transferrin receptor 1
  • CD71 transferrin receptor 1
  • TfRl transferrin receptor 1
  • CD71 transferrin receptor 1
  • the antigen binding domain comprises transferrin or a transferrin receptor-binding fragment thereof.
  • the antigen binding domain is specific to a defined tumor associated antigen, such as but not limited to FRa, CEA, 5T4, CA125, SM5-1 or CD71.
  • the tumor associated antigen can be a tumor-specific peptide-MHC complex.
  • the peptide is a neoantigen.
  • the tumor associated antigen it a peptide-heat shock protein complex.
  • the invention provides a CoStAR which comprises
  • scFv that binds to carcinoembryonic antigen (CEA), a spacer and transmembrane sequence of CD28, a CD28 signaling domain, and a CD40 signaling domain.
  • CEA carcinoembryonic antigen
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD28, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD28, a CD 137 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD28, a CD 134 signaling domain, and a CD40 signaling domain.
  • v an scFv that binds to CEA, a spacer and transmembrane sequence of CD28, a CD2 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD28, a GITR signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD28, a CD29 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD28, a CD 150 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD8, a CD28 signaling domain, and a CD40 signaling domain.
  • x an scFv that binds to CEA, a spacer and transmembrane sequence of CD8, and a CD40 signaling domain.
  • xi an scFv that binds to CEA, a spacer and transmembrane sequence of CD8, a CD 137 signaling domain, and a CD40 signaling domain.
  • xii an scFv that binds to CEA, a spacer and transmembrane sequence of CD8, a CD 134 signaling domain, and a CD40 signaling domain.
  • xiii an scFv that binds to CEA, a spacer and transmembrane sequence of CD8, a CD2 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer and transmembrane sequence of CD8, a GITR signaling domain, and a CD40 signaling domain.
  • xv. an scFv that binds to CEA, a spacer and transmembrane sequence of CD8, a CD29 signaling domain, and a CD40 signaling domain.
  • xviii an scFv that binds to CEA, a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, and a CD40 signaling domain.
  • xix an scFv that binds to CEA, a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a CD 137 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA
  • a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a CD 134 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA
  • a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a CD2 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA
  • a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a GITR signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA
  • spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a CD29 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA
  • a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a CD 150 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA, a spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a first CD40 signaling domain and a second CD40 signaling domain
  • scFv that binds to CEA
  • spacer comprising an IgG4 constant region and CD28 transmembrane sequence, a first CD40 signaling domain and a second mutated CD40 signaling domain
  • xxvii a binding domain that binds to PDL1, a short spacer and transmembrane sequence of CD28, a CD28 signaling domain, and a CD40 signaling domain.
  • xxviii a binding domain that binds to PDL1, a short spacer and transmembrane sequence of CD28, and a CD40 signaling domain.
  • xxx a binding domain that binds to CD155, CD112, or CD113, a CD28 transmembrane domain, and a CD40 signaling domain.
  • xxxi an scFv that binds to CEA, a binding domain that binds to PDL1, a short spacer and transmembrane sequence of CD28, a CD28 signaling domain, and a CD40 signaling domain.
  • xxxii an scFv that binds to CEA, a binding domain that binds to PDL1, a short spacer and transmembrane sequence of CD28, and a CD40 signaling domain.
  • xxxiii an scFv that binds to CEA, a binding domain that binds to CD155, CD112, or CD113, a short spacer and transmembrane sequence of CD28, a CD28 signaling domain, and a CD40 signaling domain.
  • scFv that binds to CEA
  • a binding domain that binds to CD155, CD112, or CD113
  • a short spacer and transmembrane sequence of CD28 a CD40 signaling domain.
  • xxxv an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain, and transmembrane sequence of CD28, and a NTRKl signaling domain
  • xxxvi an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, aNTRKl signaling domain, and a CD40 signaling domain.
  • xxxvii an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, and aNTRKl signaling domain.
  • xxxviii an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, and aNTRKl signaling domain.
  • an scFv that binds to CEA a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, a NTRK1 signaling domain, and a CD40 signaling domain.
  • xlii an scFv that binds to CEA, a spacer comprising the CD2 extracellular domain and transmembrane sequence of CD2, a CD2 signaling domain, and a CD40 signaling domain.
  • xliii an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, and a CD2 signaling domain.
  • xlvii an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, and a DAP 10 signaling domain.
  • xlviii an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, a CD40 signaling domain, and a DAP 10 signaling domain.
  • xlix an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD28 signaling domain, and a CD 134 signaling domain.
  • xlx an scFv that binds to CEA, a spacer comprising the CD28 extracellular domain and transmembrane sequence of CD28, a CD40 signaling domain, and a CD 134 signaling domain.
  • the invention provides a CoStAR which comprises an scFv that binds to MSLN linked to the spacer, transmembrane, and signaling domain structure of any one of paragraphs i-xlx.
  • the invention provides a CoStAR which comprises an scFv that binds to FolRl linked to the spacer, transmembrane, and signaling domain structure of any one of paragraphs i-xlx.
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxxiv and binds to FolRl by a binding domain which comprises an antigen-binding fragment of scFv M0V19 (SEQ ID NO:9).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxxiv and binds to CEA by a binding domain which comprises an antigen-binding fragment of scFv MFE23 (SEQ ID NO: 10).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to CEA by a binding domain which comprises an antigen-binding fragment of scFv MFE23(K>Q) (SEQ ID NO: 11).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to CEA by a binding domain which comprises an antigen-binding fragment of humanized scFv MFE23 (hMFE23) (SEQ ID NO: 12).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to CEA by a binding domain which comprises an antigen-binding fragment of scFv CEA6 (SEQ ID NO: 13).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to CEA by a binding domain which comprises an antigen-binding fragment of scFv BW431/26 (SEQ ID NO: 14).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to CEA by a binding domain which comprises an antigen-binding fragment of scFv HuT84.66(M5A) (SEQ ID NO: 15).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxxiv and binds to FolRl by a binding domain which comprises an antigen-binding fragment of scFv M0V19 (SEQ ID NO:9).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxxiv and xxxi to xxxiv and binds to MSLN by a binding domain which comprises an antigen-binding fragment of scFv SSI (SEQ ID NO: 186).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to MSLN by a binding domain which comprises an antigen-binding fragment of scFv M5 (humanized SSI) (SEQ ID NO: 187).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to MSLN by a binding domain which comprises an antigen-binding fragment of humanized scFv HN1 (SEQ ID NO: 188).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to MSLN by a binding domain which comprises an antigen-binding fragment of scFv M912 (SEQ ID NO: 189).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to MSLN by a binding domain which comprises an antigen-binding fragment of scFv HuYP218 (SEQ ID NO: 190).
  • the invention provides a CoStAR which comprises the spacer, transmembrane, and signaling domain structure of any one of i-xxvi and xxxi to xxxiv and binds to MSLN by a binding domain which comprises an antigen-binding fragment of scFv P4 (SEQ ID NO: 191).
  • any of the above can be used with a CD40, TRAF2, TRAF2/3, or TRAF6 variants provided herein, including those in Figs. 28, 67, 77A-77C, 83-89D, and 92 (excluding those in Figs. 78 and 79), and including those in Tables 2, 4-5, and 7- 14, and including SEQ ID NOS: 42, 475-479, 494-498, 505, 510-519, and 840-40839, and Consensus sequences A-C.
  • the term “specifically binds” or “is specific for” refers to measurable and reproducible interactions, such as binding between a target and an antibody or antibody moiety that is determinative of the presence of the target in the presence of a heterogeneous population of molecules, including biological molecules.
  • an antibody moiety that specifically binds to a target is an antibody moiety that binds the target with greater affinity, avidity, more readily, and/or with greater duration than its bindings to other targets.
  • an antibody moiety that specifically binds to an antigen reacts with one or more antigenic determinants of the antigen (for example a cell surface antigen or a peptide/MHC protein complex) with a binding affinity that is at least about 10 times its binding affinity for other targets.
  • one or more antigenic determinants of the antigen for example a cell surface antigen or a peptide/MHC protein complex
  • a CoStAR of the invention optionally comprises a spacer region between the antigen binding domain and the costimulatory receptor.
  • the term “spacer” refers to the extracellular structural region of a CoStAR that separates the antigen binding domain from the external ligand binding domain of the costimulatory protein. The spacer provides flexibility to access the targeted antigen and receptor ligand. In some embodiments long spacers are employed, for example to target membrane-proximal epitopes or glycosylated antigens (see Guest R.D. et al. The role of extracellular spacer regions in the optimal design of chimeric immune receptors: evaluation of four different scFvs and antigens. J. Immunother.
  • CoStARs bear short spacers, for example to target membrane distal epitopes (see Hudecek M. et al., Receptor affinity and extracellular domain modifications affect tumor recognition by ROR1 -specific chimeric antigen receptor T cells. Clin. Cancer Res. 2013;19:3153-3164; Hudecek M. et al., The nonsignaling extracellular spacer domain of chimeric antigen receptors is decisive for in vivo antitumor activity.
  • the spacer comprises all or part of or is derived from an IgG hinge, including but not limited to IgGl, IgG2, or IgG4.
  • IgG hinge a spacer comprising insertions, deletions, or mutations in an IgG hinge.
  • a spacer can comprise all or part of one or more antibody constant domains, such as but not limited to CH2 and/or CH3 domains.
  • the CH2 domain is modified so as not to bind to an Fc receptor.
  • the spacer comprises all or part of an Ig-like hinge from CD28, CD8, or other protein comprising a hinge region.
  • the spacer is from 1 and 50 amino acids in length.
  • the spacer comprises essentially all of an extracellular domain, for example a CD28 extracellular domain (i.e. from about amino acid 19, 20, 21, or 22 to about amino acid 152) or an extracellular domain of another protein, including but not limited to another TNFR superfamily member.
  • the spacer comprises a portion of an extracellular domain, for example a portion of a CD28 extracellular domain, and may lack all or most of the Ig domain.
  • the spacer includes amino acids of CD28 from about 141 to about 152 but not other portions of the CD28 extracellular domain.
  • the spacer includes amino acids of CD8 from about 128 to about 182 but not other portions of the CD8 extracellular domain.
  • the CoStAR extracellular domain comprises a linker.
  • Linkers comprise short runs of amino acids used to connect domains, for example a binding domain with a spacer or transmembrane domain.
  • a ligand binding domain will usually be connected to a spacer or a transmembrane domain by flexible linker comprising from about 5 to 25 amino acids, such as, for example, AAAGSGGSG (SEQ ID NO: 18), GGGGSGGGGSGGGGS (SEQ ID NO:431).
  • a CoStAR comprises a binding domain joined directly to a transmembrane domain by a linker, and without a spacer.
  • a CoStAR comprises a binding domain joined directly to a transmembrane by a spacer and without a linker.
  • a CoStAR comprises a full length primary costimulatory receptor which can comprise an extracellular ligand binding and intracellular signaling portion of, without limitation, CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
  • the costimulatory receptor comprises a chimeric protein, for instance comprising an extracellular ligand binding domain of one of the aforementioned proteins and an intracellular signaling domain of another of the aforementioned proteins.
  • the signaling portion of the CoStAR comprises a single signaling domain.
  • the signaling portion of the CoStAR comprises a second intracellular signaling domain such as but not limited to: CD2, CD27, CD28, CD40, CD134 (0X40), CD137 (4-1BB), CD150 (SLAM).
  • the first and second intracellular signaling domains are the same. In other embodiments, the first and second intracellular signaling domains are different.
  • the costimulatory receptor is capable of dimerization. Without being bound by theory, it is thought that CoStARs dimerize or associate with other accessory molecules for signal initiation. In some embodiments, CoStARs dimerize or associate with accessory molecules through transmembrane domain interactions. In some embodiments, dimerization or association with accessory molecules is assisted by costimulatory receptor interactions in the intracellular portion, and/or the extracellular portion of the costimulatory receptor.
  • the transmembrane domain influences CoStAR function.
  • the transmembrane domain is comprised by the full length primary costimulatory receptor domain.
  • the transmembrane domain can be that of the extracellular domain or the intracellular domain.
  • the transmembrane domain is from CD4, CD8a, CD28, or ICOS. Gueden et al.
  • the transmembrane domain comprises a hydrophobic a helix that spans the cell membrane.
  • the transmembrane domain comprises amino acids of the CD28 transmembrane domain from about amino acid 153 to about amino acid 179.
  • the transmembrane domain comprises amino acids of the CD8 transmembrane domain from about amino acid 183 to about amino acid 203.
  • the CoStARs of the invention may include several amino acids between the transmembrane domain and signaling domain.
  • the link from a CD8 transmembrane domain to a signaling domain comprises several amino acids of the CD8 cytoplasmic domain (e.g., amino acids 204-210 of CD8).
  • amino acid sequence variants of the antibody moieties or other moieties provided herein are contemplated.
  • Amino acid sequence variants of an antibody moiety may be prepared by introducing appropriate modifications into the nucleotide sequence encoding the antibody moiety, or by peptide synthesis. Such modifications include, for example, deletions from, and/or insertions into and/or substitutions of residues within the amino acid sequences of the antibody moiety. Any combination of deletion, insertion, and substitution can be made to arrive at the final construct, provided that the final construct possesses the desired characteristics, e.g., antigen-binding.
  • antibody binding domain moieties comprising one or more amino acid substitutions, deletions, or insertions are provided.
  • Sites of interest for mutational changes include the antibody binding domain heavy and light chain variable regions (VRs) and frameworks (FRs).
  • Amino acid substitutions may be introduced into a binding domain of interest and the products screened for a desired activity, e.g., retained/improved antigen binding or decreased immunogenicity.
  • amino acid substitutions may be introduced into one or more of the primary co-stimulatory receptor domain (extracellular or intracellular), secondary costimulatory receptor domain, or extracellular co-receptor domain.
  • the invention encompasses CoStAR proteins and component parts particularly disclosed herein as well as variants thereof, i.e. CoStAR proteins and component parts having at least 75%, at least 80%, at least 85%, at least 87%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, at least 99% sequence identity to the amino acid sequences particularly disclosed herein.
  • the terms “percent similarity,” “percent identity,” and “percent homology” when referring to a particular sequence are used as set forth in the University of Wisconsin GCG software program BestFit. Other algorithms may be used, e.g.
  • BLAST Altschul et al. (1990) J. Mol. Biol. 215: 405-410
  • FASTA which uses the method of Pearson and Lipman (1988) PNAS USA 85: 2444-2448.
  • Particular amino acid sequence variants may differ from a reference sequence by insertion, addition, substitution or deletion of 1 amino acid, 2, 3, 4, 5-10, 10-20 or 20-30 amino acids.
  • a variant sequence may comprise the reference sequence with 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more residues inserted, deleted or substituted. For example, 5, 10, 15, up to 20, up to 30 or up to 40 residues may be inserted, deleted or substituted.
  • a variant may differ from a reference sequence by 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more conservative substitutions.
  • Conservative substitutions involve the replacement of an amino acid with a different amino acid having similar properties.
  • an aliphatic residue may be replaced by another aliphatic residue
  • a non-polar residue may be replaced by another non-polar residue
  • an acidic residue may be replaced by another acidic residue
  • a basic residue may be replaced by another basic residue
  • a polar residue may be replaced by another polar residue or an aromatic residue may be replaced by another aromatic residue.
  • Conservative substitutions may, for example, be between amino acids within the following groups: [00314] Conservative substitutions are shown in Table 6 below.
  • Amino acids may be grouped into different classes according to common side-chain properties: a. hydrophobic: Norleucine, Met, Ala, Vai, Leu, He; b. neutral hydrophilic: Cys, Ser, Thr, Asn, Gin; c. acidic: Asp, Glu; d. basic: His, Lys, Arg; e. residues that influence chain orientation: Gly, Pro; aromatic: Trp, Tyr, Phe. Non-conservative substitutions will entail exchanging a member of one of these classes for another class.
  • the cells used in the present invention may be any lymphocyte that is useful in adoptive cell therapy, such as a T-cell or a natural killer (NK) cell, an NKT cell, a gamma/delta T-cell or T regulatory cell.
  • the cells may be allogeneic or autologous to the patient.
  • T cells or T lymphocytes are a type of lymphocyte that have a central role in cell- mediated immunity. They can be distinguished from other lymphocytes, such as B cells and natural killer cells (NK cells), by the presence of a T-cell receptor (TCR) on the cell surface.
  • TCR T-cell receptor
  • TC cells Cytotoxic T cells
  • CTLs destroy virally infected cells and tumor cells, and are also implicated in transplant rejection.
  • CTLs express the CD8 molecule at their surface.
  • CD8+ cells recognize their targets by binding to antigen associated with MHC class I, which is present on the surface of all nucleated cells.
  • MHC class I MHC class I
  • IL-10 adenosine and other molecules secreted by regulatory T cells
  • the CD8+ cells can be inactivated to an anergic state, which prevent autoimmune diseases such as experimental autoimmune encephalomyelitis.
  • Memory T cells are a subset of antigen-specific T cells that persist long-term after an infection has resolved. They quickly expand to large numbers of effector T cells upon re- exposure to their cognate antigen, thus providing the immune system with "memory” against past infections.
  • Memory T cells comprise three subtypes: central memory T cells (TCM cells) and two types of effector memory T cells (TEM cells and TEMRA cells). Memory cells may be either CD4+ or CD8+.
  • Memory T cells typically express the cell surface protein CD45RO.
  • Regulatory T cells (Treg cells), formerly known as suppressor T cells, are crucial for the maintenance of immunological tolerance. Their major role is to shut down T cell-mediated immunity toward the end of an immune reaction and to suppress auto-reactive T cells that escaped the process of negative selection in the thymus.
  • Treg cells Two major classes of CD4+ Treg cells have been described — naturally occurring Treg cells and adaptive Treg cells.
  • Naturally occurring Treg cells also known as CD4 + CD25 + FoxP3 + Treg cells
  • Naturally occurring Treg cells arise in the thymus and have been linked to interactions between developing T cells with both myeloid (CD11 c + ) and plasmacytoid (CD123 + ) dendritic cells that have been activated with TSLP.
  • Naturally occurring Treg cells can be distinguished from other T cells by the presence of an intracellular molecule called FoxP3.
  • Adaptive Treg cells also known as Tri cells or Th3 cells may originate during a normal immune response.
  • Natural Killer Cells are a type of cytolytic cell which form part of the innate immune system. NK cells provide rapid responses to innate signals from virally infected cells in an MHC independent manner. NK cells (belonging to the group of innate lymphoid cells) are defined as large granular lymphocytes (LGL) and constitute the third kind of cells differentiated from the common lymphoid progenitor generating B and T lymphocytes.
  • LGL large granular lymphocytes
  • therapeutic cells of the invention comprise autologous cells engineered to express a CoStAR.
  • therapeutic cells of the invention comprise allogeneic cells engineered to express a CoStAR.
  • Autologous cells expressing CoStARs may be advantageous in avoiding graft-versus-host disease (GVHD) due to TCR-mediated recognition of recipient alloantigens.
  • GVHD graft-versus-host disease
  • the immune system of a CoStAR recipient could attack the infused CoStAR cells, causing rejection.
  • endogenous TcR is removed from allogeneic CoStAR cells by genome editing.
  • An aspect of the invention provides a nucleic acid sequence of the invention, encoding any of the CoStARs, polypeptides, or proteins described herein (including functional portions and functional variants thereof).
  • the terms “polynucleotide”, “nucleotide”, and “nucleic acid” are intended to be synonymous with each other. It will be understood by a skilled person that numerous different polynucleotides and nucleic acids can encode the same polypeptide as a result of the degeneracy of the genetic code.
  • Nucleic acids according to the invention may comprise DNA or RNA. They may be single stranded or doublestranded. They may also be polynucleotides which include within them synthetic or modified nucleotides. A number of different types of modification to oligonucleotides are known in the art.
  • polynucleotides may be modified by any method available in the art. Such modifications may be carried out in order to enhance the in vivo activity or life span of polynucleotides of interest.
  • variant in relation to a nucleotide sequence include any substitution of, variation of, modification of, replacement of, deletion of or addition of one (or more) nucleic acid from or to the sequence.
  • the nucleic acid sequence may encode the CoStAR proteins including without limitation any one of SEQ ID NOS:42-247 or a variant thereof.
  • the nucleotide sequence may comprise a codon optimized nucleic acid sequence shown engineered for expression in human cells.
  • the invention also provides a nucleic acid sequence which comprises a nucleic acid sequence encoding a CoStAR and a further nucleic acid sequence encoding a T-cell receptor (TCR) and/or chimeric antigen receptor (CAR).
  • TCR T-cell receptor
  • CAR chimeric antigen receptor
  • the nucleic acid sequences may be joined by a sequence allowing co-expression of the two or more nucleic acid sequences.
  • the construct may comprise an internal promoter, an internal ribosome entry sequence (IRES) sequence or a sequence encoding a cleavage site.
  • the cleavage site may be self-cleaving, such that when the polypeptide is produced, it is immediately cleaved into the discrete proteins without the need for any external cleavage activity.
  • Various self-cleaving sites are known, including the Foot- and Mouth disease virus (FMDV) and the 2A self-cleaving peptide.
  • the co-expressing sequence may be an internal ribosome entry sequence (IRES).
  • the co-expressing sequence may be an internal promoter.
  • the present invention provides a vector which comprises a nucleic acid sequence or nucleic acid construct of the invention.
  • a vector may be used to introduce the nucleic acid sequence(s) or nucleic acid construct(s) into a host cell so that it expresses one or more CoStAR(s) according to the first aspect of the invention and, optionally, one or more other proteins of interest (POI), for example a TCR or a CAR.
  • POI proteins of interest
  • the vector may, for example, be a plasmid or a viral vector, such as a retroviral vector or a lentiviral vector, or a transposon-based vector or synthetic mRNA.
  • nucleic acids of the present invention may also be used for nucleic acid immunization and gene therapy, using standard gene delivery protocols. Methods for gene delivery are known in the art. See, e.g., U.S. Pat. Nos. 5,399,346, 5,580,859, 5,589,466, incorporated by reference herein in their entireties.
  • Vectors derived from retroviruses are suitable tools to achieve long-term gene transfer since they allow long-term, stable integration of a transgene or transgenes and its propagation in daughter cells.
  • the vector may be capable of transfecting or transducing a lymphocyte including a T cell or an NK cell.
  • the present invention also provides vectors in which a nucleic acid of the present invention is inserted.
  • the expression of natural or synthetic nucleic acids encoding a CoStAR, and optionally a TCR or CAR is typically achieved by operably linking a nucleic acid encoding the CoStAR and TCR/CAR polypeptide or portions thereof to one or more promoters, and incorporating the construct into an expression vector.
  • 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 recently 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
  • a suitable promoter is the immediate early cytomegalovirus (CMV) promoter sequence.
  • CMV immediate early cytomegalovirus
  • This promoter sequence is a strong constitutive promoter sequence capable of driving high levels of expression of any polynucleotide sequence operatively linked thereto.
  • Another example of a suitable promoter is Elongation Growth Factor-la (EF-la).
  • 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, MSCV promoter, MND 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 hemoglobin promoter, and the creatine kinase promoter.
  • the vectors can be suitable for replication and integration in eukaryotic cells.
  • Typical cloning vectors contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the desired nucleic acid sequence.
  • Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York), and in other virology and molecular biology manuals, see also, WO 01/96584; WO 01/29058; and U.S. Pat. No.6,326,193).
  • the constructs expressed are as shown in SEQ ID NOS:42-247.
  • the nucleic acids are multi -ci stronic constructs that permit the expression of multiple transgenes (e.g., CoStAR and a TCR and/or CAR etc.) under the control of a single promoter.
  • the transgenes e.g., CoStAR and a TCR and/or CAR etc.
  • the transgenes are separated by a self-cleaving 2A peptide.
  • 2A peptides useful in the nucleic acid constructs of the invention include F2A, P2A, T2A and E2A.
  • the nucleic acid construct of the invention is a multi -ci stronic construct comprising two promoters; one promoter driving the expression of CoStAR and the other promoter driving the expression of the TCR or CAR.
  • the dual promoter constructs of the invention are uni-directional. In other embodiments, the dual promoter constructs of the invention are bi-directional.
  • 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 transduced through viral vectors.
  • a source of cells e.g., immune effector cells, e.g., T cells or NK cells
  • T cells e.g., immune effector cells, e.g., T cells or NK cells
  • 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.
  • 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 TM gradient or by counterflow centrifugal elutriation.
  • T cell may be collected at an apheresis center and cell storage facility where T cells can be harvested, maintained, and easily transferred.
  • the T cells can be cryopreserved and stored for later use. An acceptable duration of storage may be determined and validated and can be up to 6 months, up to a year, or longer.
  • Tumor infiltrating cells are isolated and/or expanded from a tumor, for example by a fragmented, dissected, or enzyme digested tumor biopsy or mass.
  • the TILs may be produced in a two-stage process using a tumor biopsy as the starting material: Stage 1 (generally performed over 2-3 hours) initial collection and processing of tumor material using dissection, enzymatic digestion and homogenization to produce a single cell suspension which can be directly cryopreserved to stabilize the starting material for subsequent manufacture and Stage 2 which can occur days or years later.
  • Stage 2 may be performed over 4 weeks, which may be a continuous process starting with thawing of the product of Stage 1 and growth of the TIL out of the tumor starting material (about 2 weeks) followed by a rapid expansion process of the TIL cells (about 2 weeks) to increase the amount of cells and therefore dose.
  • the TILs maybe concentrated and washed prior to formulation as a liquid suspension of cells.
  • the TIL population can be transduced at any point following collection.
  • a cryopreserved TIL population is transduced to express a CoStAR following thawing.
  • a TIL population is transduced to express a CoStAR during outgrowth or initial expansion from tumor starting material.
  • a TIL population is transduced to express a CoStAR during REP, for example but not limited to from about day 8 to about day 10 of REP.
  • An exemplary TIL preparation is described in Applicant’s US patent application Serial No. 62/951,559, filed December 20, 2019.
  • T cells such as CD3+, CD28+, CD4+, CD8+, CD45RA+, and CD45RO+T cells
  • T cells are isolated by incubation with anti-CD3/anti- CD28-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. In one aspect, the incubation time period is 24 hours. Longer incubation times may be used to isolate T cells in any situation where there are few T cells as compared to other cell types, such in isolating tumor infiltrating lymphocytes (TIL) from tumor tissue or from immunocompromised individuals. Further, use of longer incubation times can increase the efficiency of capture of CD8+ T cells. Thus, by simply shortening or lengthening the time T cells are allowed to bind to the CD3/CD28 beads and/or by increasing or decreasing the ratio of beads to T cells (as described further herein), subpopulations of T cells can be preferentially selected for or against at culture initiation or at other time points during the process.
  • 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 invention. 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 CD 14, CD20, CD 16, HLA-DR, and CD8.
  • T regulatory cells are depleted by anti-CD25 conjugated beads or other similar method of selection.
  • the methods described herein can include, e.g., selection of a specific subpopulation of immune effector cells, e.g., T cells, that are a T regulatory cell-depleted population, CD25+ depleted cells, using, e.g., a negative selection technique, e.g., described herein.
  • the population of T regulatory depleted cells contains less than 30%, 25%, 20%, 15%, 10%, 5%, 4%, 3%, 2%, 1% of CD25+ cells.
  • a specific subpopulation of CoStAR effector cells that specifically bind to a target antigen can be enriched for by positive selection techniques.
  • effector cells are enriched for by incubation with target antigen-conjugated beads for a time period sufficient for positive selection of the desired abTCR effector cells.
  • the time period is about 30 minutes.
  • the time period ranges from 30 minutes to 36 hours or longer (including all ranges between these values).
  • the time period is at least one, 2, 3, 4, 5, or 6 hours.
  • the time period is 10 to 24 hours.
  • the incubation time period is 24 hours.
  • T cells for stimulation can also be frozen after a washing step. After the washing step that removes plasma and platelets, 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. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at -20° C or in liquid nitrogen.
  • the immune effector cell can be an allogeneic immune effector cell, e.g., T cell or NK cell.
  • the cell can be an allogeneic T cell, e.g., an allogeneic T cell lacking expression of endogenous T cell receptor (TCR) and/or human leukocyte antigen (HLA), e.g., HLA class I and/or HLA class II.
  • TCR endogenous T cell receptor
  • HLA human leukocyte antigen
  • a T cell lacking a functional endogenous TCR can be, e.g., engineered such that it does not express any functional TCR on its surface, engineered such that it does not express one or more subunits that comprise a functional TCR (e.g., engineered such that it does not express (or exhibits reduced expression) of TCR alpha, TCR beta, TCR gamma, TCR delta, TCR epsilon, and/or TCR zeta) or engineered such that it produces very little functional TCR on its surface.
  • the T cell can express a substantially impaired TCR, e.g., by expression of mutated or truncated forms of one or more of the subunits of the TCR.
  • substantially impaired TCR means that this TCR will not elicit an adverse immune reaction in a host.
  • a T cell described herein can be, e.g., engineered such that it does not express a functional HLA on its surface.
  • a T cell described herein can be engineered such that cell surface expression HLA, e.g., HLA class 1 and/or HLA class II, is downregulated.
  • HLA e.g., HLA class 1 and/or HLA class II
  • downregulation of HLA may be accomplished by reducing or eliminating expression of beta- 2 microglobulin (B2M).
  • the T cell can lack a functional TCR and a functional HLA, e.g., HLA class I and/or HLA class II.
  • Modified T cells that lack expression of a functional TCR and/or HLA can be obtained by any suitable means, including a knock out or knock down of one or more subunit of TCR or HLA.
  • the T cell can include a knock down of TCR and/or HLA using siRNA, shRNA, clustered regularly interspaced short palindromic repeats (CRISPR) transcription-activator like effector nuclease (TALEN), or zinc finger endonuclease (ZFN).
  • siRNA siRNA
  • shRNA clustered regularly interspaced short palindromic repeats
  • TALEN clustered regularly interspaced short palindromic repeats
  • ZFN zinc finger endonuclease
  • the allogeneic cell can be a cell which does not expresses or expresses at low levels an inhibitory molecule, e.g. a cell engineered by any method described herein.
  • the cell can be a cell that does not express or expresses at low levels an inhibitory molecule, e.g., that can decrease the ability of a CoStAR-expressing cell to mount an immune effector response.
  • inhibitory molecules examples include PD1, PD-L1, PD-L2, CTLA4, TIM3, CEACAM (e g., CEACAM-1, CEACAM-3 and/or CEACAM-5), LAG3, VISTA, BTLA, TIGIT, LAIR1, CD160, 2B4, CD80, CD86, B7-H3 (CD276), B7-H4 (VTCN1), HVEM (TNFRSF14 or CD270), KIR, A2aR, MHC class I, MHC class II, Gal9, adenosine, and TGFR beta. Inhibition of an inhibitory molecule, e.g., by inhibition at the DNA, RNA or protein level, can optimize a CAR-expressing cell performance.
  • an inhibitory nucleic acid e.g., an inhibitory nucleic acid, e.g., a dsRNA, e.g., an siRNA or shRNA, a clustered regularly interspaced short palindromic repeats (CRISPR), a transcription-activator like effector nuclease (TALEN), or a zinc finger endonuclease (ZFN), e.g., as described herein, can be used.
  • an inhibitory nucleic acid e.g., a dsRNA, e.g., an siRNA or shRNA, a clustered regularly interspaced short palindromic repeats (CRISPR), a transcription-activator like effector nuclease (TALEN), or a zinc finger endonuclease (ZFN), e.g., as described herein, can be used.
  • CRISPR clustered regularly interspaced short palindromic repeats
  • TALEN transcription-activator like effector nu
  • TCR expression and/or HLA expression can be inhibited using siRNA or shRNA that targets a nucleic acid encoding a TCR and/or HLA, and/or an inhibitory molecule described herein (e g., PD1, PD-L1, PD-L2, CTLA4, TIM3, CEACAM (e g., CEACAM- 1, CEACAM-3 and/or CEACAM-5), LAG3, VISTA, BTLA, TIGIT, LAIR1, CD 160, 2B4, CD80, CD86, B7-H3 (CD276), B7-H4 (VTCN1), HVEM (TNFRSF14 or CD270), KIR, A2aR, MHC class I, MHC class II, Gal9, adenosine, and TGFR beta), in a T cell.
  • siRNA or shRNA that targets a nucleic acid encoding a TCR and/or HLA, and/or an inhibitory molecule described herein (e g., PD1,
  • siRNA and shRNAs in T cells can be achieved using any conventional expression system, e.g., such as a lentiviral expression system.
  • exemplary shRNAs that downregulate expression of components of the TCR are described, e.g., in US Publication No.: 2012/0321667.
  • Exemplary siRNA and shRNAthat downregulate expression of HLA class I and/or HLA class II genes are described, e.g., in U.S. publication No. : US 2007/0036773.
  • CRISPR or CRISPR to inhibit TCR and/or HLA as used herein refers to a set of clustered regularly interspaced short palindromic repeats, or a system comprising such a set of repeats.
  • Cas refers to a CRISPR-associated protein.
  • CRISPR/Cas refers to a system derived from CRISPR and Cas which can be used to silence or mutate a TCR and/or HLA gene, and/or an inhibitory molecule described herein (e.g., PD1, PD-L1, PD-L2, CTLA4, TIM3, CEACAM (e g., CEACAM-1, CEACAM-3 and/or CEACAM-5), LAG3, VISTA, BTLA, TIGIT, LAIR1, CD 160, 2B4, CD80, CD86, B7-H3 (CD276), B7-H4 (VTCN1), HVEM (TNFRSF14 or CD270), KIR, A2aR, MHC class I, MHC class II, GAL9, adenosine, and TGFR beta).
  • an inhibitory molecule described herein e.g., PD1, PD-L1, PD-L2, CTLA4, TIM3, CEACAM (e g., CEACAM-1, CEACAM
  • T cells may be activated and expanded generally using methods as described, for example, in U.S. Patents 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and U.S. Patent Application Publication No. 20060121005.
  • the T cells of the invention 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 can be used.
  • 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. Immunol Meth. 227(l-2):53-63, 1999).
  • expansion can be performed using flasks or containers, or gas- permeable containers known by those of skill in the art and can proceed for 7 days, 8 days, 9 days, 10 days, 11 days, 12 days, 13 days, or 14 days, about 7 days to about 14 days, about 8 days to about 14 days, about 9 days to about 14 days, about 10 days to about 14 days, about 11 days to about 14 days, about 12 days to about 14 days, or about 13 days to about 14 days.
  • the second TIL expansion can proceed for about 14 days.
  • the expansion can be performed using non-specific T-cell receptor stimulation in the presence of interleukin-2 (IL-2) or interleukin- 15 (IL-15).
  • the nonspecific T-cell receptor stimulus can include, for example, an anti-CD3 antibody, such as about 30 ng/ml of OKT3, a mouse monoclonal anti-CD3 antibody (commercially available from OrthoMcNeil, Raritan, N.J. or Miltenyi Biotech, Auburn, Calif.) or UHCT-1 (commercially available from BioLegend, San Diego, Calif., USA).
  • CoStAR cells can be expanded in vitro by including one or more antigens, including antigenic portions thereof, such as epitope(s), of a cancer, which can be optionally expressed from a vector, such as a human leukocyte antigen A2 (HLA-A2) binding peptide, e.g., 0.3 uM MART-1 :26-35 (27L) or gpl00:209-217 (210M), optionally in the presence of a T-cell growth factor, such as 300 lU/mL IL-2 or IL-15.
  • HLA-A2 human leukocyte antigen A2
  • T-cell growth factor such as 300 lU/mL IL-2 or IL-15.
  • CoStAR cells may also be rapidly expanded by restimulation with the same antigen(s) of the cancer pulsed onto HLA-A2-expressing antigen- presenting cells.
  • the CoStAR cells can be further stimulated with, e.g., example, irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and IL- 2.
  • the stimulation occurs as part of the expansion.
  • the expansion occurs in the presence of irradiated, autologous lymphocytes or with irradiated HLA-A2+ allogeneic lymphocytes and IL-2.
  • the cell culture medium comprises IL-2. In some embodiments, the cell culture medium comprises about 1000 lU/mL, about 1500 lU/mL, about 2000 lU/mL, about 2500 lU/mL, about 3000 lU/mL, about 3500 lU/mL, about 4000 lU/mL, about 4500 lU/mL, about 5000 lU/mL, about 5500 lU/mL, about 6000 lU/mL, about 6500 lU/mL, about 7000 lU/mL, about 7500 lU/mL, or about 8000 lU/mL, or between 1000 and 2000 lU/mL, between 2000 and 3000 lU/mL, between 3000 and 4000 lU/mL, between 4000 and 5000 lU/mL, between 5000 and 6000 lU/mL, between 6000 and 7000 lU/mL, between 7000 lU/mL, between
  • the cell culture medium comprises OKT3 antibody.
  • the cell culture medium comprises about 0.1 ng/mL, about 0.5 ng/mL, about 1 ng/mL, about 2.5 ng/mL, about 5 ng/mL, about 7.5 ng/mL, about 10 ng/mL, about 15 ng/mL, about 20 ng/mL, about 25 ng/mL, about 30 ng/mL, about 35 ng/mL, about 40 ng/mL, about 50 ng/mL, about 60 ng/mL, about 70 ng/mL, about 80 ng/mL, about 90 ng/mL, about 100 ng/mL, about 200 ng/mL, about 500 ng/mL, about 1 pg/mL or between 0.1 ng/mL and 1 ng/mL, between 1 ng/mL and 5 ng/mL, between 5 ng/mL and 10 ng/mL
  • a combination of IL-2, IL-7, IL-15, and/or IL-21 are employed as a combination during the expansion.
  • IL-2, IL-7, IL- 15, and/or IL-21 as well as any combinations thereof can be included during the expansion.
  • a combination of IL-2, IL-15, and IL-21 are employed as a combination during the expansion.
  • IL-2, IL-15, and IL-21 as well as any combinations thereof can be included.
  • the expansion can be conducted in a supplemented cell culture medium comprising IL-2, OKT-3, and antigen-presenting feeder cells.
  • the expansion culture media comprises about 500 lU/mL of IL- 15, about 400 lU/mL of IL-15, about 300 lU/mL of IL-15, about 200 lU/mL of IL-15, about 180 lU/mL of IL-15, about 160 lU/mL of IL-15, about 140 lU/mL of IL-15, about 120 lU/mL of IL- 15, or about 100 lU/mL of IL-15, or about 500 lU/mL of IL-15 to about 100 lU/mL of IL-15, or about 400 lU/mL of IL- 15 to about 100 lU/mL of IL- 15 or about 300 lU/mL of IL- 15 to about 100 lU/mL of IL-15 or about 200 lU/mL of IL-15, or about 180 lU/mL of IL-15.
  • the expansion culture media comprises about 20 lU/mL of IL- 21, about 15 lU/mL of IL-21, about 12 lU/mL of IL-21, about 10 lU/mL of IL-21, about 5 lU/mL of IL-21, about 4 IU/mL of IL-21, about 3 lU/mL of IL-21, about 2 IU/mL of IL-21, about 1 lU/mL of IL-21, or about 0.5 lU/mL of IL-21, or about 20 lU/mL of IL-21 to about 0.5 lU/mL of IL-21, or about 15 lU/mL of IL-21 to about 0.5 lU/mL of IL-21, or about 12 lU/mL of IL-21 to about 0.5 lU/mL of IL-21, or about 10 lU/mL of IL-21 to about 0.5 lU/mL of IL-21,
  • the antigen-presenting feeder cells are PBMCs.
  • the ratio of CoStAR cells to PBMCs and/or antigen-presenting cells in the expansion is about 1 to 25, about 1 to 50, about 1 to 100, about 1 to 125, about 1 to 150, about 1 to 175, about 1 to 200, about 1 to 225, about 1 to 250, about 1 to 275, about 1 to 300, about 1 to 325, about 1 to 350, about 1 to 375, about 1 to 400, or about 1 to 500, or between 1 to 50 and 1 to 300, or between 1 to 100 and 1 to 200.
  • the primary stimulatory signal and the costimulatory signal for the T cell may be provided by different protocols.
  • the agents providing each signal may be in solution or coupled to a surface.
  • the agents When coupled to a surface, the agents may be coupled to the same surface (i.e., in "cis” formation) or to separate surfaces (i.e., in "trans” formation).
  • one agent may be coupled to a surface and the other agent in solution.
  • the agent providing the costimulatory signal is bound to a cell surface and the agent providing the primary activation signal is in solution or coupled to a surface. In certain aspects, both agents can be in solution.
  • the agents may be in soluble form, and then cross-linked to a surface, such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents.
  • a surface such as a cell expressing Fc receptors or an antibody or other binding agent which will bind to the agents.
  • aAPCs artificial antigen presenting cells
  • the two agents are immobilized on beads, either on the same bead, i.e., “cis,” or to separate beads, i.e., “trans.”
  • the agent providing the primary activation signal is an anti-CD3 antibody or an antigen-binding fragment thereof and the agent providing the costimulatory signal is an anti-CD28 antibody or antigen-binding fragment thereof; and both agents are co -immobilized to the same bead in equivalent molecular amounts.
  • a 1 : 1 ratio of each antibody bound to the beads for CD4+ T cell expansion and T cell growth is used.
  • a ratio of anti CD3:CD28 antibodies bound to the beads is used such that an increase in T cell expansion is observed as compared to the expansion observed using a ratio of 1 : 1. In one particular aspect an increase of from about 1 to about 3 fold is observed as compared to the expansion observed using a ratio of 1 : 1.
  • the ratio of CD3:CD28 antibody bound to the beads ranges from 100: 1 to 1 : 100 and all integer values there between.
  • more anti-CD28 antibody is bound to the particles than anti- CD3 antibody, i.e., the ratio of CD3:CD28 is less than one.
  • the ratio of anti CD28 antibody to anti CD3 antibody bound to the beads is greater than 2: 1.
  • a 1 : 100 CD3:CD28 ratio of antibody bound to beads is used. In one aspect, a 1 :75 CD3:CD28 ratio of antibody bound to beads is used. In a further aspect, a 1 :50 CD3:CD28 ratio of antibody bound to beads is used. In one aspect, a 1 :30 CD3:CD28 ratio of antibody bound to beads is used. In one preferred aspect, a 1 : 10 CD3 :CD28 ratio of antibody bound to beads is used. In one aspect, a 1 :3 CD3:CD28 ratio of antibody bound to the beads is used. In yet one aspect, a 3: 1 CD3:CD28 ratio of antibody bound to the beads is used.
  • Ratios of particles to cells from 1 :500 to 500: 1 and any integer values in between may be used to stimulate T cells or other target cells.
  • the ratio of particles to cells may depend on particle size relative to the target cell. For example, small sized beads could only bind a few cells, while larger beads could bind many.
  • the ratio of cells to particles ranges from 1 : 100 to 100: 1 and any integer values inbetween and in further aspects the ratio comprises 1 :9 to 9: 1 and any integer values in between, can also be used to stimulate T cells.
  • the ratio of anti-CD3- and anti-CD28-coupled particles to T cells that result in T cell stimulation can vary as noted above, however certain preferred values include 1 : 100, 1 :50, 1 :40, 1 :30, 1 :20, 1 : 10, 1 :9, 1 :8, 1 :7, 1 :6, 1 :5, 1 :4, 1 :3, 1 :2, 1 : 1, 2: 1, 3:1, 4: 1, 5: 1, 6: 1, 7: 1, 8: 1, 9: 1, 10: 1, and 15: 1 with one preferred ratio being at least 1 : 1 particles per T cell.
  • a ratio of particles to cells of 1 : 1 or less is used.
  • a preferred particle: cell ratio is 1 :5.
  • the ratio of particles to cells can be varied depending on the day of stimulation.
  • the ratio of particles to cells is from 1 : 1 to 10: 1 on the first day and additional particles are added to the cells every day or every other day thereafter for up to 10 days, at final ratios of from 1 : 1 to 1 : 10 (based on cell counts on the day of addition).
  • the ratio of particles to cells is 1 : 1 on the first day of stimulation and adjusted to 1 :5 on the third and fifth days of stimulation.
  • particles are added on a daily or every other day basis to a final ratio of 1 : 1 on the first day, and 1 :5 on the third and fifth days of stimulation.
  • the ratio of particles to cells is 2: 1 on the first day of stimulation and adjusted to 1 : 10 on the third and fifth days of stimulation.
  • particles are added on a daily or every other day basis to a final ratio of 1 : 1 on the first day, and 1 : 10 on the third and fifth days of stimulation.
  • ratios will vary depending on particle size and on cell size and type.
  • the most typical ratios for use are in the neighborhood of 1 : 1, 2: 1 and 3 : 1 on the first day.
  • the cells such as T cells
  • the beads and the cells are subsequently separated, and then the cells are cultured.
  • the agent-coated beads and cells prior to culture, are not separated but are cultured together.
  • the beads and cells are first concentrated by application of a force, such as a magnetic force, resulting in increased ligation of cell surface markers, thereby inducing cell stimulation.
  • Retrovirus-based gene delivery is a mature, well -characterized technology, which has been used to permanently integrate CARs into the host cell genome (Scholler J., e.g. Decade-long safety and function of retroviral-modified chimeric antigen receptor T cells. Sci. Transl. Med. 2012;4: 132ra53; Rosenberg S. A. et al., Gene transfer into humans — immunotherapy of patients with advanced melanoma, using tumor-infiltrating lymphocytes modified by retroviral gene transduction. N. Engl. J. Med. 1990;323:570-578)
  • Non-viral DNA transfection methods can also be used.
  • Singh et al describes use of the Sleeping Beauty (SB) transposon system developed to engineer CAR T cells (Singh H., et al., Redirecting specificity of T-cell populations for CD19 using the Sleeping Beauty system. Cancer Res. 2008;68:2961-2971) and is being used in clinical trials (see e.g., ClinicalTrials.gov: NCT00968760 and NCT01653717).
  • SB Sleeping Beauty
  • SB100X hyperactive transposase
  • SB100X hyperactive transposase
  • FIG. 1 shows a hyperactive transposase with approximately 100-fold enhancement in efficiency when compared to the first-generation transposase.
  • SB100X supported 35-50% stable gene transfer in human CD34(+) cells enriched in hematopoietic stem or progenitor cells.
  • Mates L. et al. Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates. Nat. Genet. 2009;41 :753-761
  • multiple transgenes can be delivered from multi ci str onic single plasmids (e.g., Thokala R.
  • Morita et al describes the piggyBac transposon system to integrate larger transgenes (Morita D. et al., Enhanced expression of anti-CD19 chimeric antigen receptor in piggyBac transposon-engineered T cells. Mol. Ther. Methods Clin. Dev. 2017;8: 131-140)
  • Nakazawa et al. describes use of the system to generate EBV-specific cytotoxic T-cells expressing HER2-specific chimeric antigen receptor (Nakazawa Y et al, PiggyBac-mediated cancer immunotherapy using EBV-specific cytotoxic T-cells expressing HER2-specific chimeric antigen receptor. Mol. Ther. 2011;19:2133-2143).
  • Manuri et al used the system to generate CD-19 specific T cells (Manuri P.V.R. et al., piggyBac transposon/transposase system to generate CD19-specific T cells for the treatment of B-lineage malignancies. Hum. Gene Ther. 2010;21 :427-437).
  • Transposon technology is easy and economical.
  • One potential drawback is the longer expansion protocols currently employed may result in T cell differentiation, impaired activity and poor persistence of the infused cells.
  • Monjezi et al describe development mini circle vectors that minimize these difficulties through higher efficiency integrations (Monjezi R. et al., Enhanced CAR T-cell engineering using non-viral Sleeping Beauty transposition from minicircle vectors. Leukemia. 2017;31 : 186-194). These transposon technologies can be used for CoStARs of the invention.
  • the present invention also relates to a pharmaceutical composition containing a vector or a CoStAR expressing cell of the invention together with a pharmaceutically acceptable carrier, diluent or excipient, and optionally one or more further pharmaceutically active polypeptides and/or compounds.
  • a pharmaceutical composition comprising a CoStAR described above and a pharmaceutically acceptable carrier.
  • a pharmaceutical composition comprising a nucleic acid encoding a CoStAR according to any of the embodiments described above and a pharmaceutically acceptable carrier.
  • a pharmaceutical composition is provided comprising an effector cell expressing a CoStAR described above and a pharmaceutically acceptable carrier.
  • Such a formulation may, for example, be in a form suitable for intravenous infusion.
  • pharmaceutically acceptable or “pharmacologically compatible” is meant a material that is not biologically or otherwise undesirable, e.g., the material may be incorporated into a pharmaceutical composition administered to a patient without causing any significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the composition in which it is contained.
  • Pharmaceutically acceptable carriers or excipients have preferably met the required standards of toxicological and manufacturing testing and/or are included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug administration.
  • An aspect of the invention provides a population of modified T cells expressing a recombinant CoStAR.
  • a suitable population may be produced by a method described above.
  • the population of modified T cells may be for use as a medicament.
  • a population of modified T cells as described herein may be used in cancer immunotherapy therapy, for example adoptive T cell therapy.
  • Other aspects of the invention provide the use of a population of modified T cells as described herein for the manufacture of a medicament for the treatment of cancer, a population of modified T cells as described herein for the treatment of cancer, and a method of treatment of cancer may comprise administering a population of modified T cells as described herein to an individual in need thereof.
  • the population of modified T cells may be autologous i.e. the modified T cells were originally obtained from the same individual to whom they are subsequently administered (i.e. the donor and recipient individual are the same).
  • a suitable population of modified T cells for administration to the individual may be produced by a method comprising providing an initial population of T cells obtained from the individual, modifying the T cells to express a cAMP PDE or fragment thereof and an antigen receptor which binds specifically to cancer cells in the individual, and culturing the modified T cells.
  • the population of modified T cells may be allogeneic i.e. the modified T cells were originally obtained from a different individual to the individual to whom they are subsequently administered (i.e. the donor and recipient individual are different).
  • the donor and recipient individuals may be HLA matched to avoid GVHD and other undesirable immune effects.
  • a suitable population of modified T cells for administration to a recipient individual may be produced by a method comprising providing an initial population of T cells obtained from a donor individual, modifying the T cells to express a CoStAR which binds specifically to cancer cells in the recipient individual, and culturing the modified T cells.
  • the recipient individual may exhibit a T cell mediated immune response against cancer cells in the recipient individual. This may have a beneficial effect on the cancer condition in the individual.
  • Cancer conditions may be characterized by the abnormal proliferation of malignant cancer cells and may include leukemias, such as AML, CML, ALL and CLL, lymphomas, such as Hodgkin lymphoma, non-Hodgkin lymphoma and multiple myeloma, and solid cancers such as sarcomas, skin cancer, melanoma, bladder cancer, brain cancer, breast cancer, uterus cancer, ovary cancer, prostate cancer, lung cancer, colorectal cancer, cervical cancer, liver cancer, head and neck cancer, oesophageal cancer, pancreas cancer, renal cancer, adrenal cancer, stomach cancer, testicular cancer, cancer of the gall bladder and biliary tracts, thyroid cancer, thymus cancer, cancer of bone, and cerebral cancer, as well as cancer of unknown primary (CUP).
  • leukemias such as AML, CML, ALL and CLL
  • lymphomas such as Hodgkin lymphoma, non-Hodgkin lymphoma and multiple myelo
  • Cancer cells within an individual may be immunologically distinct from normal somatic cells in the individual (i.e. the cancerous tumor may be immunogenic).
  • the cancer cells may be capable of eliciting a systemic immune response in the individual against one or more antigens expressed by the cancer cells.
  • the tumor antigens that elicit the immune response may be specific to cancer cells or may be shared by one or more normal cells in the individual.
  • An individual suitable for treatment as described above may be a mammal, such as a rodent (e.g. a guinea pig, a hamster, a rat, a mouse), murine (e.g. a mouse), canine (e.g. a dog), feline (e.g. a cat), equine (e.g. a horse), a primate, simian (e.g. a monkey or ape), a monkey (e.g. marmoset, baboon), an ape (e.g. gorilla, chimpanzee, orangutan, gibbon), or a human.
  • a rodent e.g. a guinea pig, a hamster, a rat, a mouse
  • murine e.g. a mouse
  • canine e.g. a dog
  • feline e.g. a cat
  • equine e.g. a horse
  • the individual is a human.
  • non-human mammals especially mammals that are conventionally used as models for demonstrating therapeutic efficacy in humans (e.g. murine, primate, porcine, canine, or rabbit animals) may be employed.
  • the term “therapeutically effective amount” refers to an amount of a CoStAR or composition comprising a CoStAR as disclosed herein, effective to "treat” a disease or disorder in an individual.
  • the therapeutically effective amount of a CoStAR or composition comprising a CoStAR as disclosed herein can reduce the number of cancer cells; reduce the tumor size or weight; inhibit (i.e., slow to some extent and preferably stop) cancer cell infiltration into peripheral organs; inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; inhibit, to some extent, tumor growth; and/or relieve to some extent one or more of the symptoms associated with the cancer.
  • a CoStAR or composition comprising a CoStAR as disclosed herein can prevent growth and/or kill existing cancer cells, it can be cytostatic and/or cytotoxic.
  • the therapeutically effective amount is a growth inhibitory amount. In some embodiments, the therapeutically effective amount is an amount that improves progression free survival of a patient.
  • the therapeutically effective amount of a CoStAR or composition comprising a CoStAR as disclosed herein can reduce the number of cells infected by the pathogen; reduce the production or release of pathogen- derived antigens; inhibit (i.e., slow to some extent and preferably stop) spread of the pathogen to uninfected cells; and/or relieve to some extent one or more symptoms associated with the infection.
  • the therapeutically effective amount is an amount that extends the survival of a patient.
  • Cells, including T and NK cells, expressing CoStARs for use in the methods of the present may either be created ex vivo either from a patient's own peripheral blood (autologous), or in the setting of a haematopoietic stem cell transplant from donor peripheral blood (allogenic), or peripheral blood from an unconnected donor (allogenic).
  • T-cells or NK cells may be derived from ex-vivo differentiation of inducible progenitor cells or embryonic progenitor cells to T-cells or NK cells.
  • T-cells expressing a CoStAR and, optionally, a CAR and/or TCR are generated by introducing DNA or RNA coding for the CoStAR and, optionally, a CAR and/or TCR, by one of many means including transduction with a viral vector, transfection with DNA or RNA.
  • T or NK cells expressing a CoStAR of the present invention and, optionally, expressing a TCR and/or CAR may be used for the treatment of haematological cancers or solid tumors.
  • a method for the treatment of disease relates to the therapeutic use of a vector or cell, including a T or NK cell, of the invention.
  • the vector, or T or NK cell may be administered to a subject having an existing disease or condition in order to lessen, reduce or improve at least one symptom associated with the disease and/or to slow down, reduce or block the progression of the disease.
  • the method of the invention may cause or promote T-cell mediated killing of cancer cells.
  • the vector, or T or NK cell according to the present invention may be administered to a patient with one or more additional therapeutic agents.
  • the one or more additional therapeutic agents can be co-administered to the patient.
  • co-administering is meant administering one or more additional therapeutic agents and the vector, or T or NK cell of the present invention sufficiently close in time such that the vector, or T or NK cell can enhance the effect of one or more additional therapeutic agents, or vice versa.
  • the vectors or cells can be administered first and the one or more additional therapeutic agents can be administered second, or vice versa.
  • the vectors or cells and the one or more additional therapeutic agents can be administered simultaneously.
  • One co-administered therapeutic agent that may be useful is IL-2, as this is currently used in existing cell therapies to boost the activity of administered cells.
  • IL-2 treatment is associated with toxicity and tolerability issues.
  • the CoStAR effector cells can be allogeneic or autologous to the patient.
  • allogeneic cells are further genetically modified, for example by gene editing, so as to minimize or prevent GVHD and/or a patient’s immune response against the CoStAR cells.
  • the CoStAR effector cells are used to treat cancers and neoplastic diseases associated with a target antigen.
  • Cancers and neoplastic diseases that may be treated using any of the methods described herein include tumors that are not vascularized, or not yet substantially vascularized, as well as vascularized tumors.
  • the cancers may comprise non- solid tumors (such as hematological tumors, for example, leukemias and lymphomas) or may comprise solid tumors.
  • Types of cancers to be treated with the CoStAR effector cells of the invention include, but are not limited to, carcinoma, blastoma, and sarcoma, and certain leukemia or lymphoid malignancies, benign and malignant tumors, and malignancies e.g., sarcomas, carcinomas, and melanomas.
  • carcinoma a malignant neoplasm
  • blastoma a malignant na
  • sarcoma e.g., sarcomas, carcinomas, and melanomas.
  • malignancies e.g., sarcomas, carcinomas, and melanomas.
  • adult tumors/cancers and pediatric tumors/cancers are also included.
  • Hematologic cancers are cancers of the blood or bone marrow.
  • leukemias include leukemias, including acute leukemias (such as acute lymphocytic leukemia, acute myelocytic leukemia, acute myelogenous leukemia and myeloblastic, promyelocytic, myelomonocytic, monocytic and erythroleukemia), chronic leukemias (such as chronic myelocytic (granulocytic) leukemia, chronic myelogenous leukemia, and chronic lymphocytic leukemia), polycythemia vera, lymphoma, Hodgkin's disease, nonHodgkin's lymphoma (indolent and high grade forms), multiple myeloma, plasmacytoma, Waldenstrom's macroglobulinemia, heavy chain disease, myelodysplastic syndrome, hairy cell leukemia and myelodysp
  • Solid tumors are abnormal masses of tissue that usually do not contain cysts or liquid areas. Solid tumors can be benign or malignant. Different types of solid tumors are named for the type of cells that form them (such as sarcomas, carcinomas, and lymphomas).
  • solid tumors such as sarcomas and carcinomas
  • solid tumors include adrenocortical carcinoma, cholangiocarcinoma, fibrosarcoma, myosarcoma, liposarcoma, chondrosarcoma, osteosarcoma, and other sarcomas, synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma, rhabdomyosarcoma, colon carcinoma, stomach cancer, lymphoid malignancy, pancreatic cancer, breast cancer, lung cancers, ovarian cancer, prostate cancer, hepatocellular carcinoma, squamous cell carcinoma, basal cell carcinoma, adenocarcinoma, sweat gland carcinoma, thyroid cancer (e.g., medullary thyroid carcinoma and papillary thyroid carcinoma), pheochromocytomas sebaceous gland carcinoma, papillary carcinoma, papillary adenocarcinomas, medullary carcinoma, bronchogenic carcinoma,
  • 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 invention 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. of Med. 319: 1676, 1988).
  • a CoStAR-expressing 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.
  • a CoStAR-expressing 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 CAR-expressing cell described herein can be administered first, and the additional agent can be administered second, or the order of administration can be reversed.
  • the CoStAR therapy and/or other therapeutic agents, procedures or modalities can be administered during periods of active disorder, or during a period of remission or less active disease.
  • the CoStAR therapy can be administered before the other treatment, concurrently with the treatment, post-treatment, or during remission of the disorder.
  • the therapy and the additional agent can be administered in an amount or dose that is higher, lower or the same than the amount or dosage of each agent used individually, e.g., as a monotherapy.
  • the administered amount or dosage of the CoStAR therapy, the additional agent (e.g., second or third agent), or all is lower (e.g., at least 20%, at least 30%, at least 40%, or at least 50%) than the amount or dosage of each agent used individually, e.g., as a monotherapy.
  • the amount or dosage of the CoStAR therapy, the additional agent (e.g., second or third agent), or all, that results in a desired effect is lower (e.g., at least 20%, at least 30%, at least 40%, or at least 50% lower) than the amount or dosage of each agent used individually, e.g., as a monotherapy, required to achieve the same therapeutic effect.
  • a CoStAR-expressing 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 FK506, antibodies, or other immunoablative agents such as CAMPATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludarabine, cyclosporin, FK506, rapamycin, mycophenolic acid, steroids, FR901228, 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 FK506, antibodies
  • immunoablative agents such as CAMPATH, anti-CD3 antibodies or other antibody therapies, cytoxin, fludarabine, cyclosporin, FK506,
  • compounds of the present invention are combined with other therapeutic agents, such as other anti-cancer agents, anti-allergic agents, anti-nausea agents (or anti-emetics), pain relievers, cytoprotective agents, and combinations thereof.
  • other therapeutic agents such as other anti-cancer agents, anti-allergic agents, anti-nausea agents (or anti-emetics), pain relievers, cytoprotective agents, and combinations thereof.
  • a CoStAR-expressing cell described herein can be used in combination with a chemotherapeutic agent.
  • chemotherapeutic agents include an anthracycline (e.g., doxorubicin (e.g., liposomal doxorubicin)), a vinca alkaloid (e.g., vinblastine, vincristine, vindesine, vinorelbine), an alkylating agent (e.g., cyclophosphamide, decarbazine, melphalan, ifosfamide, temozolomide), an immune cell antibody (e.g., alemtuzamab, gemtuzumab, rituximab, ofatumumab, tositumomab, brentuximab), an anti metabolite (including, e.g., folic acid antagonists, pyrimidine analogs, purine analogs and adenosine de
  • General Chemotherapeutic agents considered for use in combination therapies include busulfan (Myleran®), busulfan injection (Busulfex®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®),, daunorubicin hydrochloride (Cerubidine®), daunorubicin citrate liposome injection (DaunoXome®), dexamethasone, , doxorubicin hydrochloride (Adriamycin®, Rubex®), etoposide (Vepesid®), fludarabine phosphate (Fludara®), hydroxyurea (Hydrea®), Idarubicin (Idamycin®), mitoxantrone (Novantrone®), Gemt
  • general chemotherapeutic agents considered for use in combination therapies include anastrozole (Arimidex®), bicalutamide (Casodex®), bleomycin sulfate (Blenoxane®), busulfan (Myleran®), busulfan injection (Busulfex®), capecitabine (Xeloda®), N4-pentoxycarbonyl-5-deoxy-5-fluorocytidine, carboplatin (Paraplatin®), carmustine (BiCNU®), chlorambucil (Leukeran®), cisplatin (Platinol®), cladribine (Leustatin®), cyclophosphamide (Cytoxan® or Neosar®), cytarabine, cytosine arabinoside (Cytosar-U®), cytarabine liposome injection (DepoCyt®), dacarbazine (DTIC- Dom
  • Treatments can be evaluated, for example, by tumor regression, tumor weight or size shrinkage, time to progression, duration of survival, progression free survival, overall response rate, duration of response, quality of life, protein expression and/or activity.
  • Approaches to determining efficacy of the therapy can be employed, including for example, measurement of response through radiological imaging.
  • sequences include complete CoStARs and CoStAR components and are non-limiting.
  • Components include signal peptides (SP), binding domains (BD), linkers, spacers and transmembrane domains (STM), a CD28 transmembrane fragment without extracellular or intracellular sequences (STM-CD28TM), intracellular signal domains (SD) and CD40 domains and motifs.
  • SEQ ID NOS:42-247 comprise CoStARs with N-terminal signal peptides, it will be understood that the N-terminal signal peptides are removed from a mature CoStAR.
  • a mature CoStAR may lack 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 or more amino acids at the N-terminal (i.e., counted from the C-terminal end of the signal peptide).
  • Component locations within whole proteins can be confirmed from GenBank and other sources.
  • the constructs and components are illustrative as to precise sizes and extents and components can be from more than one source. Where there is more than one intracellular signaling domain or signaling fragment, the multiple domains can be in any order.
  • proteins may comprise N-terminal signal peptides when expressed
  • those signal peptides are cleaved and may be imprecisely cleaved when the proteins are expressed, and that the resulting proteins from which signal peptides are removed comprise binding domains having variation of up to about five amino acids in the location of the N-terminal amino acid.
  • An chimeric costimulatory antigen receptor which comprises: an extracellular binding domain that binds to carcinoembryonic antigen (CEA), or an extracellular binding domain that binds to mesothelin (MSLN), operatively linked to a transmembrane domain, and a first signaling domain and an intracellular domain of ICOS or a signaling fragment thereof, or a first signaling domain and an intracellular domain of NTRK1 or a signaling fragment thereof, or a first signaling domain and an intracellular domain of DAP 10 or a signaling fragment thereof, or a first signaling domain and a CD40 signaling domain or a signaling fragment thereof, or a first signaling domain and one or more of a TRAF2/TRAF3 sequence, a TRAF6 sequence, a TRAF2 sequence, or an IProx sequence.
  • CEA carcinoembryonic antigen
  • MSLN mesothelin
  • the first signaling domain comprises a signaling domain or signaling fragment of CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
  • the CoStAR of arrangement 3, wherein the second signaling domain comprises a signaling domain or signaling fragment of CD2, CD9, CD26, CD27, CD28, CD29, CD38, CD40, CD43, CD46, CD49d, CD55, CD73, CD81, CD82, CD99, CD100, CD134 (0X40), CD137 (41BB), CD150 (SLAM), CD270 (HVEM), CD278 (ICOS), CD357 (GITR), or EphB6.
  • SH3 motif KPTNKAPH, SEQ ID NO:35
  • TRAF2 motif PQE, SEQ ID NO:36, PVQE, SEQ ID NO: 37, SVQE, SEQ ID NO: 38
  • TRAF6 motif QEPQEINFP, SEQ ID NO: 39
  • PKA motif KKPTNKA, SEQ ID NO:40, SRISVQE, SEQ ID NO:41
  • the CoStAR of arrangement 1, wherein the transmembrane domain comprises the transmembrane domain sequence of SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22.
  • the CoStAR of arrangement 1, wherein the extracellular binding domain comprises an scFv, a peptide, an antibody heavy-chain variable domain, an antibody light-chain variable domain, or a CEA ligand.
  • OSM oncostatin M
  • CD8a CD8a
  • CD2 CD2
  • IL-2 interleukin-2
  • GM-CSF granulocytemacrophage colony stimulating factor
  • human IgGK human IgGK
  • a cell population which is enriched for cell expression a CoStAR of any one of arrangements 1 to 16.
  • a method for treating a disease in a subject which comprises the step of administering a cell according to any of arrangements 20 to 22, or a cell population according to arrangement 25 to the subject.
  • a protein comprising an amino acid sequence comprising a sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein: a. Xi is any amino acid, b. X 2 is any amino acid, c. X3 is P, X4 is any amino acid, d. X5 is Q, e. Xe is C or A, f. X7 is any amino acid, g. Xs is any amino acid, h. X9 is any amino acid, i. X10 is any amino acid, and j. Xu is any amino acid.
  • the sequence comprises: i. Xi is S or P, ii. X 2 is V, H, or Y, iii. X 4 is I, Q, V, iv. X7 is T or S, v. Xs is D, vi. X9 is K, D, or G, vii. X10 is T, S, G, or A, and viii. Xu is D, S, N, or D; or b. the sequence is at least 60% identical to a).
  • a protein comprising an amino acid sequence comprising a sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein: a. Xi is any amino acid, b. X 2 is any amino acid, c. X 3 is P, S, A, or T, d. X 4 is any amino acid, e. X5 is Q or E, f. X 6 is E, g. X7 is any amino acid, h. Xs is any amino acid, i. X9 is any amino acid, j. X10 is any amino acid, and k. Xu is any amino acid.
  • Xi is P, A, M, T, S, R, V, H, ii. X 2 is F, A, L, I, T, V, G, C, A, F, P, iii. X 4 is K, V, I, H, A, Q, T, E, S, iv. X 7 is C, T, E, D, S, A, v. X 8 is A, L, G, Y, I, Q, D, E, vi.
  • X 9 is F, H, K, R, P, A, G, Y, E, N, vii.
  • X10 is R, G, E, K, A, S, D, C, C, P, V, and viii.
  • Xu is S, C, D, P, W, T, A, G, E; or b. the sequence is at least 60% identical to a).
  • a protein comprising an amino acid sequence comprising a sequence of Consensus C, or X1X2X3X4X5X6, wherein: a. Xi is P, b. X 2 is any amino acid, c. X3 is E, d. X 4 is any amino acid, e. X5 is any amino acid, and f. Xe is Ac/ Ar. 37. The protein of arrangement 36, wherein the protein is part of a TRAF domain.
  • a. the sequence comprises: i. X 2 is Q, P, E, V, T, or S, ii. X 4 is I, L M, N, S, T, N, D, iii. X 5 is N, D, R, S, G, or Y; or b. the sequence is at least 60% identical to a).
  • An amino acid sequence comprising: a) one or more of SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; b) a sequence that is at least 70% identical to a sequence in a); or c) a sequence that is at least 80% similar to a).
  • TRAF domain in a CD40 protein wherein the TRAF domain comprises one or more of: a) SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; b) a sequence that is at least 70% identical to a sequence in a); or c) a sequence that is at least 80% similar to a).
  • a TRAF6 domain sequence comprising: PQEINF, PEEMSW, PPENYE, or PQENSY.
  • a TRAF2/3 domain sequence comprising: PVQET, TQEET, SKEET, AVEET, or PVQET.
  • a TRAF2 domain sequence comprising: SVQE, AVEE or PEEE.
  • a TRAF 6 or TRAF2/3 domain that comprises: a) the amino acid sequence of one of SEQ ID NOs: 475, 476, 477, 478, 479, 494, 495, 496, 498, 505, 510, 511, 512, 513, 514, 515, 516, 517, 518, or 519; b) the amino acid sequence that is at least 70% identical to a) or c) the amino acid sequence that is at least 80% similar to a).
  • Xi is any amino acid
  • b. X2 is any amino acid
  • c. X3 is P
  • X4 is any amino acid
  • X5 is Q
  • e. Xe is C or A
  • X7 is any amino acid
  • g. Xs is any amino acid
  • h. X9 is any amino acid
  • i. X10 is any amino acid
  • j. Xu is any amino acid.
  • Xi is any amino acid
  • b. X2 is any amino acid
  • c. X 3 is P, S, A, or T
  • X4 is any amino acid
  • e. X5 is Q or E
  • X 6 is E
  • g. X7 is any amino acid
  • h. Xs is any amino acid
  • i. X9 is any amino acid
  • j. X10 is any amino acid
  • k. Xu is any amino acid.
  • a TRAF6 domain that comprises an amino acid sequence of Consensus C, or X1X2X3X4X5X6, wherein a. Xi is P, b. X2 is any amino acid, c. X3 is E, d. X4 is any amino acid, e. X5 is any amino acid, and f. Xe is Ac/ Ar.
  • a CD40 domain that comprises an amino acid sequence of one or more of the following: a.
  • a TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus A, or X1X2X3X4X5X6X7X8X9X10X11, wherein i. Xi is any amino acid, ii. X2 is any amino acid, iii. X3 is P, X4 is any amino acid, iv. X5 is Q, v. Xe is C or A, vi. X7 is any amino acid, vii. Xs is any amino acid, viii. X9 is any amino acid, ix. X10 is any amino acid, and x. Xu is any amino acid.
  • a TRAF2/TRAF3 domain that comprises an amino acid sequence of Consensus B, or X1X2X3X4X5X6X7X8X9X10X11, wherein i.Xi is any amino acid, ii.X2 is any amino acid, iii.X3 is P, S, A, or T, iv.X4 is any amino acid, V.X5 is Q or E, vi.Xe is E, vii.X? is any amino acid, viii. Xs is any amino acid, ix.Xg is any amino acid, x.Xio is any amino acid, and xi.Xn is any amino acid. c.
  • a TRAF6 domain that comprises an amino acid sequence of Consensus C, or X1X2X3X4X5X6, wherein i.Xi is P, ii.X2 is any amino acid, iii .X3 is E, iv.X4 is any amino acid,
  • V.X5 is any amino acid, and vi.Xe is Ac/ Ar.
  • An chimeric costimulatory antigen receptor which comprises: an extracellular binding domain that binds to carcinoembryonic antigen (CEA), or an extracellular binding domain that binds to mesothelin (MSLN); a transmembrane domain that is linked to the extracellular binding domain, a first signaling domain; and a second signaling domain, wherein the second signaling domain comprises a variant CD40 signaling domain or a signaling fragment thereof, wherein the variant CD40 comprises a sequence of a variant TRAF2/TRAF3 sequence, or a variant TRAF6 sequence, or a variant TRAF2 sequence, wherein the variant CD40 does not comprise SEQ ID NO: 42.
  • the first signalling domain comprises a signalling domain or signaling fragment of CD28 or CD278 (ICOS).
  • the CoStAR of arrangement 55 wherein the linker comprises from about 10 to about 250 amino acids.
  • the transmembrane domain comprises a transmembrane domain from CD28, CD8, ICOS, DAP10, or NTRK.
  • the CoStAR of arrangement 55, wherein the transmembrane domain comprises the transmembrane domain sequence of SEQ ID NO:20, SEQ ID NO:21, or SEQ ID NO:22.
  • the CoStAR of arrangement 55 wherein the extracellular binding domain comprises an scFv, a peptide, an antibody heavy-chain variable domain, an antibody light-chain variable domain, or a CEA ligand.
  • a vector which comprises the nucleic acid of arrangement 61 is provided.
  • the cell of arrangement 63 wherein the cell comprises an alpha-beta T cell, gamma-delta T cell, T regulatory cell, TIL, NKT cell or NK cell.
  • a method of making the cell of any one of arrangements 63-65 which comprises the step of transducing or transfecting a cell with a vector of arrangement 62.
  • a method for preparing a population of cells that express a CoStAR of any one of arrangements 52-60 which comprises: a. detecting expression of the CoStAR on the surface of cells transfected or transduced with a vector of arrangement 62; and b. selecting cells which are identified as expressing the CoStAR.
  • a cell population which is enriched for cell expression a CoStAR of any one of arrangements 52-60.
  • a method for treating a disease in a subject which comprises the step of administering a cell according to any of arrangements 63-65, or a cell population according to arrangement 68 to the subject.
  • a protein comprising the amino acid sequence of one of SEQ ID NOs: 510-519.
  • the protein of arrangement 70 wherein the protein comprises the sequence of SEQ ID NO: 510.
  • the MFE23 CoStAR consists of a CEA-specific MFE23, humanized (hu) MFE23, CEA6, BW431/26 or huT84.66 derived single chain antibody fragment nucleotide sequence with an oncostatin Ml, CD8a, CD2, IL-2, GM-CSF or hlgGK VIII leader sequence.
  • Each CoStAR has an extracellular spacer domain derived from CD8 or CD28 or truncated CD28 and a signalling domain derived from CD28 and CD40.
  • the constructs were cloned into pSF.Lenti (Oxford Genetics) containing an MND promoter, and separated from a truncated CD34 marker gene via a P2A cleavage sequence.
  • Lentiviral Production - Lentiviral production was performed using a three-plasmid packaging system (Cell Biolabs, San Diego, USA) by mixing 10 pg of each plasmid, plus 10 pg of the pSF.Lenti lentiviral plasmid containing the transgene, together in serum free RPMI containing 50 mM CaCh. The mixture was added dropwise to a 50% confluent monolayer of 293T cells in 75 cm 2 flasks. The viral supernatants were collected at 48 and 72h post transfection, pooled and concentrated using LentiPac lentiviral supernatant concentration (GeneCopoeia, Rockville, Maryland, USA) solution according to the manufacturer’s instructions.
  • LentiPac lentiviral supernatant concentration GeneCopoeia, Rockville, Maryland, USA
  • Lentiviral supernatants were concentrated 10-fold and used to directly infect primary human T-cells in the presence of 4 pg/ml polybrene (Sigma-Aldrich, Dorset, UK). Peripheral blood mononuclear cells were isolated from normal healthy donors before activation for 24 hours with T-cell activation and expansion beads (Invitrogen) according to the manufacturer’s instructions before addition of lentiviral supernatants.
  • Cell transduction was assessed 96 hours post infection using CEA.hFc protein and anti- hFc-PE secondary, plus anti-CD34-APC or by anti-CD34-PE antibodies alone. Cells were then expanded further using xlO donor mismatched irradiated PBMC feeders at a 1 :20- 1 :200 ratio in RPMI + 10% FCS with the addition of 1 pg/ml PHA and 200 lU/ml IL-2. After 14 days the cells were stained as previous and stored ready for assay.
  • Proliferation assays were performed by first loading T-cells with 10 pM eFluor450 proliferation dye (eBioscience, UK) for 10 min at 37°C at a concentration of 1x10 ⁇ cells/ml before incubating the cells in 5 volumes of cold T-cell media for 5 min on ice. Cells were then washed excessively to remove unbound dye and added to cocultures containing tumour cells. Cells were removed at 2, 6 and 10 days, 1 :200 dilution of DRAQ7 added and the cells analysed using a MACSQuant cytometer and MACSQuantify software.
  • Cell counts for proliferation assays were performed by taking cells from the wells and staining with anti-CD2 PerCP eFluor710 antibody (eBioscience, UK) for 20 min in the dark, followed by DRAQ7 staining and counts made using a MACSQuant analyser.
  • T-cells Primary human T-cells were isolated from Buffy coats obtained from the NHSBT. T- cells were isolated by Ficoll-mediated isolation and T-cell negative isolation kits (StemCell Technologies). The isolated T-cells were activated with human T-cell activation and expansion beads (Invitrogen, UK). Cells were incubated with concentrated lentiviral particles and expanded over a number of days. The lentivirus contained the DNA sequence of the MFE.CoStAR.2A.tCD34 construct (MFE23.scFv fused to full length human CD28 co-expressed with truncated human CD34 via a 2A cleavage sequence). Successfully transduced cells were further expanded using irradiated feeders as outlined in materials and methods.
  • MFE.CoStAR.2A.tCD34 construct MFE23.scFv fused to full length human CD28 co-expressed with truncated human CD34 via a 2A cleavage sequence
  • Donor 1 transduction was measured at 22.69% (17.15 CD34+/CoStAR+ plus 5.53% CD34-/CoStAR+), donor 2 was measured at 20.73%, and donor 3 at 13.34%.
  • Cells were enriched for CoStAR expression using anti-CD34 antibodies to obtain T-cell populations greater than 90% CoStAR positive.
  • tumour cells were tested against the CEA+ tumour cell lines LoVo and LS174T.
  • the tumour cells To enable activation of the T-cells in response to the unmatched tumour lines we engineered the tumour cells to express an anti-CD3 single chain antibody fragment anchored to the cell membrane by way of a synthetic transmembrane domain and split from the GFP marker gene using an IRES element to visualise transduced cells using flow cytometry.
  • CoStAR enhanced IL- 2 secretion towards OKT3 engineered tumour cells was found in all three donors tested. The effect was most evident at E:T ratios of 8: 1 and 16: 1 and at higher E:T ratios IL-2 secretion was too low to measure accurately. At lower effector to target ratios it appeared that IL-2 secretion was saturating from non-transduced cells. These observations were repeated in LoVo cells with two of the three donors tested against LS174T with similar results (Fig. 3D & E).
  • CoStAR engineered cells went through 5,6 or 7 proliferation cycles over 6 days compared to non-engineered cells in response to LoVo- 0KT3, whereas CoStAR transduced and non-transduced cells went through an average of approximately 2 cycles over the same duration in response to wild-type LoVo.
  • CD28(IEV) is truncated such that the C-terminal motif of CD28 is the amino acid triad ‘IEV’.
  • Sequences were generated de novo by Genewiz and cloned into a lentiviral vector under an EFla promoter along with a CD34 marker gene separated from the fusion CoStAR by a 2A self-cleaving peptide.
  • Primary CD8+ T-cells were isolated using EasySep beads (StemCell Technologies) and activated with anti- CD3/anti-CD28 activation/expansion Dynabeads before addition of lentiviral particles.
  • Fig. 5 shows the IL-2 response from CD34- (CoStAR non- transduced) and CD34+ (CoStAR transduced).
  • IFNy a cytokine released under normal signal 1 conditions but enhanced by costimulation
  • CD107a a marker of degranulation
  • bcl-xL an antiapoptotic protein upregulated by costimulation.
  • Engagement of CoStAR enhanced all the effector functions analysed to varying degrees.
  • Example 2 The effect of CD28 and CD28.CD40 based CoStARs on population based cytokine secretion was compared.
  • Primary T-cells from three donors were transduced with either the CD28(IEV) truncated CoStAR, full length CD28 CoStAR or CD28.CD40 CoStAR (having the full length CD28 as shown in SEQ ID NO:439, but lacking the N terminal N and K residues) or left non-transduced.
  • T-cells were enriched for CoStAR expression using the CD34 marker gene, and following expansion cells were mixed with LoVo-OKT3 cells and IL-2 secretion analysed by ELISA (See Fig. 7).
  • Non-transduced cells on average produced 0.80 ng/ml IL-2, with CD28(IEV) and full length CD28 CoStAR producing 4.6 and 5.0 ng/ml IL-2 respectively.
  • CD28.CD40 induced 29.0 ng/ml IL-2 on average across three donors thus demonstrating a clear benefit to incorporating CD40 into the basic CD28-based CoStAR.
  • T-cells from seven donors were transduced with either CD28 or CD28.CD40 CoStARs with either an anti- CA125 (196-14) or anti-Folate receptor (MOV-19) scFv, or an anti-Folate receptor peptide (C7) antigen binding domain. Additional cells were transduced with a CD28 CoStAR harboring an anti-CEA scFv as a mismatched control. Cells were then mixed with CA125+/Folate receptor+/CEA- cell line OvCAR3 engineered to express a membrane bound OKT3 (OvCAR-OKT3).
  • OvCAR-OKT3 membrane bound OKT3
  • T-cells were engineered with a murine constant domain modified TCR which recognizes a CEA peptide (691-699) in the context of HLA-A*02 as well as the CD28 or CD28.CD40 CoStAR targeted towards cell surface CEA protein. As a control cells were also transduced with a CA125 specific CD28 CoStAR. The T-cells were mixed with HLA-A*02+/CEA+ H508 cells and cytokine production analysed by intracellular flow cytometry staining.
  • Flow cytometric gating was performed using antibodies directed towards the murine TCRP constant domain (marks the TCR engineered cells) as well as the DYKDDDDK (SEQ ID NO:449) epitope tag (marks the CoStAR engineered cells).
  • TCR-/CoStAR-, TCR+/CoStAR-, TCR-/CoStAR+ and TCR+/CoStAR+ cells were analysed in each subpopulation in either the CD4+ or CD8+ T-cells (Fig. 9).
  • CD28.CD40 CoStAR enhanced CD137 and TNFa production above TCR stimulation alone, however the TCR response in CD4+ cells was poor due to the dependency of the TCR on CD8.
  • CD8+ cells there was more robust effector activity with IL-2 and CD107a in particular showing a stronger induction in the CD28.CD40 CoStAR groups.
  • the effector activity in just the TCR+/CoStAR+ groups was plotted in CD4+ and CD8+ cells (Fig. 10).
  • CD4+ cells induction of CD137 was significantly enhanced by CD28.CD40 compared to either CEA or mismatched targeting CD28 CoStAR.
  • CD137 induction was significantly increased compared to either CEA or mismatched targeting CD28 CoStAR, whereas CD 107a induction was increased compared to the control CoStAR.
  • CD28.CD40 shows enhanced effector activity across a broad range of models and effector activities.
  • MFE23.CD28 or MFE23.CD28.CD40 CoStAR were mock transduced or transduced with MFE23.CD28 or MFE23.CD28.CD40 CoStAR, each harbouring a CD34 marker gene separated by a 2A cleavage peptide.
  • MFE23 is a single chain Fv antibody that has a high affinity for carcinoembryonic antigen (CEA).
  • CEA carcinoembryonic antigen
  • MACSTM paramagnetic selection reagents Miltenyi Biotech
  • MFE23.CD28 CoStAR strongly mediated expansion of CD34 + T cells
  • MFE23.CD28.CD40 CoStAR further enhanced expansion (Fig. 11).
  • T cells mock transduced or transfected with MFE23.CD28 or MFE23.CD28.CD40 were cocultured with LoVo-OKT3 cells at an 8: 1 effectortarget ratio in the presence (200 lU/ml) or absence of exogenous IL-2.
  • days 1, 4, 7, 11 and 18 cells were taken and the number of viable T-cells enumerated by using anti-CD2 reagents on a MACSQuant flow cytometer.
  • Fig. 12A In the absence of stimulation by tumor and IL-2, cells declined in number as would be expected (Fig. 12A).
  • Fig. 12B In the absence of stimulation but presence of IL-2 there was a more apparent survival of the cells, but no specific growth.
  • Mock transduced and T cells transduced with MFE23.CD28 or MFE23.CD28.CD40 CoStARs were then tested for cytokine production.
  • Bead array analysis was performed on supernatants obtained from T-cell/tumour cocultures.
  • Engineered T-cells were incubated at a 1 : 1 effectortarget ratio with LoVo-OKT3 cells for 24 hours and supernatant collected.
  • Conditioned supernatant was also collected from an equal number of T-cells alone, or LoVo-OKT3 cells alone.
  • IL-2 IFN-y, TNFa, IL-4, IL-5, IL-13, IL-17A, IL-17F, IL-22, IL-6, IL-10, IL-9, and IL-21 was analysed using a LegendplexTM Human TH1/TH2 cytokine panel (Biolegend) (Fig. 13 A-13M). Cytokines were either very low or undetectable in media from T-cells or tumour alone. However when cocultured with tumour cytokine production was enhanced. MFE23.CD28 enhanced production of IL-2, IL-5, IL-17A/17F, IL-10, IL-9 and IL-21 compared to mock.
  • MFE23.CD28.CD40 also enhanced production of TNFa, IL-13 and IL-22.
  • MFE23.CD28.CD40 also enhanced the production of a number of cytokines greater than that elicited by MFE23.CD28 (IL-2, IL-9 and IL-17F), but also reduced the production of some cytokines below the levels seen with MFE23.CD28 (IL-5 and IL-10).
  • Mock transduced and T cells transduced with MFE23.CD28 or MFE23.CD28.CD40 CoStARs were further tested for chemokine production.
  • Chemokines were either very low or undetectable in media from T-cells alone. However when cocultured with tumor, chemokine production was enhanced. MFE23.CD28 enhanced production of CXCL5, CXCL10, CXCL11, CCL17 and CCL20 compared to mock. However, MFE23.CD28.CD40 also enhanced production of CCL2, CXCL1 and CXCL9.
  • MFE23.CD28.CD40 also further enhanced the production of certain cytokines to a greater amount than that elicited by MFE23.CD28 (CXCL1, CXCL9, CXCL10, CXCL11, CCL17, CCL2, CXCL9, CCL5 and CCL20), while reducing the production of some cytokines below the levels seen with MFE23.CD28 (CCL4).
  • CoStARs were tested for functional activity against cancer targets.
  • Cells were transduced with CD28 or CD28.CD40 CoStARs engineered with an scFv binding domain specific for FolR or CA125 (scFv M0V19 and scFv 196-14 respectively).
  • Human folate receptor alpha represents a suitable target for a number of tumours including ovarian, head and neck, renal and lung and CA125 represents an alternative target for ovarian cancer.
  • Primary human T-cells from six healthy donors were engineered with either 196-14. CD28, 196-14.
  • CD28.CD40, MOV19.CD28 or MOV19.CD28.CD40 receptors all harbouring a DYKDDDDK epitope tag for detection.
  • Transduced cells were mixed with FolR+/CA125+ OvCAR-OKT3 cells before analysis of effector activity using intracellular staining in the epitope tag positive and negative populations.
  • Specific enhancement of effector activity determined by production of IL-2 (Fig. 15A and 15B), TNFa (Fig. 15C and 15D), CD137 (Fig. 15E and 15F), and BCL-xL (Fig.
  • Mock transduced TILs or TILs engineered with MOV19.CD28.CD40 CoStAR were evaluated for expansion and CD137 production stimulated by patient matched tumour digest (Fig. 16).
  • Three donor tumours were tested which displayed varying levels of FolR on the digest, ranging from negative (6A), low expression (6B) to high expression (6C).
  • Mock and CoStAR negative TIL in the CoStAR engineered populations of TIL matched for the FolR negative digest demonstrated similar levels of CD137 upregulation following tumour coculture which was not enhanced by the presence of CoStAR (Fig. 16D).
  • CoStAR constructs include an MFE23 (CEA specific), M0V19 (Folate receptor a specific) or 196-14 (CA125 specific) derived single chain antibody fragment nucleotide sequence with an oncostatin Ml leader sequence fused to a costimulatory domain.
  • the costimulatory domains contain an extracellular spacer region and transmembrane domain derived from human CD8 or CD28 and a signalling domain of either CD28, CD2 or CD137 and/or wild-type or mutant CD40 variants.
  • Some CoStARs detailed herein comprise a human PD1 extracellular domain fused to CD28 and CD40.
  • Receptors were cloned with a P2A cleavage sequence and a truncated form of human CD34 to permit detection of transduced cells.
  • the CoStAR nucleotide sequence was codon optimised and gene synthesised by Genewiz Inc.
  • the constructs were cloned into a third generation lentiviral vector.
  • Peripheral blood mononuclear cells were isolated from normal healthy donors before activation for 24 hours with T-cell activation and expansion beads (Invitrogen) according to the manufacturer’s instructions before addition of lentiviral supernatants.
  • Cell transduction was assessed 96 hours post infection using CEA.hFc protein (R&D Systems) and anti-hFc-PE secondary, plus anti-CD34-APC or by anti-CD34-PE antibodies alone. Cells were then expanded further using xlO donor mismatched irradiated PBMC feeders at a 1 :20- 1 :200 ratio in RPMI + 10% FCS with the addition of 30 ng/ml OKT3 and 200 lU/ml IL-2. After 14 days the cells were stained as previous and stored ready for assay.
  • Functionality assays were performed by mixing CoStAR positive or negative cells with wild-type or OKT3 engineered CEA-Positive LoVo cells. Briefly, T-cells were mixed with LoVo cells at varying ratios in 96-well plates. For flow analysis cocultures were incubated with Brefeldin and monensin and anti-CD107a antibodies for 16 hours following which cells were stained with Fixable Viability Dye ef450 (eBiosciences), fixed with 4% paraformaldehyde and then permeabilised using Fix/Perm wash buffer (BD Biosciences).
  • Fixable Viability Dye ef450 eBiosciences
  • cytokine bead array LGENDPLEXTM Human Th Cytokine Panel (12-plex)
  • chemokine bead array LGENDPLEXTM Human Proinflammatory Chemokine Panel (13-plex).
  • Proliferation assays were performed by mixing T-cells and tumour cells at an 8: 1 effectortarget ratio in complete T-cell media (TCM: RPMI supplemented with 10 % FCS, 0.01 M HEPES and 1% Penicillin/streptomycin, 50 mM P-mercaptoethanol) in the presence or absence of IL-2. Cell counts were made at indicated time points and fresh tumour cells were added in restimulation assays at a final E:T of 8: 1.
  • Cell counts for proliferation assays were performed by taking cells from the wells and staining with anti-CD2 PerCP eFluor710 antibody (eBioscience, UK) for 20 min in the dark, followed by DRAQ7 staining and counts made using a MACSQuant analyser.
  • variant receptors were generated harbouring mutations in the TRAF6 binding motif (MFE23.CD28.CD40 (PQEINF mutated to AQAINF)), the TRAF2 binding motif (MFE23.CD28.CD40 (SVQE mutated to AVQA)) or the TRAF1/2/3/5 binding motif (MFE23.CD28.CD40 (PVQET mutated to AVAEA)).
  • TRAF6 binding motif MFE23.CD28.CD40 (PQEINF mutated to AQAINF)
  • MFE23.CD28.CD40 SVQE mutated to AVQA
  • TRAF1/2/3/5 binding motif MFE23.CD28.CD40
  • Primary human T-cells isolated from three separate healthy donors were transduced with the indicated CoStARs and cells enriched for CoStAR expression via CD34. Cocultures were set up with LoVo-OKT3 cells and supernatants collected for cytokine analysis.
  • IL2 production by non -transduced cells was very low, but elevated in cells expressing the wild-type MFE23.CD28.CD40 CoStAR.
  • IL2 production was not largely affected by mutations to the SVQE, PQEINF or Q263A mutation.
  • mutation to the PVQET motif had a dramatic effect on IL2 production by T-cells.
  • CoStARs that bind to CEA -
  • the CoStAR consists of a CEA specific MFE23, humanised (hu) MFE23, CEA6, BW431/26 or huT84.66 derived single chain antibody fragment nucleotide sequence with an oncostatin Ml, CD8a, CD2, IL-2, GM-CSF or hlgGK VIII leader sequence.
  • Each CoStAR has an extracellular spacer domain derived from CD8 or CD28 or truncated CD28 and a signalling domain derived from CD28 and CD40.
  • the constructs are cloned into pSF.Lenti (Oxford Genetics) containing an MND promoter, and separated from a truncated CD34 marker gene via a P2A cleavage sequence.
  • Lentiviral Production - Lentiviral production is performed using a three-plasmid packaging system (Cell Biolabs, San Diego, USA) by mixing 10 pg of each plasmid, plus 10 pg of the pSF.Lenti lentiviral plasmid containing the transgene, together in serum free RPMI containing 50 mM CaCh. The mixture is added dropwise to a 50% confluent monolayer of 293T cells in 75 cm2 flasks. The viral supernatants are collected at 48 and 72h post transfection, pooled and concentrated using Lenti-X lentiviral supernatant concentration (Takara Bio Inc. Japan) solution according to the manufacturer’s instructions.
  • Lenti-X lentiviral supernatant concentration Takara Bio Inc. Japan
  • Lentiviral supernatants are concentrated 10- fold and used to directly infect primary human T-cells at an MOI of 3-5 in the presence of 4 pg/ml polybrene (Sigma-Aldrich, Dorset, UK).
  • Peripheral blood mononuclear cells are isolated from normal healthy donors before activation for 24 hours with T-cell activation and expansion beads (Invitrogen) according to the manufacturer’s instructions before addition of lentiviral supernatants.
  • Cell transduction is assessed 96 hours post infection using CEA.hFc protein and anti- hFc-PE secondary, plus anti-CD34-APC or by anti-CD34-PE antibodies alone.
  • xlO donor mismatched irradiated PBMC feeders at a 1 :200 ratio in T-cell media (RPMI 1640, 10% FBS, lOmM HEPES, 50 pM P -mercaptoethanol and 50 u/ml Penicillin/streptomycin), 200 lU/ml IL-2 and a final concentration of 30 ng/ml anti-CD3 (OKT3). After 12-14 days the cells are stained as previous and stored ready for assay.
  • Functionality assays are performed by mixing CoStAR positive or negative cells with wild-type or OKT3 engineered CEA positive cell lines (LoVo, HT29, SW480, H508). Briefly, T- cells are mixed with target cells at varying ratios in 96-well plates and cytokine release measured by ELISA and MSD analysis.
  • Cytotoxicity assays are performed using the xCELLigence RTCA SP real time cell analyser system (Acea).
  • a program was generated to test well conductivity (cell index) of a 96- well PET E-plate every 15 min for the duration of the experiment (up to 250 hr).
  • 50 pL T cell medium was added to the wells which were to have cell index tested and incubated at room temperature (RT) for 30 minutes.
  • the E-plate was added to the RTCA SP device and background conductivity readings measured.
  • the optimal density of target cells to seed is defined as that which reaches a stable cell index between 24- and 36- hours after the beginning of the assay and does not decrease without intervention (i.e. addition of Triton-x-100 or effector cell populations) before the end of the assay.
  • Target cells at optimal density for killing assays are counted using a quantitative method capable of dead-cell discrimination.
  • the E-plate is removed from the device and the optimal density of live cells is added to the wells containing T cell medium at a final volume of 100 pL before incubation for 30 minutes at RT.
  • the E-plate us then placed back on the analyser and cell index values acquired until a stable cell index is observed, at which point the program is paused and the E-plate removed from the RTCA SP device. Treatments are added to the appropriate wells. Treatments consist of either 100 pL T cell medium (no treatment control), or the same volume containing effector cells or 0.5 % Triton-x-100 (full lysis control). Effector cell counting uses a quantitative method capable of dead- and apoptotic-cell discrimination. The number of effectors to target cells varied depending on the experiment.
  • NCIst is the Normalised Cell Index for the sample and NCIRt is the average of Normalise Cell Index for the matching reference wells.
  • Repeat stimulation assays are performed by mixing 5xl0 4 CoStAR transduced or mock-transduced cells at an 8: 1 E:T ration with LoVo-OKT3 cells in the absence of exogenous IL-2, in triplicate well of a 96-well U-bottom plate.
  • T-cell counts are made on DI, 4 and 7 via flow cytometric assessment of numbers based on aCD2 gating, and fresh tumour cells added at seven day intervals. Relative expansion is assessed by splitting of wells and enumeration of fold change based upon the original seeding density with the proportion of cells removed for counting also factored in.
  • a model system is developed to evaluate the impact of various structural components of CEA directed CoStAR receptors. To this end the signal peptide (SP), single chain antibody fragment (scFv) and extracellular spacer (ES) are assessed for their impact on expression and function.
  • SP signal peptide
  • scFv single chain antibody fragment
  • ES extracellular spacer
  • the impact of the signal peptide on expression of the CoStAR is tested, as it is known that different signal peptides can affect expression of various recombinant proteins (REF).
  • the MFE23.CD28.CD40 CoStAR receptors are generated with various different leader sequences (which encode the desired signal peptide) sequences. These include signal peptides derived from: Oncostatin Ml (OSM), IL2, CD2, CD8a, GMCSF and hlgGK VIII. Each leader sequence is cloned in frame with the MFE23 scFv sequence to generate SP.MFE23.CD28.CD40.P2A.tCD34.
  • a Jurkat cell line model is selected to investigate the relative expression of each SP modified CoStAR relative to the tCD34 marker gene.
  • Jurkat JRT3-T3.5 T-cells are incubated with lentiviral particles at an MOI of 5. Seven days post transduction the cells are stained with anti- CD34 antibodies to stain for the transduced cells, and CEA.hFc protein followed by anti-hFc secondary antibodies to identify for the CEA CoStAR. All SP modified CoStAR variants tested are found to be expressed in the CD34+ proportion of the JRT3-T3.5 cells.
  • T-cells Primary human T-cells are isolated from Buffy coats obtained from the NHSBT. T- cells are isolated by Ficoll-mediated isolation and T-cell negative isolation kits (StemCell Technologies). The isolated T-cells are activated with human T-cell activation and expansion beads (Invitrogen, UK). Cells are incubated with concentrated lentiviral particles, encoding CEA CoStARs containing the OSM SP, and expanded over a number of days. Cells are enriched for CoStAR expression using anti-CD34 antibodies to obtain T-cell populations greater than 90% CoStAR positive before being placed in a rapid expansion protocol (REP), with irradiated buffy coat derived PBMCs as outlined in the materials and methods.
  • REP rapid expansion protocol
  • a physiologically relevant in vitro model is employed to test the impact of CoStAR on T-cell activity.
  • Transduced and non-transduced cells are tested against the CEA+ cell lines LoVo, H508, SW480 or HT29.
  • the murine CEA- cell line Ba/F3 is engineered to express CEA as a control.
  • the tumour cells are engineered to express an anti-CD3 single chain antibody fragment anchored to the cell membrane by way of a synthetic transmembrane domain and split from a GFP marker gene using an IRES element to visualise transduced cells using flow cytometry.
  • Non-transduced and CoStAR transduced T-cells are mixed at varying effectortarget ratios with wild-type or OKT3 -engineered tumour cell lines. After 24 hours coculture media is taken for IL-2 ELISA measurement. Activation dependent IL-2 secretion is observed from both CoStAR+ and CoStAR- T-cell populations from all donors in response to OKT3 engineered cells with only background IL-2 secretion seen from transduced and non-transduced T-cells in response to un-engineered tumour cells. In all donors tested, the presence of CEA CoStAR enhances effector activity (IL2, IL3, CXCL10) towards OKT3 engineered CEA+ tumour lines.
  • IL2, IL3, CXCL10 effector activity
  • Cocultures with Ba/F3 cells demonstrate the targeted approach of the CEA CoStARs.
  • Coculture of CEA CoStAR engineered cells with Ba/F3 or Ba/F3-CEA does not result in specific IL2 release whereas incubation with Ba/F3-OKT3 enhances IL-2 secretion.
  • incubation of T-cells with Ba/F3-OKT3/CEA significantly enhances IL2 secretion compared to Ba/F3-OKT3 alone.
  • TIL are engineered with CEA specific CoStAR constructs.
  • tumours are digested and analysed for CEA expression using flow cytometry.
  • Tumour digests testing positive are engineered with CEA CoStARs.
  • engineered and matched non-engineered TIL are mixed with either tumour digest, or where available, matched autologous tumour lines.
  • the presence of the CEA CoStAR enhances specific effector activity as measured by IFNy and IL-2 compared to cells which are mock transduced.
  • Anti-MSLN CoStARs comprising different scFv antigen-binding domains (Table 8) were compared for surface expression on T cells from healthy donors.
  • T cells from healthy donor (HD) PBMCs were lentivirus transduced, at a multiplicity of infection (MOI) 5, with six variable scFV constructs against mesothelin (MSNL) that possessed CD28.CD40 signaling domains.
  • MOI multiplicity of infection
  • MSNL mesothelin
  • Non-transduced (MOCK) cells were used as controls.
  • Cells were sorted using CD34 microbeads and underwent a rapid expansion protocol (REP) for 14 days.
  • IxlO 5 cells were assessed for transduction efficiency either via surface detection of the marker gene tCD34 or CoStAR molecule using an anti-CD34-APC (black) or anti- MSLN-PE (red) antibody, respectively. (Fig. 19). The results represent 3 biological replicates.
  • Cytokine production was assessed in CoStAR transduced HD T cells cocultured with target cell lines.
  • a variety of CoStARs comprising different anti-MSLN binding domains, spacers, or transmembrane domains were tested.
  • Nontransduced (MOCK) and anti-MSNL CoStAR transduced HD T cells were cocultured with engineered OVCAR3 target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1.25xl0 4 ) for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted. Cytokine concentrations were determined for IL-2 (Fig. 20A) IFNy (Fig. 20B) and TNFa (Fig. 20C) following cocultures with OVCAR-3 or OVCAR3-OKT3 cell lines. Non-treated T cells were used as a control. The results represent 1-3 biological replicates with 3 technical replicates each.
  • Nontransduced (MOCK) and anti-MSNL CoStAR transduced HD T cells were cocultured with engineered K562 target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1.25xl0 4 ) for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted. Cytokine concentrations were determined for IL-2 (Fig. 21 A) IFNy (Fig. 21B) and TNFa (Fig. 21C) following cocultures with K562-MSNL or K562-MSNL-OKT3 cell lines. Non-treated T cells were used as a control. The results represent 1-3 biological replicates with 3 technical replicates each. [00475] Anti-CEA CoStAR Expression
  • Anti-CEA CoStAR expression was evaluated for anti-CEA CoStARs comprising differing signal peptides (Table 11) or scFv antigen binding domains (Table 12).
  • T cells from healthy donor PBMCs were lentivirus transduced at a multiplicity of infection (MOI) 5, with the MFE23 scFV constructs against the carcinoembryonic antigen 5 (CEA) that possessed CD28.CD40 domains.
  • the constructs had variations in the signal peptide and non-transduced (MOCK) cells were used as controls.
  • Cells were sorted using CD34 microbeads and underwent a rapid expansion protocol (REP) for 14 days. Following expansion, IxlO 5 cells were assessed for transduction efficiency (Fig.
  • T cells from healthy donor PBMCs were also lentivirus transduced, at a multiplicity of infection (MOI) 5, with variable scFV constructs against the carcinoembryonic antigen 5 (CEA) that possessed CD28.CD40 domains.
  • MOI multiplicity of infection
  • CEA carcinoembryonic antigen 5
  • Fig. 1 T cells from healthy donor PBMCs were also lentivirus transduced, at a multiplicity of infection (MOI) 5, with variable scFV constructs against the carcinoembryonic antigen 5 (CEA) that possessed CD28.CD40 domains.
  • CCA carcinoembryonic antigen 5
  • Cytokine production was assessed in CoStAR transduced HD T cells cocultured with Lovo target cell lines. CoStARs comprising different anti -CEA binding domains (Table 12) were tested. Nontransduced (MOCK) and anti-CEA CoStAR transduced HD T cells were cocultured with engineered target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1 ,25xl0 4 ) for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted. Cytokine concentrations were determined for IL-2 (Fig. 24A) IFNy (Fig. 24B) and TNFa (Fig. 24C) following cocultures with Lovo or Lovo-OKT3 cell lines. Non-treated T cells were used as a control. The results represent 1 biological replicate with 3 technical replicates.
  • Cytokine production was also assessed in CoStAR transduced HD T cells cocultured with K562 target cell lines.
  • cells were cocultured with engineered target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1.25xl0 4 ) for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted and cytokine concentrations were determined for IL-2 (Fig. 25A) IFNy (Fig. 25B) and TNFa (Fig. 25C) following cocultures with K562.CEACAM5 or K562.CEACAM5.OKT3 cell lines. Non-treated T cells were used as a control.
  • T cells from healthy donor PBMCs were lentivirus transduced at a multiplicity of infection (MOI) 5, with the hMF23 scFV constructs against the carcinoembryonic antigen 5 (CEA) that possessed CD28.CD40 domains.
  • CCA carcinoembryonic antigen 5
  • Cells were sorted using CD34 microbeads and underwent a rapid expansion protocol (REP) for 14 days. Following expansion, IxlO 5 cells were assessed for transduction efficiency (Fig.
  • Cytokine production was assessed in CoStAR transduced HD T cells cocultured with Lovo target cell lines. As above, cells were cocultured with engineered target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1.25xl0 4 ) for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted and cytokine concentrations were determined for IL-2 (Fig. 27A) IFNy (Fig. 27B) and TNFa (Fig. 27C) following cocultures with Lovo or Lovo-OKT3 cell lines. Non-treated T cells were used as a control.
  • E:T effector to target
  • CoStARs were constructed to test intracellular signaling domains.
  • Fig. 28 and Table 14 depict anti-CEA CoStARs comprising an hMFE23 CEA-binding domain with intracellular signaling domains comprising CD40, CD134, CD137, CD2, ICOS, DAP10, andNTRKl signaling elements.
  • T cells from healthy donor PBMCs were lentivirus transduced at a multiplicity of infection (MOI) 5 with the hMF23 scFV constructs against the carcinoembryonic antigen 5 (CEA).
  • MOI multiplicity of infection
  • CEA carcinoembryonic antigen 5
  • Nontransduced (MOCK) cells were used as controls.
  • Cells were sorted using CD34 microbeads and underwent a rapid expansion protocol (REP) for 14 days. Following expansion, IxlO 5 cells were assessed for transduction efficiency (Fig.
  • CoStAR transduced cells were phenotypically characterized. Following outgrowth and REP, IxlO 5 cells were assessed for the differentiation subtype using flow cytometry.
  • T cells from HD PBMCs of three donors were lentivirus transduced with the hMF23 scFV constructs of Fig. 28.
  • Cells were sorted using CD34 microbeads and underwent a rapid expansion protocol (REP) for 14 days. Following outgrowth and REP, IxlO 5 cells were assessed for the differentiation subtype compared to non-transduced cells using flow cytometry. T cell phenotypes are depicted in Fig. 30 as a proportion of CD3 cells.
  • Cytokine secretion anti-CEA hFME23 CoStAR transduced T cells was assessed by coculture with K562 target cells.
  • Nontransduced (MOCK) and anti-CEA CoStAR transduced HD T cells were cocultured with engineered target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1.25xl0 4 ) for 24 hours and MSD immunoassay was performed to evaluate the concentration of cytokines secreted. Cytokine concentrations for IL-2 (Fig. 31 A) ZFNy (Fig. 3 IB) and TNFa (Fig. 31C), following cocultures with K562.CEACAM5 (signal 2) or K562.CEACAM5.OKT3 (signal 1+2) cell lines are shown. Non-treated T cells were used as a control.
  • Nontransduced (MOCK) and anti-CEA CoStAR transduced HD T cells were cocultured with engineered target cell lines at an effector to target (E:T) ratio of 1 : 1 (IxlO 5 : IxlO 5 ) for 16 hours in the presence of Brefeldin A and cytokine producing cells were measured using intracellular flow cytometry.
  • E:T effector to target
  • cytokine producing cells were measured using intracellular flow cytometry.
  • Frequency of IL-2 (Fig. 32A) IFNy (Fig. 32B) and TNFa (Fig. 32C) expressing cells following cocultures with K562.CEACAM5 (signal 2) or K562.CEACAM5.OKT3 (signal 1+2) cell lines are shown.
  • Nontreated T cells were used as a control.
  • HD T cells were transduced with hMFE23 anti-CEA CoStARs and cocultured with engineered target cells.
  • Nontransduced (MOCK) and anti-CEA CoStAR transduced HD T cells were cocultured with K562.CEACAM5.OKT3 engineered target cell lines at an effector to target (E:T) ratio of 8: 1 (IxlO 5 : 1 ,25xl0 4 ) on Day 0.
  • Nontransduced (MOCK) cells were used as controls.
  • E:T effector to target
  • HD T cells transduced with hMFE23 anti-CEA CoStARs and cocultured with K562.CEACAM5.OKT3 engineered target cell lines as above were sampled for counting on Day 6 to evaluate fold expansion (Fig. 34). Cells were counted by flow cytometry using DRAQ7 for live cell discrimination and CD2 to enumerate the T cells.
  • Cells were enriched for CD34 marker expression, expanded following the rapid expansion protocol (REP) and frozen for subsequent experiments. After thaw, cells were rested for 3-4 days in complete RPMI supplemented with IL-2 and their transduction rate was determined looking at the CD34 marker gene expression. The viability and absolute count were assessed after overnight IL-2 starvation using DRAQ-7 (1 :200) by flow cytometry (Novocyte) and data were analysed using the NovoExpress 1.5.0 software. Transduced T cells were cocultured in absence of IL-2 with LoVo (CCL-229TM from ATCC) or LoVo.OKT3.GFP tumor cells at 8: 1 effector to target ratio. After 24 hours, supernatants were collected and frozen.
  • LoVo CCL-229TM from ATCC
  • LoVo.OKT3.GFP tumor cells at 8: 1 effector to target ratio. After 24 hours, supernatants were collected and frozen.
  • LoVo and LoVo.OKT3.GFP naturally express CEA and PD-L1 on their surface, conferring signal 2 through the CoStAR alone (LoVo) or associated with signal 1 (LoVo.OKT3.GFP) to the transduced T cells.
  • Cocultures were performed in triplicates and corresponding negative (T cells alone, tumor cells alone) and positive (PMA + ionomycin) controls were included in the experiment. After thaw, secreted IL-2 was detected by ELISA and the absorbance was measured using the FLUOstar Omega microplate reader and subsequently analysed with the Omega MARS 3.42 R5 software (Fig. 36A). Each dot represents the mean of triplicates for one donor. Note that negative controls (T cells alone, tumor cells alone) were all below the detection range.
  • Non-transduced (Non-Td) and anti-FOLRl CoStAR transduced (Td) TILs were generated using a 24-day protocol. Briefly, aliquots of OC digest were thawed and transduced with anti-FOLRl CoStAR lentivirus at a multiplicity of infection (MOI) of 5 at 48h and 72h. Cells were then expanded for 8 days (outgrowth), and then subjected to a rapid expansion protocol (REP) with allogeneic irradiated peripheral blood mononuclear cells (PBMCs) for 12 days.
  • MOI multiplicity of infection
  • PBMCs peripheral blood mononuclear cells
  • TIL CD4/CD8 ratio and anti-FOLRl CoStAR transduction efficiency was measured.
  • TILs were phenotypically characterized for their differentiation status, expression of co-inhibitory and co-stimulatory markers, T cell subsets and cytokine producing potential using flow cytometric panels.
  • TIL T cell media (TCM) for outgrowth consists of 450 mL of GIBCO custom P158718 media with 50 mL of heat inactivated Fetal Bovine Serum, gentamycin (10 pg/mL) / amphotericin (0.25 pg/mL) and vancomycin (50 pg/mL).
  • Complete rapid expansion protocol (REP) media consists of 460 mL of GIBCO custom P158718 with 40 mL human AB serum, gentamycin (10 pg/mL) / amphotericin (0.25 pg/mL) and vancomycin (50 pg/mL).
  • TILs were then centrifuged at 400 x g for 5 minutes, resuspended at a concentration of 1 x 10 6 cells/mL, placed into an appropriate vessel with 3000 lU/mL IL-2 and rested for two days in a 5% CO2 incubator set to 37°C.
  • IL-2 was added at a concentration of 3000 lU/mL and the cells were placed in a 5% CO2 incubator set to 37°C. [00503] On day 4, the cells were collected, washed once with complete TIL TCM, and resuspended in the same volume of fresh complete TIL TCM as on day 3 for the second day of transduction. Transduction was performed using the anti-FOLRl CoStAR lentivirus at an MOI of 5 and IL-2 at 3000 lU/mL was added to the cells prior to placing them in a 5% CO2 incubator set to 37°C for 8 days. IL-2 (3000 lU/mL) was added to the cells every 2-3 days until D13.
  • TILs were then assessed for transduction efficiency by staining 1 x 10 5 cells of each sample with antibodies against CD3, CD4, CD8, CoStAR and a viability stain.
  • DNA was extracted from 1 x 10 6 cells from each sample using the DNeasy Blood & Tissue Kit following the manufacturer’s instructions. Isolated DNA was used to analyze the vector copy number (VCN) using Droplet Digital PCR (ddPCR) and primers specific to the anti-FOLRl CoStAR and the reference gene Poly(rC) binding protein 2 (PCBP2). For subsequent experiments 2-5 x 10 7 cells were rested in fresh complete REP TIL TCM for 3 days with IL-2 (3000 lU/mL).
  • ddPCR Droplet Digital PCR
  • PCBP2 Poly(rC) binding protein 2
  • Remaining TIL were resuspended in cryoprotectant and aliquoted to cryovials, cooled to -80°C overnight, and then transferred to -150 °C for short term storage. Cryopreserved TIL were thawed in a 37 °C water bath, washed once with PBS by centrifugation at 400 x g for 5 minutes, then underwent an identical rest period as described above prior to experimentation.
  • Non-Td and Td cells from four donors were rested for 3 days in REP TCM media with IL-2 (3000 lU/mL). Subsequently, the cells were harvested, washed once with media by centrifugation at 400 x g for 5 minutes, resuspended in fresh complete REP TIL TCM, counted using Novocyte 3005, and resuspended at a concentration of 1 x 10 6 cells/mL. Cytometric evaluation ofTILs was performed on 1 x 10 5 cells per well, in triplicates, using four flow cytometry panels.
  • Cell subpopulations including Tregs, were assessed using antibodies against CD3, CD4, CD25, forkhead box Protein 3 (FOXP3), T cell receptor alpha beta (TCRaP), T cell receptor gamma delta (TCRyb), CD56, CD127, CoStAR, and a viability stain.
  • Cytokine production upon mitogenic stimulation was assessed using antibodies against CD3, CD4, CD8, IL-22, TNFa, IL- 17A, IFNy, CoStAR, and a viability stain.
  • TILs were activated by addition of PMA (50 ng/mL) / ionomycin (1 pg/mL), and Brefeldin A (1000 x) and placed in a 5% CO2 incubator set to 37°C for four hours. Following activation, TILs were collected, centrifuged at 400 x g for 5 minutes, counted, and 1 x 10 5 cells were seeded in triplicate for cytometric analysis. For all flow cytometry panels, fixation and permeabilization was performed using BD Cytofix/Cytoperm per manufacturer’s instructions.
  • recombinant human FOLR1 with Fc tag (rhFOLRl-FC) was used for the detection of anti-FOLRl CoStAR cells, and the populations of interest were reported from CoStAR- subset for the Non-Td TILs, and both CoStAR- and CoStAR+ fractions from the Td TILs (anti-FOLRl CoStAR- Td TILs and anti-FOLRl CoStAR+ Td TILs). Further subset characterization was performed on these populations.
  • Differentiation status was as follows: a lymphocyte gate followed by doublet and dead cell exclusion, CD3+, CD4+ and CD8+ gates. From all three populations (CD3+, CD4+, and CD8+), further analysis was performed on the T cell fractions of interest. To characterize the different T cell memory subsets, CD45RA+CD45RO- and CD45RA-CD45RO+ cells were gated from CD3+ cells. CD45RO+CCR7+ and CD45RO+CCR7- populations were then gated from CD45RA-CD45RO+ cells.
  • the central memory T cells (Tcm; CD45RO+CCR7+CD95+CD27+) cells and effector memory T cells (Tern; CD45RO+CCR7-CD95+CD27+/-) cells were further gated. Additionally, CD45RA+CCR7+ and CD45RA+CCR7- populations were gated from CD45RA+CD45RO- cells.
  • Tscm stem cell memory T cells
  • Tn naive T cells
  • Tte terminal effector T cells
  • the gating strategy employed for characterizing coinhibitory and costimulatory molecules included doublet and dead cell exclusion. Gating of CD4+ and CD8+ and CoStAR+/- cells was performed and populations were further analyzed for CD137, PD-1, CTLA-4, LAG-3, TIM-3 and SLAM expression.
  • the gating strategy employed for characterizing T cell subtypes included doublet and dead cell exclusion and a CD3+ gate. Using these populations, the expression of TCRaP, TCRyb, and CD56 was assessed. Subsequently, the CD3+CD4+ cells were gated for expression of TCRaP and CD56, and further analysis of the CD3+CD4+TCRaP+ population for CD25 and CD127 expression was performed. Using the CD25+CD127- gate the FOXP3+ cells were gated to determine the population of Tregs. Therefore, Tregs are defined as CD3+TCRab+CD4+ CD25+CD127-FOXP3+ and CoStAR+/- depending on the population assessed.
  • the gating strategy employed for characterizing intracellular cytokine production included doublet and dead cell exclusion, CD3+, CD4+, and CD8+ gates. CoStAR expression analysis on the different populations was performed followed by further analysis of the frequency of cells expressing IL-22, IL-17A, TNFa, and IFNy. [00517] Clinical Characteristics
  • CD4 and CD8 population composition in the product indicated most cells were CD4 ⁇ with levels ranging between 53.0-58.7% and fewer CD8 ⁇ cells (30.8-38.2%). CD4 ⁇ CD8 ⁇ and CD4- CD8- cells were also detected at low levels ranging between 3.47-4.43% and 3.19-6.97%, respectively. There were no significant differences between the Non-Td, anti-FOLRl CoStAR- Td, and anti-FOLRl CoStAR ⁇ Td TILs with regards to the CD4/CD8 cell composition (Fig. 40). [00520] The TILs were further characterized to determine whether anti-FOLRl CoStAR modification impacted TIL function.
  • Tn, Tscm, Tcm, Tern and Tte were assessed from CD3 ⁇ , CD4 ⁇ and CD8 ⁇ T cell compartments of Non-Td, anti-FOLRl CoStAR- Td and anti-FOLRl CoStAR ⁇ Td TILs (Fig. 41A-C). Results show that majority of TILs were Tern across the CD3 ⁇ (63.2-78.6%), CD4 ⁇ (76.9-88.8%) and CD8 ⁇ (48.3-66.9%) populations. Tcm cell frequencies were between 6.28-15.7%, 6.72-17.5% and 5.18-11.7% for CD3 ⁇ , CD4 ⁇ and CD8 ⁇ TILs, respectively. Tte cells made up 14.8-15.9% of bulk CD3 ⁇ TILs.
  • CD8+ and CD4+ TILs were assessed for the expression of CD 137, PD-1, CTLA-4, LAG-3, TIM-3 and SLAM (Fig. 42).
  • CD4+ TILs expression for all three populations of interest were in the range of 39.8-47.7%, 61.0-64.4%, 52.7-57.6, and 65.6-72.1% for LAG-3, PD-1, SLAM, and TIM-3, respectively.
  • CD8+ TILs expression ranged between 86.7-88.2%, 38.2- 46.5%, 61.5-67.2%, and 90.0-94.3% for LAG-3, PD-1, SLAM, and TIM-3, respectively.
  • CTLA- 4 ranged between 8.92-15.2% and 4.10-7.29%, and CD137 was 2.80-8.30% and 7.70-17.1%, for CD4+ and CD8+ cells, respectively.
  • PD-1+ TIL frequency was only higher in comparison to the anti-FOLRl- Td TILs but not the Non-Td TILs (46.5 ⁇ 21.1% vs 38.2 ⁇ 19.6% vs 40.6 ⁇ 26.8%, respectively).
  • CoStAR modification of TILs for coinhibitory or costimulatory marker expression was little observed except for the slight but significant increase in the frequency of CD8+ CD137+, CTLA4+, and PD-1+ TILs.
  • T cell subset frequency was assessed in TIL samples, using markers for Treg detection in addition to the expression of TCRaP and TCRyb.
  • the majority of the CD3+ cells expressed TCRaP (90.0-93.5%) with relatively few TCRyb cells (1.35-3.08%) detected (Fig. 43A) and no differences were observed between the three populations.
  • the detection frequencies were 0.63 ⁇ 0.48%, 0.66 ⁇ 0.36% and 0.93 ⁇ 0.63% for non-Td, anti-FOLRl CoStAR- and anti-FOLRl CoStAR+ Td TILs, respectively (Fig. 43B).
  • the detection frequencies were 0.63 ⁇ 0.48%, 0.66 ⁇ 0.36% and 0.93 ⁇ 0.63% for non-Td, anti-FOLRl CoStAR- and anti-FOLRl CoStAR+ Td TILs, respectively (Fig. 43B).
  • the detection frequencies were 0.63 ⁇ 0.48%, 0.66 ⁇ 0.36% and 0.93 ⁇ 0.63% for non-Td, anti-FOLRl CoStAR- and anti-FOLRl CoStAR+ Td TILs, respectively (Fig. 43B).
  • TILs were assessed the ability of the cells to produce cytokines upon mitogenic activation using PMA/ionomycin.
  • the Non-Td and Td TILs were activated for 4 hours using PMA/ionomycin and then stained for IFNy, IL-22, IL-17A, and TNFa from CD3+, CD4+, and CD8+ cells.
  • high frequencies of CD3+ TILs expressing TNFa (61.8-73-6%) and IFNY (32.5-42.0%), and lower frequencies of IL-22 (4.74-8.07%) and IL-17A (5.74-11.0%) expressing cells were detected (Fig. 44A).
  • TNFa+ cells were higher in anti- FOLR1 CoStAR+ Td compared to anti-FOLRl CoStAR- Td TILs (73.6 ⁇ 14% vs 61.8 ⁇ 18.3%), but not Non-Td TILs (72.1 ⁇ 9.20%).
  • CD4+ TILs high frequencies of cells expressing TNFa (54.3-67.2%), and lower frequencies of IFNy (19.3-26.2%), IL-22 (7.63-10.5%) and IL-17A (12.0-20.2%) expressing cells were detected (Fig. 44B).
  • Complete rapid expansion protocol (REP) medium consisted of 460 mL GIBCO custom Pl 58718 supplemented with 40 mL human AB serum, gentamycin (10 pg/mL) / amphotericin (0.25 pg/mL) and vancomycin (50 pg/mL).
  • Complete T cell medium (TCM) consisted of 450 mL RPMI 1640 GlutaMAXTM Supplement HEPES medium supplemented with 5 mL Penicillin-Streptomycin, 500 pL 2 -Mercaptoethanol (50 mM), and 50 mL Fetal Bovine Serum (FBS).
  • Non-Td and Td TILs from five OC samples were produced as described in ITIL-306- NC-010 and the transduction percentages are shown in Table 17.
  • TILs were either used directly after the REP or upon thaw from long-term cry opreservation (-150°C; stored in cryoprotectant consisting of FBS with 10 % DMSO). ovarian cancer TILs were thawed using a 37°C water bath, transferred to a 50 mL Falcon tube with 10 mL of complete REP TCM, centrifuged at 400 x g for 5 minutes and resuspended in complete REP TCM.
  • Both post-REP and post- thaw TILs were counted using the NovoCyte 3005 Flow Cytometer System following DRAQ7 dead cell exclusion and a CD2+ count and placed in T75 flasks at a density of IxlO 6 cells/mL in complete REP TCM supplemented with 3000 lU/ml of interleukin 2 (IL-2). The cells were then placed in a 5% CO2 incubator set to 37°C for 2-3-days. Before the assay, TILs were resuspended in complete REP TCM at a density of IxlO 6 cells/mL without IL-2 and placed in a 5% CO2 incubator set to 37°C overnight.
  • IL-2 interleukin 2
  • the quantification of FOLR1 expression was conducted according to the following gating strategy: a cell gate (forward scatter- height [FSC]-H vs side scatter-height [SSC]-H), then a doublet exclusion gate (SSC-H vs side scatter-area [SSC-A]) followed by a dead cell exclusion gate (SSC-A vs Fixable Viability dye eFluor 450).
  • the CD2-cells were then gated from which the frequency of the FOLR1+ cells were quantified (SSC-A vs FOLR1-PE).
  • Non-Td and anti-FOLRl CoStAR Td TILs were cocultured at a 1 : 1 effector to target ratio (E:T, IxlO 5 TILs : IxlO 5 target cells) with either autologous tumor digests, K-562, or OVCAR-3 derived engineered cell lines as targets.
  • Cocultures took place in 96 well round bottom plates with 200 pL complete TCM supplemented with lx Brefeldin A and were incubated in a 5% CO2 incubator set to 37°C for 16 hours.
  • TILs or target cells alone were used as negative controls, and positive control TILs were activated with 50 ng/mL phorbol-myristate-acetate (PMA) and 1 pg/mL ionomycin. All conditions were performed in triplicates.
  • PMA phorbol-myristate-acetate
  • cytokine production was performed using a panel with antibodies against CD3, CD4, CD8, CoStAR (anti-idiotype 19.1 primary and anti-mouse IgGl secondary antibodies), tumor necrosis factor alpha (TNFa), IL-2, and a viability stain. Following the 16-hour incubation, cocultures were harvested by centrifugation at 500 x g for 4 minutes. The supernatant was discarded, and samples were analyzed by flow cytometry. Briefly, cells were labelled using 100 pl of fixable viability dye (1 : 1000 diluted in PBS) and incubated for 10 minutes at room temperature.
  • cells were washed using BD stain buffer, centrifuged at 500 x g for 4 minutes, and cell pellets were resuspended in 100 pl of BD stain buffer with FcR blocking reagent for 10 minutes at room temperature.
  • cells were washed once with BD stain buffer and fixed using 4% paraformaldehyde (PF A) for 15 minutes at room temperature.
  • PF A paraformaldehyde
  • Cells were then resuspended in 100 pl of BD stain buffer with CD3, CD4, CD8, anti-mouse IgGl, TNFa, and IL-2 and incubated at 4°C for 25 minutes. Following two more wash steps using BD perm/wash buffer, cell pellets were resuspended in 100 pl of BD stain buffer for acquisition on NovoCyte 3005 Flow Cytometer System.
  • CD3+ cells were gated from the live gate (SSC-A vs CD3-A) and then CD4+ and CD8+ cells were gated from the CD3+ gate (CD4-A vs CD8-A).
  • TNFa and IL-2 producing cells were reported from the CoStAR negative (-) subset for the Non-Td TILs, and both CoStAR- and CoStAR positive (+) fractions from the Td TILs (anti-FOLRl CoStAR- Td TILs and anti-FOLRl CoStAR+ Td TILs).
  • non-Td and anti-FOLRl CoStAR Td TILs were cocultured at a 1 : 1 ratio (E:T, 1x105 TILs : IxlO 5 target cells) with autologous tumor digests and at a 8: 1 ratio (E:T, IxlO 5 TILs : 1.25xl0 4 target cells) with K-562 or BA/F3 derived engineered cell lines. Cocultures were performed in 200 pL complete TCM in triplicate.
  • TILs or target cells alone were used as negative controls, and TILs activated with 50 ng/mL phorbol-myristate-acetate (PMA) and 1 pg/mL ionomycin were used as a positive control.
  • PMA phorbol-myristate-acetate
  • ionomycin 1 pg/mL ionomycin
  • Non-Td and anti-FOLRl CoStAR Td TILs were cocultured at a 1 : 1 ratio (E:T, IxlO 5 TILs : IxlO 5 target cells) with BA/F3 derived engineered cell lines. Cocultures were performed in 96 well round bottom plates with 200 pL complete TCM in triplicate, and incubated for 20 hours in a 5% CO2 incubator set to 37°C. TILs and target cells were cultured alone as negative controls.
  • Target cell counts were enumerated by flow cytometry after doublet and dead cell exclusion.
  • CD2-cells were gated from the live gate (SSC-A vs CD2-A) and quantified by the absolute count function of the NovoCyte 3005 Flow Cytometer System.
  • Non-Td or Td TILs in 100 pL TCM were added to OVCAR-3 derived engineered cell lines (E:T ratios of 1 :5 and 1 :30, respectively). These were incubated at room temperature for 30 minutes prior to 169 hours of further cell index readings upon the RTCA Analyzer (37 °C, 5 % CO2). Control conditions included wells containing target cell lines alone, target cell lines with 0.5 % Triton X-100 added at OC TIL loading time-point (full lysis control), and TILs alone.
  • the normalized cell index (NCI) was determined according to manufacturer’s instructions using RTCA software pro.
  • IL-2+ or TNFa+ TILs were detected in tumor digests cultured overnight (16 hours) alone with brefeldin A.
  • IL-2+ and TNFa+ TILs were detected upon 16-hour coculture of expanded TIL with autologous tumor digest (Fig. 46).
  • CD4+ anti-FOLRl CoStAR+ Td TILs were characterized by significantly higher frequency of IL-2 producing cells compared to Non-Td TILs with a marked 6.56-fold increase (12.0 ⁇ 12.9% vs 1.83 ⁇ 0.55%) (Fig. 46A).
  • CD4+ anti-FOLRl CoStAR+ Td TILs also had a 3.33-fold increase in IL-2 producing cell frequencies compared to anti-FOLRl CoStAR- Td TILs (12.0 ⁇ 12.9% vs 3.61 ⁇ 3.10%).
  • a slight but significant increase in the number of anti-FOLRl CoStAR+ CD4 T cells producing TNFa (6.96 ⁇ 3.56%) when cultured alone relative to anti- FOLRl CoStAR- Td TILs (2.58 ⁇ 1.60%), but not Non-Td TILs (3.31 ⁇ 3.62%) was also detected (Fig. 46C).
  • TNFa+ cells Upon coculture with the autologous digest, TNFa+ cells seemed to increase in frequency in the anti-FOLRl CoStAR ⁇ Td TIL population, although a statistically significant difference compared to anti-FOLRl CoStAR- Td and Non-Td TILs was not observed (32.3% vs 17.8% vs 11.6%).
  • CD8+ TNFa producing cell frequencies were increased in the anti-FOLRl CoStAR+ Td TILs relative to anti-FOLRl CoStAR-Td and Non-Td TILs, however, these differences did not reach statistical significance (22.6% vs 12.5% vs 10.5%) (Fig. 46D).
  • TNFa 55.0 pg/mL vs 18.2 pg/mL, Fig. 47B
  • IL-13 152 pg/mL vs 48.4 pg/mL, Fig. 47C
  • TNFa 55.0 pg/mL vs 18.2 pg/mL, Fig. 47B
  • IL-13 152 pg/mL vs 48.4 pg/mL, Fig. 47C
  • MHC blocking antibodies prevent TCRs from engaging their target and mediating TCR signaling.
  • Non-Td and Td TILs were cocultured with autologous tumor digest in the presence of MHC blocking, or irrelevant isotype control antibodies, and TIL anti-tumor activity was measured by ZFNy release (Fig. 48).
  • CoStAR modification enhanced the cytokine production in response to autologous tumor (Fig. 47)
  • percentage reduction relative to TILs cocultured with autologous digest without blocking agents was assessed. The percentage of cytokine release was not significantly different between Non-Td and Td TILs in any of the conditions assessed.
  • Intracellular flow cytometry was used to enumerate cytokine producing cells after 16- hour coculture with engineered K-562 and OVCAR-3 cell lines (Fig. 49).
  • IL-2 producing cell frequencies in response to K-562 and K-562-FOLR1 were minimal for CD4+ (1.47-4.17%) and CD8+ (0.23-3.73%) cells across all populations of interest (Fig. 49A).
  • Culture with K-562-OKT3 resulted in IL-2+ cell frequencies of 23.0-34.0% and 20.0-39.7% for CD4+ and CD8+ cell populations, respectively.
  • TILs cultured alone or cocultured with OVCAR-3 were characterized by minimal frequencies of IL-2 producing cells for both CD4+ (0.78-1.38%) and CD8+ (0.22-0.80%) populations (Fig. 49A).
  • Upon stimulation with both signals provided by the OVCAR-3-OKT3 cell line a significant increase in the frequency of IL-2 producing cells was observed by the anti- FOLRl CoStAR+ Td TILs (39.1 ⁇ 14.5%) in the CD4+ population with a 1.74- and a 2.46-fold increase in comparison to anti-FOLRl CoStAR- Td TILs (22.4 ⁇ 14.0%) and Non-Td TILs (15.9 ⁇ 9.47%), respectively.
  • anti-FOLRl CoStAR+ Td TILs (34.1 ⁇ 13.2%) demonstrated a 2.65- and 2.36-fold increase in IL-2 producing cell frequencies compared to anti-FOLRl CoStAR- Td TILs (12.9 ⁇ 10.2%) and Non-Td TILs (14.5 ⁇ 9.58%), respectively.
  • CD4+ TNFa positive cell frequencies were significantly higher in the anti-FOLRl CoStAR+ Td TILs cocultured with K-562-OKT3 compared to anti-FOLRl CoStAR- Td TILs (75.9 ⁇ 8.35% vs 66.2 ⁇ 5.04%), and with K-562-FOLR1 compared to Non-Td TILs (12.6 ⁇ 7.08% vs 0.73 ⁇ 0.34%) (Fig. 49B). No significance was observed in the same conditions for the CD8+ TNFa positive cell populations.
  • MSD immunoassay was used to evaluate levels of secreted cytokines upon coculture with K-562 and BA/F3 engineered cell lines (Table 18). Cytokine secretion was minimal in cocultures with wild type cell lines or those engineered to express signal 2 alone (Fig. 50). IL-2 release stimulated by K-562-OKT3-FOLR1 cell lines was higher in the Td TILs (2682 pg/mL) compared to the Non-Td TILs (521.5 pg/mL) demonstrating a 5.14-fold increase (Fig. 50A).
  • IL-2 secretion was 9.31-fold higher in the Td TILs compared to Non- Td TILs (Fig. 50A).
  • Significantly higher TNFa production was also detected in Td TILs compared to Non-Td TILs when cocultured with K-562-OKT3-FOLR1 (2337 pg/ml vs 1211 pg/mL, 1.93- fold increase) and BA/F3-OKT3-FOLR1 (900.3 pg/mL vs 278.0 pg/mL, 3.24-fold increase).
  • IL- 13 and IFNy production was also significantly higher upon stimulation with cell lines expressing both signals (Fig. 50C-D). More specifically, in response to stimulation with K- 562-OKT3-FORL1 Td TILs secreted high levels of IL-13 (1590 pg/mL) compared with Non-Td TILs (587.0 pg/mL), showing a 2.71fold higher secretion by OKT3-FORL1 Td TILs. Similarly, a 2.26-fold higher amount of IFNy was observed in OKT3-FORL1 Td TILs (194559 pg/mL) vs Non-Td TILs (86183 pg/mL).
  • IL-13 and IFNy concentrations were significantly elevated in Td TILs cocultured with BA/F3-OKT3-FOLR1 over Non-Td TILs in the same conditions with a 4.35- (983.9 pg/mL vs 226.1 pg/mL) and 5.13-fold (65594 pg/mL vs 12786 pg/mL) greater cytokine secretion, respectively (Fig. 50C-D).
  • CD40 signaling motif mutant constructs CTP198, CTP197, CTP196, CTP199, and CTP195 were designed and individually incorporated into a CD40 wild type signaling motif, which contained the CD34 marker gene for sorting (Fig. 61). These constructs were then expressed in vitro, and screened for transcriptional changes compared to wild type CD40 (data not shown).
  • TRAF domains and their influence on CoStAR signalling can be monitored by a series of mutations to either inhibit TRAF binding, inhibit expression of TRAF, modulate the TRAF binding motif, or swap TRAF domains.
  • TRAF domains of CD40 were swapped in the constructs as shown in Table 17, and in Fig. 67. There was a total of 12 mutant CD40 constructs generated, as well as one wild type CD40 construct, and one “mock” construct of a CoStAR without CD40.
  • Each construct was transduced into primary human pan T cells obtained from STEM cell (#Cat 70024) from one of three donors.
  • the proliferation of TRAF variant T cells expressing each construct was then assessed in a co-culture with Ba/f3.1uc.puro.FOLRl.OKT3 at an effector to target ratio of 8:1.
  • the proliferation experiment pipeline was conducted as shown in Figs. 62A- 62B. These experiments were conducted in 96 well plates, wherein cells were treated with or without 200 units/mL IL-2 to activate dynabeads.
  • TRAF variant CoStAR T cells For the manufacturing of TRAF variant CoStAR T cells, cells were transduced after two days, dynabeads were removed at day 5, and flow cytometry was then used to detect the expression of CoStAR at day 6 (Fig. 62A). Day 9-23 then followed 14 days of REP.
  • TRAF variant proliferation experiment cells were given 200 units/mL IL-2 for three days, followed by one day of IL-2 starvation. On day 4, flow cytometry was again used to detect expression of CoStAR. Cells were co-cultured with Ba/f3.1uc.puro.FOLRl.OKT3 at an effector to target ratio of 8: 1 on day 5. On days 12, 19, and 26, proliferation was assessed (as “Days 7, 14, and 21” in the figures). In addition, supernatant was collected when changing media for cytokine MSD analysis and a short term 24 co-culture experiment was set up for cytokine MSD analysis.
  • CTP411 and CTP413 had increased proliferation with and without IL-2 for HD donor 702C in comparison to CD28-CD40 CoSTAR (CTP205) and CD28 CoStAR (CTP343) by day 21 of the co-culture.
  • CTP410 had improved proliferation in the presence of IL-2 only in comparison to CD28-CD40 CoSTAR (CTP205) by day 21.
  • CTP408 (TRAF2/3 variant), CTP409 & CTP410 (TRAF2 variant), CTP411, CTP412 (TRAF6 variants) and CTP421 had increased proliferation in comparison to CD28-CD40 CoSTAR (CTP205) and CD28 CoStAR (CTP343) when treated with IL-2 by day 7.
  • CD28-CD40 CoStAR (CTP205) had the highest rate of proliferation for donor HD 1004 without IL-2.
  • CD28-CD40 CoStAR (CTP205) had the highest rate of proliferation for donor HD 2000 with IL-2 .
  • CTP411 (TRAF 6 variant) had the highest rate of proliferation for donor HD 2000 without IL-2 in comparison to CD28-CD40 CoSTAR (CTP205) and CD28 CoStAR (CTP343).
  • M0V19 CoStAR contains the variable heavy (VH) and variable light (VL) chains of the anti-folate receptor antibody M0V19 (Figini et al. 1998 and CAA68252.1 and CAA68253.1).
  • the heavy and light chains were joined with a codon optimised for human nucleotide sequence encoding a S(G4S)x3 serine-glycine linker region in the orientation of VH-VL, with addition of a codon optimised for human sequence for the OSM signal peptide. Following the VL region a codon optimised for human sequence encoding a AAA(GSG)x2 motif was included.
  • the signalling domain consists of a fusion of codon optimised for human sequences for CD28 (NP_006130.1: residues 21-220) fused directly to CD40 (NP_001241.1: residues 216-277). Constructs were gene synthesised by GenScript and cloned into pSF.Lenti (Oxford Genetics).
  • Lentiviral production was performed using a three- plasmid packaging system by mixing 10 pg of each packaging plasmid, plus 10 pg of the pSF.Lenti lentiviral plasmid containing the transgene, together in serum free RPMI containing 50 mM CaCL. The mixture was added dropwise to a 50% confluent monolayer of 293T cells in 75 cm 2 flasks. The viral supernatants were collected at 48 and 72h post transfection, pooled and concentrated using LentiPac lentiviral supernatant concentration (GeneCopoeia, Rockville, Maryland, USA) solution according to the manufacturer’s instructions.
  • LentiPac lentiviral supernatant concentration GeneCopoeia, Rockville, Maryland, USA
  • Lentiviral supernatants titrated on Jurkat T cells and then used to directly infect primary human T cells at an MOI 5 in the presence of 4 pg/ml polybrene (Sigma- Aldrich).
  • Human peripheral blood pan T-cells (StemCell Technologies) were activated for 24 hours with DynabeadsTM Human T-activator beads (Invitrogen) according to the manufacturer’s instructions before addition of lentiviral supernatants.
  • Cell transduction was assessed 4 days post infection using FRa.hFc protein (Aero Biosystems) and anti-IgG-PE secondary (Sigma- Aldrich). Cells were then expanded further using xlO donor mismatched irradiated PBMC feeders at a 1 :200 ratio in RPMI + 10% FCS with the addition of 30 ng/mL OKT3 and 200 lU/mL IL-2 After 14 days the cells were cryopreserved ready for assay. After thaw the cells were rested for 3 days and then starved for 24-48 h in the absence of 11-2 prior to assay set up. Cells were also stained for CoStAR expression 24 h prior to assay set up.
  • Functionality assays were performed by mixing CoStAR positive or negative cells with Ba/F3 cells expressing a membrane anchored OKT3 single chain antibody fragment.
  • 5xl0 4 T cells were mixed with 6,250 target cells (E:T 8: 1) at day 0, in the preence and absence of exogenous IL-2 (200IU/mL) and T cell counts made after 7 days. Additional Ba/F3 target cells were added at 8: 1 at day 7, with multiple rounds of stimulation performed up to day 21.
  • TRAF domains in the TRAF2, 2/3 and 6 regions which were assigned randomly based on the TRAF consensus sequences, CD28 followed by just the TRAF2/3 binding domain flanked by 5 C- and N-terminal amino acids, or CD28 alone (lacking the entirety of the TRAF domain containing CD40 regions assigned here as MOV19.CD28 or ACD40). Additional mock transduced cells were included.
  • Fig. 68 outlines the transduction levels for each receptor and each donor.
  • CoStAR expression was normalized to the expression of the lowest transduction efficiency in each individual donor using excess mock transduced cells. By doing this we were able to start each donor at an equivalent transduction level to mitigate any effect that expression might have on overall performance.
  • donor 702C this was A2-6 at 30.4%, and for donors 1004 and 2000 this was the 2 -2/3-6 variant at 27.3 and 42.6% respectively.
  • T cells were cocultured with Ba/F3-OKT3 cells at an E:T of 8: 1 in the presence and absence of 200IU/mL IL-2 and counts made at days 7, 14 and 21 in the presence and absence of exogenous IL-2.
  • Fold change compared to base line was plotted for each donor and each receptor and also for all three donors combined.
  • swapping the TRAF6 domain did not dramatically impair the function of CoStAR compared to the wild-type receptor, and in some instances an enhancement in proliferation was observed, particularly at day 21 (Figs. 69A-69F and 73 A-73D). This effect was still observable in the absence of IL-2 but was less pronounced.
  • TRAF2/3 domain from CD40 to a basic CD28 CoStAR was not sufficient to mediate an enhancement in activity compared to the wild type receptor, and random TRAF domains based on consensus sequences were equally less efficient than the wildtype receptor and mediating T cell proliferation in the presence and absence of IL-2, particularly the latter (Figs. 73A-73D and 74A-74D).
  • the inventors also assessed cytokine production from CoStAR variant T-cells. To this end, coculture experiments were set up between T cells and BA/F3.OKT3.FRa cells (providing signal 1 and 2). Supernatants were harvested after 20 hours and analysed for TNFa, IL-2 and IFNy secretion by MSD (Figs. 90A-90C). In general, wild type CD28.CD40 CoStAR+ cells induced greater cytokine production compared to mock transduced counterparts, and CoStAR containing CD28 alone (ACD40).
  • TRAF variantions were more variable but clearerst with IL-2 as a readout where variations to the TRAF2/3 domain (PVQE-TQEE, PVQE-SKEE and PVQE-AVEE) generally reduced IL-2 production compared to wild-type receptor, as did variants to the TRAF2 domain (SVQE-AVEE and SVQE-PEEE).
  • Variations to the TRAF6 domain had more variable effects, but noticeably the PQEINF-PPENYE variant had a noticeable effect on increasing all three cytokines analysed compared to the wildtype receptor.
  • Transduced T cells were cocultured in absence of IL-2 for 6-8 days with LoVo.OKT3.GFP tumor cells at 8: 1 effector to target ratio, changing half of the culture medium every 3-4 days.
  • LoVo.OKT3.GFP naturally expresses CEA and PD-L1 on their surface, conferring both signal 2 and signal 1 (0KT3) to the transduced T cells.
  • the viability and absolute count were assessed, and live T cells were rechallenged for an additional week with fresh LoVo.OKT3.GFP tumor cells as described above.
  • the viability and absolute count were measured, and the fold expansion was calculated (Fig. 91B), and IL-2 levels were assessed (Fig. 91 A).

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Abstract

La présente invention concerne un récepteur antigénique chimérique costimulateur (CoStAR) utile dans une thérapie cellulaire adoptive (ACT), ainsi que les cellules comprenant le CoStAR. Le CoStAR peut agir en tant que modulateur de l'activité cellulaire améliorant les réponses à des antigènes définis. La présente invention concerne également des protéines du CoStAR, des acides nucléiques codant celles-ci et leurs utilisations thérapeutiques.
PCT/US2023/060937 2022-01-20 2023-01-19 Récepteurs fournissant une costimulation ciblée destinée à une thérapie cellulaire adoptive WO2023141530A2 (fr)

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