US20200368283A1 - Non-hla restricted t cell receptors and uses thereof - Google Patents

Non-hla restricted t cell receptors and uses thereof Download PDF

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US20200368283A1
US20200368283A1 US16/990,185 US202016990185A US2020368283A1 US 20200368283 A1 US20200368283 A1 US 20200368283A1 US 202016990185 A US202016990185 A US 202016990185A US 2020368283 A1 US2020368283 A1 US 2020368283A1
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cell
antigen
tcr
locus
certain embodiments
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Michel Sadelain
Jorge A. Mansilla-Soto
Justin Eyquem
Anton Dobrin
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Memorial Sloan Kettering Cancer Center
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Memorial Sloan Kettering Cancer Center
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Priority to US16/990,185 priority Critical patent/US20200368283A1/en
Priority to US17/075,142 priority patent/US11229669B2/en
Publication of US20200368283A1 publication Critical patent/US20200368283A1/en
Priority to US17/505,515 priority patent/US12036244B2/en
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    • A61K38/177—Receptors; Cell surface antigens; Cell surface determinants
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    • A61K39/4631—Chimeric Antigen Receptors [CAR]
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    • A61K39/4632—T-cell receptors [TCR]; antibody T-cell receptor constructs
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    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
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    • A61K39/464416—Receptors for cytokines
    • A61K39/464417—Receptors for tumor necrosis factors [TNF], e.g. lymphotoxin receptor [LTR], CD30
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    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
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    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
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    • C07K2317/56—Immunoglobulins specific features characterized by immunoglobulin fragments variable (Fv) region, i.e. VH and/or VL
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    • C12N2510/00—Genetically modified cells

Definitions

  • the presently disclosed subject matter provides methods and compositions for enhancing the immune response toward cancers and pathogens. It relates to novel designs of T cell receptors (TCRs) and engineered immunoresponsive cells comprising the same.
  • TCRs T cell receptors
  • the engineered immunoresponsive cells comprising the novel TCRs are antigen-directed.
  • Adoptive immunotherapy using antigen recognizing receptors has shown remarkable clinical results in the treatment of leukemia and is one of the most promising new strategies to treat cancer.
  • CARs chimeric antigen receptors
  • current clinical protocols employ autologous T cells and randomly integrating vectors, including gamma-retroviral, lentiviral and transposons, which all result in semi-random integration and variable expression of the CAR owing to transgene variegation.
  • the conjunction of autologous cell sourcing and random vector integration is prone to generating cell products with variable potency.
  • novel designs of antigen recognizing receptors having consistent potency and increased ability to detect low levels of target antigen.
  • the presently disclosed subject matter generally provides HLA-independent (or non-HLA restricted) T cell receptors (referred to as “HI-TCRs”) that bind to an antigen of interest in an HLA-independent manner and immunoresponsive cells comprising thereof.
  • HLA-TCRs HLA-independent T cell receptors
  • the presently disclosed subject matter also provides methods of using such cells for inducing and/or enhancing an immune response to a target antigen, and/or treating and/or preventing neoplasia or other diseases/disorders where an increase in an antigen-specific immune response is desired.
  • TCR T cell receptor
  • the constant domain comprises a native or modified TRAC peptide, and/or a native or modified TRBC peptide. In certain embodiments, the constant domain is capable of forming a homodimer or a heterodimer with another constant domain.
  • the recombinant TCR is expressed from an expression cassette placed in an endogenous TRAC locus and/or a TRBC locus of an immunoresponsive cell.
  • the placement of the recombinant TCR expression cassette disrupts or abolishes the endogenous expression of a TCR comprising a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell.
  • the placement of the recombinant TCR expression cassette prevents or eliminates mispairing between the recombinant TCR and a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell.
  • the antigen binding chain is capable of associating with a CD3 ⁇ polypeptide.
  • the antigen binding chain upon binding to an antigen, is capable of activating the CD3 ⁇ polypeptide associated to the antigen binding chain.
  • the activation of the CD3 ⁇ polypeptide is capable of activating an immunoresponsive cell.
  • the CD3 ⁇ polypeptide can be endogenous or exogenous.
  • the CD3 ⁇ polypeptide is endogenous and is endogenous and integrated in the native CD3 ⁇ complex.
  • the CD3 ⁇ polypeptide is exogenous and optionally integrated with a co-stimulatory molecule selected from the group consisting of a CD28 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS polypeptide, a DAP-10 polypeptide and any combination thereof.
  • the antigen binding chain further comprises a co-stimulatory region, wherein the recombinant TCR, upon binding to an antigen, is capable of stimulating an immunoresponsive cell.
  • the co-stimulatory region can include a co-stimulatory molecule selected from the group consisting of a CD28 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS polypeptide, a DAP-10 polypeptide and any combination thereof.
  • the co-stimulatory region comprises a CD28 polypeptide.
  • the recombinant TCR is capable of associating with a CD3 complex. In certain embodiments, the recombinant TCR is capable of integrating with a CD3 complex and providing HLA-independent antigen recognition. In certain embodiments, the CD3 complex is endogenous. In certain embodiments, the recombinant TCR replaces an endogenous TCR in a CD3/TCR complex.
  • the extracellular antigen-binding domain is capable of dimerizing with another extracellular antigen-binding domain.
  • the extracellular antigen-binding domain can include a ligand for a cell-surface receptor, a receptor for a cell surface ligand, an antigen binding portion of an antibody or a fragment thereof or an antigen binding portion of a TCR.
  • the extracellular antigen-binding domain comprises a heavy chain variable region (V H ) of an antibody, or a VHH from a camelid V H -only antibody and/or a light chain variable region (V L ) of an antibody.
  • V H heavy chain variable region
  • V L light chain variable region
  • the extracellular antigen-binding domain is capable of dimerizing with another extracellular antigen-binding domain.
  • the extracellular antigen-binding domain comprises a V H of an antibody, wherein the human, murine, or camelid V H is capable of dimerizing with another extracellular antigen-binding domain comprising a V L of the antibody and form a fragment variable (Fv).
  • the extracellular antigen-binding domain comprises a V L of an antibody, wherein the V L is capable of dimerizing with another extracellular antigen-binding domain comprising a V H of the antibody and form a fragment variable (Fv).
  • the recombinant TCR binds to a tumor antigen.
  • the tumor antigen can be selected from the group consisting of CD19, MUC16, MUC1, CA1X, CEA, CD8, CD7, CD10, CD20, CD22, CD30, CLL1, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, EGP-2, EGP-40, EpCAM, erb-B2,3,4, FBP, Fetal acetylcholine receptor, folate receptor-a, GD2, GD3, HER-2, hTERT, a2, K-light chain, KDR, LeY, L1 cell adhesion molecule, MAGE-A1, Mesothelin, ERBB2, MAGEA3, p53, MART1, GP100, Proteinase3 (PR1), Tyrosinase, Survivin, hTERT, EphA2, NKG2D ligands, NY-ES0-1, on
  • the recombinant TCR exhibits greater antigen sensitivity than a CAR targeting the same antigen. In certain embodiments, the recombinant TCR is capable of inducing an immune response when binds to an antigen that has a low density on the surface of a tumor cell. In certain embodiments, the antigen that has a low density on the cell surface has below about 2,000 molecules per cell.
  • the presently disclosed subject matter further provides immunoresponsive cells comprising a recombinant TCR described herein.
  • the expression cassette of at least one antigen binding chain of the recombinant TCR is placed at an endogenous gene locus of the immunoresponsive cell.
  • the expression cassettes of two antigen binding chains of the recombinant TCR are placed at an endogenous gene locus of the immunoresponsive cell, wherein the two antigen binding chains are capable of dimerization.
  • the placement of the expression cassette of the recombinant TCR can disrupt or abolish the endogenous expression of a TCR comprising a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell, whereby preventing or eliminating mispairing between the recombinant TCR and a native TCR chain and/or a native TCR ⁇ chain in the immunoresponsive cell.
  • the endogenous gene locus can be a CD3 ⁇ locus, a CD3 ⁇ locus, a CD247 locus, a B2M locus, a TRAC locus, a TRBC locus or a TRGC locus or a TRDC locus.
  • the endogenous gene locus is a TRAC locus and/or a TRBC locus.
  • the endogenous gene locus can include a modified transcription terminator region.
  • the modified transcription terminator region comprises a genomic element selected from the group consisting of a TK transcription terminator, a GCSF transcription terminator, a TCRA transcription terminator, an HBB transcription terminator, a bovine growth hormone transcription terminator, a SV40 transcription terminator and a P2A element; the P2A element allows the use of the endogenous transcription terminator of the targeted gene.
  • one or more other endogenous T cell receptor locus in the cell is modified to eliminate the expression of an endogenous TCR chain.
  • the one or more other endogenous T cell receptor loci are further modified to express a gene of interest.
  • the gene of interest can be an anti-tumor cytokine, a co-stimulatory molecule ligand, a tracking gene or a suicide gene.
  • one or more endogenous TCR loci are further modified to incorporate a sequence encoding co-stimulatory signaling domain(s) to generate a TCR chain containing such signaling domain(s) at the carboxy terminus.
  • the immunoresponsive cell is selected from the group consisting of a T cell, a cytotoxic T lymphocyte (CTL), a regulatory T cell, a Natural Killer T (NKT) cell, a human embryonic stem cell, and a pluripotent stem cell from which lymphoid cells may be differentiated.
  • the immunoresponsive cell is autologous.
  • the immunoresponsive cell further comprises at least one exogenous co-stimulatory ligand.
  • the co-stimulatory ligand is selected from the group consisting of CD80, CD86, 41BBL, CD275, CD40L, OX40L and any combination thereof.
  • the cell further comprises or consists of one exogenous co-stimulatory ligand.
  • the one exogenous co-stimulatory ligand is CD80 or 4-1BBL.
  • the cell further comprises or consists of two exogenous co-stimulatory ligands.
  • the two exogenous co-stimulatory ligands are CD80 and 4-1BBL.
  • the immunoresponsive cell further comprises at least one chimeric costimulatory receptor (CCR).
  • CCR chimeric costimulatory receptor
  • the CCR comprising a co-stimulatory molecule selected from the group consisting of a CD28 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS polypeptide, a DAP-10 polypeptide and any combination thereof.
  • the presently disclosed subject matter also provides pharmaceutical compositions comprising the immunoresponsive cell(s) disclosed herein and a pharmaceutically acceptable excipient.
  • the pharmaceutical composition can be used for treating a neoplasia.
  • the method comprises administering to the subject an effective amount of the immunoresponsive cells described herein or the pharmaceutical composition described herein.
  • the presently disclosed subject matter also provides methods of treating or preventing a neoplasm.
  • the method comprises administering to the subject an effective amount of the immunoresponsive cells described herein or the pharmaceutical composition described herein.
  • the neoplasm can be selected from the group consisting of blood cancer, B cell leukemia, multiple myeloma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia, non-Hodgkin's lymphoma and adenocarcinoma.
  • the neoplasm is B cell leukemia, multiple myeloma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia, or non-Hodgkin's lymphoma, and the recombinant TCR binds to CD19.
  • the neoplasm is B cell leukemia, multiple myeloma, acute lymphoblastic leukemia (ALL), chronic lymphocytic leukemia, an adenocarcinoma, or non-Hodgkin's lymphoma
  • the recombinant TCR binds to CD19, MUC16, MUC1, CA1X, CEA, CD8, CD7, CD10, CD20, CD22, CD30, CLL1, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, EGP-2, EGP-40, EpCAM, erb-B2,3,4, FBP, Fetal acetylcholine receptor, folate receptor-a, GD2, GD3, HER-2, hTERT, IL-13R-a2, K-light chain, KDR, LeY, L1 cell adhesion molecule, MAGE-A1, Mesothelin (MSLN), ERBB2, MAGEA
  • ALL acute
  • the presently disclosed subject matter further provides methods for producing an antigen-specific immunoresponsive cell.
  • the method comprises introducing into an immunoresponsive cell a nucleic acid sequence encoding a recombinant TCR described herein.
  • the nucleic acid sequence can be comprised in a vector.
  • the expression cassette of at least one antigen binding chain of the recombinant TCR is placed at an endogenous gene locus of the immunoresponsive cell.
  • the expression cassettes of two antigen binding chains of the recombinant TCR are placed at an endogenous gene locus of the immunoresponsive cell, wherein the two antigen binding chains are capable of dimerization.
  • the endogenous gene locus can be a CD3 ⁇ locus, a CD3 ⁇ locus, a CD247locus, a B2M locus, a TRAC locus, a TRBC locus, a TRDC locus and/or a TRGC locus.
  • the endogenous gene locus is a TRAC locus or a TRBC locus.
  • the placement of the expression cassette of the recombinant TCR disrupts or abolishes the endogenous expression of a TCR comprising a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell, whereby preventing or eliminating mispairing between the recombinant TCR and a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell.
  • the endogenous gene locus comprises a modified transcription terminator region.
  • the modified transcription terminator region comprises a genomic element selected from the group consisting of a TK transcription terminator, a GCSF transcription terminator, a TCRA transcription terminator, an HBB transcription terminator, a bovine growth hormone transcription terminator, an SV40 transcription terminator and a P2A element.
  • a genomic element selected from the group consisting of a TK transcription terminator, a GCSF transcription terminator, a TCRA transcription terminator, an HBB transcription terminator, a bovine growth hormone transcription terminator, an SV40 transcription terminator and a P2A element.
  • one or more other endogenous T cell receptor locus in the cell is modified to eliminate the expression of an endogenous TCR chain.
  • the one or more other endogenous T cell receptor locus are further modified to express a gene of interest.
  • the gene of interest is an anti-tumor cytokine, a co-stimulatory molecule ligand, a tracking gene or a suicide gene.
  • the presently disclosed subject matter further provides nucleotide acids encoding a recombinant TCR described herein, and nucleic acid compositions comprising a recombinant TCR described herein.
  • the nucleic acid sequences are comprised in a vector.
  • the presently disclosed subject matter also provides vectors comprising the nucleic acid composition described herein.
  • kits comprising a recombinant TCR described herein, an immunoresponsive cell described herein, a pharmaceutical composition described herein, a nucleic acid composition described herein, or a vector described herein.
  • the kit further comprises written instructions for treating and/or preventing a neoplasm, a pathogen infection, an autoimmune disorder, or an allogeneic transplant.
  • Illustrative neoplasms for which the presently disclosed subject matter can be used include, but are not limited to leukemias (e.g., acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia a, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, chronic leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia), polycythemia vera, lymphoma (Hodgkin's disease, non-Hodgkin's disease), Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors such as sarcomas and carcinomas (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angio
  • the presently disclosed subject matter further provides use of any recombinant TCR, any pharmaceutical composition or any immunoresponsive cell disclosed herein for used in a therapy.
  • FIGS. 1A-1E depict HLA-Independent TCR-based Chimeric Antigen Receptor HIT (HIT-CAR, i.e., HI-TCR or HIT) and gene targeting strategy at the TRAC locus in human T cells.
  • FIG. 1A depicts schematic representation of the T Cell Receptor (TCR), the B Cell Receptor (BCR), a Chimeric Antigen Receptor (CAR) and the HLA-Independent TCR-based Chimeric Antigen Receptor (HIT-CAR, i.e., HI-TCR or HIT).
  • FIG. 1B depicts CRISPR/Cas9-targeted integration of the 3 receptors into the TRAC locus.
  • FIG. 1C depicts representative TCR/Mouse F(ab′)2 flow cytometry plots 4 days after TRAC targeting.
  • the TCR antibody epitope recognize the constant chain of the TCR alpha and beta.
  • FTL firefly luciferase
  • NALM-6 targets cells
  • FIGS. 2A-2B depict expression and therapeutic efficacy of HI-TCR.
  • FIG. 2A depicts representative TCR/Mouse F(ab′)2 flow cytometry plots 4 days after TRAC targeting.
  • FIG. 2B depicts Kaplan-Meier analysis of the mice survival where NALM-6-bearing mice were treated with 5 ⁇ 10 5 CAR T cells.
  • FIGS. 3A-3E depict gene targeting strategy and expression of NYESO TCR.
  • FIG. 3A depicts schematic representation of the NYESO TCR genes integrated into the TCR alpha or beta chain.
  • FIG. 3B depicts representative TCR-V-beta-1 flow cytometry plots 4 days after TRAC or TRBC targeting.
  • FIG. 3D depicts schematic representation of a co-targeting into both the TCR alpha and the TCR beta.
  • E Representative TCR-V-beta-1/4-1BBL flow cytometry plots 4 days after TRAC and TRBC co-targeting.
  • FIGS. 4A-4C depict strategy of integrating a CAR into a TRAC locus and modulation the expression by various transcriptional termination signals/3′ unstranslated regions (3′UTR).
  • FIG. 4A depicts schematic representation of the 1928z CAR gene integrated into the TRAC locus.
  • Poly A black box
  • FIG. 4B depicts representative CAR flow plots 3 days after TRAC (left panel). and geometric mean fluorescence intensity (gMFI), MFI, and Median values for the CAR-expressing population (right panel). Boxed is the original 3′UTR sequence of bovine growth hormone poly A.
  • FIGS. 5A and 5B depict efficacy of genetically integrated CARs with different 3′UTR sequences.
  • FIGS. 6A-6C depict HIT gene targeting at the TRAC locus in human T cells.
  • FIG. 6A depicts CRISPR/Cas9-targeted CAR or HIT gene integration into the TRAC locus. Top, TRAC locus; middle, rAAV6 containing the CAR cassette flanked by homology arms; bottom, rAAV6 containing the HIT cassette flanked by homology arms.
  • FIG. 6B depicts representative CAR/HIT flow plots 4 days after transfection of T cells with Cas9 mRNA and TRAC gRNA and addition of AAV6. CAR and HIT surface protein were detected using a goat anti-mouse IgG.
  • FIGS. 7A-7B depict HIT T cells outperform CAR T cells at killing target cells expressing low antigen levels.
  • Nalm6 cell line expressing firefly luciferase
  • FIG. 7B depicts cytotoxic activity using an 4h bioluminescence assay, using NALM6 as targets cells expressing different CD19 levels and CAR (red squares) or HIT (blue circles) T cells at 1:1 effector (E): target (T) ratio.
  • FIGS. 8A-8C depict HIT T cells outperform CAR T cells at killing target cells expressing low antigen levels. Cytotoxic activity using an 18 h bioluminescence assay, using NALM6 as targets cells expressing different CD19 levels (indicated at the right), which were incubated with untransduced T cells ( FIG. 8A ), CAR T cells ( FIG. 8B ), and HIT T cells ( FIG. 8C ) at different effector (E): target (T) ratios.
  • FIGS. 9A-9D depict HIT T cells expressing costimulatory ligands outperform CAR T cells in controlling established B-ALL tumor with very low CD19 levels.
  • FIG. 9A depicts untransduced (black) vs CAR (red) T cells.
  • FIG. 9B depicts CAR (red) vs HIT (green) T cells.
  • FIG. 9C depicts T cells expressing HIT alone (green), HIT+CD80 co-stimulatory ligand (orange), HIT+41BBL co-stimulatory ligand (pink), or HIT+CD80+41BBL co-stimulatory ligands (blue).
  • FIG. 9D depicts mouse survival analysis.
  • FIGS. 10A-10C depict that baseline TRAC-CAR expression can be controlled by distinct 3′UTR sequences without affecting cell surface replenishment kinetic after antigen encounter.
  • FIG. 10A depicts CRISPR/Cas9-targeted CAR gene integration into the TRAC locus.
  • the targeting construct (AAV) contains the 1928z CAR coding sequence followed by a 3′UTR sequence, flanked by sequences homologous to the TRAC locus (LHA and RHA, left and right homology arm).
  • FIG. 10B depicts each 3′UTR sequence provides different CAR surface levels (measured by FACS).
  • FIG. 10C depicts CAR T cells were stimulated once (indicated by a red arrow) with CD19-expressing 3T3 cells, and CAR MFI was measured every 24h over a 3-day period. All CAR T cells show similar CAR expression regulation.
  • the presently disclosed subject matter provides HLA-independent (or non-HLA restricted) T cell receptors (referred to as “HI-TCRs”) that bind to an antigen of interest in an HLA-independent manner.
  • the HI-TCRs are TCR molecules where the TCR variable domain is replaced by the variable domain from an antibody (Fv), resulting in a FvTCR.
  • the HI-TCR can bind to a tumor antigen or a pathogen antigen.
  • the presently disclosed subject matter also provides cells, including genetically modified immunoresponsive cells (e.g., T cells, NKT cells, or CTL cells) comprising the presently disclosed HI-TCR.
  • binding of the antigen by the HI-TCR is capable of activating the immunoresponsive cell.
  • the presently disclosed subject matter also provides methods of using such cells for inducing and/or enhancing an immune response to a target antigen, and/or treating and/or preventing neoplasia or other diseases/disorders where an increase in an antigen-specific immune response is desired.
  • the term “about” or “approximately” means within an acceptable error range for the particular value as determined by one of ordinary skill in the art, which will depend in part on how the value is measured or determined, i.e., the limitations of the measurement system. For example, “about” can mean within 3 or more than 3 standard deviations, per the practice in the art. Alternatively, “about” can mean a range of up to about 20%, e.g., up to about 10%, up to about 5%, or up to about 1% of a given value. Alternatively, particularly with respect to biological systems or processes, the term can mean within an order of magnitude, e.g., within about 5-fold or within about 2-fold, of a value.
  • an immunoresponsive cell By “activates an immunoresponsive cell” is meant induction of signal transduction or changes in protein expression in the cell resulting in initiation of an immune response. For example, when CD3 Chains cluster in response to ligand binding and immunoreceptor tyrosine-based inhibition motifs (ITAMs) a signal transduction cascade is produced.
  • ITAMs immunoreceptor tyrosine-based inhibition motifs
  • a formation of an immunological synapse occurs that includes clustering of many molecules near the bound receptor (e.g. CD4 or CD8, CD3 ⁇ / ⁇ / ⁇ / ⁇ , etc.). This clustering of membrane bound signaling molecules allows for ITAM motifs contained within the CD3 chains to become phosphorylated.
  • This phosphorylation in turn initiates a T cell activation pathway ultimately activating transcription factors, such as NF- ⁇ B and AP-1.
  • transcription factors induce global gene expression of the T cell to increase IL-2 production for proliferation and expression of master regulator T cell proteins in order to initiate a T cell mediated immune response.
  • an immunoresponsive cell By “stimulates an immunoresponsive cell” is meant a signal that results in a robust and sustained immune response. In various embodiments, this occurs after immune cell (e.g., T-cell) activation or concomitantly mediated through receptors including, but not limited to, CD28, CD137 (4-1BB), OX40, CD40 and ICOS.
  • immune cell e.g., T-cell
  • receptors including, but not limited to, CD28, CD137 (4-1BB), OX40, CD40 and ICOS.
  • Receiving multiple stimulatory signals can be important to mount a robust and long-term T cell mediated immune response. T cells can quickly become inhibited and unresponsive to antigen. While the effects of these co-stimulatory signals may vary, they generally result in increased gene expression in order to generate long lived, proliferative, and anti-apoptotic T cells that robustly respond to antigen for complete and sustained eradication.
  • antigen recognizing receptor refers to a receptor that is capable of activating an immune or immunoresponsive cell (e.g., a T-cell) in response to its binding to an antigen.
  • antigen recognizing receptors include native or endogenous T cell receptors (“TCRs”), and chimeric antigen receptors (“CARs”).
  • the term “antibody” means not only intact antibody molecules, but also fragments of antibody molecules that retain immunogen-binding ability. Such fragments are also well known in the art and are regularly employed both in vitro and in vivo. Accordingly, as used herein, the term “antibody” means not only intact immunoglobulin molecules but also the well-known active fragments F(ab′) 2 , and Fab. F(ab′) 2 , and Fab fragments that lack the Fc fragment of intact antibody, clear more rapidly from the circulation, and may have less non-specific tissue binding of an intact antibody (Wahl et al., J. Nucl. Med. 24:316-325 (1983).
  • antibodies include whole native antibodies, bispecific antibodies; chimeric antibodies; Fab, Fab′, single chain V region fragments (scFv), fusion polypeptides, and unconventional antibodies.
  • an antibody is a glycoprotein comprising at least two heavy (H) chains and two light (L) chains inter-connected by disulfide bonds.
  • Each heavy chain is comprised of a heavy chain variable region (abbreviated herein as V H ) and a heavy chain constant (C H ) region.
  • the heavy chain constant region is comprised of three domains, CH1, CH2 and CH3.
  • Each light chain is comprised of a light chain variable region (abbreviated herein as V L ) and a light chain constant C L region.
  • the light chain constant region is comprised of one domain, C L .
  • the V H and V L regions can be further sub-divided into regions of hypervariability, termed complementarity determining regions (CDR), interspersed with regions that are more conserved, termed framework regions (FR).
  • CDR complementarity determining regions
  • FR framework regions
  • Each V H and V L is composed of three CDRs and four FRs arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, FR4.
  • the variable regions of the heavy and light chains contain a binding domain that interacts with an antigen.
  • the constant regions of the antibodies may mediate the binding of the immunoglobulin to host tissues or factors, including various cells of the immune system (e.g., effector cells) and the first component (C1 q) of the classical complement system.
  • CDRs are defined as the complementarity determining region amino acid sequences of an antibody which are the hypervariable regions of immunoglobulin heavy and light chains. See, e.g., Kabat et al., Sequences of Proteins of Immunological Interest, 4th U. S. Department of Health and Human Services, National Institutes of Health (1987). Generally, antibodies comprise three heavy chain and three light chain CDRs or CDR regions in the variable region. CDRs provide the majority of contact residues for the binding of the antibody to the antigen or epitope. In certain embodiments, the CDRs regions are delineated using the Kabat system (Kabat, E. A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242).
  • single-chain variable fragment is a fusion protein of the variable regions of the heavy (V H ) and light chains (V L ) of an immunoglobulin covalently linked to form a V H ::V L heterodimer.
  • the V H and V L are either joined directly or joined by a peptide-encoding linker (e.g., 10, 15, 20, 25 amino acids), which connects the N-terminus of the V H with the C-terminus of the V L , or the C-terminus of the V H with the N-terminus of the V L .
  • the linker is usually rich in glycine for flexibility, as well as serine or threonine for solubility.
  • Single chain Fv polypeptide antibodies can be expressed from a nucleic acid including V H - and V L -encoding sequences as described by Huston, et al. (Proc. Nat. Acad. Sci. USA, 85:5879-5883, 1988). See, also, U.S. Pat. Nos. 5,091,513, 5,132,405 and 4,956,778; and U.S. Patent Publication Nos. 20050196754 and 20050196754.
  • Antagonistic scFvs having inhibitory activity have been described (see, e.g., Zhao et al., Hyrbidoma (Larchmt) 2008 27(6):455-51; Peter et al., J Cachexia Sarcopenia Muscle 2012 Aug. 12; Shieh et al., J Imunol 2009 183(4):2277-85; Giomarelli et al., Thromb Haemost 2007 97(6):955-63; Fife eta., J Clin Inst 2006 116(8):2252-61; Brocks et al., Immunotechnology 1997 3(3):173-84; Moosmayer et al., Ther Immunol 1995 2(10:31-40).
  • affinity is meant a measure of binding strength. Affinity can depend on the closeness of stereochemical fit between antibody combining sites and antigen determinants, on the size of the area of contact between them, and/or on the distribution of charged and hydrophobic groups. As used herein, the term “affinity” also includes “avidity”, which refers to the strength of the antigen-antibody bond after formation of reversible complexes. Methods for calculating the affinity of an antibody for an antigen are known in the art, including, but not limited to, various antigen-binding experiments, e.g., functional assays (e.g., flow cytometry assay).
  • chimeric antigen receptor refers to a molecule comprising an extracellular antigen-binding domain that is fused to an intracellular signaling domain that is capable of activating or stimulating an immunoresponsive cell, and a transmembrane domain.
  • the extracellular antigen-binding domain of a CAR comprises a scFv.
  • the scFv can be derived from fusing the variable heavy and light regions of an antibody. Alternatively or additionally, the scFv may be derived from Fab's (instead of from an antibody, e.g., obtained from Fab libraries).
  • the scFv is fused to the transmembrane domain and then to the intracellular signaling domain.
  • the CAR has a high binding affinity or avidity for the antigen.
  • nucleic acid molecules include any nucleic acid molecule that encodes a polypeptide of interest or a fragment thereof. Such nucleic acid molecules need not be 100% homologous or identical with an endogenous nucleic acid sequence, but may exhibit substantial identity. Polynucleotides having “substantial identity” or “substantial homology” to an endogenous sequence are typically capable of hybridizing with at least one strand of a double-stranded nucleic acid molecule. By “hybridize” is meant a pair to form a double-stranded molecule between complementary polynucleotide sequences (e.g., a gene described herein), or portions thereof, under various conditions of stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods Enzymol. 152:399; Kimmel, A. R. (1987) Methods Enzymol. 152:507).
  • stringent salt concentration will ordinarily be less than about 750 mM NaCl and 75 mM trisodium citrate, e.g., less than about 500 mM NaCl and 50 mM trisodium citrate, or less than about 250 mM NaCl and 25 mM trisodium citrate.
  • Low stringency hybridization can be obtained in the absence of organic solvent, e.g., formamide, while high stringency hybridization can be obtained in the presence of at least about 35% formamide, e.g., at least about 50% formamide.
  • Stringent temperature conditions will ordinarily include temperatures of at least about 30° C., at least about 37° C., or at least about 42° C.
  • Varying additional parameters, such as hybridization time, the concentration of detergent, e.g., sodium dodecyl sulfate (SDS), and the inclusion or exclusion of carrier DNA, are well known to those skilled in the art. Various levels of stringency are accomplished by combining these various conditions as needed. In certain embodiments, hybridization will occur at 30° C. in 750 mM NaCl, 75 mM trisodium citrate, and 1% SDS. In certain embodiments, hybridization will occur at 37° C. in 500 mM NaCl, 50 mM trisodium citrate, 1% SDS, 35% formamide, and 100 ⁇ g/ml denatured salmon sperm DNA (ssDNA).
  • SDS sodium dodecyl sulfate
  • hybridization will occur at 42° C. in 250 mM NaCl, 25 mM trisodium citrate, 1% SDS, 50% formamide, and 200 ⁇ g/ml ssDNA. Useful variations on these conditions will be readily apparent to those skilled in the art.
  • wash stringency conditions can be defined by salt concentration and by temperature. As above, wash stringency can be increased by decreasing salt concentration or by increasing temperature.
  • stringent salt concentration for the wash steps can be less than about 30 mM NaCl and 3 mM trisodium citrate, e.g., less than about 15 mM NaCl and 1.5 mM trisodium citrate.
  • Stringent temperature conditions for the wash steps will ordinarily include a temperature of at least about 25° C., of at least about 42° C., or of at least about 68° C. In certain embodiments, wash steps will occur at 25° C.
  • wash steps will occur at 42° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. In certain embodiments, wash steps will occur at 68° C. in 15 mM NaCl, 1.5 mM trisodium citrate, and 0.1% SDS. Additional variations on these conditions will be readily apparent to those skilled in the art. Hybridization techniques are well known to those skilled in the art and are described, for example, in Benton and Davis (Science 196:180, 1977); Grunstein and Rogness (Proc. Natl. Acad.
  • substantially identical or “substantially homologous” is meant a polypeptide or nucleic acid molecule exhibiting at least about 50% homologous or identical to a reference amino acid sequence (for example, any one of the amino acid sequences described herein) or nucleic acid sequence (for example, any one of the nucleic acid sequences described herein).
  • a reference amino acid sequence for example, any one of the amino acid sequences described herein
  • nucleic acid sequence for example, any one of the nucleic acid sequences described herein.
  • such a sequence is at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 99%, or at least about 100% homologous or identical to the sequence of the amino acid or nucleic acid used for comparison.
  • Sequence identity can be measured by using sequence analysis software (for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705, BLAST, BESTFIT, GAP, or PILEUP/PRETTYBOX programs). Such software matches identical or similar sequences by assigning degrees of homology to various substitutions, deletions, and/or other modifications. Conservative substitutions typically include substitutions within the following groups: glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid, asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. In an exemplary approach to determining the degree of identity, a BLAST program may be used, with a probability score between e-3 and e-100 indicating a closely related sequence.
  • sequence analysis software for example, Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology
  • analog is meant a structurally related polypeptide or nucleic acid molecule having the function of a reference polypeptide or nucleic acid molecule.
  • ligand refers to a molecule that binds to a receptor. In certain embodiments, the ligand binds to a receptor on another cell, allowing for cell-to-cell recognition and/or interaction.
  • disease is meant any condition, disease or disorder that damages or interferes with the normal function of a cell, tissue, or organ, e.g., neoplasia, and pathogen infection of cell.
  • an “effective amount” is meant an amount sufficient to have a therapeutic effect. In certain embodiments, an “effective amount” is an amount sufficient to arrest, ameliorate, or inhibit the continued proliferation, growth, or metastasis (e.g., invasion, or migration) of a neoplasia.
  • enforcing tolerance is meant preventing the activity of self-reactive cells or immunoresponsive cells that target transplanted organs or tissues.
  • endogenous is meant a nucleic acid molecule or polypeptide that is normally expressed in a cell or tissue.
  • exogenous is meant a nucleic acid molecule or polypeptide that is not endogenously present in a cell, or not present at a level sufficient to achieve the functional effects obtained when over-expressed.
  • the term “exogenous” would therefore encompass any recombinant nucleic acid molecule or polypeptide expressed in a cell, such as foreign, heterologous, and over-expressed nucleic acid molecules and polypeptides.
  • exogenous nucleic acid is meant a nucleic acid not present in a native wild-type cell; for example, an exogenous nucleic acid may vary from an endogenous counterpart by sequence, by position/location, or both.
  • an exogenous nucleic acid may have the same or different sequence relative to its native endogenous counterpart; it may be introduced by genetic engineering into the cell itself or a progenitor thereof, and may optionally be linked to alternative control sequences, such as a non-native promoter or secretory sequence.
  • heterologous nucleic acid molecule or polypeptide is meant a nucleic acid molecule (e.g., a cDNA, DNA or RNA molecule) or polypeptide that is not normally present in a cell or sample obtained from a cell.
  • This nucleic acid may be from another organism, or it may be, for example, an mRNA molecule that is not normally expressed in a cell or sample.
  • immunoresponsive cell is meant a cell that functions in an immune response or a progenitor, or progeny thereof.
  • modulate is meant positively or negatively alter.
  • exemplary modulations include a about 1%, about 2%, about 5%, about 10%, about 25%, about 50%, about 75%, or about 100% change.
  • alteration is meant to alter positively by at least about 5%.
  • An alteration may be by about 5%, about 10%, about 25%, about 30%, about 50%, about 75%, about 100% or more.
  • alter is meant to alter negatively by at least about 5%.
  • An alteration may be by about 5%, about 10%, about 25%, about 30%, about 50%, about 75%, or even by about 100%.
  • isolated cell is meant a cell that is separated from the molecular and/or cellular components that naturally accompany the cell.
  • isolated refers to material that is free to varying degrees from components which normally accompany it as found in its native state. “Isolate” denotes a degree of separation from original source or surroundings. “Purify” denotes a degree of separation that is higher than isolation.
  • a “purified” or “biologically pure” protein is sufficiently free of other materials such that any impurities do not materially affect the biological properties of the protein or cause other adverse consequences. That is, a nucleic acid or peptide is purified if it is substantially free of cellular material, viral material, or culture medium when produced by recombinant DNA techniques, or chemical precursors or other chemicals when chemically synthesized.
  • Purity and homogeneity are typically determined using analytical chemistry techniques, for example, polyacrylamide gel electrophoresis or high performance liquid chromatography.
  • the term “purified” can denote that a nucleic acid or protein gives rise to essentially one band in an electrophoretic gel.
  • modifications for example, phosphorylation or glycosylation, different modifications may give rise to different isolated proteins, which can be separately purified.
  • antigenic determinant refers to a domain capable of specifically binding a particular antigenic determinant or set of antigenic determinants present on a cell.
  • Linker shall mean a functional group (e.g., chemical or polypeptide) that covalently attaches two or more polypeptides or nucleic acids so that they are connected to one another.
  • a “peptide linker” refers to one or more amino acids used to couple two proteins together (e.g., to couple V H and V L domains).
  • the linker comprises a sequence set forth in GGGGSGGGGSGGGGS [SEQ ID NO: 31].
  • Neoplasm is meant a disease characterized by the pathological proliferation of a cell or tissue and its subsequent migration to or invasion of other tissues or organs. Neoplasia growth is typically uncontrolled and progressive, and occurs under conditions that would not elicit, or would cause cessation of, multiplication of normal cells.
  • Neoplasia can affect a variety of cell types, tissues, or organs, including but not limited to an organ selected from the group consisting of bladder, bone, brain, breast, cartilage, glia, esophagus, fallopian tube, gallbladder, heart, intestines, kidney, liver, lung, lymph node, nervous tissue, ovaries, pancreas, prostate, skeletal muscle, skin, spinal cord, spleen, stomach, testes, thymus, thyroid, trachea, urogenital tract, ureter, urethra, uterus, and vagina, or a tissue or cell type thereof.
  • Neoplasia include cancers, such as sarcomas, carcinomas, or plasmacytomas (malignant tumor of the plasma cells).
  • the neoplasm is a solid tumor.
  • Illustrative neoplasms for which the presently disclosed subject matter can be used include, but are not limited to leukemias (e.g., acute leukemia, acute lymphocytic leukemia, acute myelocytic leukemia a, acute myeloblastic leukemia, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute monocytic leukemia, acute erythroleukemia, chronic leukemia, chronic myelocytic leukemia, chronic lymphocytic leukemia), polycythemia vera, lymphoma (Hodgkin's disease, non-Hodgkin's disease), Waldenstrom's macroglobulinemia, heavy chain disease, and solid tumors such as sarcomas and carcinomas (e.g., fibrosarcoma, myxosarcoma, liposarcoma, chondrosarcoma, osteogenic sarcoma, chordoma, angio
  • receptor is meant a polypeptide, or portion thereof, present on a cell membrane that selectively binds one or more ligand.
  • a T cell that recognizes a tumor can expresses a receptor (e.g., a TCR or CAR) that binds to a tumor antigen.
  • a receptor e.g., a TCR or CAR
  • scFv-antigen binding by a cell expressing a CAR and an scFv may be compared to the level of scFv-antigen binding in a corresponding cell expressing CAR alone.
  • secreted is meant a polypeptide that is released from a cell via the secretory pathway through the endoplasmic reticulum, Golgi apparatus, and as a vesicle that transiently fuses at the cell plasma membrane, releasing the proteins outside of the cell.
  • leader sequence is meant a peptide sequence (e.g., 5, 10, 15, 20, 25 or 30 amino acids) present at the N-terminus of newly synthesized proteins that directs their entry to the secretory pathway.
  • exemplary leader sequences include, but is not limited to, the IL-2 signal sequence: MYRMQLLSCIALSLALVTNS [SEQ ID NO: 12] (human), MYSMQLASCVTLTLVLLVNS [SEQ ID NO: 13] (mouse); the kappa leader sequence: METPAQLLFLLLLWLPDTTG [SEQ ID NO: 14] (human), METDTLLLWVLLLWVPGSTG [SEQ ID NO: 15] (mouse); the CD8 leader sequence: MALPVTALLLPLALLLHAARP [SEQ ID NO: 16] (human); the truncated human CD8 signal peptide: MALPVTALLLPLALLLHA [SEQ ID NO: 28] (human); the albumin signal sequence: MKWVTFISL
  • telomere binding binds is meant a polypeptide or fragment thereof that recognizes and binds to a biological molecule of interest (e.g., a polypeptide), but which does not substantially recognize and bind other molecules in a sample, for example, a biological sample, which naturally includes a presently disclosed polypeptide.
  • a biological molecule of interest e.g., a polypeptide
  • tumor antigen refers to an antigen (e.g., a polypeptide) that is uniquely or differentially expressed on a tumor cell compared to a normal or non-IS neoplastic cell.
  • a tumor antigen includes any polypeptide expressed by a tumor that is capable of activating or inducing an immune response via an antigen recognizing receptor (e.g., CD19, MUC-16) or capable of suppressing an immune response via receptor-ligand binding (e.g., CD47, PD-L1/L2, B7.1/2).
  • an antigen recognizing receptor e.g., CD19, MUC-16
  • receptor-ligand binding e.g., CD47, PD-L1/L2, B7.1/2
  • treatment refers to clinical intervention in an attempt to alter the disease course of the individual or cell being treated, and can be performed either for prophylaxis or during the course of clinical pathology.
  • Therapeutic effects of treatment include, without limitation, preventing occurrence or recurrence of disease, alleviation of symptoms, diminishment of any direct or indirect pathological consequences of the disease, preventing metastases, decreasing the rate of disease progression, amelioration or palliation of the disease state, and remission or improved prognosis.
  • a treatment can prevent deterioration due to a disorder in an affected or diagnosed subject or a subject suspected of having the disorder, but also a treatment may prevent the onset of the disorder or a symptom of the disorder in a subject at risk for the disorder or suspected of having the disorder.
  • mammals include, but are not limited to, humans, primates, farm animals, sport animals, rodents and pets.
  • Non-limiting examples of non-human animal subjects include rodents such as mice, rats, hamsters, and guinea pigs;
  • immunocompromised refers to a subject who has an immunodeficiency.
  • the subject is very vulnerable to opportunistic infections, infections caused by organisms that usually do not cause disease in a person with a healthy immune system, but can affect people with a poorly functioning or suppressed immune system.
  • HLA-Independent T Cell Receptor HLA-Independent T Cell Receptor
  • the present disclosure provides an HI-TCR that binds to an antigen of interest in an HLA-independent manner.
  • binding of the antigen is capable of activating an immunoresponsive cell comprising the HI-TCR.
  • the HI-TCR comprises an antigen binding chain.
  • the antigen binding chain comprises an extracellular antigen-binding domain.
  • the extracellular antigen-binding domain is derived from a scFv, Fab, or antibody of murine, human or camelid (e.g., lama ) origin.
  • the antigen binding chain further comprises a constant domain.
  • the HI-TCR binds to a tumor antigen.
  • Any tumor antigen (antigenic peptide) can be used in the tumor-related embodiments described herein.
  • Sources of antigen include, but are not limited to, cancer proteins.
  • the antigen can be expressed as a peptide or as an intact protein or portion thereof.
  • the intact protein or a portion thereof can be native or mutagenized.
  • tumor antigens include carbonic anhydrase IX (CA1X), carcinoembryonic antigen (CEA), CD8, CD7, CD10, CD19, CD20, CD22, CD30, CD33, CLL1, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, CD123, CD44V6, an antigen of a cytomegalovirus (CMV) infected cell (e.g., a cell surface antigen), epithelial glycoprotein-2 (EGP-2), epithelial glycoprotein-40 (EGP-40), epithelial cell adhesion molecule (EpCAM), receptor tyrosine-protein kinases erb-B2,3,4 (erb-B2,3,4), folate-binding protein (FBP), fetal acetylcholine receptor (AChR), folate receptor- ⁇ , Ganglioside G2 (GD2), Ganglioside G3 (GD3), human Epidermal Growth
  • CMV
  • the HI-TCR binds to CD19. In certain embodiments, the HI-TCR binds to a human CD19 polypeptide. In certain embodiments, the human CD19 polypeptide comprises the amino acid sequence set forth in SEQ ID NO: 11.
  • the HI-TCR binds to the extracellular domain of a CD19 protein.
  • the HI-TCR binds to a pathogen antigen, e.g., for use in treating and/or preventing a pathogen infection or other infectious disease, for example, in an immunocompromised subject.
  • pathogen includes a virus, bacteria, fungi, parasite and protozoa capable of causing disease.
  • Retroviridae e.g. human immunodeficiency viruses, such as HIV-1 (also referred to as HDTV-III, LAVE or HTLV-III/LAV, or HIV-III; and other isolates, such as HIV-LP; Picornaviridae (e.g. polio viruses, hepatitis A virus; enteroviruses, human Coxsackie viruses, rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause gastroenteritis); Togaviridae (e.g. equine encephalitis viruses, rubella viruses); Flaviridae (e.g.
  • Coronoviridae e.g. coronaviruses
  • Rhabdoviridae e.g. vesicular stomatitis viruses, rabies viruses
  • Filoviridae e.g. ebola viruses
  • Paramyxoviridae e.g. parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus
  • Orthomyxoviridae e.g. influenza viruses
  • Bungaviridae e.g.
  • African swine fever virus African swine fever virus
  • Non-limiting examples of bacteria include Pasteurella, Staphylococci, Streptococcus, Escherichia coli, Pseudomonas species , and Salmonella species.
  • infectious bacteria include but are not limited to, Helicobacter pyloris, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria sps (e.g. M. tuberculosis, M. avium, M. intracellulare, M. kansaii, M.
  • the pathogen antigen is a viral antigen present in Cytomegalovirus (CMV), a viral antigen present in Epstein Barr Virus (EBV), a viral antigen present in Human Immunodeficiency Virus (HIV), or a viral antigen present in influenza virus.
  • CMV Cytomegalovirus
  • EBV Epstein Barr Virus
  • HAV Human Immunodeficiency Virus
  • influenza virus a viral antigen present in influenza virus.
  • the antigen binding chain comprises an extracellular antigen-binding domain.
  • the extracellular antigen-binding domain specifically binds to an antigen, e.g., a tumor antigen or a pathogen antigen, e.g., those disclosed in Section 2.1.
  • the extracellular antigen-binding domain is capable of dimerizing with another extracellular antigen-binding domain (e.g., forming a fragment variable (Fv)), wherein the dimerized antigen-binding domains (e.g., an Fv) specifically bind to an antigen, e.g., a tumor antigen or a pathogen antigen.
  • Fv fragment variable
  • the extracellular antigen-binding domain comprises a ligand for a cell-surface receptor. In certain embodiments, the extracellular antigen-binding domain comprises a receptor for a cell surface ligand.
  • the extracellular antigen-binding domain specifically binds to an antigen, e.g., a tumor antigen or a pathogen antigen.
  • the antigen binding chain is capable of forming a dimer with another antigen binding chain.
  • the HI-TCR comprises a heterodimer comprising two different antigen binding chains.
  • the HI-TCR comprises a homodimer comprising two identical antigen binding chains.
  • the antigen binding chains dimerize through one or more disulfide-links.
  • the antigen binding chain is capable of forming a trimer or oligomer with one or more identical or different antigen binding chains.
  • the extracellular antigen-binding domain is capable of dimerizing with another extracellular antigen-binding domain (e.g., forming a fragment variable (Fv)), wherein the dimerized antigen-binding domains (e.g., a Fv) specifically bind to an antigen, e.g., a tumor antigen or a pathogen antigen.
  • another extracellular antigen-binding domain e.g., forming a fragment variable (Fv)
  • the dimerized antigen-binding domains e.g., a Fv
  • an antigen e.g., a tumor antigen or a pathogen antigen.
  • the extracellular antigen-binding domain of the HI-TCR (for example, an Fv or an analog thereof) binds to an antigen with a dissociation constant (K d ) of about 2 ⁇ 10 ⁇ 7 M or less.
  • K d dissociation constant
  • the K d is about 2 ⁇ 10 ⁇ 7 M or less, about 1 ⁇ 10 ⁇ 7 M or less, about 9 ⁇ 10 ⁇ 8 M or less, about 1 ⁇ 10 ⁇ 8 M or less, about 9 ⁇ 10 ⁇ 9 M or less, about 5 ⁇ 10 ⁇ 9 M or less, about 4 ⁇ 10 ⁇ 9 M or less, about 3 ⁇ 10 ⁇ 9 or less, about 2 ⁇ 10 ⁇ 9 M or less, or about 1 ⁇ 10 ⁇ 9 M or less.
  • the K d is about 3 ⁇ 10 ⁇ 9 M or less. In certain non-limiting embodiments, the K d is from about 1 ⁇ 10 ⁇ 9 M to about 3 ⁇ 10 ⁇ 7 M. In certain non-limiting embodiments, the K d is from about 1.5 ⁇ 10 ⁇ 9 M to about 3 ⁇ 10 ⁇ 7 M. In certain non-limiting embodiments, the K d is from about 1.5 ⁇ 10 ⁇ 9 M to about 2.7 ⁇ 10 ⁇ 7 M.
  • Binding of the extracellular antigen-binding domain can be confirmed by, for example, enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), FACS analysis, bioassay (e.g., growth inhibition), or Western Blot assay.
  • ELISA enzyme-linked immunosorbent assay
  • RIA radioimmunoassay
  • FACS FACS analysis
  • bioassay e.g., growth inhibition
  • Western Blot assay Western Blot assay.
  • Each of these assays generally detect the presence of protein-antibody complexes of particular interest by employing a labeled reagent (e.g., an antibody, or an Fv) specific for the complex of interest.
  • the Fv can be radioactively labeled and used in a radioimmunoassay (RIA) (see, for example, Weintraub, B., Principles of Radioimmunoassays, Seventh Training Course on Radioligand Assay Techniques, The Endocrine Society, March, 1986, which is incorporated by reference herein).
  • the radioactive isotope can be detected by such means as the use of a ⁇ counter or a scintillation counter or by autoradiography.
  • the extracellular antigen-binding domain is labeled with a fluorescent marker.
  • Non-limiting examples of fluorescent markers include green fluorescent protein (GFP), blue fluorescent protein (e.g., EBFP, EBFP2, Azurite, and mKalama1), cyan fluorescent protein (e.g., ECFP, Cerulean, and CyPet), and yellow fluorescent protein (e.g., YFP, Citrine, Venus, and YPet).
  • GFP green fluorescent protein
  • blue fluorescent protein e.g., EBFP, EBFP2, Azurite, and mKalama1
  • cyan fluorescent protein e.g., ECFP, Cerulean, and CyPet
  • yellow fluorescent protein e.g., YFP, Citrine, Venus, and YPet
  • the extracellular antigen-binding domain comprises an antigen binding portion of a TCR.
  • the extracellular antigen-binding domain comprises an antigen binding portion of an antibody or a fragment thereof.
  • the extracellular antigen-binding domain comprises a heavy chain variable region (V H ) and/or a light chain variable region (V L ) of an antibody.
  • the extracellular antigen-binding domain comprises a single-chain variable fragment (scFv).
  • the extracellular antigen-binding domain comprises a heavy chain-only antibodies (VHH).
  • the extracellular antigen-binding domain comprises a Fab, which is optionally crosslinked.
  • the extracellular antigen-binding domain comprises a F(ab) 2 .
  • any of the foregoing molecules can be comprised in a fusion protein with a heterologous sequence to form the extracellular antigen-binding domain.
  • the extracellular antigen-binding domain comprises a heavy chain variable region (V H ) and/or a light chain variable region (V L ) of an antibody, wherein the V H or the V L is capable of dimerizing with another extracellular antigen-binding domain comprising a V L or a V H (e.g., forming a fragment variable (Fv)).
  • the Fv is a human Fv.
  • the Fv is a humanized Fv.
  • the Fv is a murine Fv.
  • the Fv is identified by screening a Fv phage library with an antigen-Fc fusion protein.
  • Additional extracellular antigen-binding domains targeting an interested antigen can be obtained by sequencing an existing scFv or a Fab region of an existing antibody targeting the same antigen.
  • the dimerized extracellular antigen-binding domain of a presently disclosed HI-TCR is a murine Fv.
  • the dimerized extracellular antigen-binding domain is an Fv that binds to a human CD19 polypeptide.
  • the extracellular antigen-binding domain is an Fv, which comprises the amino acid sequence of SEQ ID NO: 9 and specifically binds to a human CD19 polypeptide (e.g., a human CD19 polypeptide comprising the amino acid sequence set forth in SEQ ID NO: 11).
  • the nucleotide sequence encoding the amino acid sequence of SEQ ID NO: 9 is set forth in SEQ ID NO: 10.
  • the Fv comprises a heavy chain variable region (V H ) comprising the amino acid sequence set forth in SEQ ID NO: 7.
  • the Fv comprises a light chain variable region (V L ) comprising the amino acid sequence set forth in SEQ ID NO: 8.
  • the Fv comprises V H comprising the amino acid sequence set forth in SEQ ID NO: 7 and a V L comprising the amino acid sequence set forth in SEQ ID NO: 8.
  • the extracellular antigen-binding domain comprises a V H comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous or identical to SEQ ID NO: 7.
  • the extracellular antigen-binding domain comprises a V H comprising an amino acid sequence that is at least about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% homologous or identical to SEQ ID NO: 7.
  • the extracellular antigen-binding domain comprises a V H comprising the amino sequence set forth in SEQ ID NO: 7.
  • the extracellular antigen-binding domain comprises a V L comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous to SEQ ID NO: 8.
  • the extracellular antigen-binding domain comprises a V L comprising an amino acid sequence that is at least about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% homologous or identical to SEQ ID NO: 8.
  • the extracellular antigen-binding domain comprises a V L comprising the amino acid sequence set forth in SEQ ID NO: 8.
  • the extracellular antigen-binding domain comprises a V H comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous to SEQ ID NO: 7, and a V L comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous or identical to SEQ ID NO: 8.
  • the extracellular antigen-binding domain comprises a V H comprising the amino acid sequence set forth in SEQ ID NO: 7 and a V L comprising the amino acid sequence set forth in SEQ ID NO: 8.
  • the Fv comprises a heavy chain variable region (V H ) comprising the amino acid sequence set forth in SEQ ID NO: 44.
  • the Fv comprises a light chain variable region (V L ) comprising the amino acid sequence set forth in SEQ ID NO: 45.
  • the Fv comprises V H comprising the amino acid sequence set forth in SEQ ID NO: 44 and a V L comprising the amino acid sequence set forth in SEQ ID NO: 45.
  • the extracellular antigen-binding domain comprises a V H comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous or identical to SEQ ID NO: 44.
  • the extracellular antigen-binding domain comprises a V H comprising an amino acid sequence that is at least about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% homologous or identical to SEQ ID NO: 44.
  • the extracellular antigen-binding domain comprises a V H comprising the amino sequence set forth in SEQ ID NO: 44.
  • the extracellular antigen-binding domain comprises a V L comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous to SEQ ID NO: 45.
  • the extracellular antigen-binding domain comprises a V L comprising an amino acid sequence that is at least about 80%, about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99% homologous or identical to SEQ ID NO: 45.
  • the extracellular antigen-binding domain comprises a V L comprising the amino acid sequence set forth in SEQ ID NO: 45.
  • the extracellular antigen-binding domain comprises a V H comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous to SEQ ID NO: 44, and a V L comprising an amino acid sequence that is at least about 80% (e.g., at least about 85%, at least about 90%, or at least about 95%) homologous or identical to SEQ ID NO: 45.
  • the extracellular antigen-binding domain comprises a V H comprising the amino acid sequence set forth in SEQ ID NO: 44 and a V L comprising the amino acid sequence set forth in SEQ ID NO: 45.
  • the extracellular antigen-binding domain comprises a V H CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 1, or a conservative modification thereof, a V H CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 2 or a conservative modification thereof, and a V H CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 3, a conservative modification thereof.
  • the extracellular antigen-binding domain comprises a V H CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 1, a V H CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 2, and a V H CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 3.
  • the extracellular antigen-binding domain comprises a V L CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 4 or a conservative modification thereof, a V L CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 5 or a conservative modification thereof, and a V L CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 6 or a conservative modification thereof.
  • the extracellular antigen-binding domain comprises a V L CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 4, a V L CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 5, and a V L CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 6.
  • the extracellular antigen-binding domain comprises a V H CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 1 or a conservative modification thereof, a V H CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 2 or a conservative modification thereof, a V H CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 3, a conservative modification thereof, a V L CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 4 or a conservative modification thereof, a V L CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 5 or a conservative modification thereof, and a V L CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 6 or a conservative modification thereof.
  • the extracellular antigen-binding domain comprises a V H CDR1 comprising amino acids having the sequence set forth in SEQ ID NO: 1, a V H CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 2, a V H CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 3, a V L CDR1 comprising the amino acid sequence set forth in SEQ ID NO: 4, a V L CDR2 comprising the amino acid sequence set forth in SEQ ID NO: 5 and a V L CDR3 comprising the amino acid sequence set forth in SEQ ID NO: 6.
  • a conservative sequence modification refers to an amino acid modification that does not significantly affect or alter the binding characteristics of the presently disclosed HI-TCR comprising the amino acid sequence.
  • Conservative modifications can include amino acid substitutions, additions and deletions. Modifications can be introduced into the Fv of the presently disclosed HI-TCR by standard techniques known in the art, such as site-directed mutagenesis and PCR-mediated mutagenesis. Amino acids can be classified into groups according to their physicochemical properties such as charge and polarity. Conservative amino acid substitutions are ones in which the amino acid residue is replaced with an amino acid within the same group.
  • amino acids can be classified by charge: positively-charged amino acids include lysine, arginine, histidine, negatively-charged amino acids include aspartic acid, glutamic acid, neutral charge amino acids include alanine, asparagine, cysteine, glutamine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine.
  • positively-charged amino acids include lysine, arginine, histidine
  • negatively-charged amino acids include aspartic acid
  • glutamic acid neutral charge amino acids include alanine, asparagine, cysteine, glutamine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine.
  • amino acids can be classified by polarity: polar amino acids include arginine (basic polar), asparagine, aspartic acid (acidic polar), glutamic acid (acidic polar), glutamine, histidine (basic polar), lysine (basic polar), serine, threonine, and tyrosine; non-polar amino acids include alanine, cysteine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, and valine.
  • one or more amino acid residues within a CDR region can be replaced with other amino acid residues from the same group and the altered antibody can be tested for retained function (i.e., the functions set forth in (c) through (1) above) using the functional assays described herein.
  • no more than one, no more than two, no more than three, no more than four, no more than five residues within a specified sequence or a CDR region are altered.
  • V H and/or V L amino acid sequences having at least about 80%, at least about 85%, at least about 90%, or at least about 95% e.g., about 81%, about 82%, about 83%, about 84%, about 85%, about 86%, about 87%, about 88%, about 89%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, or about 99%
  • a specific sequence e.g., SEQ ID NOs: 7, and 8 8
  • substitutions e.g., conservative substitutions
  • a target antigen e.g., CD19
  • a total of 1 to 10 amino acids are substituted, inserted and/or deleted in a specific sequence (e.g., SEQ ID NOs: 7, and 8).
  • substitutions, insertions, or deletions occur in regions outside the CDRs (e.g., in the FRs) of the extracellular antigen-binding domain.
  • the extracellular antigen-binding domain comprises V H and/or V L sequence selected from the group consisting of SEQ ID NOs: 7, and 8, including post-translational modifications of that sequence (SEQ ID NOs: 7 and 8).
  • the percent homology between two amino acid sequences is equivalent to the percent identity between the two sequences.
  • the comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm.
  • the percent homology between two amino acid sequences can be determined using the algorithm of E. Meyers and W. Miller (Comput. Appl. Biosci., 4:11-17 (1988)) which has been incorporated into the ALIGN program (version 2.0), using a PAM120 weight residue table, a gap length penalty of 12 and a gap penalty of 4.
  • the percent homology between two amino acid sequences can be determined using the Needleman and Wunsch (J. Mol. Biol.
  • amino acids sequences of the presently disclosed subject matter can further be used as a “query sequence” to perform a search against public databases to, for example, identify related sequences.
  • search can be performed using the XBLAST program (version 2.0) of Altschul, et al. (1990) J. Mol. Biol. 215:403-10.
  • Gapped BLAST can be utilized as described in Altschul et al., (1997) Nucleic Acids Res. 25(17):3389-3402.
  • the default parameters of the respective programs e.g., XBLAST and NBLAST
  • the antigen binding chain further comprises a constant domain.
  • the constant domain comprises a hinge/spacer region and a transmembrane domain.
  • the constant domain is capable of forming a homodimer or a heterodimer with another constant domain.
  • the constant domain dimerizes through one or more disulfide-links.
  • the antigen binding chain is capable of forming a trimer or oligomer with one or more identical or different constant domains.
  • the constant domain comprises a T cell receptor constant region, e.g., T cell receptor alpha constant region (TRAC), T cell receptor beta constant region (TRBC, e.g., TRBC1 or TRBC2), T cell receptor gamma constant region (TRGC, e.g., TRGC1 or TRGC2), T cell receptor delta constant region (TRDC) or any variants or functional fragments thereof.
  • T cell receptor constant region e.g., T cell receptor alpha constant region (TRAC), T cell receptor beta constant region (TRBC, e.g., TRBC1 or TRBC2), T cell receptor gamma constant region (TRGC, e.g., TRGC1 or TRGC2), T cell receptor delta constant region (TRDC) or any variants or functional fragments thereof.
  • T cell receptor constant region e.g., T cell receptor alpha constant region (TRAC), T cell receptor beta constant region (TRBC, e.g., TRBC1 or TRBC2), T cell receptor gamma constant region (TR
  • the constant domain of a presently disclosed HI-TCR comprises a native or modified TRAC peptide.
  • the TRAC polypeptide comprises an amino acid sequence that is at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or at least about 100% homologous or identical to the amino acid sequence set forth in SEQ ID NO:38, which is provided below), or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the TRAC polypeptide has an amino acid sequence that is at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or at least about 100% homologous or identical to the amino acid sequence encoded by a transcript expressed by the gene of NCBI Genbank ID: 28755, NG 001332.3, range 925603 to 930229 (SEQ ID NO:29, which is provided below), or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • [SEQ ID NO: 29] 1 atatccagaa ccctgaccct gccgtgtacc agctgagaga ctctaaatcc agtgacaagt 61 ctgtctgcct attcaccgat tttgattctc aaacaaatgt gtcacaaagt aaggattctg 121 atgtgtatat cacagacaaa actgtgctag acatgaggtc tatggacttc aagagcaaca 181 gtgctgtggc ctggagcaac aaatctgact ttgcatgtgtgc aaacgccttc aacaacagca 241 ttattccaga agacaccttc ttccccagcc caggtaaggg cagctt
  • an “TRAC nucleic acid molecule” refers to a polynucleotide encoding an TRAC polypeptide.
  • the constant domain of a presently disclosed HI-TCR comprises a native or modified TRBC peptide. In certain embodiments, the constant domain of a presently disclosed HI-TCR comprises a native or modified TRBC2 peptide. In certain embodiments, the TRBC2 polypeptide comprises an amino acid sequence that is at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or at least about 100% homologous or identical to the amino acid sequence set forth in SEQ ID NO:39, which is provided below, or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the constant domain of a presently disclosed HI-TCR comprises a native or modified TRBC1 peptide.
  • the TRBC1 polypeptide comprises an amino acid sequence that is at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or at least about 100% homologous or identical to the amino acid sequence set forth in SEQ ID NO:40, which is provided below, or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the TRBC polypeptide has an amino acid sequence that is at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99% or at least about 100% homologous or identical to the amino acid sequence encoded by a transcript expressed by a gene of NCBI Genbank ID: 28639, NG 001333.2, range 645749 to 647196 (TRBC1, SEQ ID NO: 30), NCBI Genbank ID: 28638, NG 001333.2 range 655095 to 656583 (TRBC2, SEQ ID NO:31) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • an “TRBC nucleic acid molecule” refers to a polynucleotide encoding an TRBC polypeptide.
  • the constant domain of a presently disclosed HI-TCR comprises a native or modified TRGC peptide. In certain embodiments, the constant domain of a presently disclosed HI-TCR comprises a native or modified TRGC1 peptide. In certain embodiments, the TRGC1 polypeptide has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or 100% homologous or identical to the amino acid sequence set forth in SEQ ID NO: 42, which is provided below.
  • the constant domain of a presently disclosed HI-TCR comprises a native or modified TRGC2 peptide.
  • the TRGC2 polypeptide has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or 100% homologous or identical to the amino acid sequence set forth in SEQ ID NO: 43, which is provided below.
  • the TRGC polypeptide has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or 100% homologous or identical to the amino acid sequence encoded by a transcript expressed by a gene of NCBI Genbank ID: 6966, NG 001336.2, range 108270 to 113860 (TRGC1, SEQ ID NO: 32), NCBI Genbank ID: 6967, NG 001336.2, range 124376 to 133924 (TRGC2, SEQ ID NO: 33) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • an “TRGC nucleic acid molecule” refers to a polynucleotide encoding an TRGC polypeptide.
  • the constant domain of a presently disclosed HI-TCR comprises a native or modified TRDC peptide.
  • the TRDC polypeptide has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or 100% homologous or identical to the amino acid sequence set forth in SEQ ID NO: 41, which is provided below.
  • T cell receptor constant region comprises a hinge/spacer region that links the extracellular antigen-binding domain to the constant domain.
  • the hinge/spacer region can be flexible enough to allow the antigen binding domain to orient in different directions to facilitate antigen recognition.
  • the hinge/spacer region can be the hinge region from IgG1, or the CH2CH3 region of immunoglobulin and portions of CD3, a portion of a CD28 polypeptide, a portion of a CD8 polypeptide, a variation of any of the foregoing which is at least about 80%, at least about 85%, at least about 90%, or at least about 95% homologous or identical thereto, or a synthetic spacer sequence.
  • the hinge/spacer region of the CAR can comprise a native or modified hinge region of a CD3 ⁇ polypeptide, a CD40 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, a CD166 peptide, a CD166 peptide, a CD8a peptide, a CD8b peptide, an ICOS polypeptide, an ICAM-1 peptide, a CTLA-4 peptide, a synthetic peptide (not based on a protein associated with the immune response), or a combination thereof.
  • a presently disclosed HI-TCR comprises an antigen binding chain, which does not comprise an intracellular domain.
  • the antigen binding chain is capable of associating with a CD3 ⁇ polypeptide.
  • the antigen binding chain comprises a constant domain, which is capable of associating with a CD3 ⁇ polypeptide.
  • the CD3 ⁇ polypeptide is endogenous.
  • the CD3 ⁇ polypeptide is exogenous.
  • binding of the antigen binding chain to an antigen is capable of activating the CD3 ⁇ polypeptide associated to the antigen binding chain.
  • the exogenous CD3 ⁇ polypeptide is fused to or integrated with a costimulatory molecule disclosed herein.
  • a presently disclosed HI-TCR comprises an antigen binding chain that comprises an intracellular domain.
  • the intracellular domain comprises a CD3 ⁇ polypeptide.
  • binding of the antigen binding chain to an antigen is capable of activating the CD3 ⁇ polypeptide of the antigen binding chain.
  • the activated CD3 ⁇ polypeptide can activate and/or stimulate an immunoresponsive cell (e.g., a cell of the lymphoid lineage, e.g., a T cell).
  • CD3 ⁇ comprises three immunoreceptor tyrosine-based activation motifs (ITAM1, ITAM2 and ITAM3), three basic-rich stretch (BRS) regions (BRS1, BRS2 and BRS3), and transmits an activation signal to the cell (e.g., a cell of the lymphoid lineage, e.g., a T cell) after antigen is bound to the antigen binding chain.
  • the intracellular signaling domain of the CD3 ⁇ -chain is the primary transmitter of signals from endogenous TCRs.
  • the CD3 ⁇ polypeptide comprises or has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous to the sequence having a NCBI Reference No: NP_932170 (SEQ ID NO: 17), NCBI Reference No: NP_000725.1 (SEQ ID NO: 18) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the CD3 ⁇ polypeptide comprises or has an amino acid sequence that is a consecutive portion of SEQ ID NO: 17, which is at least 20, or at least 30, or at least 40, or at least 50, and up to 164 amino acids in length.
  • the CD3 ⁇ polypeptide comprises or has an amino acid sequence of amino acids 1 to 164, 1 to 50, 50 to 100, 100 to 150, or 150 to 164 of SEQ ID NO: 17.
  • the CD3 ⁇ polypeptide comprises or has an amino acid sequence of amino acids 52 to 164 of SEQ ID NO: 17.
  • SEQ ID NO: 17 is provided below:
  • the intracellular signaling domain comprises a human CD3 ⁇ polypeptide.
  • the human CD3 ⁇ polypeptide can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to SEQ ID NO: 18 or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • SEQ ID NO: 18 is provided below:
  • SEQ ID NO: 19 An exemplary nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 18 is set forth in SEQ ID NO: 19, which is provided below.
  • a presently disclosed HI-TCR comprises an antigen binding chain that comprises an intracellular domain, wherein the intracellular domain comprises a co-stimulatory region.
  • the intracellular domain comprises a co-stimulatory region and a CD3 ⁇ polypeptide.
  • the intracellular domain comprises a co-stimulatory region and does not comprise a CD3 ⁇ polypeptide.
  • the co-stimulatory region comprises at least one co-stimulatory molecule, which can provide optimal lymphocyte activation.
  • co-stimulatory molecules refer to cell surface molecules other than antigen receptors or their ligands that are required for an efficient response of lymphocytes to antigen.
  • the at least one co-stimulatory signaling region can include a CD28 polypeptide, a 4-1BB polypeptide, an OX40 polypeptide, an ICOS polypeptide, a DAP-10 polypeptide, or a combination thereof.
  • the co-stimulatory molecule can bind to a co-stimulatory ligand, which is a protein expressed on cell surface that upon binding to its receptor produces a co-stimulatory response, i.e., an intracellular response that effects the stimulation provided when an antigen binds to its CAR molecule.
  • Co-stimulatory ligands include, but are not limited to CD80, CD86, CD70, OX40L, and 4-1BBL.
  • a 4-1BB ligand i.e., 4-1BBL
  • 4-1BB also known as “CD137”
  • CARs comprising an intracellular signaling domain that comprises a co-stimulatory signaling region comprising 4-1BB, ICOS or DAP-10 are disclosed in U.S. Pat. No. 7,446,190, which is herein incorporated by reference in its entirety.
  • the co-stimulatory region of an antigen binding chain of a HI-TCR comprises a co-stimulatory signaling region that comprises a CD28 polypeptide.
  • the CD28 polypeptide can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or 100% homologous or identical to the sequence having a NCBI Reference No: P10747 or NP_006130 (SEQ ID NO: 20), or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the CD28 polypeptide comprises or has an amino acid sequence that is a consecutive portion of SEQ ID NO: 20 which is at least 20, or at least 30, or at least 40, or at least 50, and up to 220 amino acids in length.
  • the CD28 polypeptide comprises or has an amino acid sequence of amino acids 1 to 220, 1 to 50, 50 to 100, 100 to 150, 114 to 220, 150 to 200, or 200 to 220 of SEQ ID NO: 20.
  • the co-stimulatory region comprises a co-stimulatory signaling region that comprises a CD28 polypeptide comprising or having an amino acid sequence of amino acids 180 to 220 of SEQ ID NO: 20.
  • [SEQ ID NO: 20] 1 MLRLLLALNL FPSIQVTGNK ILVKQSPMLV AYDNAVNLSC KYSYNLFSRE FRASLHKGLD 61 SAVEVCVVYG NYSQQLQVYS KTGFNCDGKL GNESVTFYLQ NLYVNQTDIY FCKIEVMYPP 121 PYLDNEKSNG TIIHVKGKHL CPSPLFPGPS KPFWVLVVVG GVLACYSLLV TVAFIIFWVR 181 SKRSRLLHSD YMNMTPRRPG PTRKHYQPYA PPRDFAAYRS
  • the co-stimulatory region comprises a human intracellular signaling domain of CD28.
  • the human intracellular signaling domain of CD28 can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to SEQ ID NO: 21 or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • SEQ ID NO: 21 is provided below:
  • SEQ ID NO: 22 An exemplary nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 21 is set forth in SEQ ID NO: 22, which is provided below.
  • the co-stimulatory region comprises a co-stimulatory signaling region that comprises two co-stimulatory molecules, e.g., co-stimulatory signaling regions of CD28 and 4-1BB or co-stimulatory signaling regions of CD28 and OX40.
  • 4-1BB can act as a tumor necrosis factor (TNF) ligand and have stimulatory activity.
  • the 4-1BB polypeptide can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to the sequence having a NCBI Reference No: P41273 or NP_001552 (SEQ ID NO: 23) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • SEQ ID NO: 23 is provided below:
  • a “4-1BB nucleic acid molecule” refers to a polynucleotide encoding a 4-1BB polypeptide.
  • the co-stimulatory region comprises an intracellular signaling domain of 4-1BB.
  • the intracellular signaling domain of 4-1BB can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to SEQ ID NO: 24 or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • SEQ ID NO: 24 is provided below: KRGRKKLLYI FKQPFMRPVQ TTQEEDGCSC RFPEEEEGGC EL [SEQ ID NO: 24].
  • SEQ ID NO: 27 An exemplary nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 24 is set forth in SEQ ID NO: 27, which is provided below.
  • An OX40 polypeptide can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to the sequence having a NCBI Reference No: P43489 or NP_003318 (SEQ ID NO: 25), or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • SEQ ID NO: 25 is provided below:
  • an “OX40 nucleic acid molecule” refers to a polynucleotide encoding an OX40 polypeptide.
  • An ICOS polypeptide can comprise or have an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to the sequence having a NCBI Reference No: NP_036224 (SEQ ID NO: 26) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • SEQ ID NO: 26 is provided below:
  • an “ICOS nucleic acid molecule” refers to a polynucleotide encoding an ICOS polypeptide.
  • mutation sites and/or junction between domains/motifs/regions of the CAR derived from different proteins are de-immunized.
  • a presently disclosed HI-TCR is capable of associating with a CD3 complex (also known as “T-cell co-receptor”).
  • the HI-TCR and the CD3 complex form an antigen recognizing receptor complex similar to a native TCR/CD3 complex.
  • the CD3 complex is endogenous.
  • the CD3 complex is exogenous.
  • the presently disclosed HI-TCR replaces a native and/or an endogenous TCR in the CD3/TCR complex.
  • the CD3 complex comprises a CD3 ⁇ chain, a CD3 ⁇ chain, and two CD3 ⁇ chains.
  • the CD3 ⁇ chain comprises or has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to NCBI reference number: NP_000064.1 (SEQ ID NO: 34, which is provided below) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the CD3 ⁇ chain comprises or has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to NCBI reference numbers: NP_000723.1 (SEQ ID NO: 35, which is provided below), NP_001035741.1 (SEQ ID NO: 36, which is provided below) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the CD3 ⁇ chain comprises or has an amino acid sequence that is at least about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99% or about 100% homologous or identical to NCBI reference number: NP_000724.1 (SEQ ID NO: 37, which is provided below) or fragments thereof, and/or may optionally comprise up to one or up to two or up to three conservative amino acid substitutions.
  • the recombinant TCR exhibits a greater antigen sensitivity than a CAR targeting the same antigen.
  • the recombinant TCR is capable of inducing an immune response when binding to an antigen that has a low density on the surface of a tumor cell.
  • immunoresponsive cells comprising a presently disclosed HI-TCR can be used to treat a subject having tumor cells with a low expression level of a surface antigen, e.g., from a relapse of a disease, wherein the subject received treatment which leads to residual tumor cells.
  • the tumor cells have a low density of a target molecule on the surface of the tumor cells.
  • a target molecule having a low density on the cell surface has a density of less than about 5,000 molecules per cell, less than about 4,000 molecules per cell, less than about 3,000 molecules per cell, less than about 2,000 molecules per cell, less than about 1,500 molecules per cell, less than about 1,000 molecules per cell, less than about 500 molecules per cell, less than about 200 molecules per cell, or less than about 100 molecules per cell.
  • a target molecule having a low density on the cell surface has a density of less than about 2,000 molecules per cell.
  • a target molecule having a low density on the cell surface has a density of less than about 1,500 molecules per cell.
  • a target molecule having a low density on the cell surface has a density of less than about 1,000 molecules per cell. In certain embodiments, a target molecule having a low density on the cell surface has a density of between about 4,000 molecules per cell and about 2,000 molecules per cell, between about 2,000 molecules per cell and about 1,000 molecules per cell, between about 1,500 molecules per cell and about 1,000 molecules per cell, between about 2,000 molecules per cell and about 500 molecules per cell, between about 1,000 molecules per cell and about 200 molecules per cell, or between about 1,000 molecules per cell and about 100 molecules per cell.
  • a presently disclosed HI-TCR comprises two antigen binding chains, e.g., VL-TRAC and VH-TRBC, which are capable of dimerizing, wherein the HI-TCR binds to CD19 (e.g., human CD19).
  • a presently disclosed HI-TCR comprises an antigen binding chain that comprises an extracellular antigen-binding domain of a V L domain of an antibody and a constant domain of TRAC.
  • the antibody binds to CD19 (e.g., human CD19).
  • the antigen binding chain is designated as “VL-TRAC”.
  • a presently disclosed HI-TCR comprises an antigen binding chain that comprises an extracellular antigen-binding domain of a V H domain of an antibody and a constant domain of TRBC.
  • the antibody binds to CD19 (e.g., human CD19).
  • the antigen binding chain is designated as “VH-TRBC”.
  • the presently disclosed subject matter provides immunoresponsive cells comprising a presently disclosed HI-TCR.
  • the HI-TCR is capable of activating the immunoresponsive cell.
  • the immunoresponsive cells Upon binding to the antigen, the immunoresponsive cells exhibit cytolytic effects towards cells bearing the antigen.
  • the immunoresponsive cells comprising the HI-TCR exhibits comparable or better therapeutic potency compared to cells comprising a chimeric antigen receptor (CAR) targeting the same antigen.
  • the immunoresponsive cells comprising the HI-TCR exhibit comparable or better cytolytic effects compared to cells comprising a chimeric antigen receptor (CAR) targeting the same antigen.
  • the immunoresponsive cells comprising the HI-TCR secrete anti-tumor cytokines.
  • the cytokines secreted by the immunoresponsive cells include, but are not limited to, TNF ⁇ , IFN ⁇ and IL2.
  • the immunoresponsive cells of the presently disclosed subject matter can be cells of the lymphoid lineage.
  • the lymphoid lineage comprising B, T and natural killer (NK) cells, provides for the production of antibodies, regulation of the cellular immune system, detection of foreign agents in the blood, detection of cells foreign to the host, and the like.
  • immunoresponsive cells of the lymphoid lineage include T cells, Natural Killer T (NKT) cells, and precursors thereof including embryonic stem cells, and pluripotent stem cells (e.g., those from which lymphoid cells may be differentiated).
  • T cells can be lymphocytes that mature in the thymus and are chiefly responsible for cell-mediated immunity. T cells are involved in the adaptive immune system.
  • the T cells of the presently disclosed subject matter can be any type of T cells, including, but not limited to, helper T cells, cytotoxic T cells, memory T cells (including central memory T cells, stem-cell-like memory T cells (or stem-like memory T cells), and two types of effector memory T cells: e.g., T EM cells and T EMRA cells, Regulatory T cells (also known as suppressor T cells), Natural killer T cells, Mucosal associated invariant T cells, and ⁇ T cells.
  • Cytotoxic T cells CTL or killer T cells
  • TTL are a subset of T lymphocytes capable of inducing the death of infected somatic or tumor cells.
  • a patient's own T cells may be genetically modified to target specific antigens through the introduction of an HI-TCR.
  • the immunoresponsive cell is a T cell.
  • the T cell can be a CD4 + T cell or a CD8 + T cell.
  • the T cell is a CD4 + T cell.
  • the T cell is a CD8 + T cell.
  • the immunoresponsive cell comprises an exogenous or a recombinant (e.g., the cell is transduced with) at least one co-stimulatory ligand.
  • the immunoresponsive cell co-expresses the HI-TCR and the at least one exogenous co-stimulatory ligand.
  • the interaction between the HI-TCR and at least one exogenous co-stimulatory ligand provides a non-antigen-specific signal important for full activation of an immunoresponsive cell (e.g., T cell).
  • Co-stimulatory ligands include, but are not limited to, members of the tumor necrosis factor (TNF) superfamily, and immunoglobulin (Ig) superfamily ligands.
  • TNF is a cytokine involved in systemic inflammation and stimulates the acute phase reaction. Its primary role is in the regulation of immune cells.
  • TNF superfamily share a number of common features. The majority of TNF superfamily members are synthesized as type II transmembrane proteins (extracellular C-terminus) containing a short cytoplasmic segment and a relatively long extracellular region.
  • TNF superfamily members include, but are not limited to, nerve growth factor (NGF), CD40L (CD40L)/CD154, CD137L/4-1BBL, TNF- ⁇ , CD134L/OX40L/CD252, CD27L/CD70, Fas ligand (FasL), CD30L/CD153, tumor necrosis factor beta (TNF ⁇ )/lymphotoxin-alpha (LT ⁇ ), lymphotoxin-beta (LT ⁇ ), CD257/B cell-activating factor (BAFF)/Blys/THANK/Tall-1, glucocorticoid-induced TNF Receptor ligand (GITRL), and TNF-related apoptosis-inducing ligand (TRAIL), LIGHT (TNFSF14).
  • NGF nerve growth factor
  • CD40L CD40L
  • CD154 CD137L/4-1BBL
  • TNF- ⁇ CD134L/OX40L/CD252, CD27L/CD70
  • the immunoglobulin (Ig) superfamily is a large group of cell surface and soluble proteins that are involved in the recognition, binding, or adhesion processes of cells. These proteins share structural features with immunoglobulins—they possess an immunoglobulin domain (fold).
  • Immunoglobulin superfamily ligands include, but are not limited to, CD80 and CD86, both ligands for CD28.
  • the at least one co-stimulatory ligand is selected from the group consisting of 4-1BBL, CD275, CD80, CD86, CD70, OX40L, CD48, TNFRSF14, and combinations thereof.
  • the immunoresponsive cell comprises or consists of one exogenous or recombinant co-stimulatory ligand.
  • the one exogenous or recombinant co-stimulatory ligand is 4-1BBL or CD80. In certain embodiments, the one exogenous or recombinant co-stimulatory ligand is 4-1BBL. In certain embodiments, the immunoresponsive cell comprises or consists of two exogenous or recombinant co-stimulatory ligands. In certain embodiments, the two exogenous or recombinant co-stimulatory ligands are 4-1BBL and CD80.
  • the immunoresponsive cell can comprise or be transduced with at least one chimeric co-stimulatory receptor (CCR).
  • CCR chimeric co-stimulatory receptor
  • the term “chimeric co-stimulatory receptor” or “CCR” refers to a chimeric receptor that binds to an antigen, and, upon its binding to the antigen, provides a co-stimulatory signal to a cell (e.g., a T cell) comprising the CCR, but does not alone provide an activation signal to the cell.
  • CCR is described in Krause, et al., J. Exp. Med. (1998); 188(4):619-626, and US20020018783, which is incorporated by reference in its entirety.
  • CCRs mimic co-stimulatory signals, but unlike, CARs, do not provide a T-cell activation signal, e.g., CCRs lack a CD3 ⁇ polypeptide.
  • CCRs provide co-stimulation, e.g., a CD28-like signal, in the absence of the natural co-stimulatory ligand on the antigen-presenting cell.
  • a combinatorial antigen recognition i.e., use of a CCR in combination with a CAR, can augment T-cell reactivity against the dual-antigen expressing T cells, thereby improving selective tumor targeting. See WO2014/055668, which is incorporated by reference in its entirety.
  • Kloss et al. describe a strategy that integrates combinatorial antigen recognition, split signaling, and, critically, balanced strength of T-cell activation and co-stimulation to generate T cells that eliminate target cells that express a combination of antigens while sparing cells that express each antigen individually (Kloss et al., Nature Biotechnology (2013); 31(1):71-75, the content of which is incorporated by reference in its entirety).
  • T-cell activation requires CAR-mediated recognition of one antigen, whereas co-stimulation is independently mediated by a CCR specific for a second antigen.
  • the combinatorial antigen recognition approach diminishes the efficiency of T-cell activation to a level where it is ineffective without rescue provided by simultaneous CCR recognition of the second antigen.
  • the CCR comprises an extracellular antigen-binding domain that binds to a second antigen, a transmembrane domain, and a co-stimulatory signaling region that comprises at least one co-stimulatory molecule. In certain embodiments, the CCR does not alone deliver an activation signal to the cell.
  • co-stimulatory molecules include CD28, 4-1BB, OX40, ICOS, DAP-10 and any combination thereof.
  • the co-stimulatory signaling region of the CCR comprises one co-stimulatory signaling molecule. In certain embodiments, the one co-stimulatory signaling molecule is CD28. In certain embodiments, the one co-stimulatory signaling molecule is 4-1BB.
  • the co-stimulatory signaling region of the CCR comprises two co-stimulatory signaling molecules.
  • the two co-stimulatory signaling molecules are CD28 and 4-1BB.
  • a second antigen is selected so that expression of both the first antigen and the second antigen is restricted to the targeted cells (e.g., cancerous tissue or cancerous cells).
  • the extracellular antigen-binding domain can be a scFv, a Fab, a F(ab) 2 , or a fusion protein with a heterologous sequence to form the extracellular antigen-binding domain.
  • the CCR is co-expressed with a HI-TCR binding to an antigen that is different from the antigen to which the CCR binds, e.g., the HI-TCR binds to a first antigen and the CCR binds to a second antigen.
  • Types of human lymphocytes of the presently disclosed subject matter include, without limitation, peripheral donor lymphocytes, e.g., those disclosed in Sadelain, M., et al. 2003 Nat Rev Cancer 3:35-45 (disclosing peripheral donor lymphocytes genetically modified to express CARs), in Morgan, R. A., et al. 2006 Science 314:126-129 (disclosing peripheral donor lymphocytes genetically modified to express a full-length tumor antigen-recognizing T cell receptor complex comprising the ⁇ and ⁇ heterodimer), in Panelli, M. C., et al. 2000 J Immunol 164:495-504; Panelli, M. C., et al.
  • TILs tumor infiltrating lymphocytes
  • AAPCs artificial antigen-presenting cells
  • the immunoresponsive cells can be autologous, non-autologous (e.g., allogeneic), or derived in vitro from engineered progenitor or stem cells.
  • the presently disclosed immunoresponsive cells are capable of modulating the tumor microenvironment.
  • Tumors have a microenvironment that is hostile to the host immune response involving a series of mechanisms by malignant cells to protect themselves from immune recognition and elimination.
  • This “hostile tumor microenvironment” comprises a variety of immune suppressive factors including infiltrating regulatory CD4 + T cells (Tregs), myeloid derived suppressor cells (MDSCs), tumor associated macrophages (TAMs), immune suppressive cytokines including TGF- ⁇ , and expression of ligands targeted to immune suppressive receptors expressed by activated T cells (CTLA-4 and PD-1).
  • the unpurified source of CTLs may be any known in the art, such as the bone marrow, fetal, neonate or adult or other hematopoietic cell source, e.g., fetal liver, peripheral blood or umbilical cord blood.
  • hematopoietic cell source e.g., fetal liver, peripheral blood or umbilical cord blood.
  • Various techniques can be employed to separate the cells. For instance, negative selection methods can remove non-CTLs initially.
  • mAbs are particularly useful for identifying markers associated with particular cell lineages and/or stages of differentiation for both positive and negative selections.
  • a large proportion of terminally differentiated cells can be initially removed by a relatively crude separation.
  • magnetic bead separations can be used initially to remove large numbers of irrelevant cells.
  • at least about 80%, usually at least about 70% of the total hematopoietic cells will be removed prior to cell isolation.
  • Procedures for separation include, but are not limited to, density gradient centrifugation; resetting; coupling to particles that modify cell density; magnetic separation with antibody-coated magnetic beads; affinity chromatography; cytotoxic agents joined to or used in conjunction with a mAb, including, but not limited to, complement and cytotoxins; and panning with antibody attached to a solid matrix, e.g. plate, chip, elutriation or any other convenient technique.
  • Techniques for separation and analysis include, but are not limited to, flow cytometry, which can have varying degrees of sophistication, e.g., a plurality of color channels, low angle and obtuse light scattering detecting channels, impedance channels.
  • the cells can be selected against dead cells, by employing dyes associated with dead cells such as propidium iodide (PI).
  • the cells are collected in a medium comprising 2% fetal calf serum (FCS) or 0.2% bovine serum albumin (BSA) or any other suitable, e.g., sterile, isotonic medium.
  • FCS fetal calf serum
  • BSA bovine serum albumin
  • an immunoresponsive cell e.g., a T cell or an NKT cell
  • a retroviral vector either gamma-retroviral or lentiviral
  • a polynucleotide encoding an HI-TCR can be cloned into a retroviral vector and expression can be driven from its endogenous promoter, from the retroviral long terminal repeat, or from a promoter specific for a target cell type of interest.
  • Non-viral vectors may be used as well.
  • a retroviral vector is generally employed for transduction, however any other suitable viral vector or non-viral delivery system can be used.
  • the HI-TCR can be constructed with an auxiliary molecule (e.g., a cytokine) in a single, multicistronic expression cassette, in multiple expression cassettes of a single vector, or in multiple vectors.
  • elements that create polycistronic expression cassette include, but is not limited to, various viral and non-viral Internal Ribosome Entry Sites (IRES, e.g., FGF-1 IRES, FGF-2 IRES, VEGF IRES, IGF-II IRES, NF- ⁇ B IRES, RUNX1 IRES, p53 IRES, hepatitis A IRES, hepatitis C IRES, pestivirus IRES, aphthovirus IRES, picornavirus IRES, poliovirus IRES and encephalomyocarditis virus IRES) and cleavable linkers (e.g., 2A peptides, e.g., P2A, T2A, E2A and F2A peptides).
  • IRES Internal Ribosome Entry Sites
  • cleavable linkers e.g., 2A peptides, e.g., P2A, T2A, E2A and F2A
  • Combinations of retroviral vector and an appropriate packaging line are also suitable, where the capsid proteins will be functional for infecting human cells.
  • Various amphotropic virus-producing cell lines are known, including, but not limited to, PA12 (Miller, et al. (1985) Mol. Cell. Biol. 5:431-437); PA317 (Miller, et al. (1986) Mol. Cell. Biol. 6:2895-2902); and CRIP (Danos, et al. (1988) Proc. Natl. Acad. Sci. USA 85:6460-6464).
  • Non-amphotropic particles are suitable too, e.g., particles pseudotyped with VSVG, RD114 or GALV envelope and any other known in the art.
  • Possible methods of transduction also include direct co-culture of the cells with producer cells, e.g., by the method of Bregni, et al. (1992) Blood 80:1418-1422, or culturing with viral supernatant alone or concentrated vector stocks with or without appropriate growth factors and polycations, e.g., by the method of Xu, et al. (1994) Exp. Hemat. 22:223-230; and Hughes, et al. (1992) J. Clin. Invest. 89:1817.
  • transducing viral vectors can be used to modify an immunoresponsive cell.
  • the chosen vector exhibits high efficiency of infection and stable integration and expression (see, e.g., Cayouette et al., Human Gene Therapy 8:423-430, 1997; Kido et al., Current Eye Research 15:833-844, 1996; Bloomer et al., Journal of Virology 71:6641-6649, 1997; Naldini et al., Science 272:263-267, 1996; and Miyoshi et al., Proc. Natl. Acad. Sci. U.S.A. 94:10319, 1997).
  • viral vectors that can be used include, for example, adenoviral, lentiviral, and adena-associated viral vectors, vaccinia virus, a bovine papilloma virus, or a herpes virus, such as Epstein-Barr Virus (also see, for example, the vectors of Miller, Human Gene Therapy 15-14, 1990; Friedman, Science 244:1275-1281, 1989; Eglitis et al., BioTechniques 6:608-614, 1988; Tolstoshev et al., Current Opinion in Biotechnology 1:55-61, 1990; Sharp, The Lancet 337:1277-1278, 1991; Cornetta et al., Nucleic Acid Research and Molecular Biology 36:311-322, 1987; Anderson, Science 226:401-409, 1984; Moen, Blood Cells 17:407-416, 1991; Miller et al., Biotechnology 7:980-990, 1989; LeGal La Salle et al., Science 259:988
  • Retroviral vectors are particularly well developed and have been used in clinical settings (Rosenberg et al., N. Engl. J. Med 323:370, 1990; Anderson et al., U.S. Pat. No. 5,399,346).
  • Non-viral approaches can also be employed for genetic modification of an immunoresponsive cell.
  • a nucleic acid molecule can be introduced into an immunoresponsive cell by administering the nucleic acid in the presence of lipofection (Feigner et al., Proc. Natl. Acad. Sci. U.S.A. 84:7413, 1987; Ono et al., Neuroscience Letters 17:259, 1990; Brigham et al., Am. J. Med. Sci.
  • Transplantation of normal genes into the affected tissues of a subject can also be accomplished by transferring a normal nucleic acid into a cultivatable cell type ex vivo (e.g., an autologous or heterologous primary cell or progeny thereof), after which the cell (or its descendants) are injected into a targeted tissue or are injected systemically.
  • Recombinant receptors can also be derived or obtained using transposases or targeted nucleases (e.g. Zinc finger nucleases, meganucleases, or TALE nucleases, CRISPR). Transient expression may be obtained by RNA electroporation.
  • recombinant receptors can be introduced by a transposon-based vector.
  • the transposon-based vector comprises a transposon (a.k.a. a transposable element).
  • the transposon can be recognized by a transposase.
  • the transposase is a Sleeping Beauty transposase.
  • CRISPR Clustered regularly-interspaced short palindromic repeats
  • the system includes Cas9 (a protein able to modify DNA utilizing crRNA as its guide), CRISPR RNA (crRNA, contains the RNA used by Cas9 to guide it to the correct section of host DNA along with a region that binds to tracrRNA (generally in a hairpin loop form) forming an active complex with Cas9), trans-activating crRNA (tracrRNA, binds to crRNA and forms an active complex with Cas9), and an optional section of DNA repair template (DNA that guides the cellular repair process allowing insertion of a specific DNA sequence).
  • Cas9 a protein able to modify DNA utilizing crRNA as its guide
  • CRISPR RNA CRISPR RNA
  • tracrRNA trans-activating crRNA
  • Cas9 DNA that guides the cellular repair process allowing insertion of a specific DNA sequence.
  • CRISPR/Cas9 often employs a plasmid to transfect the target cells.
  • the crRNA needs to be designed for each application as this is the sequence that Cas9 uses to identify and directly bind to the target DNA in a cell.
  • the repair template carrying CAR expression cassette need also be designed for each application, as it must overlap with the sequences on either side of the cut and code for the insertion sequence.
  • Multiple crRNA's and the tracrRNA can be packaged together to form a single-guide RNA (sgRNA). This sgRNA can be joined together with the Cas9 gene and made into a plasmid in order to be transfected into cells.
  • a zinc-finger nuclease is an artificial restriction enzyme, which is generated by combining a zinc finger DNA-binding domain with a DNA-cleavage domain.
  • a zinc finger domain can be engineered to target specific DNA sequences which allows a zinc-finger nuclease to target desired sequences within genomes.
  • the DNA-binding domains of individual ZFNs typically contain a plurality of individual zinc finger repeats and can each recognize a plurality of basepairs.
  • the most common method to generate new zinc-finger domain is to combine smaller zinc-finger “modules” of known specificity.
  • the most common cleavage domain in ZFNs is the non-specific cleavage domain from the type IIs restriction endonuclease FokI.
  • ZFNs can be used to insert the CAR expression cassette into genome.
  • the HR machinery searches for homology between the damaged chromosome and the homologous DNA template, and then copies the sequence of the template between the two broken ends of the chromosome, whereby the homologous DNA template is integrated into the genome.
  • Transcription activator-like effector nucleases are restriction enzymes that can be engineered to cut specific sequences of DNA. TALEN system operates on almost the same principle as ZFNs. They are generated by combining a transcription activator-like effectors DNA-binding domain with a DNA cleavage domain. Transcription activator-like effectors (TALEs) are composed of 33-34 amino acid repeating motifs with two variable positions that have a strong recognition for specific nucleotides. By assembling arrays of these TALEs, the TALE DNA-binding domain can be engineered to bind desired DNA sequence, and thereby guide the nuclease to cut at specific locations in genome.
  • TALEs Transcription activator-like effector nucleases
  • cDNA expression for use in polynucleotide therapy methods can be directed from any suitable promoter (e.g., the human cytomegalovirus (CMV), simian virus 40 (SV40), or metallothionein promoters), and regulated by any appropriate mammalian regulatory element or intron (e.g. the elongation factor 1a enhancer/promoter/intron structure).
  • CMV human cytomegalovirus
  • SV40 simian virus 40
  • metallothionein promoters regulated by any appropriate mammalian regulatory element or intron (e.g. the elongation factor 1a enhancer/promoter/intron structure).
  • enhancers known to preferentially direct gene expression in specific cell types can be used to direct the expression of a nucleic acid.
  • the enhancers used can include, without limitation, those that are characterized as tissue- or cell-specific enhancers.
  • regulation can be mediated by the cognate regulatory sequences or, if desired, by regulatory sequences derived from a heterologous source, including any of the promoters or regulatory elements described above.
  • the resulting cells can be grown under conditions similar to those for unmodified cells, whereby the modified cells can be expanded and used for a variety of purposes.
  • an HI-TCR, a costimulatory ligand, a CCR or any other molecule/transgene disclosed herein is expressed by an immunoresponsive cell through a modified genomic locus.
  • an expression cassette of the transgene is integrated into a targeted genomic locus of an immunoresponsive cell through targeted genome editing methods.
  • the targeted genomic locus can be CD3 ⁇ , CD3 ⁇ , CD247, B2M, TRAC, TRBC1, TRBC2, TRGC1 and/or TRGC2 loci.
  • an HI-TCR is expressed by an immunoresponsive cell through a modified endogenous T cell receptor locus.
  • an HI-TCR expression cassette is integrated at an endogenous T cell receptor locus.
  • the HI-TCR expression cassette is integrated within the T cell receptor alpha locus (TRA, GenBank ID: 6955).
  • the HI-TCR expression cassette is integrated within the T cell receptor beta locus (TRB, GenBank ID: 6957).
  • the HI-TCR expression cassette is integrated within the T cell receptor gamma locus (TRG, GenBank ID: 6965).
  • the HI-TCR expression cassette comprises an extracellular antigen-binding domain that is integrated in the first exon of a TCR constant domain locus, so that the extracellular antigen-binding domain and the TCR constant domain are comprised in one antigen binding chain of the HI-TCR.
  • the TCR constant domain locus can be TRAC, TRBC1, TRBC2, TRGC1, or TRGC2.
  • the HI-TCR expression cassette comprises an extracellular antigen-binding domain that is integrated in the first exon of a TRAC locus, so that the extracellular antigen-binding domain and a TRAC peptide are comprised in a first antigen binding chain of the HI-TCR.
  • the HI-TCR expression cassette further comprises a second antigen binding chain, which optionally comprises an extracellular antigen-binding domain and a TRBC peptide.
  • the HI-TCR expression cassette comprises an extracellular antigen-binding domain that is integrated in the first exon of a TRBC locus, so that the extracellular antigen-binding domain and a TRBC peptide are comprised in a first antigen binding chain of the HI-TCR.
  • the HI-TCR expression cassette further comprises a second antigen binding chain, which optionally comprises an extracellular antigen-binding domain and a TRAC peptide.
  • the expression cassette comprises elements that create polycistronic expression cassette, e.g., a cleavable peptide, e.g., a 2A peptide.
  • the recombinant TCR is expressed from an expression cassette placed in an endogenous TRAC locus and/or a TRBC locus of an immunoresponsive cell.
  • the placement of the recombinant TCR expression cassette disrupts or abolishes the endogenous expression of a TCR comprising a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell.
  • the placement of the recombinant TCR expression cassette prevents or eliminates mispairing between the recombinant TCR and a native TCR ⁇ chain and/or a native TCR ⁇ chain in the immunoresponsive cell.
  • a CRISPR system is used to modify T cell receptor locus.
  • the CRISPR system targets exon 1 of a human TRAC locus.
  • the CRISPR system comprises a guide RNA (gRNA) that targets exon 1 of a human TRAC locus.
  • a zinc-finger nuclease is used to modify an endogenous T cell receptor locus.
  • a TALEN system is used to modify an endogenous T cell receptor locus.
  • one endogenous T cell receptor locus in a cell when one endogenous T cell receptor locus in a cell is modified to express one or more antigen binding chain of an HI-TCR, one or more other endogenous T cell receptor locus in the cell are modified to eliminate the endogenous expression of the endogenous TCR chain.
  • the one or more other endogenous T cell receptor locus are further modified to express a gene of interest, e.g., an anti-tumor cytokine (e.g., IL-2, IL-12, TNF ⁇ , and INF ⁇ ), a co-stimulatory molecule ligand (e.g., 4-1BBL), a tracking gene (e.g., eGFP) or a suicide gene.
  • a gene of interest e.g., an anti-tumor cytokine (e.g., IL-2, IL-12, TNF ⁇ , and INF ⁇ )
  • a co-stimulatory molecule ligand e.g.,
  • the expression of an HI-TCR expression cassette integrated into a targeted genomic locus is driven by an endogenous promoter/enhancer of the genomic locus. In certain embodiments, the expression of an HI-TCR expression cassette integrated into a targeted genomic locus is driven by a modified promoter/enhancer introduced to the genomic locus. Any targeted genome editing methods can be used to modify the promoter/enhancer region of a targeted genomic locus, and thereby enhancing or modifying the expression of an HI-TCR in an immunoresponsive cell.
  • the modification comprises replacement of an endogenous promoter with a constitutive promoter or an inducible promoter, or insertion of a constitutive promoter or inducible promoter to the promoter region of a targeted genomic locus.
  • a constitutive promoter is positioned on a targeted genomic locus to drive gene expression of the HI-TCR.
  • Eligible constitutive promoters include, but are not limited to, a CMV promoter, an EF1a promoter, a SV40 promoter, a PGK1 promoter, a Ubc promoter, a beta-actin promoter, and a CAG promoter.
  • conditional or inducable promoter is positioned on a targeted genomic locus to drive gene expression of the HI-TCR.
  • conditional promoters include a tetracycline response element (TRE) promoter and an estrogen response element (ERE) promoter.
  • TRE tetracycline response element
  • ERP estrogen response element
  • enhancer elements can be placed in regions other than the promoter region.
  • the expression of an HI-TCR expression cassette integrated into a targeted genomic locus is regulated by an endogenous transcription terminator of the genomic locus.
  • the expression of an HI-TCR expression cassette integrated into a targeted genomic locus is regulated by a modified transcription terminator introduced to the genomic locus. Any targeted genome editing methods can be used to modify the transcription terminator region of a targeted genomic locus, and thereby modifying the expression of an HI-TCR in an immunoresponsive cell.
  • the modification comprises replacement of an endogenous transcription terminator with an alternative transcription terminator, or insertion of an alternative transcription terminator to the transcription terminator region of a targeted genomic locus.
  • the alternative transcription terminator comprises a 3′UTR region or a ploy A region of a gene. In certain embodiments, the alternative transcription terminator is endogenous. In certain embodiments, the alternative transcription terminator is exogenous. In certain embodiments, alternative transcription terminators include, but are not limited to, a TK transcription terminator, a GCSF transcription terminator, a TCRA transcription terminator, an HBB transcription terminator, a bovine growth hormone transcription terminator, an SV40 transcription terminator and a P2A element.
  • Any targeted genome editing methods can be used to modify the promoter/enhancer region and/or the transcription terminator region of a targeted genomic locus.
  • a CRISPR system is used to modify the promoter/enhancer region and/or the transcription terminator region of a targeted genomic locus.
  • zinc-finger nucleases are used to modify the promoter/enhancer region and/or the transcription terminator region of a targeted genomic locus.
  • a TALEN system is used to modify the promoter/enhancer region and/or the transcription terminator region of a targeted genomic locus.
  • the components of a selected genome editing method are delivered as DNA constructs in one or more plasmids.
  • the components are delivered via viral vectors.
  • Common delivery methods include but is not limited to, electroporation, microinjection, gene gun, impalefection, hydrostatic pressure, continuous infusion, sonication, magnetofection, adeno-associated viruses, envelope protein pseudotyping of viral vectors, replication-competent vectors cis and trans-acting elements, herpes simplex virus, and chemical vehicles (e.g., oligonucleotides, lipoplexes, polymersomes, polyplexes, dendrimers, inorganic Nanoparticles, and cell-penetrating peptides).
  • Modification can be made anywhere within a targeted genomic locus, or anywhere that can impact gene expression of a targeted genomic locus.
  • the modification occurs upstream of the transcriptional start site of a targeted genomic locus.
  • the modification occurs between the transcriptional start site and the protein coding region of a targeted genomic locus.
  • the modification occurs downstream of the protein coding region of a targeted genomic locus.
  • the modification occurs upstream of the transcriptional start site of a targeted genomic locus, wherein the modification produces a new transcriptional start site.
  • polypeptides e.g., CD19, CD8, CD28, CD3, CD40, 4-1BB, OX40, CD84, CD166, CD8a, CD8b, ICOS, ICAM-1, TRAC, TRBC1, TRBC2, TRGC1, TRGC2, CD3 ⁇ , CD3 ⁇ , CD3 ⁇ and CTLA-4) or fragments thereof that are modified in ways that enhance their anti-neoplastic activity when expressed in an immunoresponsive cell.
  • the presently disclosed subject matter provides methods for optimizing an amino acid sequence or nucleic acid sequence by producing an alteration in the sequence. Such alterations may include certain mutations, deletions, insertions, or post-translational modifications.
  • the presently disclosed subject matter further includes analogs of any naturally-occurring polypeptide disclosed herein (including, but not limited to, CD19, CD8, CD28, CD3, CD40, 4-1BB, OX40, CD84, CD166, CD8a, CD8b, ICOS, ICAM-1, TRAC, TRBC1, TRBC2, TRGC1, TRGC2, CD3 ⁇ , CD3 ⁇ , CD3 ⁇ and CTLA-4).
  • Analogs can differ from a naturally-occurring polypeptide disclosed herein by amino acid sequence differences, by post-translational modifications, or by both.
  • Analogs can exhibit at least about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99% or more homologous to all or part of a naturally-occurring amino, acid sequence of the presently disclosed subject matter.
  • the length of sequence comparison is at least 5, 10, 15 or 20 amino acid residues, e.g., at least 25, 50, or 75 amino acid residues, or more than 100 amino acid residues.
  • a BLAST program may be used, with a probability score between e ⁇ 3 and e ⁇ 100 indicating a closely related sequence.
  • Modifications include in vivo and in vitro chemical derivatization of polypeptides, e.g., acetylation, carboxylation, phosphorylation, or glycosylation; such modifications may occur during polypeptide synthesis or processing or following treatment with isolated modifying enzymes.
  • Analogs can also differ from the naturally-occurring polypeptides by alterations in primary sequence.
  • a fragment means at least 5, 10, 13, or 15 amino acids. In certain embodiments, a fragment comprises at least 20 contiguous amino acids, at least 30 contiguous amino acids, or at least 50 contiguous amino acids. In certain embodiments, a fragment comprises at least 60 to 80, 100, 200, 300 or more contiguous amino acids.
  • Fragments can be generated by methods known to those skilled in the art or may result from normal protein processing (e.g., removal of amino acids from the nascent polypeptide that are not required for biological activity or removal of amino acids by alternative mRNA splicing or alternative protein processing events).
  • Non-protein analogs have a chemical structure designed to mimic the functional activity of a protein disclosed herein. Such analogs may exceed the physiological activity of the original polypeptide.
  • Methods of analog design are well known in the art, and synthesis of analogs can be carried out according to such methods by modifying the chemical structures such that the resultant analogs increase the anti-neoplastic activity of the original polypeptide when expressed in an immunoresponsive cell. These chemical modifications include, but are not limited to, substituting alternative R groups and varying the degree of saturation at specific carbon atoms of a reference polypeptide.
  • the protein analogs are relatively resistant to in vivo degradation, resulting in a more prolonged therapeutic effect upon administration.
  • Assays for measuring functional activity include, but are not limited to, those described in the Examples below.
  • compositions comprising the presently disclosed immunoresponsive cells can be provided systemically or directly to a subject for inducing and/or enhancing an immune response to an antigen and/or treating and/or preventing a neoplasia, pathogen infection, or infectious disease.
  • the presently disclosed immunoresponsive cells or compositions comprising thereof are directly injected into an organ of interest (e.g., an organ affected by a neoplasia).
  • the presently disclosed immunoresponsive cells or compositions comprising thereof are provided indirectly to the organ of interest, for example, by administration into the circulatory system (e.g., the tumor vasculature).
  • Expansion and differentiation agents can be provided prior to, during or after administration of the cells or compositions to increase production of T cells, NKT cells, or CTL cells in vitro or in vivo.
  • the presently disclosed immunoresponsive cells can be administered in any physiologically acceptable vehicle, normally intravascularly, although they may also be introduced into bone or other convenient site where the cells may find an appropriate site for regeneration and differentiation (e.g., thymus). Usually, at least about 1 ⁇ 10 5 cells will be administered, eventually reaching about 1 ⁇ 10 10 or more.
  • the presently disclosed immunoresponsive cells can comprise a purified population of cells. Those skilled in the art can readily determine the percentage of the presently disclosed immunoresponsive cells in a population using various well-known methods, such as fluorescence activated cell sorting (FACS). Suitable ranges of purity in populations comprising the presently disclosed immunoresponsive cells are about 50% to about 55%, about 5% to about 60%, and about 65% to about 70%.
  • the purity is about 70% to about 75%, about 75% to about 80%, or about 80% to about 85%. In certain embodiments, the purity is about 85% to about 90%, about 90% to about 95%, and about 95% to about 100%. Dosages can be readily adjusted by those skilled in the art (e.g., a decrease in purity may require an increase in dosage).
  • the cells can be introduced by injection, catheter, or the like.
  • compositions can be pharmaceutical compositions comprising the presently disclosed immunoresponsive cells or their progenitors and a pharmaceutically acceptable carrier.
  • Administration can be autologous or heterologous.
  • immunoresponsive cells, or progenitors can be obtained from one subject, and administered to the same subject or a different, compatible subject.
  • Peripheral blood derived immunoresponsive cells or their progeny e.g., in vivo, ex vivo or in vitro derived
  • a therapeutic composition of the presently disclosed subject matter e.g., a pharmaceutical composition comprising a presently disclosed immunoresponsive cell
  • it can be formulated in a unit dosage injectable form (solution, suspension, emulsion).
  • compositions comprising the presently disclosed immunoresponsive cells can be conveniently provided as sterile liquid preparations, e.g., isotonic aqueous solutions, suspensions, emulsions, dispersions, or viscous compositions, which may be buffered to a selected pH.
  • sterile liquid preparations e.g., isotonic aqueous solutions, suspensions, emulsions, dispersions, or viscous compositions, which may be buffered to a selected pH.
  • Liquid preparations are normally easier to prepare than gels, other viscous compositions, and solid compositions. Additionally, liquid compositions are somewhat more convenient to administer, especially by injection. Viscous compositions, on the other hand, can be formulated within the appropriate viscosity range to provide longer contact periods with specific tissues.
  • Liquid or viscous compositions can comprise carriers, which can be a solvent or dispersing medium containing, for example, water, saline, phosphate buffered saline, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like) and suitable mixtures thereof.
  • carriers can be a solvent or dispersing medium containing, for example, water, saline, phosphate buffered saline, polyol (for example, glycerol, propylene glycol, liquid polyethylene glycol, and the like) and suitable mixtures thereof.
  • Sterile injectable solutions can be prepared by incorporating the genetically modified immunoresponsive cells in the required amount of the appropriate solvent with various amounts of the other ingredients, as desired.
  • Such compositions may be in admixture with a suitable carrier, diluent, or excipient such as sterile water, physiological saline, glucose, dextrose, or the like.
  • the compositions can also be lyophilized.
  • the compositions can contain auxiliary substances such as wetting, dispersing, or emulsifying agents (e.g., methylcellulose), pH buffering agents, gelling or viscosity enhancing additives, preservatives, flavoring agents, colors, and the like, depending upon the route of administration and the preparation desired.
  • Standard texts such as “REMINGTON'S PHARMACEUTICAL SCIENCE”, 17th edition, 1985, incorporated herein by reference, may be consulted to prepare suitable preparations, without undue experimentation.
  • compositions which enhance the stability and sterility of the compositions, including antimicrobial preservatives, antioxidants, chelating agents, and buffers, can be added.
  • antimicrobial preservatives for example, parabens, chlorobutanol, phenol, sorbic acid, and the like.
  • Prolonged absorption of the injectable pharmaceutical form can be brought about by the use of agents delaying absorption, for example, aluminum monostearate and gelatin. According to the presently disclosed subject matter, however, any vehicle, diluent, or additive used would have to be compatible with the genetically modified immunoresponsive cells or their progenitors.
  • compositions can be isotonic, i.e., they can have the same osmotic pressure as blood and lacrimal fluid.
  • the desired isotonicity of the compositions may be accomplished using sodium chloride, or other pharmaceutically acceptable agents such as dextrose, boric acid, sodium tartrate, propylene glycol or other inorganic or organic solutes.
  • Sodium chloride can be particularly for buffers containing sodium ions.
  • Viscosity of the compositions can be maintained at the selected level using a pharmaceutically acceptable thickening agent.
  • a pharmaceutically acceptable thickening agent for example, methylcellulose is is readily and economically available and is easy to work with.
  • suitable thickening agents include, for example, xanthan gum, carboxymethyl cellulose, hydroxypropyl cellulose, carbomer, and the like.
  • concentration of the thickener can depend upon the agent selected. The important point is to use an amount that will achieve the selected viscosity.
  • liquid dosage form e.g., whether the composition is to be formulated into a solution, a suspension, gel or another liquid form, such as a time release form or liquid-filled form.
  • the quantity of cells to be administered will vary for the subject being treated. In a one embodiment, between about 10 4 and about 10 10 , between about 10 5 and about 10 9 , or between about 10 6 and about 10 8 of the presently disclosed immunoresponsive cells are administered to a human subject. More effective cells may be administered in even smaller numbers. In certain embodiments, at least about 1 ⁇ 10 8 , about 2 ⁇ 10 8 , about 3 ⁇ 10 8 , about 4 ⁇ 10 8 , or about 5 ⁇ 10 8 of the presently disclosed immunoresponsive cells are administered to a human subject. The precise determination of what would be considered an effective dose may be based on factors individual to each subject, including their size, age, sex, weight, and condition of the particular subject. Dosages can be readily ascertained by those skilled in the art from this disclosure and the knowledge in the art.
  • any additives in addition to the active cell(s) and/or agent(s) are present in an amount of 0.001 to 50% (weight) solution in phosphate buffered saline, and the active ingredient is present in the order of micrograms to milligrams, such as about 0.0001 to about 5 wt %, about 0.0001 to about 1 wt %, about 0.0001 to about 0.05 wt % or about 0.001 to about 20 wt %, about 0.01 to about 10 wt %, or about 0.05 to about 5 wt %.
  • any composition to be administered to an animal or human the followings can be determined: toxicity such as by determining the lethal dose (LD) and LD50 in a suitable animal model e.g., rodent such as mouse; the dosage of the composition(s), concentration of components therein and timing of administering the composition(s), which elicit a suitable response.
  • toxicity such as by determining the lethal dose (LD) and LD50 in a suitable animal model e.g., rodent such as mouse
  • the dosage of the composition(s), concentration of components therein and timing of administering the composition(s), which elicit a suitable response Such determinations do not require undue experimentation from the knowledge of the skilled artisan, this disclosure and the documents cited herein. And, the time for sequential administrations can be ascertained without undue experimentation.
  • the presently disclosed subject matter provides methods for inducing and/or increasing an immune response in a subject in need thereof.
  • the presently disclosed immunoresponsive cells and compositions comprising thereof can be used for treating and/or preventing a neoplasia in a subject.
  • the presently disclosed immunoresponsive cells and compositions comprising thereof can be used for prolonging the survival of a subject suffering from a neoplasia.
  • the presently disclosed immunoresponsive cells and compositions comprising thereof can also be used for treating and/or preventing a pathogen infection or other infectious disease in a subject, such as an immunocompromised human subject.
  • Such methods comprise administering the presently disclosed immunoresponsive cells in an amount effective or a composition (e.g., pharmaceutical composition) comprising thereof to achieve the desired effect, be it palliation of an existing condition or prevention of recurrence.
  • the amount administered is an amount effective in producing the desired effect.
  • An effective amount can be provided in one or a series of administrations.
  • An effective amount can be provided in a bolus or by continuous perfusion.
  • immunoresponsive cells comprising a HI-TCR disclosed herein can be used to treat a subject having tumor cells with a low expression level of a surface antigen, e.g., from a relapse of a disease, wherein the subject received treatment which leads to residual tumor cells.
  • the tumor cells have low density of a target molecule on the surface of the tumor cells
  • a target molecule having a low density on the cell surface has a density of less than about 5,000 molecules per cell, less than about 4,000 molecules per cell, less than about 3,000 molecules per cell, less than about 2,000 molecules per cell, less than about 1,500 molecules per cell, less than about 1,000 molecules per cell, less than about 500 molecules per cell, less than about 200 molecules per cell, or less than about 100 molecules per cell.
  • a target molecule having a low density on the cell surface has a density of less than about 2,000 molecules per cell.
  • a target molecule having a low density on the cell surface has a density of less than about 1,500 molecules per cell.
  • a target molecule having a low density on the cell surface has a density of less than about 1,000 molecules per cell. In certain embodiments, a target molecule having a low density on the cell surface has a density of between about 4,000 molecules per cell and about 2,000 molecules per cell, between about 2,000 molecules per cell and about 1,000 molecules per cell, between about 1,500 molecules per cell and about 1,000 molecules per cell, between about 2,000 molecules per cell and about 500 molecules per cell, between about 1,000 molecules per cell and about 200 molecules per cell, or between about 1,000 molecules per cell and about 100 molecules per cell.
  • immunoresponsive cells comprising a HI-TCR disclosed herein can be used to treat a subject having a relapse of a disease, wherein the subject received immunoresponsive cells (e.g., T cells) comprising a CAR comprising an intracellular signaling domain that comprises a co-stimulatory signaling domain comprising a 4-1BB polypeptide (e.g., a 4-1BBz CAR).
  • the tumor cells have a low density of a tumor specific antigen on the surface of the tumor cells.
  • the disease is CD19 + ALL.
  • the tumor cells have a low density of CD19 on the tumor cells.
  • Such methods comprise administering the presently disclosed immunoresponsive cells in an amount effective or a composition (e.g., pharmaceutical composition) comprising thereof to achieve the desired effect, alleviation of an existing condition or prevention of recurrence.
  • an “effective amount” is an amount sufficient to effect a beneficial or desired clinical result upon treatment.
  • An effective amount can be administered to a subject in one or more doses.
  • an effective amount is an amount that is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of the disease, or otherwise reduce the pathological consequences of the disease.
  • the effective amount is generally determined by the physician on a case-by-case basis and is within the skill of one in the art. Several factors are typically taken into account when determining an appropriate dosage to achieve an effective amount. These factors include age, sex and weight of the subject, the condition being treated, the severity of the condition and the form and effective concentration of the immunoresponsive cells administered.
  • cell doses in the range of about 10 6 -10 10 are typically infused.
  • T cells are induced that are specifically directed against the specific antigen.
  • the modified cells can be administered by any method known in the art including, but not limited to, intravenous, subcutaneous, intranodal, intratumoral, intrathecal, intrapleural, intraperitoneal and directly to the thymus.
  • the presently disclosed subject matter provides methods for treating and/or preventing a neoplasia in a subject.
  • the method can comprise administering an effective amount of the presently disclosed immunoresponsive cells or a composition comprising thereof to a subject having a neoplasia.
  • Non-limiting examples of neoplasia include blood cancers (e.g. leukemias, lymphomas, and myelomas), ovarian cancer, breast cancer, bladder cancer, brain cancer, colon cancer, intestinal cancer, liver cancer, lung cancer, pancreatic cancer, prostate cancer, skin cancer, stomach cancer, glioblastoma, throat cancer, melanoma, neuroblastoma, adenocarcinoma, glioma, soft tissue sarcoma, and various carcinomas (including prostate and small cell lung cancer).
  • blood cancers e.g. leukemias, lymphomas, and myelomas
  • ovarian cancer breast cancer, bladder cancer, brain cancer, colon cancer, intestinal cancer, liver cancer, lung cancer, pancreatic cancer, prostate cancer, skin cancer, stomach cancer, glioblastoma, throat cancer, melanoma, neuroblastoma, adenocarcinoma, glioma, soft tissue sarcoma, and various carcinomas (including
  • Suitable carcinomas further include any known in the field of oncology, including, but not limited to, astrocytoma, fibrosarcoma, myxosarcoma, liposarcoma, oligodendroglioma, ependymoma, medulloblastoma, primitive neural ectodermal tumor (PNET), chondrosarcoma, osteogenic sarcoma, pancreatic ductal adenocarcinoma, small and large cell lung adenocarcinomas, chordoma, angiosarcoma, endotheliosarcoma, squamous cell carcinoma, bronchoalveolarcarcinoma, epithelial adenocarcinoma, and liver metastases thereof, lymphangiosarcoma, lymphangioendotheliosarcoma, hepatoma, cholangiocarcinoma, synovioma, mesothelioma, Ewing's
  • the neoplasm is selected from the group consisting of blood cancers (e.g. leukemias, lymphomas, and myelomas), ovarian cancer, prostate cancer, breast cancer, bladder cancer, brain cancer, colon cancer, intestinal cancer, liver cancer, lung cancer, pancreatic cancer, prostate cancer, skin cancer, stomach cancer, glioblastoma, and throat cancer.
  • the presently disclosed immunoresponsive cells and compositions comprising thereof can be used for treating and/or preventing blood cancers (e.g., leukemias, lymphomas, and myelomas) or ovarian cancer, which are not amenable to conventional therapeutic interventions.
  • the neoplasm is a solid tumor.
  • the subjects can have an advanced form of disease, in which case the treatment objective can include mitigation or reversal of disease progression, and/or amelioration of side effects.
  • the subjects can have a history of the condition, for which they have already been treated, in which case the therapeutic objective will typically include a decrease or delay in the risk of recurrence.
  • Suitable human subjects for therapy typically comprise two treatment groups that can be distinguished by clinical criteria.
  • Subjects with “advanced disease” or “high tumor burden” are those who bear a clinically measurable tumor.
  • a clinically measurable tumor is one that can be detected on the basis of tumor mass (e.g., by palpation, CAT scan, sonogram, mammogram or X-ray; positive biochemical or histopathologic markers on their own are insufficient to identify this population).
  • a pharmaceutical composition is administered to these subjects to elicit an anti-tumor response, with the objective of palliating their condition.
  • reduction in tumor mass occurs as a result, but any clinical improvement constitutes a benefit.
  • Clinical improvement includes decreased risk or rate of progression or reduction in pathological consequences of the tumor.
  • a second group of suitable subjects is known in the art as the “adjuvant group.” These are individuals who have had a history of neoplasia, but have been responsive to another mode of therapy.
  • the prior therapy can have included, but is not restricted to, surgical resection, radiotherapy, and traditional chemotherapy.
  • these individuals have no clinically measurable tumor.
  • they are suspected of being at risk for progression of the disease, either near the original tumor site, or by metastases.
  • This group can be further subdivided into high-risk and low-risk individuals. The subdivision is made on the basis of features observed before or after the initial treatment. These features are known in the clinical arts, and are suitably defined for each different neoplasia.
  • Features typical of high-risk subgroups are those in which the tumor has invaded neighboring tissues, or who show involvement of lymph nodes.
  • Another group have a genetic predisposition to neoplasia but have not yet evidenced clinical signs of neoplasia. For instance, women testing positive for a genetic mutation associated with breast cancer, but still of childbearing age, can wish to receive one or more of the immunoresponsive cells described herein in treatment prophylactically to prevent the occurrence of neoplasia until it is suitable to perform preventive surgery.
  • the presently disclosed subject matter provides methods for treating and/or preventing a pathogen infection (e.g., viral infection, bacterial infection, fungal infection, parasite infection, or protozoal infection) in a subject, e.g., in an immunocompromised subject.
  • the method can comprise administering an effective amount of the presently disclosed immunoresponsive cells or a composition comprising thereof to a subject having a pathogen infection.
  • a pathogen infection e.g., viral infection, bacterial infection, fungal infection, parasite infection, or protozoal infection
  • the method can comprise administering an effective amount of the presently disclosed immunoresponsive cells or a composition comprising thereof to a subject having a pathogen infection.
  • Exemplary viral infections susceptible to treatment include, but are not limited to, Cytomegalovirus (CMV), Epstein Barr Virus (EBV), Human Immunodeficiency Virus (HIV), and influenza virus infections.
  • a potential solution to this problem is engineering a suicide gene into the presently disclosed immunoresponsive cells.
  • Suitable suicide genes include, but are not limited to, Herpes simplex virus thymidine kinase (hsv-tk), inducible Caspase 9 Suicide gene (iCasp-9), and a truncated human epidermal growth factor receptor (EGFRt) polypeptide.
  • the suicide gene is an EGFRt polypeptide.
  • the EGFRt polypeptide can enable T cell elimination by administering anti-EGFR monoclonal antibody (e.g., cetuximab).
  • EGFRt can be covalently joined to the upstream of the antigen-recognizing receptor of a presently disclosed CAR.
  • the suicide gene can be included within the vector comprising nucleic acids encoding a presently disclosed CAR.
  • a prodrug designed to activate the suicide gene e.g., a prodrug (e.g., AP1903 that can activate iCasp-9) during malignant T-cell transformation (e.g., GVHD) triggers apoptosis in the suicide gene-activated CAR-expressing T cells.
  • a prodrug e.g., AP1903 that can activate iCasp-9
  • GVHD malignant T-cell transformation
  • kits for inducing and/or enhancing an immune response and/or treating and/or preventing a neoplasia or a pathogen infection in a subject.
  • the kit comprises an effective amount of presently disclosed immunoresponsive cells or a pharmaceutical composition comprising thereof.
  • the kit comprises a sterile container; such containers can be boxes, ampules, bottles, vials, tubes, bags, pouches, blister-packs, or other suitable container forms known in the art.
  • Such containers can be made of plastic, glass, laminated paper, metal foil, or other materials suitable for holding medicaments.
  • the kit includes an isolated nucleic acid molecule encoding an HI-TCR disclosed herein which is directed toward an antigen of interest in expessible form, which may optionally be comprised in one or more vectors.
  • the immunoresponsive cells and/or nucleic acid molecules are provided together with instructions for administering the cells or nucleic acid molecules to a subject having or at risk of developing a neoplasia or pathogen or immune disorder.
  • the instructions generally include information about the use of the composition for the treatment and/or prevention of neoplasia or a pathogen infection.
  • the instructions include at least one of the following: description of the therapeutic agent; dosage schedule and administration for treatment or prevention of a neoplasia, pathogen infection, or immune disorder or symptoms thereof; precautions; warnings; indications; counter-indications; over-dosage information; adverse reactions; animal pharmacology; clinical studies; and/or references.
  • the instructions may be printed directly on the container (when present), or as a label applied to the container, or as a separate sheet, pamphlet, card, or folder supplied in or with the container.
  • TCR locus designed to alter the antigen specificity of human T cells without disrupting or bypassing their CD3 complex, which physiologically controls and regulates T cell activation.
  • the T cell lost its endogenous T cell receptor and acquired the ability to recognize antigen independent of HLA, making use of its CD3 complex, which is otherwise bypassed when using CARs.
  • the recombinant TCR-like molecule i.e., HI-TCR, FvTCR or HIT-CAR
  • the recombined receptor signals via the CD3 complex which can either be intact (i.e., in its physiological composition) or augmented through the non-covalent incorporation of costimulatory domains.
  • TCR and TCR-like T cells A novel strategy for one-step generation of TCR and TCR-like T cells was developed by integrating a TCR or TCR-like gene with a distinct variable domain for a predetermined antigen. This resulted in the expression of the new TCR/TCR-like gene under the control of the endogenous TCR promoter (alpha, beta or both) with concomitant disruption of surface expression of the endogenous TCR.
  • a strategy for one-step generation of universal CAR T cells were developed by targeting the integration of a promoter-less CAR gene cassette in the TCR alpha constant chain (TRAC) first exon. This resulted in CAR expression under the control of the endogenous TCR alpha promoter with concomitant disruption of the TCR alpha gene expression, leading to lack of TCR expression at the cell surface.
  • CAR gene targeting at the TRAC locus was accomplished through homologous recombination (HR) by using a site-specific nuclease (e.g. CRISPR/Cas9) and an AAV donor template.
  • HR homologous recombination
  • the present strategy permitted the generation of T cells with a unique specificity, which was encoded by a chimeric TCR receptor containing a specific antigen-binding domain.
  • the antigen-binding domain was derived from either an Immunoglobulin (i.e. Fv fragment), a ligand for a cell-surface receptor or a TCR ( ⁇ or ⁇ ).
  • the hybrid Immunoglobulin-TCR chimeric antigen receptor i.e., HIT-CAR, FvTCR or HI-TCR
  • the ⁇ 6TCR allowed the T cell to recognize a target cell in an HLA-independent manner. Inserting a new ⁇ TCR could be accomplished in the same way but would result in HLA-restricted antigen recognition.
  • FIG. 1A shows schematic representation of the T Cell Receptor (TCR), the B Cell Receptor (BCR), a Chimeric Antigen Receptor (CAR) and the HLA-Independent TCR-based Chimeric Antigen Receptor (i.e., HIT-CAR, FvTCR or HI-TCR).
  • CRISPR/Cas9-targeted integration of the three receptors into the TRAC locus is shown in FIG. 1B .
  • the engineered HIT-CAR targets CD19.
  • Cell surface expression of HIT-CAR (i.e., HI-TCR) from TRAC locus is show in FIG. 1C .
  • Cytolitic effects and proliferation of HIT-CAR (i.e., HI-TCR or FvTCR) T cells are shown in FIGS. 1D and 1E respectively.
  • HIT-CAR i.e., HI-TCR or FvTCR
  • HIT-CAR HI-TCR or FvTCR
  • FIG. 2A HIT-CAR T cells combining target gene disruption and HIT-CAR (i.e., HI-TCR or FvTCR) targeted insertion in a single step as shown in FIG. 2A .
  • These T cells exhibited in vitro and in vivo tumor lysis activity similar to the previously characterized TRAC-CAR T cells expressing the 1928z CAR as shown in FIG. 2B .
  • antigen interaction induced down-regulation of the HIT-CAR (i.e., HI-TCR or FvTCR) T cells which was dependent of the number of antigen-dependent stimulations.
  • these HIT-CAR (i.e., HI-TCR or FvTCR) T cells were useful for the development of off-the-shelf immunotherapy.
  • Targets other than CD19 can be employed for immunotherapy.
  • Schematic representation of the NYESO TCR genes integrated into the TCR alpha or beta chain is shown in FIG. 3A .
  • Cell surface expressions of TRAC-NYESO-TCR and TRBC-NYESO-TCR i.e., HI-TCRs or FvTCRs
  • FIG. 3B Representative TCR-V-beta-1 flow cytometry plots 4 days after TRAC or TRBC targeting are shown in FIG. 3B .
  • Cytotoxic activity of the engineered T cells is shown in FIG. 3C .
  • Schematic representation of an alternative design of co-targeting into both the TCR alpha and the TCR beta is shown in FIG.
  • FIG. 3D where a NYESO-HI-TCR was placed in the TRAC locus and 4-1BBL expression cassette was placed in TRBC locus.
  • Cell surface expressions of the TRAC-NYESO-TCR and TRBC-4-1BBL are shown in FIG. 3E .
  • a variant approach was also provided in which a costimulatory domain is non-covalently inserted into the CD3 complex, which provides supraphysiological antigen sensing and activation. This is achieved by fusing the costimulatory domain to one or both TCR chains. Moreover, two costimulatory dosages are possible, by ether fusing the costimulatory domain to one or both modified TCR chains (i.e., antigen binding chains).
  • HI-TCR exhibited greater sensitivity in comparison to CARs.
  • Human T cells edited to replace endogenous TCR with HI-TCR acquired the ability to engage lower antigen densities and kill such cells.
  • Table 2 shows in vitro cytotoxic activity of HI-TCR cells.
  • HI-TCR or CD19-CAR was introduced at the endogenous TRAC locus of human peripheral T cells via CRISPR/Cas9-mediated gene editing and AAV6 donor vectors. Five days post-gene targeting, T cells (6, 30, or 150 thousands) were incubated with 250 thousands Nalm6 leukemia cells that express different CD19 levels (from very low to high levels).
  • FIG. 4A shows schematic representation of the CD28z CAR gene integrated into the TRAC locus.
  • Poly A black box
  • bGH bovine growth hormone
  • 3′UTRs including the endogenous TRAC 3′UTR, were shown to increase CAR surface expression levels ( FIGS. 4B and 4C ), which produced CAR-T cells with improved in vivo cytotoxic activity ( FIGS. 5A and 5B ). These 3′UTRs can also be used to regulate precise and predictable gene expression of any HI-TCR disclosed herein.
  • TRAC locus permit the generation of T cells expressing optimal levels of HI-TCR that like the physiological TCR but unlike CARs, take advantage of the endogenous T cell activating machinery (the CD3 complex and downstream signaling elements). This approach can advance both autologous and allogeneic T cell therapies.
  • T-iPS-derived T cells are pluripotent stem cells obtained through reprogramming of peripheral T lymphocytes. These T-iPS cells therefore contain a rearranged T-cell receptor, either an ⁇ or a ⁇ TCR, which can be modified using gene-editing technologies.
  • T cells obtained from T-iPS cells through directed differentiation express the rearranged TCR, which can be detected and sequenced. Using this sequence, one can determine the precise location of the rearranged variable domain in the genome of T-iPS cells. Using nucleases that specifically target this rearranged variable domain and a donor DNA containing a TCR variable domain of known specificity, one can replace the endogenous variable domain with the new one.
  • This approach requires two steps of gene editing: one targeting the a (or ⁇ ) chain, and the other the ⁇ (or ⁇ ) chain.
  • the approach can be performed in a single step since only two alleles need to be modified.
  • the TCR chains can be modified to express any HI-TCR disclose herein.
  • FIG. 1A CRISPR/Cas9-targeted integration of the three receptors into the TRAC locus is shown in FIG. 1A .
  • the engineered HIT-CAR targets CD19.
  • Cell surface expression of HIT-CAR (i.e., HI-TCR) from TRAC locus is show in FIGS. 6B and 6C .
  • Cytolitic effects and proliferation of HIT-CAR (i.e., HI-TCR or FvTCR) T cells are shown in FIGS. 7A,7B and 8A-8C .
  • these data show that HIT T cells outperformed CAR-T cells at killing target cells expressing low antigen levels.
  • the HI-TCR T cells were engineered to co-express costimulatory ligands.
  • the T cells were transferred with retroviral SFG vectors coding for CD80, 41BBL or both.
  • 5 days after expanding these cells ex vivo 4e5 TRAC-CAR or TRAC-HI-TCR positive T cells were injected into NSG mice bearing NALM6 cells expressing very low level of CD19.
  • the TRAC-HI-TCR T cells we either expressing CD80, 41BBL, both ligand or none. Bioluminescence was used to assess the tumor burden every week and follow the survival of the mice.
  • the TRAC-CAR T cells were not able to control the tumor with very low levels of CD19 and all the mice were terminally ill by day 30.
  • the HI-TCR T cells initially controlled the tumor burden, however the mice relapsed by day 10 and were terminally ill by day 40.
  • the addition of costimulatory ligands to the HI-TCR T cells improved the anti-tumor activity with an optimal response when the HI-TCR T cells co-expressed CD80 and 4-1BBL. This improved activity resulted in a long-term control of NALM6 expressing very low levels of CD19.
  • FIGS. 10A-10C further demonstrate that baseline TRAC-CAR expression can be controlled by distinct 3′UTR sequences without affecting cell surface replenishment kinetic after antigen encounter.
  • the TRAC-CAR T cells were engineered the same way as previously described, so that the all the constructs were under the transcriptional control of the TRAC endogenous promoter. It was observed that by modifying the 3′UTR (that includes polyA signal), the baseline expression level were modulated ( FIG. 10B ). When these different TRAC-CAR T cells were cultivated on CD19 expressing tumor cells, a drop in the CAR cell surface expression followed by a replenishment was observed by flow cytometry ( FIG. 10 C). The different 3′UTR changed the baseline expression level but they retained the same replenishment kinetic and the final expression level was similar to the baseline.
  • HI-TCR targeting CD70 and a HI-TCR targeting CD22 were also created.
  • HI-TCR targeting an interested antigen can be created by sequencing an existing scFv or a Fab region of an existing antibody targeting the same antigen to obtain the extracellular antigen-binding domain.

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