NKp80-BINDING PROTEINS AND USES THEREOF
Engineered immune cells with NKp80-binding proteins inhibit NK cell cytotoxicity, addressing transplantation rejection and enhancing allogeneic cell survival and treating NK cell-related diseases.
Patent Information
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Filing Date
- 2025-09-19
- Publication Date
- 2026-03-26
AI Technical Summary
Natural killer (NK) cells contribute to transplantation rejection by targeting donor cells, particularly in allogeneic settings, necessitating a solution to inhibit or block NKp80 to prevent host-versus-graft responses.
Engineered immune cells expressing NKp80-binding proteins, such as anti-NKp80 single domain antibodies (sdAbs) or chimeric antigen receptors (CARs), which block or do not activate NKp80, are developed to inhibit NK cell cytotoxicity and prolong the survival of allogeneic cells.
The engineered immune cells effectively reduce host-versus-graft responses and enhance the persistence of allogeneic cells, offering a safer alternative to deep lymphodepletion regimens and potentially treating NK cell-related diseases like renal cell carcinoma, lymphoma, and acute myeloid leukemia.
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Abstract
Description
NKp80-BINDING PROTEINS AND USES THEREOFCROSS REFERENCE TO RELATED APPLICATIONSThis application claims benefit of priority of International Patent Application No. PCT / CN2024 / 120119 filed on 20 September 2024, the content of which is incorporated herein by reference in its entirety.SUBMISSION OF SEQUENCE LISTING ON XML FILEThe content of the following submission on XML file is incorporated herein by reference in its entirety: a computer readable form (CRF) of the Sequence Listing (file name: IEC250484PCT SEQUENCE LISTING. XML, date recorded: September 16, 2025, size: 35.3 KB) .FIELD OF DISCLOSURE
[0001] The present disclosure relates to an engineered immune cell resisting transplantation rejection and also relates to a method for resisting transplantation rejection.BACKGROUND
[0002] Natural killer (NK) cells are effector lymphocytes deriving from common lymphoid progenitors and represent 5–10%of circulating lymphocytes. NK cells are natural cytotoxic cells, but, unlike cytotoxic T lymphocytes, they do not require antigen exposure to mediate their effect. NK cells can engage in cytolytic effector activity via direct lysis in the absence of MHC-I molecules (i.e., “missing self” ) and in antibody-dependent cellular cytotoxicity (ADCC) upon interaction of CD16 expressed by NK cells and an Fc domain of an antibody.
[0003] NKp80 (also known as killer cell lectin-like receptor subfamily F, member 1 (KLRF1) or CLEC5C) is a type II transmembrane C-type lectin-like receptor that induces NK-cell mediated cytotoxicity and cytokine production through interaction with its ligand, AICL (activation-induced C-type lectin) . NKp80 contains an atypical hemi-immunoreceptor tyrosine-based activation motif at the amino terminus of its cytoplasmic domain crucially involved in triggering NK cell cytotoxicity. NKp80 is expressed on the cell surface of nearly all NK cells as a homodimer and is also expressed on a subset of effector memory CD8 T cells and γδ T cells. NKp80 augments NK cell responses toward malignant and nonmalignant myeloid cells.
[0004] NK cells have been implicated in the advancement of various diseases or disorders, including autoimmune diseases. For example, NK cells were found to reduce the engraftment of donor lymphoid cells (e.g., stem cells) following bone marrow transplantation (see, e.g., Davis et al. (2015) Biol Blood Marrow Transplant. 21 (2) : 242-249) .
[0005] The disclosure of all publications, patents, patent applications and published patent applications referred to herein are hereby incorporated by reference in their entirety. BRIEF SUMMARY
[0006] The present disclosure in one aspect provides an engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain. In some embodiments, the NKp80-binding protein i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80 positive cells; optionally wherein the NKp80 positive cells are NK cells.
[0007] In some embodiments, the engineered immune cells described above comprise an NKp80-binding protein that comprises an NKp80 binding domain, wherein the NKp80 binding domain is selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, a single chain Fv (scFv) , a single domain antibody (sdAb) , and a peptide ligand specifically binding to NKp80. In some embodiments, the NKp80 binding domain is an sdAb ( “anti-NKp80 sdAb” ) . In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1, a CDR2, and a CDR3 having the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; (v) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15; and / or (vi) a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16.
[0008] In some embodiments according to any of the engineered immune cells described above, the NKp80-binding protein is a CAR comprising an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, wherein the antigen binding domain comprises the NKp80 binding domain. In some embodiments, transmembrane domain is derived from the group consisting of CD8α, CD4, CD28, 4-1BB, CD80, CD86, CD152, and PD-1. In some embodiments, the transmembrane domain is derived from CD8α. In some embodiments, the intracellular signaling domain is derived from the group consisting of CD3ζ, FcRγ, FcRβ, CD3γ, CD3δ, CD3ε, CD5, CD22, CD79a, CD79b, DAP12, and CD66d. In some embodiments, the intracellular signaling domain is derived from CD3ζ. In some embodiments, the CAR further comprises an intracellular co-stimulatory signaling domain. In some embodiments, the intracellular co-stimulatory signaling domain is derived from a co-stimulatory molecule selected from the group consisting of CD27, CD28, CD137, OX40, CD40, PD-1, LFA-1, ICOS, CD2, CD7, LIGHT, NKG2C, B7-H3, TNFRSF9, TNFRSF4, TNFRSF8, CD40LG, ITGB2, KLRC2, TNFRSF18, TNFRSF14, HAVCR1, LGALS9, DAP10, DAP12, CD83, ligands of CD83, and any combination thereof. In some embodiments, the intracellular co-stimulatory signaling domain is derived from a cytoplasmic domain of CD28. In some embodiments, the CAR further comprises a hinge domain located between the antigen binding domain and the transmembrane domain. In some embodiments, the hinge domain is derived from CD8α. In some embodiments, the NKp80-binding protein comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 34-37.
[0009] In some embodiments according to any of the engineered immune cells described above, the NKp80-binding protein further comprises a signal peptide at its N-terminus. In some embodiments, the signal peptide is derived from CD8α.
[0010] In some embodiments according to any of the engineered immune cells described above, the NKp80-binding protein further comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80. In some embodiments, the engineered immune cell further comprises a second antigen binding protein, wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80. In some embodiments, the second antigen is a disease-associated antigen or disease-specific antigen selected from the group consisting of: a cancer-associated antigen or a cancer-specific antigen, an infectious disease-associated antigen or an infectious disease-specific antigen, an inflammatory disorder-associated antigen or an inflammatory disorder-specific antigen, and an autoimmune-associated antigen or an autoimmune-specific antigen. In some embodiments, the disease-associated antigen or disease-specific antigen is a cancer-associated antigen or a cancer-specific antigen. In some embodiments, the cancer-associated antigen or cancer-specific antigen is selected from the group consisting of CD19, CD20, CD22, BCMA, DLL3, B7H3, PD-L1, PD-L2, CLL1, GPC3, GU2CYC, CD7, CD38, CD41, CD123, Claudin 18.2, Claudin 6, NKG2D, GPRC5D, CD70, and any combination thereof.
[0011] In some embodiments according to any of the engineered immune cells described above, the second antigen binding protein is a second CAR comprising the second antigen binding domain, a second transmembrane domain, and a second intracellular signaling domain. In some embodiments, the CAR further comprises a second signal peptide at its N-terminus, and / or a second hinge domain.
[0012] In some embodiments according to any of the engineered immune cells described above, the engineered immune cell is selected from the group consisting of a T cell, an NK cell, a B cell, a monocyte, a dendritic cell, and any combination thereof. In some embodiments, the engineered immune cell a T cell. In some embodiments, the T cell is an αβ T cell or a γδ T cell. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous NKp80. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous B2M.
[0013] The present disclosure in another aspect provides an antibody construct comprising an sdAb that binds to NKp80 ( “anti-NKp80 sdAb” ) , wherein the anti-NKp80 sdAb comprises a CDR1, a CDR2, and a CDR3 having the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16. In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16.
[0014] In some embodiments according to the anti-NKp80 antibody construct described above, the anti-NKp80 antibody construct is a chimeric receptor. In some embodiments, the chimeric receptor is a CAR. In some embodiments, the CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37.
[0015] The present disclosure in another aspect provides methods of treating and / or reducing the severity of a condition, disease, or disorder in an individual in need thereof, comprising administering to the individual an effective amount of any of the engineered immune cells described above (or a pharmaceutical composition thereof) . In some embodiments, the condition, disease, or disorder is cancer. In some embodiments, the condition, disease, or disorder is host-versus-graft (HvG) response. In some embodiments, the condition, disease, or disorder is an NK cell-associated disease or a disease associated with cells that express NKp80 (e.g., an NKp80-associated cancer) . In some embodiments, the NK cell-associated disease is HvG or an NK cell malignancy. In some embodiments, the individual is human. In some embodiments, the engineered immune cell is allogeneic to the individual.
[0016] The present disclosure in another aspect provides methods of preventing and / or reducing the risk of developing HvG in an individual, comprising administering to the individual a therapeutically effective amount of any of the engineered immune cells described above (or a pharmaceutical composition thereof) . In some embodiments, the individual is human. In some embodiments, the engineered immune cell is allogeneic to the individual.
[0017] The present disclosure in another aspect provides methods of depleting NK cells in a first population of cells, comprising exposing the first population of cells to a second population of cells comprising any of the engineered immune cells described above (or a pharmaceutical composition thereof) , wherein the exposing results in depletion of NK cells in the first population.
[0018] The present disclosure in another aspect provides methods of: i) prolonging in vivo persistence, and / or ii) reducing HvG response of an immune cell, comprising modifying the immune cell to express an NKp80-binding protein that comprises an NKp80 binding domain. In some embodiments, the NKp80-binding protein is any of the anti-NKp80 antibody constructs described above.
[0019] The present disclosure in another aspect provides an isolated nucleic acid encoding any of the NKp80-binding proteins described above (e.g., anti-NKp80 CARs described herein) or any of the anti-NKp80 antibody constructs described above. In some embodiments, the CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37. In some embodiments, the anti-NKp80 antibody construct comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12 or 16.
[0020] Also provided are vectors encoding the nucleic acids described herein; host cells comprising said nucleic acids or vectors; and pharmaceutical compositions comprising any of the engineered immune cells described herein and a pharmaceutically acceptable excipient.BRIEF DESCRIPTION OF THE DRAWINGS
[0021] FIG. 1 shows the expression of NKp80 and NKG2A on primary NK cells and primary T cells from peripheral blood mononuclear cells (PBMCs) .
[0022] FIG. 2 shows the expression of NKp80 on Raji. Luc cells that were constructed to overexpress NKp80. From left to right: Unstained, Transduced, MACS-P1 and MACS-P20, which correspond to unstained cells, transduced cells, cells from the 1st passage after enrichment, and cells from the 20th passage after enrichment, respectively.
[0023] FIG. 3 shows the in vitro cytotoxicity of anti-NKp80 CAR-T cells against NKp80-positive Raji. Luc cells at an effector-to-target (E: T) ratio of 10: 1 or 5: 1. UnT, untransduced T cells (control) ; M2981-T, T cells expressing M2981 CAR that comprises the anti-NKp80 VHH AS327466; M2986-T, T cells expressing M2986 CAR that comprises the anti-NKp80 VHH AS327860; M3040-T, T cells expressing M3040 CAR that comprises the anti-NKp80 VHH AS328653; M3056-T, T cells expressing M3056 CAR that comprises the anti-NKp80 VHH AS331499.
[0024] FIGs. 4A-4B show the cytokine release of IFN-γ (FIG. 4A) and TNFα (FIG. 4B) from anti-NKp80 CAR-T cells co-cultured with NKp80-positive Raji. Luc cells at an E: T ratio of 5: 1. UnT, untransduced T cells (control) ; M2981-T, AS327466-CAR T cells ; M2986-T, AS327860-CAR T cells; M3040-T, AS328653-CAR T cells; M3056-T, AS331499-CAR T cells.
[0025] FIGs. 5A-5B show the expression levels of NKp80 (FIG. 5A) and NKG2A (FIG. 5B) on primed NK cells. NC, negative control (i.e., unstained cells) ; SSC, side scatter.
[0026] FIG. 6 shows the in vitro cytotoxicity of anti-NKG2A CAR-T cells and anti-NKp80 CAR-T cells against primed NK cells at an E: T ratio of 1: 1 or 1: 5. UnT, untransduced T cells (control) ; M2969-T, T cells expressing anti-NKG2A CAR; M2981-T, AS327466-CAR T cells ; M2986-T, AS327860-CAR T cells; M3040-T, AS328653-CAR T cells; M3056-T, AS331499-CAR T cells.
[0027] FIG. 7 shows the in vitro cytotoxicity of anti-NKG2A CAR-T cells and anti-NKp80 CAR-T cells against primary NK cells at an E: T ratio of 2: 1 or 1: 1. UnT, untransduced T cells (control) ; M2981-T, AS327466-CAR T cells ; M2986-T, AS327860-CAR T cells; M3040-T, AS328653-CAR T cells; M3056-T, AS331499-CAR T cells.
[0028] FIGs. 8A-8B show the NK cell or T cell number during anti-NKG2A B2M knock-out (KO) CAR-T cells and anti-NKp80 B2M knock-out CAR-T cells co-culture with PBMC at an E:T ratio of 1: 25, respectively. FIG. 8A shows the fold-change of primary NK cells over 6 days of co-culture with each T cell group. FIG. 8B shows the fold-change of B2M KO T cell numbers for each T cell group over 6 days of co-culture with primary NK cells. B2M KO-T, T cells with knocked out B2M that do not express any CAR; M2969 B2M KO-T, anti-NKG2A CAR T cells with knocked out B2M; M2981 B2M KO-T, AS327466-CAR T cells with knocked out B2M; M3056 B2M KO-T, AS331499-CAR T cells with knocked out B2M.DETAILED DESCRIPTION
[0029] The present disclosure is based on a finding that NKp80 is highly expressed on primary NK cells from PBMCs, even higher than NKG2A, and is lowly expressed on T cells. This makes NKp80 suitable as a target or antigen to inhibit or prevent host NK cell killing, e.g., in an allogeneic transplantation therapy.
[0030] The present disclosure in one aspect provides engineered immune cells, wherein the engineered immune cells comprise an NKp80-binding protein comprising an NKp80 binding domain (e.g., an anti-NKp80 sdAb) . In some embodiments, the engineered immune cells further comprise a second antigen-binding protein (e.g., CAR) that specifically binds to a second antigen, wherein the second antigen is not NKp80. In some embodiments, the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, an NK cell, a B cell, a monocyte, a dendritic cell, and any combination thereof. In some embodiments, the engineered immune cell is further engineered to reduce or eliminate the expression and / or function of endogenous TCR, B2M, and / or NKp80. Pharmaceutical compositions comprising thereof, methods of making thereof, and methods of use thereof are also provided.
[0031] The present disclosure in another aspect provides anti-NKp80 antibody constructs, for example anti-NKp80 single domain antibodies ( “anti-NKp80 sdAb” ) or anti-NKp80 sdAb CARs.
[0032] Also provided herein are methods of making the engineered immune cells and / or the anti-NKp80 antibody constructs provided herein, and methods of treating and / or preventing host-versus-graft (HvG) symptoms, NK-cell disease, and / or cancer using the engineered immune cells and / or anti-NKp80 antibody constructs provided herein.
[0033] The engineered immune cells of the instant disclosure are engineered to express an NKp80-binding protein (e.g., anti-NKp80 CAR) that comprises an NKp80 binding domain, wherein the NKp80-binding protein blocks NKp80 and / or does not activate NPKp80, and optionally a second antigen-binding protein (e.g., CAR) that does not bind NKp80. The second antigen binding protein (e.g., second CAR) , is selected for its suitability for therapeutic treatment of a condition, disorder, or disease, such as a cancer, in a patient. For example, the second antigen binding protein may be a second CAR that recognizes an antigen that is expressed by or is characteristic of cells that associate with, cause, induce, promote, etc. the condition, disorder, or disease, e.g. cancer cells. The NKp80-binding protein, e.g., anti-NKp80 CAR, targets the NKp80 protein that is expressed on host immune cells, for example, NK cells or a subset of T cells. Thus, the engineered immune cell can defend itself against HvG, thereby prolonging the survival of the allogeneic cells after administration. Alternatively, one antigen binding protein, e.g. one tandem CAR, may comprise both “therapeutic” binding activity of a second antigen binding domain and the NKp80 binding activity of the NKp80 antigen binding domain. The present disclosure therefore provides a method of increasing persistence of allogeneic immune cells and / or reducing HvG response against allogeneic immune cells, e.g., allogeneic CAR-T cells or any other allogeneic CAR immune cell (e.g. CAR NK cell) , wherein the method comprises engineering the immune cell (e.g., CAR-T cell, CAR-NK cell, CAR-monocyte) to express an NKp80-binding protein such as an anti-NKp80 CAR. In some embodiments, the immune cell further expresses or is further engineered to express a second antigen binding protein (e.g., a second CAR) that targets a second antigen that is associated with or causes a condition, disorder, or disease (e.g., cancer) .
[0034] The approaches provided herein potentially provide a safer alternative to deep lymphodepletion regimens, because NKp80-negative immune cells are not expected to be targeted by the NKp80-binding protein, thus avoiding long-term immunosuppression. Additionally, NKp80 is also expressed by malignant NK cells in a variety of NK neoplasms, including renal cell carcinoma, lymphoma and acute myeloid leukemia. Hence the provided engineered immune cells and methods herein can also be used to treat NK cell related diseases such as NK cell cancer. Engineering immune cells, such as T cells, to express chimeric receptors (e.g., CAR) against NKp80 and a second target (e.g., a cancer-specific target, such as CD19 and / or CD20) , either as separate CARs or as a single tandem CAR with dual specificity, may therefore enhance the efficacy and persistence of the engineered immune cells (e.g., CAR-T cells) while reducing allogeneic graft rejection by the host immune system. Thus, approaches provided herein would increase the likelihood of success of allogeneic adoptive cell therapy and permit an “off-the-shelf” cell therapy approach to address a multitude of diseases. I. Definitions
[0035] Techniques and procedures described or referenced herein include those that are generally well understood and / or commonly employed using conventional methodology by those skilled in the art, such as, for example, the widely utilized methodologies described in Sambrook et al., Molecular Cloning: A Laboratory Manual (3d ed. 2001) ; Current Protocols in Molecular Biology (Ausubel et al. eds., 2003) ; Therapeutic Monoclonal Antibodies: From Bench to Clinic (An ed. 2009) ; Monoclonal Antibodies: Methods and Protocols (Albitar ed. 2010) ; and Antibody Engineering Vols 1 and 2 (Kontermann and Dübel eds., 2d ed. 2010) . Unless otherwise defined herein, technical and scientific terms used in the present description have the meanings that are commonly understood by those of ordinary skill in the art. For purposes of interpreting this specification, the following description of terms will apply and whenever appropriate, terms used in the singular will also include the plural and vice versa. In the event that any description of a term set forth conflicts with any document incorporated herein by reference, the description of the term set forth below shall control.
[0036] The term “antibody, ” “immunoglobulin, ” or “Ig” is used interchangeably herein, and is used in the broadest sense and specifically covers, for example, monoclonal antibodies (including agonist, antagonist, neutralizing antibodies, full length or intact monoclonal antibodies) , antibody compositions with polyepitopic or monoepitopic specificity, polyclonal or monovalent antibodies, multivalent antibodies, multispecific antibodies (e.g., bispecific antibodies so long as they exhibit the desired biological activity) , formed from at least two intact antibodies, single chain antibodies, and fragments thereof (e.g., domain antibodies) , as described below. An antibody can be human, humanized, chimeric and / or affinity matured, as well as an antibody from other species, for example, mouse, rabbit, llama, etc. The term “antibody” is intended to include a polypeptide product of B cells within the immunoglobulin class of polypeptides that is able to bind to a specific molecular antigen and is composed of two identical pairs of polypeptide chains, wherein each pair has one heavy chain (about 50-70 kDa) and one light chain (about 25 kDa) , each amino-terminal portion of each chain includes a variable region of about 100 to about 130 or more amino acids, and each carboxy-terminal portion of each chain includes a constant region. See, e.g., Antibody Engineering (Borrebaeck ed., 2d ed. 1995) ; and Kuby, Immunology (3d ed. 1997) . Antibodies also include, but are not limited to, synthetic antibodies, recombinantly produced antibodies, antibodies including from Camelidae species (e.g., llama or alpaca) or their humanized variants, intrabodies, anti-idiotypic (anti-Id) antibodies, and functional fragments (e.g., antigen binding fragments) of any of the above, which refers to a portion of an antibody heavy or light chain polypeptide that retains some or all of the binding activity of the antibody from which the fragment was derived. Non-limiting examples of functional fragments (e.g., antigen binding fragments) include single-chain Fvs (scFv) (e.g., including monospecific, bispecific, etc. ) , Fab fragments, F (ab’) fragments, F (ab) 2 fragments, F (ab’) 2 fragments, disulfide-linked Fvs (dsFv) , Fd fragments, Fv fragments, sdAb, diabody, triabody, tetrabody, and minibody. In particular, antibodies provided herein include immunoglobulin molecules and immunologically active portions of immunoglobulin molecules, for example, antigen-binding domains or molecules that contain an antigen-binding site that binds to an antigen (e.g., one or more CDRs of an antibody) . Such antibody fragments can be found in, for example, Harlow and Lane, Antibodies: A Laboratory Manual (1989) ; Mol. Biology and Biotechnology: A Comprehensive Desk Reference (Myers ed., 1995) ; Huston et al., 1993, Cell Biophysics 22: 189-224; Plückthun and Skerra, 1989, Meth. Enzymol. 178: 497-515; and Day, Advanced Immunochemistry (2d ed. 1990) . The antibodies provided herein can be of any class (e.g., IgG, IgE, IgM, IgD, and IgA) or any subclass (e.g., IgG1, IgG2, IgG3, IgG4, IgA1, and IgA2) of immunoglobulin molecule. Antibodies may be agonistic antibodies or antagonistic antibodies. Antibodies may be neither agonistic nor antagonistic.
[0037] An “antigen” is a structure to which an antibody can selectively bind. A target antigen may be a polypeptide, carbohydrate, nucleic acid, lipid, hapten, or other naturally occurring or synthetic compound. The target antigen can be a polypeptide. An antigen may be associated with a cell, for example, is present on or in a cell.
[0038] “Single-chain Fv” also abbreviated as “sFv” or “scFv” are antibody fragments that comprise the VH and VL antibody domains connected into a single polypeptide chain. The scFv polypeptide may further comprise a polypeptide linker between the VH and VL domains which enables the scFv to form the desired structure for antigen binding. For a review of the scFv, see Pluckthun in The Pharmacology of Monoclonal Antibodies, vol. 113, Rosenburg and Moore eds., Springer-Verlag, New York, pp. 269-315 (1994) .
[0039] The term “heavy chain-only antibody” or “HCAb” refers to a functional antibody, which comprises heavy chains, but lacks the light chains usually found in 4-chain antibodies. For example, camelid animals (such as camels, llamas, or alpacas) are known to produce HCAbs.
[0040] “Single domain antibody” or “sdAb” as used herein refers to a single monomeric variable antibody domain and which is capable of antigen binding. Single domain antibodies include VHH domains as described herein. Examples of single domain antibodies include, but are not limited to, antibodies naturally devoid of light chains such as those from Camelidae species (e.g., llama) , single domain antibodies derived from conventional 4-chain antibodies, engineered antibodies and single domain scaffolds other than those derived from antibodies. Single domain antibodies (e.g., VHH domains) may be derived from any species including, but not limited to mouse, human, camel, llama, goat, rabbit, and bovine. For example, a single domain antibody can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, alpaca, and guanaco, as described herein. Other species besides Camelidae may produce heavy chain antibodies naturally devoid of light chain; VHHs derived from such other species are within the scope of the disclosure. The single domain antibody (e.g., VHH domain) provided herein has a structure of FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4. Single domain antibodies may be genetically fused or chemically conjugated to another molecule (e.g., an agent) as described herein. Single domain antibodies may be part of a bigger binding molecule (e.g., a multispecific antibody or a chimeric antigen receptor) .
[0041] The terms “binds” or “binding” refer to an interaction between molecules including, for example, to form a complex. Interactions can be, for example, non-covalent interactions including hydrogen bonds, ionic bonds, hydrophobic interactions, and / or van der Waals interactions. A complex can also include the binding of two or more molecules held together by covalent or non-covalent bonds, interactions, or forces. The strength of the total non-covalent interactions between a single antigen-binding site on a binding molecule and a single epitope of a target molecule, such as an antigen, is the affinity of the binding molecule or functional fragment for that epitope. The ratio of dissociation rate (koff) to association rate (kon) of a binding molecule (e.g., an antibody) to a monovalent antigen (koff / kon) is the dissociation constant KD, which is inversely related to affinity. The lower the KD value, the higher the affinity of the molecule. The value of KD varies for different complexes of binding molecule and its target antigen and depends on both kon and koff. The dissociation constant KD for a binding molecule against its target provided herein can be determined using any method provided herein or any other method well known to those skilled in the art. The affinity at one binding site does not always reflect the true strength of the interaction between a binding molecule and a target antigen. When complex antigens containing multiple, repeating antigenic determinants, such as a polyvalent antigen, come in contact with antibodies containing multiple binding sites, the interaction of antibody with antigen at one site will increase the probability of a reaction at a second site. The strength of such multiple interactions between a multivalent antibody and antigen is called the avidity.
[0042] In connection with the binding molecules described herein terms such as “bind to, ” “that specifically bind to, ” and analogous terms are also used interchangeably herein and refer to binding molecules of antigen binding domains that specifically bind to an antigen, such as a polypeptide. A binding molecule or antigen binding domain that binds to or specifically binds to an antigen can be identified, for example, by immunoassays, or other techniques known to those of skill in the art. A binding molecule or antigen binding domain may bind to or specifically bind to an antigen when it binds to an antigen with higher affinity than to any cross-reactive antigen as determined using experimental techniques, such as radioimmunoassay (RIA) and enzyme linked immunosorbent assay (ELISA) . Typically, a specific or selective reaction will be at least twice background signal or noise and may be more than 10 times background. See, e.g., Fundamental Immunology 332-36 (Paul ed., 2d ed. 1989) for a discussion regarding binding specificity. The extent of binding of a binding molecule or antigen binding domain to a “non-target” protein may be less than about 10%of the binding of the binding molecule or antigen binding domain to its particular target antigen, for example, as determined by fluorescence activated cell sorting (FACS) analysis or RIA. A binding molecule or antigen binding domain that binds to an antigen includes one that is capable of binding the antigen with sufficient affinity such that the binding molecule is useful, for example, as a therapeutic and / or diagnostic agent in targeting the antigen. A binding molecule or antigen binding domain that binds to an antigen may have a dissociation constant (KD) of ≤ 1μM, ≤ 100 nM, ≤ 10 nM, ≤ 1 nM, or ≤ 0.1 nM. In certain embodiments, a binding molecule or antigen binding domain binds to an epitope of an antigen that is conserved among the antigen from different species.
[0043] The binding molecules or antigen binding domains can comprise “chimeric” sequences in which a portion of the heavy and / or light chain is identical with or homologous to corresponding sequences in antibodies derived from a particular species or belonging to a particular antibody class or subclass, while the remainder of the chain (s) is identical with or homologous to corresponding sequences in antibodies derived from another species or belonging to another antibody class or subclass, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (see U.S. Pat. No. 4,816,567; and Morrison et al., 1984, Proc. Natl. Acad. Sci. USA 81: 6851-55) . Chimeric sequences may include humanized sequences.
[0044] In certain embodiments, the binding molecules or antigen binding domains can comprise portions of “humanized” forms of nonhuman (e.g., camelid, murine, non-human primate) antibodies that include sequences from human immunoglobulins (e.g., recipient antibody) in which the native CDR residues are replaced by residues from the corresponding CDR of a nonhuman species (e.g., donor antibody) such as camelid, mouse, rat, rabbit, or nonhuman primate having the desired specificity, affinity, and capacity. In some instances, one or more FR region residues of the human immunoglobulin sequences are replaced by corresponding nonhuman residues. Furthermore, humanized antibodies can comprise residues that are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance. A humanized antibody heavy or light chain can comprise substantially all of at least one or more variable regions, in which all or substantially all of the CDRs correspond to those of a nonhuman immunoglobulin and all or substantially all of the FRs are those of a human immunoglobulin sequence. The humanized antibody may comprise at least a portion of an immunoglobulin constant region (Fc) , typically that of a human immunoglobulin. For further details, see, Jones et al., Nature 321: 522-25 (1986) ; Riechmann et al., Nature 332: 323-29 (1988) ; Presta, Curr. Op. Struct. Biol. 2: 593-96 (1992) ; Carter et al., Proc. Natl. Acad. Sci. USA 89: 4285-89 (1992) ; U.S. Pat. Nos: 6,800,738; 6,719,971; 6,639,055; 6,407,213; and 6,054,297.
[0045] The binding molecules or antigen binding domains can comprise portions of a “fully human antibody” or “human antibody, ” wherein the terms are used interchangeably herein and refer to an antibody that comprises a human variable region and, for example, a human constant region. The binding molecules may comprise an antibody sequence. In specific embodiments, the terms refer to an antibody that comprises a variable region and constant region of human origin. “Fully human” antibodies, in certain embodiments, can also encompass antibodies which bind polypeptides and are encoded by nucleic acid sequences which are naturally occurring somatic variants of human germline immunoglobulin nucleic acid sequence. The term “fully human antibody” includes antibodies having variable and constant regions corresponding to human germline immunoglobulin sequences as described by Kabat et al. (See Kabat et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91-3242) . A “human antibody” is one that possesses an amino acid sequence which corresponds to that of an antibody produced by a human and / or has been made using any of the techniques for making human antibodies. This definition of a human antibody specifically excludes a humanized antibody comprising non-human antigen-binding residues. Human antibodies can be produced using various techniques known in the art, including phage-display libraries (Hoogenboom and Winter, J. Mol. Biol. 227: 381 (1991) ; Marks et al., J. Mol. Biol. 222: 581 (1991) ) and yeast display libraries (Chao et al., Nature Protocols 1: 755-68 (2006) ) . Also available for the preparation of human monoclonal antibodies are methods described in Cole et al., Monoclonal Antibodies and Cancer Therapy 77 (1985) ; Boerner et al., J. Immunol. 147 (1) : 86-95 (1991) ; and van Dijk and van de Winkel, Curr. Opin. Pharmacol. 5: 368-74 (2001) . Human antibodies can be prepared by administering the antigen to a transgenic animal that has been modified to produce such antibodies in response to antigenic challenge, but whose endogenous loci have been disabled, e.g., mice (see, e.g., Jakobovits, Curr. Opin. Biotechnol. 6 (5) : 561-66 (1995) ; Brüggemann and Taussing, Curr. Opin. Biotechnol. 8 (4) : 455-58 (1997) ; and U.S. Pat. Nos. 6,075,181 and 6,150,584 regarding XENOMOUSETM technology) . See also, for example, Li et al., Proc. Natl. Acad. Sci. USA 103: 3557-62 (2006) regarding human antibodies generated via a human B-cell hybridoma technology.
[0046] The binding molecules or antigen binding domains can comprise portions of a “recombinant human antibody, ” wherein the phrase includes human antibodies that are prepared, expressed, created, or isolated by recombinant means, such as antibodies expressed using a recombinant expression vector transfected into a host cell, antibodies isolated from a recombinant, combinatorial human antibody library, antibodies isolated from an animal (e.g., a mouse or cow) that is transgenic and / or transchromosomal for human immunoglobulin genes (see, e.g., Taylor, L. D. et al., Nucl. Acids Res. 20: 6287-6295 (1992) ) or antibodies prepared, expressed, created or isolated by any other means that involves splicing of human immunoglobulin gene sequences to other DNA sequences. Such recombinant human antibodies can have variable and constant regions derived from human germline immunoglobulin sequences (See 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) . In certain embodiments, however, such recombinant human antibodies are subjected to in vitro mutagenesis (or, when an animal transgenic for human Ig sequences is used, in vivo somatic mutagenesis) and thus the amino acid sequences of the VH and VL regions of the recombinant antibodies are sequences that, while derived from and related to human germline VH and VL sequences, may not naturally exist within the human antibody germline repertoire in vivo.
[0047] In certain embodiments, the binding molecules or antigen binding domains can comprise a portion of a “monoclonal antibody, ” wherein the term as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, e.g., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts or well-known post-translational modifications such as amino acid isomerization or deamidation, methionine oxidation or asparagine or glutamine deamidation, each monoclonal antibody will typically recognize a single epitope on the antigen. In specific embodiments, a “monoclonal antibody, ” as used herein, is an antibody produced by a single hybridoma or other cell. The term “monoclonal” is not limited to any particular method for making the antibody. For example, the monoclonal antibodies useful in the present disclosure may be prepared by the hybridoma methodology first described by Kohler et al., Nature 256: 495 (1975) , or may be made using recombinant DNA methods in bacterial or eukaryotic animal or plant cells (see, e.g., U.S. Pat. No. 4,816,567) . The “monoclonal antibodies” may also be isolated from phage antibody libraries using the techniques described in Clackson et al., Nature 352: 624-28 (1991) and Marks et al., J. Mol. Biol. 222: 581-97 (1991) , for example. Other methods for the preparation of clonal cell lines and of monoclonal antibodies expressed thereby are well known in the art. See, e.g., Short Protocols in Molecular Biology (Ausubel et al. eds., 5th ed. 2002) .
[0048] A typical 4-chain antibody unit is a heterotetrameric glycoprotein composed of two identical light (L) chains and two identical heavy (H) chains. In the case of IgGs, the 4-chain unit is generally about 150,000 daltons. Each L chain is linked to an H chain by one covalent disulfide bond, while the two H chains are linked to each other by one or more disulfide bonds depending on the H chain isotype. Each H and L chain also has regularly spaced intrachain disulfide bridges. Each H chain has at the N-terminus, a variable domain (VH) followed by three constant domains (CH) for each of the α and γ chains and four CH domains for μ and ε isotypes. Each L chain has at the N-terminus, a variable domain (VL) followed by a constant domain (CL) at its other end. The VL is aligned with the VH, and the CL is aligned with the first constant domain of the heavy chain (CH1) . Particular amino acid residues are believed to form an interface between the light chain and heavy chain variable domains. The pairing of a VH and VL together forms a single antigen-binding site. For the structure and properties of the different classes of antibodies, see, for example, Basic and Clinical Immunology 71 (Stites et al. eds., 8th ed. 1994) ; and Immunobiology (Janeway et al. eds., 5th ed. 2001) .
[0049] The term “Fab” or “Fab region” refers to an antibody region that binds to antigens. A conventional IgG usually comprises two Fab regions, each residing on one of the two arms of the Y-shaped IgG structure. Each Fab region is typically composed of one variable region and one constant region of each of the heavy and the light chain. More specifically, the variable region and the constant region of the heavy chain in a Fab region are VH and CH1 regions, and the variable region and the constant region of the light chain in a Fab region are VL and CL regions. The VH, CH1, VL, and CL in a Fab region can be arranged in various ways to confer an antigen binding capability according to the present disclosure. For example, VH and CH1 regions can be on one polypeptide, and VL and CL regions can be on a separate polypeptide, similarly to a Fab region of a conventional IgG. Alternatively, VH, CH1, VL and CL regions can all be on the same polypeptide and oriented in different orders as described in more detail the sections below.
[0050] The term “variable region, ” “variable domain, ” “V region, ” or “V domain” refers to a portion of the light or heavy chains of an antibody that is generally located at the amino-terminal of the light or heavy chain and has a length of about 120 to 130 amino acids in the heavy chain and about 100 to 110 amino acids in the light chain, and are used in the binding and specificity of each particular antibody for its particular antigen. The variable region of the heavy chain may be referred to as “VH” . The variable region of the light chain may be referred to as “VL” . The term “variable” refers to the fact that certain segments of the variable regions differ extensively in sequence among antibodies. The V region mediates antigen binding and defines specificity of a particular antibody for its particular antigen. However, the variability is not evenly distributed across the 110-amino acid span of the variable regions. Instead, the V regions consist of less variable (e.g., relatively invariant) stretches called framework regions (FRs) of about 15-30 amino acids separated by shorter regions of greater variability (e.g., extreme variability) called “hypervariable regions” that are each about 9-12 amino acids long. The variable regions of heavy and light chains each comprise four FRs, largely adopting a β sheet configuration, connected by three hypervariable regions, which form loops connecting, and in some cases form part of, the βsheet structure. The hypervariable regions in each chain are held together in close proximity by the FRs and, with the hypervariable regions from the other chain, contribute to the formation of the antigen-binding site of antibodies (see, e.g., Kabat et al., Sequences of Proteins of Immunological Interest (5th ed. 1991) ) . The constant regions are not involved directly in binding an antibody to an antigen, but exhibit various effector functions, such as participation of the antibody in antibody dependent cellular cytotoxicity (ADCC) and complement dependent cytotoxicity (CDC) . The variable regions differ extensively in sequence between different antibodies. The variable region may be a human variable region.
[0051] The term “variable region residue numbering according to Kabat” or “amino acid position numbering as in Kabat” , and variations thereof, refer to the numbering system used for heavy chain variable regions or light chain variable regions of the compilation of antibodies in Kabat et al., supra. Using this numbering system, the actual linear amino acid sequence may contain fewer or additional amino acids corresponding to a shortening of, or insertion into, an FR or CDR of the variable domain. For example, a heavy chain variable domain may include a single amino acid insert (residue 52a according to Kabat) after residue 52 and three inserted residues (e.g., residues 82a, 82b, and 82c, etc. according to Kabat) after residue 82. The Kabat numbering of residues may be determined for a given antibody by alignment at regions of homology of the sequence of the antibody with a “standard” Kabat numbered sequence. The Kabat numbering system is generally used when referring to a residue in the variable domain (approximately residues 1-107 of the light chain and residues 1-113 of the heavy chain) (e.g., Kabat et al., supra) . The “EU numbering system” or “EU index” is generally used when referring to a residue in an immunoglobulin heavy chain constant region (e.g., the EU index reported in Kabat et al., supra) . The “EU index as in Kabat” refers to the residue numbering of the human IgG 1 EU antibody. Other numbering systems have been described, for example, by AbM, Chothia, Contact, IMGT, and AHon.
[0052] The term “heavy chain” when used in reference to an antibody refers to a polypeptide chain of about 50-70 kDa, wherein the amino-terminal portion includes a variable region of about 120 to 130 or more amino acids, and a carboxy-terminal portion includes a constant region. The constant region can be one of five distinct types, (e.g., isotypes) referred to as alpha (α) , delta (δ) , epsilon (ε) , gamma (γ) , and mu (μ) , based on the amino acid sequence of the heavy chain constant region. The distinct heavy chains differ in size: α, δ, and γ contain approximately 450 amino acids, while μ and ε contain approximately 550 amino acids. When combined with a light chain, these distinct types of heavy chains give rise to five well known classes (e.g., isotypes) of antibodies, IgA, IgD, IgE, IgG, and IgM, respectively, including four subclasses of IgG, namely IgG1, IgG2, IgG3, and IgG4.
[0053] The term “light chain” when used in reference to an antibody refers to a polypeptide chain of about 25 kDa, wherein the amino-terminal portion includes a variable region of about 100 to about 110 or more amino acids, and a carboxy-terminal portion includes a constant region. The approximate length of a light chain is 211 to 217 amino acids. There are two distinct types, referred to as kappa (κ) or lambda (λ) based on the amino acid sequence of the constant domains.
[0054] As used herein, the terms “hypervariable region, ” “HVR, ” “Complementarity Determining Region, ” and “CDR” are used interchangeably. A “CDR” refers to one of three hypervariable regions (H1, H2 or H3) within the non-framework region of the immunoglobulin (Ig or antibody) VH β-sheet framework, or one of three hypervariable regions (L1, L2 or L3) within the non-framework region of the antibody VL β-sheet framework. CDR1, CDR2 and CDR3 in VH domain are also referred to as HCDR1, HCDR2 and HCDR3, respectively. CDR1, CDR2 and CDR3 in VL domain are also referred to as LCDR1, LCDR2 and LCDR3, respectively. Accordingly, CDRs are variable region sequences interspersed within the framework region sequences.
[0055] CDR regions are well known to those skilled in the art and have been defined by well-known numbering systems. For example, the Kabat Complementarity Determining Regions (CDRs) are based on sequence variability and are the most commonly used (see, e.g., Kabat et al., supra; Nick Deschacht et al., J Immunol 2010; 184: 5696-5704) . Chothia refers instead to the location of the structural loops (see, e.g., Chothia and Lesk, J. Mol. Biol. 196: 901-17 (1987) ) . The end of the Chothia CDR-H1 loop when numbered using the Kabat numbering convention varies between H32 and H34 depending on the length of the loop (this is because the Kabat numbering scheme places the insertions at H35A and H35B; if neither 35A nor 35B is present, the loop ends at 32; if only 35A is present, the loop ends at 33; if both 35A and 35B are present, the loop ends at 34) . The AbM hypervariable regions represent a compromise between the Kabat CDRs and Chothia structural loops, and are used by Oxford Molecular’s AbM antibody modeling software (see, e.g., Antibody Engineering Vol. 2 (Kontermann and Dübel eds., 2d ed. 2010) ) . The “contact” hypervariable regions are based on an analysis of the available complex crystal structures. Another universal numbering system that has been developed and widely adopted is ImMunoGeneTics (IMGT) Information (Lafranc et al., Dev. Comp. Immunol. 27 (1) : 55-77 (2003) ) . IMGT is an integrated information system specializing in immunoglobulins (IG) , T-cell receptors (TCR) , and major histocompatibility complex (MHC) of human and other vertebrates. Herein, the CDRs are referred to in terms of both the amino acid sequence and the location within the light or heavy chain. As the “location” of the CDRs within the structure of the immunoglobulin variable domain is conserved between species and present in structures called loops, by using numbering systems that align variable domain sequences according to structural features, CDR and framework residues are readily identified. This information can be used in grafting and replacement of CDR residues from immunoglobulins of one species into an acceptor framework from, typically, a human antibody. An additional numbering system (AHon) has been developed by Honegger and Plückthun, J. Mol. Biol. 309: 657-70 (2001) . Correspondence between the numbering system, including, for example, the Kabat numbering and the IMGT unique numbering system, is well known to one skilled in the art (see, e.g., Kabat, supra; Chothia and Lesk, supra; Martin, supra; Lefranc et al., supra) . The residues from each of these hypervariable regions or CDRs are exemplified in Table A below. Table A. Exemplary CDRs According to Various Numbering Systems
[0056] The boundaries of a given CDR may vary depending on the scheme used for identification. Thus, unless otherwise specified, the terms “CDR” and “complementary determining region” of a given antibody or region thereof, such as a variable region, as well as individual CDRs (e.g., CDR-H1, CDR-H2) of the antibody or region thereof, should be understood to encompass the complementary determining region as defined by any of the known schemes described herein above. In some instances, the scheme for identification of a particular CDR or CDRs is specified, such as the CDR as defined by the IMGT, Kabat, Chothia, or Contact method. In other cases, the particular amino acid sequence of a CDR is given. It should be noted CDR regions may also be defined by any combination of various numbering systems, e.g., a combination of Kabat and Chothia numbering systems, a combination of Kabat and AbM numbering systems, or a combination of Kabat and IMGT numbering systems. Therefore, the term such as “aCDR1 as set forth in a specific VH” includes any CDR1 as defined by the exemplary CDR numbering systems described above but is not limited thereby. Once a variable region (e.g., a VH or VL) is given, those skilled in the art would understand that CDRs within the region can be defined by different numbering systems or combinations thereof.
[0057] The term “hypervariable region, ” “HVR, ” or “HV, ” when used herein refers to the regions of an antibody variable domain which are hypervariable in sequence and / or form structurally defined loops. Generally, single-domain antibodies comprise three HVRs (or CDRs) : HVR1 (or CDR1) , HVR2 (or CDR2) , and HVR3 (or CDR3) . HVR3 (or CDR3) displays the most diversity of the three HVRs and is believed to play a unique role in conferring fine specificity to antibodies. See, e.g., Hamers-Casterman et al., Nature 363: 446-448 (1993) ; Sheriff et al., Nature Struct. Biol. 3: 733-736 (1996) . Hypervariable regions may comprise “extended hypervariable regions” as follows: 24-36 or 24-34 (L1) , 46-56 or 50-56 (L2) , and 89-97 or 89-96 (L3) in the VL, and 26-35 or 26-35A (H1) , 50-65 or 49-65 (H2) , and 93-102, 94-102, or 95-102 (H3) in the VH.
[0058] The term “constant region” or “constant domain” refers to a carboxy terminal portion of the light and heavy chain which is not directly involved in binding of the antibody to antigen but exhibits various effector function, such as interaction with the Fc receptor. The term refers to the portion of an immunoglobulin molecule having a more conserved amino acid sequence relative to the other portion of the immunoglobulin, the variable region, which contains the antigen binding site. The constant region may contain the CH1, CH2, and CH3 regions of the heavy chain and the CL region of the light chain.
[0059] The term “framework” or “FR” refers to those variable region residues flanking the CDRs. FR residues are present, for example, in chimeric, humanized, human, domain antibodies, diabodies, linear antibodies, and bispecific antibodies. FR residues are those variable domain residues other than the hypervariable region residues or CDR residues.
[0060] The term “Fc region” herein is used to define a C-terminal region of an immunoglobulin heavy chain, including, for example, native sequence Fc regions, recombinant Fc regions, and variant Fc regions. Although the boundaries of the Fc region of an immunoglobulin heavy chain might vary, the human IgG heavy chain Fc region is often defined to stretch from an amino acid residue at position Cys226, or from Pro230, to the carboxyl-terminus thereof. The C-terminal lysine (residue 447 according to the EU numbering system) of the Fc region may be removed, for example, during production or purification of the antibody, or by recombinantly engineering the nucleic acid encoding a heavy chain of the antibody. Accordingly, a composition of intact antibodies may comprise antibody populations with all K447 residues removed, antibody populations with no K447 residues removed, and antibody populations having a mixture of antibodies with and without the K447 residue. A “functional Fc region” possesses an “effector function” of a native sequence Fc region. Exemplary “effector functions” include C1q binding; CDC; Fc receptor binding; ADCC; phagocytosis; downregulation of cell surface receptors (e.g., B cell receptor) , etc. Such effector functions generally require the Fc region to be combined with a binding region or binding domain (e.g., an antibody variable region or domain) and can be assessed using various assays known to those skilled in the art. A “variant Fc region” comprises an amino acid sequence which differs from that of a native sequence Fc region by virtue of at least one amino acid modification (e.g., substituting, addition, or deletion) . In certain embodiments, the variant Fc region has at least one amino acid substitution compared to a native sequence Fc region or to the Fc region of a parent polypeptide, for example, from about one to about ten amino acid substitutions, or from about one to about five amino acid substitutions in a native sequence Fc region or in the Fc region of a parent polypeptide. The variant Fc region herein can possess at least about 80%homology with a native sequence Fc region and / or with an Fc region of a parent polypeptide, or at least about 90%homology therewith, for example, at least about 95%homology therewith.
[0061] As used herein, an “epitope” is a term in the art and refers to a localized region of an antigen to which a binding molecule (e.g., an antibody) can specifically bind. An epitope can be a linear epitope or a conformational, non-linear, or discontinuous epitope. In the case of a polypeptide antigen, for example, an epitope can be contiguous amino acids of the polypeptide (a“linear” epitope) or an epitope can comprise amino acids from two or more non-contiguous regions of the polypeptide (a “conformational, ” “non-linear” or “discontinuous” epitope) . It will be appreciated by one of skill in the art that, in general, a linear epitope may or may not be dependent on secondary, tertiary, or quaternary structure. For example, a binding molecule may bind to a group of amino acids regardless of whether they are folded in a natural three-dimensional protein structure. A binding molecule may require amino acid residues making up the epitope to exhibit a particular conformation (e.g., bend, twist, turn or fold) in order to recognize and bind the epitope.
[0062] “Percent (%) amino acid sequence identity” and “homology” with respect to a peptide, polypeptide or antibody sequence are defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in the specific peptide or polypeptide sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN or MEGALIGNTM (DNASTAR) software. Those skilled in the art can determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full length of the sequences being compared.
[0063] The term “specificity” refers to selective recognition of an antigen binding protein (such as a CAR or an antibody) for a particular epitope of an antigen. Natural antibodies, for example, are monospecific. The term “multispecific” as used herein denotes that an antigen binding protein has two or more antigen-binding sites of which at least two bind different epitopes. “Bispecific” as used herein denotes that an antigen binding protein has two different antigen-binding specificities. The term “monospecific” as used herein denotes an antigen binding protein that has one or more binding sites each of which bind the same epitope.
[0064] The term “valent” as used herein denotes the presence of a specified number of binding sites in an antigen binding protein (such as a CAR or an antibody) . A natural antibody for example or a full-length antibody has two binding sites and is bivalent. As such, the terms “trivalent” , “tetravalent” , “pentavalent” and “hexavalent” denote the presence of two binding site, three binding sites, four binding sites, five binding sites, and six binding sites, respectively, in an antigen binding protein.
[0065] As used herein, a first antibody or fragment thereof “competes” for binding to a target antigen / epitope with a second antibody or fragment thereof when the first antibody or fragment thereof inhibits the target antigen / epitope binding of the second antibody of fragment thereof by at least about 50% (such as at least about any one of 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 98%or 99%) in the presence of an equimolar concentration of the first antibody or fragment thereof, or vice versa. A high throughput process for “binning” antibodies based upon their cross-competition is described in WO 2003 / 048731.
[0066] As used herein, a cell is considered "positive" for a cell-surface marker if it expresses the marker on its cell-surface in amounts sufficient to be detected using methods known to those of skill in the art, such as contacting a cell with an antibody that binds specifically to that marker, and subsequently performing flow cytometric analysis of such a contacted cell to determine whether the antibody is specifically bound the cell. It is to be understood that while a cell may express messenger RNA for a cell-surface marker, in order to be considered positive for the compositions and methods described herein, the cell must express the marker of interest on its surface. Similarly, a cell is considered "negative" for a cell-surface marker if it does not express the marker on its surface in amounts sufficient to be detected using methods known to those of skill in the art, such as contacting a cell with an antibody that binds specifically to that marker and subsequently performing flow cytometric analysis of such a contacted cell to determine whether the antibody is bound the cell.
[0067] The term “transplantation immune rejection” or “transplantation rejection” refers to such an immunological response, in which after a graft, such as a heterologous tissue, organ, or cell is transplanted into a host, the exogenous graft as an “exogenous component” is recognized by the host's immune system, and the immune system initiates an attack on the graft and tries to destruct and remove it.
[0068] The term “host” refers to a recipient who receives transplantation of a graft. In some embodiments, it may be an individual, such as a human, who receives transplantation of exogenous cells.
[0069] A “blocking” antibody or an “antagonist” antibody is one that inhibits or reduces a biological activity of the antigen to which it binds. In some embodiments, the blocking antibodies or antagonist antibodies substantially or completely inhibit the biological activity of the antigen. The NKp80 binding protein or NKp80 binding domain of the disclosure may block or not active the interaction between NKp80 and its ligand and, thus, signaling through NKp80. The NKp80 activation can be measured via any known method, including but not limited to detecting NK cell IFN-γ secretion. An "agonist" or activating antibody is one that enhances or initiates signaling by the antigen to which it binds. In some embodiments, the agonist antibodies cause or activate the signaling without the presence of the natural ligand. The NKp80 binding protein or NKp80 binding domain of the disclosure may cause or activate the NKp80 signaling.
[0070] “Chimeric antigen receptor” or “CAR” as used herein refers to genetically engineered receptors, which can be used to graft one or more antigen specificity onto immune effector cells, such as T cells. Some CARs are also known as “artificial T-cell receptors, ” “chimeric T cell receptors, ” or “chimeric immune receptors. ” The CAR may comprise an extracellular antigen binding domain specific for one or more antigens (such as tumor antigens) , a transmembrane domain, and an intracellular signaling domain of a T cell and / or other receptors. “CAR-T cell” refers to a T cell that expresses a CAR.
[0071] The terms “polypeptide” and “peptide” and “protein” are used interchangeably herein and refer to polymers of amino acids of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid, including but not limited to, unnatural amino acids, as well as other modifications known in the art. It is understood that, because the polypeptides of this disclosure may be based upon antibodies or other members of the immunoglobulin superfamily, a “polypeptide” can occur as a single chain or as two or more associated chains.
[0072] “Polynucleotide” or “nucleic acid, ” as used interchangeably herein, refers to polymers of nucleotides of any length and includes DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, modified nucleotides or bases, and / or their analogs, or any substrate that can be incorporated into a polymer by DNA or RNA polymerase or by a synthetic reaction. A polynucleotide may comprise modified nucleotides, such as methylated nucleotides and their analogs. “Oligonucleotide, ” as used herein, refers to short, generally single-stranded, synthetic polynucleotides that are generally, but not necessarily, fewer than about 200 nucleotides in length. The terms “oligonucleotide” and “polynucleotide” are not mutually exclusive. The description above for polynucleotides is equally and fully applicable to oligonucleotides. A cell that produces a binding molecule of the present disclosure may include a parent hybridoma cell, as well as bacterial and eukaryotic host cells into which nucleic acids encoding the antibodies have been introduced. Unless specified otherwise, the left-hand end of any single-stranded polynucleotide sequence disclosed herein is the 5′end; the left-hand direction of double-stranded polynucleotide sequences is referred to as the 5′direction. The direction of 5′to 3′addition of nascent RNA transcripts is referred to as the transcription direction; sequence regions on the DNA strand having the same sequence as the RNA transcript that are 5′to the 5′end of the RNA transcript are referred to as “upstream sequences” ; sequence regions on the DNA strand having the same sequence as the RNA transcript that are 3′to the 3′end of the RNA transcript are referred to as “downstream sequences. ”
[0073] An “isolated nucleic acid” is a nucleic acid, for example, an RNA, DNA, or a mix of nucleic acids, which is substantially separated from other genome DNA sequences as well as proteins or complexes such as ribosomes and polymerases, which naturally accompany a native sequence. An “isolated” nucleic acid molecule is one which is separated from other nucleic acid molecules which are present in the natural source of the nucleic acid molecule. Moreover, an “isolated” nucleic acid molecule, such as a cDNA molecule, can be substantially free of other cellular material, or culture medium when produced by recombinant techniques, or substantially free of chemical precursors or other chemicals when chemically synthesized. In a specific embodiment, one or more nucleic acid molecules encoding an antibody as described herein are isolated or purified. The term embraces nucleic acid sequences that have been removed from their naturally occurring environment and includes recombinant or cloned DNA isolates and chemically synthesized analogues or analogues biologically synthesized by heterologous systems. A substantially pure molecule may include isolated forms of the molecule. Specifically, an “isolated” nucleic acid molecule encoding a CAR or an antibody described herein is a nucleic acid molecule that is identified and separated from at least one contaminant nucleic acid molecule with which it is ordinarily associated in the environment in which it was produced.
[0074] Unless otherwise specified, a “nucleotide sequence encoding an amino acid sequence” includes all nucleotide sequences that are degenerate versions of each other and that encode the same amino acid sequence. The phrase nucleotide sequence that encodes a protein or an RNA may also include introns to the extent that the nucleotide sequence encoding the protein may in some versions contain an intron (s) .
[0075] The term “control sequences” refers to DNA sequences necessary for the expression of an operably linked coding sequence in a particular host organism. The control sequences that are suitable for prokaryotes, for example, include a promoter, optionally an operator sequence, and a ribosome binding site. Eukaryotic cells are known to utilize promoters, polyadenylation signals, and enhancers.
[0076] As used herein, the term “operatively linked, ” and similar phrases (e.g., genetically fused) , when used in reference to nucleic acids or amino acids, refer to the operational linkage of nucleic acid sequences or amino acid sequence, respectively, placed in functional relationships with each other. For example, an operatively linked promoter, enhancer elements, open reading frame, 5′ and 3′ UTR, and terminator sequences result in the accurate production of a nucleic acid molecule (e.g., RNA) . In some embodiments, operatively linked nucleic acid elements result in the transcription of an open reading frame and ultimately the production of a polypeptide (i.e., expression of the open reading frame) . As another example, an operatively linked peptide is one in which the functional domains are placed with appropriate distance from each other to impart the intended function of each domain.
[0077] The term “vector” refers to a substance that is used to carry or include a nucleic acid sequence, including for example, a nucleic acid sequence encoding a binding molecule (e.g., an antibody) as described herein, in order to introduce a nucleic acid sequence into a host cell. Vectors applicable for use include, for example, expression vectors, plasmids, phage vectors, viral vectors, episomes, and artificial chromosomes, which can include selection sequences or markers operable for stable integration into a host cell’s chromosome. Additionally, the vectors can include one or more selectable marker genes and appropriate expression control sequences. Selectable marker genes that can be included, for example, provide resistance to antibiotics or toxins, complement auxotrophic deficiencies, or supply critical nutrients not in the culture media. Expression control sequences can include constitutive and inducible promoters, transcription enhancers, transcription terminators, and the like, which are well known in the art. When two or more nucleic acid molecules are to be co-expressed (e.g., both an antibody heavy and light chain or an antibody VH and VL) , both nucleic acid molecules can be inserted, for example, into a single expression vector or in separate expression vectors. For single vector expression, the encoding nucleic acids can be operationally linked to one common expression control sequence or linked to different expression control sequences, such as one inducible promoter and one constitutive promoter. The introduction of nucleic acid molecules into a host cell can be confirmed using methods well known in the art. Such methods include, for example, nucleic acid analysis such as Northern blots or polymerase chain reaction (PCR) amplification of mRNA, immunoblotting for expression of gene products, or other suitable analytical methods to test the expression of an introduced nucleic acid sequence or its corresponding gene product. It is understood by those skilled in the art that the nucleic acid molecules are expressed in a sufficient amount to produce a desired product and it is further understood that expression levels can be optimized to obtain sufficient expression using methods well known in the art.
[0078] The term “host” as used herein refers to an animal, such as a mammal (e.g., a human) .
[0079] The term “host cell” as used herein refers to a particular subject cell that may be transfected with a nucleic acid molecule and the progeny or potential progeny of such a cell. Progeny of such a cell may not be identical to the parent cell transfected with the nucleic acid molecule due to mutations or environmental influences that may occur in succeeding generations or integration of the nucleic acid molecule into the host cell genome.
[0080] As used herein, the term “autologous” is meant to refer to any material derived from the same individual to whom it is later to be re-introduced into the individual.
[0081] “Allogeneic” refers to a graft derived from a different individual of the same species.
[0082] The term “transfected” or “transformed” or “transduced” as used herein refers to a process by which exogenous nucleic acid is transferred or introduced into the host cell. A “transfected” or “transformed” or “transduced” cell is one which has been transfected, transformed or transduced with exogenous nucleic acid. The cell includes the primary subject cell and its progeny.
[0083] The term “pharmaceutically acceptable” as used herein means being approved by a regulatory agency of the Federal or a state government, or listed in United States Pharmacopeia, European Pharmacopeia, or other generally recognized Pharmacopeia for use in animals, and more particularly in humans.
[0084] The term “effective amount” or “therapeutically effective amount” as used herein refers to an amount of an agent or a combination of agents, sufficient to treat a specified disorder, condition, or disease such as ameliorate, palliate, lessen, and / or delay one or more of its symptoms. In some embodiments, an effective amount is an amount sufficient to delay development of the specified disorder, condition, or disease. In some embodiments, an effective amount is an amount sufficient to prevent or delay recurrence of the specified disorder, condition, or disease. An effective amount can be administered in one or more administrations. In reference to host-versus-graft (HvG) symptoms, an effective amount comprises an amount sufficient to prevent, reduce, or eliminate a response by the host immune system against allogeneic cells that have been administered to the host. In reference to cancer, an effective amount comprises an amount sufficient to cause a tumor to shrink and / or to decrease the growth rate of the tumor (such as to suppress tumor growth) or to prevent or delay other unwanted cell proliferation. The effective amount of the drug or composition may: (i) reduce the number of cancer cells; (ii) reduce tumor size; (iii) inhibit, retard, slow to some extent and preferably stop cancer cell infiltration into peripheral organs; (iv) inhibit (i.e., slow to some extent and preferably stop) tumor metastasis; (v) inhibit tumor growth; (vi) prevent or delay occurrence and / or recurrence of tumor; and / or (vii) relieve to some extent one or more of the symptoms associated with the cancer.
[0085] The terms “subject, ” “individual, ” and “patient” may be used interchangeably. As used herein, in certain embodiments, a subject or an individual is a mammal, such as a non-primate or a primate (e.g., human) . In specific embodiments, the individual is a human. In one embodiment, the individual is a mammal, e.g., a human, diagnosed with a disease or disorder, or at risk of developing a disease or disorder.
[0086] As used herein, the terms “treat, ” “treatment” and “treating” is an approach for obtaining beneficial or desired results including clinical results. For purposes of this disclosure, beneficial or desired clinical results include, but are not limited to, one or more of the following: alleviating one or more symptoms resulting from the disease, diminishing the extent of the disease, stabilizing the disease (e.g., preventing or delaying the worsening of the disease) , preventing or delaying the spread (e.g., metastasis) of the disease, preventing or delaying the recurrence of the disease, delay or slowing the progression of the disease, ameliorating the disease state, providing a remission (partial or total) of the disease, decreasing the dose of one or more other medications required to treat the disease, delaying the progression of the disease, increasing the quality of life, and / or prolonging survival. Also encompassed by “treatment” is a reduction of pathological consequence of cancer and / or HvG symptoms. The methods of the disclosure contemplate any one or more of these aspects of treatment. The term “treating” includes both managing and ameliorating the disease. The terms “manage, ” “managing, ” and “management” refer to the beneficial effects that a subject derives from a therapy which does not necessarily result in a cure of the disease.
[0087] The terms “prevent, ” “preventing, ” and “prevention” refer to reducing the likelihood of the onset (or recurrence) of a disease, disorder, condition, or associated symptom (s) (e.g., a cancer or HvG) .
[0088] As used herein, “delaying” the development of cancer means to defer, hinder, slow, retard, stabilize, and / or postpone development of the disease. This delay can be of varying lengths of time, depending on the history of the disease and / or individual being treated. As is evident to one skilled in the art, a sufficient or significant delay can, in effect, encompass prevention, in that the individual does not develop the disease. A method that “delays” development of cancer is a method that reduces probability of disease development in a given time frame and / or reduces the extent of the disease in a given time frame, when compared to not using the method. Such comparisons are typically based on clinical studies, using a statistically significant number of individuals. Cancer development can be detectable using standard methods, including, but not limited to, computerized axial tomography (CAT Scan) , Magnetic Resonance Imaging (MRI) , abdominal ultrasound, clotting tests, arteriography, or biopsy. Development may also refer to cancer progression that may be initially undetectable and includes occurrence, recurrence, and onset.
[0089] The terms “about” and “approximately” mean within 20%, within 15%, within 10%, within 9%, within 8%, within 7%, within 6%, within 5%, within 4%, within 3%, within 2%, within 1%, or less of a given value or range.
[0090] As used in the present disclosure and claims, the singular forms “a” , “an” and “the” include plural forms unless the context clearly dictates otherwise.
[0091] It is understood that wherever embodiments are described herein with the term “comprising” otherwise analogous embodiments described in terms of “consisting of” and / or “consisting essentially of” are also provided. It is also understood that wherever embodiments are described herein with the phrase “consisting essentially of” otherwise analogous embodiments described in terms of “consisting of” are also provided.
[0092] The term “between” as used in a phrase as such “between A and B” or “between A-B” refers to a range including both A and B.
[0093] The term “and / or” as used in a phrase such as “A and / or B” herein is intended to include both A and B; A or B; A (alone) ; and B (alone) . Likewise, the term “and / or” as used in a phrase such as “A, B, and / or C” is intended to encompass each of the following embodiments: A, B, and C; A, B, or C; A or C; A or B; B or C; A and C; A and B; B and C; A (alone) ; B (alone) ; and C (alone) . II. Engineered Immune Cells
[0094] In one aspect, there is provided an engineered immune cell (e.g., engineered T cell) comprising an NKp80-binding protein that comprises an NKp80 binding domain. In some embodiments, the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the NKp80-binding protein is an anti-NKp80 chimeric receptor. The anti-NKp80 chimeric receptor may be an anti-NKp80 engineered TCR, an anti-NKp80 cTCR, an anti-NKp80 TAC, or an anti-NKp80 CAR. In some embodiments, the anti-NKp80 chimeric receptor is an anti-NKp80 CAR, such as any of the anti-NKp80 CARs described herein. In some embodiments, the engineered immune cell further comprises a second antigen binding protein (e.g., CAR, engineered TCR, cTCR, or TAC) , wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen (e.g., a tumor antigen) , and wherein the second antigen is not NKp80. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, NK cell, B cell, monocyte, dendritic cell, and any combination thereof. In some embodiments, the engineered immune cell is a T cell, such as an αβ T cell or a γδ T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reduced by at least about 20%, such as by at least about any of 30%, 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 96%, 97%, 98%, 99%, or more) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function.
[0095] In some embodiments, the NKp80-binding protein is an anti-NKp80 CAR, such as an anti-NKp80 sdAb CAR (e.g., any of the anti-NKp80 sdAb CARs described herein) . Hence in some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) expressing an anti-NKp80 CAR or comprising a nucleic acid encoding an anti-NKp80 CAR, wherein the anti-NKp80 CAR comprises: (i) an NKp80 binding domain (e.g., sdAb, scFv, or Fab) ; (ii) an optional hinge domain (e.g., derived from CD8α, CD28, or IgG4) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; and (iv) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) . The intracellular co-stimulatory signaling domain can be at the N-terminus or the C-terminus of the intracellular signaling domain. In some embodiments, the NKp80 binding domain is selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to NKp80. In some embodiments, the NKp80 binding domain is an anti-NKp80 sdAb. In some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) expressing an anti-NKp80 CAR or comprising a nucleic acid encoding an anti-NKp80 CAR, wherein the anti-NKp80 CAR comprises from N’ to C’: (i) an anti-NKp80 sdAb (e.g., any of the anti-NKp80 sdAbs provided herein) ; (ii) an optional hinge domain (e.g., derived from CD8α, CD28, or IgG4) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; and (iv) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) , such as between the transmembrane domain and the intracellular signaling domain. In some embodiments, the anti-NKp80 CAR further comprises a second antigen binding domain (e.g., sdAb, scFv, or Fab) that specifically recognizes a second target antigen that is not NKp80 (e.g., a tumor antigen) . The second antigen binding domain can be at the N-terminus of the NKp80 binding domain or can be between the NKp80 binding domain and the optional hinge domain. In some embodiments, the engineered immune cell further comprises a second antigen binding protein (e.g., CAR, engineered TCR, cTCR, or TAC) , wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen (e.g., a tumor antigen) , and wherein the second antigen is not NKp80. In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 CAR comprises two or more anti-NKp80 sdAbs connected in tandem. In some embodiments, each anti-NKp80 sdAb comprises an anti-NKp80 VHH domain. In some embodiments, the anti-NKp80 CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 34-37. In some embodiments, the nucleic acid encoding the anti-NKp80 CAR further encodes a signal peptide (e.g., comprising the amino acid sequence of SEQ ID NO: 21) N-terminal to the anti-NKp80 CAR. In some embodiments, the anti-NKp80 CAR further comprises a protein tag (e.g., FLAG) , such as located between the signal peptide and the NKp80 binding domain. Thus, in some embodiments, there is provided an engineered immune cell comprising an anti-NKp80 CAR comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 17-20. In some embodiments, the anti-NKp80 CAR: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, e.g., NK cells. In some embodiments, the engineered immune cell is capable of inhibiting or killing primary NK cells obtained from PBMCs from a donor. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, NK cell, B cell, monocyte, dendritic cell, and any combination thereof, such as a T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function.
[0096] In some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) expressing an anti-NKp80 CAR or comprising a nucleic acid encoding an anti-NKp80 CAR, wherein the anti-NKp80 CAR comprises: (i) an NKp80 binding domain (e.g., sdAb, scFv, or Fab) and a second antigen binding domain (e.g., sdAb, scFv, or Fab) that specifically recognizes a second antigen that is not NKp80 (e.g., tumor antigen) ; (ii) an optional hinge domain (e.g., derived from CD8α) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; and (iv) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) . The intracellular co-stimulatory signaling domain can be at the N-terminus or the C-terminus of the intracellular signaling domain. In some embodiments, the NKp80 binding domain is an anti-NKp80 sdAb (e.g., any of the anti-NKp80 sdAbs provided herein) . The second antigen binding domain can be at the N-terminus of the NKp80 binding domain, or can be between the NKp80 binding domain and the optional hinge domain. In some embodiments, the anti-NKp80 CAR: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, e.g., NK cells. In some embodiments, the engineered immune cell is capable of inhibiting or killing cells that express the second antigen. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, NK cell, B cell, monocyte, dendritic cell, and any combination thereof, such as a T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function.
[0097] In some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) comprising: (a) a first nucleic acid encoding an NKp80-binding protein that comprises an NKp80 binding domain (e.g., an anti-NKp80 chimeric receptor, such as anti-NKp80 CAR) ; and (b) a second nucleic acid encoding a second antigen binding protein, wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen (e.g., tumor antigen) , and wherein the second antigen is not NKp80. In some embodiments, the second antigen binding protein is a second chimeric receptor (e.g., CAR, engineered TCR, cTCR, or TAC) . In some embodiments, the second chimeric receptor is a second CAR comprising the second antigen binding domain, an optional second hinge, a second transmembrane domain, and a second intracellular signaling domain. In some embodiments, the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the engineered immune cell is capable of inhibiting or killing cells that express the second antigen. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, NK cell, B cell, monocyte, dendritic cell, and any combination thereof, such as a T cell. In some embodiments, the engineered immune cell is further engineered to not express or to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function.
[0098] The first nucleic acid encoding the NKp80-binding protein and the second nucleic acid encoding the second antigen binding protein can be on different vectors or on the same vector. In some embodiments, the first nucleic acid and the second nucleic acid are on the same vector and under the control of separate promoters (can be the same or different) . In some embodiments, the first nucleic acid and the second nucleic acid are on the same vector and are under the control of a single / same promoter. In some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) comprising: (a) a first nucleic acid encoding an NKp80 binding protein (e.g., an anti-NKp80 chimeric receptor, such as an anti-NKp80 CAR) ; and (b) a second nucleic acid encoding a second antigen binding protein (e.g., a second chimeric receptor, such as a second CAR) , wherein the second antigen binding protein comprises a second antigen binding domain (e.g., sdAb, scFv, or Fab) that specifically binds to a second antigen (e.g., tumor antigen) , wherein the second antigen is not NKp80; wherein the first nucleic acid and the second nucleic acid are on the same vector and under the control of separate promoters (can be the same or different) . In some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) comprising: (a) a first nucleic acid encoding an NKp80 binding protein (e.g., an anti-NKp80 chimeric receptor, such as an anti-NKp80 CAR) ; and (b) a second nucleic acid encoding a second antigen binding protein (e.g., a second chimeric receptor, such as a second CAR) , wherein the second antigen binding protein comprises a second antigen binding domain (e.g., sdAb, scFv, or Fab) that specifically binds to a second antigen (e.g., tumor antigen) , wherein the second antigen is not NKp80; wherein the first nucleic acid and the second nucleic acid are on the same vector and under the control of a single promoter, and wherein the first nucleic acid and the second nucleic acid are connected via a linking nucleic acid (e.g., IRES, or encoding a cleavable linker such as 2A peptide) . The first nucleic acid can be downstream or upstream of the second nucleic acid. In some embodiments, the linking nucleic acid encodes a P2A, E2A, or a T2A amino acid sequence. In some embodiments, there is provided an engineered immune cell (e.g., engineered T cell) comprising: (a) a first nucleic acid encoding an NKp80 binding protein (e.g., an anti-NKp80 chimeric receptor, such as an anti-NKp80 CAR) ; and (b) a second nucleic acid encoding a second antigen binding protein (e.g., a second chimeric receptor, such as a second CAR) , wherein the second antigen binding protein comprises a second antigen binding domain (e.g., sdAb, scFv, or Fab) that specifically binds to a second antigen (e.g., tumor antigen) , wherein the second antigen is not NKp80; wherein the first nucleic acid and the second nucleic acid are on different vectors. In some embodiments, the anti-NKp80 CAR comprises from N’ to C’ : (i) an anti-NKp80 sdAb (e.g., any of the anti-NKp80 sdAbs provided herein) ; (ii) an optional hinge domain (e.g., derived from CD8α) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; and (iv) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the second antigen binding protein is a second CAR comprising the second antigen binding domain, an optional second hinge domain, a second transmembrane domain (e.g., derived from CD8α) , and a second intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR and / or the second CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) , which can either be at the N’ or C’ of the intracellular signaling domain (or second intracellular signaling domain) . In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 CAR comprises two or more anti-NKp80 sdAbs, such as connected in tandem, wherein each anti-NKp80 sdAb comprises a VHH domain independently selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 34-37. In some embodiments, the first nucleic acid and / or the second nucleic acid further encodes a signal peptide (e.g., SEQ ID NO: 21) N-terminal to the NKp80-binding protein and / or the N-terminal of the second antigen binding protein. In some embodiments, the NKp80 binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the engineered immune cell is capable of inhibiting or killing cells that express the second antigen. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, NK cell, B cell, monocyte, dendritic cell, and any combination thereof, such as a T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the NKp80 binding protein is an anti-NKp80 CAR comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37. A. NKp80-binding protein and second antigen binding protein
[0099] Provided herein are antigen binding proteins that specifically bind to NKp80 (NKp80-binding proteins) and / or a second antigen that is not NKp80. In some embodiments, the NKp80-binding proteins comprise an NKp80 binding domain. In some embodiments, the NKp80-binding protein further comprises a second or more antigen binding domains (e.g., sdAb, scFv) , optionally wherein the second or more antigen binding domains do not bind to NKp80. Any of the anti-NKp80 antibody constructs described herein (e.g., anti-NKp80 sdAbs, or anti-NKp80 sdAb CAR) can be used as the NKp80 binding domain or NKp80-binding protein herein.
[0100] The NKp80-binding protein can comprise multiple antigen binding domains that specifically recognize the same antigen (e.g., NKp80) or different antigens (e.g., NKp80 and a second antigen that is not NKp80, such as a disease-associated antigen) . In some instances, the NKp80-binding protein comprises multiple antigen binding domains that specifically recognize different epitopes from the same antigen (e.g., NKp80 or a second antigen that is not NKp80) . In some instances, the NKp80-binding protein comprise multiple antigen binding domains that specifically recognize the same epitope from the same antigen (e.g., NKp80) .
[0101] In some embodiments, the expression of NKp80 and / or a second antigen that is not NKp80 on a target cell (e.g., NK cell) can be measured using flow cytometry or microscopy paired with antibody staining, ELISA, western blotting, quantitative or semi-quantitative real-time PCR, etc. In some embodiments, NKp80 activity within the target cell can be measured by assessing NK cell degranulation, cytokine release, and / or NK cell-mediated cytolysis of target cells. NK cell degranulation can be analyzed, e.g., by assessing relevant markers such as LAMP-1, CD107a (see, e.g., Shabrish et al. (2016) J Immunol Res. 2016: 3769590, hereby incorporated by reference in its entirety) . Cytokine release can be analyzed via, e.g., flow cytometry, ELISpot, ELISA, and / or western blotting. NK cell-mediated cytolysis of target cells can be analyzed by assessing the specific cytolysis of target cells incubated in co-culture with NK cells, e.g., according to standard methods in the field. Activity of the second antigen within the target cell can be assessed using assays designed for the specific antigen.
[0102] In some embodiments, the NKp80-binding protein binds to NKp80 (e.g., human NKp80) with a dissociation constant (KD) of ≤ 1μM, ≤ 100 nM, ≤ 10 nM, ≤ 1 nM, ≤ 0.1 nM, ≤ 0.01 nM, or ≤ 0.001 nM (e.g., about 10-8 M or less, such as any of from about 10-8 M to about 10-13 M, from about 10-9 M to about 10-13 M, from about 10-10 M to about 10-13 M, or from about 10-11 M to about 10-13 M) . In some embodiments, the second antigen binding protein binds to the second antigen (e.g., human second antigen) with a dissociation constant (KD) of ≤ 1μM, ≤ 100 nM, ≤10 nM, ≤ 1 nM, ≤ 0.1 nM, ≤ 0.01 nM, or ≤ 0.001 nM (e.g., about 10-8 M or less, such as any of from about 10-8 M to about 10-13 M, from about 10-9 M to about 10-13 M, from about 10-10 M to about 10-13 M, or from about 10-11 M to about 10-13 M) . A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present disclosure, including by RIA, for example, performed with an antibody of interest and its antigen (Chen et al., 1999, J. Mol Biol 293: 865-81) ; by biolayer interferometry (BLI) or surface plasmon resonance (SPR) assays by using, for example, an Red96 system, or by using, for example, a TM-2000 or a TM-3000. An “on-rate” or “rate of association” or “association rate” or “kon” may also be determined with the same BLI or SPR techniques described above using, for example, the Red96, the TM-2000, or the TM-3000 system.
[0103] In some embodiments, the NKp80-binding protein comprises (or consists of, or consists essentially of) an NKp80 binding domain. In some embodiments, the second antigen binding protein comprises (or consists of, or consists essentially of) a second antigen binding domain, wherein the second antigen is not NKp80. In some embodiments, the NKp80 binding domain and the second antigen binding domain each individually comprises (or consists of, or consists essentially of) a full-length antibody, an sdAb, a Fab, a Fab’ , a Fab’ -SH, a F (ab’ ) 2, a (Fab’ ) 2, an Fv, an scFv, or a peptide ligand specifically binding to NKp80 or to the second antigen. In some embodiments, the NKp80 binding domain is an anti-NKp80 sdAb and / or the second antigen binding domain is an sdAb. In some embodiments, the NKp80 binding domain is an anti-NKp80 scFv and / or the second antigen binding domain is an scFv. In some embodiments, the NKp80 binding domain is an anti-NKp80 full-length antibody and / or the second antigen binding domain is a full-length antibody, wherein each comprises an Fc region of any antibody class or isotype, such as IgG1, IgG2, IgG3, or IgG4. In some embodiments, the Fc region has reduced or minimized effector function.
[0104] The NKp80-binding protein or the NKp80 binding domain can bind NKp80 derived from any organism, including but not limited to, dogs, cats, pigs, cows, sheep, goats, horses, rats, rabbits, hamsters, guinea pigs, monkeys, mice, and humans. In some embodiments, the NKp80-binding protein binds human NKp80. Any NKp80-binding proteins available can be used here, including but are not limited to, MAB1900 (e.g., BioTechne) , 5D12 (e.g., BioLegend) , REA845 (e.g., Miltenyi Biotec) , ab198928 (e.g., AbCam) , ab256809 (e.g., AbCam) , MA152 (e.g., Beckman Coulter) , LAP171 (e.g., Vitale et al. (2001) Eur J Immunol. 31 (1) : 233-242) , etc., the contents of which are incorporated herein by reference in its entirety.
[0105] In some embodiments, the NKp80 binding domain and / or the second antigen binding domain is each individually selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to NKp80 and / or to the second antigen. In some embodiments, the NKp80 binding domain and / or the second antigen binding domain can also be selected from a VH, a VL, an scFv-scFv, an Fv, a minibody, a diabody, a domain antibody variant (dAb) , a camelid antibody (VHH) , a fibronectin 3 domain variant, an ankyrin repeat variant, and other NKp80-specific or second antigen-specific binding domains derived from other protein scaffolds. In some embodiments, the NKp80 binding domain and / or the second antigen binding domain comprises a heavy chain variable domain (VH) and a light chain variable domain (VL) , wherein the VH comprises H-CDR1, H-CDR2, and H-CDR3, and the VL comprises L-CDR1, L-CDR2, and L-CDR3. In some embodiments, the NKp80 binding domain and / or the second antigen binding domain comprises a single domain (i.e., VHH) , wherein the single domain comprises a CDR1, CDR2, and CDR3. In some embodiments, the CDR positions are determined according to Kabat or AbM numbering scheme.
[0106] In some embodiments, the NKp80 binding domain is an sdAb ( “anti-NKp80 sdAb” ) , such as any of the anti-NKp80 sdAbs described herein. For example, in some embodiments, the anti-NKp80 sdAb comprises a CDR1, a CDR2, and a CDR3, and wherein the CDR1, CDR2, and CDR3 have the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16.
[0107] In some embodiments, a NKp80 binding domain and / or the second antigen binding domain may be used to screen a library of the complementary variable region to identify an NKp80 binding domain and / or the second antigen binding domain with desirable properties, such as increased affinity for NKp80 and / or for the second antigen. Such methods are described, for example, in Portolano et al., J. Immunol. (1993) 150: 880-887; Clarkson et al., Nature (1991) 352: 624-628; and Klimka et al., British Journal of Cancer (2000) 83: 252-260; Beiboer et al., J. Mol. Biol. (2000) 296: 833-849; and Rader et al., PNAS (1998) 95: 8910-8915; the contents of each of which are incorporated herein by reference in their entirety.
[0108] In some embodiments, NKp80-binding protein and / or the second antigen binding protein comprises one or more post-translational modifications.
[0109] Functional epitopes can be mapped by combinatorial alanine scanning. In this process, a combinatorial alanine-scanning strategy can be used to identify amino acids in the NKp80 protein that are necessary for interaction with NKp80-binding proteins and / or to identify amino acids in the second antigen protein that are necessary for interaction with the second antigen binding domain. In some embodiments, the epitope is conformational and crystal structure of NKp80-binding proteins bound to NKp80 and / or of second antigen binding proteins bound to the second antigen may be employed to identify the epitopes.
[0110] In some embodiments, there is also provided an NKp80-binding protein that competes with any one of the NKp80-binding proteins described herein for binding to NKp80 (e.g., same NKp80 epitope, overlapping NKp80 epitope) .
[0111] Competition assays may be used to identify an NKp80-binding protein that competes with any of the NKp80-binding proteins described herein for binding to NKp80. Competition assays can be used to determine whether two antigen binding proteins bind the same epitope by recognizing identical or sterically overlapping epitopes, or one antigen binding protein competitively inhibits binding of another antigen binding protein to the antigen. In certain embodiments, such a competing antigen binding protein binds to the same epitope that is bound by any of the NKp80-binding proteins described herein. Exemplary competition assays include, but are not limited to, routine assays such as those provided in Harlow and Lane (1988) Antibodies: A Laboratory Manual ch. 14 (Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. ) . Detailed exemplary methods for mapping an epitope to which an antigen binding proteins binds are provided in Morris (1996) "Epitope Mapping Protocols, " in Methods in Molecular Biology vol. 66 (Humana Press, Totowa, N.J. ) . In some embodiments, two antigen binding proteins are said to bind to the same epitope if each blocks binding of the other by about 50%or more (e.g., at least about any of 60%, 70%, 80%, 90%, 95%, or more) . In some embodiments, the antigen binding protein that competes with any of the NKp80-binding proteins described herein is a humanized antibody, a human antibody, a multispecific antibody, a monoclonal antibody, a multivalent antibody, a conjugated antibody, or a chimeric antibody. In some embodiments, the competing antigen-binding protein is a full-length antibody, a Fab, a Fab’, a Fab’-SH, a F (ab’) 2, an Fv, an scFv, a peptide ligand specifically binding to NKp80, or any combinations thereof.
[0112] The NKp80-binding protein and / or the second antigen binding protein (e.g., sdAb, scFv, Fab, or full-length antibody) can be generated by a variety of methods known in the art (see, e.g., U.S. Pat. Nos. 6,291,161; 6,291,158) . Sources of NKp80-binding proteins and / or second antigen binding proteins include monoclonal antibody or antigen-binding fragments thereof from various species, including human, camelid (from camels, dromedaries, or llamas; Hamers-Casterman et al. (1993) Nature, 363: 446 and Nguyen et al. (1998) J. Mol. Biol., 275: 413) , shark (Roux et al. (1998) Proc. Nat'l. Acad. Sci. (USA) 95: 11804) , fish (Nguyen et al. (2002) Immunogenetics, 54: 39) , rodent, avian, or ovine. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is derived from a human or humanized antibody. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is chimeric. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is derived from a fully human antibody, for example, developed using phage-display, yeast-display, or transgenic mice bearing human Ig genes. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is murine. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is monovalent. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is multivalent. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is multivalent and monospecific.
[0113] In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is selected from the group consisting of: an antibody, a chimeric receptor, an antibody-drug conjugate (ADC) , an antibody-siRNA conjugate (ARC) , an antibody-oligonucleotide conjugate (AOC) , an antibody-detection tag conjugate, and an immunocytokine. In some embodiments, the NKp80-binding protein and / or the second antigen binding protein is a chimeric receptor (i.e., anti-NKp80 chimeric receptor and / or second chimeric receptor) . In some embodiments, the anti-NKp80 chimeric receptor and / or the second chimeric receptor is each individually selected from the group consisting of a chimeric antigen receptor (CAR) , a T cell antigen coupler (TAC) , a T cell antigen coupler-like (TAC-like) , and a chimeric T cell receptor (cTCR) .
[0114] There is also provided a NKG2A-binding protein, wherein the NKG2A-binding protein is an anti-NKG2A CAR. The anti-NKG2A CAR may comprise from N-terminus to C-terminus: (a) an anti-NKG2A scFv; (b) a hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . The anti-NKG2A scFv may comprise the amino acid sequence of SEQ ID NO: 27. The anti-NKG2A CAR may comprise the amino acid sequence of SEQ ID NO: 28. B. Chimeric receptors
[0115] In some embodiments, the NKp80-binding protein is a chimeric receptor comprising an antigen binding domain, wherein the antigen binding domain is the NKp80 binding domain. In some embodiments, the NKp80-binding protein further comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80.
[0116] The NKp80-targeted chimeric receptor can be any chimeric receptor that specifically recognizes NKp80 and is capable of activating the engineered immune cell (e.g., inducing cytokine secretion, and / or inducing NKp80-mediated immune cell cytotoxicity) . In some embodiments, the anti-NKp80 chimeric receptor is an anti-NKp80 T cell receptor (TCR) , an anti-NKp80-targeted chimeric TCR (cTCR) , an anti-NKp80 T cell antigen coupler (TAC) , an anti-NKp80 T cell antigen coupler-like (TAC) -like, or an anti-NKp80 chimeric antigen receptor (CAR) . In some embodiments, the engineered immune cells can further comprise a second antigen-binding protein that comprises an antigen-binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80. In some embodiments, the second antigen-binding protein is also a chimeric receptor (e.g., a second TCR, cTCR, TAC, TAC-like, or CAR) .
[0117] In some embodiments, the anti-NKp80 chimeric receptor is a CAR (hereinafter also referred to as “anti-NKp80 CAR” ) . The anti-NKp80 CAR may comprise from N-terminus to C-terminus: (a) an antigen binding domain specifically recognizing NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) ; (b) an optional hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an optional intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . The anti-NKp80 CAR may comprise from N-terminus to C-terminus: (a) an antigen binding domain specifically recognizing NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) ; (b) an optional hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular signaling domain (e.g., derived from CD3ζ) ; and (e) an optional intracellular co-stimulatory signaling domain (e.g., derived from CD28) . In some embodiments, the antigen binding domain of the anti-NKp80 CAR is an anti-NKp80 sdAb, e.g., any of the anti-NKp80 sdAbs described herein. The two or more antigen-binding fragments can be the same or different. The two or more antigen-binding fragments can recognize the same epitope or different epitopes of NKp80. In some embodiments, the anti-NKp80 CAR comprises from N-terminus to C-terminus: (a) an anti-NKp80 sdAb (e.g., any of the anti-NKp80 sdAbs provided herein) ; (b) a hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the transmembrane domain is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 24. In some embodiments, the intracellular signaling domain is derived from CD3ζ, such as comprising the amino acid sequence of SEQ ID NO: 26. In some embodiments, the intracellular co-stimulatory signaling domain is derived from a cytoplasmic domain of CD28, such as comprising the amino acid sequence of SEQ ID NO: 25. In some embodiments, the hinge domain is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 23. In some embodiments, the anti-NKp80 CAR further comprises a signal peptide N-terminal to the antigen binding domain specifically recognizing NKp80. In some embodiments, the signal peptide is derived from a CD8α propeptide, such as comprising the amino acid sequence of SEQ ID NO: 21. In some embodiments, the NKp80 CAR further comprises a protein tag located between the signal peptide and the antigen binding domain specifically recognizing NKp80. In some embodiments, the protein tag is a FLAG tag comprising the amino acid sequence of SEQ ID NO: 22.
[0118] In some embodiments, the anti-NKp80 CAR comprises from N’ to C’ : (a) an anti-NKp80 sdAb; (b) an optional hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; and (d) an intracellular signaling domain (e.g., derived from CD3ζ) ; wherein the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 CAR comprises at least two anti-NKp80 sdAbs connected in tandem, wherein each anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence independently selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. The two or more anti-NKp80 sdAbs can be the same or different. In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain, such as an intracellular co-stimulatory signaling domain comprising a cytoplasmic domain of CD28. In some embodiments, the intracellular co-stimulatory signaling domain is at the C-terminus of the intracellular signaling domain. In some embodiments, the intracellular co-stimulatory signaling domain is at the N-terminus of the intracellular signaling domain. Hence in some embodiments, the anti-NKp80 CAR comprises from N’ to C’ : (a) an anti-NKp80 sdAb; (b) a hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 24. In some embodiments, the intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 26. In some embodiments, the hinge domain comprises the amino acid sequence of SEQ ID NO: 23. In some embodiments, the intracellular co-stimulatory signaling domain comprises the amino acid sequence of SEQ ID NO: 25. In some embodiments, the anti-NKp80 CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 34-37. In some embodiments, the anti-NKp80 CAR further comprises a signal peptide N-terminal to the anti-NKp80 sdAb. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 21. In some embodiments, the anti-NKp80 CAR further comprises a protein tag located between the signal peptide and the anti-NKp80 sdAb. In some embodiments, the protein tag is a FLAG tag comprising the amino acid sequence of SEQ ID NO: 22. In some embodiments, the anti-NKp80 CAR comprising the signal peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20.
[0119] In some embodiments, the anti-NKp80 chimeric receptor is an engineered TCR (hereinafter also referred to as “anti-NKp80 TCR” ) . The anti-NKp80 TCR may comprise: i) an antigen binding domain that comprises a Vα and a Vβ (or a Vδ and a Vγ) derived from a wildtype TCR together specifically recognizing NKp80, wherein the Vα, the Vβ, or both (or the Vδ, the Vγ, or both) , comprise one or more mutations (e.g., insertions, deletions, or substitutions, such as conservative substitutions) in one or more CDRs relative to the wild type TCR; and ii) a transmembrane domain (TM) derived from a TCR molecule (e.g., TCRα / TCRβ, or TCRδ / TCRγ) . The anti-NKp80 TCR can be a single chain TCR (scTCR) or a dimeric TCR (dTCR) . For example, the anti-NKp80 TCR may comprise: i) a first polypeptide chain comprising from N’ to C’ : Vα (e.g., Vα variant) –Cα –TMα –optional TCRα cytoplasmic domain (cytoTCRα) , and ii) a second polypeptide chain comprising from N’ to C’ : Vβ (e.g., Vβvariant) –Cβ –TMβ –optional cytoTCRβ; wherein the Vα and the Vβ form an antigen binding domain that specifically recognizes NKp80. The anti-NKp80 TCR may comprise: i) a first polypeptide chain comprising from N’ to C’ : Vγ (e.g., Vγ variant) –Cγ –TMγ –optional cytoTCRγ, and ii) a second polypeptide chain comprising from N’ to C’ : Vδ (e.g., Vδ variant) –Cδ –TMδ –optional cytoTCRδ; wherein the Vγ and the Vδ form an antigen binding domain that specifically recognizes an NKp80-MHC complex. The anti-NKp80 TCR may bind to the same cognate peptide-MHC bound by the wildtype TCR. The anti-NKp80 TCR may bind to the same cognate peptide-MHC with higher affinity compared to that bound by the wildtype TCR. The anti-NKp80 TCR may bind to the same cognate peptide-MHC with lower affinity compared to that bound by the wildtype TCR. The anti-NKp80 TCR may bind to a non-cognate peptide-MHC not bound by the wildtype TCR. The anti-NKp80 TCR may not comprise an intracellular signaling domain. The anti-NKp80 TCR may further comprise a hinge domain (or a connecting domain) between the TCR Ig-like constant domain and the TCR transmembrane domain, such as a hinge domain derived from TCRα / TCRβ or TCRδ / TCRγ.
[0120] In some embodiments, the anti-NKp80 chimeric receptor is a chimeric T cell receptor (cTCR; hereinafter also referred to as “anti-NKp80-targeted cTCR” ) . The anti-NKp80-targeted cTCR may comprise: i) an antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) , and ii) a full-length TCR subunit, wherein the TCR subunit is selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3γ, CD3ε, and CD3δ; wherein the antigen binding domain is fused (directly or indirectly) to the N-terminus of the full-length TCR subunit. In some embodiments, the TCR subunit is CD3ε. In some embodiments, the anti-NKp80-targeted cTCR comprises from N’ to C’: i) an antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) , ii) an optional extracellular domain (ECD) or portion thereof derived from a first TCR subunit, and iii) a transmembrane domain derived from a second TCR subunit; wherein the first TCR subunit and the second TCR subunit are independently selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3γ, CD3ε, and CD3δ. The anti-NKp80-targeted cTCR can be incorporated into a functional TCR complex along with other endogenous TCR subunits and confer antigen specificity to the TCR complex. The antigen binding domain of the anti-NKp80 cTCR may be selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to NKp80. The anti-NKp80-targeted cTCR antigen binding domain may be fused to the N-terminus of the full-length or a portion thereof of CD3ε, CD3γ, or CD3δ. The anti-NKp80-targeted cTCR antigen binding domain may be fused to the N-terminus of a TCRα molecule (with or without the Vα domain) , and / or the N-terminus of a TCRβmolecule (with or without the Vβ domain) . The cTCR antigen binding domain may be fused to the N-terminus of a TCRγ molecule (with or without the Vγ domain) , and / or the N-terminus of a TCRδ molecule (with or without the Vδ domain) . The anti-NKp80-targeted cTCR may not comprise an intracellular signaling domain. The anti-NKp80-targeted cTCR may comprise an intracellular signaling domain, such as the intracellular signaling domain of CD3γ, CD3ε, or CD3δ. The anti-NKp80-targeted cTCR intracellular signaling domain and the anti-NKp80-targeted cTCR transmembrane domain can be derived from the same TCR subunit, e.g., both from CD3ε, both from CD3ε, or both from CD3δ. The anti-NKp80-targeted cTCR antigen binding domain and the first TCR subunit (full-length or an ECD portion thereof) can be fused via a linker (such as a GS linker) . In some embodiments, the anti-NKp80-targeted cTCR antigen binding domain is fused to the N-terminus of the transmembrane domain via an optional linker or hinge domain. The anti-NKp80-targeted cTCR may further comprise a hinge domain between the ECD portion derived from the first TCR subunit and the transmembrane domain derived from the second TCR subunit. In some embodiments, the anti-NKp80-targeted cTCR comprises from N-terminus to C-terminus: (a) an antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of anti-NKp80 sdAbs provided herein) ; (b) an optional linker, (c) an optional extracellular domain of a first TCR subunit (e.g., CD3ε) or a portion thereof, (d) an optional hinge domain, (e) a transmembrane domain derived from a second TCR subunit (e.g., CD3ε) , and (f) an optional cytoplasmic domain (e.g., optional intracellular signaling domain) ; wherein the first and second TCR subunits are independently selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. The first and second TCR subunits can be the same or different. In some embodiments, the anti-NKp80-targeted cTCR comprises from N-terminus to C-terminus: (a) an anti-NKp80 scFv or sdAb (e.g., any of the anti-NKp80 sdAbs described herein) ; (b) an optional linker, and (c) a full-length CD3ε, CD3γ, or CD3δ.
[0121] In some embodiments, the anti-NKp80 chimeric receptor is a T cell antigen coupler (TAC; hereinafter also referred to as “anti-NKp80 TAC” ) . The anti-NKp80 TAC may comprise: (a) an anti-NKp80 binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) ; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a TCR subunit (e.g., CD3ε) ; (d) an optional second linker; (e) an optional extracellular domain derived from a first TCR co-receptor (such as CD4, CD28, or CD8, e.g., CD8α) ; (f) a transmembrane comprising a transmembrane of a second TCR co-receptor (such as CD4, CD28, or CD8, e.g., CD8α) ; and (g) an optional intracellular signaling domain comprising intracellular signaling domain of a third TCR co-receptor (such as CD4, CD28, or CD8, e.g., CD8α) . In some embodiments, the first, second, and third TCR co-receptors are the same (e.g., all CD4) . In some embodiments, the first, second, and third TCR co-receptors are different. For example, in some embodiments, the TAC comprises: (a) an anti-NKp80 binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a TCR subunit (e.g., CD3ε) ; (d) an optional second linker; and (e) a full length TCR co-receptor (e.g., CD4, CD8 (e.g., CD8α) , or CD28) . T cells expressing TACs may be referred to herein as “TAC-T. ”
[0122] In some embodiments, the anti-NKp80 chimeric receptor is an anti-NKp80 T cell antigen coupler (TAC) -like chimeric receptor (hereinafter also referred to as “anti-NKp80 TAC-like receptor” ) . The anti-NKp80 TAC-like receptor may comprise: (a) an anti-NKp80 binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) ; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a first TCR subunit (e.g., CD3ε) ; (d) an optional second linker; (e) an optional extracellular domain of a second TCR subunit (e.g., CD3ε) or a portion thereof; (f) a transmembrane domain comprising a transmembrane domain of a third TCR subunit (e.g., CD3ε) ; and (g) an optional intracellular signaling domain comprising an intracellular signaling domain of a fourth TCR subunit (e.g., CD3ε) ; wherein the first, second, third, and fourth TCR subunits are all selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. In some embodiments, the first, second, third, and fourth TCR subunits are the same (e.g., CD3ε) . In some embodiments, the second, third, and fourth TCR subunits are the same (e.g., CD3ε) . In some embodiments, the first, second, third, and fourth TCR subunits are different. In some embodiments, the second, third, and fourth TCR subunits are the same (e.g., CD3ε) but different from the first TCR subunit (e.g., TCRα) . In some embodiments, the anti-NKp80 TAC-like chimeric receptor comprises: (a) an anti-NKp80 binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) ; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a first TCR subunit (e.g., CD3ε) ; (d) an optional second linker; and (e) a full length second TCR subunit (e.g., CD3ε) ; wherein the first and second TCR subunits are both selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. In some embodiments, the first and second TCR subunits are the same (e.g., both CD3ε) . In some embodiments, the first (e.g., TCRα) and second (e.g., CD3ε) TCR subunits are different. T cells expressing TAC-like chimeric receptors are referred herein as “TAC-like-T. ”
[0123] In some embodiments, there is provided an NKp80-binding protein (e.g., anti-NKp80 chimeric receptor, such as anti-NKp80 CAR) that comprises an antigen-binding domain that specifically binds to NKp80, wherein the NKp80-binding protein further comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80. In some embodiments, the NKp80-binding protein is an anti-NKp80 chimeric receptor. In some embodiments, the anti-NKp80 chimeric receptor is a CAR. The anti-NKp80 CAR may comprise from N-terminus to C-terminus: (a) an antigen binding domain specifically recognizing NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) and a second antigen binding domain that specifically recognizes a second antigen that is not NKp80; (b) an optional hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an optional intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . The CAR may comprise from N-terminus to C-terminus: (a) an antigen binding domain specifically recognizing NKp80 (e.g., any of the anti-NKp80 sdAbs provided herein) and a second antigen binding domain that specifically recognizes a second antigen that is not NKp80; (b) an optional hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular signaling domain (e.g., derived from CD3ζ) ; and (e) an optional intracellular co-stimulatory signaling domain (e.g., derived from CD28) . The anti-NKp80 antigen binding domain and / or the second antigen binding domain of the anti-NKp80 CAR may be selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, a single chain Fv (scFv) , a single domain antibody (sdAb) specifically binding to NKp80, and peptide ligand specifically binding to NKp80 and / or a second antigen that is not NKp80. In some embodiments, the anti-NKp80 antigen binding domain of the CAR is an anti-NKp80 sdAb. In some embodiments, the anti-NKp80 CAR comprises from N-terminus to C-terminus: (a) an anti-NKp80 sdAb (e.g., any of the anti-NKp80 sdAbs provided herein) and a second antigen binding domain that specifically recognizes a second antigen that is not NKp80; (b) a hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) , either at the N-terminus or C-terminus of the intracellular signaling domain. The second antigen binding domain can be at the N-terminus or C-terminus of the anti-NKp80 antigen-binding domain, either fused directly or via a linker. In some embodiments, the transmembrane domain is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 24. In some embodiments, the intracellular signaling domain is derived from CD3ζ, such as comprising the amino acid sequence of SEQ ID NO: 26. In some embodiments, the intracellular co-stimulatory signaling domain is derived from a cytoplasmic domain of CD28, such as comprising the amino acid sequence of SEQ ID NO: 25. In some embodiments, the hinge domain is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 23. In some embodiments, the CAR further comprises a signal peptide N-terminal to the anti-NKp80 antigen binding domain and the second antigen binding domain. In some embodiments, the signal peptide is derived from a CD8α propeptide, such as comprising the amino acid sequence of SEQ ID NO: 21. In some embodiments, the CAR further comprises a protein tag located between the signal peptide and: (i) the anti-NKp80 antigen binding domain, wherein the anti-NKp80 antigen binding domain is located N-terminal to the second antigen binding domain; or (ii) the second antigen binding domain, wherein the second antigen binding domain is located N-terminal to the anti-NKp80 antigen binding domain. In some embodiments, the protein tag is a FLAG tag comprising the amino acid sequence of SEQ ID NO: 22.
[0124] In some embodiments, there is provided an anti-NKp80 CAR comprising from N’ to C’: (a) an anti-NKp80 sdAb and a second antigen binding domain (e.g., scFv, sdAb, or a ligand) that specifically recognizes a second antigen that is not NKp80; (b) an optional hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; and (d) an intracellular signaling domain (e.g., derived from CD3ζ) ; wherein the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the second antigen binding domain specifically binds to a second antigen selected from the group consisting of a cancer-associated antigen or a cancer-specific antigen; an infectious disease-associated antigen or an infectious disease-specific antigen; an inflammatory disorder-associated antigen or an inflammatory disorder-specific antigen; and an autoimmune-associated antigen or an autoimmune-specific antigen. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the second antigen binding domain specifically binds to a cancer-associated antigen or a cancer-specific antigen, such as selected from the group consisting of CD19, CD20, CD22, BCMA, DLL3, B7H3, PD-L1, PD-L2, CLL1, GPC3, GU2CYC, CD7, CD38, CD41, CD123, Claudin 18.2, Claudin 6, NKG2D, GPRC5D, CD70, and any combination thereof. In some embodiments, the anti-NKp80 CAR comprises at least two anti-NKp80 sdAbs connected in tandem, wherein each anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence independently selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the two or more anti-NKp80 sdAbs are further connected with the second antigen binding domain in tandem. Hence in some embodiments, the anti-NKp80 CAR comprises from N’ to C’ : (a) an anti-NKp80 sdAb and a second antigen binding domain that specifically recognizes a second antigen that is not NKp80; (b) a hinge domain (e.g., derived from CD8α) ; (c) a transmembrane domain (e.g., derived from CD8α) ; (d) an intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the CAR further comprises an intracellular co-stimulatory signaling domain, such as an intracellular co-stimulatory signaling domain comprising a cytoplasmic domain of CD28. The intracellular co-stimulatory signaling domain can be at the C-terminus or the N-terminus of the intracellular signaling domain. The second antigen binding domain can be at the N-terminus or C-terminus of the anti-NKp80 sdAb, either fused directly or via a linker. In some embodiments, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 24. In some embodiments, the intracellular signaling domain comprises the amino acid sequence of SEQ ID NO: 26. In some embodiments, the hinge domain comprises the amino acid sequence of SEQ ID NO: 23. In some embodiments, the intracellular co-stimulatory signaling domain comprises the amino acid sequence of SEQ ID NO: 25. In some embodiments, the CAR further comprises a signal peptide N-terminal to the anti-NKp80 sdAb and the second antigen binding domain. In some embodiments, the signal peptide comprises the amino acid sequence of SEQ ID NO: 21. In some embodiments, the CAR further comprises a protein tag located between the signal peptide and: (i) the anti-NKp80 sdAb, wherein the anti-NKp80 sdAb is located N-terminal to the second antigen binding domain; or (ii) the second antigen binding domain, wherein the second antigen binding domain is located N-terminal to the anti-NKp80 sdAb. In some embodiments, the protein tag is a FLAG tag comprising the amino acid sequence of SEQ ID NO: 22.
[0125] In some embodiments, the engineered immune cell further comprises a second antigen binding protein, wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen, and wherein the second antigen is not NKp80. In some embodiments, the second antigen binding protein is a second chimeric receptor (e.g., CAR, cTCR, engineered TCR, or TAC) .
[0126] In some embodiments, the second chimeric receptor is a CAR (hereinafter also referred to as “second CAR” ) . The second CAR may comprise from N-terminus to C-terminus: (a) a second antigen binding domain specifically recognizing a second antigen, wherein the second antigen is not NKp80; (b) an optional second hinge domain (e.g., derived from CD8α) ; (c) a second transmembrane domain (e.g., derived from CD8α) ; (d) an optional second intracellular co-stimulatory signaling domain (e.g., derived from CD28 or 4-1BB) ; and (e) a second intracellular signaling domain (e.g., derived from CD3ζ or a chimeric signaling domain (CMSD) ) . The second CAR may comprise from N-terminus to C-terminus: (a) a second antigen binding domain specifically recognizing a second antigen, wherein the second antigen is not NKp80; (b) an optional second hinge domain (e.g., derived from CD8α) ; (c) a second transmembrane domain (e.g., derived from CD8α) ; (d) a second intracellular signaling domain (e.g., derived from CD3ζ) ; and (e) an optional second intracellular co-stimulatory signaling domain (e.g., derived from CD28) . The second antigen binding domain of the second CAR may be selected from the group consisting of a ligand, a Fab, a Fab’, a (Fab’) 2, an Fv, a single chain Fv (scFv) , a single domain antibody (sdAb) specifically binding to the second antigen, and a peptide ligand specifically binding to the second antigen. In some embodiments, the second antigen binding domain comprises two or more antigen-binding fragments (e.g., scFv or sdAb) specifically recognizing a second antigen, wherein the second antigen is not NKp80, such as connected in tandem. The two or more antigen-binding fragments can be the same or different. The two or more antigen-binding fragments can recognize the same epitope or different epitopes of the second antigen. In some embodiments, the second CAR comprises from N-terminus to C-terminus: (a) a second antigen binding domain specifically recognizing a second antigen, wherein the second antigen is not NKp80; (b) a second hinge domain (e.g., derived from CD8α) ; (c) a second transmembrane domain (e.g., derived from CD8α) ; (d) a second intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (e) a second intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the second transmembrane domain is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 24. In some embodiments, the second intracellular signaling domain is derived from CD3ζ, such as comprising the amino acid sequence of SEQ ID NO: 26. In some embodiments, the second intracellular co-stimulatory signaling domain is derived from a cytoplasmic domain of CD28, such as comprising the amino acid sequence of SEQ ID NO: 25. In some embodiments, the second hinge domain is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 23. In some embodiments, the second CAR further comprises a second signal peptide N-terminal to the second antigen binding domain specifically recognizing the second antigen. In some embodiments, the second signal peptide is derived from a CD8α propeptide, such as comprising the amino acid sequence of SEQ ID NO: 21. In some embodiments, the second CAR further comprises a second protein tag located between the second signal peptide and the second antigen binding domain specifically recognizing the second antigen. In some embodiments, the second protein tag is a FLAG tag comprising the amino acid sequence of SEQ ID NO: 22. In some embodiments, the second antigen is a disease-associated antigen or disease-specific antigen selected from the group consisting of: a cancer-associated antigen or a cancer-specific antigen; an infectious disease-associated antigen or an infectious disease-specific antigen; an inflammatory disorder-associated antigen or an inflammatory disorder-specific antigen; and an autoimmune-associated antigen or an autoimmune-specific antigen. In some embodiments, the disease-associated antigen or disease-specific antigen is a cancer-associated antigen or a cancer-specific antigen. In some embodiments, the cancer-associated antigen or cancer-specific antigen is selected from the group consisting of CD19, CD20, CD22, BCMA, DLL3, B7H3, PD-L1, PD-L2, CLL1, GPC3, GU2CYC, CD7, CD38, CD41, CD123, Claudin 18.2, Claudin 6, NKG2D, GPRC5D, CD70, and any combination thereof.
[0127] In some embodiments, the second chimeric receptor is an engineered TCR (hereinafter referred to as “second engineered TCR” ) . The second engineered TCR may comprise: i) a second antigen binding domain that comprises a Vα and a Vβ (or a Vδ and a Vγ) derived from a wildtype TCR together specifically recognizing a second antigen that is not NKp80, wherein the Vα, the Vβ, or both (or the Vδ, the Vγ, or both) , comprise one or more mutations (e.g., insertions, deletions, or substitutions, such as conservative substitutions) in one or more CDRs relative to the wild type TCR; and ii) a second transmembrane domain (TM) derived from a TCR molecule (e.g., TCRα / TCRβ, or TCRδ / TCRγ) . The second engineered TCR can be a single chain TCR (scTCR) or a dimeric TCR (dTCR) . For example, the second engineered TCR may comprise: i) a first polypeptide chain comprising from N’ to C’ : Vα (e.g., Vα variant) –Cα –TMα –optional TCRα cytoplasmic domain (cytoTCRα) , and ii) a second polypeptide chain comprising from N’ to C’ : Vβ (e.g., Vβ variant) –Cβ –TMβ –optional cytoTCRβ; wherein the Vα and the Vβ form a second antigen binding domain that specifically recognizes a second antigen that is not NKp80. The second engineered TCR may comprise: i) a first polypeptide chain comprising from N’ to C’ : Vγ (e.g., Vγ variant) –Cγ –TMγ –optional cytoTCRγ, and ii) a second polypeptide chain comprising from N’ to C’ : Vδ (e.g., Vδ variant) –Cδ –TMδ –optional cytoTCRδ; wherein the Vγ and the Vδ form a second antigen binding domain that specifically recognizes a second antigen that is not NKp80 complexed with MHC. The second engineered TCR may bind to the same cognate peptide-MHC bound by the wildtype TCR. The second engineered TCR may bind to the same cognate peptide-MHC with higher affinity compared to that bound by the wildtype TCR. The second engineered TCR may bind to the same cognate peptide-MHC with lower affinity compared to that bound by the wildtype TCR. The second engineered TCR may bind to a non-cognate peptide-MHC not bound by the wildtype TCR. The second engineered TCR may not comprise an intracellular signaling domain. The second engineered TCR may further comprise a second hinge domain (or a connecting domain) between the TCR Ig-like constant domain and the second TCR transmembrane domain, such as a second hinge domain derived from TCRα / TCRβ or TCRδ / TCRγ.
[0128] In some embodiments, the second chimeric receptor is a chimeric T cell receptor (hereinafter referred to as “second cTCR” ) . The second cTCR may comprise: i) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes a second antigen that is not NKp80, and ii) a full-length TCR subunit, wherein the TCR subunit is selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3γ, CD3ε, and CD3δ; wherein the second antigen binding domain is fused (directly or indirectly) to the N-terminus of the full-length TCR subunit. In some embodiments, the second cTCR comprises from N’ to C’ : i) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes a second antigen that is not NKp80, ii) an optional extracellular domain (ECD) or portion thereof derived from a first TCR subunit, and iii) a transmembrane domain derived from a second TCR subunit; wherein the first TCR subunit and the second TCR subunit are independently selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3γ, CD3ε, and CD3δ. The second cTCR can be incorporated into a functional TCR complex along with other endogenous TCR subunits and confer antigen specificity to the TCR complex. The second antigen binding domain of the second cTCR may be selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to the second antigen. The second cTCR antigen binding domain may be fused to the N-terminus of the full-length or a portion thereof of CD3ε, CD3γ, or CD3δ. The second cTCR antigen binding domain may be fused to the N-terminus of a TCRα molecule (with or without the Vα domain) , and / or the N-terminus of a TCRβ molecule (with or without the Vβ domain) . The second cTCR antigen binding domain may be fused to the N-terminus of a TCRγ molecule (with or without the Vγ domain) , and / or the N-terminus of a TCRδ molecule (with or without the Vδ domain) . The second cTCR may not comprise an intracellular signaling domain. The second cTCR may comprise an intracellular signaling domain, such as the intracellular signaling domain of CD3γ, CD3ε, or CD3δ. The second cTCR intracellular signaling domain and the second cTCR transmembrane domain can be derived from the same TCR subunit, e.g., both from CD3ε, both from CD3ε, or both from CD3δ. The second cTCR antigen binding domain and the first TCR subunit (full-length or an ECD portion thereof) can be fused via a linker (such as a GS linker) . In some embodiments, the second cTCR antigen binding domain is fused to the N-terminus of the second transmembrane domain via an optional second linker or second hinge domain. The second cTCR may further comprise a second hinge domain between the ECD portion derived from the first TCR subunit and the second transmembrane domain derived from the second TCR subunit. In some embodiments, the second cTCR comprises from N-terminus to C-terminus: (a) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically recognizes a second antigen that is not NKp80; (b) an optional second linker, (c) an optional extracellular domain of a first TCR subunit (e.g., CD3ε) or a portion thereof, (d) an optional second hinge domain, (e) a second transmembrane domain derived from a second TCR subunit (e.g., CD3ε) , and (f) an optional second cytoplasmic domain (e.g., optional intracellular signaling domain) ; wherein the first and second TCR subunits are independently selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. The first and second TCR subunits can be the same or different. In some embodiments, the second cTCR comprises from N-terminus to C-terminus: (a) an scFv or sdAb that specifically recognizes a second antigen, wherein the second antigen is not NKp80; (b) an optional second linker, and (c) a full-length CD3ε, CD3γ, or CD3δ.
[0129] In some embodiments, the second chimeric receptor is a second T cell antigen coupler (TAC) . The second TAC may comprise: (a) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically binds to a second antigen that is not NKp80; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a TCR subunit (e.g., CD3ε) ; (d) an optional second linker; (e) an optional extracellular domain derived from a first TCR co-receptor (such as CD4, CD28, or CD8, e.g., CD8α) ; (f) a transmembrane comprising a transmembrane of a second TCR co-receptor (such as CD4, CD28, or CD8, e.g., CD8α) ; and (g) an optional intracellular signaling domain comprising intracellular signaling domain of a third TCR co-receptor (such as CD4, CD28, or CD8, e.g., CD8α) . In some embodiments, the first, second, and third TCR co-receptors are the same (e.g., all CD4) . In some embodiments, the first, second, and third TCR co-receptors are different. For example, in some embodiments, the second TAC comprises: (a) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically binds to a second antigen that is not NKp80; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a TCR subunit (e.g., CD3ε) ; (d) an optional second linker; and (e) a full length TCR co-receptor (e.g., CD4, CD8 (e.g., CD8α) , or CD28) .
[0130] In some embodiments, the second chimeric receptor is a second T cell antigen coupler (TAC) -like chimeric receptor. The second TAC-like receptor may comprise: (a) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically binds to a second antigen that is not NKp80; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a first TCR subunit (e.g., CD3ε) ; (d) an optional second linker; (e) an optional extracellular domain of a second TCR subunit (e.g., CD3ε) or a portion thereof; (f) a transmembrane domain comprising a transmembrane domain of a third TCR subunit (e.g., CD3ε) ; and (g) an optional intracellular signaling domain comprising an intracellular signaling domain of a fourth TCR subunit (e.g., CD3ε) ; wherein the first, second, third, and fourth TCR subunits are all selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. In some embodiments, the first, second, third, and fourth TCR subunits are the same (e.g., CD3ε) . In some embodiments, the second, third, and fourth TCR subunits are the same (e.g., CD3ε) . In some embodiments, the first, second, third, and fourth TCR subunits are different. In some embodiments, the second, third, and fourth TCR subunits are the same (e.g., CD3ε) but different from the first TCR subunit (e.g., TCRα) . In some embodiments, the second TAC-like chimeric receptor comprises: (a) a second antigen binding domain comprising an antibody or antigen-binding fragment thereof (e.g., scFv, Fab, or sdAb) that specifically binds to a second antigen that is not NKp80; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a first TCR subunit (e.g., CD3ε) ; (d) an optional second linker; and (e) a full length second TCR subunit (e.g., CD3ε) ; wherein the first and second TCR subunits are both selected from the group consisting of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. In some embodiments, the first and second TCR subunits are the same (e.g., both CD3ε) . In some embodiments, the first (e.g., TCRα) and second (e.g., CD3ε) TCR subunits are different.
[0131] Each component of the anti-NKp80 chimeric receptors and the second chimeric receptors and optionally additional regions are described in more detail below.Antigen binding domains
[0132] In some embodiments, the NKp80 binding domain of the chimeric receptor is selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to NKp80. In some embodiments, the second antigen binding domain of the second chimeric receptor is selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to the second antigen. NKp80 binding domain:
[0133] In some embodiments, the NKp80-targeted chimeric receptor or the anti-NKp80 antigen binding domain comprises a means for specifically recognizing NKp80. In some embodiments, the antigen binding domain of the chimeric receptor (e.g., cTCR or CAR) is selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to NKp80. In some embodiments, the anti-NKp80 chimeric receptor is a TCR comprising an NKp80 binding domain that comprises a Vα and a Vβ (or a Vδ and a Vγ) . In some embodiments, the antigen binding domain is an anti-NKp80 scFv or an anti-NKp80 Fab. In some embodiments, the antigen binding domain is an anti-NKp80 sdAb. In some embodiments, the antigen binding domain is monospecific and monovalent. In some embodiments, the antigen binding domain is monospecific (e.g., specifically binding to the same NKp80 epitope) and multivalent. In some embodiments, the antigen binding domain is multispecific (e.g., specifically binding to different NKp80 epitopes) and multivalent.
[0134] The chimeric receptor antigen binding domain can specifically recognize NKp80 of any source. In some embodiments, the NKp80 is a human NKp80. In some embodiments, the NKp80 is from any of mice, rats, hamsters, guinea pigs, rabbits, chinchillas, cats, dogs, horses, donkeys, cows, goats, sheep, deer, monkeys, apes, etc. In some embodiments, the chimeric receptor antigen binding domain specifically recognizes human NKp80. In some embodiments, the chimeric receptor antigen binding domain does not cross-react with NKp80 from a non-human species. In some embodiments, the chimeric receptor antigen binding domain cross-reacts with NKp80 from a non-human species, such as mouse, rat, or monkey (e.g., cynomolgus monkey) NKp80. Using an antigen binding domain that cross-reacts with NKp80 from a non-human species can help extrapolate animal study data to human clinical trials. NKp80 recognized by the chimeric receptor antigen binding domain can be wildtype NKp80 or mutant NKp80.
[0135] Any NKp80-binding proteins and / or anti-NKp80 antibody constructs specifically recognizing NKp80 can be used in the chimeric receptor antigen binding domains described herein. Exemplary NKp80-binding proteins or anti-NKp80 antibody constructs include but are not limited to, the antibody moiety contained in MAB1900 (e.g., BioTechne) , 5D12 (e.g., BioLegend) , REA845 (e.g., Miltenyi Biotec) , ab198928 (e.g., AbCam) , ab256809 (e.g., AbCam) , MA152 (e.g., Beckman Coulter) , LAP171 (e.g., Vitale et al. (2001) Eur J Immunol. 31 (1) : 233-242., the contents of which are incorporated herein by reference in its entirety) , etc. Anti-NKp80 single domain antibody (sdAb)
[0136] In some embodiments, the NKp80 antigen binding domain comprises (or consists of, or consists essentially of) one or more anti-NKp80 sdAbs, such as two or more anti-NKp80 sdAbs connected in tandem. In some embodiments, the NKp80 antigen binding domain comprises (or consists of, or consists essentially of) an anti-NKp80 sdAb. Any of the anti-NKp80 sdAbs described in the “III. Anti-NKp80 antibody constructs” section can be used herein.
[0137] In some embodiments, the anti-NKp80 sdAb binds to human NKp80. NKp80 (UniProtKB: Q9NZS2) is a type II transmembrane C-type lectin-like receptor that is expressed on the cell surface of nearly all NK cells as well as a subset of effector memory CD8 T cells and γδ T cells. NK cells have been implicated in the advancement of various diseases or disorders, including autoimmune diseases such as systemic lupus erythematosus (SLE) , Syndrome, rheumatoid arthritis, type I diabetes (T1D) , and autoimmune liver disease (ALD) ; graft rejection; and NK cell neoplasms, e.g., NK cell leukemia, NK cell lymphoma, or blastoid NK cell lymphoma.
[0138] In some embodiments, the anti-NKp80 sdAb modulates one or more NKp80 activities. In some embodiments, the anti-NKp80 sdAb is an antagonist antibody. In some embodiments, the anti-NKp80 sdAb blocks NKp80. In some embodiments, the anti-NKp80 sdAb does not activate NKp80. In some embodiments, the anti-NKp80 sdAb blocks NKp80 without activating NKp80.
[0139] In some embodiments, the anti-NKp80 sdAb binds to NKp80 (e.g., human NKp80) with a dissociation constant (KD) of ≤ 1μM, ≤ 100 nM, ≤ 10 nM, ≤ 1 nM, ≤ 0.1 nM, ≤ 0.01 nM, or ≤0.001 nM (e.g., about 10-8 M or less, such as any of from about 10-8 M to about 10-13 M, from about 10-9 M to about 10-13 M, from about 10-10 M to about 10-13 M, or from about 10-11 M to about 10-13 M) . A variety of methods of measuring binding affinity are known in the art, any of which can be used for purposes of the present disclosure, including by RIA, for example, performed with the an antibody of interest and its antigen (Chen et al., 1999, J. Mol Biol 293: 865-81) ; by biolayer interferometry (BLI) or surface plasmon resonance (SPR) assays by using, for example, an Red96 system, or by using, for example, a TM-2000 or a TM-3000. An “on-rate” or “rate of association” or “association rate” or “kon” may also be determined with the same BLI or SPR techniques described above using, for example, the Red96, the TM-2000, or the TM-3000 system.
[0140] In some embodiments, the anti-NKp80 sdAb comprises a VNAR domain. In some embodiments, the anti-NKp80 sdAb comprises a VHH domain. In some embodiments, the anti-NKp80 sdAb comprises from N’ to C’ : FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4. In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1, a CDR2, and a CDR3 having the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16, or a variant of any CDR thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3, or a variant of any CDR thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7, or a variant of any CDR thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11, or a variant of any CDR thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (v) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15, or a variant of any CDR thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; and / or (vi) a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) . In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of any one of SEQ ID NOs: 1, 5, 9, and 13, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (ii) a CDR2 comprising the amino acid sequence of any one of SEQ ID NOs: 2, 6, 10, and 14, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; and (iii) a CDR3 comprising the amino acid sequence of any one of SEQ ID NOs: 3, 7, 11, and 15. In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1, a CDR2, and a CDR3 having the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NOs: 4, 8, 12, or 16; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; (v) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15; and / or (vi) a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 sdAb comprises a CDR1 comprising the amino acid sequence of any one of SEQ ID NOs: 1, 5, 9, and 13, a CDR2 comprising the amino acid sequence of any one of SEQ ID NOs: 2, 6, 10, and 14, and a CDR3 comprising the amino acid sequence of any one of SEQ ID NOs: 3, 7, 11, and 15. In some embodiments, the anti-NKp80 sdAb comprises one, two, or all three CDRs of a VHH of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 sdAb comprises CDR1, CDR2, and CDR3 of a VHH of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 sdAb is camelid. In some embodiments, the anti-NKp80 sdAb is humanized. In some embodiments, the anti-NKp80 sdAb comprises an acceptor human framework, e.g., a human immunoglobulin framework or a human consensus framework. CDR sequences can be determined according to well-known numbering systems / schemes, such as any of IMGT, Kabat, AbM, Chothia, and Contact numbering scheme, or a combination thereof. In some embodiments, the CDRs are determined according to AbM numbering scheme.
[0141] In some embodiments, the anti-NKp80 sdAb comprises one, two, three, or all four framework regions of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 sdAb comprises one, two, three, or all four framework regions derived from a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 sdAb comprises all four framework regions derived from a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 sdAb is camelid. In some embodiments, the anti-NKp80 sdAb is humanized. In some embodiments, the anti-NKp80 sdAb comprises an acceptor human framework, e.g., a human immunoglobulin framework or a human consensus framework.
[0142] In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (ii) a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; and (iii) a CDR3 comprising the amino acid sequence of SEQ ID NO: 3, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) . In some embodiments, the anti-NKp80 sdAb comprises: a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3. In some embodiments, the anti-NKp80 sdAb is camelid. In some embodiments, the anti-NKp80 sdAb is humanized. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of SEQ ID NO: 4, or a variant thereof having at least about 85% (e.g., at least about any of 90%, 95%, 96%, 96%, 98%, 99%, or more) sequence identity to SEQ ID NO: 4.
[0143] In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (ii) a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; and (iii) a CDR3 comprising the amino acid sequence of SEQ ID NO: 7, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) . In some embodiments, the anti-NKp80 sdAb comprises: a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and (iii) a CDR3 comprising the amino acid sequence of SEQ ID NO: 7. In some embodiments, the anti-NKp80 sdAb is camelid. In some embodiments, the anti-NKp80 sdAb is humanized. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of SEQ ID NO: 8, or a variant thereof having at least about 85% (e.g., at least about any of 90%, 95%, 96%, 96%, 98%, 99%, or more) sequence identity to SEQ ID NO: 8.
[0144] In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (ii) a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; and (iii) a CDR3 comprising the amino acid sequence of SEQ ID NO: 11, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) . In some embodiments, the anti-NKp80 sdAb comprises: a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11. In some embodiments, the anti-NKp80 sdAb is camelid. In some embodiments, the anti-NKp80 sdAb is humanized. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of SEQ ID NO: 12, or a variant thereof having at least about 85% (e.g., at least about any of 90%, 95%, 96%, 96%, 98%, 99%, or more) sequence identity to SEQ ID NO: 12.
[0145] In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; (ii) a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) ; and (iii) a CDR3 comprising the amino acid sequence of SEQ ID NO: 15, or a variant thereof comprising up to 5 (e.g., 5, 4, 3, 2, or 1) amino acid variations (e.g., insertion, deletion, or substitution, such as conservative substitution) . In some embodiments, the anti-NKp80 sdAb comprises: a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the anti-NKp80 sdAb is camelid. In some embodiments, the anti-NKp80 sdAb is humanized. In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of SEQ ID NO: 16, or a variant thereof having at least about 85% (e.g., at least about any of 90%, 95%, 96%, 96%, 98%, 99%, or more) sequence identity to SEQ ID NO: 16.
[0146] In some embodiments, the anti-NKp80 sdAb comprises a VHH having at least about any of 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or 100%sequence identity to an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the VHH with sequence variation contains substitutions (e.g., conservative substitutions) , insertions, and / or deletions relative to the reference sequence, but the anti-NKp80 sdAb comprising that variant sequence retains the ability to bind to NKp80. In some embodiments, a total of 1 to 10 amino acids have been substituted, inserted and / or deleted in an amino acid sequence selected from the group consisting of any of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, substitutions, insertions, and / or deletions occur in regions outside the CDRs (i.e., in the FRs) . In some embodiments, the anti-NKp80 sdAb comprises a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 antigen binding domain comprises: (i) two or more anti-NKp80 sdAbs connected in tandem, wherein each anti-NKp80 sdAb comprises a VHH domain; and / or (ii) at least one anti-NKp80 sdAb and a second antigen binding domain (e.g., scFv, sdAb, Fab) that specifically recognizes a second antigen that is not NKp80. The two or more antigen binding domains can be the same or different. The two or more antigen-binding fragments can recognize the same epitope or different epitopes of NKp80 and / or a second antigen that is not NKp80. In some embodiments, the at least two anti-NKp80 VHH domains are selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the anti-NKp80 antigen binding domain comprising one or more anti-NKp80 VHH domains selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16 contains post-translational modifications.
[0147] Functional epitopes can be mapped, e.g., by combinatorial alanine scanning, to identify amino acids in the NKp80 protein that are necessary for interaction with anti-NKp80 sdAbs provided herein. Conformational and crystal structure of anti-NKp80 sdAb bound to NKp80 may be employed to identify the epitopes. In some embodiments, the anti-NKp80 sdAb specifically binds to the same NKp80 epitope as any of the anti-NKp80 sdAbs provided herein. In some embodiments, the anti-NKp80 sdAb specifically binds to the same NKp80 epitope as an anti-NKp80 sdAb comprising a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16.
[0148] In some embodiments, the anti-NKp80 sdAb specifically binds to NKp80 competitively with any one of the anti-NKp80 sdAbs described herein. In some embodiments, the anti-NKp80 sdAb specifically binds to NKp80 competitively with an anti-NKp80 sdAb comprising a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, competitive binding may be determined using an ELISA assay. Additional antigen binding domains
[0149] In some embodiments, the anti-NKp80 chimeric receptor further comprises a second antigen binding domain that comprises a means for specifically recognizing a second antigen. In some embodiments, the second antigen is not NKp80. In other embodiments, the second antigen binding protein (e.g., second CAR) further comprises one or more additional (e.g., a second, third, fourth, or more) antigen binding domains, wherein the one or more additional antigen binding domains specifically bind to one or more additional antigens that are not an NKp80 antigen. In some embodiments, the second antigen is selected from the group consisting of a cancer-associated antigen or a cancer-specific antigen, an infectious disease-associated antigen or an infectious disease-specific antigen, an inflammatory disorder-associated antigen or an inflammatory disorder-specific antigen, and an autoimmune-associated antigen or an autoimmune-specific antigen. In some embodiments, the second antigen is a cancer-associated antigen or a cancer-specific antigen. In some embodiments, the cancer-associated antigen or cancer-specific antigen is selected from the group consisting of CD19, CD20, CD22, BCMA, DLL3, B7H3, PD-L1, PD-L2, CLL1, GPC3, GU2CYC, CD7, CD38, CD41, CD123, Claudin 18.2, Claudin 6, NKG2D, GPRC5D, CD70, and any combination thereof. In some embodiments, the second antigen binding domain is selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to the second antigen. In some embodiments, the second antigen binding domain is an scFv or a Fab fragment. In some embodiments, the second antigen binding domain is an sdAb. In some embodiments, the second antigen binding domain is monospecific and monovalent. In some embodiments, the second antigen binding domain is monospecific (e.g., specifically binding to the same antigenic epitope) and multivalent. In some embodiments, the second antigen binding domain is multispecific (e.g., specifically binding to different antigenic epitopes) and multivalent. In some embodiments, the second antigen is from a human. In some embodiments, the second antigen is from any of mice, rats, hamsters, guinea pigs, rabbits, chinchillas, cats, dogs, horses, donkeys, cows, goats, sheep, deer, monkeys, apes, etc. In some embodiments, the second antigen binding domain specifically recognizes a human second antigen. In some embodiments, the second antigen binding domain does not cross-react with a second antigen from a non-human species. In some embodiments, the second antigen binding domain cross-reacts with a second antigen from a non-human species, such as mouse, rat, or monkey (e.g., cynomolgus monkey) . Any second antigen binding proteins or second antibody constructs specifically recognizing the second antigen can be used in the second antigen binding domain of the second antigen binding protein (e.g., second chimeric receptor) described herein.
[0150] In some embodiments, the second chimeric receptor comprises a second antigen binding domain that comprises a means for specifically recognizing a second antigen. In some embodiments, the second antigen is not NKp80. In some embodiments, the second antigen is selected from the group consisting of a cancer-associated antigen or a cancer-specific antigen, an infectious disease-associated antigen or an infectious disease-specific antigen, an inflammatory disorder-associated antigen or an inflammatory disorder-specific antigen, and an autoimmune-associated antigen or an autoimmune-specific antigen. In some embodiments, the second antigen is a cancer-associated antigen or a cancer-specific antigen. In some embodiments, the cancer-associated antigen or cancer-specific antigen is selected from the group consisting of CD19, CD20, CD22, BCMA, DLL3, B7H3, PD-L1, PD-L2, CLL1, GPC3, GU2CYC, CD7, CD38, CD41, CD123, Claudin 18.2, Claudin 6, NKG2D, GPRC5D, CD70, and any combination thereof. In some embodiments, the second antigen binding domain of the second chimeric receptor (e.g., cTCR or CAR) is selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically binding to the second antigen. In some embodiments, the second antigen binding domain is an scFv or a Fab fragment. In some embodiments, the second antigen binding domain is an sdAb. In some embodiments, the second chimeric receptor is a TCR comprising a second antigen binding domain that comprises a Vα and a Vβ (or a Vδ and a Vγ) . In some embodiments, the second antigen binding domain is monospecific and monovalent. In some embodiments, the second antigen binding domain is monospecific (e.g., specifically binding to the same antigenic epitope) and multivalent. In some embodiments, the second antigen binding domain is multispecific (e.g., specifically binding to different antigenic epitopes) and multivalent. In some embodiments, the second antigen binding domain comprises two or three domains that binds to different antigens, optionally wherein each domain is an antibody. In some embodiments, the second antigen binding domain comprises a CD19 binding domain and a CD20 binding domain. In some embodiments, the second antigen is from a human. In some embodiments, the second antigen is from any of mice, rats, hamsters, guinea pigs, rabbits, chinchillas, cats, dogs, horses, donkeys, cows, goats, sheep, deer, monkeys, apes, etc. In some embodiments, the second antigen binding domain specifically recognizes a human second antigen. In some embodiments, the second antigen binding domain does not cross-react with a second antigen from a non-human species. In some embodiments, the second antigen binding domain cross-reacts with a second antigen from a non-human species, such as mouse, rat, or monkey (e.g., cynomolgus monkey) . Any second antigen binding proteins or second antibody constructs specifically recognizing the second antigen can be used in the second antigen binding domain of the second antigen binding protein (e.g., second chimeric receptor) described herein.Transmembrane domain
[0151] The anti-NKp80 (i.e., the first) and / or second chimeric receptors (e.g., anti-NKp80 CAR and / or second CAR) of the present disclosure comprise a transmembrane domain that can be directly or indirectly fused to the extracellular antigen binding domain. Any protein structure that is thermodynamically stable in a cell membrane, such as a eukaryotic cell membrane, can be used as the transmembrane domain herein. The transmembrane domain may be derived either from a natural or from a synthetic source. For example, it can be a synthetic, non-naturally occurring protein segment, e.g., a hydrophobic protein segment that is thermodynamically stable in a cell membrane. The transmembrane domain can be derived from a wildtype protein, or contains one or more mutations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) . A transmembrane domain containing one or more mutations can be employed to avoid mispairing with endogenous protein, e.g., endogenous TCR complex component (s) , in order to enhance correct chimeric receptor assembly and / or expression level.
[0152] In some embodiments, the first chimeric receptor is an anti-NKp80 CAR. In some embodiments, the transmembrane domain of the first CAR is derived from a Type I single-pass membrane protein. In some embodiments, transmembrane domains from multi-pass membrane proteins may also be compatible for use in any of the CARs described herein (e.g., the first CAR and / or the second CAR) . Multi-pass membrane proteins may comprise a complex of (at least 2, 3, 4, 5, 6, 7 or more) alpha helices or a beta sheet structure. In some embodiments, the N-terminus and the C-terminus of a multi-pass membrane protein are present on opposing sides of the lipid bilayer, e.g., the N-terminus of the protein is present on the cytoplasmic side of the lipid bilayer and the C-terminus of the protein is present on the extracellular side.
[0153] In some embodiments, the transmembrane domain of the first CAR and / or the second CAR is derived from a molecule selected from the group consisting of: an α, β or ζ chain of a TCR, CD28, CD3ε, CD45, CD4, CD5, CD8, CD9, CD16, CD22, CD33, CD37, CD64, CD80, CD86, CD134, 4-1BB (CD137) , CD154, KIRDS2, OX40, CD2, CD27, LFA-1 (CD11a, CD18) , ICOS (CD278) , 4-1BB (CD137) , GITR, CD40, BAFFR, HVEM (LIGHTR) , SLAMF7, NKp80 (KLRF1) , CD160, Claudin-6, IL-2Rβ, IL-2Rγ, IL-7Ra, ITGA1, VLA1, CD49a, ITGA4, IA4, CD49D, ITGA6, VLA-6, CD49f, ITGAD, CD11d, ITGAE, CD103, ITGAL, CD11a, LFA-1, ITGAM, CD11b, ITGAX, CD11c, ITGB1, CD29, ITGB2, CD18, LFA-1, ITGB7, TNFR2, DNAM1 (CD226) , SLAMF4 (CD244, 2B4) , CD84, CD96 (Tactile) , CEACAM1, CRT AM, Ly9 (CD229) , CD160 (BY55) , PSGL1, CDIOO (SEMA4D) , SLAMF6 (NTB-A, Ly108) , SLAM (SLAMF1, CD150, IPO-3) , BLAME (SLAMF8) , SELPLG (CD162) , LTBR, PAG / Cbp, NKp44, NKp30, NKp46, NKG2D, and NKG2C. In some embodiments, the transmembrane domain is derived from a molecule selected from the group consisting of CD8α, CD4, CD28, CD137, CD80, CD86, CD152, and PD-1.
[0154] In some specific embodiments, the transmembrane domain of the first CAR and / or the second CAR is derived from CD8α. In some embodiments, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 24.Hinge domain
[0155] The anti-NKp80 (i.e., the first) and / or second chimeric receptors of the present disclosure (e.g., anti-NKp80 and / or second engineered TCR, cTCR, or CAR) may comprise a hinge domain that is located between the extracellular antigen binding domain and the transmembrane domain. A hinge domain is an amino acid segment that is generally found between two domains of a protein and may allow for flexibility of the protein and movement of one or both of the domains relative to one another. Any amino acid sequence that provides such flexibility and movement of the extracellular antigen binding domain relative to the transmembrane domain of the effector molecule can be used. A peptide linker (e.g., any of those described in the “Peptide Linker” subsection below) can be used as a hinge domain. The hinge domain may confer stability to a multi-chain chimeric receptor, such as by forming disulfide-bond between two polypeptide chains of a chimeric receptor (e.g., a CH1-CL pair hinge domain, or an antibody hinge region pair) .
[0156] The hinge domain may contain about 10-100 amino acids, e.g., about any one of 15-75 amino acids, 20-50 amino acids, or 30-60 amino acids. In some embodiments, the hinge domain may be at least about any one of 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 40, 45, 50, 55, 60, 65, 70, or 75 amino acids in length.
[0157] The hinge domain can be a hinge domain of a naturally occurring protein. Hinge domains of any protein known in the art to comprise a hinge domain are compatible for use in the chimeric receptors described herein. In some embodiments, the hinge domain is at least a portion of a hinge domain of a naturally occurring protein and confers flexibility to the chimeric receptor. In some embodiments, the hinge domain is derived from CD28. In some embodiments, the hinge domain is derived from IgG4. In some embodiments, the hinge domain is derived from CD8α. In some embodiments, the hinge domain is a portion of the hinge domain of CD8α, e.g., a fragment containing at least 15 (e.g., 20, 25, 30, 35, or 40) consecutive amino acids of the hinge domain of CD8α. In some embodiments, the hinge domain derived from CD8α comprises the amino acid sequence of SEQ ID NO: 23.
[0158] Non-naturally occurring peptides may also be used as hinge domains for the chimeric receptors described herein. In some embodiments, the hinge domain between the C-terminus of the extracellular antigen binding domain and the N-terminus of the transmembrane domain is a peptide linker, such as a (GGGGS) n linker (e.g., SEQ ID NO: 31) , wherein n can be an integer of at least 1, e.g., 1, 2, 3, 4, or more; or a (GxS) n linker, wherein x and n, independently can be an integer of at least 1, such as between 3 and 12, including 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12. In some embodiments, the peptide linker comprises the amino acid sequence of SEQ ID NO: 29 or 30.Intracellular signaling domain
[0159] The intracellular signaling domain is responsible for activation of at least one of the normal effector functions of the immune effector cell expressing the anti-NKp80 (i.e., the first) and / or second chimeric receptors (e.g., anti-NKp80 and / or second CAR or cTCR) . The term “effector function” refers to a specialized function of a cell, such as in the killing of diseased cells such as tumor cells, or in the inhibition of tumor growth and / or inhibition of tumor development, including inhibition of tumor dissemination and metastasis. Effector function of a T cell, for example, may be cytolytic activity or helper activity including the secretion of cytokines. Thus, the term “intracellular signaling domain” refers to the portion of a protein which transduces the effector function signal and directs the cell to perform a specialized function. While usually the entire intracellular signaling domain can be employed, in many cases it is not necessary to use the entire chain. To the extent that a truncated portion of the intracellular signaling domain is used, such truncated portion may be used in place of the intact chain as long as it transduces the effector function signal. The term intracellular signaling domain is thus meant to include any truncated portion of the intracellular signaling domain sufficient to transduce the effector function signal.
[0160] In some embodiments, the intracellular signaling domain comprises (or consists essentially of, or consists of) a primary intracellular signaling domain of an immune effector cell. In some embodiments, the first chimeric receptor and / or the second chimeric receptor comprises an intracellular signaling domain consisting essentially of a primary intracellular signaling domain of an immune effector cell. “Primary intracellular signaling domain” refers to intracellular signaling sequence that acts in a stimulatory manner to induce immune effector functions. In some embodiments, the primary intracellular signaling domain contains a signaling motif known as immunoreceptor tyrosine-based activation motif, or ITAM. An “ITAM, ” as used herein, is a conserved protein motif that is generally present in the tail portion of signaling molecules expressed in many immune cells. ITAMs within signaling molecules are important for signal transduction within the cell, which is mediated at least in part by phosphorylation of tyrosine residues in the ITAM following activation of the signaling molecule. ITAMs may also function as docking sites for other proteins involved in signaling pathways. Exemplary ITAM-containing primary intracellular signaling sequences include those derived from CD3ζ, FcεRIβ, FcεRIγ, CD3γ, CD3δ, CD3ε, DAP12, CNAIP / NFAM1, STAM-1, STAM-2, Moesin, CD5, CD22, CD79a, CD79b, DAP12 and CD66d (CEACAM3) . The primary intracellular signaling domain may comprise a chimeric signaling domain (CMSD) . The CMSD may comprise one or a plurality of immune-receptor Tyrosine-based Activation Motifs (CMSD ITAMs) . In some embodiments, the plurality of CMSD ITAMs are optionally connected by one or more linkers (CMSD linkers) . The CMSD ITAMs may be derived from an ITAM-containing parent molecule selected from the group consisting of CD3ε, CD3δ, CD3γ, Igα (CD79a) , Igβ (CD79b) , FcεRIβ, FcεRIγ, DAP12, CNAIP / NFAM1, STAM-1, STAM-2, and Moesin. Details of the CMSD can be found, e.g., in PCT Application Publication No. WO2021037221, which is incorporated herein by reference in its entirety.
[0161] In some embodiments, the first CAR and / or the second CAR of the present disclosure comprises an intracellular signaling domain, e.g., comprises an ITAM-containing primary intracellular signaling domain, or a functional primary intracellular signaling domain. In some embodiments, the first CAR and / or the second CAR comprises an intracellular signaling domain (e.g., a primary intracellular signaling domain) derived from CD3ζ. In some embodiments, the intracellular signaling domain (e.g., the primary intracellular signaling domain) derived from CD3ζ comprises the amino acid sequence of SEQ ID NO: 26.Intracellular co-stimulatory signaling domain
[0162] Many immune effector cells require co-stimulation, in addition to stimulation of an antigen-specific signal (e.g., the primary signal) , to promote cell proliferation, differentiation and survival, as well as to activate effector functions of the cell. In some embodiments, the first chimeric receptor and / or the second chimeric receptor of the present disclosure (e.g., first CAR and / or second CAR) comprises at least one co-stimulatory signaling domain. The term “co-stimulatory signaling domain, ” as used herein, refers to at least a portion of a protein that mediates a secondary or co-stimulatory signal transduction within a cell to induce an immune response such as an effector function. The intracellular co-stimulatory signaling domain can act in an antigen-independent manner to provide a secondary or co-stimulatory signal to immune cells. The co-stimulatory signaling domain of the first chimeric receptor and / or the second chimeric receptor described herein can be an intracellular signaling domain from a co-stimulatory protein, which transduces a secondary or co-stimulatory signal and modulates responses mediated by immune cells, such as T cells, NK cells, macrophages, neutrophils, or eosinophils. The term "co-stimulatory molecule" refers to a cognate binding partner on an immune cell (such as T cell) that specifically binds with a co-stimulatory ligand, thereby mediating a co-stimulatory response by the immune cell, such as, but not limited to, proliferation and survival. In some embodiments, the co-stimulatory molecule selected from the group consisting of CD27, CD28, CD137, OX40, CD40, PD-1, LFA-1, ICOS, CD2, CD7, LIGHT, NKG2C, B7-H3, TNFRSF9, TNFRSF4, TNFRSF8, CD40LG, ITGB2, KLRC2, TNFRSF18, TNFRSF14, HAVCR1, LGALS9, DAP10, DAP12, CD83, the Toll / Interleukin-1 receptor (TIR) domain of Toll-like receptor 2 (TLR2) , and ligands of CD83.
[0163] In some embodiments, the first chimeric receptor and / or the second chimeric receptor comprises a single intracellular co-stimulatory signaling domain. In some embodiments, the first chimeric receptor and / or the second chimeric receptor comprises two or more (such as about any of 2, 3, 4, or more) intracellular co-stimulatory signaling domains. In some embodiments, the first chimeric receptor and / or the second chimeric receptor comprises two or more of the same co-stimulatory signaling domains. In some embodiments, the first chimeric receptor and / or the second chimeric receptor comprises two or more co-stimulatory signaling domains from different co-stimulatory proteins, such as any two or more co-stimulatory proteins described herein. In some embodiments, the first chimeric receptor and / or the second chimeric receptor (e.g., first cTCR and / or second cTCR) lacks a functional primary intracellular signaling domain but comprises one or more intracellular co-stimulatory signaling domains. In some embodiments, the first chimeric receptor and / or the second chimeric receptor (e.g., first cTCR and / or second cTCR) lacks any primary intracellular signaling domain but comprises one or more intracellular co-stimulatory signaling domains. In some embodiments, the first chimeric receptor and / or the second chimeric receptor (e.g., first CAR and / or second CAR) comprises an intracellular signaling domain (e.g., derived from CD3ζ) and one or more intracellular co-stimulatory signaling domains. In some embodiments, the one or more intracellular co-stimulatory signaling domains and the primary intracellular signaling domain (such as intracellular signaling domain of CD3ζ) are fused to each other via optional peptide linkers. The primary intracellular signaling domain and the one or more intracellular co-stimulatory signaling domains may be arranged in any suitable order. In some embodiments, the one or more intracellular co-stimulatory signaling domains are located between the transmembrane domain and the primary intracellular signaling domain (such as intracellular signaling domain of CD3ζ) . In some embodiments, the one or more intracellular co-stimulatory signaling domains are located at the C-terminus of the primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the primary intracellular signaling domain (e.g., derived from CD3ζ) is located in between two intracellular co-stimulatory signaling domains. Multiple co-stimulatory signaling domains may provide additive or synergistic stimulatory effects.
[0164] In some embodiments, the first chimeric receptor and / or the second chimeric receptor of the present disclosure (e.g., first CAR and / or second CAR) further comprises an intracellular co-stimulatory signaling domain derived from the cytoplasmic domain of CD28. In some embodiments, the first chimeric receptor and / or the second chimeric receptor (e.g., first CAR and / or second CAR) comprises an intracellular co-stimulatory signaling domain comprising the amino acid sequence of SEQ ID NO: 25. In some embodiments, the first CAR and / or the second CAR comprises an intracellular signaling domain of CD3ζ and an intracellular co-stimulatory signaling domain of CD28.
[0165] Also within the scope of the present disclosure are variants of any of the intracellular co-stimulatory signaling domains described herein, such that the variant intracellular co-stimulatory signaling domain is capable of modulating the immune response of the immune cell. The intracellular co-stimulatory signaling domain may comprise up to 10 amino acid residue variations (e.g., 1, 2, 3, 4, 5, or 8) as compared to a wild-type counterpart. Mutation of amino acid residues of the intracellular co-stimulatory signaling domain may result in: i) an increase in signaling transduction and enhanced stimulation of immune responses relative to intracellular co-stimulatory signaling domains that do not comprise the mutation; or ii) a decrease in signaling transduction and reduced stimulation of immune responses relative to intracellular co-stimulatory signaling domains that do not comprise the mutation.Signal Peptide
[0166] The anti-NKp80 (i.e. the first) and / or second chimeric receptors of the present disclosure may comprise a signal peptide (also known as a signal sequence) at the N-terminus of the polypeptide. In general, signal peptides are peptide sequences that target a polypeptide to the desired site in a cell. In some embodiments, the signal peptide targets the first chimeric receptor and / or the second chimeric receptor to the secretory pathway of the cell and will allow for integration and anchoring of the chimeric receptor into the lipid bilayer. Signal peptides including signal sequences of naturally occurring proteins or synthetic, non-naturally occurring signal sequences, which are compatible for use in the chimeric receptors described herein, will be evident to one of skill in the art. In some embodiments, the signal peptide is derived from a molecule selected from the group consisting of CD8α, GM-CSF receptor α, and IgG1 heavy chain. In some embodiments, the signal peptide is derived from a CD8α propeptide, e.g., human CD8α, such as comprising the amino acid sequence of SEQ ID NO: 21.Protein Tag
[0167] The first chimeric receptor and / or the second chimeric receptor of the present disclosure may comprise one or more protein tags, such as between different components of the anti-NKp80 (i.e., the first) chimeric receptor and / or second chimeric receptor (e.g., between the signal peptide and the antigen binding domain, or between the antigen binding domain and the transmembrane domain) , and / or at the N-terminus of the anti-NKp80 chimeric receptor and / or the second chimeric receptor and / or the C-terminus of the anti-NKp80 chimeric receptor and / or the second chimeric receptor.
[0168] Protein tags can include, e.g., affinity tags, solubilization tags, chromatography tags, epitope tags, or fluorescence tags. In some embodiments, the protein tag is a chromatography tag, such as but not limited to a FLAG tag or a polyglutamate tag. In some embodiments, the protein tag is an epitope tag, such as but not limited to any of an ALFA-tag, a V5-tag, a Myc-tag, an HA-tag, a Spot-tag, a T7-tag, or an NE-tag. In some embodiments, the protein tag is a fluorescence tag, such as but not limited to green fluorescent protein (GFP) , red fluorescent protein (RFP) , yellow fluorescent protein (YFP) , cyan fluorescent protein (CFP) , blue fluorescent protein (BFP) , enhanced green fluorescent protein (eGFP) , enhanced yellow fluorescent protein (eYFP) , dsRed, mFruits, mCherry, tagRFP, eqFP611, Dronpa, EosFP, etc.
[0169] In some embodiments, the first chimeric receptor and / or the second chimeric receptor comprises a protein tag located between the first signal peptide and the first antigen binding domain and / or the second signal peptide and the second antigen binding domain. In some embodiments, the protein tag is a FLAG tag comprising the amino acid sequence of SEQ ID NO: 22.Peptide Linker
[0170] The anti-NKp80 (i.e., the first) chimeric receptor and / or the second chimeric receptor of the present disclosure may comprise one or more peptide linkers, such as between different components of the anti-NKp80 chimeric receptor and / or the second chimeric receptor (e.g., between two or more intracellular co-stimulatory signaling domains, between intracellular co-stimulatory signaling domain and primary intracellular signaling domain, or between the antigen binding domain and the transmembrane domain) , and / or within one chimeric receptor component (e.g., antigen binding domain, such as within an scFv, or for connecting two or more antibody moieties in tandem) .
[0171] Each peptide linker in an anti-NKp80 chimeric receptor and / or a second chimeric receptor may have the same or different length and / or sequence depending on the structural and / or functional features of the antibody moieties and / or the various domains. Each peptide linker may be selected and optimized independently. The length, the degree of flexibility and / or other properties of the peptide linker (s) used in the anti-NKp80 and / or second chimeric receptors may have some influence on properties, including but not limited to the affinity, specificity, or avidity for one or more particular antigens or epitopes. For example, longer peptide linkers may be selected to ensure that two adjacent domains do not sterically interfere with one another. A short peptide linker may be disposed between the transmembrane domain and the primary intracellular signaling domain of a an anti-NKp80 chimeric receptor and / or a second chimeric receptor (e.g., anti-NKp80 CAR and / or a second CAR) , or between the transmembrane domain and the intracellular co-stimulatory signaling domain of an anti-NKp80 chimeric receptor and / or a second chimeric receptor (e.g., anti-NKp80 CAR and / or second CAR) . In some embodiment, the peptide linker comprises flexible residues (such as glycine and serine) so that the adjacent domains are free to move relative to each other. For example, a glycine-serine doublet can be a suitable peptide linker.
[0172] The peptide linker can be of any suitable length. The peptide linker may be at least about any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 50, 75, 100 or more amino acids (aa) long. The peptide linker may be no more than about any of 100, 75, 50, 40, 35, 30, 25, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5 or fewer aa long. In some embodiments, the length of the peptide linker is any of about 1 aa to about 10 aa, about 1 aa to about 20 aa, about 1 aa to about 30 aa, about 5 aa to about 15 aa, about 10 aa to about 25 aa, about 5 aa to about 30 aa, about 10 aa to about 30 aa, about 30 aa to about 50 aa, about 50 aa to about 100 aa, or about 1 aa to about 100 aa. In some embodiments, the peptide linker is about 10 aa to about 20 aa, such as about 15 aa.
[0173] The peptide linker may have a naturally occurring sequence, or a non-naturally occurring sequence. For example, a sequence derived from the hinge region of heavy chain only antibodies may be used as the linker. See, for example, WO1996 / 34103. In some embodiments, the peptide linker is a flexible linker. Exemplary flexible linkers include but not limited to glycine polymers (G) n, glycine-serine polymers, glycine-alanine polymers, alanine-serine polymers, threonine-serine, and other flexible linkers known in the art. Other linkers known in the art, for example, as described in WO2016014789, WO2015158671, WO2016102965, US20150299317, WO2018067992, US7741465, Colcher et al., J. Nat. Cancer Inst. 82: 1191-1197 (1990) , and Bird et al., Science 242: 423-426 (1988) may also be included in the chimeric receptors provided herein, the disclosure of each of which is incorporated herein by reference in their entirety.
[0174] In some embodiments, the peptide linker is (GGGGS) n (SEQ ID NO: 31) , wherein n is an integer of at least 1 (e.g., 1, 2, 3, 4, or more) . In some embodiments, the peptide linker is (GxS) n, wherein x and n independently can be an integer of at least 1, such as between 3 and 12 (e.g., 3, 4, 5, 6, 7, 8, 9, 10, 11, 12) . In some specific embodiments, the peptide linker comprises the amino acid sequence of SEQ ID NO: 29 or 30. C. Nucleic acids and vectors encoding antigen binding proteins
[0175] In one aspect, the present disclosure provides nucleic acids and vectors for cloning and expressing any one of the NKp80 binding proteins (e.g., NKp80-targeted chimeric receptors such as anti-NKp80 CARs) and / or the second antigen binding protein (e.g., second chimeric receptor such as second CARs) described herein. In some embodiments, the vector is suitable for replication and integration in eukaryotic cells, such as mammalian cells. In some embodiments, the vector is a viral vector. Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus (AAV) vectors, lentiviral vector, retroviral vectors, vaccinia vector, herpes simplex viral vector, and derivatives thereof. Viral vector technology is well known in the art and is described, for example, in Sambrook et al. (2001, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York) , and in other virology and molecular biology manuals.
[0176] A number of viral based systems have been developed for gene transfer into mammalian cells. For example, retroviruses provide a convenient platform for gene delivery systems. The heterologous nucleic acid can be inserted into a vector and packaged in retroviral particles using techniques known in the art. The recombinant virus can then be isolated and delivered to the engineered mammalian cell in vitro or ex vivo. A number of retroviral systems are known in the art. In some embodiments, adenovirus vectors are used. A number of adenovirus vectors are known in the art. In some embodiments, lentivirus vectors are used. In some embodiments, self-inactivating lentiviral vectors are used. The lentiviral vectors can be used to transduce a mammalian cell (such as primary human T cells) using methods known in the art. Vectors derived from retroviruses such as lentivirus are suitable tools to achieve long-term gene transfer, because they allow long-term, stable integration of a transgene and its propagation in progeny cells. Lentiviral vectors also have low immunogenicity, and can transduce non-proliferating cells. In some embodiments, the vector encoding the chimeric receptor is a lentiviral vector.
[0177] In some embodiments, there is provided a nucleic acid encoding the NKp80 binding protein and a second antigen binding protein. In some embodiments, there is provided a second nucleic acid encoding the second antigen binding protein. In some embodiments, the first nucleic acid and the second nucleic acid are located on the same vector. In some embodiments, the first nucleic acid and the second nucleic acid are located on different vectors (i.e., a first vector and a second vector) . In some embodiments, the first vector and the second vector are both transduced into an immune cell in order to generate the engineered immune cell of the present disclosure. In some embodiments, the first vector and the second vector are transduced simultaneously into an immune cell. In some embodiments, the first vector and the second vector are transduced concurrently into an immune cell. In some embodiments, the first vector and the second vector are transduced sequentially into an immune cell. The first vector can be transduced first into an immune cell before or after the second vector. In some embodiments, the immune cell already comprises the second nucleic acid encoding the second antigen binding protein, or already expresses the second antigen binding protein, then only the first nucleic acid is introduced into the immune cell.
[0178] In some embodiments, there is provided a vector (e.g., a first vector) comprising any one of the nucleic acids encoding an NKp80 binding protein (e.g., NKp80-targeted chimeric receptor, such as any of the anti-NKp80 CARs described herein) . The nucleic acid can be cloned into the vector using any known molecular cloning methods in the art, including, for example, using restriction endonuclease sites and one or more selectable markers.
[0179] In some embodiments, the nucleic acid or the vector encoding thereof that encodes the NKp80 binding protein (e.g., NKp80-targeted chimeric receptor, such as anti-NKp80 CAR) and / or the second antigen binding protein (e.g., second chimeric receptor, such as second CAR) further encodes a signal peptide (e.g., comprising the amino acid sequence of SEQ ID NO: 21) at the N-terminus. In some embodiments, the nucleic acid encodes a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37.
[0180] In some embodiments, the first nucleic acid encoding the NKp80 binding protein and / or the second nucleic acid encoding the second antigen binding protein is operably linked to a promoter. Varieties of promoters have been explored for gene expression in mammalian cells, and any of the promoters known in the art may be used in the present disclosure. Promoters may be roughly categorized as constitutive promoters or regulated promoters, such as inducible promoters. In some embodiments, the first nucleic acid and / or the second nucleic acid are under the control of a promoter. In some embodiments, the promoter is selected from the group consisting of a phosphoglycerate kinase (PGK) promoter (e.g., PGK-1 promoter) , a Rous Sarcoma Virus (RSV) promoter, an Simian Virus 40 (SV40) promoter, a cytomegalovirus (CMV) immediate early (IE) gene promoter, an elongation factor 1 alpha (EF1-α) promoter, a ubiquitin-C (UBQ-C) promoter, a cytomegalovirus CMV) enhancer / chicken beta-actin (CAG) promoter, polyoma enhancer / herpes simplex thymidine kinase (MC1) promoter, a beta actin (β-ACT) promoter, a myeloproliferative sarcoma virus enhancer, negative control region deleted, d1587rev primer-binding site substituted (MND) promoter, an NFAT promoter, a promoter, and an NFκB promoter. In some embodiments, the promoter is an hEF1α promoter.
[0181] In some embodiments, there is provide a vector (e.g., viral vector, such as lentiviral vector) comprising: a first nucleic acid encoding an NKp80-targeted chimeric receptor (e.g., any of the chimeric receptors described herein, such as anti-NKp80 CAR) , and a second nucleic acid encoding a second chimeric receptor (e.g., a chimeric receptor targeting a disease antigen such as a cancer antigen, such as any cancer antigen known in the art) . In some embodiments, the first nucleic acid and the second nucleic acid are under the control of the same promoter. In some embodiments, the first nucleic acid and the second nucleic acid are under the control of different promoters. The first nucleic acid can be at the 5′or the 3′of the second nucleic acid.
[0182] In some embodiments, there is provided a first vector (e.g., viral vector, such as lentiviral vector) comprising a first nucleic acid encoding an NKp80-targeted chimeric receptor (e.g., any of the chimeric receptors described herein, such as anti-NKp80 CAR) , and a second vector (e.g., viral vector, such as lentiviral vector) comprising a second nucleic acid encoding a second chimeric receptor (e.g., a second chimeric receptor targeting a disease antigen such as a cancer antigen, such as any cancer antigen known in the art) . In some embodiments, the first vector and the second vector can be transduced into a cell or administered to an individual (e.g., human) separately. In some embodiments, the first vector and the second vector can be transduced into a cell or administered to an individual sequentially. In some embodiments, the first vector and the second vector can be transduced into a cell or administered to an individual concurrently. In some embodiments, the first vector and the second vector can be transduced into a cell or administered to an individual simultaneously.
[0183] In some embodiments, there is provided a vector (e.g., viral vector, such as lentiviral vector) comprising: a first nucleic acid encoding an NKp80 binding protein (e.g., NKp80-targeted chimeric receptor as described herein, such as anti-NKp80 CAR) , and a second nucleic acid encoding a second antigen binding protein (e.g., a second chimeric receptor, such as a second chimeric receptor that targets a disease antigen such as a cancer antigen, such as any cancer antigen known in the art) , wherein the first nucleic acid and the second nucleic acid are under the control of the same promoter. In some embodiments, the first nucleic acid is upstream of the second nucleic acid. In some embodiments, the first nucleic acid is downstream of the second nucleic acid. In some embodiments, the first nucleic acid and the second nucleic acid are connected via a linking nucleic acid encoding a cleavable linker, such as a 2A peptide. In some embodiments, the 2A peptide is P2A, T2A, E2A, or F2A. In some embodiments, the first nucleic acid and the second nucleic acid are connected via a linking nucleic acid of IRES sequence. In some embodiments, the first nucleic acid encodes an anti-NKp80 CAR comprising the amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37.
[0184] In some embodiments, the vector further contains a selectable marker gene or a reporter gene to select cells expressing the chimeric receptor from the population of host cells transfected with the nucleic acid (s) or the vector (s) (e.g., lentiviral vector) . Both selectable markers and reporter genes may be flanked by appropriate regulatory sequences to enable expression in the host cells. For example, the vector may contain transcription and translation terminators, initiation sequences, and promoters useful for regulation of the expression of the nucleic acid sequences.
[0185] In some embodiments, the vector further encodes a FLAG-tag sequence. In some embodiments, the FLAG-tag sequence is at the N-terminus of the chimeric receptor. In some embodiments, the FLAG-tag sequence is between the signal peptide and the anti-NKp80 antigen binding domain. In some embodiments, the FLAG-tag comprises the amino acid sequence of SEQ ID NO: 22. D. Immune Cells
[0186] Any immune cells can be used herein to make the engineered immune cells. See “VI. Methods of Making Engineered Immune Cells” section below for generation methods. The present disclosure provides engineered immune cells that comprise any of the antigen binding proteins (e.g., NKp80-binding protein, such as anti-NKp80 CAR, and / or second antigen binding protein, such as second CAR) , any of the nucleic acids, and / or any of the vectors described herein.
[0187] One aspect of the present disclosure provides an engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain. In some embodiments, the NKp80-binding protein: (i) blocks NKp80; and / or (ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells. In some embodiments, the NKp80-positive cells are natural killer (NK) cells.
[0188] In some embodiments, there is provided an engineered immune cell comprising: (a) an NKp80-binding protein that comprises an NKp80 binding domain (e.g., a first chimeric receptor that specifically binds to NKp80, such as any of the anti-NKp80 chimeric receptors described herein, i.e., anti-NKp80 CAR) ; and (b) a second antigen binding protein that comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80 (e.g., a second chimeric receptor that does not bind to NKp80) .
[0189] In some embodiments, the engineered immune cell comprises a polypeptide encoding an NKp80-binding protein (e.g., any of the NKp80-binding proteins described herein, such as anti-NKp80 CAR) . In some embodiments, the NKp80-binding protein is an anti-NKp80 CAR comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37.
[0190] The engineered immune cells can be further genetically modified to enhance one or more functions (such as to further enhance NKp80-targeting abilities and / or to enhance immune cell persistence in vitro and / or in vivo, e.g., by reducing recognition by a host immune cell that could trigger an HvG response) . In some embodiments, the engineered immune cells are genetically modified to reduce or abolish the expression and / or function of an endogenous TCR. In some embodiments, the engineered immune cells are genetically modified to reduce or abolish the expression and / or function of an endogenous B2M. In some embodiments, the engineered immune cells can be genetically modified to reduce or abolish the expression and / or function of an endogenous NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the engineered immune cells are genetically modified to reduce or abolish the expression and / or function of an endogenous HLA-A and / or HLA-B. In some embodiments, the engineered immune cells are further genetically modified using any one or more standard technique such as by using siRNA, CRISPR / Cas system, meganucleases, TALENs, etc.
[0191] In some embodiments, the immune cell is selected from the group consisting of a T cell, a monocyte, a dendritic cell, a macrophage, a B cell, an NK cell, and any combination thereof. In some embodiments, the T cell is selected from the group consisting of a killer T cell (Tc, cytotoxic T lymphocyte, or CTL) , a helper T cell (Th) , a regulatory T cell (Treg) , an αβ T cell, a γδ T cell, a natural killer T (NKT) cell, and any combination thereof. In some embodiments, the immune cell is an immune effector cell that can exhibit immune effector functions. For example, immune effector cells comprise T cells (cytotoxic T cells, helper T cells, tumor infiltrating T cells) , B cells, NK cells, neutrophils, macrophages, and dendritic cells. The immune effector cell may express FcγRIII and perform ADCC effector function. Examples of immune effector cells which mediate ADCC include peripheral blood mononuclear cells (PBMC) , NK cells, monocytes, cytotoxic T cells, neutrophils, and eosinophils.
[0192] In some embodiments, the engineered immune cell is generated from PBMC. In some embodiments, the engineered immune cell is a T cell. The engineered T cells may be αβ T cells, or γδ T cells. The engineered T cells may be γδ T cells, wherein the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the engineered T cells are polyclonal γδT cells, Vδ1 T cells, or Vδ2 T cells. In some embodiments, the engineered T cells are CD4+ / CD8-, CD4- / CD8+, CD4+ / CD8+, or CD4- / CD8-. In some embodiments, the engineered T cells produce IL-2, IFN-γ, and / or TNF-α upon expressing the antigen binding protein (s) (e.g., the NKp80-binding protein such as an anti-NKp80 CAR and / or a second antigen binding protein) and binding to the target cells, such as NKp80-positive NK cells. In some embodiments, the engineered T cells lyse antigen-specific (e.g., NKp80-expressing) target cells upon expressing the antigen binding protein (s) and binding to the target cells. In some embodiments, the antigen-specific target cells are NKp80-positive NK cells.
[0193] In some embodiments, the engineered immune cell is an NK cell. In other embodiments, the engineered immune cell is made from established cell lines, for example, NK-92 cells.
[0194] In some embodiments, the engineered immune cell is derived from a stem cell. In some embodiments, the stem cell is a hematopoietic stem cell, pluripotent stem cell, induced pluripotent stem cell, or embryonic stem cell. In some embodiments, the stem cell is engineered to express the NKp80-binding protein described herein and allowed to differentiate into a mature immune cell (e.g., T cell) .
[0195] Immune cells for making the engineered immune cells described herein can be from any sources, such as derived from related (e.g., an individual, such as a human, having host-versus-graft (HvG) symptoms to be treated) or unrelated (e.g., healthy individual) humans, non-human animals, cell lines, or cultures. In some embodiments, the engineered immune cell is allogeneic (e.g., derived from a healthy individual) . In some embodiments, the engineered immune cell is autologous (e.g., derived from the individual having HvG symptoms to be treated) . III. NKp80 Antibody Constructs
[0196] The present disclosure also provides novel anti-NKp80 antibody constructs. Any of the anti-NKp80 antibody constructs described herein can be used as the NKp80-binding protein described herein. Any of the anti-NKp80 antibody constructs described herein can either be expressed by the engineered immune cells or be provided separately. Any of the antigen binding domains comprised in the NKp80-binding proteins described herein can be used within the anti-NKp80 antibody constructs.
[0197] In one aspect, there is provided an anti-NKp80 antibody construct comprising (or consisting of, or consisting essentially of) any of the anti-NKp80 sdAbs described herein. In some embodiments, the anti-NKp80 antibody construct is a transmembrane molecule, such as any of the anti-NKp80 chimeric receptors described herein. In some embodiments, the anti-NKp80 antibody construct is a secreted molecule.
[0198] The anti-NKp80 antibody construct can bind NKp80 derived from any organism, including but not limited to, dogs, cats, pigs, cows, sheep, goats, horses, rats, rabbits, hamsters, guinea pigs, monkeys, mice, and humans. In some embodiments, the anti-NKp80 antibody construct binds human NKp80.
[0199] In some embodiments, the anti-NKp80 antibody construct is an sdAb (anti-NKp80 sdAb) . In some embodiments, the anti-NKp80 sdAb comprises a single domain (i.e., VHH) , wherein the single domain comprises a CDR1, CDR2, and CDR3. In some embodiments, the CDR positions are determined according to Kabat or AbM numbering scheme.
[0200] In some embodiments, the anti-NKp80 sdAb comprises a CDR1, a CDR2, and a CDR3, and wherein the CDR1, CDR2, and CDR3 have the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16. In some embodiments, the anti-NKp80 sdAb comprises: (i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1; a CDR2 comprising the amino acid sequence of SEQ ID NO: 2; a CDR3 comprising the amino acid sequence of SEQ ID NO: 3; (ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5; a CDR2 comprising the amino acid sequence of SEQ ID NO: 6; a CDR3 comprising the amino acid sequence of SEQ ID NO: 7; (iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9; a CDR2 comprising the amino acid sequence of SEQ ID NO: 10; a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or (iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13; a CDR2 comprising the amino acid sequence of SEQ ID NO: 14; a CDR3 comprising the amino acid sequence of SEQ ID NO: 15. In some embodiments, the affinity of such anti-NKp80 sdAb for NKp80 (e.g., human NKp80) is comparable (e.g., within about 2-fold difference) to that of a reference antibody comprising a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. In some embodiments, the affinity of such anti-NKp80 sdAb for NKp80 (e.g., human NKp80) is at least about 2-fold (e.g., at least about any of 5, 10, 50, 100, 1000, or more folds) of that of a reference antibody comprising a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16.
[0201] In some embodiments, the NKp80 antibody construct specifically recognizing NKp80 is an sdAb ( “anti-NKp80 sdAb” ) , wherein the anti-NKp80 sdAb comprises a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16, or a variant thereof having at least about 80% (e.g., at least about any of 85%, 90%, 95%, 96%, 97%, 98%, 99%or more) amino acid sequence homology to an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16. One or more amino acid variations (e.g., insertions, deletions, and / or substitutions, such as conserved substitutions) can be in one or more of the CDRs. One or more amino acid variations can be in one or more of the framework regions (FRs) . Two or more amino acid variations may be in both CDRs and FRs. In some embodiments, anti-NKp80 sdAb comprises one or more post-translational modifications.
[0202] In some embodiments, the anti-NKp80 antibody construct can include, but is not limited to, an anti-NKp80 antibody or antigen binding fragment thereof, an anti-NKp80 chimeric receptor (e.g., an anti-NKp80 TCR, anti-NKp80-targeted cTCR, anti-NKp80 TAC, anti-NKp80 CAR, etc. ) , an anti-NKp80 antibody-drug conjugate (ADC) , an anti-NKp80 antibody-detection tag conjugate, an anti-NKp80 antibody-oligonucleotide conjugate (AOC) , a vaccine, etc. IV. Pharmaceutical Compositions and Kits
[0203] Also provided are pharmaceutical compositions comprising any of the engineered immune cells described herein (e.g., engineered immune cell expressing an NKp80-binding protein, such as an NKp80-targeted chimeric receptor, e.g., an anti-NKp80 CAR) , and optionally a pharmaceutically acceptable excipient. Also provided are pharmaceutical compositions comprising any of the antibody constructs, nucleic acids encoding thereof, or viral vectors comprising thereof described herein, and optionally a pharmaceutically acceptable excipient. Any excipient suitable for the storage and administration of engineered immune cells and / or protein constructs (e.g., NKp80-binding proteins, anti-NKp80 antibody constructs, and / or antigen-binding proteins described herein) can be used herein. The excipient may not affect the viability and / or bioactivity of the encoded NKp80-binding protein (e.g., anti-NKp80 CAR) and / or a second antigen-binding protein (e.g., second CAR) of the engineered immune cells.
[0204] “Excipient” means a pharmaceutically acceptable material, composition, or vehicle, such as a liquid or solid filler, diluent, solvent, or encapsulating material. Excipients include, for example, encapsulating materials or additives such as absorption accelerators, antioxidants, binders, buffers, carriers, coating agents, coloring agents, diluents, disintegrating agents, emulsifiers, extenders, fillers, flavoring agents, humectants, lubricants, perfumes, preservatives, propellants, releasing agents, sterilizing agents, sweeteners, solubilizers, wetting agents and mixtures thereof. The term “excipient” can also refer to a diluent, adjuvant (e.g., Freunds’ adjuvant (complete or incomplete) or vehicle.
[0205] Excipients may be pharmaceutically acceptable excipients. Examples of pharmaceutically acceptable excipients include buffers, such as phosphate, citrate, and other organic acids; antioxidants, including ascorbic acid; low molecular weight (e.g., fewer than about 10 amino acid residues) polypeptide; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers, such as polyvinylpyrrolidone; amino acids, such as glycine, glutamine, asparagine, arginine, or lysine; monosaccharides, disaccharides, and other carbohydrates, including glucose, mannose, or dextrins; chelating agents, such as EDTA; sugar alcohols, such as mannitol or sorbitol; salt-forming counterions, such as sodium; and / or nonionic surfactants, such as TWEENTM, polyethylene glycol (PEG) , and PLURONICSTM. Other examples of pharmaceutically acceptable excipients are described in Remington and Gennaro, Remington’s Pharmaceutical Sciences (18th ed. 1990) .
[0206] In one embodiment, each component is “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of a pharmaceutical formulation, and suitable for use in contact with the tissue or organ of humans and animals without excessive toxicity, irritation, allergic response, immunogenicity, or other problems or complications, commensurate with a reasonable benefit / risk ratio. See, e.g., Lippincott Williams &Wilkins: Philadelphia, PA, 2005; Handbook of Pharmaceutical Excipients, 6th ed.; Rowe et al., Eds.; The Pharmaceutical Press and the American Pharmaceutical Association: 2009; Handbook of Pharmaceutical Additives, 3rd ed.; Ash and Ash Eds.; Gower Publishing Company: 2007; Pharmaceutical Preformulation and Formulation, 2nd ed.; Gibson Ed.; CRC Press LLC: Boca Raton, FL, 2009. In some embodiments, pharmaceutically acceptable excipients are nontoxic to the cell or mammal being exposed thereto at the dosages and concentrations employed. In some embodiments, a pharmaceutically acceptable excipient is an aqueous pH buffered solution.
[0207] Excipients may be sterile liquids, such as water and oils, including those of petroleum, animal, vegetable, or synthetic origin, such as peanut oil, soybean oil, mineral oil, sesame oil, and the like. Water is an exemplary excipient when a composition (e.g., a pharmaceutical composition) is administered intravenously. Saline solutions and aqueous dextrose and glycerol solutions can also be employed as liquid excipients, particularly for injectable solutions. An excipient can also include starch, glucose, lactose, sucrose, gelatin, malt, rice, flour, chalk, silica gel, sodium stearate, glycerol monostearate, talc, sodium chloride, dried skim milk, glycerol, propylene, glycol, water, ethanol, and the like. The composition, if desired, can also contain minor amounts of wetting or emulsifying agents, or pH buffering agents. Compositions can take the form of solutions, suspensions, emulsion, powders (e.g., freeze-dried) , sustained-release formulations, and the like. In some embodiments, the composition can be reconstituted.
[0208] Compositions, including pharmaceutical compositions, may contain a binding molecule (e.g., an antibody) , for example, in isolated or purified form, together with a suitable amount of excipients.
[0209] In some embodiments, there is provided a pharmaceutical composition comprising: i) an engineered immune cell (e.g., engineered T cell) expressing an NKp80-binding protein that comprises an NKp80 binding domain (e.g., any of the NKp80-binding proteins described herein, such as an NKp80-targeted chimeric receptor (e.g., anti-NKp80 CAR) ) , and optionally ii) a pharmaceutically acceptable excipient.
[0210] In other embodiments, provided herein is a pharmaceutical composition comprising: i) an engineered immune cell comprising: (a) a first nucleic acid encoding an NKp80-binding protein that comprises an NKp80 binding domain, such as an NKp80-targeted chimeric receptor (e.g., an anti-NKp80 CAR) , and (b) a second nucleic acid encoding a second antigen binding protein, wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80; and ii) optionally a pharmaceutically acceptable excipient.
[0211] The choice of excipient may be determined in part by the particular cell, binding molecule, antibody construct, viral vector, and / or by the method of administration. Accordingly, there are a variety of suitable formulations. A. Pharmaceutical Composition Formulation
[0212] Suitable pharmaceutically acceptable excipient for engineered immune cells, NKp80-binding proteins, or anti-NKp80 antibody constructs thereof may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide) ; and preservatives. The pharmaceutically acceptable excipient may contain autologous serum, such as human serum. In some embodiments, the pharmaceutically acceptable excipient is non-toxic, biocompatible, non-immunogenic, biodegradable, and can avoid recognition by the host’s defense mechanism. The excipient may also contain adjuvants such as preserving stabilizing, wetting, emulsifying agents, and the like. The pharmaceutically acceptable excipient may enhance the stability of the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs. The final form may be sterile and may also be able to pass readily through an injection device such as a hollow needle. The proper viscosity may be achieved and maintained by the proper choice of excipients.
[0213] In some embodiments, the pharmaceutical composition is formulated to have a pH in the range of about 4.5 to about 9.0, including for example pH ranges of about any one of 5.0 to about 8.0, about 6.5 to about 7.5, or about 6.5 to about 7.0. The pharmaceutical composition can also be made to be isotonic with blood by the addition of a suitable tonicity modifier, such as glycerol.
[0214] Typically, acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers, antioxidants including ascorbic acid, methionine, Vitamin E, sodium metabisulfite; preservatives, isotonicifiers, stabilizers, metal complexes (e.g., Zn-protein complexes) ; chelating agents such as EDTA and / or non-ionic surfactants.
[0215] Buffers may be used to control the pH in a range which optimizes the therapeutic effectiveness, especially if stability is pH dependent. Suitable buffering agents for use with the present disclosure include both organic and inorganic acids and salts thereof. For example, citrate, phosphate, succinate, tartrate, fumarate, gluconate, oxalate, lactate, acetate. Additionally, buffers may comprise histidine and trimethylamine salts such as Tris.
[0216] Preservatives may be added to retard microbial growth. Suitable preservatives for use with the present disclosure include octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium halides (e.g., chloride, bromide, iodide) , benzethonium chloride; thimerosal, phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol, 3-pentanol, and m-cresol.
[0217] Tonicity agents, sometimes known as “stabilizers” can be present to adjust or maintain the tonicity of liquid in a composition. When used with large, charged biomolecules such as proteins and antibodies, they are often termed “stabilizers” because they can interact with the charged groups of the amino acid side chains, thereby lessening the potential for inter and intra-molecular interactions. Exemplary tonicity agents include polyhydric sugar alcohols, trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol and mannitol.
[0218] Additional exemplary excipients include: (1) bulking agents, (2) solubility enhancers, (3) stabilizers and (4) agents preventing denaturation or adherence to the container wall. Such excipients include: polyhydric sugar alcohols (enumerated above) ; amino acids such as alanine, glycine, glutamine, asparagine, histidine, arginine, lysine, ornithine, leucine, 2-phenylalanine, glutamic acid, threonine, etc.; organic sugars or sugar alcohols such as sucrose, lactose, lactitol, trehalose, stachyose, mannose, sorbose, xylose, ribose, ribitol, myoinisitose, myoinisitol, galactose, galactitol, glycerol, cyclitols (e.g., inositol) , polyethylene glycol; sulfur containing reducing agents, such as urea, glutathione, thioctic acid, sodium thioglycolate, thioglycerol, α-monothioglycerol and sodium thio sulfate; low molecular weight proteins such as human serum albumin, bovine serum albumin, gelatin or other immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; monosaccharides (e.g., xylose, mannose, fructose, glucose; disaccharides (e.g., lactose, maltose, sucrose) ; trisaccharides such as raffinose; and polysaccharides such as dextrin or dextran.
[0219] In order for the pharmaceutical compositions to be used for in vivo administration, they are preferably sterile. The pharmaceutical composition may be rendered sterile by filtration through sterile filtration membranes. The pharmaceutical compositions herein generally can be placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
[0220] Various compositions and delivery systems are known and can be used with the therapeutic agents provided herein, including, but not limited to, encapsulation in liposomes, microparticles, microcapsules, recombinant cells capable of expressing the chimeric receptor, NKp80-binding proteins, and / or anti-NKp80 antibody constructs, construction of a nucleic acid as part of a retroviral or other vector, etc.
[0221] In some embodiments, the pharmaceutical composition must meet certain standards for administration to an individual (e.g., a human) . For example, the United States Food and Drug Administration has issued regulatory guidelines setting standards for cell-based immunotherapeutic products, including 21 CFR 610 and 21 CFR 610.13. Methods are known in the art to assess the appearance, identity, purity, safety, and / or potency of pharmaceutical compositions. In some embodiments, the pharmaceutical composition is substantially free of extraneous protein capable of producing allergenic effects, such as proteins of an animal source used in cell culture other than the engineered immune cells. In some embodiments, “substantially free” is less than about any of 10%, 5%, 1%, 0.1%, 0.01%, 0.001%, 1 ppm or less of total volume or weight of the pharmaceutical composition. In some embodiments, the pharmaceutical composition is prepared in a GMP-level workshop. In some embodiments, the pharmaceutical composition comprises less than about 5 EU / kg body weight / hr of endotoxin for parenteral administration. In some embodiments, at least about 70%of the engineered immune cells in the pharmaceutical composition are alive for intravenous administration. In some embodiments, the pharmaceutical composition has a “no growth” result when assessed using a 14-day direct inoculation test method as described in the United States Pharmacopoeia (USP) . In some embodiments, prior to administration of the pharmaceutical composition, a sample including both the engineered immune cells and the pharmaceutically acceptable excipient should be taken for sterility testing approximately about 48-72 hours prior to the final harvest (or coincident with the last re-feeding of the culture) . In some embodiments, the pharmaceutical composition is free of mycoplasma contamination. In some embodiments, the pharmaceutical composition is free of detectable microbial agents. In some embodiments, the pharmaceutical composition is free of communicable disease agents, such as HIV type I, HIV type II, HBV, HCV, Human T-lymphotropic virus, type I; and Human T-lymphotropic virus, type II. In some embodiments, the pharmaceutical composition is free of viral (e.g., lentivirus) components during manufacture. B.Kits
[0222] In some embodiments, there is provided a kit comprising any of the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs (or nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical composition thereof) described herein. In some embodiments, the kit may further comprise instruction (s) on methods of using the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs (or nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical composition thereof) , such as uses or methods described herein. The kits described herein may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, intravenous injectors or drips, and package inserts with instructions for performing any methods described herein.
[0223] In some embodiments, the kit and / or composition comprises a culture medium used in the methods provided herein, whether provided individually as components, in any combination, or as the culture medium admixed with cells (e.g., any of the engineered immune cells described herein) . In some embodiments, the kit comprises reagents suitable for expanding the engineered immune cells, such as media, cytokine, ITSEA, and human albumin serum.
[0224] The components of the kits may be packaged either in aqueous media or in lyophilized form. The container means of the kits may include at least one vial, test tube, flask, bottle, syringe, or other container means, into which a component may be placed, and preferably, suitably aliquoted. Where there is more than one component in the kit, the kit also will generally contain a second, third, or other additional container into which the additional components may be separately placed. However, various combinations of components may be comprised in a vial. The kits of the present disclosure also will typically include a means for containing any of the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs (or nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical composition thereof) described herein, and any other reagent containers in close confinement for commercial sale. Such containers may include injection or blow molded plastic containers into which the desired vials are retained, for example.
[0225] In some embodiments, the kits may further comprise instruction (s) on methods of making or methods of treatment using any of the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs (or nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical composition thereof) described herein, such as methods of making or methods of treatment described herein. V. Methods of Treating Disease
[0226] The present disclosure provides a method of treating or preventing host-versus-graft (HvG) responses in an individual (e.g., human) in need thereof, comprising administering to the individual an effective amount of any of the engineered immune cells (e.g., engineered T cells) , NKp80-binding proteins, and / or anti-NKp80 antibody constructs provided herein, and / or any of the pharmaceutical compositions provided herein. In some embodiments, the engineered immune cell comprises an NKp80-binding protein that comprises an NKp80 binding domain, wherein the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the individual is human.
[0227] Also provided are methods of treating a condition, disease, or disorder (e.g., cancer) in an individual (e.g., human) in need thereof, comprising administering to the individual a therapeutically effective amount of any of the engineered immune cells (e, g., engineered T cells) , NKp80-binding proteins, and / or anti-NKp80 antibody constructs provided herein, and / or any of the pharmaceutical compositions provided herein. In some embodiments, the engineered immune cell is allogeneic to the individual. In some embodiments, the engineered immune cell does not trigger a response from the host (i.e., individual’s ) immune system. In some embodiments, the engineered immune cell comprises an NKp80-binding protein that comprises an NKp80 binding domain, wherein the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is further capable of inhibiting or killing the target cells (e.g., the NKp80 cells and / or the cancer cells) . In some embodiments, the engineered immune cell comprises a second antigen binding protein that comprises a second antigen binding domain that recognizes a tumor associated antigen and / or a tumor specific antigen. In some embodiments, the NKp80-binding protein of the engineered immune cell further comprises a second antigen binding domain that recognizes a disease-or disorder-associated or specific antigen (e.g., a tumor-associated antigen (TAA) and / or a tumor-specific antigen (TSA) ) . In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the individual is human.
[0228] Also provided are methods of preventing, treating, reducing the risk of developing, and / or reducing the severity of HvG in an individual (e.g., human) , comprising administering to the individual in need thereof a therapeutically effective amount of any of the engineered immune cells (e.g., engineered T cells) , NKp80-binding proteins, and / or anti-NKp80 antibody constructs provided herein, and / or any of the pharmaceutical compositions provided herein. In some embodiments, there is provided a preventing, treating, reducing the risk of developing, and / or reducing the severity of HvG in an individual, comprising administering to the individual an effective amount of any of the engineered immune cells provided herein. In some embodiments, the engineered immune cell comprises an NKp80-binding protein that comprises an NKp80 binding domain, wherein the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells. In some embodiments, the NKp-80 positive cells are natural killer (NK) cells. In some embodiments, the individual is human.
[0229] Also provided are methods of depleting NK cells in a first population of cells, comprising exposing the first population of cells to a second population of cells comprising any of the engineered immune cells (e.g., engineered T cells) provided herein and / or any of the pharmaceutical compositions provided herein, wherein the exposing results in depletion of NK cells in the first population. In some embodiments, the exposing the first population of cells to a second population of cells comprising any of the engineered immune cells (e.g., engineered T cells) provided herein and / or any of the pharmaceutical compositions provided herein occurs in vitro, such as in a cell culture (i.e., a cell co-culture of the first population of cells and the second population of cells) . In some embodiments, the exposing the first population of cells to a second population of cells comprising any of the engineered immune cells (e.g., engineered T cells) provided herein and / or any of the pharmaceutical compositions provided herein occurs in vivo, such as in an individual (e.g., human) , for example after the individual has received an adoptive cellular transfer of the second population of cells, wherein the second population of cells comprises any of the engineered immune cells (e.g., engineered T cells) provided herein and / or any of the pharmaceutical compositions provided herein; wherein the first population of cells is from the individual (e.g., a first population of cells comprising cells from the individual’s host immune cells) . In some embodiments, the engineered immune cell comprises an NKp80-binding protein that comprises an NKp80 binding domain, wherein the NKp80-binding protein: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the individual is human.
[0230] Also provided are methods of treating an NK cell-associated disease or a disease associated with cells that express NKp80 in an individual (e.g., human) in need thereof, comprising administering to the individual a therapeutically effective amount of any of the engineered immune cells (e.g., engineered T cells) , NKp80-binding proteins, and / or anti-NKp80 antibody constructs provided herein, and / or any of the pharmaceutical compositions provided herein. In some embodiments, the NK cell-associated disease or the disease associated with cells that express NKp80 is HvG or an autoimmune disease. In some embodiments, the autoimmune disease is selected from the group consisting of systemic lupus erythematosus (SLE) , Syndrome, rheumatoid arthritis, type I diabetes (T1D) , and autoimmune liver disease (ALD) . In some embodiments, the HvG or autoimmune disease is characterized by an increase (e.g., by about any of 1-, 2-, 2.5-, 3-, 3.5-, 4-, 4.5-, 5-, 6-, 7-, 8-, 9-, 10-, 15-, 20-, 25-, 30-, 35-, 40-, 50-, 100-, 1000-fold, or more) in the number of NK cells, such as total NK cells and / or activated NK cells. In some embodiments, the increase in the number of NK cells correlates to an increase in NKp80 expression in the affected tissue and / or systemically. The expressed NKp80 can either be a wild-type form or a mutant form (e.g., constitutively active, or with increased activity, or with reduced or absent activity) . In some embodiments, the NK cell-associated disease or the disease associated with cells that express NKp80 is an NK cell malignancy. In some embodiments, the NK cell malignancy is selected from the group consisting of NK cell leukemia, NK cell lymphoma, and blastoid NK cell lymphoma. In some embodiments, the NKp80-binding protein or anti-NKp80 antibody construct: i) blocks NKp80; and / or ii) does not activate NKp80. In some embodiments, the engineered immune cell is capable of inhibiting or killing NKp80-positive cells, such as NK cells. In some embodiments, the individual is human.
[0231] A cancer can be associated with the increased expression of a tumor associated antigen (TAA) or tumor specific antigen (TSA) , e.g., over-expression compared to a healthy state, or mis-expression in the cancer cells that is different from a healthy state (e.g., not expressed by corresponding healthy cells or tissues) . Such cancers may be further associated with one or more additional antigens (e.g., abnormal expression or overexpression of the one or more additional antigens) , e.g., over-expression compared to a healthy state, or mis-expression at a location different from a healthy state. In some instances, the cancer is heterogeneous such that the cancer cells may express different levels of TSAs / TAAs and / or may express different TSAs / TAAs across the cancer cell milieu. Thus, in some instances, the cancer may present with increased expression of a first TSA / TAA and, over the course of administering a therapy targeting that first TSA / TAA, the cancer composition may shift by downregulating the expression of the first TSA / TAA and / or upregulating the expression of a second TSA / TAA.
[0232] In some embodiments, there is provided a method of treating, preventing, reducing the risk of developing, and / or reducing the severity of an HvG response in an individual (e.g., human) , comprising administering to the individual an effective amount of an engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain; wherein the NKp80-binding protein is an anti-NKp80 CAR comprising: (i) the NKp80 binding domain (e.g., scFv, sdAb, or Fab) ; (ii) an optional hinge domain (e.g., derived from CD8α) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; and (iv) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) , which can be at the N’ or C’ of the intracellular signaling domain. In some embodiments, the anti-NKp80 CAR further comprises a second antigen binding domain that specifically binds to a second antigen that is not NKp80. In some embodiments, the engineered immune cell further comprises a second antigen binding protein comprising a second antigen binding domain that specifically binds to a second antigen that is not NKp80. In some embodiments, there is provided a method of treating or preventing an HvG response in an individual (e.g., human) , comprising administering to the individual any of the engineered immune cells provided herein, for example, an engineered immune cell as described in Section II. In some embodiments, the engineered immune cell is an engineered T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the anti-NKp80 CAR comprises the amino acid sequence of any of SEQ ID NOs: 34-37.
[0233] In some embodiments, there is provided a method of treating an NK cell-associated disease or a disease associated with cells that express NKp80 in an individual (e.g., human) , comprising administering to the individual a therapeutically effective amount of an engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain; wherein the NKp80-binding protein is an anti-NKp80 CAR comprising: (i) the NKp80 binding domain (e.g., scFv, sdAb, or Fab) ; (ii) an optional hinge domain (e.g., derived from CD8α) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; and (iv) an intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the anti-NKp80 CAR further comprises an intracellular co-stimulatory signaling domain (e.g., derived from CD28) , which can be at the N’ or C’ of the intracellular signaling domain. In some embodiments, there is provided a method of treating an NK cell-associated disease or a disease associated with cells that express NKp80 in an individual (e.g., human) , comprising administering to the individual any of the engineered immune cells provided herein, for example, an engineered immune cell as described in Section II.In some embodiments, the engineered immune cell is an engineered T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the NK cell-associated disease is HvG, or an autoimmune disease, for example systemic lupus erythematosus (SLE) , Syndrome, rheumatoid arthritis, type I diabetes (T1D) , and autoimmune liver disease (ALD) . In some embodiments, the NK cell-associated disease is an NK cell malignancy, for example NK cell leukemia, NK cell lymphoma, or blastoid NK cell lymphoma. In some embodiments, the anti-NKp80 CAR comprises the amino acid sequence of any of SEQ ID NOs: 34-37.
[0234] In some embodiments, there is provided a method of depleting NK cells in a first population of cells, comprising exposing the first population of cells to a second population of cells comprising an engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain; wherein the NKp80-binding protein is an anti-NKp80 chimeric receptor; and wherein the anti-NKp80 chimeric receptor comprises: (i) the NKp80 binding domain (e.g., scFv, sdAb, or Fab) ; (ii) an optional hinge domain (e.g., derived from CD8α) ; (iii) a transmembrane domain (e.g., derived from CD8α) ; (iv) an optional intracellular co-stimulatory signaling domain (e.g., derived from CD28) ; and (v) an intracellular signaling domain (e.g., derived from CD3ζ) ; wherein the exposing results in depletion of NK cells in the first population. In some embodiments, there is provided a method of depleting NK cells in a first population of cells (for example, in an individual (e.g., human) ) , comprising exposing the first population of cells to a second population of cells comprising the engineered immune cell provided herein, for example, an engineered immune cell as described in Section II (e.g., comprising administering the engineered immune cell provided herein to an individual, such as a human) , wherein the exposing results in depletion of NK cells in the first population. In some embodiments, the engineered immune cell is a T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function. In some embodiments, the anti-NKp80 CAR comprises the amino acid sequence of any of SEQ ID NOs: 34-37.
[0235] In some embodiments, the methods of treatment or prevention described herein can achieve one or more of the following biological activities: (1) killing (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%) NKp80-positive cells; (2) inhibiting (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%) proliferation of NKp80-positive cells; (3) inducing (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 1.5, 2, 3, 4, 5, 10, 20, or more folds) T cell expansion in the presence of NKp80-positive cells; and / or (4) reducing (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%) the number of NKp80-positive cells (including reducing the size of NKp80-positive tumors) . In some embodiments, the methods of treatment or prevention described herein can achieve one or more of the following therapeutic effects: (1) alleviating (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%) one or more symptoms in an individual (e.g., human) having NKp80-positive cells; (2) prolonging survival, such as prolonging the survival of the individual by at least any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, or 24 months, or more; (3) prolonging time to NKp80-associated disease progression, such as prolonging the time to disease progression by at least any of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 weeks, or more; (4) preventing, inhibiting, or reducing (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, or 100%) the likelihood of the recurrence of an NKp80-associated disease; and / or (5) increasing, enhancing, or stimulating (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 1.5, 2, 3, 4, 5, 10, 20, or more folds) an immune response or function in a subject by activating effector cells (e.g., T cells) in the presence of NKp80-positive cells. In some embodiments, the engineered immune cells (e.g., engineered T cells) administered to the individual have increased or enhanced (e.g., increasing at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 100%, 1.5, 2, 3, 4, 5, 10, 20, or more folds) priming, activation, proliferation, IFN-γ cytokine production, and / or cytolytic activity relative to non-engineered immune cells. In some embodiments, the individual is a human.
[0236] The methods provided herein may be practiced in a primary therapeutic setting, i.e., wherein the methods being carried out are the primary / definitive therapy. In some embodiments, the method may be carried out before or in conjunction with the primary / definitive therapy. In some embodiments, the method is used to treat an individual (such as a human) who has previously been treated. Any of the methods of treatment provided herein may be used to treat an individual (such as a human) who has not previously been treated. In some embodiments, the method is used as a first line therapy. In some embodiments, the method is used as a second line therapy.
[0237] The methods described herein are suitable for treating a variety of cancers with reduced or no HvG responses and a variety of NK cell-associated diseases or a disease associated with cells that express NKp80, including HvG responses, graft rejection, autoimmune diseases, and cell malignancies. The methods are applicable to diseases of all stages, including early-stage disease, tissue-localized disease, systemic disease, disease in remission (e.g., autoimmune disease or malignancy or cancer in remission) , early-stage cancer, non-metastatic cancer, primary cancer, advanced cancer, locally advanced cancer, metastatic cancer, or cancer in remission. The methods described herein may be used as a first therapy, second therapy, third therapy, or combination therapy with other types of therapies known in the art. In some embodiments, the method is for treating a cancer or an NK cell-associated disease with a first therapy, second therapy, third therapy, or combination therapy with other types of therapies comprises administration of one or more immunosuppressive agents such as calcineurin inhibitors, targets of rapamycin, interleukin-2 (IL-2) α-chain blockers, inhibitors of inosine monophosphate dehydrogenase, inhibitors of dihydrofolic acid reductase, corticosteroids, and immunosuppressive antimetabolites, wherein the NK cell-associated disease is any one of HvG responses, graft rejection, or an autoimmune disease. In some embodiments, the method is for treating a cancer or an NK cell-associated disease with a first therapy, second therapy, third therapy, or combination therapy with other types of therapies comprises administration of one or more of chemotherapy, surgery, radiation, gene therapy, immunotherapy, bone marrow transplantation, stem cell transplantation, targeted therapy, cryotherapy, ultrasound therapy, photodynamic therapy, radio-frequency ablation or the like, in an adjuvant setting or a neoadjuvant setting. In some embodiments, the cancer or NK cell-associated disease (e.g., the NK cell cancer or autoimmune disease) has been refractory to prior therapy.
[0238] Any of the methods described herein of: (i) treating or preventing host-versus-graft responses in an individual in need thereof; (ii) treating an NK cell-associated disease or a disease associated with cells that express NKp80 in an individual in need thereof; (iii) preventing, treating, reducing the risk of developing, and / or reducing the severity of HvG in an individual; and / or (iv) depleting NK cells (e.g., depleting NK cells within an individual) , further comprise any suitable methods for the administration of an engineered immune cell (e.g., an engineered immune cell comprising any of the anti-NKp80 CARs described herein) . In some embodiments, the engineered immune cell is administered in a single composition. “Administration” used herein encompasses all above administration situation, including direct administration and indirect administration.
[0239] Exemplary routes of administration of any of the engineered immune cells (e.g., engineered T cells) , NKp80-binding proteins, and / or anti-NKp80 antibody constructs described herein (or nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical compositions thereof) include, but are not limited to, intravenous, intracavitary, intraarterial, intramuscular, subcutaneous, parenteral, or intraperitoneal routes, or be delivered into lymph glands, body spaces, organs, or tissues known to contain NKp80-positive target cells. In some embodiments, the engineered immune cells, anti-NKp80 antibody constructs or, nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical compositions thereof, are administered intravenously, such as by infusion. Intravenous infusion can be at any suitable rate. For example, in some embodiments, the engineered immune cells and / or anti-NKp80 antibody constructs described herein can be infused to an individual (e.g., human) in need thereof over a period of time no more than about any of 24 hours, 20 hours, 18 hours, 10 hours, 8 hours, 6 hours, 4 hours, 2 hours, 1 hours, 30 minutes, or less.
[0240] In some embodiments, the methods provided herein comprise administration of any of the engineered immune cells described herein or pharmaceutical compositions thereof, for example at a range of about ten thousand to about 100 billion cells and / or ten thousand to about 100 billion cells per kilogram of body weight. In some embodiments, the engineered immune cells or pharmaceutical composition thereof is administered at a dosage of at least about any of 104, 105, 106, 107, 108, or 109 cells / kg of body weight of the individual. In some embodiments, the engineered immune cell co-expressing the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) and a second antigen-binding protein (e.g., second chimeric receptor) is administered at a dose less than that when the engineered immune cell expresses the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) only. Dosages may vary depending on attributes particular to the cancer and / or patient and / or other treatments. The method may occur without or with the administration of one or more cytokines.
[0241] The dosing regimen of the engineered immune, NKp80-binding proteins, and / or anti-NKp80 antibody constructs described herein, nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical compositions thereof, administered to the individual (such as a human) may vary with the particular composition, the method of administration, and the particular type of disease or disorder being treated. In some embodiments, the effective amount of the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs, nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical compositions thereof, is below the level that induces a toxicological effect (i.e., an effect above a clinically acceptable level of toxicity) or is at a level where a potential side effect can be controlled or tolerated when the composition is administered to the individual.
[0242] In some embodiments, the pharmaceutical composition provided herein contains the engineered immune cells, NKp80 binding proteins, and / or anti-NKp80 antibody constructs described herein (or nucleic acids or vectors (e.g., viral vectors) encoding thereof) in amounts effective to treat or prevent the condition, disease, or disorder (e.g., autoimmune disease, HvG responses, and / or NK cell disease (e.g., cancer) ) , such as a therapeutically effective or prophylactically effective amount. Therapeutic or prophylactic efficacy in some embodiments is monitored by periodic assessment of treated subjects. For repeated administrations over several days or longer, depending on the condition, the treatment is repeated until a desired suppression of cancer symptoms occurs. However, other dosage regimens may be useful and can be determined.
[0243] The optimal dosage and treatment regime for a particular patient can be determined by one skilled in the art of medicine by monitoring the patient for signs of disease and adjusting the treatment accordingly. In certain embodiments, once the engineered immune cells (either expressing the anti-NKp80 chimeric receptor alone or co-expressing the anti-NKp80 chimeric receptor and a second chimeric receptor) , NKp80-binding proteins, and / or anti-NKp80 antibody constructs are administered to an individual (e.g., human) , the biological activity of the engineered immune cell populations, NKp80-binding proteins, and / or anti-NKp80 antibody constructs is measured by any of a number of known methods. Parameters to assess include specific binding of an engineered immune cell or non-engineered immune cell (e.g., bystanders) to antigen, in vivo, e.g., by imaging, or ex vivo, e.g., by ELISA or flow cytometry. In certain embodiments, the ability of the engineered immune cells or non-engineered immune cells (e.g., bystanders) to destroy target cells can be measured using any suitable method known in the art, such as cytotoxicity assays described in, for example, Kochenderfer et al., J. Immunotherapy, 32(7) : 689-702 (2009) , and Herman et al. J. Immunological Methods, 285 (1) : 25-40 (2004) . In certain embodiments, the biological activity of the engineered immune cells or non-engineered immune cells (e.g., bystanders) also can be measured by assaying expression and / or secretion of certain cytokines, such as CD107a, IFNγ, IL-2, and TNFα. In some aspects, the biological activity is measured by assessing clinical outcome, such as reduction (e.g., by at least about 50%, such as by at least about any of 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or more) in NK cell number or a reduction in disease severity (for example, reduced symptoms of graft rejection, such as reduced severity of the symptoms of graft rejection) .
[0244] In some embodiments, the individual to whom the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs described herein (or nucleic acids or vectors (e.g., viral vectors) encoding thereof, or pharmaceutical composition thereof) are administered is a primate, such as a human, monkey, gorilla, chimpanzee, etc. In some embodiments, the individual is a human. The individual can be male or female and can be any suitable age, including infant, juvenile, adolescent, adult, and geriatric individuals. In some embodiments, the individual is a mammal, including but are not limited to, mice, rats, hamsters, guinea pigs, rabbits, chinchillas, cats, dogs, horses, donkeys, cows, goats, sheep, deer, monkeys, apes, etc. In some embodiments, the individual is a livestock. In some embodiments, the individual is a companion animal. In some examples, the individual is a validated animal model for disease, adoptive cell therapy, and / or for assessing toxic outcomes. VI. Methods of Making Engineered Immune Cells, NKp80-Binding Proteins, and Anti- NKp80 Antibody Constructs
[0245] Also provided are methods of making any of the engineered immune cells (e.g., an engineered T cell) described herein, such as engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain. Also provided are methods of making any of the NKp80-binding proteins and / or anti-NKp80 antibody constructs described herein. Methods of cloning vector construction, protein expression and purification, cell preparation (e.g., enrichment and / or activation) and transfection, etc., are well-known in the art. Any of the isolated nucleic acids and vectors described under Section II. C. “Nucleic acids and vectors encoding antigen binding proteins” can be used herein to make the engineered immune cells, NKp80-binding proteins, and / or anti-NKp80 antibody constructs. Also see Examples 1 and 2 for exemplary making methods.Engineered Immune Cells
[0246] In some embodiments, there is provided a method of making an engineered immune cell (e.g., an engineered T cell) , wherein the engineered immune cell comprises an NKp80-binding protein (e.g., anti-NKp80 chimeric receptor, such as anti-NKp80 CAR) that comprises an NKp80 binding domain; wherein the method comprises: introducing into a population of immune cells a first nucleic acid encoding the NKp80-binding protein (e.g., anti-NKp80 CAR) and optionally a second nucleic acid encoding a second antigen binding protein (e.g., second chimeric receptor, such as a second CAR) that comprises a second antigen binding domain that specifically binds to a second antigen, wherein the second antigen is not NKp80. In some embodiments, the method further comprises providing (e.g., obtaining, isolating, or harvesting) the population of immune cells before introducing the first nucleic acid and / or the second nucleic acid. Hence in some embodiments, the engineered immune cell is made from a method comprising providing, obtaining, isolating, or harvesting a population of immune cells and introducing into the population of immune cells a first nucleic acid encoding the NKp80-binding protein and optionally a second nucleic acid encoding the second antigen-binding protein. In some embodiments, the first nucleic acid and the second nucleic acid are on different vectors. In some embodiments, the first nucleic acid and the second nucleic acid are introduced into the population of immune cells simultaneously. In some embodiments, the first nucleic acid is introduced into the population of immune cells before introducing the second nucleic acid. In some embodiments, the method further comprises isolating and / or enriching a plurality of engineered immune cells expressing the NKp80-binding protein, then introducing into the isolated / enriched plurality of engineered immune cells the second nucleic acid encoding the second antigen-binding protein. In some embodiments, the second nucleic acid is introduced into the population of immune cells before introducing the first nucleic acid. In some embodiments, the method further comprises isolating and / or enriching a plurality of engineered immune cells expressing the second antigen-binding protein, then introducing into the isolated / enriched plurality of engineered immune cells the first nucleic acid encoding the NKp80-binding protein. In some embodiments, the first nucleic acid and the second nucleic acid are on the same vector (e.g., under the control of the same promoter or different promoters) . In some embodiments, the method further comprises isolating and / or enriching a plurality of engineered immune cells that express both the NKp80-binding protein (e.g., NKp80-targeted chimeric receptor) and the second antigen-binding protein (e.g., second chimeric receptor) . In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, an NK cell, a B cell, a monocyte, a dendritic cell, and any combination thereof. In some embodiments, the engineered immune cell is a T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce (e.g., reducing at least about 20%) the expression and / or function of endogenous TCR, B2M, and / or NKp80 (e.g., using standard gene editing methods known in the art, such as genetic recombineering, CRISPR / Cas system, TALENs, meganucleases, siRNA, shRNA, and the like) . In some embodiments, the anti-NKp80 CAR comprises the amino acid sequence of any of SEQ ID NOs: 34-37.
[0247] In some embodiments, the first nucleic acid and the second nucleic acid are introduced into the population of immune cells simultaneously. In some embodiments, the first nucleic acid and the second nucleic acid are on the same vector. In some embodiments, the first nucleic acid and the second nucleic acid are on the same vector and under the control of separate promoters, wherein the separate promoters are the same promoter or different promoters. In some embodiments, the first nucleic acid and the second nucleic acid are on the same vector and under the control of the same promoter, wherein the first nucleic acid and the second nucleic acid are connected via a linking nucleic acid encoding a cleavable linker, such as a self-cleaving peptide. In some embodiments, the self-cleaving peptide is selected from the group consisting of T2A, P2A, E2A, and F2A.
[0248] In some embodiments, there is provided a method of making an engineered immune cell (e.g., engineered T cell) , comprising modifying an immune cell to express (a) a first nucleic acid encoding an NKp80-binding protein (e.g., any of the NKp80-binding proteins described herein, such as anti-NKp80 chimeric receptor) ; and optionally (b) a second nucleic acid encoding a second antigen binding protein (e.g., any of the second antigen binding proteins described herein, such as second chimeric receptor) ) ; wherein the first nucleic acid and the second nucleic acid are on the same vector and under the control of the same promoter or wherein the first nucleic acid and the second nucleic acid are on different vectors; wherein the first nucleic acid and the second nucleic acid are connected via a linking nucleic acid (e.g., IRES, or encoding a cleavable linker such as 2A peptide) when located on the same vector; and wherein the method comprises: (a) providing a population of immune cells, and (b) introducing into the population of immune cells the vector (s) comprising the first nucleic acid and the second nucleic acid. The first nucleic acid can be upstream or downstream of the second nucleic acid when located on the same vector. In some embodiments, the first nucleic acid encodes a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37. In some embodiments, the engineered immune cell is selected from the group consisting of a T cell, an NK cell, a B cell, a monocyte, a dendritic cell, and any combination thereof. In some embodiments, the engineered immune cell is a T cell. In some embodiments, the engineered immune cell is further engineered to eliminate or reduce expression and / or function of endogenous TCR, B2M, and / or NKp80. In some embodiments, the engineered immune cell has normal (i.e., average or median native immune cell levels of) endogenous NKp80 expression and / or function.
[0249] Also provided are methods of: i) prolonging in vivo persistence of an immune cell, and / or ii) reducing HvG response of an immune cell, comprising modifying the immune cell to express any of the NKp80-binding proteins that comprise an NKp80 binding domain provided herein and optionally a second antigen binding domain, thereby generating an engineered immune cell (e.g., an engineered T cell) , such as any of the engineered immune cells described herein. In some embodiments, the NKp80-binding protein is an anti-NKp80 CAR comprising an NKp80 binding domain, a transmembrane domain, and an intracellular signaling domain. In some embodiments, the NKp80-binding protein (e.g., anti-NKp80 CAR) further comprises a second antigen binding domain, wherein the second antigen binding domain binds to a second antigen that is not NKp80. In some embodiments, the immune cell expresses or is further modified to express a second antigen binding protein (e.g., a second CAR) , wherein the second antigen binding protein comprises a third antigen binding domain, and wherein the third antigen binding domain binds to a third antigen (e.g., a cancer antigen) . In some embodiments, the anti-NKp80 CAR comprises the amino acid sequence of any of SEQ ID NOs: 34-37.
[0250] In some embodiments, the first nucleic acid and / or the second nucleic acid are introduced into the population of immune cells via a viral vector. Examples of viral vectors include, but are not limited to, adenoviral vectors, adeno-associated virus (AVV) vectors, lentiviral vector, retroviral vectors, herpes simplex viral vector, and derivatives thereof.
[0251] In some embodiments, the first nucleic acid and / or the second nucleic acid are under the control of a promoter, such as any of the promoters described in Section II. C. above.
[0252] In some embodiments, the engineered immune cell is prepared by introducing the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) into the immune cell, such as a T cell. In some embodiments, the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) is introduced to the immune cell by transfecting the immune cell with any one of the isolated nucleic acids or vectors described herein. In some embodiments, the immune cell (e.g., engineered immune cell expressing the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor, such as anti-NKp80 CAR) is further engineered to express a second antigen-binding protein (e.g., a second chimeric receptor, such as a second CAR) , by transfecting any one of the isolated nucleic acids or vectors described herein. In some embodiments, the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) is introduced to the immune cell by inserting proteins into the cell membrane while passing cells through a microfluidic system, such as CELL (see, e.g., U.S. Patent Application Publication No. 20140287509) .
[0253] Methods of introducing vectors or isolated nucleic acids into a mammalian cell are known in the art. The vectors described can be transferred into an immune effector cell by physical, chemical, or biological methods.
[0254] Physical methods for introducing an isolated nucleic acid or vector into an immune cell include calcium phosphate precipitation, lipofection, particle bombardment, microinjection, electroporation, and the like. Methods for producing cells comprising vectors and / or exogenous nucleic acids are well-known in the art. See, e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York. In some embodiments, the vector is introduced into the cell by electroporation.
[0255] Biological methods for introducing an isolated nucleic acid or vector into an immune cell include the use of DNA and RNA vectors. Viral vectors have become the most widely used method for inserting genes into mammalian, e.g., human cells.
[0256] Chemical means for introducing an isolated nucleic acid or vector into an immune cell include colloidal dispersion systems, such as macromolecule complexes, nanocapsules, microspheres, beads, and lipid-based systems including oil-in-water emulsions, micelles, mixed micelles, and liposomes. An exemplary colloidal system for use as a delivery vehicle in vitro is a liposome (e.g., an artificial membrane vesicle) .
[0257] RNA molecules encoding any of the NKp80-binding proteins (e.g., anti-NKp80 chimeric receptors) and / or optional second antigen-binding proteins (e.g., second chimeric receptors) described herein may be prepared by a conventional method (e.g., in vitro transcription) and then introduced into the immune cells via known methods such as mRNA electroporation. See, e.g., Rabinovich et al., Human Gene Therapy 17: 1027-1035 (2006) .
[0258] The transduced or transfected immune cell can be propagated ex vivo after introduction of the vector or isolated nucleic acid. For example, the transduced or transfected immune cell can be cultured to propagate for at least about any of 1 day, 2 days, 3 days, 4 days, 5 days, 6 days, 7 days, 9 days, 10 days, 12 days, or 14 days. The transduced or transfected immune cells may be further evaluated or screened to select the engineered mammalian cell, e.g., expressing the chimeric receptor, or expressing both the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) and the optional second antigen-binding protein (e.g., second chimeric receptor) .
[0259] Reporter genes may be used for identifying potentially transfected cells and for evaluating the functionality of regulatory sequences. In general, a reporter gene is a gene that is not present in or expressed by the recipient organism or tissue and that encodes a polypeptide whose expression is manifested by some easily detectable property, e.g., enzymatic activity. Expression of the reporter gene is assayed at a suitable time after the DNA has been introduced into the recipient cells. Suitable reporter genes may include genes encoding luciferase, beta-galactosidase, chloramphenicol acetyl transferase, secreted alkaline phosphatase, or the green fluorescent protein gene (e.g., Ui-Tei et al. FEBS Letters 479: 79-82 (2000) ) . Suitable expression systems are well known and may be prepared using known techniques or obtained commercially.
[0260] Other methods to confirm the presence of the nucleic acid encoding the NKp80-binding proteins (e.g., anti-NKp80 chimeric receptors) and / or optional second antigen-binding proteins (e.g., second chimeric receptors) in the engineered immune cell, include, for example, molecular biological assays well known to those of skill in the art, such as Southern and Northern blotting, RT-PCR and PCR; biochemical assays, such as detecting the presence or absence of a particular peptide, e.g., by immunological methods (such as ELISAs and Western blots) .
[0261] In some embodiments, the engineered immune cell is a T cell. T cells for use in expansion and genetic modification can be obtained from a number of sources, including peripheral blood mononuclear cells, bone marrow, lymph node tissue, cord blood, thymus tissue, tissue from a site of infection, ascites, pleural effusion, spleen tissue, and tumors. In some embodiments, any number of T cell lines available in the art, may be used. For example, T cells can be obtained from a unit of blood collected from a subject using any number of techniques known to the skilled artisan, such as FicollTM separation. In some embodiments, cells from the circulating blood of an individual are obtained by apheresis. The apheresis product typically contains lymphocytes, including T cells, monocytes, granulocytes, B cells, other nucleated white blood cells, red blood cells, and platelets. The cells collected by apheresis may be washed to remove the plasma fraction and to place the cells in an appropriate buffer or media for subsequent processing steps. In some embodiments, the cells are washed with phosphate buffered saline (PBS) . In some embodiments, the wash solution lacks calcium and may lack magnesium or may lack many if not all divalent cations. Initial activation steps in the absence of calcium may lead to magnified activation. As those of ordinary skill in the art would readily appreciate a washing step may be accomplished by methods known to those in the art, such as by using a semi-automated “flow-through” centrifuge (for example, the Cobe 2991 cell processor, the Baxter CytoMate, or the Haemonetics Cell Saver 5) according to the manufacturer's instructions. After washing, the cells may be resuspended in a variety of biocompatible buffers, such as, for example, Ca2+-free, Mg2+-free PBS, PlasmaLyte A, or other saline solution with or without buffer. Alternatively, the undesirable components of the apheresis sample may be removed, and the cells directly resuspended in culture media.
[0262] T cells can be isolated from peripheral blood lymphocytes by lysing the red blood cells and depleting the monocytes, for example, by centrifugation through a PERCOLLTM gradient or by counterflow centrifugal elutriation. A specific subpopulation of T cells, such as CD3+, CD28+, CD4+, CD8+, CD45RA+, and CD45RO+ T cells, can be further isolated by positive or negative selection techniques. For example, in some embodiments, T cells are isolated by incubation with anti-CD3 / anti-CD28 (i.e., 3×28) -conjugated beads, such as M-450 CD3 / CD28 T, for a time period sufficient for positive selection of the desired T cells. In some embodiments, the time period is about 30 minutes. In a further embodiment, the time period ranges from about 30 minutes to about 36 hours or longer and all integer values there between, such as about 10 to about 24 hours. In a further embodiment, the time period is at least about 1, 2, 3, 4, 5, or 6 hours. For isolation of T cells from patients with leukemia, use of longer incubation times, such as 24 hours, can increase cell yield. Longer incubation times may be used to isolate T cells in any situation where there are few T cells as compared to other cell types, such in isolating T cells from tumor tissue or from immune-compromised individuals. Further, use of longer incubation times can increase the efficiency of capture of CD8+ T cells. For example, by simply shortening or lengthening the time T cells are allowed to bind to the CD3 / CD28 beads and / or by increasing or decreasing the ratio of beads to T cells, subpopulations of T cells can be preferentially selected for or against at culture initiation or at other time points during the process. Additionally, by increasing or decreasing the ratio of anti-CD3 and / or anti-CD28 antibodies on the beads or other surface, subpopulations of T cells can be preferentially selected for or against at culture initiation or at other desired time points. The skilled artisan would recognize that multiple rounds of selection can also be used. It may be desirable to perform the selection procedure and use the “unselected” cells in the activation and expansion process. “Unselected” cells can also be subjected to further rounds of selection.
[0263] In some embodiments, the population of immune cells are enriched for CD4+ and / or CD8+ cells. In some embodiments, the population of immune cells are enriched for both CD4+and CD8+ cells, such as by using CD4 Nanobeads and CD8 Nanobeads. In some embodiments, the population of immune cells are activated before introducing the nucleic acid encoding the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) and / or optional second antigen-binding protein (e.g., second chimeric receptor) into the immune cells, such as by using anti-CD3 / CD28 particles. The enrichment of CD4+ and / or CD8+ cells may be performed before introducing the nucleic acid encoding the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) and / or optional second antigen-binding protein (e.g., second chimeric receptor) into the population of immune cells. The enrichment of CD4+ and / or CD8+ cells may be performed after introducing the nucleic acid encoding the NKp80-binding protein (e.g., anti-NKp80 chimeric receptor) and / or optional second antigen-binding protein (e.g., second chimeric receptor) into the population of immune cells (e.g., a mixture of PBMC) .
[0264] In some embodiments, the cells may be incubated on a rotator for varying lengths of time at varying speeds at 2-10℃, or at room temperature.
[0265] T cells for stimulation can also be frozen after a washing step. Without being bound by theory, the freeze and subsequent thaw step may provide a more uniform product by removing granulocytes and to some extent monocytes in the cell population. After the washing step that removes plasma and platelets, the cells may be suspended in a freezing solution. While many freezing solutions and parameters are known in the art and will be useful in this context, one method involves using PBS containing 20%DMSO and 8%human serum albumin, or culture media containing 10%dextran 40 and 5%dextrose, 20%human serum albumin and 7.5%DMSO, or 31.25%plasmalyte-A, 31.25%dextrose 5%, 0.45%NaCl, 10%dextran 40 and 5%dextrose, 20%human serum albumin, and 7.5%DMSO or other suitable cell freezing media containing for example, Hespan and PlasmaLyte A. The cells then are frozen to -80℃ at a rate of 1℃ per minute and stored in the vapor phase of a liquid nitrogen storage tank. Other methods of controlled freezing may be used as well as uncontrolled freezing immediately at -20℃ or in liquid nitrogen.
[0266] In some embodiments, cryopreserved cells are thawed and washed as described herein and allowed to rest for one hour at room temperature prior to activation.
[0267] In some embodiments, prior to or after genetic modification of the T cells expressing the NKp80-binding proteins (e.g., anti-NKp80 chimeric receptors) or co-expressing the NKp80-binding proteins and second antigen-binding proteins (e.g., second chimeric receptors) described herein, the T cells can be activated and expanded generally using methods as described, for example, in U.S. Pat. Nos. 6,352,694; 6,534,055; 6,905,680; 6,692,964; 5,858,358; 6,887,466; 6,905,681; 7,144,575; 7,067,318; 7,172,869; 7,232,566; 7,175,843; 5,883,223; 6,905,874; 6,797,514; 6,867,041; and U.S. Patent Application Publication No. 20060121005.
[0268] Generally, T cells can be expanded by contact with a surface having attached thereto an agent that stimulates a CD3 / TCR complex associated signal and a ligand that stimulates a co-stimulatory molecule on the surface of the T cells. In particular, T cell populations may be stimulated as described herein, such as by contact with an anti-CD3 antibody, or antigen binding fragment thereof, or an anti-CD2 antibody immobilized on a surface, or by contact with a protein kinase C activator (e.g., bryostatin) in conjunction with a calcium ionophore. For co-stimulation of an accessory molecule on the surface of the T cells, a ligand that binds the accessory molecule is used. For example, a population of T cells can be contacted with an anti-CD3 antibody and an anti-CD28 antibody, under conditions appropriate for stimulating proliferation of the T cells. To stimulate proliferation of either CD4+ T cells or CD8+ T cells, an anti-CD3 antibody and an anti-CD28 antibody can be used. Examples of an anti-CD3 antibody include UCHT1, OKT3, HIT3a (BioLegend, San Diego, US) can be used as can other methods commonly known in the art (Graves J, et al., J. Immunol. 146: 2102 (1991) ; Li B, et al., Immunology 116: 487 (2005) ; Rivollier A, et al., Blood 104: 4029 (2004) ) . Examples of an anti-CD28 antibody include 9.3, B-T3, XR-CD28 (Diaclone, Besancon, France) can be used as can other methods commonly known in the art (Berg et al., Transplant Proc. 30 (8) : 3975-3977 (1998) ; Haanen et al., J. Exp. Med. 190(9) : 13191328 (1999) ; Garland et al., J. Immunol Meth. 227 (1-2) : 53-63 (1999) ) .
[0269] In addition to CD4 and CD8 markers, other phenotypic markers vary significantly, but in large part, reproducibly during the course of the cell expansion process. Thus, such reproducibility enables the ability to tailor an activated T cell product for specific purposes.NKp80-binding proteins and / or anti-NKp80 antibody constructs
[0270] The NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein each may be prepared by any of the known protein expression and purification methods in the art. DNA sequence encoding the NKp80-binding proteins and / or the anti-NKp80 antibody constructs can be fully synthesized. After obtaining such sequence, it is cloned into a suitable expression vector, then transfected into a suitable host cell. The transfected host cells are cultured, and the supernatant is harvested and purified to obtain the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. In some embodiments, the host cell is lysed to obtain the expressed NKp80-binding proteins and / or the anti-NKp80 antibody constructs.
[0271] In some embodiments, the present application provides isolated nucleic acids encoding one or more of the polypeptides of any one of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. The isolated nucleic acids may be DNA or RNA.
[0272] In some embodiments, the isolated nucleic acid is inserted into a vector, such as an expression vector, a viral vector, or a cloning vector. Hence also provided are vectors comprising any of the isolated nucleic acids described herein. For expression of the nucleic acids, the vector may be introduced into a host cell to allow expression of the nucleic acids within the host cell. The expression vectors may contain a variety of elements for controlling expression, including, without limitation, promoter sequences, transcription initiation sequences, enhancer sequences, selectable markers, and signal sequences. These elements may be selected as appropriate by a person of ordinary skill in the art. For example, the promoter sequence (s) may be selected to promote the transcription of the polynucleotide in the vector. Suitable promoter sequences include, without limitation, T7 promoter, T3 promoter, SP6 promoter, beta-actin promoter, EF1a promoter, CMV promoter, and SV40 promoter. Enhancer sequences may be selected to enhance the transcription of the nucleic acids. Selectable markers may be selected to allow selection of the host cells inserted with the vector from those cells lacking the vector, for example, the selectable markers may be genes that confer antibiotic resistance. Signal sequences may be selected to allow the expressed polypeptide to be transported outside of the host cell.
[0273] In some embodiments, there is provided an isolated host cell comprising any of the isolated nucleic acids or vectors encoding the polypeptide portion of any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. In some embodiments, there is provided an isolated host cell expressing any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. In some embodiments, two or more polypeptides of any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein are encoded by a single vector. In some embodiments, two or more polypeptides of any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein are encoded by two or more vectors. The host cells containing the vector may be useful in expression or cloning of the isolated nucleic acids. Suitable host cells can include, without limitation, prokaryotic cells, fungal cells, yeast cells, or higher eukaryotic cells such as mammalian cells. The expression of antibody constructs in prokaryotic cells such as E. coli is well established in the art. For a review, see for example Pluckthun, A. BioTechnology 9: 545-551 (1991) . Expression in eukaryotic cells in culture is also available to those skilled in the art as an option for production of antibody constructs, see reviews, for example Ref, M. E. (1993) Curr. Opinion Biotech. 4: 573-576; Trill J. J. et al. (1995) Curr. Opinion Biotech 6: 553-560. Higher eukaryotic cells, in particular those derived from multicellular organisms can be used for expression of glycosylated polypeptides. Suitable higher eukaryotic cells include, without limitation, invertebrate cells and insect cells, and vertebrate cells. In some embodiments, the host cell is E. coli. In some embodiments, the host cell is a Chinese hamster ovary (CHO) cell or an HEK293 cell.
[0274] The vector can be introduced to the host cell using any suitable methods known in the art, including, but not limited to, DEAE-dextran mediated delivery, calcium phosphate precipitate method, cationic lipids mediated delivery, liposome mediated transfection, electroporation, microprojectile bombardment, receptor-mediated gene delivery, delivery mediated by polylysine, histone, chitosan, and peptides. Standard methods for transfection and transformation of cells for expression of a vector of interest are well known in the art. In some embodiments, the host cells comprise two or more vectors each encoding a polypeptide of any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. The two or more vectors can be introduced into the host cells at a same ratio, or at different ratios. In some embodiments, the host cells comprise a single vector comprising isolated nucleic acids encoding two or more polypeptides of any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. The two or more nucleic acids encoding the two or more polypeptides of the NKp80-binding protein and / or the anti-NKp80 antibody construct can be under the same promoter control, or different promoter controls. For example, two or more nucleic acids under the same promoter control can be connected via an IRES sequence, or a sequence encoding a self-cleaving peptide (e.g., P2A, T2A) .
[0275] In some embodiments, the present application provides methods of making any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein, comprising i) culturing an isolated host cell comprising any of the isolated nucleic acids described herein or any of the vectors described herein, or any of the isolated host cells described herein (e.g., a host cell comprising any of the isolated nucleic acids or vectors described herein) , under a condition suitable for the expression of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs, and ii) obtaining the expressed NKp80-binding proteins and / or the anti-NKp80 antibody constructs from said host cell (e.g., from the cell culture, or by lysing the host cell) . The isolated host cells are cultured under conditions that allow expression of the isolated nucleic acids inserted in the vectors. Suitable conditions for expression of polynucleotides may include, without limitation, suitable medium, suitable density of host cells in the culture medium, presence of necessary nutrients, presence of supplemental factors, suitable temperatures and humidity, and absence of microorganism contaminants. A person with ordinary skill in the art can select the suitable conditions as appropriate for the purpose of the expression. In some embodiments, the methods of making further comprise purifying any of the obtained NKp80-binding proteins and / or the anti-NKp80 antibody constructs.
[0276] In some embodiments, the polypeptides expressed by the host cell can assemble together (e.g., form a polypeptide complex such as a dimer) and produce any of the NKp80-binding proteins and / or the anti-NKp80 antibody constructs described herein. In some embodiments, the polypeptide complex may be formed inside the host cell. For example, the polypeptide complex may be formed inside the host cell with the aid of relevant enzymes and / or cofactors. In some embodiments, the polypeptide complex may be sec...
Claims
1.An engineered immune cell comprising an NKp80-binding protein that comprises an NKp80 binding domain.2.The engineered immune cell of claim 1, wherein the NKp80-binding protein:i) blocks NKp80; and / orii) does not activate NKp80.3.The engineered immune cell of claim 1 or 2, wherein the engineered immune cell is capable of inhibiting or killing NKp80 positive cells; optionally wherein the NKp80 positive cells are natural killer (NK) cells.4.The engineered immune cell of any one of claims 1-3, wherein the NKp80 binding domain is selected from the group consisting of a Fab, a Fab’ , a (Fab’ ) 2, an Fv, a single chain Fv (scFv) , a single domain antibody (sdAb) , and a peptide ligand specifically binding to NKp80.5.The engineered immune cell of claim 4, wherein the NKp80 binding domain is an sdAb (“anti-NKp80 sdAb” ) .6.The engineered immune cell of claim 5, wherein the anti-NKp80 sdAb comprises:(i) a CDR1, a CDR2, and a CDR3 having the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16;(ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3;(iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7;(iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11;(v) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15; and / or(vi) a VHH comprising the amino acid sequence of any one of SEQ ID NOs: 4, 8, 12, and 16.7.The engineered immune cell of any one of claims 1-6, wherein the NKp80-binding protein is a chimeric antigen receptor (CAR) comprising an antigen binding domain, a transmembrane domain, and an intracellular signaling domain, and wherein the antigen binding domain comprises the NKp80 binding domain.8.The engineered immune cell of claim 7, wherein the transmembrane domain is derived from the group consisting of CD8α, CD4, CD28, 4-1BB, CD80, CD86, CD152, and PD-1; optionally wherein the transmembrane domain is derived from CD8α.9.The engineered immune cell of claim 7 or 8, wherein the intracellular signaling domain is derived from the group consisting of CD3ζ, FcRγ, FcRβ, CD3γ, CD3δ, CD3ε, CD5, CD22, CD79a, CD79b, DAP12, and CD66d; optionally wherein the intracellular signaling domain is derived from CD3ζ.10.The engineered immune cell of any one of claims 7-9, wherein the CAR further comprises an intracellular co-stimulatory signaling domain.11.The engineered immune cell of claim 10, wherein the intracellular co-stimulatory signaling domain is derived from a co-stimulatory molecule selected from the group consisting of CD27, CD28, CD137, OX40, CD40, PD-1, LFA-1, ICOS, CD2, CD7, LIGHT, NKG2C, B7-H3, TNFRSF9, TNFRSF4, TNFRSF8, CD40LG, ITGB2, KLRC2, TNFRSF18, TNFRSF14, HAVCR1, LGALS9, DAP10, DAP12, CD83, ligands of CD83, and any combination thereof; optionally wherein the intracellular co-stimulatory signaling domain is derived from a cytoplasmic domain of CD28.12.The engineered immune cell of any one of claims 7-11, wherein the CAR further comprises a hinge domain located between the antigen binding domain and the transmembrane domain; optionally wherein the hinge domain is derived from CD8α.13.The engineered immune cell of any one of claims 7-12, wherein the CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 34-37.14.The engineered immune cell of any one of claims 1-13, wherein the NKp80-binding protein further comprises a signal peptide at its N-terminus; optionally wherein the signal peptide is derived from CD8α.15.The engineered immune cell of any one of claims 1-14, wherein the NKp80-binding protein further comprises a second antigen binding domain that specifically binds to a second antigen, and wherein the second antigen is not NKp80.16.The engineered immune cell of any one of claims 1-14, wherein the engineered immune cell further comprises a second antigen binding protein, wherein the second antigen binding protein comprises a second antigen binding domain that specifically binds to a second antigen, and wherein the second antigen is not NKp80.17.The engineered immune cell of claim 15 or 16, wherein the second antigen is a disease-associated antigen or disease-specific antigen selected from the group consisting of: a cancer-associated antigen or a cancer-specific antigen, an infectious disease-associated antigen or an infectious disease-specific antigen, an inflammatory disorder-associated antigen or an inflammatory disorder-specific antigen, and an autoimmune-associated antigen or an autoimmune-specific antigen.18.The engineered immune cell of claim 17, wherein the disease-associated antigen or disease-specific antigen is a cancer-associated antigen or a cancer-specific antigen; optionally wherein the cancer-associated antigen or cancer-specific antigen is selected from the group consisting of CD19, CD20, CD22, BCMA, DLL3, B7H3, PD-L1, PD-L2, CLL1, GPC3, GU2CYC, CD7, CD38, CD41, CD123, Claudin 18.2, Claudin 6, NKG2D, GPRC5D, CD70, and any combination thereof.19.The engineered immune cell of any one of claims 16-18, wherein the second antigen binding protein is a second CAR comprising the second antigen binding domain, a second transmembrane domain, and a second intracellular signaling domain; optionally wherein the second CAR further comprises a second signal peptide at its N-terminus, and / or a second hinge domain.20.The engineered immune cell of any one of claims 1-19, wherein the engineered immune cell is selected from the group consisting of a T cell, an NK cell, a B cell, a monocyte, a dendritic cell, and any combination thereof.21.The engineered immune cell of claim 20, wherein the engineered immune cell is a T cell; optionally wherein the T cell is an αβ T cell or a γδ T cell.22.The engineered immune cell of claim 20 or 21, wherein the engineered immune cell has normal endogenous NKp80 expression and / or function.23.The engineered immune cell of claim 20 or 21, wherein the engineered immune cell is further engineered to eliminate or reduce the expression and / or function of endogenous NKp80.24.The engineered immune cell of any one of claims 21-23, wherein the T cell is engineered to eliminate or reduce the expression and / or function of endogenous TCR.25.The engineered immune cell of any one of claims 21-24, wherein the T cell is engineered to eliminate or reduce the expression and / or function of endogenous B2M.26.A pharmaceutical composition comprising the engineered immune cell of any one of claims 1-25, and a pharmaceutically acceptable excipient.27.A method of treating and / or reducing the severity of a condition, disease, or disorder in an individual in need thereof, comprising administering to the individual a therapeutically effective amount of the engineered immune cell of any one of claims 1-25, or the pharmaceutical composition of claim 26.28.The method of claim 27, wherein the condition, disease, or disorder is host-versus-graft (HvG) response or cancer.29.The method of claim 27, wherein the condition, disease, or disorder is an NK cell-associated disease or a disease associated with cells that express NKp80.30.The method of claim 29, wherein the NK cell-associated disease is an NK cell malignancy.31.A method of preventing and / or reducing the risk of developing HvG in an individual, comprising administering to the individual a therapeutically effective amount of the engineered immune cell of any one of claims 1-25, or the pharmaceutical composition of claim 26.32.The method of any one of claims 27-31, wherein the individual is human.33.The method of any one of claims 27-32, wherein the engineered immune cell is allogeneic to the individual.34.A method of depleting NK cells in a first population of cells, comprising exposing the first population of cells to a second population of cells comprising the engineered immune cell of any one of claims 1-25 or the pharmaceutical composition of claim 26, wherein the exposing results in depletion of NK cells in the first population.35.An antibody construct comprising an sdAb that binds to NKp80 ( “anti-NKp80 sdAb” ) , wherein the anti-NKp80 sdAb comprises a CDR1, a CDR2, and a CDR3 having the amino acid sequences of the CDR1, CDR2, and CDR3, respectively, as set forth in SEQ ID NO: 4, 8, 12, or 16.36.The anti-NKp80 antibody construct of claim 35, wherein the anti-NKp80 sdAb comprises:(i) a CDR1 comprising the amino acid sequence of SEQ ID NO: 1, a CDR2 comprising the amino acid sequence of SEQ ID NO: 2, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 3;(ii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 5, a CDR2 comprising the amino acid sequence of SEQ ID NO: 6, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 7;(iii) a CDR1 comprising the amino acid sequence of SEQ ID NO: 9, a CDR2 comprising the amino acid sequence of SEQ ID NO: 10, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 11; or(iv) a CDR1 comprising the amino acid sequence of SEQ ID NO: 13, a CDR2 comprising the amino acid sequence of SEQ ID NO: 14, and a CDR3 comprising the amino acid sequence of SEQ ID NO: 15.37.The anti-NKp80 antibody construct of claim 35 or 36, wherein the anti-NKp80 sdAb comprises a VHH comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 4, 8, 12, and 16.38.The anti-NKp80 antibody construct of any one of claims 35-37, wherein the anti-NKp80 antibody construct is a chimeric receptor.39.The anti-NKp80 antibody construct of claim 38, wherein the chimeric receptor is a CAR.40.The anti-NKp80 antibody construct of claim 39, wherein the CAR comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 17-20 and 34-37.41.A method of i) prolonging in vivo persistence, and / or ii) reducing HvG response of an immune cell, comprising modifying the immune cell to express an NKp80-binding protein that comprises an NKp80 binding domain.42.The method of claim 41, wherein the NKp80-binding protein is the anti-NKp80 antibody construct of any one of claims 35-40.
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