Engineered il-15 constructs and uses thereof
Engineered immune cells with an IL-15 construct improve therapeutic cell expansion and persistence, addressing limitations in ACT by enhancing in vivo efficacy and safety.
Patent Information
- Application Number
- PCT/CN2025/126990
- Authority / Receiving Office
- WO · WO
- Patent Type
- Applications
- Current Assignee / Owner
- Priority Date
- 2024-10-12
- Filing Date
- 2025-10-11
- Publication Date
- 2026-04-16
AI Technical Summary
Existing adoptive cell therapy (ACT) approaches face challenges with limited expansion and persistence of therapeutic cells, such as CAR-T and CAR-NK cells, within the tumor microenvironment, leading to exhaustion and potential cytokine release syndrome from systemic cytokine administration.
Engineered immune cells expressing an IL-15 construct comprising an IL-15 moiety and a transmembrane domain derived from DAP12, which enhances cell expansion and persistence while reducing bystander cell killing and systemic cytotoxicity.
The engineered cells demonstrate superior in vitro and in vivo expansion, persistence, and cytotoxicity against target cells, with reduced host immune cell activation and graft rejection, offering enhanced ACT benefits and improved patient survival.
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Abstract
Description
ENGINEERED IL-15 CONSTRUCTS AND USES THEREOFCROSS REFERENCE TO RELATED APPLICATION
[0001] This application claims benefit of priority of International Patent Application No. PCT / CN2024 / 124484 filed on October 12, 2024, the content of which is incorporated herein by reference in its entirety. SEQUENCE STATEMENT
[0002] This application contains a Sequence Listing that has been submitted electronically as an XML file named “IEC250347PCT-seql. xml. ” The XML file, created on October 11, 2025, is 84,605 bytes in size. The material in the XML file is hereby incorporated by reference in its entirety. FIELD OF THE PRESENT APPLICATION
[0003] The present application generally relates to engineered cells (e.g., engineered immune cells) comprising an IL-15 construct. IL-15 constructs, compositions comprising the engineered immune cells, methods for treating of a disease (e.g., cancer) using the compositions, and methods of promoting persistence and / or expansion of a cell (e.g., immune cell) using the IL-15 constructs, are also provided. BACKGROUND OF THE PRESENT APPLICATION
[0004] Adoptive cell therapy or adoptive cell transfer (ACT) is becoming an ever more important treatment paradigm, particularly in the treatment of cancer. ACT refers to the transfer of therapeutic cells, most typically immune cells, into a patient. These cells may have originated from the patient (i.e., autologous therapy) or from another individual of the same species (i.e., allogeneic therapy) . The goal of ACT is to improve functions and characteristics of the immune system in the patient. Specially, in cancer immunotherapy, the goal of ACT is to trigger an immune response against the cancer. Although T cells are most often used in ACT, other immune cell types such as natural killer (NK) cells, lymphocytes (e.g., tumor-infiltrating lymphocytes or TILs) , dendritic cells and myeloid cells have also been applied.
[0005] Ideally, the therapeutic cells that are infused to a patient receiving an ACT (or reinfused in case of autologous therapy) will expand and persist in the patient. However, many factors are known to lead to decreased therapeutic cell number and / or function in ACT. For example, therapeutic cells such as CAR-T or CAR-NK cell populations are known to exhibit limited expansion or replicative senescence within a tumor microenvironment (TME) , potentially leading to exhaustion of the population and failure of ACT.
[0006] One strategy that has been employed to promote persistence and expansion of ACT therapeutic cells in vivo is administration of cytokines known to promote proliferation of the therapeutic cell to the individual receiving ACT. For example, clinical trials demonstrated that systemic administration (subcutaneous or intravenous) of recombinant human interleukin-15 (rhIL-15) was able to promote robust in vivo NK-cell expansion and promote remission in 32%of acute myeloid leukemia patients receiving both lymphodepleting chemotherapy and haploidentical NK cell ACT (see, e.g., Cooley et al., Blood Adv., 2019, 3 (13) : 1970–1980, which is herein incorporated by reference in its entirety) . However, these same trials resulted in over half of all patients receiving rhIL-15 developed cytokine release syndrome (CRS) , demonstrating the deleterious effects systemic treatment approaches have on patients.
[0007] The disclosures of all publications, patents, patent applications and published patent applications referred to herein are hereby incorporated herein by reference in their entirety. BRIEF SUMMARY OF THE DISCLOSURE
[0008] The present application in one aspect provides engineered immune cells comprising an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12.
[0009] In some embodiments according to the engineered immune cells described above, the IL-15 moiety is derived from a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the IL-15 moiety is a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the IL-15 moiety is a functional fragment of the mature wildtype human IL-15 polypeptide. In some embodiments, the IL-15 moiety is a functional variant of the mature wildtype human IL-15 polypeptide.
[0010] In some embodiments according to any of the engineered immune cells described above, the transmembrane domain is derived from a wildtype human DAP12 polypeptide comprising the amino acid sequence of SEQ ID NO: 17. In some embodiments, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 18. In some embodiments, the transmembrane domain is a functional variant of the transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18.
[0011] In some embodiments according to any of the engineered immune cells described above, the IL-15 construct further comprises a hinge domain between the IL-15 moiety and the transmembrane domain derived from DAP12. In some embodiments, the hinge domain is derived from CD8. In some embodiments, the hinge domain comprises the amino acid sequence of SEQ ID NO: 21.
[0012] In some embodiments according to any of the engineered immune cells described above, the IL-15 construct does not comprise a functional intracellular signaling domain.
[0013] In some embodiments according to any of the engineered immune cells described above, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 29 or 46.
[0014] In some embodiments according to any of the engineered immune cells described above, the IL-15 construct further comprises a signal peptide at the N-terminus. In some embodiments, the signal peptide is derived from DAP12. In some embodiments, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 2 or 45.
[0015] In some embodiments according to any of the engineered immune cells described above, the engineered immune cell further comprises a chimeric receptor. In some embodiments, the chimeric receptor is selected from the group consisting of an engineered T cell receptor (TCR) , a chimeric antigen receptor (CAR) , a chimeric TCR (cTCR) , a T cell antigen coupler (TAC) , and a TAC-like engineered receptor. In some embodiments, the chimeric receptor is a CAR comprising an extracellular antigen binding domain, a transmembrane domain, and a primary intracellular signaling domain. In some embodiments, the extracellular antigen binding domain of the CAR comprises an antigen-binding moiety specifically recognizing a target antigen, such as BCMA. In some embodiments, the antigen-binding moiety is an sdAb. In some embodiments, the transmembrane domain of the CAR is not derived from DAP12. In some embodiments, the transmembrane domain of the CAR is derived from CD8. In some embodiments, the CAR further comprises a hinge domain between the extracellular antigen binding domain and the transmembrane domain. In some embodiments, the hinge domain of the CAR is derived from CD8. In some embodiments, the primary intracellular signaling domain of the CAR is derived from CD3ζ. In some embodiments, the CAR further comprises a costimulatory intracellular signaling domain. In some embodiments, the costimulatory intracellular signaling domain is derived from 4-1BB. In some embodiments, the CAR comprises the amino acid sequence of SEQ ID NO: 31.
[0016] In some embodiments according to any of the engineered immune cells described above, the engineered immune cell is selected from the group consisting of: T cell, NK cell, NKT cell, PBMC, macrophage, and monocyte. In some embodiments, the engineered immune cell is an NK cell. In some embodiments, the NK cell is further modified to increase the expression and / or function of, e.g., overexpress, one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9. In some embodiments, the NK cell is further modified to reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules.
[0017] In some embodiments according to any of the engineered immune cells described above, the IL-15 construct is encoded by a first nucleic acid, the chimeric receptor is encoded by a second nucleic acid, optionally wherein the first nucleic acid and the second nucleic acid are present on a single vector (e.g., viral vector) . In some embodiments, the first nucleic acid and the second nucleic acid are operably linked to a single promoter. In some embodiments, the first nucleic acid and the second nucleic acid are connected by a linking sequence, such as a linking sequence encoding a 2A self-cleaving peptide (e.g., P2A) . In some embodiments, the single vector encodes the amino acid sequence of SEQ ID NO: 8 or 47.
[0018] The present application in another aspect provides an IL-15 construct comprising an IL-15 moiety and a transmembrane domain derived from DAP12. In some embodiments, the IL-15 construct further comprises a hinge domain between the IL-15 moiety and the transmembrane domain derived from DAP12. In some embodiments, the hinge domain is derived from CD8. In some embodiments, the IL-15 construct comprises the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46.
[0019] The present application in another aspect provides an isolated nucleic acid encoding any of the IL-15 constructs described herein. Also provided are vectors comprising any of the isolated nucleic acids described herein. In some embodiments, the vector is a viral vector. In some embodiments, the vector further comprises a second nucleic acid encoding a chimeric receptor. In some embodiments, the chimeric receptor is a CAR comprising an extracellular antigen binding domain, a transmembrane domain, and a primary intracellular signaling domain. In some embodiments, the nucleic acid encoding the IL-15 construct and the second nucleic acid are operably linked to a single promoter and are connected by a linking sequence. In some embodiments, the linking sequence encodes a 2A self-cleaving peptide. In some embodiments, the vector encodes the amino acid sequence of SEQ ID NO: 8 or 47.
[0020] The present application in another aspect provides an engineered immune cell expressing any one of the IL-15 constructs described herein, any of the isolated nucleic acids described herein, or any of the vectors described herein. In some embodiments, the engineered immune cell is selected from the group consisting of: T cell, NK cell, NKT cell, PBMC, macrophage, and monocyte. In some embodiments, the engineered immune cell is an NK cell. In some embodiments, the NK cell is further modified to increase the expression and / or function of, e.g., overexpress, one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9. In some embodiments, the NK cell is further modified to reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules.
[0021] The present application in another aspect provides a pharmaceutical composition comprising any of the engineered immune cells described herein, the isolated nucleic acids described herein, or any of the vectors described herein.
[0022] The present application in another aspect provides a method of treating a disease or condition in an individual, comprising administering to the individual an effective amount of any of the engineered immune cells described herein, or any of the pharmaceutical compositions described herein. In some embodiments, the disease or condition is cancer, an autoimmune disorder, or an infection, such as an autoimmune disorder. In some embodiments, the engineered immune cell is allogeneic. In some embodiments, the individual is a human.
[0023] The present application in another aspect provides a method of making any of the engineered immune cells described herein, comprising introducing into an immune cell any of the isolated nucleic acids described herein or any of the vectors described herein. In some embodiments, the immune cell expresses a chimeric receptor (e.g., a CAR) . In some embodiments, the method further comprises introducing into the immune cell a second nucleic acid encoding a chimeric receptor (e.g., a CAR) . In some embodiments, the immune cell is selected from the group consisting of: T cell, NK cell, NKT cell, PBMC, macrophage, and monocyte, such as an NK cell. In some embodiments, the NK cell is further modified to increase the expression and / or function of, e.g., overexpress, one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9. In some embodiments, the NK cell is further modified to reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules.
[0024] The present application in another aspect provides a method of promoting persistence and / or expansion of an immune cell, comprising introducing into the immune cell any of the isolated nucleic acids described herein or any of the vectors described herein. In some embodiments, the method further comprises introducing into the immune cell a second nucleic acid encoding a chimeric receptor (e.g., CAR) . In some embodiments, the immune cell expresses a chimeric receptor (e.g., CAR) . In some embodiments, the immune cell is selected from the group consisting of: T cell, NK cell, NKT cell, PBMC, macrophage, and monocyte, such as an NK cell. In some embodiments, the method further comprises modifying the NK cell to increase the expression and / or function of, e.g., overexpress, one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9. In some embodiments, the NK cell is further modified to reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules.BRIEF DESCRIPTION OF THE DRAWINGS
[0025] FIG. 1 shows in vitro short-term cytotoxicity of IL-15 armored BCMA CAR-NK cells against NCI-H929 cells (4 hours co-culture, E: T = 4: 1, 1: 1, 0.25: 1, or 0.0625: 1) .
[0026] FIGs. 2A-2C show the in vitro long-term cytotoxicity of IL-15 armored BCMA CAR-NK cells under 3 rounds of repeated antigen stimulation of NCI-H929 cells at low ET ratios. FIG. 2A shows the assay conditions. FIG. 2B and FIG. 2C show the CAR-NK cell cytotoxicity under antigen stimulation at E: T ratio of 1: 5 or 1: 10, respectively.
[0027] FIG. 3 shows the in vitro expansion of IL-15 armored BMCA CAR-NK cells (Armor-1, Armor-2, and Armor-3) in culture medium without cytokine.
[0028] FIG. 4A shows the effect of IL-15 armored CAR-NK cells (HLA-A2 positive) on the expansion of HLA-A2 negative allo-NK cells in co-culture. FIG. 4B shows the amplification of HLA-A2 positive IL-15 armored CAR-NK cells in co-cultured system with HLA-A2 negative allo-NK cells. Un-transduced HLA-A2 positive NK cells (Un-NK) served as control.
[0029] FIG. 5 shows the human IL-15 detection from cell supernatant of IL-15 armored BMCA CAR-NK cells (Armor-1, Armor-2, Armor-3) , unarmored NK cell control, and medium only control.
[0030] FIGs. 6A-6D show in vivo evaluation of armored CAR-NK cells in NCI-H929-luc bearing NCG model. Un-transduced NK cells (Un-NK, i.p. ) , Armor-1 armored BCMA CAR-NK cells, Armor-2 armored BCMA CAR-NK cells were evaluated in a NCG mouse model (NOD_Prkdcem26Cd52 / NjuCrl) having a multiple myeloma tumor xenograft with a BCMA-positive tumor cell line -NCI-H929. Mice in vehicle group were treated with HBSS (- / -) , intravenously. FIG. 6A shows quantification of mean tumor flux over the days following CAR-NK infusion. FIG. 6B show the representative luciferase imaging of treatment mice over the course of the experiment. FIG. 6C shows mouse body weight over the course of the experiment. FIG. 6D shows the survival curve of mice subjected to each treatment condition.
[0031] FIGs. 7A-7C show the impact of various armors on CAR-NK rejections by allogenic PBMC. FIG. 7A is the schematic of experiment design. FIG. 7B shows the CAR-NK percentage (graft) in total cells 8 days after mixed lymphocyte (MLR) . FIG. 7C shows the T cell activation markers in PBMC (host) . DETAILED DESCRIPTION OF THE DISCLOSURE
[0032] The present application in one aspect provides an engineered cell (e.g., engineered immune cell, such as CAR-NK cell or CAR-T cell) comprising an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12. The application is in part based on inventors’ insight and observation that such IL-15 construct expressed on the surface of engineered cells (e.g., engineered immune cells) can effectively reduce the by-stander killing effect on surrounding cells compared to other membrane-bound IL-15 constructs, or when the IL-15 construct is in a soluble (e.g., secreted) format, demonstrating unexpected safety profile. Further, engineered cells (e.g., engineered immune cells, such as CAR-NK cell or CAR-T cell) expressing the IL-15 construct comprising a transmembrane domain derived from DAP12 demonstrate: (i) superior in vitro and in vivo expansion and persistence; (ii) higher graft rate and less host immune cell activation, indicating less host-versus-graft (HvG) rejection; (iii) superior in vitro and in vivo cytotoxicity against target cells (e.g., tumor cells expressing a target antigen recognized by CAR) ; and (iv) higher patient survival rate, either compared to other membrane-bound IL-15 constructs, or when the IL-15 construct is in a soluble (e.g., secreted) format. Accordingly, the advantages conferred to engineered cells (e.g., engineered immune cells) comprising an IL-15 construct, including superior expansion / persistence of said cells in vivo, may enhance the benefits of ACT. Moreover, the membrane-bound IL-15 construct is not cleaved from cell membrane, which can avoid undesired systemic cytotoxicity.
[0033] The present application also provides IL-15 constructs comprising an IL-15 moiety and a transmembrane domain derived from DAP12, isolated nucleic acids and vectors encoding thereof, methods of making any of the engineered cells (e.g., engineered immune cells, such as CAR-T or CAR-NK cell) described herein using thereof, and methods of promoting persistence and / or expansion of a cell (e.g., immune cell, such as CAR-T or CAR-NK cell) using thereof. Pharmaceutical compositions comprising the engineered cells (e.g., engineered immune cells, such as CAR-NK cell or CAR-T cell) expressing the membrane-bound IL-15 constructs described herein, and methods of using thereof in treating disease or conditions (e.g., cancer, autoimmune disease, or infection) using thereof, are also provided. I. Definitions
[0034] The term “antibody” or “antibody moiety” includes monoclonal antibodies as well as antibody fragments (e.g., Fab, F (ab′) 2, and Fv) . The term “immunoglobulin” (Ig) is used interchangeably with “antibody” herein. The term antibody includes conventional four-chain antibodies, and single-domain antibodies, such as heavy-chain only antibodies or fragments thereof, e.g., VHH.
[0035] 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. Camelid animals (such as camels, llamas, or alpacas) are known to produce HCAbs.
[0036] The term “single-domain antibody” or “sdAb” refers to a single antigen-binding polypeptide having three complementary determining regions (CDRs) . The sdAb alone is capable of binding to the antigen without pairing with a corresponding CDR-containing polypeptide. A sdAb can be derived from antibodies raised in Camelidae species, for example in camel, llama, dromedary, or alpaca and guanaco. In some cases, single-domain antibodies are engineered from camelid HCAbs, and their heavy chain variable domains are referred herein as “VHHs” (Variable domain of the heavy chain of the Heavy chain antibody) . Camelid sdAb is one of the smallest known antigen-binding antibody fragments (see, e.g., Hamers-Casterman et al., Nature 363: 446-8 (1993) ; Greenberg et al., Nature 374: 168-73 (1995) ; Hassanzadeh-Ghassabeh et al., Nanomedicine (Lond) , 8: 1013-26 (2013) ) . A basic VHH has the following structure from the N-terminus to the C-terminus: FR1-CDR1-FR2-CDR2-FR3-CDR3-FR4, in which FR1 to FR4 refer to framework regions 1 to 4, respectively, and in which CDR1 to CDR3 refer to the complementarity determining regions 1 to 3.
[0037] The term “constant domain” 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 domain, which contains the antigen-binding site. The constant domain contains the CH1, CH2 and CH3 domains (collectively, CH) of the heavy chain and the CHL (or CL) domain of the light chain.
[0038] The “variable region” or “variable domain” of an antibody refers to the amino-terminal domains of the heavy or light chain of the antibody. The variable domains of the heavy chain and light chain may be referred to as “VH” and “VL” , respectively. These domains are generally the most variable parts of the antibody (relative to other antibodies of the same class) and contain the antigen binding sites. Heavy-chain only antibodies from the Camelid species have a single heavy chain variable region, which is referred to as “VHH” . VHH is thus a special type of VH.
[0039] The “light chains” of antibodies (immunoglobulins) from any mammalian species can be assigned to one of two clearly distinct types, called kappa ( “κ” ) and lambda ( “λ” ) , based on the amino acid sequences of their constant domains.
[0040] “Antibody fragments” comprise a portion of an intact antibody, preferably comprising the antigen-binding region thereof. In some embodiments, the antibody fragment described herein is an antigen-binding fragment. Examples of antibody fragments include, but are not limited to Fab, Fab′, F (ab′) 2 and Fv fragments; diabodies; linear antibodies (see U.S. Pat. No. 5,641,870, Example 2; Zapata et al., Protein Eng. 8 (10) : 1057-1062 (1995) ) ; single-chain antibody (scFv) molecules; single-domain antibodies (such as VHH) , and multispecific antibodies formed from antibody fragments. Papain digestion of antibodies produced two identical antigen-binding fragments, called “Fab” fragments, and a residual “Fc” fragment, a designation reflecting the ability to crystallize readily. The Fab fragment consists of an entire L chain along with the variable domain of the H chain (VH) , and the first constant domain of one heavy chain (CH1) . Each Fab fragment is monovalent with respect to antigen binding, i.e., it has a single antigen-binding site. Pepsin treatment of an antibody yields a single large F (ab′) 2 fragment that roughly corresponds to two disulfide linked Fab fragments having different antigen-binding activity and is still capable of cross-linking antigen. Fab′fragments differ from Fab fragments by having a few additional residues at the carboxy-terminus of the CH1 domain including one or more cysteines from the antibody hinge region. Fab′-SH is the designation herein for Fab′in which the cysteine residue (s) of the constant domains bear a free thiol group. F (ab′) 2 antibody fragments originally were produced as pairs of Fab′fragments, which have hinge cysteines between them. Other chemical couplings of antibody fragments are also known.
[0041] “Single-chain Fv” or “scFv” antibody fragments comprise the VH and VL domains of antibody, wherein these domains are present in a single polypeptide chain. Generally, the scFv polypeptide further comprises 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 scFv, see, e.g., Pluckthün, The Pharmacology of Monoclonal Antibodies. Springer Berlin Heidelberg, 1994.269-315.
[0042] 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) .
[0043] The term “Complementarity Determining Region” or “CDR” are used to refer to hypervariable regions as defined by the Kabat system. See Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991)
[0044] A number of HVR delineations are in use and are encompassed herein. The Kabat Complementarity Determining Regions (CDRs) are based on sequence variability and are the most commonly used (Kabat et al., Sequences of Proteins of Immunological Interest, 5th Ed. Public Health Service, National Institutes of Health, Bethesda, Md. (1991) ) . Other numbering systems have been described, for example, by AbM, Chothia, Contact, IMGT, and AHon. Chothia refers instead to the location of the structural loops (Chothia and Lesk, J. Mol. Biol. 196: 901-917 (1987) ) . The AbM HVRs represent a compromise between the Kabat HVRs and Chothia structural loops, and are used by Oxford Molecular's AbM antibody modeling software. The “contact” HVRs are based on an analysis of the available complex crystal structures. The residues from each of these HVRs are noted below in Table A. Table A. HVR delineations.
[0045] HVRs may comprise “extended HVRs” 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 (H1) , 50-65 or 49-65 (H2) and 93-102, 94-102, or 95-102 (H3) in the VH. The variable domain residues are numbered according to Kabat et al., supra, for each of these definitions.
[0046] The expression “variable-domain residue-numbering as in Kabat” or “amino-acid-position numbering as in Kabat, ” and variations thereof, refers to the numbering system used for heavy-chain variable domains or light-chain variable domains 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, a FR or HVR 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 of H2 and inserted residues (e.g. residues 82a, 82b, and 82c, etc. according to Kabat) after heavy-chain FR 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) . Unless indicated otherwise herein, the numbering of the residues in an immunoglobulin heavy chain is that of the EU index as in Kabat et al., supra. The “EU index as in Kabat” refers to the residue numbering of the human IgG1 EU antibody.
[0047] “Framework” or “FR” residues are those variable-domain residues other than the HVR residues as herein defined.
[0048] The term “Fc region” or “fragment crystallizable region” herein is used to define a C-terminal region of an immunoglobulin heavy chain, including native-sequence 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 usually 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. Suitable native-sequence Fc regions for use in the antibodies described herein include human IgG1, IgG2 (IgG2A, IgG2B) , IgG3 and IgG4.
[0049] As use herein, the term “binds” , “specifically binds to” or is “specific for” refers to measurable and reproducible interactions such as binding between a target and a ligand (or an antibody moiety) , which is determinative of the presence of the target in the presence of a heterogeneous population of molecules including biological molecules. For example, a ligand (or an antibody moiety) that binds to or specifically binds to a target is a ligand (or an antibody moiety) that binds this target with greater affinity, avidity, more readily, and / or with greater duration than it binds to other targets. The extent of binding of a ligand (or an antibody moiety) to an unrelated target may be less than about 10%of the binding of the ligand (or an antibody moiety) to the target as measured, e.g., by a radioimmunoassay (RIA) . In certain embodiments, a ligand (or an antibody moiety) that specifically binds to a target has a dissociation constant (Kd) of ≤ 1μM, ≤ 100 nM, ≤10 nM, ≤ 1 nM, or ≤ 0.1 nM. In certain embodiments, a ligand (or an antibody moiety) specifically binds to a region on a protein that is conserved among the proteins from different species. In another embodiment, specific binding can include, but does not require exclusive binding.
[0050] 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.
[0051] “Percent (%) amino acid sequence identity” and “homology” with respect to a polypeptide 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 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. For example, polypeptides having at least 70%, 85%, 90%, 95%, 98%or 99%identity to specific polypeptides described herein and preferably exhibiting substantially the same functions, as well as polynucleotide encoding such polypeptides, are contemplated.
[0052] 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. 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.
[0053] 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.
[0054] 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 PCT Publication No. WO 03 / 48731.
[0055] As used herein, the term “express” refers to transcription of a DNA to an RNA (e.g., mRNA) , or translation of a nucleic acid into a protein. Proteins may be expressed and remain intracellular, become a component of the cell surface membrane, or be secreted into extracellular matrix or medium.
[0056] An “isolated nucleic acid” is a nucleic acid, for example, an RNA, DNA, or a mixed 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 acids encoding an IL-15 construct or chimeric receptor 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 an IL-15 construct or chimeric receptor 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.
[0057] 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) .
[0058] Nucleic acid is “operably linked” when it is placed into a functional relationship with another nucleic acid sequence. For example, DNA for a presequence or secretory leader is operably linked to DNA for a polypeptide if it is expressed as a preprotein that participates in the secretion of the polypeptide; a promoter or enhancer is operably linked to a coding sequence if it affects the transcription of the sequence; or a ribosome binding site is operably linked to a coding sequence if it is positioned so as to facilitate translation. Generally, “operably linked” means that the DNA sequences being linked are contiguous, and, in the case of a secretory leader, contiguous and in reading frame. However, enhancers do not have to be contiguous. Linking is accomplished by ligation at convenient restriction sites. If such sites do not exist, the synthetic oligonucleotide adaptors or linkers are used in accordance with conventional practice.
[0059] The term “vector, ” as used herein, refers to a nucleic acid molecule capable of propagating another nucleic acid to which it is linked. The term includes the vector as a self-replicating nucleic acid structure as well as the vector incorporated into the genome of a host cell into which it has been introduced. Certain vectors are capable of directing the expression of nucleic acids to which they are operatively linked. Such vectors are referred to herein as “expression vectors. ”
[0060] 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 a cell, which has been transfected, transformed or transduced with exogenous nucleic acid.
[0061] 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.
[0062] As used herein, the expressions “cell” , “cell line” , and “cell culture” are used interchangeably and all such designations include progeny. Thus, the words “transfectants” and “transfected cells” include the primary subject cell and cultures derived there from without regard for the number of transfers. It is also understood that not all progeny may be precisely identical in DNA content, due to deliberate or inadvertent mutations. Variant progeny that has the same function or biological activity as screened for in the originally transformed cell are included.
[0063] “Primary cells"refer to cells taken directly from living tissue (i.e. biopsy material) and established for growth in vitro, which have undergone very few population doublings and are therefore more representative of the main functional components and characteristics of tissues from which they are derived from, in comparison to continuous tumorigenic or artificially immortalized cell lines.
[0064] The term “in vivo” refers to inside the body of the organism from which the cell is obtained. “Ex vivo” or “in vitro” means outside the body of the organism from which the cell is obtained.
[0065] As used herein, the term “autologous” refers to any material derived from the same individual to whom it is later to be re-introduced into the individual.
[0066] “Allogeneic” refers to a graft derived from a different individual of the same species.
[0067] The term “recombinant” refers to a biomolecule, e.g., a gene or protein, that (1) has been removed from its naturally occurring environment, (2) is not associated with all or a portion of a polynucleotide in which the gene is found in nature, (3) is operatively linked to a polynucleotide which it is not linked to in nature, or (4) does not occur in nature. The term “recombinant” can be used in reference to cloned DNA isolates, chemically synthesized polynucleotide analogs, or polynucleotide analogs that are biologically synthesized by heterologous systems, as well as proteins and / or mRNAs encoded by such nucleic acids.
[0068] As used herein, the term “derived from” when made in reference to a domain or protein described herein refers to a domain or protein that is obtained from the relevant domain or protein with or without additional modifications (e.g., by recombinant expression or de novo synthesis) . The term encompasses domains with naturally occurring sequences, and domains with sequences carrying mutations. A domain derived from a particular protein can have an amino acid sequence that is at least about any of 60%, 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99%, or 100%identical to the relevant domain of the particular protein from which it is derived. A domain derived from a particular protein can be from a natural or a synthetic source. For example, a transmembrane domain derived from DAP12 can have a sequence that is identical to the transmembrane domain of DAP12, or having at least about 60%, 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%or 99%sequence identity to the transmembrane domain of DAP12.
[0069] The term “tolerogenic factor” as used herein include immunosuppressive factors or immune-regulatory factors that modulate or affect the ability of a cell to be recognized by the immune system of a host or recipient subject upon administration, transplantation, or engraftment. Typically, a tolerogenic factor is a factor that induces immunological tolerance to an engineered cell, such as engineered primary cell, so that the engineered cell is not targeted, such as rejected, by the host immune system of a recipient. Hence, a tolerogenic factor may be a hypoimmunity factor. Examples of tolerogenic factors include immune cell inhibitory receptors (e.g. CD47) , proteins that engage immune cell inhibitory receptors, checkpoint inhibitors and other molecules that reduce innate or adaptive immune recognition. Tolerogenic factors may induce immunological tolerance, such as achieving one or more of the following effects: (i) increasing (e.g., increasing at least about any of 10%, 20%, 50%, 70%, 90%, 1-fold, 2-fold, 5-fold, or more) the success rate of transplantation or engraft; (ii) increasing persistence of the grafted cells (e.g., any of the engineered cells described herein) ; (iii) reducing (e.g., reducing at least about any of 10%, 20%, 50%, 70%, 90%, 95%, or 100%) immune clearance of the grafted cells (e.g., any of the engineered cells described herein) ; and (iv) reducing (e.g., reducing at least about any of 10%, 20%, 50%, 70%, 90%, 95%, or 100%) the level of host cell-mediated rejection.
[0070] As used herein, the term “overexpress” generally refers to any amount greater than an expression level exhibited by a reference standard. The terms “overexpress, ” “overexpressing, ” “overexpressed” and “overexpression” in the present disclosure refer an expression of a gene product or a polypeptide at a level greater than the expression of the same gene product or polypeptide prior to a genetic alteration of the host cell or in a comparable host which has not been genetically altered at defined conditions. If a host cell does not comprise a given gene product, it is possible to introduce the gene product into the host cell for expression; in this case, any detectable expression is encompassed by the term “overexpression. ”
[0071] As used herein, “treatment” or “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 the disease. The methods of the present application contemplate any one or more of these aspects of treatment.
[0072] The term “prevent, ” and similar words such as “prevented, ” “preventing” etc., indicate an approach for preventing, inhibiting, or reducing the likelihood of the recurrence of, a disease or condition, e.g., cancer. It also refers to delaying the recurrence of a disease or condition or delaying the recurrence of the symptoms of a disease or condition. As used herein, “prevention” and similar words also includes reducing the intensity, effect, symptoms and / or burden of a disease or condition prior to recurrence of the disease or condition.
[0073] As used herein, “delaying” the development of a disease 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. A method that “delays” development of a disease 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. Disease 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 disease progression that may be initially undetectable and includes occurrence, recurrence, and onset.
[0074] The term “effective amount” used herein refers to an amount of an agent sufficient to treat a specified disorder, condition or disease such as ameliorate, palliate, lessen, and / or delay one or more of its symptoms. 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. In some embodiments, an effective amount is an amount sufficient to delay development. In some embodiments, an effective amount is an amount sufficient to prevent or delay recurrence. An effective amount can be administered in one or more administrations. 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.
[0075] As used herein, an “individual” or a “subject” refers to a mammal, including, but not limited to, human, bovine, horse, donkey, sheep, goat, feline, canine, rodent, or primate. In some embodiments, the individual is a human.
[0076] It is understood that embodiments of the present application described herein include “consisting” and / or “consisting essentially of” embodiments.
[0077] Reference to “about” a value or parameter herein includes (and describes) variations (e.g., within ± 10%) that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X” .
[0078] As used herein, reference to “not” a value or parameter generally means and describes “other than” a value or parameter. For example, the method is not used to treat cancer of type X means the method is used to treat cancer of types other than X.
[0079] The term “about X-Y” used herein has the same meaning as “about X to about Y. ”
[0080] As used herein and in the appended claims, the singular forms “a” , “an” , and “the” include plural referents unless the context clearly dictates otherwise.
[0081] The term “and / or” as used herein a phrase such as “A and / or B” is intended to include both A and B; A or B; A (alone) ; and B (alone) . Likewise, the term “and / or” as used herein 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 Cells Expressing an IL-15 Construct
[0082] In one aspect, there is provided an engineered cell (e.g., an engineered immune cell such as a CAR-expressing immune cell) comprising an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12 (e.g., a DAP12 transmembrane domain comprising SEQ ID NO: 18, or functional variants thereof) . In some embodiments, there is provided an engineered cell (e.g., an engineered immune cell such as a CAR-expressing immune cell) expressing any of the IL-15 constructs described hereinafter. In some embodiments, the engineered cell further expresses a chimeric receptor (e.g., CAR, such as an anti-BCMA CAR) . In some embodiments, the IL-15 moiety is a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the IL-15 moiety is a functional fragment or functional variant of a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the IL-15 moiety comprises the amino acid sequence of any of SEQ ID NOs: 48 and 50-67. In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR, such as anti-BCMA CAR) is not derived from DAP12 or cannot interact with the transmembrane domain of the IL-15 construct. In some embodiments, the engineered cell is an engineered stem cell such as embryonic stem cells (ESC) , pluripotent stem cell (PSC) , induced pluripotent stem cells (iPSCs) , or hematopoietic stems cells (HSCs) . In some embodiments, the engineered cell is a cell (e.g., immune cell) differentiated from an engineered stem cell. In some embodiments, the engineered cell is an engineered immune cell. In some embodiments, the engineered immune cell is selected from the group consisting of T cell, NK cell, NKT cell, B cell, macrophage, monocyte, cytokine-induced killer (CIK) cell, and peripheral blood mononuclear cell (PBMC) . In some embodiments, the engineered immune cell is an NK cell, such as CAR-NK cell. In some embodiments, the NK cell is further modified to reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules. In some embodiments, the NK cell is further modified to increase the expression and / or function of, such as overexpress, one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9.
[0083] In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12, wherein the IL-15 moiety is a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the transmembrane domain is derived from a wildtype human DAP12 polypeptide comprising the amino acid sequence of SEQ ID NO: 17. In some embodiments, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 18. In some embodiments, the transmembrane domain of the IL-15 construct is a functional variant of the transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18. In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12, wherein the transmembrane domain derived from DAP12 comprises the amino acid sequence of SEQ ID NO: 18. In some embodiments, the IL-15 construct further comprises a hinge domain between the IL-15 moiety and the transmembrane domain derived from DAP12. In some embodiments, the hinge domain is derived from CD8 (e.g., a CD8 hinge comprising the amino acid sequence of SEQ ID NO: 21) . In some embodiments, the IL-15 construct comprises from N’ to C’: an IL-15 moiety (e.g., a mature wildtype human IL-15 polypeptide, such as SEQ ID NO: 1) , a hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., a DAP12 transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18, or functional variants thereof) . In some embodiments, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 32. In some embodiments, the IL-15 construct does not comprise a functional intracellular signaling domain. In some embodiments, the IL-15 construct does not comprise an intracellular domain (e.g., intracellular signaling domain) , such as not comprising any cytoplasmic sequence. In alternate embodiments, the IL-15 construct comprises an intracellular domain (e.g., intracellular signaling domain) . In some embodiments, the intracellular domain comprises a co-stimulatory intracellular signaling domain. In some embodiments, the IL-15 construct comprises a non-functional primary intracellular signaling domain (e.g., ITAM-mutated to abolish signaling function) . In some embodiments, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 29 or 46. In some embodiments, the IL-15 construct further comprises a signal peptide at the N-terminus, such as a signal peptide derived from DAP12 (e.g., a DAP12 signal peptide comprising the amino acid sequence of SEQ ID NO: 16) . In some embodiments, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 2 or 45. In some embodiments, the engineered cell is an engineered immune cell selected from the group consisting of T cell, NK cell, NKT cell, B cell, macrophage, monocyte, CIK cell, and PBMC. In some embodiments, the engineered cell is an engineered stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., immune cell) differentiated therefrom. In some embodiments, the engineered immune cell is an NK cell, such as CAR-NK cell.
[0084] In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising: (i) an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., human mature IL-15 polypeptide comprising SEQ ID NO: 1) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., a DAP12 transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18, or functional variants thereof) ; and (ii) a chimeric receptor. In some embodiments, the IL-15 construct further comprises a signal peptide at the N-terminus (e.g., a DAP12 signal peptide comprising the amino acid sequence of SEQ ID NO: 16) . In some embodiments, the chimeric receptor is selected from the group consisting of an engineered T cell receptor (TCR) , a chimeric antigen receptor (CAR) , a chimeric TCR (cTCR) , a T cell antigen coupler (TAC) , and a TAC-like engineered receptor. In some embodiments, the chimeric receptor is a CAR comprising an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA, pathogen-specific antigen, or autoimmune or inflammatory disease-associated target antigen) , a transmembrane domain, and a primary intracellular signaling domain. Hence in some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising: (i) an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1, or a functional variant thereof) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., a DAP12 transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18, or functional variants thereof) ; and (ii) a CAR comprising an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA) , a transmembrane domain, and a primary intracellular signaling domain. In some embodiments, the IL-15 construct comprises the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46. In some embodiments, the extracellular antigen binding domain comprises one or more antigen-binding moieties (e.g., sdAb or scFv) specifically recognizing one or more epitopes of one or more target antigens (e.g., BCMA) . In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., sdAb or scFv) connected in tandem. In some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen, such as BCMA) ; (c) an optional hinge domain (e.g., derived from CD8α) ; (d) a transmembrane domain (e.g., derived from CD8α) ; and (e) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb specifically recognizing a first epitope (e.g., a first tumor epitope, such as BCMA) ; (c) an optional linker (e.g., GG or a GS linker comprising the amino acid sequence of SEQ ID NO: 13) ; (d) a second sdAb specifically recognizing a second epitope (e.g., a second tumor epitope, such as BCMA) ; (e) an optional hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; and (g) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the CAR further comprises a costimulatory intracellular signaling domain (e.g., derived from 4-1BB) , which can be situated between the transmembrane domain and the primary intracellular signaling domain, or at the C-terminus of the primary intracellular signaling domain. In some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb specifically recognizing a first epitope (e.g., a first tumor epitope, such as BCMA) ; (c) an optional linker (e.g., GG or a GS linker comprising the amino acid sequence of SEQ ID NO: 13) ; (d) a second sdAb specifically recognizing a second epitope (e.g., a second tumor epitope, such as BCMA) ; (e) a hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; (g) a costimulatory intracellular signaling domain (e.g., derived from 4-1BB) ; and (h) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR) is not derived from DAP12. In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR) (e.g., derived from or not derived from DAP12) cannot interact with the transmembrane domain of the IL-15 construct. In some embodiments, the first sdAb and the second sdAb are both anti-BCMA sdAbs. In some embodiments, the first or second anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 34, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 35, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 36. In some embodiments, the second or first anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 38, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 39, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 40. In some embodiments, the first and / or second anti-BCMA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 33 or 37. In some embodiments, the CAR comprises a signal peptide (e.g., SEQ ID NO: 19) at the N-terminus. In some embodiments, the CAR is an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising: (i) an IL-15 construct comprising the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46; and (ii) an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, the engineered cell is an engineered immune cell selected from the group consisting of T cell, NK cell, NKT cell, B cell, macrophage, monocyte, CIK cell, and PBMC. In some embodiments, the engineered immune cell is an NK cell, such as CAR-NK cell. In some embodiments, the engineered cell is an engineered stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., immune cell) differentiated therefrom.
[0085] In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising: (i) a first nucleic acid encoding an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., human mature IL-15 polypeptide comprising SEQ ID NO: 1) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., a DAP12 transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18, or functional variants thereof) ; and (ii) a second nucleic acid encoding a chimeric receptor (e.g., CAR, cTCR, engineered TCR, TAC, or TAC-like engineered receptor) . In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising (i) a first nucleic acid encoding an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1, or a functional variant thereof) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., a DAP12 transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18, or a functional variant thereof) ; and (ii) a second nucleic acid encoding a CAR, wherein the CAR comprises from N’ to C’: (a) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA) , (b) an optional hinge domain (e.g., derived from CD8α) , (c) a transmembrane domain (e.g., derived from CD8α) , and (d) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., sdAb or scFv) connected in tandem. In some embodiments, the CAR further comprises a costimulatory intracellular signaling domain (e.g., derived from 4-1BB) , which can be situated between the transmembrane domain and the primary intracellular signaling domain, or at the C-terminus of the primary intracellular signaling domain. In some embodiments, the CAR comprises from N’ to C’: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb specifically recognizing a first epitope (e.g., a first tumor epitope, such as BCMA) ; (c) an optional linker (e.g., GG or a GS linker comprising the amino acid sequence of SEQ ID NO: 13) ; (d) a second sdAb specifically recognizing a second epitope (e.g., a second tumor epitope, such as BCMA) ; (e) a hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; (g) a costimulatory intracellular signaling domain (e.g., derived from 4-1BB) ; and (h) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR) is not derived from DAP12. In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR) (e.g., derived from or not derived from DAP12) cannot interact with the transmembrane domain of the IL-15 construct. In some embodiments, the IL-15 construct comprises the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46. In some embodiments, the first sdAb and the second sdAb are both anti-BCMA sdAbs. In some embodiments, the first or second anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 34, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 35, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 36. In some embodiments, the second or first anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 38, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 39, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 40. In some embodiments, the first and / or second anti-BCMA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 33 or 37. In some embodiments, the CAR is an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. The first nucleic acid and the second nucleic acids can be on a single vector or on different vectors. In some embodiments, the vector is a viral vector, such as a lentiviral vector or retroviral vector. In some embodiments, the first nucleic acid and the second nucleic acid are on a single vector. In some embodiments, the first nucleic acid and the second nucleic acid are operably linked to different promoters on the single vector. In some embodiments, the first nucleic acid and the second nucleic acid are operably linked to a single promoter on the single vector. The first nucleic acid can be at the 5’ or the 3’ of the second nucleic acid on the single vector. In some embodiments, the first nucleic acid and the second nucleic acid are connected by a linking sequence, such as IRES, or a linking sequence encoding a 2A self-cleaving peptide (e.g., P2A or T2A) . In some embodiments, the engineered cell is an engineered immune cell selected from the group consisting of T cell, NK cell, NKT cell, B cell, macrophage, monocyte, CIK cell, and PBMC. In some embodiments, the engineered immune cell is an NK cell, such as CAR-NK cell. In some embodiments, the engineered cell is an engineered stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., immune cell) differentiated therefrom.
[0086] In some embodiments, the first nucleic acid encoding the IL-15 construct and the second nucleic acid encoding the chimeric receptor (e.g., CAR) are on a single vector, and the first nucleic acid and the second nucleic acid are operably linked to a single promoter. In some embodiments, the first nucleic acid and the second nucleic acid are connected by a linking sequence, such as IRES, or a linking sequence encoding a 2A self-cleaving peptide (e.g., P2A or T2A) . The first nucleic acid can be at the 5’ or the 3’ of the second nucleic acid on the vector. Hence in some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising a vector (e.g., viral vector, such as retroviral vector) , wherein the vector comprises from 5’ to 3’: (i) a promoter (e.g., hEF1α promoter) ; (ii) a first nucleic acid encoding an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., human mature IL-15 polypeptide comprising SEQ ID NO: 1) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., human DAP12 transmembrane domain comprising SEQ ID NO: 18) ; (iii) a linking sequence (e.g., IRES, or a sequence encoding a 2A self-cleaving peptide such as P2A or T2A) ; and (iv) a second nucleic acid encoding a chimeric receptor (e.g., CAR, cTCR, engineered TCR, TAC, or TAC-like engineered receptor) . In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising a vector (e.g., viral vector, such as retroviral vector) , wherein the vector comprises from 5’ to 3’: (i) a promoter (e.g., hEF1α promoter) ; (ii) a second nucleic acid encoding a chimeric receptor (e.g., CAR, cTCR, engineered TCR, TAC, or TAC-like engineered receptor) ; (iii) a linking sequence (e.g., IRES, or a sequence encoding a 2A self-cleaving peptide such as P2A or T2A) ; and (iv) a first nucleic acid encoding an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., human mature IL-15 polypeptide comprising SEQ ID NO: 1) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., human DAP12 transmembrane domain comprising SEQ ID NO: 18) . In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising a vector (e.g., viral vector, such as retroviral vector) , wherein the vector comprises from 5’ to 3’: (i) a promoter (e.g., hEF1α promoter) ; (ii) a second nucleic acid encoding a CAR, wherein the CAR comprises from N’ to C’: (a) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA) , (b) an optional hinge domain (e.g., derived from CD8α) , (c) a transmembrane domain (e.g., derived from CD8α) , and (d) a primary intracellular signaling domain (e.g., derived from CD3ζ) ; (iii) a linking sequence (e.g., IRES, or a sequence encoding a 2A self-cleaving peptide such as P2A or T2A) ; and (iv) a first nucleic acid encoding an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety (e.g., human mature IL-15 polypeptide comprising SEQ ID NO: 1) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., human DAP12 transmembrane domain comprising SEQ ID NO: 18) . In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., sdAb or scFv) connected in tandem. In some embodiments, the CAR further comprises a costimulatory intracellular signaling domain (e.g., derived from 4-1BB) , which can be situated between the transmembrane domain and the primary intracellular signaling domain, or at the C-terminus of the primary intracellular signaling domain. In some embodiments, the CAR comprises from N’ to C’: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb specifically recognizing a first epitope (e.g., a first tumor epitope, such as BCMA) ; (c) an optional linker (e.g., GG or SEQ ID NO: 13) ; (d) a second sdAb specifically recognizing a second epitope (e.g., a second tumor epitope, such as BCMA) ; (e) a hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; (g) a costimulatory intracellular signaling domain (e.g., derived from 4-1BB) ; and (h) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR) is not derived from DAP12. In some embodiments, the transmembrane domain of the chimeric receptor (e.g., CAR) (e.g., derived from or not derived from DAP12) cannot interact with the transmembrane domain of the IL-15 construct. In some embodiments, the IL-15 construct comprising the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46. In some embodiments, the first sdAb and the second sdAb are both anti-BCMA sdAbs. In some embodiments, the first or second anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 34, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 35, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 36. In some embodiments, the second or first anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 38, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 39, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 40. In some embodiments, the first and / or second anti-BCMA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 33 or 37. In some embodiments, the CAR is an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, there is provided an engineered cell (e.g., engineered immune cell) comprising a vector (e.g., viral vector, such as retroviral vector) , wherein the vector comprises from 5’ to 3’: (i) a promoter (e.g., hEF1α promoter) ; (ii) a second nucleic acid encoding an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31; (iii) a linking sequence (e.g., IRES, or a sequence encoding a 2A self-cleaving peptide such as P2A or T2A) ; and (iv) a first nucleic acid encoding an IL-15 construct comprising the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46. In some embodiments, the vector (e.g., viral vector, such as retroviral vector) encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 8 or 47. In some embodiments, the engineered cell is an engineered immune cell selected from the group consisting of T cell, NK cell, NKT cell, B cell, macrophage, monocyte, CIK cell, and PBMC. In some embodiments, the engineered cell is an engineered stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., immune cell) differentiated therefrom. In some embodiments, the engineered immune cell is an NK cell, such as CAR-NK cell. A. IL-15 Constructs
[0087] The engineered cells (e.g., engineered immune cells) described herein comprise a nucleic acid (e.g., a first nucleic acid) encoding an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12. The IL-15 construct in some embodiments stimulates the expansion, function (e.g., cytotoxicity) , proliferation, and / or persistence of the immune cells expressing it, such as NK cells. The present application in one aspect provides any of the IL-15 constructs described herein.
[0088] Hence in some embodiments, there is provided an IL-15 construct (e.g., isolated IL-15 construct) comprising an IL-15 moiety and a transmembrane domain derived from DAP12. In some embodiments, the IL-15 construct comprises from N’ to C’: an IL-15 moiety (e.g., a mature wildtype human IL-15 polypeptide, such as SEQ ID NO: 1) , and a transmembrane domain derived from DAP12 (e.g., SEQ ID NO: 18) . In some embodiments, the IL-15 construct comprises from N’ to C’: an IL-15 moiety (e.g., a mature wildtype human IL-15 polypeptide, such as SEQ ID NO: 1) , a hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., SEQ ID NO: 18) . In some embodiments, the IL-15 construct comprises from N’ to C’: a signal peptide (any of SEQ ID NOs: 16, 19, 25, and 30, such as SEQ ID NO: 16) , an IL-15 moiety (e.g., a mature wildtype human IL-15 polypeptide, such as SEQ ID NO: 1) , a hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., SEQ ID NO: 18) .
[0089] In some embodiments, there is provided an IL-15 construct comprising the amino acid sequence of SEQ ID NO: 29 or 46. In some embodiments, the IL-15 construct further comprises a signal peptide (e.g., derived from DAP12, such as SEQ ID NO: 16) at the N-terminus. In some embodiments, there is provided an IL-15 construct comprising the amino acid sequence of SEQ ID NO: 2 or 45. IL-15 moieties
[0090] Interleukin-15 (IL-15) is a cytokine known to play a role in the development of inflammatory and protective immune responses, for example in response to microbial invaders and / or parasite invaders. IL-15 may modulate immune cell responses, including activation and / or proliferation of the immune cells. Without being bound by theory, IL-15 is known to stimulate the proliferation of natural killer (NK) cells, T-cells, and / or B-cells. In particular, IL-15 has been described as promoting NK cell differentiation, proliferation, activation, and / or homeostasis (see, for example, Huntington et al., J. Exp. Med., 2009, 206 (1) : 25-34; Carson et al., J. Exp. Med., 1994, 180 (4) : 139501403; and Ranson et al., Blood, 2003, 101 (12) : 4887-4893, all of which are herein incorporated by reference in their entireties) . In other instances, IL-15 has been shown to stimulate cytotoxic T lymphocyte (CD8+ T cell) proliferation and cytotoxicity (Waldmann, 2006, Nat. Rev. Immunol., 6: 595-601, which is herein incorporated by reference in its entirety) .
[0091] In some embodiments, the IL-15 moieties described herein can bind to a trimeric IL-15R (IL-15 receptor) complex. The IL-15 receptor consists of three polypeptides, the type-specific IL-15 ( "IL-15Rα" ) , the IL-2 / IL-15Rβ ( "IL-15Rβ" ) , and the common gamma chain ( "γc" ) shared by various cytokines. In some embodiments, the IL-15 moiety is capable of binding the alpha-chain ( "IL-15Rα" ) , the common beta-chain ( "IL-15Rβ" ) , and / or the common gamma-chain ( "IL-15Rγc" ) .
[0092] Without being bound by theory, while wildtype IL-15 is not membrane-bound, IL-15 is most commonly expressed through its high affinity binding to IL-15Rα receptors on the surface of IL-15-producing cells, and is more rarely secreted in its soluble form (as described in, for example, Musso et al., 1999, Blood, 93: 3531-3539, which is herein incorporated by reference in its entirety) . IL-15 is a 162 amino acid-long, four-helix bundle with an “up-up-down-down” topology like many short-chain helical cytokines. The four A, B, C, and D helices of IL-15 are connected through AB loops and CD loops, respectively, wherein the CD loop comprises two disulfide bridges. The IL-15-IL-15Rα complex, which presents IL-15 in trans to neighboring cells, includes the carboxy-terminal half of the IL-15Rα sushi domain for perching of IL-15. IL-15 binding to IL-15Rα occurs at the interface core formed around the C’D-loop bulge of the IL-15Rα receptor (involving Arg35, Ala37 and Gly38) , which fitted into a shallow, concave surface composed of the AB (Thr24, Tyr26) and CD loops (Glu89 and, via water, Glu93) , and the B helix (Glu46 and Gln48) of IL-15. More details on the structure of IL-15 alone and in complex with IL-15Rα can be found, for example, in Chirifu et al., 2007, Nature Immunology, 8: 9: 1001-1007, which herein incorporated by reference in its entirety.
[0093] IL-15 heterodimerizes IL-2Rβ and the common IL-2Rγ receptor subunits expressed on the surface of target cells for activation of said cells. Binding of IL-15 to IL-2R subunits transduces downstream activation of the Jak-STAT, PI3K-Akt, and Ras-MAPK pathways in order to stimulate cell-specific responses to IL-15 signaling (Johnston et al., PNAS, 1995, 92: 8705-8709, which is herein incorporated by reference in its entirety) . IL-15 within the IL-15-IL-15Rα complex may possess restricted conformational freedom of its AB and CD loops, which may decrease energetic barriers to binding and thereby increase the affinity of IL-15 for IL-2Rβ in trans. In fact, IL-15 within the IL-15-IL-15Rα complex has been shown to bind to IL-2Rβ with a KD of 3 nM, an affinity increase of approximately 150-fold over soluble IL-15. More details on the binding of IL-15 to IL-2Rβ can be found, for instance, in Ring et al., Nature Immunology, 2012, 13 (12) : 1187-1195, which is herein incorporated by reference in its entirety.
[0094] In some embodiments, the IL-15 moiety comprises (or consists essentially of, or consists of) an IL-15 polypeptide. In some embodiments, the IL-15 polypeptide is a full-length IL-15 molecule. In some embodiments, the IL-15 polypeptide comprises a functional fragment of an IL-15 molecule. In some embodiments, the IL-15 polypeptide is a human IL-15 polypeptide.
[0095] The IL-15 moiety can be derived from an IL-15 polypeptide of any source, including but not limited to, human, bovine, horse, donkey, sheep, goat, feline, canine, rodent (e.g., mouse, rat, hamster, rabbit, chinchilla) , or primate (e.g., monkey, chimpanzee, gorilla) . In some embodiments, the IL-15 moiety is derived from a human IL-15 polypeptide. The IL-15 moiety may or may not comprise a propeptide sequence (e.g., SEQ ID NO: 28) . The IL-15 moiety may or may not comprise a signal peptide (e.g., SEQ ID NO: 25) .
[0096] In some embodiments, the IL-15 moiety is derived from a mature wildtype human IL-15 polypeptide, such as a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments the IL-15 moiety has an amino acid sequence that has at least about 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or 99% (or more) sequence identity to SEQ ID NO: 1. In some embodiments, the IL-15 moiety is a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1. In some embodiments, the IL-15 moiety is a functional fragment of a wildtype human IL-15 polypeptide (e.g., mature wildtype human IL-15 polypeptide) . In some embodiments, the functional fragment of a wildtype human IL-15 polypeptide comprises at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or more amino acid length of SEQ ID NO: 1.
[0097] In some embodiments, the IL-15 moiety is a functional variant of a mature wildtype human IL-15 polypeptide. In some embodiments, the functional variant of mature wildtype human IL-15 polypeptide can contain no more than any of 50, 40, 30, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conserved substitution) relative to SEQ ID NO: 1. In some embodiments, the IL-15 moiety is a variant IL-15 described in US20240209050, the content of which is incorporated herein by reference in its entirety. In some embodiments, the IL-15 polypeptide comprises an amino acid substitution at one or more positions selected from the group consisting of 3, 8, 23, 25, 26, 58, 61, 62, 72, and 89, wherein the amino acid position is reference to SEQ ID NO: 1. Exemplary variant IL-15 polypeptide sequences and their corresponding mutations are listed in Table B below. In some embodiments, the IL-15 moiety comprises the amino acid sequence of any of SEQ ID NOs: 48 and 50-67. Table B. Exemplary variant IL-15 polypeptides
[0098] As used herein, the term “functional fragment” or “functional variant” of an IL-15 polypeptide refers to a fragment or a variant (e.g., mutant) of a wildtype IL-15 polypeptide (e.g., wildtype human IL-15) that can achieve at least about 10% (e.g., at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100%, 110%, 120%, 150%, 200%, 300%, or more) functional activity of the wildtype IL-15 polypeptide. In some embodiments, the functional activity comprises binding to an IL-15 receptor (one, two, or all of IL-15Rα, IL-15Rβ, and γc) , which can be as measured by, for example, by a radioimmunoassay (RIA) , ELISA, or surface plasmon resonance (SPR) . In some embodiments, the functional activity comprises activating IL-15 signal pathway (e.g., one or more of JAK-STAT, PI3K-Akt, and Ras-MAPK signaling pathways; also see Johnston et al., PNAS, 1995, 92: 8705-8709) , which can be as measured, for example, by phosphorylation of components in the signaling pathway, gene expression profiles, and / or reporter assays. In some embodiments, the functional activity comprising stimulating target cell (e.g., immune cell such as NK cell or T cell) function (e.g., proliferation, expansion, persistence, inducing cytokine secretion, and / or cytotoxicity) , which can be measured, for example, by target cell killing assays and FACS. Also see exemplary functional tests in Examples 2-5.
[0099] In some embodiments, the IL-15 moiety induces inflammatory cytokine secretion by the modified immune cell (e.g., a CAR-NK cell) . Exemplary inflammatory cytokines include, but are not limited to, e.g., IFN-γ, TNF-α, and GM-CSF. In some embodiments, the functional capacity of the IL-15 moiety to induce cytokine release is measured by in serum immunoassays, such as enzyme-linked immunosorbent assay (ELISA) , chemiluminescent immunoassays (CIA) , or flow cytometry. In some embodiments, the inflammatory cytokine secretion levels are measured in a cell-based assay. In some embodiments, the inflammatory cytokine secretion levels are measured in vivo.
[0100] In some embodiments, the functional variant of IL-15 polypeptide (e.g., human IL-15) induces less (e.g., at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or more less) inflammatory cytokine secretion by an immune cell (e.g., NK cell, T cell) , compared to a wildtype IL-15 polypeptide. Exemplary inflammatory cytokines include, but are not limited to, e.g., IFN-γ, TNF-α, and GM-CSF. Transmembrane domain derived from DAP12
[0101] DNAX-Activation Protein 12 (DAP12) is a transmembrane tyrosine-kinase binding adaptor protein which non-covalently associates with activating receptors found on the surface of a variety of immune cells. DAP12 is also known as TYRO protein tyrosine kinase-binding protein or TYROBP. Interaction of DAP12 has been shown to mediate signaling and cell activation following association with several cell surface receptors. Specifically, DAP12 is a disulfide-linked homodimer that associates with several activating receptors expressed on the surface of NK cells through the acidic aspartic acid (D) residue within its transmembrane domain, including but not limited to CD94 / NKG2C or NKG2E, KIR2DS, and NKp44. These receptors share the common feature of comprising a basic amino acid residue (e.g., lysine (K) or arginine (R) ) within their transmembrane domain to facilitate the non-covalent interaction with the acidic residue of the DAP12 transmembrane domain. Signaling to any of these receptors, for example, is transduced through their interaction with DAP12, which bears an immunoreceptor tyrosine-based activation motif (ITAM) in its cytoplasmic domain. Specifically, ligand binding to these receptors results in phosphorylation of ITAM of DAP12, such as performed through Src family kinases. Phosphorylated ITAM of DAP12 therein serves as a docking site for the SH2 domains of downstream kinases such as ZAP-70 and Syk kinases, which further transduce the signal to control NK cell gene activation and functionality. More information on DAP12-mediated signal transduction is disclosed, for instance, in Lanier and Bakker, Immunology Today, 2000, 21 (12) : 611-614; McVicar et al., The Journal of Biological Chemistry, 1998, 273 (49) : 32934-32942; Campbell et al., The International Journal of Biochemistry &Cell Biology, 1999, 31 (6) : 621-636, and Turnbull &Colonna, Nature Reviews Immunology, 2007, 7: 155-161; all of which are herein incorporated by reference in their entireties.
[0102] DAP12 modulates signal transduction in NK cells and, by extension, can modulate NK cell function itself. For example, increased NK cell proliferation following viral infection in mouse models has been shown to depend in part on DAP12-mediated signal transduction following binding of the murine NK cell receptor Ly49H to its virally encoded ligand, m157 (see, e.g., French et al., The Journal of Immunology, 2006, 177 (8) : 4981-4990, which is herein incorporated by reference in its entirety) . As another example, human NK cells engineered with chimeric antigen receptors (CAR) comprising an anti-PSCA single-chain AB fragment scFv (AM1) fused to a DAP12 polypeptide (including DAP12 ITAM) demonstrated improved cytotoxicity against PSCA-positive tumor cells when compared with CAR comprising a CD3ζ intracellular signaling domain. Improved cytotoxicity was showed to be due at least in part to phosphorylation of DAP12-associated ZAP-70 kinase and subsequent release of IFNγ following recognition of PSCA-positive tumor cells, demonstrating the modulating effect of DAP12 on NK cell function (Topfer et al., The Journal of Immunology, 2015, 194 (7) : 3201-3212, which is herein incorporated by reference in its entirety) .
[0103] In some embodiments, the IL-15 construct comprises a transmembrane domain derived from DAP12 (e.g., human DAP12) . In some embodiments, the transmembrane domain is derived from a wildtype human DAP12 polypeptide, such as comprising the amino acid sequence of SEQ ID NO: 17. In some embodiments, the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 18. In some embodiments, the transmembrane domain comprises an amino acid sequence that has at least about 70% (e.g., at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 18.
[0104] In some embodiments, the transmembrane domain derived from DAP12 is a functional variant of the transmembrane domain comprising the amino acid sequence of SEQ ID NO: 18. In some embodiments, the functional variant of the transmembrane domain derived from DAP12 can contain no more than any of 20, 18, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conserved substitution) relative to SEQ ID NO: 18. A “functional variant” of a DAP12 transmembrane domain described herein refers to a variant (e.g., mutant) of a wildtype DAP12 (e.g., wildtype human DAP12) transmembrane domain that can achieve at least about 10% (e.g., at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 100%, 110%, 120%, 150%, 200%, 300%, or more) functional activity of the wildtype DAP12 transmembrane domain. The functional activity can comprise one or both of: (i) anchoring the IL-15 construct to the cell membrane; and (ii) transducing cellular signals via interacting with and / or recruiting other transmembrane molecules (e.g., DAP12-associated receptors such as KIR gene family, CD94 / NKG2C or NKG2E, and NKp44 on NK cell membrane) . The functional activity can be measured by, for example, FACS, phosphorylation of components in the signaling pathway, gene expression profiles, and / or reporter assays. Hinge domains
[0105] The IL-15 construct of the present disclosure may comprise a hinge domain that is located between the IL-15 moiety and the transmembrane domain derived from DAP12. 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 IL-15 moiety relative to the transmembrane domain derived from DAP12 can be used. The hinge domain can be a peptide linker, or a hinge domain (or fragment thereof) of antibodies, such as an IgG, IgA, IgM, IgE, or IgD. Any of the peptide linkers described in the “Peptide Linker” subsection below can be used herein as a hinge domain. The hinge domain can be a hinge domain of a naturally occurring protein (e.g., derived from CD8α) , or a non-naturally occurring peptide. In some embodiments, the hinge domain of the IL-15 construct is derived from CD8α (e.g., human CD8α) . In some embodiments, the hinge domain of the IL-15 construct is derived from CD28 (e.g., human CD28) . In some embodiments, the hinge domain of the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 21. In some embodiments, the hinge domain of the IL-15 construct comprises an amino acid sequence that has at least about 70% (such as at least about any of 75%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 21. IL-15 construct intracellular domains
[0106] In some embodiments, the IL-15 construct does not comprise any intracellular amino acid sequence or domain. In some embodiments, the IL-15 construct comprises an intracellular amino acid sequence (can be sequence of signaling domain or not signaling domain) . Without being bound by theory, an intracellular amino acid sequence can comprise cytoplasmic amino acid residues that are immediately C-terminal to a transmembrane domain of a transmembrane protein (e.g., the transmembrane domain of DAP12) . The intracellular domain amino acid sequence of the IL-15 construct can be derived from DAP12 or from another transmembrane protein. In some embodiments, the IL-15 construct comprises an intracellular co-stimulatory signaling domain. In some embodiments, the IL-15 construct does not comprise a DAP12 intracellular signaling domain. In some embodiments, the IL-15 construct does not comprise amino acids 62-113 or 64-113 of DAP12 comprising the amino acid sequence of SEQ ID NO: 17.
[0107] In some embodiments, the IL-15 construct comprises one or more (e.g., 10, 9, 8, 7, 6, 5, 4, 3, 2, or 1) intracellular amino acid residues that are immediately C-terminal to the transmembrane domain derived from DAP12 transmembrane, such as to increase the stability of the IL-15 construct on the cell membrane. For example, in some embodiments, the IL-15 construct comprises a transmembrane domain derived from DAP12 and intracellular amino acid residues (e.g., 1, 2, 3, 4, or 5 residues) derived from a DAP12 intracellular domain. In some embodiments, the transmembrane domain derived from DAP12 and the intracellular amino acid residues together comprise the amino acid sequence of SEQ ID NO: 32. In some embodiments, the transmembrane domain derived from DAP12 and the intracellular amino acid residues together comprise an amino acid sequence that has at least about 70% (e.g., at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 32. In some embodiments, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 32.
[0108] In some embodiments, the IL-15 construct does not comprise a functional intracellular signaling domain. For example, the IL-15 construct can comprise a non-functional primary intracellular signaling domain, or the IL-15 construct does not comprise an intracellular signaling domain. In some embodiments, the IL-15 construct may comprise a primary intracellular signaling domain with mutated ITAM (s) that abolishes the signal transduction function of the primary intracellular signaling domain (i.e., non-functional intracellular signaling domain) . In some embodiments, the IL-15 construct does not comprise a functional DAP12 intracellular signaling domain (e.g., an ITAM cytoplasmic domain) . In some embodiments, the IL-15 construct comprises a non-functional intracellular domain (e.g. a non-functional DAP12-derived primary intracellular signaling domain, or a cytoplasmic portion without signaling function) . In some embodiments, the IL-15 construct comprises an intracellular or cytoplasmic sequence (e.g., 1, 2, 3, 4, or 5 intracellular amino acid residues immediately C-terminal to the transmembrane domain derived from DAP12, such as to increase the stability and / or function of the IL-15 construct on the cell membrane) , but does not comprise any intracellular signaling domain (neither primary intracellular signaling domain nor co-stimulatory intracellular signaling domain) . In some embodiments, the IL-15 construct comprises a non-functional intracellular domain derived from DAP12 (e.g., a portion of DAP12 intracellular domain without signaling function) . Without being bound by theory, a non-functional intracellular domain can be any cytoplasmic domain of a transmembrane protein normally involved in signal transduction that has an altered, truncated, and / or mutated amino acid sequence that removes / abolishes said signal transduction functionality. For example, a non-functional DAP12 intracellular domain comprises an amino acid sequence wherein ITAM phosphorylation function has been reduced or removed entirely. In some embodiments, a non-functional DAP12 intracellular domain comprises a truncated DAP12 intracellular amino acid sequence. In some embodiments, the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 32, wherein the amino acid sequence comprises a non-functional DAP12 intracellular domain / sequence. In some embodiments, inclusion of a non-functional intracellular domain improves the stability and / or function of the IL-15 construct. IL-15 construct signal peptides
[0109] The IL-15 construct of the present disclosure may further comprise a signal peptide (also known as a signal sequence) at the N-terminus of the IL-15 moiety. 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 IL-15 construct to the secretory pathway of the cell and will allows for integration and anchoring of the IL-15 construct into the lipid bilayer of cell membrane. During or following translocation of the IL-15 construct to the cell membrane, the signal peptide may be cleaved. Signal peptides including signal sequences of naturally occurring proteins or synthetic, non-naturally occurring signal sequences, which are compatible for use in the IL-15 constructs 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, DAP12, IgE, and IgG1 heavy chain. In some embodiments, the signal peptide is derived from a CD8α propeptide, e.g., human CD8α. In some embodiments, the signal peptide is derived from a DAP12 propeptide, e.g., human DAP12. In some embodiments, the signal peptide is derived from IL-15 (e.g., human IL-15) . In some embodiments, the signal peptide is derived from IgE (e.g., human IgE) . In some embodiments, the signal peptide comprises the amino acid sequence of any of SEQ ID NOs: 16, 19, 25, and 30, such as SEQ ID NO: 16. B. Chimeric Receptors
[0110] The engineered cells (e.g., engineered immune cells) described herein may further express one or more chimeric receptors. In some embodiments, the chimeric receptor comprises i) an extracellular antigen binding domain specifically recognizing a target antigen, and ii) a transmembrane domain. In some embodiments, the chimeric receptor is a chimeric antigen receptor (CAR) , an engineered T cell receptor (TCR) , a chimeric TCR (cTCR) , a T cell antigen coupler (TAC) , or a TAC-like engineered receptor. In some embodiments, the chimeric receptor is a CAR (e.g., anti-BCMA CAR) .
[0111] In some embodiments, the chimeric receptor is encoded by a heterologous nucleic acid operably linked to a promoter (such as a constitutive promoter or an inducible promoter) . The engineered cells (e.g., engineered immune cells) thus in some embodiments comprise a second nucleic acid encoding a chimeric receptor. In some embodiments, the chimeric receptor is introduced to the engineered cell (e.g., engineered immune cell) by inserting proteins into the cell membrane while passing cells through a microfluidic system, such as CELL (see, for example, U.S. Patent Application Publication No. 20140287509) . The chimeric receptor may enhance the function of the engineered cells (e.g., engineered immune cells) , such as by targeting the engineered cells to target cells (e.g., cancer cell) , by transducing signals, and / or by enhancing cytotoxicity of the engineered cells.Chimeric Antigen Receptor (CAR)
[0112] In some embodiments, the chimeric receptor is a CAR, such as any CAR known in the art or described herein. In some embodiments, the CAR comprises i) an extracellular antigen binding domain specifically recognizing a target antigen, ii) a transmembrane domain, and iii) an intracellular signaling domain (e.g., a primary intracellular signaling domain, such as derived from CD3ζ) . In some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen, such as BCMA) ; (c) an optional hinge domain (e.g., derived from CD8α) ; (d) a transmembrane domain (e.g., derived from CD8α) ; (e) an optional co-stimulatory intracellular signaling domain (e.g., derived from 4-1BB) ; and (f) a primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen, such as BCMA) ; (c) an optional hinge domain (e.g., derived from CD8α) ; (d) a transmembrane domain (e.g., derived from CD8α) ; (e) a primary intracellular signaling domain (e.g., derived from CD3ζ) ; and (f) an optional co-stimulatory intracellular signaling domain (e.g., derived from 4-1BB) . In some embodiments, the transmembrane domain of the CAR is not derived from DAP12. In some embodiments, the transmembrane domain of the CAR is derived from CD8, such as comprising the amino acid sequence of SEQ ID NO: 22. In some embodiments, the hinge domain of the CAR is derived from CD8, such as comprising the amino acid sequence of SEQ ID NO: 21. In some embodiments, the primary intracellular signaling domain is derived from CD3ζ, such as comprising the amino acid sequence of SEQ ID NO: 24. In some embodiments, the costimulatory intracellular signaling domain is derived from 4-1BB, such as comprising the amino acid sequence of SEQ ID NO: 23. In some embodiments, the CAR is an anti-BMCA CAR.
[0113] In some embodiments, the extracellular antigen binding domain of the CAR comprise two or more sdAbs connected in tandem, specifically recognizing one or more epitopes of one or more target antigens (e.g., BCMA) . Hence, in some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb (e.g., SEQ ID NO: 33) specifically recognizing a first epitope (e.g., a first tumor epitope, such as BCMA) ; (c) an optional linker (e.g., any of GG and SEQ ID NOs: 12, 13, and 26) ; (d) a second sdAb (e.g., SEQ ID NO: 37) specifically recognizing a second epitope (e.g., a second tumor epitope, such as BCMA) ; (e) an optional hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; (g) an optional co-stimulatory intracellular signaling domain (e.g., derived from 4-1BB) ; and (h) an primary intracellular signaling domain (e.g., derived from CD3ζ) . In some embodiments, the CAR comprises from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb (e.g., SEQ ID NO: 33) specifically recognizing a first epitope (e.g., a first tumor epitope, such as BCMA) ; (c) an optional linker (e.g., any of GG and SEQ ID NOs: 12, 13, and 26) ; (d) a second sdAb (e.g., SEQ ID NO: 37) specifically recognizing a second epitope (e.g., a second tumor epitope, such as BCMA) ; (e) an optional hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; (g) an primary intracellular signaling domain (e.g., derived from CD3ζ) ; and (h) an optional co-stimulatory intracellular signaling domain (e.g., derived from 4-1BB) .
[0114] In some embodiments, the CAR is an anti-BCMA sdAb CAR comprising from N-terminus to C-terminus: (a) an optional signal peptide (e.g., derived from CD8α) ; (b) a first sdAb specifically recognizing a first epitope of BCMA (first anti-BCMA sdAb) ; (c) an optional linker (e.g., any of GG and SEQ ID NOs: 12, 13, and 26) ; (d) a second sdAb specifically recognizing a second epitope of BCMA (second anti-BCMA sdAb) ; (e) an optional hinge domain (e.g., derived from CD8α) ; (f) a transmembrane domain (e.g., derived from CD8α) ; (g) an optional co-stimulatory intracellular signaling domain (e.g., derived from 4-1BB) ; and (h) an primary intracellular signaling domain (e.g., derived from CD3ζ) ; wherein the first anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 34, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 35, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 36; and wherein the second anti-BCMA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 38, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 39, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 40. In some embodiments, the first anti-BCMA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 33.In some embodiments, the second anti-BCMA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 37. In some embodiments, the CAR is an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 31, or a variant thereof having at least about 70% (such as at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 31. In some embodiments, the CAR comprises a signal peptide at the N-terminus, e.g., SEQ ID NO: 19. In some embodiments, the CAR is an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6, or a variant thereof having at least about 70% (such as at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 6.
[0115] In some embodiments, the engineered cell (e.g., engineered immune cell) comprises a second nucleic acid encoding a CAR. Many CARs targeting different tumor antigens known in the field can be used herein, such as CAR targeting BMCA. CARs that can be used herein include, but are not limited to, those described in US9447194, US11253546, US10442867, US10174095, US10316101, US10383929, US10934363, US11021542, US11066475, US11939389, US12006369, US20200023010, US20200261501, US20210128619, and US20220218745, the contents of each of which are incorporated herein by reference in their entirety. Extracellular antigen binding domain
[0116] The extracellular antigen binding domain of the CAR may comprise (e.g., consist of, or consist essentially of) an antigen-binding moiety selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically recognizing the target antigen, or a combination thereof. The extracellular antigen binding domain can be monovalent or multivalent. The extracellular antigen binding domain can be monospecific or multispecific. In some embodiments, the extracellular antigen binding domain of the CAR comprise one or more antigen-binding moieties (e.g., scFv or sdAb) specifically recognizing one or more epitopes of one or more target antigens. In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., scFv or sdAb) connected in tandem. In some embodiments, the two or more antigen-binding moieties specifically recognize two or more epitopes of the same target antigen (e.g., BCMA) . The two or more antigen-binding moieties can be the same or different. The two or more antigen-binding moieties can recognize the same epitope or different epitopes. In some embodiments, the antigen-binding moiety is an antibody moiety (e.g., sdAb) .
[0117] In some embodiments, the extracellular antigen binding domain of the CAR comprises an (e.g., one or more) antibody moiety (e.g., scFv or sdAb) specifically recognizing a (e.g., one or more) target epitope or target antigen (e.g., tumor antigen, autoimmune disease antigen, viral or bacterial antigen) . In some embodiments, the target antigen is a pathogen-specific antigen, such as a viral antigen, a bacterial antigen, a fungal antigen (e.g., from Aspergillus or Candida) , or a parasitic antigen. In some embodiments, the viral antigen is from Herpes simplex virus (HSV) , respiratory syncytial virus (RSV) , metapneumovirus (hMPV) , rhinovirus, parainfluenza (NV) , Epstein-Barr virus (EBV) , Cytomegalovirus (CMV) , JC virus (John Cunningham virus) , BK virus, HIV, Zika virus, human coronavirus, norovirus, encephalitis virus, or Ebola. In some embodiments, the target antigen is associated with an autoimmune or inflammatory disease. In some embodiments, the target antigen is selected from the group consisting of BCMA, AFP, CLL1, CD4, GPC2, GPC3, GPRC5D, GUCY2C (GCC) , CD19, MUC16, MUC1, CAIX, CEA, CD8, CD7, CD10, CD20, CD22, CD30, CD33, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, CD228, EGP-2, EGP-40, EpCAM, ERBB2 (HER-2) , ERBB3, ERBB4, FBP, fetal acetylcholine receptor, folate receptor-α, GD2, GD3, hTERT, IL-13R-α2, κ-light chain, KDR, LeY, L1 cell adhesion molecule, MAGE-A1, mesothelin, MAGEA3, p53, MART1, GP100, proteinase-3 (PR3) , tyrosinase, survivin, hTERT, EphA2, NY-ESO-1, h5T4, PSCA, PSMA, ROR1, TAG-72, VEGF-R2, WT-1, CD123, CD44V6, NKCS1, IGF1R, EGFR, EGFR-VIII, Claudin 18.2, Claudin 6, NKG2D, Delta-like 3 (DLL3) , CD70, CS-1, c-Met, Glycolipid F77, PD-L1, and PD-L2. In some embodiments, the target antigen is a tumor antigen, such as tumor-specific antigens (TSA) or tumor-associated antigen (TAA) . In some embodiments, the tumor antigen is selected from the group consisting of CD19, BCMA, Claudin 18.2, NY-ESO-1, VEGFR2, MAGE-A3, CD20, CD22, CD33, CD38, CEA, EGFR, GD2, HER2, IGF1R, mesothelin, PSMA, ROR1, GPC3, GUCY2C, DLL3, GPRC5D, CLL1, WT1, and combinations thereof. In some embodiments, the tumor antigen or epitope is BCMA.
[0118] In some embodiments, the extracellular antigen binding domain specifically recognizes BCMA. In some embodiments, the extracellular antigen binding domain comprises one or more antibody moieties (e.g., sdAb) specifically recognizing BMCA. In some embodiments, the extracellular antigen binding domain comprises from N’ to C’: a first anti-BCMA sdAb (e.g., SEQ ID NO: 33 or 37) –an optional linker (e.g., GG, or SEQ ID NO: 12 or 13) –a second anti-BCMA sdAb (e.g., SEQ ID NO: 37 or 33) . Any of the anti-BCMA sdAbs (or VHHs) disclosed in US10934363 can be used herein in the extracellular antigen binding domain, the content of which is incorporated herein by reference in its entirety.
[0119] In some embodiments, the anti-BMCA sdAb comprises (i) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 34, or a variant thereof comprising up to 3 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) ; (ii) an HCDR2 comprising the amino acid sequence of SEQ ID NO: 35, or a variant thereof comprising up to 3 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) ; and (iii) an HCDR3 comprising the amino acid sequence of SEQ ID NO: 36, or a variant thereof comprising up to 3 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) . In some embodiments, the anti-BMCA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 34, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 35, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 36. In some embodiments, the anti-BMCA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 33, or a variant thereof having at least about 70% (e.g., at least about any of 75%, 80%, 85%, 90%, 95%, 99%, or more) sequence identity to SEQ ID NO: 33.
[0120] In some embodiments, the anti-BMCA sdAb comprises (i) an HCDR1 comprising the amino acid sequence of SEQ ID NO: 38, or a variant thereof comprising up to 3 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) ; (ii) an HCDR2 comprising the amino acid sequence of SEQ ID NO: 39, or a variant thereof comprising up to 3 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) ; and (iii) an HCDR3 comprising the amino acid sequence of SEQ ID NO: 40, or a variant thereof comprising up to 3 amino acid variations (e.g., insertion, deletion, and / or substitution, such as conservative substitution) . In some embodiments, the anti-BMCA sdAb comprises an HCDR1 comprising the amino acid sequence of SEQ ID NO: 38, an HCDR2 comprising the amino acid sequence of SEQ ID NO: 39, and an HCDR3 comprising the amino acid sequence of SEQ ID NO: 40. In some embodiments, the anti-BMCA sdAb comprises a VHH domain comprising the amino acid sequence of SEQ ID NO: 37, or a variant thereof having at least about 70% (e.g., at least about any of 75%, 80%, 85%, 90%, 95%, 99%, or more) sequence identity to SEQ ID NO: 37.
[0121] In some embodiments, the anti-BMCA sdAb specifically binds to BCMA competitively with any one of the anti-BMCA sdAbs described herein. In some embodiments, the anti-BMCA sdAb specifically binds to BCMA competitively with an anti-BMCA sdAb comprising a VHH comprising the amino acid sequence of any one of SEQ ID NO: 33 or 37. In some embodiments, competitive binding may be determined using an ELISA assay. Transmembrane domain
[0122] The transmembrane domain of the chimeric receptor 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. In some embodiments, the transmembrane domain of the 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 of the CAR is not derived from DAP12. In some embodiments, the transmembrane domain of the CAR (e.g., derived from or not derived from DAP12) cannot interact with the transmembrane domain of the IL-15 construct. In some embodiments, the transmembrane domain of the CAR is derived from CD8α or CD28. In some embodiments, the transmembrane domain of the CAR comprises an amino acid sequence having at least about 70% (such as at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 22. In some embodiments, the transmembrane domain of the CAR comprises the amino acid sequence of SEQ ID NO: 22. In some embodiments, the CAR comprises the amino acid sequence of SEQ ID NO: 41 (comprising transmembrane domain and immediate cytoplasmic sequence) .
[0123] Methods of testing the interaction (e.g., multimerization) of two or more membrane-bound proteins are well-known in the art, including but not limited to, co-immunoprecipitation (co-IP; e.g., followed by Western blot) , fluorescence cross-correlation spectroscopy (FCS) , resonance energy transfer (FRET) , and brightness and diffusion global analysis (BDGA) . Hinge domain
[0124] The CAR of the present disclosure may comprise a hinge domain between the extracellular antigen binding domain and the transmembrane domain. Any of the hinge domains described in the “hinge domains” subsection of the “A. IL-15 Constructs” section above can be used herein in the chimeric receptor herein (e.g., CAR) . In some embodiments, the hinge domain of the CAR is derived from CD8α, such as comprising the amino acid sequence of SEQ ID NO: 21. In some embodiments, the hinge domain of the CAR comprises an amino acid sequence having at least about 70% (such as at least about any of 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 21. Primary intracellular signaling domain
[0125] In some embodiments, the CAR comprises an intracellular signaling domain consisting essentially of (or consisting 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, and CD66d (CEACAM3) . In some embodiments, the intracellular signaling domain of the CAR comprises (or consists essentially of, or consists of) a primary intracellular signaling domain, such as an CD3ζ intracellular signaling domain. In some embodiments, the intracellular signaling domain of the CAR comprises an amino acid sequence having at least about 70% (such as at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 24. In some embodiments, the intracellular signaling domain (or primary intracellular signaling domain) of the CAR is a CD3ζintracellular signaling domain comprising the amino acid sequence of SEQ ID NO: 24. Co-stimulatory intracellular signaling domain
[0126] 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 CAR further comprises at least one co-stimulatory intracellular signaling domain. The term “co-stimulatory intracellular 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 co-stimulatory intracellular signaling domain can act in an antigen-independent manner to provide a secondary or co-stimulatory signal to immune cells. The co-stimulatory intracellular signaling domain of the CAR 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 or NK 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. Activation of a co-stimulatory intracellular signaling domain in a host cell (e.g., an immune cell) may induce the cell to increase or decrease the production and secretion of cytokines, phagocytic properties, proliferation, differentiation, survival, and / or cytotoxicity. The co-stimulatory intracellular signaling domain of any co-stimulatory molecule may be compatible for use in the CAR described herein. The type (s) of co-stimulatory intracellular signaling domain is selected based on factors such as the type of the immune effector cells in which the CAR would be expressed (e.g., T cells, NK cells, macrophages, neutrophils, or eosinophils) and the desired immune effector function (e.g., ADCC effect) . In some embodiments, the co-stimulatory molecule is selected from the group consisting of CD27, CD28, 4-1BB (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, and ligands of CD83. In some embodiments, the co-stimulatory intracellular signaling domain is derived from 4-1BB. In some embodiments, the co-stimulatory intracellular signaling domain of the CAR comprises an amino acid sequence having at least about 70% (such as at least about any of 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99%, or more) sequence identity to SEQ ID NO: 23. In some embodiments, the co-stimulatory intracellular signaling domain of the CAR is a 4-1BB co-stimulatory intracellular signaling domain comprising the amino acid sequence of SEQ ID NO: 23. Chimeric receptor signal peptide
[0127] The CAR of the present disclosure may further comprise a signal peptide (also known as a signal sequence) at the N-terminus of the polypeptide (e.g., N’ of the extracellular antigen binding domain) . In some embodiments, the signal peptide of the chimeric receptor targets the chimeric receptor (e.g., CAR) to the secretory pathway of the cell and will allow for integration and anchoring of the chimeric receptor into the lipid bilayer. Any of the signal peptide described in the “IL-15 construct signal peptides” subsection of the “A. IL-15 Constructs” section above can be used herein in the chimeric receptor herein (e.g., CAR) . In some embodiments, the signal peptide of the chimeric receptor (e.g., CAR) is derived from a CD8α propeptide, e.g., human CD8α. In some embodiments, the signal peptide of the chimeric receptor (e.g., CAR) comprises the amino acid sequence of any of SEQ ID NOs: 16, 19, 25, and 30, such as SEQ ID NO: 19. Peptide linker
[0128] The chimeric receptor (e.g., CAR) may comprise one or more peptide linkers, such as between different components of the chimeric receptor (e.g., between two or more co-stimulatory intracellular signaling domains, between co-stimulatory intracellular signaling domain and primary intracellular signaling domain, or between the extracellular antigen binding domain and the transmembrane domain) , and / or within one chimeric receptor component (e.g., between two or more antigen-binding moieties within the extracellular antigen binding domain, such as within an scFv, or for connecting two or more antigen-binding moieties (e.g., antibody moieties, such as sdAb) in tandem) .
[0129] Each peptide linker in a chimeric receptor (e.g., CAR) may have the same or different length and / or sequence depending on the structural and / or functional features of the antigen-binding moieties (e.g., 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 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. 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, the disclosure of which is incorporated herein by reference in its entirety. 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 (e.g., CAR) provided herein, the disclosure of each of which is incorporated herein by reference in their entirety.
[0130] 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) (SEQ ID NO: 68) . In some embodiments, the (GxS) n linker comprises the amino acid sequence of SEQ ID NO: 12. In some embodiments, the peptide linker comprises the amino acid sequence of SEQ ID NO: 13. In some embodiments, the peptide linker comprises the amino acid sequence of SEQ ID NO: 26. In some embodiments, the peptide linker comprises the amino acid sequence of GG, GGS, or GGGS (SEQ ID NO: 69) .Engineered T cell receptor (TCR)
[0131] In some embodiments, the chimeric receptor is an engineered TCR. The engineered TCR may comprise i) an extracellular antigen binding domain that comprises a Vα and a Vβ (or a Vδand a Vγ) derived from a wildtype TCR together specifically recognizing a target antigen (e.g., tumor antigen such as BCMA, autoimmune disease antigen, viral or bacterial antigen, or cognate peptide-MHC) , wherein the Vα, the Vβ, or both (or the Vδ, the Vγ, or both) comprise one or more mutations (e.g., insertions, deletions, and / or substitutions, such as conservative substitutions) in one or more CDRs relative to the wild type TCR; and ii) a transmembrane domain derived from a TCR molecule (e.g., TCRα / TCRβ, or TCRδ / TCRγ) . The engineered TCR can be a single chain TCR (scTCR) or a dimeric TCR (dTCR) . For example, the 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 an extracellular antigen binding domain that specifically recognizes a target antigen (e.g., BCMA, or complex of MHC and a peptide of BCMA) . The 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 an extracellular antigen binding domain that specifically recognizes a target antigen (e.g., BCMA, or complex of MHC and a peptide of BCMA) . The engineered TCR may bind to the same cognate peptide-MHC bound by the wildtype TCR. The engineered TCR may bind to the same cognate peptide-MHC with higher affinity compared to that bound by the wildtype TCR. The engineered TCR may bind to the same cognate peptide-MHC with lower affinity compared to that bound by the wildtype TCR. The engineered TCR may bind to a non-cognate peptide-MHC not bound by the wildtype TCR. The engineered TCR may not comprise an intracellular signaling domain (e.g., does not comprise a primary intracellular signaling domain) . In some embodiments, the engineered TCR does not comprise a functional intracellular signaling domain. In some embodiments, the engineered TCR comprises the cytoplasmic domain of TCRα, TCRβ, TCRδ, or TCRγ. The engineered 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 / TCRβor TCRδ / TCRγ, or any of the peptide linkers and hinge domains described herein. Any of the target antigens described herein, or a complex of MHC and a peptide of the target antigen described herein, may be recognized by an engineered TCR described herein.Chimeric TCR (cTCR)
[0132] In some embodiments, the chimeric receptor is a chimeric TCR (cTCR) . The cTCR may comprise: i) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA, autoimmune disease antigen, viral or bacterial antigen) , 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 extracellular antigen binding domain is fused (directly or indirectly) to the N-terminus of the full-length TCR subunit. The cTCR may comprise an optional extracellular domain (ECD) or portion thereof derived from a TCR subunit. For example, the cTCR may comprise from N’ to C’: i) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA) , ii) an optional 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 cTCR can be incorporated into a functional TCR complex along with other endogenous TCR subunits and confer antigen specificity to the TCR complex. Any of the extracellular antigen binding domains described under the “Chimeric Antigen Receptor (CAR) ) section above can be used herein as the extracellular antigen binding domain of the cTCR. The extracellular antigen binding domain of the cTCR may comprise one or more antigen-binding moieties selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically recognizing the target antigen. In some embodiments, the extracellular antigen binding domain of the cTCR comprise one or more antigen-binding moieties (e.g., scFv, sdAb, or peptide ligand) specifically recognizing one or more epitopes of one or more target antigens (e.g., BCMA) . In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., scFv, sdAb, or peptide ligand) connected in tandem. The cTCR extracellular antigen binding domain may be fused to the N-terminus of the full-length or a portion thereof of CD3ε, CD3γ, or CD3δ. The cTCR extracellular 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 cTCR extracellular 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 Vδdomain) . The cTCR may or may not comprise an intracellular signaling domain (e.g., does not comprise a primary intracellular signaling domain) . In some embodiments, the cTCR comprises the cytoplasmic domain of TCRα, TCRβ, TCRδ, or TCRγ. The cTCR may comprise an intracellular signaling domain, such as the intracellular signaling domain of CD3γ, CD3ε, or CD3δ. The cTCR intracellular domain (e.g., intracellular signaling domain, or cytoplasmic amino acid residues) and the cTCR transmembrane domain can be derived from the same TCR subunit, e.g., both from CD3ε, both from CD3ε, both from CD3δ, both from TCRα, both from TCRβ, both from TCRγ, or both from TCRδ. The cTCR extracellular antigen binding domain and the TCR subunit (full-length or an ECD portion thereof) can be fused via a linker (such as a GS linker) . In some embodiments, the extracellular antigen binding domain is fused to the N-terminus of the transmembrane domain via an optional linker or hinge domain. The cTCR may further comprise a hinge domain between the ECD portion derived from a first TCR subunit and a transmembrane domain derived from a second TCR subunit. In some embodiments, the cTCR comprises from N-terminus to C-terminus: (a) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., BCMA) ; (b) an optional linker, (c) an optional extracellular domain of a first TCR subunit or a portion thereof, (d) an optional hinge domain, (e) a transmembrane domain derived from a second TCR subunit, 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. Any of the target antigens described under the “Extracellular antigen binding domain” subsection above may be recognized by a cTCR described herein.T cell antigen coupler (TAC)
[0133] In some embodiments, the chimeric receptor is a T cell antigen coupler (TAC) comprising: (a) an extracellular antigen binding domain specifically recognizing a target antigen (e.g., tumor antigen such as BCMA, autoimmune disease antigen, viral or bacterial antigen) ; (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) ; (f) a transmembrane comprising a transmembrane derived from a second TCR co-receptor (such as CD4, CD28, or CD8) ; and (g) an optional intracellular signaling domain comprising an intracellular signaling domain derived from a third TCR co-receptor (such as CD4, CD28, or CD8) . The TCR subunit can be any of TCRα, TCRβ, TCRγ, TCRδ, CD3ε, CD3γ, and CD3δ. In some embodiments, the first, second, and third TCR co-receptors are the same (e.g., all CD4) . In some embodiments, at least two of the first, second, and third TCR co-receptors are different. For example, in some embodiments, the TAC comprises: (a) an extracellular antigen binding domain specifically recognizing one or more epitopes of a target antigen (e.g., tumor antigen such as BCMA) ; (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, or CD28) . Any of the extracellular antigen binding domains described under the “Chimeric Antigen Receptor (CAR) ) section above can be used herein as the extracellular antigen binding domain of the TAC. The extracellular antigen binding domain of the TAC may comprise one or more antigen-binding moieties selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically recognizing the target antigen. In some embodiments, the extracellular antigen binding domain of the TAC comprise one or more antigen-binding moieties (e.g., scFv, sdAb, or peptide ligand) specifically recognizing one or more epitopes of one or more target antigens (e.g., BCMA) . In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., scFv, sdAb, or peptide ligand) connected in tandem. Any of the target antigens described under the “Extracellular antigen binding domain” subsection above may be recognized by a TAC described herein.TAC-like engineered receptor
[0134] In some embodiments, the chimeric receptor is a TAC-like engineered receptor comprising: (a) an extracellular antigen binding domain specifically recognizing one or more epitopes of a target antigen (e.g., tumor antigen such as BCMA, autoimmune disease antigen, or pathogen-specific antigen) ; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a first TCR subunit; (d) an optional second linker; (e) an optional extracellular domain derived from a second TCR subunit or a portion thereof; (f) a transmembrane domain comprising a transmembrane domain derived from a third TCR subunit; and (g) an optional intracellular domain (e.g., intracellular signaling domain) comprising an intracellular domain (e.g., intracellular signaling domain) derived from a fourth TCR subunit; wherein the first, second, third, and fourth TCR subunits are independently 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. In some embodiments, the second, third, and fourth TCR subunits are the same. In some embodiments, at least two of the first, second, third, and fourth TCR subunits are different. In some embodiments, the second, third, and fourth TCR subunits are the same but different from the first TCR subunit. In some embodiments, the TAC-like engineered receptor comprises: (a) an extracellular antigen binding domain specifically recognizing one or more epitopes of a target antigen (e.g., BCMA) ; (b) an optional first linker; (c) an extracellular TCR binding domain that specifically recognizes the extracellular domain of a first TCR subunit; (d) an optional second linker; and (e) a full length second TCR subunit; wherein the first and second TCR subunits are independently 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. In some embodiments, the first and second TCR subunits are different. Any of the extracellular antigen binding domains described under the “Chimeric Antigen Receptor (CAR) ) section above can be used herein as the extracellular antigen binding domain of the TAC-like engineered receptor. The extracellular antigen binding domain of the TAC-like engineered receptor may comprise one or more antigen-binding moieties selected from the group consisting of a Fab, a Fab’, a (Fab’) 2, an Fv, an scFv, an sdAb, and a peptide ligand specifically recognizing the target antigen. In some embodiments, the extracellular antigen binding domain of the TAC-like engineered receptor comprise one or more antigen-binding moieties (e.g., scFv, sdAb, or peptide ligand) specifically recognizing one or more epitopes of one or more target antigens (e.g., BCMA) . In some embodiments, the extracellular antigen binding domain comprises two or more antigen-binding moieties (e.g., scFv, sdAb, or peptide ligand) connected in tandem. Any of the target antigens described under the “Extracellular antigen binding domain” subsection above may be recognized by a TAC-like engineered receptor described herein.
[0135] These examples are merely illustrative in nature and are not limiting to the present embodiments, as any chimeric receptors can be present in the engineered cells (e.g., engineered immune cells) . These non-limiting examples of chimeric receptors (e.g., CAR, engineered TCR, cTCR, TAC, and TAC-like engineered receptors) and any other chimeric receptor construct could be encoded by the second nucleic acid disclosed herein. C. Nucleic Acids and Vectors
[0136] The engineered cells (e.g., engineered immune cells) described herein comprise one or more nucleic acids (or heterologous nucleic acid sequence (s) ) encoding any one of the IL-15 constructs and / or chimeric receptors (e.g., CAR) described herein. In some embodiments, the nucleic acid is a DNA. In some embodiments, the nucleic acid is an RNA. In some embodiments, the nucleic acid is linear. In some embodiments, the nucleic acid is circular. In some embodiments, the IL-15 constructs and / or chimeric receptors (e.g., CAR) described herein is expressed by introducing the nucleic acid or the vector comprising a sequence encoding the IL-15 constructs and / or chimeric receptors (e.g., CAR) into a cell in vivo (in vivo cell therapy) or in vitro (including autologous cell therapy and allogeneic cell therapy) .
[0137] The one or more nucleic acids encoding any one of the IL-15 constructs and / or chimeric receptors (e.g., CAR) described herein may be operably linked to one or more regulatory sequences. Exemplary regulatory sequences that control the transcription and / or translation of a coding sequence are known in the art and may include, but not limited to, a promoter, additional elements for proper initiation, regulation and / or termination of transcription (e.g. polyA transcription termination sequences) , mRNA transport (e.g. nuclear localization signal sequences) , processing (e.g. splicing signals) , stability (e.g. introns and non-coding 5′and 3′sequences) , translation (e.g. an initiator Met, tripartite leader sequences, IRES ribosome binding sites, signal peptides, etc. ) , and insertion site for introducing an insert into the viral vector. In some embodiments, the regulatory sequence is a promoter, a transcriptional enhancer and / or a sequence that allows for proper expression of the IL-15 construct and / or the chimeric receptor.
[0138] The term “regulatory sequence” or “control sequence” refers to a DNA sequence that affects the expression of a coding sequence to which it is operably linked. The nature of such regulatory sequences differs depending upon the host organism. In prokaryotes, regulatory sequences generally include promoters, optionally an operator sequence, ribosomal binding sites, and terminators. In eukaryotes, regulatory sequences include promoters, polyadenylation signals, terminators and, in some instances, enhancers, or sequences recognized by transactivators or transcription factors.
[0139] A regulatory sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the regulatory sequences. 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.
[0140] As used herein, a “promoter” or a “promoter region” refers to a segment of DNA or RNA that controls transcription of the DNA or RNA to which it is operatively linked. The promoter region includes specific sequences that are involved in RNA polymerase recognition, binding and transcription initiation. In addition, the promoter includes sequences that modulate recognition, binding and transcription initiation activity of RNA polymerase (i.e., binding of one or more transcription factors) . These sequences can be cis acting or can be responsive to trans acting factors. Promoters, depending upon the nature of the regulation, can be constitutive or regulated. Regulated promoters can be inducible or environmentally responsive (e.g. respond to cues such as pH, anaerobic conditions, osmoticum, temperature, light, or cell density) . Many such promoter sequences are known in the art. See, for example, U.S. Pat. Nos. 4,980,285; 5,631,150; 5,707,928; 5,759,828; 5,888,783; 5,919,670, and Sambrook, et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Press (1989) .
[0141] In some embodiments, the promoter is an endogenous promoter. For example, a nucleic acid encoding the IL-15 construct or chimeric receptor may be knocked-in to the genome of an engineered cell (e.g., engineered immune cell) downstream of an endogenous promoter using any methods known in the art, such as using the CRISPR / Cas9 method. In some embodiments, the endogenous promoter is a promoter for an abundant protein, such as beta-actin. In some embodiments, the endogenous promoter is an inducible promoter, for example, inducible by an endogenous activation signal of the engineered cell (e.g., engineered immune cell) . In some embodiments, wherein the engineered immune cell is a T cell, the promoter is a T cell activation-dependent promoter (such as an IL-2 promoter, an NFAT promoter, or an NFκB promoter) . In some embodiments, wherein the engineered immune cell is an NK cell, the promoter is an NK cell activation-dependent promoter (such as an IL-2 promoter, an NFAT promoter, an NFκB promoter, an MHCI (HLA-A, HLA-B, HLA-C, HLA-E, or HLA-F) promoter, a KIR (KIR2DS1, KIR2DS4, or KIR3DS1) promoter) . In some embodiments, the promoter is a heterologous promoter.
[0142] 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 heterologous nucleic acid sequence encoding the IL-15 construct or chimeric receptor is operably linked to a constitutive promoter. In some embodiments, the heterologous nucleic acid sequence encoding the IL-15 construct or chimeric receptor is operably linked to an inducible promoter.
[0143] Constitutive promoters allow heterologous genes (also referred to as transgenes) to be expressed constitutively in the host cells. Exemplary constitutive promoters contemplated herein include, but are not limited to, Cytomegalovirus (CMV) promoters, human elongation factors-1alpha (hEF1α) , ubiquitin C promoter (UbiC) , phosphoglycerokinase promoter (PGK) , simian virus 40 early promoter (SV40) , and chicken β-Actin promoter coupled with CMV early enhancer (CAGG) . The efficiencies of such constitutive promoters on driving transgene expression have been widely compared in a huge number of studies. In some embodiments, the promoter is a hEF1αpromoter.
[0144] In some embodiments, the promoter is an inducible promoter. Inducible promoters belong to the category of regulated promoters. The inducible promoter can be induced by one or more conditions, such as a physical condition, microenvironment of the engineered cells (e.g., engineered immune cell, such as engineered CAR-NK cell) , or the physiological state of the engineered cell, an inducer (i.e., an inducing agent) , or a combination thereof. In some embodiments, the inducing condition does not induce the expression of endogenous genes in the engineered cell (e.g., engineered immune cell such as engineered CAR-NK cell) , and / or in the subject that receives the pharmaceutical composition. In some embodiments, the inducing condition is selected from the group consisting of: inducer, irradiation (such as ionizing radiation, light) , temperature (such as heat) , redox state, tumor environment, and the activation state of the engineered cell (e.g., engineered immune cell such as engineered CAR-NK cell) .
[0145] The heterologous nucleic acid sequences (s) described herein can be present in a heterologous gene expression cassette, which comprises one or more protein-coding sequences and optionally one or more promoters. In some embodiments, the heterologous gene expression cassette comprises a single protein-coding sequence. In some embodiments, the heterologous gene expression cassette comprises two or more protein-coding sequences driven by a single promoter (i.e., polycistronic) . In some embodiments, the heterologous gene expression cassette further comprises one or more regulatory sequences (such as 5’UTR, 3’UTR, enhancer sequence, IRES, transcription termination sequence) , recombination sites, one or more selection markers (such as antibiotic resistance gene, reporter gene, etc. ) , signal sequence, or combinations thereof. In some embodiments, a first nucleic acid encoding the IL-15 construct is fused to a second nucleic acid encoding a chimeric receptor via another nucleic acid sequence (e.g., linking sequence) encoding a self-cleavable linker, such as P2A, T2A, E2A, or F2A peptide, or an Internal Ribosome Entry Sites (IRES) linking sequence.
[0146] In some embodiments, the heterologous nucleic acid sequence (s) are present in a vector. A vector can be used 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, 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.
[0147] In some embodiments, the engineered cell (e.g., engineered immune cell) comprises a vector comprising a first nucleic acid encoding an IL-15 construct (e.g., any of the IL-15 constructs described herein) . In some embodiments, the engineered cell (e.g., engineered immune cell) comprises a vector comprising a first nucleic acid encoding an IL-15 construct and a second nucleic acid encoding a chimeric receptor (e.g., CAR) .
[0148] In some embodiments, the vector is a non-viral vector (e.g., lipid nanoparticles (LNPs) ) . In some embodiments, the vector is a virus-like particles (VLPs) , or enveloped delivery vehicles (EDVs) .
[0149] 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.
[0150] 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 therapeutic cell (e.g., engineered immune cell) in vitro or ex vivo. A number of retroviral systems are known in the art. In some embodiments, adenovirus vectors are used. In some embodiments, lentivirus vectors are used. In some embodiments, self-inactivating lentiviral vectors are used. For example, self-inactivating lentiviral vectors can be packaged with protocols known in the art. The resulting lentiviral vectors can be used to transduce a mammalian cell (such as human NK cells and / or 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 IL-15 construct and / or the chimeric receptor is a retroviral vector.
[0151] In some embodiments, the vector is a non-viral vector, such as a plasmid, or an episomal expression vector.
[0152] In some embodiments, the vector is an expression vector. “Expression vector” is a construct that can be used to transform a selected host and provides for expression of a coding sequence in the selected host. Expression vectors can for instance be cloning vectors, binary vectors or integrating vectors. Expression comprises transcription of the nucleic acid molecule preferably into a translatable mRNA. Regulatory elements ensuring expression in eukaryotic cells are well known to those skilled in the art. In the case of eukaryotic cells, they comprise normally promoters ensuring initiation of transcription and optionally poly-A signals ensuring termination of transcription and stabilization of the transcript. Examples of regulatory elements permitting expression in eukaryotic host cells are AOX1 or GAL1 promoter in yeast or the CMV-, SV40-, RSV-promoter (Rous sarcoma virus) , CMV-enhancer, SV40-enhancer or a globin intron in mammalian and other animal cells. Furthermore, depending on the expression system used leader sequences capable of directing the polypeptide to a cellular compartment or secreting it into the medium may be added to the coding sequence of the recited nucleic acid sequence and are well known in the art. The leader sequence (s) is (are) assembled in appropriate phase with translation, initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein, or a portion thereof, into the periplasmic space or extracellular medium. Optionally, the nucleic acid sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product. Suitable expression vectors are known in the art such as Okayama-Berg cDNA expression vector pcDV1 (Pharmacia) , pEF-Neo, pCDM8, pRc / CMV, pcDNA1, pcDNA3 (Invitrogen) , pEF-DHFR and pEF-ADA, (Raum et al., Cancer Immunol Immunother (2001) 50 (3) , 141-150) or pSPORT1 (GIBCO BRL) .
[0153] In some embodiments, the vector is a non-viral vector. In some embodiments, the non-viral vector is or includes a polynucleotide, e.g., a DNA or RNA polynucleotide, that is suitable for transduction and / or transfection by any suitable and / or known non-viral method for gene delivery, such as but not limited to microinjection, electroporation, transient cell compression or squeezing (e.g., as described in Lee, et al. (2012) Nano Lett 12: 6322-27) , lipid-mediated transfection, peptide-mediated delivery, or a combination thereof.
[0154] In some embodiments, the vector comprises or is a polymer. In some embodiments, the polymer comprises a polymer nanoparticle. In some embodiments, the vector comprises or is a lipid nanoparticle. In some embodiments, the vector comprises or is a cell penetrating peptide.
[0155] Any viral vectors described herein can be introduced into a cell in vivo using any suitable techniques known in the art. The viral based systems can be engineered to target (i.e. infect) a range of cells, target a narrow subset of cells, or target a specific type of cell. In general, the envelope protein chosen for the viral based systems will determine the viral tropism. In some embodiments, the virus used in the viral based systems can be pseudotyped to target a specific cell type of interest. For example, the envelope protein on the viral vectors can be modified to have reduced binding affinity to its natural receptor on host cells and the viral vectors can be modified to display a ligand (e.g., antibody or fragment thereof) that specifically binds to a cell surface marker. In some embodiments, the cell is an immune cell. Exemplary envelope proteins include, but are not limited to, VSV-G (vesicular stomatitis virus glycoprotein) , COCAL-G (cocal virus glycoprotein) and their known mutants that have a reduced binding affinity with low-density lipoprotein receptor (LDL-R) . Accordingly, one skilled in the art can select the appropriate tropism, pseudotype, and / or envelope protein that are well known for targeting a desired cell type.
[0156] A number of non-viral vectors have also been developed for gene transfer into mammalian cells. The non-viral vectors include but are not limited to, lipid nanoparticles (LNPs) , and stimuli-responsive polymer / inorganic nanoparticles. Any non-viral vectors described herein can be introduced into a cell in vivo using any suitable techniques known in the art. In some embodiments, LNPs are used. In some embodiments, LNPs are conjugated to a ligand (e.g., antibody or fragment thereof) that specifically binds to a cell surface marker (targeting moiety) . In some embodiments, the cell is an immune cell.
[0157] In some embodiments, the vector comprises at least one targeting moiety that specifically targets a T cell (e.g., αβT, γδT, NKT) , an NK cell, a spleen, or a lymph node.
[0158] In some embodiments, the vector comprises at least one targeting moiety that binds CD2, CD3, CD4, CD5, CD6, CD7, CD8, TCR, CD9, CD11a, CD16, CD18, CD25, CD27, CD28, CD44, CD45, CD45RA, CD45RB, CD45RO, CD47, CD53, CD56, CD57, CD62L, CD63, CD69, CD80, CD81, CD82, CD94, CD95, CD103, CD122, CD127, CD137, CD161, CD183 (CXCR3) , CD184 (CXCR4) , CD185 (CXCR5) , CD193 (CCR3) , CD194 (CCR4) , CD195 (CCR5) , CD196 (CCR6) , CD197 (CCR7) , CCR10, CTLA4, DNAM1, HLA-DR, ICOS, 4-1BB, AhR, IL-2 receptor, IL-6ST, IL-7 receptor, IL-15 receptor, KAR receptors, KIR receptors, KIR2DL1, KIR3D51, KIR3DS1, LAG3, NKG2A, NKG2C, NKG2D, NKp30, NKp44, NKp46, NTBA, OX40, P2RX7, PD1, SIGLEC-7, TIGIT, TIM3, TLR2, TLR4, TLR5. In some embodiments, the vector comprises at least one targeting moiety that binds CD2, CD3, CD4, CD5, CD7, TCR, CD8, CD56, CD16, and / or NKG2D. In some embodiments, the targeting moiety described above is an antibody or fragment thereof (e.g., scFv, VHHs) .
[0159] Exemplary targeting moieties can be found in e.g., US 11, 174, 481 B2, US 11, 191, 784 B2, US 2015 / 0320693 A1, WO 2022 / 058298 A1, US 11, 337, 929 B2, US 11, 324, 837 B2, and WO 2017 / 165683 A1, the contents of which are hereby incorporated in their entirety.
[0160] In some embodiments, there is provided an isolated nucleic acid (e.g., a first nucleic acid, either DNA or RNA) encoding any of the IL-15 constructs described herein. In some embodiments, there is provided a vector (e.g., viral vector, such as retroviral vector; non-viral vector, such as LNP; virus-like particles (VLPs) ; enveloped delivery vehicles (EDVs) ) or virus (e.g., AAV, retrovirus, or lentivirus) comprising any of such isolated nucleic acids. In some embodiments, the vector further comprises a second nucleic acid encoding a chimeric receptor (e.g., any of the chimeric receptors described herein) . In some embodiments, the chimeric receptor is a CAR comprising an extracellular antigen binding domain, a transmembrane domain, and a primary intracellular signaling domain. In some embodiments, the nucleic acid encoding the IL-15 construct and the second nucleic acid are operably linked to a single promoter and are connected by a linking sequence (e.g., IRES, or encoding a 2A self-cleaving peptide) .
[0161] In some embodiments, there is provide a vector (e.g., viral vector, such as lentiviral vector or retroviral vector; non-viral vector, such as LNP; virus-like particles (VLPs) ; enveloped delivery vehicles (EDVs) ) or virus (e.g., AAV, retrovirus, or lentivirus) comprising: a first nucleic acid encoding an IL-15 construct (e.g., any of the IL-15 constructs described herein) , and a second nucleic acid encoding a chimeric receptor (e.g., any of the chimeric receptors described herein, such as a CAR (e.g., anti-BCMA CAR) ) . In some embodiments, the first nucleic acid and the second nucleic acid are under the control of a single promoter. In some embodiments, the first nucleic acid and the second nucleic acid are connected by a linking sequence (e.g., IRES, or encoding a 2A self-cleaving peptide such as any of P2A, T2A, E2A, and F2A) . In some embodiments, the first nucleic acid and second nucleic acid are under the control of different promoters. In some embodiments, there is provided a vector (e.g., viral vector, such as retroviral vector) comprising from 5’ to 3’: a promoter (e.g., hEF1α promoter) -a second nucleic acid encoding a chimeric receptor (e.g., CAR, such as comprising the amino acid sequence of SEQ ID NO: 6 or 31) -a linking sequence (e.g., IRES, or encoding P2A or T2A) -a first nucleic acid encoding an IL-15 construct (e.g., comprising the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46) . In some embodiments, there is provided a vector (e.g., viral vector, such as retroviral vector) encoding a polypeptide comprising the amino acid sequence of SEQ ID NO: 8 or 47. In some embodiments, there is provided a vector (e.g., viral vector, such as retroviral vector) comprising from 5’ to 3’: a promoter (e.g., hEF1α promoter) -a first nucleic acid encoding an IL-15 construct (e.g., comprising the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46) -a linking sequence (e.g., IRES, or encoding P2A or T2A) -a second nucleic acid encoding a chimeric receptor (e.g., CAR, such as comprising the amino acid sequence of SEQ ID NO: 6 or 31) .
[0162] In some embodiments, the IL-15 construct described herein is encoded by a first nucleic acid and the chimeric receptor (e.g., CAR) is encoded by a second nucleic acid. The first nucleic acid and the second nucleic acid can be present on a single vector or different vectors. In some embodiments, the first nucleic acid further encodes an IL-15 construct signal peptide (e.g., comprising the amino acid sequence of SEQ ID NO: 16) N-terminal to the IL-15 construct. In some embodiments, there is provided an isolated nucleic acid (e.g., a first nucleic acid) encoding a polypeptide comprising the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46. In some embodiments, the second nucleic acid further encodes a chimeric receptor signal peptide (e.g., comprising the amino acid sequence of SEQ ID NO: 19) N-terminal to the chimeric receptor. In some embodiments, the second nucleic acid encodes a polypeptide comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, the chimeric receptor (e.g., multi-chain chimeric receptor) is encoded by a second set of two or more nucleic acids (e.g., either on the same vector or on different vectors, under the control of the same promoter or different promoters) . When the chimeric receptor contains two or more polypeptide chains to be expressed, each polypeptide chain may comprise a signal peptide fused to the N-terminus. When the two or more polypeptide chains are to be expressed from a single vector and under a single promoter control, the nucleic acids encoding the two or more polypeptide chains may be connected via a linking sequence encoding a cleavable linker (e.g., 2A peptide) or a linking sequence of IRES. In some embodiment, the nucleic acids described herein can be introduced into a cell in vivo using any suitable techniques known in the art. In some embodiments, the cell is an immune cell. In some embodiments, the nucleic acids can be modified to make it suitable for in vivo gene therapy.
[0163] In some embodiments, there is provided a vector (e.g., viral vector, such as lentiviral vector or retroviral vector; non-viral vector, such as LNP; virus-like particles (VLPs) ; enveloped delivery vehicles (EDVs) or virus (e.g., AAV, retrovirus, or lentivirus) encoding an anti-BCMA CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31, and an IL-15 construct comprising the amino acid sequence of any of SEQ ID NOs: 3-5, 42, and 43. The nucleic acid encoding the IL-15 construct comprising the amino acid sequence of any of SEQ ID NOs: 3-5, 42, and 43 can be at 5’ or 3’ of the nucleic acid encoding the anti-BCMA CAR on the vector. In some embodiments, there is provided a vector or virus encoding a polypeptide comprising the amino acid sequence of any of SEQ ID NOs: 9-11 and 44.
[0164] Methods for making recombinant viruses (e.g., AAV, retrovirus, lentivirus) encoding any of the IL-15 constructs and / or chimeric receptors (e.g., CAR) described herein are also provided herein. In some embodiments, the method comprises introducing a nucleic acid encoding any of the IL-15 constructs described herein, one or more envelope vectors comprising one or more nucleic acids encoding one or more viral glycoproteins, and one or more packaging vectors comprising one or more nucleic acids encoding one or more packaging proteins, into a producer cell, thereby producing the recombinant virus. In some embodiments, the method further comprises introducing into the producer cell a second nucleic acid encoding any of the chimeric receptors described herein. The nucleic acid encoding the IL-15 construct and the nucleic acid encoding the chimeric receptor can be on the same vector or different vectors. In some embodiments, the method further comprises isolating the recombinant virus.
[0165] The recombinant virus provided for herein can be produced or made by, for example, culturing the producer cell under conditions sufficient to make the recombinant virus. In some embodiments, the producer cell already comprises one or more nucleic acids that encode the components to produce the recombinant virus. These can be structural or non-structural viral components or proteins. Producer cell lines are known in the art and can be modified with a molecule of interest to produce the recombinant virus of interest. Any suitable producer cell line known in the art can be used, such as HEK293, 293T, HeLa, D-17, MDCK, BHK and Cf2Th cells.
[0166] Engineered cells (e.g., engineered immune cells such as T cell or NK cell) comprising any of the isolated nucleic acids or vectors described herein are also provided.
[0167] The engineered cells (e.g., engineered immune cells) described herein can further comprise one or more third, fourth, and so on, nucleic acid (s) for genetic modifications. For example, in some embodiments the engineered cell (e.g., engineered immune cell) further comprises a nucleic acid (e.g., encoding CRISPR / Cas) for B2M knockdown or knockout. Engineered cells (e.g., engineered immune cells) and methods of making thereof are further discussed in section IV below. D. Cell types
[0168] Any cells (e.g., immune cells) can be used herein to make the engineered cells (e.g., engineered immune cells) . In some embodiments, the engineered cells are engineered immune cells. In some embodiments, the immune cells are in vivo cells (e.g., cells in an individual) . In some embodiments, the engineered immune cells are produced in vivo. In some embodiments, the engineered cells are engineered stem cells. In some embodiments, the stem cell is a hematopoietic stem cell (HSC) , pluripotent stem cell (PSC) , induced pluripotent stem cell (iPSC) , or embryonic stem cell (ESC) . In some embodiments, the engineered cell is a cell (e.g., immune cell) derived from or differentiated from an engineered stem cell. In some embodiments, the stem cell is engineered to express the IL-15 construct and / or the chimeric receptor (e.g. a CAR) described herein and allowed to differentiate into a mature engineered cell (e.g., mature engineered immune cell, such as an NK cell) . See “VI. Methods of Making Engineered Cells” section below for generation methods. The present disclosure provides engineered cells (e.g., engineered immune cells) that comprise any of the IL-15 constructs, any of the nucleic acids encoding said IL-15 constructs, and / or any of the vectors encoding said IL-15 constructs described herein. The present disclosure provides engineered cells (e.g., engineered immune cells) that further comprise any of the chimeric receptors (e.g., anti-BMCA CAR) , any of the nucleic acids and / or any of the vectors described herein encoding the chimeric receptors. In some embodiments, the engineered cells (e.g., engineered immune cells) comprise any one of the IL-15 constructs described herein and any one of the chimeric receptors described herein.
[0169] The engineered cells (e.g., engineered immune cells) can be further genetically modified to enhance (e.g., increasing at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 1-fold, 1.5-fold, 2-fold, 5-fold, 10-fold, or more) one or more functions (such as to further enhance anti-tumor cytotoxicity 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 cells (e.g., engineered immune cells such as CAR-T cell) are genetically modified to reduce (e.g., reducing at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or more) or abolish the expression and / or function of an endogenous TCR. In some embodiments, the engineered cells (e.g., engineered immune cells) are genetically modified to reduce or abolish the expression and / or function of an endogenous B2M. In some embodiments, the engineered cells (e.g., 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 cell (e.g., 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 cells (e.g., engineered immune cells) are further genetically modified using any one or more standard technique such as by using siRNA, CRISPR / Cas system, meganucleases, transcription activator-like effector nucleases (TALENs) , zinc finger nucleases (ZFNs) , etc.
[0170] In some embodiments, the engineered cell is an engineered immune cell. In some embodiments, the engineered 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, a natural killer T (NKT) cell, and any combination thereof. In some embodiments, the engineered immune cell is peripheral blood mononuclear cell (PBMC) . 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, an NKT cell, and any combination thereof. In some embodiments, the engineered 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 PBMC, NK cells, monocytes, cytotoxic T cells, neutrophils, and eosinophils.
[0171] In some embodiments, the engineered immune cell is generated from PBMC. In some embodiments, the engineered immune cell is an NK cell. In some embodiments, the engineered NK cell is further modified to reduce (e.g., reducing at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or more) the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules. In some embodiments, the engineered NK cell is further modified to increase (e.g., increasing at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 1-fold, 2-fold, 5-fold, or more) the expression and / or function of, e.g., overexpress, one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9. In some embodiments, the engineered NK cells are CD16+, CD38+, CD56+ / NCAM-1+, CD57+, CD3-, CD3- / CD56+, CD7+, CD127-, Nkp46+, T-bet+, Eomes+, KIR Family receptor+, NKG2A+, NKG2D+, NKp30+, NKp44+, and / or NKp80+, or any combination thereof. In some embodiments, the engineered NK cells produce IFNγ, TNFα, and / or GM-CSF upon activation. In some embodiments, the engineered NK cells (e.g., CAR-NK) lyse target cells upon recognition and binding to the target cells. In some embodiments, the engineered immune cell is made from established cell lines, for example, NK-92 cells.
[0172] In some embodiments, the engineered immune cell is a T cell. The engineered T cells may be αβ T cells, or γδ T cells. In some embodiments, the engineered T cells are CD4+ / CD8-, CD4- / CD8+, CD4+ / CD8+, CD4- / CD8-, or combinations thereof. In some embodiments, the engineered T cells produce IL-2, TFN, and / or TNF upon activation.
[0173] Also see immune cells described in Section “IV. Methods of Making Engineered Cells and IL-15 Constructs” below.
[0174] Cells (e.g., immune cells or stem cells) for making the engineered cells (e.g., engineered immune cells) described herein can be from any sources, such as derived from related (e.g., an individual, such as a human to be treated) or unrelated (e.g., healthy individual) humans, non-human animals, cell lines, or cultures. In some embodiments, the engineered cell (e.g., engineered immune cell) is allogeneic (e.g., derived from a healthy individual) . In some embodiments, the engineered cell (e.g., engineered immune cell) is autologous (e.g., derived from the individual to be treated) . III. Pharmaceutical Compositions
[0175] Also provided are compositions comprising any of the engineered cells (e.g., engineered immune cells) described herein (e.g., CAR-NK cells comprising any of the IL-15 constructs described herein) . The composition may comprise any number of the engineered cells (e.g., engineered immune cells) . In some embodiments, the composition comprises a single engineered cell (e.g., engineered immune cell) . In some embodiments, the composition comprises at least about any of 1, 10, 100, 1000, 104, 105, 106, 107, 108 or more engineered cells (e.g., engineered immune cells) . In some embodiments, there is provided a pharmaceutical composition comprising any of the engineered cells (e.g., engineered immune cells) described herein (e.g., an allogeneic CAR-NK cell comprising any of the IL-15 constructs described herein) , and a pharmaceutically acceptable carrier.
[0176] Further provided are compositions comprising one or more nucleic acids, vectors (e.g., a viral vector, such as retroviral vector) , or viruses (e.g., AAV, retrovirus or lentivirus) encoding any of the IL-15 constructs (e.g., any of SEQ ID NOs: 2, 29, 45, and 46) and / or chimeric receptor (e.g., CAR, such as SEQ ID NO: 6 or 31) described herein. In other embodiments, the nucleic acid (s) or vector (s) is packaged into a nanoparticle, such as a lipid nanoparticle. The nucleic acid (s) , vector (s) , or virus (es) encoding any one or more of the IL-15 constructs described herein can be packaged and / or formulated for in vitro, ex vivo, and / or in vivo administration as known in the art, e.g., Tan et al. (2020) J Control Release. 323: 240–252, hereby incorporated by reference in its entirety. In some embodiments, there is provided a pharmaceutical composition comprising any of the nucleic acid (s) , vector (s) , or virus (es) described herein which encode any of the IL-15 constructs and / or chimeric receptor (e.g., CAR) described herein, and a pharmaceutically acceptable carrier.
[0177] In some embodiments, provided herein is a pharmaceutical composition comprising: (a) a first nucleic acid comprising a sequence encoding a IL-15 construct (e.g., any of SEQ ID NOs: 2, 29, 45, and 46) , and (b) a second nucleic acid comprising a sequence encoding a chimeric receptor (e.g., CAR, such as SEQ ID NO: 6 or 31) provided herein, and ii) optionally a pharmaceutically acceptable excipient.
[0178] In some embodiments, provided herein is a pharmaceutical composition comprising: i) a vector comprising (a) a first nucleic acid comprising a sequence encoding a IL-15 construct (e.g., any of SEQ ID NOs: 2, 29, 45, and 46) , and (b) a second nucleic acid comprising a sequence encoding a chimeric receptor (e.g., CAR, such as SEQ ID NO: 6 or 31) provided herein, and ii) optionally a pharmaceutically acceptable excipient.
[0179] In some embodiments, provided herein is a pharmaceutical composition comprising: i) a first vector comprising a nucleic acid comprising a sequence encoding a IL-15 construct (e.g., any of SEQ ID NOs: 2, 29, 45, and 46) ; ii) a second vector comprising a nucleic acid comprising a sequence encoding a chimeric receptor (e.g., CAR, such as SEQ ID NO: 6 or 31) provided herein; and iii) optionally a pharmaceutically acceptable excipient.
[0180] Also provided are the compositions (e.g., pharmaceutical compositions) for use in any one of the treatment methods described herein, and use of the compositions (e.g., pharmaceutical compositions) in preparation of a medicament for any one of the treatment methods described herein. A. Pharmaceutical Compositions
[0181] “Carriers” as used herein include pharmaceutically acceptable carriers, excipients, or stabilizers which are nontoxic to the cells or individual being exposed thereto at the dosages and concentrations employed. Often the physiologically acceptable carrier is an aqueous pH buffered solution. Examples of suitable pharmaceutical carriers are well known in the art and include phosphate buffered saline solutions, water, emulsions, such as oil / water emulsions, various types of wetting agents, sterile solutions, etc. Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed.
[0182] Pharmaceutical compositions comprising such carriers can be formulated by well-known conventional methods. The solvent or diluent is preferably isotonic, hypotonic or weakly hypertonic and has a relatively low ionic strength. Representative examples include sterile water, physiological saline (e.g., sodium chloride) , Ringer's solution, glucose, trehalose or saccharose solutions, Hank's solution, and other aqueous physiologically balanced salt solutions (see, for example, the most current edition of Remington: The Science and Practice of Pharmacy, A. Gennaro, Lippincott, Williams&Wilkins) .
[0183] In some embodiment, each component is “pharmaceutically acceptable” in the sense of being compatible with the other ingredients of a pharmaceutical composition, 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, a pharmaceutically acceptable excipient is an aqueous pH buffered solution.
[0184] The pharmaceutical compositions described herein may be administered via any suitable routes. In some embodiments, the pharmaceutical composition is administered parenterally (e.g., intravenously or subcutaneously) , intraluminally, intra-arterially (into an artery) , intrathecally, intramuscularly, or locally (e.g., intratumorally) . In some embodiments, the pharmaceutical composition is administered intravenously (e.g., through a peripheral or central catheter) . In some embodiments, the pharmaceutical composition is administered to the individual via infusion or injection. In some embodiments, the pharmaceutical composition is administered directly to the target site, e.g., by biolistic delivery to an internal or external target site or by catheter to a site in an artery. In some embodiments, the pharmaceutical composition is administered locally, e.g., intratumorally. Administrations may use conventional syringes and needles or any compound or device available in the art capable of facilitating or improving delivery of the active agent (s) in the subject.
[0185] Preparations for parenteral administration include sterile aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic / aqueous solutions, emulsions, or suspensions, including saline and buffered media. Parenteral vehicles include sodium chloride solution, Ringer's dextrose, dextrose and sodium chloride, lactated Ringer's, or fixed oils. Intravenous vehicles include fluid and nutrient replenishers, electrolyte replenishers (such as those based on Ringer's dextrose) , and the like. Preservatives and other additives may also be present such as, for example, antimicrobials, antioxidants, chelating agents, and inert gases and the like. In addition, the pharmaceutical composition of the present disclosure might comprise proteinaceous carriers, like, e.g., serum albumin or immunoglobulin, preferably of human origin.
[0186] In some embodiments, the pharmaceutical composition is suitably buffered for human use. Suitable buffers include without limitation phosphate buffer (e.g. PBS) , bicarbonate buffer, and / or Tris buffer capable of maintaining a physiological or slightly basic pH (e.g., from approximately pH 7 to approximately pH 9, such as about pH 7 to about pH 7.6) . In some embodiments, the pharmaceutical composition can also be made to be isotonic with blood by the addition of a suitable tonicity modifier, such as glycerol.
[0187] Tonicity agents, sometimes known as “stabilizers” are present to adjust or maintain the tonicity of liquid in a composition. Tonicity agents may include polyhydric sugar alcohols, preferably trihydric or higher sugar alcohols, such as glycerin, erythritol, arabitol, xylitol, sorbitol, and / or mannitol.
[0188] Suitable non-ionic surfactants can be used in the pharmaceutical composition include polysorbates (20, 40, 60, 65, 80, etc. ) , polyoxamers (184, 188, etc. ) , polyols, polyoxyethylene sorbitan monoethers ( etc. ) , lauromacrogol 400, polyoxyl 40 stearate, polyoxyethylene hydrogenated castor oil 10, 50 and 60, glycerol monostearate, sucrose fatty acid ester, methyl cellulose and carboxymethyl cellulose. Anionic detergents that can be used include sodium lauryl sulfate, dioctyle sodium sulfosuccinate and dioctyl sodium sulfonate. Cationic detergents include benzalkonium chloride or benzethonium chloride.
[0189] In some embodiments, the pharmaceutical composition is contained in a single-use vial, such as a single-use sealed vial. In some embodiments, the pharmaceutical composition is contained in a multi-use vial. In some embodiments, the pharmaceutical composition is contained in bulk in a container.
[0190] In some embodiments, the pharmaceutical composition is formulated for fresh infusion or cryopreserved for later administration.
[0191] In some embodiments, the pharmaceutical composition must meet certain standards for administration to an individual. 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 therapeutic cells. In some embodiments, “substantially free” is less than about any of 10%, 5%, 1%, 0.1%, 0.01%, 0.001%, 1ppm 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 therapeutic 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 therapeutic 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) . The pharmaceutical composition may be free of mycoplasma contamination, free of detectable microbial agents, and / or 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. B. Kits
[0192] Also provided are kits, unit dosages, and articles of manufacture comprising any one of the engineered cells (e.g., engineered immune cells) described herein, or any of the isolated nucleic acids or vectors described herein which encode any one of the IL-15 constructs and / or chimeric receptors (e.g., CAR) described herein.
[0193] In some embodiments, a kit is provided which contains any one of the pharmaceutical compositions described herein and preferably provides instructions for its use. In some embodiments, there is provided a kit comprising: (a) any one of the engineered cells (e.g., engineered immune cells) described herein, isolated nucleic acid (s) , vector (s) (e.g., viral vectors) , or virus (e.g., AAV, retrovirus, or lentivirus) encoding any of the IL-15 constructs and / or chimeric receptors described herein, or pharmaceutical composition comprising thereof; and (b) instructions for use in any one of the treatment or producing methods described herein. The kits 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.
[0194] In some embodiments, the kit 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 cells such as engineered immune cells described herein) . In some embodiments, the kit comprises reagents suitable for expanding the engineered cells (e.g., engineered immune cells) , such as media, cytokine, ITSEA, and human albumin serum.
[0195] 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 invention also will typically include a means for containing any of the engineered cells (e.g., engineered immune cells) described herein, isolated nucleic acid (s) , vector (s) (e.g., viral vectors) , or virus (e.g., AAV, retrovirus, or lentivirus) encoding any of the IL-15 constructs and / or chimeric receptors described herein, or pharmaceutical composition comprising thereof, 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.
[0196] In some embodiments, the kits may further comprise instruction (s) on methods of making or methods of treatment using any of the engineered cells (e.g., engineered immune cells) described herein, isolated nucleic acid (s) , vector (s) (e.g., viral vectors) , or virus (e.g., AAV, retrovirus, or lentivirus) encoding any of the IL-15 constructs and / or chimeric receptors described herein, or pharmaceutical composition comprising thereof, such as any of the methods of making or methods of treatment described herein. IV. Methods of Making Engineered Cells
[0197] Also provided are methods of making any of the engineered cells (e.g., engineered immune cells such as engineered CAR-NK cells) described herein, such as an engineered cell (e.g., engineered immune cell) comprising any of the IL-15 constructs (e.g., any of SEQ ID NOs: 2, 29, 45, and 46) and / or chimeric receptors (e.g., CAR, such as SEQ ID NO: 6 or 31) described herein. Also provided are methods of making any of the IL-15 constructs and / or chimeric receptors 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” can be used herein to make the engineered cells (e.g., engineered immune cells) , IL-15 constructs and / or chimeric receptors. Also see Example 1 for exemplary making methods, and Examples 2-5 for testing methods.
[0198] In some embodiments, there is provided a method of making any of the engineered cells (e.g., engineered immune cells, such as an engineered CAR-NK cell) described herein, wherein the method comprises introducing into a population of precursor cells (e.g., precursor immune cells or stem cells) any of the isolated nucleic acid (s) or vector (s) described herein encoding the IL-15 construct and / or chimeric receptor (e.g., by contacting the precursor cells with any of the recombinant viruses (e.g., AAV or retrovirus) described herein) . In some embodiments, there is provided a method of making an engineered cell (e.g., engineered immune cell) , comprising introducing into a population of precursor cell (e.g., precursor immune cells or stem cells) a nucleic acid (e.g., first nucleic acid) or a vector (e.g., viral vector) encoding an IL-15 construct (e.g., any of the IL-15 constructs described herein) , wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12. In some embodiments, the method further comprises introducing into the population of precursor cells (e.g., precursor immune cells or stem cells) a second nucleic acid encoding a chimeric receptor (e.g., CAR, such as anti-BCMA CAR) . The second nucleic acid can be introduced into the population of precursor cells (e.g., precursor immune cells or stem cells) before or after introducing the first nucleic acid. In some embodiments, the first and second nucleic acids are introduced into the population of precursor cells (e.g., precursor immune cells or stem cells) simultaneously, such as using different vectors or using a single vector. In some embodiments, the precursor cell (e.g., precursor immune cell or stem cell) expresses a chimeric receptor (e.g., CAR, such as anti-BCMA CAR) before introducing the nucleic acid encoding the IL-15 construct. In some embodiments, the method further comprises providing (e.g., harvesting and / or isolating from an individual) the population of precursor cells (e.g., precursor immune cells or stem cells) before introducing any nucleic acid. In some embodiments, the method further comprises isolating and / or enriching (e.g., via FACS) a plurality of engineered cell (e.g., engineered immune cells) that express the IL-15 construct and / or the chimeric receptor. In some embodiments, the precursor immune cell is selected from the group of T cell, NK cell, NKT cell, B cell, macrophage, monocyte, CIK cell, and PBMC. In some embodiments, the precursor cell is a stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., an immune cell) differentiated therefrom. In some embodiments, the method further comprises modifying the precursor cell (e.g., precursor immune cell or stem cell) or the engineered cell (e.g., engineered immune cell) to reduce (e.g., reducing at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or more) the expression and / or function of one or more factors involved in host-versus-graft (HvG) response and / or graft-versus-host (GvH) response. In some embodiments, the precursor cell is an NK cell.
[0199] In some embodiments, the method further comprises modifying the precursor cell (e.g., precursor NK cell) or the engineered cell (e.g., engineered NK cell) to reduce (e.g., reducing at least about any of 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, or more) the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules, such as via siRNA, shRNA, clustered regularly interspaced short palindromic repeats / Cas protein (CRISPR / Cas) , transcription activator-like (TAL) effector nucleases (TALEN) , or Zinc finger nucleases (ZNF) , etc. techniques, or by expressing a dominant negative protein or fragment thereof. In some embodiments, DNA or RNA editing can be employed, such as gene knockout (KO) or gene knockdown (KD) . Reduction of MHC I and / or MHC II molecule expression and / or function can be accomplished, for example, by one or more of the following: (1) knockout or knockdown the polymorphic HLA alleles (HLA-A, HLA-B, HLA-C) and MHC-II genes directly; (2) knockout or knockdown B2M and / or TAP1, which will prevent surface trafficking of all MHC-I molecules; (3) knockout or knockdown of CIITA, which will prevent surface trafficking of all MHC-II molecules; and / or (4) knockout or knockdown of components of the MHC enhanceosomes, such as NLRC5, RFX5, RFXANK, RFXAP, IRF1, NF-Y (including NFY-A, NFY-B, NFY-C) , and CIITA that are critical for HLA expression. In some embodiments, the method comprises knocking out TCR gene and / or B2M (β-2-microglobulin) gene of precursor cell or the engineered cell. For example, in some embodiments, the method further comprises introducing one or more additional nucleic acids into the cell (e.g., precursor cell such as precursor immune cell or stem cell, or engineered cell such as engineered immune cell) , wherein the one or more additional nucleic acids encode components of a CRISPR / Cas system, e.g., a third nucleic acid encoding a gRNA which target a nucleic acid sequence encoding a factor involved in HvG response and / or GvH response, and a fourth nucleic acid encoding a Cas (e.g., Cas9) .
[0200] In some embodiments, the method further comprises modifying the precursor cell (e.g., precursor immune cell such as NK cell, or stem cell) or the engineered cell (e.g., engineered immune cell) to increase (e.g., increasing at least about any of 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95%, 99%, 1-fold, 2-fold, 5-fold, or more) the expression and / or function of, e.g., overexpress, one or more tolerogenic factors. The one or more tolerogenic factors may be selected from the group consisting of HLA Class I histocompatibility antigen, alpha chain E (HLA-E) , CD47, CD24, CD26, CD27, CD31, CD35, CD200, human leukocyte antigen-C (HLA-C) , human leukocyte antigen-G (HLA-G) , programmed death-ligand 1 (PD-L1) , indoleamine 2, 3-dioxygenase 1 (IDO1) , CTLA4-Ig, C1 esterase inhibitor (C1-inhibitor) , IL-10, IL-35, Fas ligand (FASL) , double homeobox, 4 (DUX4) , chemokine (C-C motif) ligand 21 (CCL21) , milk fat globule-EGF factor 8 protein (MFGE8) , serpin family B member 9 (SERPINB9) , and any combination thereof. In some embodiments, the precursor cell (e.g., precursor NK cell) or the engineered cell (e.g., engineered NK cell) may be modified to overexpress one or more tolerogenic factors. In some embodiments, the method comprises introducing into a population of precursor cells (e.g., precursor immune cells or stem cells) or engineered cells (e.g., engineered NK cell, such as CAR-NK cells) a nucleic acid encoding one or more tolerogenic factors. In some embodiments, the overexpression of one or more endogenous tolerogenic factors may be achieved by modifying one or more regulating elements (e.g., promoter) of the genes encoding the endogenous tolerogenic factors. In some embodiments, increasing the function of one or more tolerogenic factors in a cell may comprise mutating (e.g., gain-of-function mutation) a gene encoding the one or more tolerogenic factors, such that the mutant version of the one or more tolerogenic factors has higher activity compared to the non-mutated version. In some embodiments, overexpression and / or mutation for increasing function of a tolerogenic factor may be achieved by a gene editing system known in the art (e.g., CRISPR / Cas, TALENs, or ZFNs) . In some embodiments, overexpression of the one or more tolerogenic factors may be achieved by knocking in an exogenous nucleic acid sequence encoding the one or more tolerogenic factors.
[0201] In some embodiments, there is provided a method of making an engineered cell (e.g., engineered immune cell such as an engineered CAR-NK cell) , wherein the engineered cell comprises: (1) a first nucleic acid encoding an IL-15 construct that comprises an IL-15 moiety and a transmembrane domain derived from DAP12 (e.g., any of the IL-15 constructs described herein, such as any of SEQ ID NOs: 2, 29, 45, and 46) ; and optionally (2) a second nucleic acid encoding a chimeric receptor (e.g., CAR, such as SEQ ID NO: 6 or 31) ; wherein the method comprises introducing into a population of precursor cells (e.g., precursor immune cells or stem cells) the first nucleic acid and optionally the second nucleic acid. In some embodiments, the method further comprises providing (e.g., harvesting and / or isolating from a sample from an individual or directly from the individual) the population of precursor cells (e.g., precursor immune cells or stem cells) before introducing the first nucleic acid and / or the second nucleic acid. Hence in some embodiments, the engineered cell (e.g., engineered immune cell) is made from a method comprising: (a) providing a population of precursor cells (e.g., precursor immune cells or stem cells) , and (b) introducing into the population of precursor cells (i) a first nucleic acid encoding an IL-15 construct that comprises an IL-15 moiety and a transmembrane domain derived from DAP12 (e.g., any of the IL-15 constructs described herein) , and (ii) optionally a second nucleic acid encoding a chimeric receptor (e.g., CAR) . 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 precursor cells (e.g., precursor immune cells or stem cells) simultaneously. In some embodiments, the first nucleic acid is introduced into the population of precursor cells (e.g., precursor immune cells or stem cells) before introducing the second nucleic acid. In some embodiments, the method further comprises isolating and / or enriching a plurality of engineered cells (e.g., engineered immune cells) expressing the IL-15 construct, then introducing into the plurality of engineered cells expressing the IL-15 construct the second nucleic acid encoding the chimeric receptor (e.g., CAR) . In some embodiments, the second nucleic acid is introduced into the population of precursor cells (e.g., precursor immune cells or stem cells) before introducing the first nucleic acid. In some embodiments, the method further comprises isolating and / or enriching a plurality of engineered cells (e.g., engineered immune cells) expressing the chimeric receptor (e.g., CAR) , then introducing into the plurality of engineered cells expressing the chimeric receptor the first nucleic acid encoding the IL-15 construct. In some embodiments, the first nucleic acid and the second nucleic acid are on a single 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 cells (e.g., engineered immune cells) that express both the IL-15 construct and the chimeric receptor (e.g., CAR) . In some embodiments, the engineered cell is an engineered immune cell selected from the group consisting of a T cell, an NK cell, an NKT cell, a B cell, a macrophage, a monocyte, a dendritic cell, a CIK cell, a PBMC, and any combination thereof. In some embodiments, the engineered cell is an engineered stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., immune cell) differentiated therefrom. In some embodiments, the engineered immune cell is an NK cell.
[0202] Also provided are methods of: i) promoting persistence and / or expansion of a cell (e.g., an immune cell) , ii) reducing the by-stander killing effect on surrounding cells (e.g., host cells) by a cell (e.g., immune cell) , and / or iii) reducing HvG response of a cell (e.g., immune cell) , comprising modifying the cell to express an IL-15 construct comprising an IL-15 moiety and a transmembrane domain derived from DAP12 (any of the IL-15 constructs provided herein, such as any of SEQ ID NOs: 2, 29, 45, and 46) . In some embodiments, there is provided a method of: i) promoting persistence and / or expansion of a cell (e.g., an immune cell, such as CAR-expressing immune cell) , ii) reducing the by-stander killing effect on surrounding cells (e.g., host cells) by a cell (e.g., an immune cell, such as CAR-expressing immune cell) , and / or iii) reducing HvG response of a immune cell (e.g., an immune cell, such as CAR-expressing immune cell) , comprising introducing into the cell a nucleic acid (e.g., first nucleic acid) encoding an IL-15 construct (any of the IL-15 constructs provided herein, such as any of SEQ ID NOs: 2, 29, 45, and 46) , wherein the IL-15 construct comprises an IL-15 moiety (e.g., comprising SEQ ID NO: 1) , an optional hinge domain (e.g., derived from CD8, such as SEQ ID NO: 21) , and a transmembrane domain derived from DAP12 (e.g., comprising SEQ ID NO: 18) . In some embodiments, the cell (e.g., immune cell) expresses a chimeric receptor (e.g., CAR) before introducing the nucleic acid (e.g., first nucleic acid) encoding the IL-15 construct. In some embodiments, the method further comprises introducing into the cell (e.g., immune cell) a second nucleic acid encoding a chimeric receptor (e.g., CAR) . The second nucleic acid can be introduced into the cell (e.g. immune cell) before or after introducing the first nucleic acid. In some embodiments, the first and second nucleic acids are introduced into the cell (e.g. immune cell) simultaneously, such as using different vectors or using a single vector. In some embodiments, the chimeric receptor is an anti-BCMA sdAb CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, the cell is an immune cell selected from the group consisting of a T cell, an NK cell, an NKT cell, a B cell, a macrophage, a monocyte, a dendritic cell, a CIK cell, a PBMC, and any combination thereof. In some embodiments, the cell is a stem cell (such as ESC, PSC, iPSCs, or HSCs) or a cell (e.g., immune cell) differentiated therefrom. In some embodiments, the immune cell is an NK cell, such as CAR-NK. In some embodiments, the method of: i) promoting persistence and / or expansion of a cell (e.g., immune cell) , ii) reducing the by-stander killing effect on surrounding cells (e.g., host cells) by a cell (e.g., immune cell) , and / or iii) reducing HvG response of a cell (e.g., immune cell) is compared to a method using a reference cell (e.g., reference immune cell, such as CAR-expressing immune cell) that does not express the IL-15 construct.
[0203] Graft-versus-host (GvH) response can happen when donor immune cells (e.g., T cells) recognize the recipient’s cells as foreign, resulting in attack of the recipient’s healthy tissues. GvH disease (GvHD) can be mediated by TCR on the surface of donor T cells, which recognize HLA on the host cells as foreign and initiate the attack by the donor T cells. Host-versus-graft (HvG) response can happen when immune cells (e.g., T cells) in the recipient (i.e., host) recognize the donor cells as foreign, resulting in attack of the donor cells and graft rejection. HvG disease (HvGD) can be mediated by TCRs on the surface of host T cells, which recognize HLA on the donor cells as foreign and initiate the attack by the host T cells. In some embodiments, the HvG response is mediated by host T cells. In some embodiments, the HvG response is mediated by host NK cells.
[0204] In some embodiments, the first nucleic acid encoding the IL-15 construct and the second nucleic acid encoding the chimeric receptor (e.g., CAR) are introduced into the population of precursor cells (e.g. precursor immune cells or stem cells) simultaneously. In some embodiments, the first nucleic acid and the second nucleic acid are on a single vector. The first nucleic acid can be upstream or downstream of the second nucleic acid when located on a single vector. In some embodiments, the first nucleic acid and the second nucleic acid are on a single 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 a single vector and under the control of a single promoter, wherein the first nucleic acid and the second nucleic acid are connected via a linking sequence, such as IRES, or a sequence 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. In some embodiments, the cleavable linker is a P2A peptide comprising the amino acid sequence of SEQ ID NO: 7.
[0205] In some embodiments, the first nucleic acid and / or the second nucleic acid are introduced into the cells (e.g. 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.
[0206] 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.
[0207] In some embodiments, the nucleic acids are introduced into the cells (e.g. immune cells) by transfecting any one of the isolated nucleic acids or vectors described herein. Methods of introducing vectors or isolated nucleic acids into a mammalian cell are known in the art. The vectors described herein can be transferred into a cell (e.g. an immune cell) by physical, chemical, or biological methods. In some embodiments, the IL-15 constructs and / or chimeric receptors (e.g., CAR) described herein is expressed by introducing a nucleic acid comprising a sequence encoding the IL-15 constructs and / or chimeric receptors (e.g., CAR) into a cell in vivo (in vivo cell therapy) or in vitro (including autologous cell therapy and allogeneic cell therapy) . In some embodiments, the cell is an immune cell.
[0208] Physical methods for introducing an isolated nucleic acid or vector into a precursor 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.
[0209] Biological methods for introducing an isolated nucleic acid or vector into a precursor 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.
[0210] Chemical means for introducing an isolated nucleic acid or vector into a precursor 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) .
[0211] RNA molecules encoding any of the IL-15 constructs and / or chimeric receptors described herein may be prepared by a conventional method (e.g., in vitro transcription) and then introduced into the precursor cells via known methods such as mRNA electroporation. See, e.g., Rabinovich et al., Human Gene Therapy 17: 1027-1035 (2006) .
[0212] The transduced or transfected precursor cell can be propagated ex vivo after introduction of the vector or isolated nucleic acid. For example, the transduced or transfected cells (e.g., 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 cells (e.g., immune cells) may be further evaluated or screened to select the engineered mammalian cell, e.g., expressing the IL-15 construct and / or chimeric receptor.
[0213] 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.
[0214] Other methods to confirm the presence of the nucleic acid, 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) .
[0215] In some embodiments, the chimeric receptor and / or the IL-15 construct described herein is introduced to the cell (e.g., 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) .
[0216] In some embodiments, the cell (e.g., precursor cell or 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 PBMCs, 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.
[0217] T cells can be isolated from PBMCs 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.
[0218] Enrichment of a T cell population by negative selection can be accomplished with a combination of antibodies directed to surface markers unique to the negatively selected cells. One method is cell sorting and / or selection via negative magnetic immunoadherence or flow cytometry that uses a cocktail of monoclonal antibodies directed to cell surface markers present on the cells negatively selected. For example, to enrich for CD4+ cells by negative selection, a monoclonal antibody cocktail typically includes antibodies to CD14, CD20, CD11b, CD16, HLA-DR, and CD8. It may be desirable to enrich for or positively select for regulatory T cells which typically express CD4+, CD25+, CD62Lhi, GITR+, and FoxP3+. Alternatively, in certain embodiments, T regulatory cells are depleted by anti-CD25 conjugated beads or other similar method of selection.
[0219] For isolation of a desired population of cells by positive or negative selection, the concentration of cells and surface (e.g., particles such as beads) can be varied. It may be desirable to significantly decrease the volume in which beads and cells are mixed together (i.e., increase the concentration of cells) , to ensure maximum contact of cells and beads. Using high concentrations may result in increased cell yield, cell activation, and cell expansion. Further, use of high cell concentrations may allow more efficient capture of cells that may weakly express target antigens of interest, such as CD28-negative T cells, or from samples where there are many tumor cells present (i.e., leukemic blood, tumor tissue, etc. ) . Such populations of cells may have therapeutic value and would be desirable to obtain. In some embodiments, using high concentration of cells allows more efficient selection of CD8+ T cells that normally have weaker CD28 expression.
[0220] 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.
[0221] 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. Many freezing solutions and parameters are known in the art and will be useful in this context. The cells can be 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.
[0222] In some embodiments, cryopreserved cells are thawed and washed as described herein and allowed to rest (e.g., for one hour) at room temperature prior to activation.
[0223] In some embodiments, prior to or after genetic modification of the T cells 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.
[0224] 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) ) .
[0225] In addition to CD4 and CD8 markers of T cells, 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.
[0226] In some embodiments, the cell (e.g., precursor cell or engineered immune cell) is an NK cell. NK cells are lymphoid cells that participate in immune reactions. They have the functions of killing of tumor cells, cells undergoing oncogenic transformation and other abnormal cells in a living body, and are important components of innate immunological surveillance mechanisms. NK cells possess mechanisms distinguishing between “foreign” or potential target cells and healthy “self” cells via a multitude of inhibitory and activating receptors that engage MHC class I molecules, MHC class I-like molecules, and molecules unrelated to MHC (Caliguiri, Blood 2008, 112: 461-69) . Cells (e.g., T cells such as allogeneic T cells) with reduced or absent HLA class I expression are targeted by NK cells as “foreign, ” leading to rejection reactions (Liu et al. Curr. Res. Transl. Med. 2018; 66: 39–42) .
[0227] NK cells express characteristic NK cell surface receptors, and lack both TCR rearrangement and T cell, B cell, monocyte and / or macrophage cell surface markers. NK cells exhibit cytotoxicity by releasing small cytoplasmic granules of proteins (perforin and granzyme) that cause the target cell to die by apoptosis. Killing is triggered in a contact-dependent, non-phagocytotic process which does not require prior sensitization to an antigen. Human NK cells are characterized by the presence of the cell-surface markers CD16 and CD56, and the absence of the T cell receptor (CD3) . Human bone marrow-derived NK cells are further characterized by the CD2+CD16+CD56+CD3-phenotype, further containing the T-cell receptor zeta-chain [zeta (Q-TCR] , and often characterized by NKp46, NKp30 or NKp44. Inhibitory NK cell receptors include HLA-E (CD94 / NKG2A) ; HLA-C (group 1 or 2) , KIR2DL; KIR3DL (HLA-B Bw4) and HLA-A3 or A4 + peptide. Activating NK cell receptors include HLA-E (CD94 / NKG2C) ; KIR2DS (HLA-C) and KIR3DS (HLA-Bw4) . Other receptors include the NK cell receptor protein-1 (termed NK1.1 in mice) and the low affinity receptor for the Fc portion of IgG (FcyRIII; CD16) .
[0228] Methods of isolation, culture, induction, expansion, and enrichment of NK cells are well known in the art, e.g., US9, 938, 498, or Magee et al. ( “Chapter Nine -Isolation, culture and propagation of natural killer cells, ” Natural Killer Cells, Basic Science and Clinical Application, 2010, Pages 125-135) . For example, FACS with antibodies against NK cell specific markers can be used for NK cell isolation and / or enrichment. In some embodiments, NK cells can be isolated by enriching CD56+ cells. In some embodiments, NK cells can be isolated by depleting CD3+cells.
[0229] NK cells of the present invention may be derived from any source which comprises such cells. NK cells are found in many tissues, and can be obtained, for example, from lymph nodes, spleen, liver, lungs, intestines, deciduas and can also be obtained from iPSCs or ESCs. Typically, cord blood, peripheral blood, mobilized peripheral blood and bone marrow, which contain heterogeneous lymphocyte cell populations, are used to provide large numbers of NK cells for research and clinical use. In some embodiments, the method comprises culturing a population of NK cells derived from one of cord blood, peripheral blood or bone marrow. In some embodiments, NK cells are cultured from a heterogeneous cell population comprising NK cells, CD3-cells and CD3+ cells. In one embodiment the CD3+ fraction is greater than the CD3-NK cell fraction, as is typical of bone marrow, cord blood or peripheral blood. In some embodiments, the NK cell population is selected or enriched for NK cells. In some embodiments NK cells can be propagated from fresh cell populations, while other embodiments propagate NK cells from stored cell populations (such as cryopreserved and thawed cells) or previously cultured cell populations. In some embodiments, NK cells are from a cell line, such as In some embodiments, the NK cells are a homogenous NK cell population (i.e., express the same cell surface markers) . In some embodiments, the NK cells are a heterogeneous NK cell population. In some embodiments, the NK cells are a selected NK cell population, e.g., CD56+CD3-NK cells, CD56+CD16+CD3-NK cells, or CD56+CD16-CD3-NK cells. Methods for selection of NK cells according to phenotype are well known in the art, e.g., immunodetection or FACS analysis.
[0230] Methods for enriching and isolating lymphocytes are well known in the art, and appropriate methods can be selected based on the desired population. For example, in one approach, the source material is enriched for lymphocytes by removing red blood cells. In its simplest form, removal of red blood cells can involve centrifugation of unclotted whole blood or bone marrow. Based on density red blood cells are separated from lymphocytes and other cells. The lymphocyte rich fractions can then be selectively recovered. Lymphocytes and their progenitors can also be enriched by centrifugation using separation mediums such as standard Lymphocyte Separation Medium (LSM) available from a variety of commercial sources. Alternatively, lymphocytes / progenitors can be enriched using various affinity-based procedures. Numerous antibody mediated affinity preparation methods are known in the art such as antibody conjugated magnetic beads. Lymphocyte enrichment can also be performed using commercially available preparations for negatively selecting unwanted cells, such as FICOLL-HYPAQUETM and other density gradient mediums formulated for the enrichment of whole lymphocytes, T cells or NK cells. V. Methods of Treatment
[0231] One aspect of the present application relates to methods of treating a disease or condition in an individual (such as a human individual) , comprising administering to the individual an effective amount of any of the engineered cells (e.g. engineered immune cells) comprising an IL-15 construct described herein, nucleic acid (s) , vector (s) (such as viral vector) , or virus (es) (e.g., AAV, retrovirus, or lentivirus) encoding any of the IL-15 constructs and / or chimeric receptor (e.g., CAR) described herein, or pharmaceutical composition comprising thereof. Hence in some embodiments, there is provided a method of treating a disease or condition in an individual (e.g., human) , comprising administering to the individual an effective amount of an engineered cell (e.g., an engineered immune cell such as an engineered NK cell) comprising an IL-15 construct (e.g., any of the IL-15 constructs described herein, e.g., any of SEQ ID NOs: 2, 29, 45, and 46) (or a pharmaceutical composition comprising thereof) , wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12. In some embodiments, the engineered cell (e.g. the engineered immune cell) further expresses a chimeric receptor, such as CAR, e.g., anti-BCMA CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, the engineered cell (e.g. engineered immune cell) is allogenic. In some embodiments, the engineered cell (e.g. engineered immune cell) is autologous. The present application contemplates gene therapy using nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, lentivirus or retrovirus) encoding any of the IL-15 constructs described herein (optionally further using the nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, retrovirus or lentivirus) encoding any of the chimeric receptors described herein) . In some embodiments, there is provided a method of treating a disease or condition in an individual (e.g., human) , comprising administering (e.g., i.v. or s.c. ) to the individual an effective amount of a nucleic acid, a vector (such as viral vector) , or a virus (e.g., AAV, retrovirus or lentivirus) encoding an IL-15 construct (e.g., any of the IL-15 constructs described herein, e.g., any of SEQ ID NOs: 2, 29, 45, and 46) (or a pharmaceutical composition comprising the nucleic acid or vector) , wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12. In some embodiments, the method further comprises administering (e.g., i.v. or s.c. ) to the individual an effective amount of a nucleic acid, a vector (such as viral vector) , or a virus (e.g., AAV, retrovirus or lentivirus) encoding a chimeric receptor, such as CAR, e.g., anti-BCMA CAR comprising the amino acid sequence of SEQ ID NO: 6 or 31. In some embodiments, the disease or condition is cancer (e.g., BCMA-positive cancer) , an autoimmune disorder, or an infection (or infectious disease) .
[0232] The present application contemplates engineered cells (e.g. engineered immune cells, such as IL-15 construct-expressing immune cells) , as well as nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, retrovirus, or lentivirus) encoding any of the IL-15 constructs described herein, that can be administered either alone or in any combination with another therapy (e.g., antibody therapy or immune cell therapy) , and in at least some aspects, together with a pharmaceutically acceptable carrier or excipient. In some embodiments, prior to administration, the engineered cells (e.g. engineered immune cells) , or nucleic acids, vectors, or viruses, may be combined with suitable pharmaceutical carriers and excipients that are well known in the art.
[0233] In some embodiments, the methods described herein are suitable for treating a solid cancer. The methods are applicable to cancers of all stages, including early stage, advanced stage and metastatic cancer. The methods described herein may be used as a first therapy, second therapy, third therapy, or combination therapy with other types of cancer therapies known in the art, such as 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.
[0234] In some embodiments, the cancer is a solid cancer, such as selected from the group consisting of colon cancer, rectal cancer, renal-cell carcinoma, liver cancer, non-small cell carcinoma of the lung, cancer of the small intestine, cancer of the esophagus, melanoma, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous or intraocular malignant melanoma, uterine cancer, ovarian cancer, rectal cancer, cancer of the anal region, stomach cancer, testicular cancer, uterine cancer, carcinoma of the fallopian tubes, carcinoma of the endometrium, carcinoma of the cervix, carcinoma of the vagina, carcinoma of the vulva, Hodgkin's Disease, non-Hodgkin's lymphoma, cancer of the endocrine system, cancer of the thyroid gland, cancer of the parathyroid gland, cancer of the adrenal gland, sarcoma of soft tissue, cancer of the urethra, cancer of the penis, solid tumors of childhood, cancer of the bladder, cancer of the kidney or ureter, carcinoma of the renal pelvis, neoplasm of the central nervous system (CNS) , primary CNS lymphoma, tumor angiogenesis, spinal axis tumor, brain stem glioma, pituitary adenoma, Kaposi's sarcoma, epidermoid cancer, squamous cell cancer, T-cell lymphoma, environmentally induced cancers, combinations of said cancers, and metastatic lesions of said cancers.
[0235] In some embodiments, the cancer is a hematologic cancer, such as selected from the group consisting of chronic lymphocytic leukemia (CLL) , acute leukemias, acute lymphoid leukemia (ALL) , B-cell acute lymphoid leukemia (B-ALL) , T-cell acute lymphoid leukemia (T-ALL) , chronic myelogenous leukemia (CIVIL) , B cell prolymphocytic leukemia, blastic plasmacytoid dendritic cell neoplasm, Burkitt's lymphoma, diffuse large B cell lymphoma (DLBCL) , follicular lymphoma (FL) , hairy cell leukemia, small cell-or a large cell-follicular lymphoma, malignant lymphoproliferative conditions, MALT lymphoma, mantle cell lymphoma, marginal zone lymphoma, multiple myeloma, myelodysplasia and myelodysplastic syndrome, non-Hodgkin's lymphoma, Hodgkin's lymphoma, plasmablastic lymphoma, plasmacytoid dendritic cell neoplasm, Waldenstrom macroglobulinemia, and pre-leukemia.
[0236] In some embodiments, when the engineered cell (e.g. engineered immune cell) expresses an anti-BCMA chimeric receptor (e.g., CAR, such as any of the anti-BCMA CARs described herein) , the methods described herein can be suitable for treating BCMA-positive cancer. In some embodiments, BCMA-positive cancer is a hematological cancer, such as multiple myeloma (MM) , Hodgkin's lymphoma, non-Hodgkin's lymphoma (NHL) (e.g., diffuse large B-cell lymphoma (DLBCL) , follicular lymphoma (FL) , mantle cell lymphoma (MCL) , Burkitt lymphoma) , leukemias, and glioblastoma.
[0237] In some embodiments, the cancer is multiple myeloma. In some embodiments, the cancer is stage I, stage II or stage III, and / or stage A or stage B multiple myeloma based on the Durie-Salmon staging system. In some embodiments, the cancer is stage I, stage II or stage III multiple myeloma based on the International staging system published by the International Myeloma Working Group (IMWG) . In some embodiments, the cancer is monoclonal gammopathy of undetermined significance (MGUS) . In some embodiments, the cancer is asymptomatic (smoldering / indolent) myeloma. In some embodiments, the cancer is symptomatic or active myeloma. In some embodiments, the cancer is refractory multiple myeloma. In some embodiments, the cancer is metastatic multiple myeloma. In some embodiments, the individual did not respond to a previous treatment for multiple myeloma. In some embodiments, the individual has progressive disease after a previous treatment of multiple myeloma. In some embodiments, the individual has previously received at least about any one of 2, 3, 4, or more treatment for multiple myeloma. In some embodiments, the cancer is relapsed multiple myeloma.
[0238] In some embodiments, the methods described herein are suitable for treating an autoimmune disease. Autoimmune disease, or autoimmunity, is the failure of an organism to recognize its own constituent parts (down to the sub-molecular levels) as “self, ” which results in an immune response against its own cells and tissues. Any disease that results from such an aberrant immune response is termed an autoimmune disease. Examples of autoimmune diseases include, but are not limited to, acute idiopathic thrombocytopenic purpura, chronic idiopathic thrombocytopenic purpura, dermatomyositis. Sydenham's chorea, myasthenia gravis, systemic lupus erythematosus, lupus nephritis, rheumatic fever, polyglandular syndromes, bullous pemphigoid, diabetes mellitus, Henoch-Schonlein purpura, post-streptococcalnephritis, erythema nodosum. Takayasu's arteritis, Addison's disease, rheumatoid arthritis, multiple sclerosis, sarcoidosis, ulcerative colitis, erythema multiforme, IgA nephropathy, polyarteritis nodosa, ankylosing spondylitis, Goodpasture's syndrome, thromboangitisubiterans, syndrome, primary biliary cirrhosis, Hashimoto's thyroiditis, thyrotoxicosis, scleroderma, chronic active hepatitis, polymyositis / dermatomyositis, polychondritis, pamphigus vulgaris, Wegener's granulomatosis, membranous nephropathy, amyotrophic lateral sclerosis, tabes dorsalis, giant cell arteritis / polymyalgia, pemiciousanemia, rapidly progressive glomerulonephritis, psoriasis, and fibrosing alveolitis. In some embodiments, the autoimmune disease is Coeliac disease, diabetes mellitus type 1 (IDDM) , systemic lupus erythematosus (SLE) , syndrome, multiple sclerosis (MS) , Hashimoto's thyroiditis, Graves' disease, idiopathic thrombocytopenic purpura, or rheumatoid arthritis (RA) . The most common treatments for autoimmune diseases are corticosteroids and cytotoxic drugs, which can be very toxic. These drugs also suppress the entire immune system, can result in serious infection, and have adverse effects on the bone marrow, liver, and kidneys.
[0239] The methods described herein are also suitable for treating various infection or infectious diseases in an individual. The methods are applicable to any relevant type of infection, including but not limited to viral infections, bacterial infections, fungal infections, parasitic infections, and / or any other type of pathogenic infection. The infectious disease may be an infection by a virus selected from the group of HIV, HTLV, Hepatitis C Virus, Hepatitis B Virus, Human Cytomegalovirus (CMV) , HSV, RSV, metapneumovirus (hMPV) , rhinovirus, parainfluenza (NV) , EBV, JC virus (John Cunningham virus) , BK virus, Zika virus, coronavirus, norovirus, encephalitis virus, or Ebola. The infectious disease may be an infection by opportunistic fungal infections such as invasive aspergillosis. In some embodiments, the fungal infection is from Aspergillus or Candida.
[0240] In some embodiments, the methods described herein are suitable for treating or preventing HvG response or HvGD. In some embodiments, the methods described herein are suitable for treating or preventing GvH response or GvHD.
[0241] In some embodiments, the individual, to whom the engineered cells (e.g. engineered immune cells) , nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, retrovirus, or lentivirus) , or pharmaceutical compositions thereof described herein 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. In some embodiments, the engineered cells (e.g. engineered immune cells) are allogenic. In some embodiments, the engineered cells (e.g. engineered immune cells) are autologous.
[0242] Any suitable methods for the administration of an engineered cell (e.g. engineered immune cell) , nucleic acids, vectors (e.g., viral vector) , viruses (e.g., AAV, lentivirus or retrovirus) , or pharmaceutical compositions thereof can be used herein. The route of administration is in accordance with any known and accepted methods, such as by single or multiple bolus or infusion over a long period of time in a suitable manner, e.g., injection or infusion by intravenous, intraperitoneal, intratumoral, intraarterial, or intralesional routes, or by sustained release or extended-release means. In some embodiments, the engineered cell (e.g. engineered immune cell) or pharmaceutical compositions thereof is administered intravenously, such as by infusion. In some embodiments, the engineered cell (e.g. engineered immune cell) or pharmaceutical composition thereof is administered intratumorally. In some embodiments, the nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, lentivirus or retrovirus) encoding any of the IL-15 constructs described herein (optionally further the nucleic acids, vectors (e.g., viral vector) , or viruses encoding any of the chimeric receptors described herein) , or pharmaceutical compositions thereof, are administered intravenously, intramuscularly, subcutaneously, or intratumorally.
[0243] In some embodiments, the pharmaceutical composition provided herein contains the engineered cells (e.g. engineered immune cells) , nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, lentivirus or retrovirus) in amounts effective to treat or prevent the disease or disorder, 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 disease symptoms occurs. However, other dosage regimens may be useful and can be determined.
[0244] Dosages and desired drug concentration of engineered cells (e.g. engineered immune cells) , nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, lentivirus or retrovirus) of the present invention may vary depending on the particular use envisioned. The determination of the appropriate dosage or route of administration is well within the skill of an ordinary artisan. Animal experiments provide reliable guidance for the determination of effective doses for human therapy. Interspecies scaling of effective doses can be performed following the principles laid down by Mordenti, J. and Chappell, W. “The Use of Interspecies Scaling in Toxicokinetics, ” In Toxicokinetics and New Drug Development, Yacobi et al., Eds, Pergamon Press, New York 1989, pp. 42-46. Different formulations will be effective for different treatments and different disorders, and that administration intended to treat a specific organ or tissue may necessitate delivery in a manner different from that to another organ or tissue.
[0245] In some embodiments, a subject may be administered the range of about ten thousand to about 100 billion cells and / or that amount of cells per kilogram of body weight. In some embodiments, the engineered cell (e.g. engineered immune cell) 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. Dosages may vary depending on attributes particular to the disease or disorder and / or patient and / or other treatments. The method may occur without or with the administration of one or more cytokines. The cytokine may be IL-2, IL-7, IL-12, IL-21, and / or IL-15. The method may occur without or with one or more chemokines. The chemokine may be CCL19 and / or CCL21.
[0246] In some embodiments, the engineered cells (e.g. engineered immune cells) and / or pharmaceutical composition thereof is administered for a single time. In some embodiments, the engineered cell (e.g. engineered immune cell) or pharmaceutical composition thereof is administered for multiple times (such as any of 2, 3, 4, 5, 6, or more times) , such as multiple times in a week, in a month, in 6 months, in a year, etc. In some embodiments, the engineered cell (e.g. engineered immune cell) or pharmaceutical composition thereof is administered once or multiple times during a dosing cycle. A dosing cycle can be, e.g., 1, 2, 3, 4, 5 or more week (s) , or 1, 2, 3, 4, 5, or more month (s) . In some embodiments, a dosing cycle can be one week that involves two or more doses within the week. The administration frequency and duration of the engineered cell (e.g., engineered immune cell) among two or more dosing cycles can be the same or different. In some embodiments, the nucleic acids, vectors (e.g., viral vector) , viruses (e.g., AAV, lentivirus or retrovirus) , or pharmaceutical composition thereof described herein are administered one or more times. 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 cells (e.g. engineered immune cells) , nucleic acids, vectors (e.g., viral vector) , or viruses (e.g., AAV, lentivirus or retrovirus) are administered to a mammal (e.g., a human) , the biological activity of the engineered cell populations (e.g. engineered immune cell populations) is measured by any of a number of known methods. Parameters to assess include specific binding of an engineered cell (e.g. an engineered immune cell) or non-engineered cell (e.g., bystanders, such as non-engineered engineered immune cell) 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 cells (e.g. engineered immune cells) or non-engineered cells (e.g., bystanders, such as non-engineered engineered immune cell) 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 Hermans et al. J. Immunological Methods, 285 (1) : 25-40 (2004) . In certain embodiments, the biological activity of the engineered cells (e.g. engineered immune cells) or non-engineered cells (e.g., bystanders, such as non-engineered engineered immune cell) also can be measured by assaying expression and / or secretion of certain cytokines, such as CD107a, IFNγ, IL-2, and TNFα. In some embodiments, the biological activity is measured by assessing clinical outcome, such as reduction in tumor burden or load.EXAMPLESExample 1: Preparation of CAR-NK cells expressing exemplary IL-15 constructs
[0247] Exemplary CAR-NK cells expressing exogenously introduced IL-15 armor are constructed and tested. For example, in this and following examples, BCMA CAR-NK cells expressing different IL-15 armors were constructed to exemplify the present invention. Other CAR constructs can also be used. 1.1. Construction of IL-15 armored chimeric antigen receptors (CARs)
[0248] To construct IL-15 armored anti-BCMA CAR, a nucleic acid sequence encoding anti-BCMA sdAb CAR and a nucleic acid sequence encoding an exemplary IL-15 construct were chemically synthesized and cloned into a pre-modified retroviral vector, both downstream and operably linked to a single constitutive hEF1α promoter for in vitro transcription. The anti-BCMA sdAb CAR comprises from N-terminus to C-terminus: two anti-BCMA sdAbs connected in tandem (SEQ ID NOs: 33 and 37) , a CD8α hinge domain (SEQ ID NO: 21) , a CD8αtransmembrane domain (SEQ ID NO: 22) , a CD137 co-stimulatory signaling domain (SEQ ID NO: 23) , and a CD3ζ primary intracellular signaling domain (SEQ ID NO: 24) . IL-15 constructs comprising different hinges (including hinges derived from different proteins and hinges of different lengths) and transmembrane proteins were designed. A secreted version of IL-15 armor (Armor-3) was also designed as a control. Exemplary IL-15 constructs comprise the amino acid sequence of SEQ ID NO: 2 (Armor-1) , SEQ ID NO: 3 (Armor-2) , SEQ ID NO: 4 (Armor-3; secreted) , and SEQ ID NO: 5 (Armor-4) , respectively. Table 1 shows the structure of each exemplary IL-15 construct and the resulting armored anti-BCMA CAR.
[0249] Transient retroviral supernatants were produced according to the methods outlined in Blood (2006) 108 (12) : 3890–3897, the content of which is incorporated herein by reference in its entirety. Table 1. Structures of IL-15 armored CAR-NK 1.2. IL-15 armored CAR-NK cell preparation NK cell expansion:
[0250] Human peripheral blood mononuclear cells (PBMCs) were purchased from HemaCare Corporation. PBMCs were thawed and co-cultured with K562 cells (chronic myelogenous leukemia (CML) cell line, lacking surface expression of HLA class I and II molecules) genetically modified to express membrane bound IL-15 and 4-1BB ligand (K562-mb15-41BBL) , which could stimulate cytotoxic NK cells generation. See Fujisaki et al., Cancer Res. 2009; 69 (9) : 4010-7. Cultures were expanded using stem cell growth medium (SCGM; Cell Genix, Freiburg) supplemented with 200 IU / mL of IL-2. After 7 days of culture, cells were collected and purified using anti-CD3 dynabeads (Miltenyi, Cat#11365D) to remove T cells. Remaining NK cells were then cultured in SCGM supplemented with 200 IU / mL of IL-2. Virus Transduction of NK Cells:
[0251] NK cells were collected and suspended at a concentration of 0.25×l06 cells in 2 mL of RPMI-1640 medium. The NK cells were then incubated with retrovirus supernatant obtained from section 1.1 above in a 37 ℃ incubator overnight. Supernatant volume is determined on a per-batch basis, and NK cells are treated with a multiplicity of infection (MOI) of about 1. Following overnight incubation, cells were gently centrifuged and replaced with the fresh SCGM containing 200 IU / mL of IL-2.
[0252] Transduced NK cells were maintained in SCGM with 200 IU / mL of IL-2 and used for experiments after 10 to 20 days of expansion in culture. Example 2 In vitro screening of IL-15 armored CAR-NK
[0253] The “IL-15 armored” anti-BCMA CAR-NK cells obtained from Example 1 were tested for functionality using in vitro short-term and long-term cell killing assays.
[0254] For in vitro short-term cytotoxicity assay, various IL-15 armored anti-BCMA CAR-NK cells were incubated with NCI-H929 cells (BCMA-positive multiple myeloma cell line) for 4 hours at Effector : Target (E: T) ratio of 4: 1, 1: 1, 0.25: 1 or 0.0625: 1. Un-transduced NK cells ( “Un-NK” ) were similarly incubated with NCI-H929 cells as negative control. After incubation, the cell mixture was stained with 7-aminoactinomycin D (7-AAD) to mark dead cell. 7-AAD is a fluorescent DNA binding dye that is membrane impermeant and therefore generally excluded from viable cells. The percentage of cytotoxicity on target cells was calculated by 7-AAD+%: 7-AAD+cells / Target cells*100%. As shown in FIG. 1, IL-15 Armor-1, Armor-2, and Armor-3 armored CAR-NK cells all showed increased anti-tumor killing capacity in the short-term assay compared to the un-transduced NK cells (Un-NK) . In particular, Armor-1-and Armor-3-armored BCMA CAR-NK showed improved short-term killing capacity than Armor-2-armored BCMA CAR-NK cells.
[0255] FIGs. 2A-2C show in vitro long-term killing capacity and persistence test of Armor-1-and Armor-2-armored BCMA-CAR NK cells against NCI-H929 cells (E: T ratio as shown in FIG. 2A) . As shown in FIG. 2A, the armored CAR-NK cells were initially co-cultured with NCI-H929 cells at day 0, and the co-cultures were stimulated with fresh NCI-H929 cells every 24 hours. Before each stimulation, samples were collected and analyzed by flow cytometry to determine percentage of CAR-expressing cells within the co-culture (CAR%) and percentage of target cell lysis (tumor cell lysis %) at each timepoint (see black arrows) . As shown in FIG. 2B and FIG. 2C, during 3 rounds of repeated antigen stimulation at low E: T ratio (1: 5 or 1: 10) , both Armor-1 and Armor-2 armored BCMA CAR-NK cells showed higher cytotoxicity against target cells compared to un-transduced NK cell control; while Armor-1-armored BCMA CAR-NK cells showed increased anti-tumor efficacy over Armor-2-armored BCMA CAR-NK cells. The percentage of CAR-expressing cells within the co-culture (CAR%) also showed persistence of both Armor-1-and Armor-2-armored BCMA-CAR NK cells throughout the 3-day testing period (data not shown) .
[0256] FIG. 3 shows in vitro expansion of Armor-1-, Armor-2-, and Armor-3-armored BCMA CAR-NK cells in culture medium without added cytokines. Prior to the assay, the CAR-NK cells were washed with cytokine-free medium and cultured in cytokine-free medium for about 24 hours. The cells were then counted, seeded on a 24-well plate, and cultured in cytokine-free medium for an additional 5 days. Cells were collected and counted at day 3 and day 5, and flow cytometry was performed at each timepoint to analyze the CAR%in each culture. As shown in FIG. 3, Armor-1-armored BCMA CAR-NK cells showed increased expansion over Armor-2-and Armor-3-armored BCMA CAR-NK cells. These expansion results likely correlate with the anti-tumor cytotoxicity of the CAR NK cell population armored with the respective IL-15 armor constructs, as shown in FIGs. 2B-2C. Example 3 By-stander effect analysis of membrane-bound IL-15 armored CAR-NK
[0257] To analyze the potential by-stander effect of IL-15 armored BCMA CAR-NK cells on surrounding cells (e.g., host non-engineered NK cells) , IL-15 armored BCMA CAR-NK cells from HLA-A2 positive donors (HLA-A2+) were generated using the methods described in Example 1. First, IL-15 armored BCMA CAR-NK cells were washed with cytokine-free medium and cultured in a 37℃ incubator overnight. A second batch of un-transduced allo-NK cells (allo-NK from HLA-A2 negative donor) was thawed. Then the IL-15 armored BCMA CAR-NK cells (HLA-A2+) and allo-NK cells (HLA-A2-) were seeded in a 24-well plate at a ratio of 2: 1, and incubated in cytokine-free medium for 72 hours. Co-culture of un-transduced NK cells from HLA-A2+ donor (Un-NK) with un-transduced NK cells from HLA-A2-donor (allo-NK) was used as negative control for following analysis. Un-NK cells from HLA-A2-donor (allo-NK) cultured with human IL-15 (100 ng / ml) was used as positive control for NK expansion.
[0258] FIG. 4A shows the fold-expansion of the surrounding allo-NK cells from HLA-A2-donors when co-cultured with Armor-1, Armor-2-, Armor-3-and Armor-4-BCMA CAR-NK cells (HLA-A2+) . Armor-1-CAR-NK cells (HLA-A2+) did not show any significant difference in by-stander effect on surrounding allo-NK cells (HLA-A2-) when compared to the control group co-cultured with untransduced-NK cells (un-NK, HLA-A2+) . Armor-2-CAR-NK cells (HLA-A2+) displayed increased killed of the surrounding allo-NK cells, resulting in a decreased allo-NK fold-expansion relative to un-NK controls. Both Armor-3-and Armor-4-CAR NK cells displayed stimulated fold-expansion of surrounding allo-NK cells relative to un-NK controls. However, the induced expansion on allo-NK cells by Armor-3-and Armor-4 was still less than the positive control (no HLA-A2+ cells, only secreted version of IL-15) .
[0259] FIG. 4B shows the expansion of IL-15 armored CAR-NK cells (HLA-A2+) in the co-culture system with HLA-A2-allo-NK cells. Armored CAR-NK cells and un-transduced NK cells all showed expansion over the 6-day duration. Here, Armor-1-CAR-NK cells displayed significant expansion without a significant by-stander effect on surrounding cells (as evidenced by FIG. 4A) . Armor-2-CAR-NK cells showed decreased expansion relative to un-NK cells, likely because of host-versus-graft (HvG) effect from the allo-NK cells (HLA-A2-) and / or the naturally lower expansion rate of Armor-2-CAR-NK cells (as evidenced by FIG. 3) . The expansion of Armor-3-CAR-NK cells appeared to stall by day 6 of co-culture.
[0260] To analyze whether membrane-bound IL-15 can be cleaved from cell membrane, the armored CAR-NK cells were seeded in a 24-well plate and supernatants were collected at 72 hours. FIG. 5 shows the hIL-15 level in the supernatant tested using a commercial ELISA kit (R&D Cat#DB0800370) . Armor-3-CAR NK cells which comprises the secreting form of IL-15 armor, showed elevated levels of IL-15 in culture medium, whereas Armor-1-and Armor-2-CAR-NK showed no significant levels of IL-15 in the cell membrane. These results show that there is no significant IL-15 cleavage in IL-15 constructs comprising membrane-bound IL-15, suggesting that these armors may have a better safety profile and avoid potential systemic activation in the host immune system compared to using secreted version of IL-15. Example 4 In vivo evaluation of IL-15 Armor-1 and Armor-2 armored CAR-NK cells
[0261] Based on above results, IL-15 Armor-1 and Armor-2 armored BCMA CAR-NK cells were chosen for further evaluation in vivo.
[0262] To create BCMA tumor xenograft models, NCG mice were injected intravenously with NCI-H929-Luc cells (BCMA positive multiple myeloma cell line NCI-H929 #ATCC CRL-9068TM transduced with Luciferase) at 1×106 cells / mouse. Twelve to fourteen days later, tumor engrafted NCG mice (NCI-H929-Luc model) were treated with the un-transduced NK cells (Un-NK) , Armor-1-armored BCMA CAR-NK cells, and Armor-2-armored BCMA CAR-NK cells. Each mouse was infused with 2 million of each NK cell population at day 0, and tumor size was monitored using in vivo bioluminescence imaging (BLI, PerkinElmer Lumina LT In Vivo Imaging System) for 36 days following NK cell administration, tumor flux corresponds to tumor size. Mice in the Vehicle group were treated with HBSS (- / -) . Mice not inoculated with NCI-H929-Luc cells served as blank control.
[0263] As shown in FIG. 6A and FIG. 6B, mice receiving Armor-1-armored BCMA CAR-NK cells showed significant anti-tumor efficacy. Mice receiving Armor-2-armored BCMA CAR-NK cells demonstrated less anti-tumor efficacy during the first 2 weeks post-NK cell infusion when compared to Armor-1-armored BCMA CAR-NK treatment group.
[0264] FIG. 6C shows the changes to mouse body weight over the course of the experiment, and FIG. 6D shows the survival curve of each treatment group. As shown in FIG. 6D, mice in the Armor-2-armored BMCA CAR NK group died between day 21 and day 25, even earlier than the Un-NK treated group and the Vehicle group, indicating that this armor may be cytotoxic to the mice, likely due to the by-stander effect against host allo-NK cells (see FIG. 4A) . On the contrary, mice in the Armor-1-armored BCMA CAR-NK cell treatment group survived longer than all other treatment groups while reaching normal body weight by the end of study (see FIG. 6C) .
[0265] Overall, Armor-1-armored BCMA CAR-NK cells have improved anti-tumor efficacy, better persistence and / or expansion capacity, and lower toxicity against allogeneic host cells compared to BCMA CAR-NK cells bearing Armor-2 in xenograft mouse models. Example 5: IL-15 Armor-1 armored CAR-NK shows less HvG rejection.
[0266] Armors expressed on allogenic CAR-NK may stimulate host immune systems to reject grafted CAR-NK cells (HvG rejection) . To investigate the potential impact of armor expression on CAR-NK rejection in a host immune environment, a one-way mixed lymphocyte (MLR) assay was carried out. 0.4 × 106 BCMA CAR-NK cells were first treated with 0.8 μg / ml mitomycin C to stop their proliferation, then co-cultured with 3 × 106 allogenic PBMC in stem cell growth medium (SCGM; Cell Genix, Freiburg) supplemented with 200 IU / mL of IL-2. After 8 days of co-culturing, the percent of CAR-NK (graft) and CD71 expression on T cells in PBMC was determined using flow cytometry. FIG. 7A outlines the protocol for this experiment. BCMA CAR-NK cells without any IL-15 armor served as control.
[0267] As shown in FIG. 7B, comparing to no armored BCMA CAR-NK, Armor-1 armored CAR-NK showed comparable graft percentage, while Armor-4 and Armor-3 armored BCMA CAR-NK cells had dramatically decreased graft percentage, suggesting the HvG rejection is strongly elicited.
[0268] Consistently, as shown in FIG. 7C, Armor-1 armored BCMA CAR-NK also led to less T cell activation compared to Armor-4 and Armor-3 armored CAR-NK cells. These data suggest that IL-15 Armor-1 did not lead to increased rejection by allogenic PBMC. SEQUENCE LISTING SEQ ID NO: 1 Mature wild type hIL-15 SEQ ID NO: 2 DAP12 SP –mature IL-15 -CD8 H -DAP12 TM with 2 intracellular aa SEQ ID NO: 3 IL-15 SP -mature IL-15 -CD8 H -CD8α TM with 3 intracellular aa SEQ ID NO: 4 Secreting IL-15 SEQ ID NO: 5 IgE SP –IL-15 –linker -IL15Rα without intracellular domain SEQ ID NO: 6 BCMA CAR (CD8α SP –VHH1 –VHH2 –CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζintracellular) SEQ ID NO: 7 P2A SEQ ID NO: 8 DAP12 SP -IL-15 -CD8 H -DAP12 TM armored BCMA CAR (CD8α SP –VHH1 –VHH2 – CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζ intracellular –P2A -DAP12 SP –mature IL-15 -CD8 hinge -DAP12 TM with 2 intracellular aa) SEQ ID NO: 9 IL-15 SP -IL-15-CD8h-CD8α TM armored BCMA CAR (CD8α SP –VHH1 –VHH2 –CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζ intracellular –P2A –IL-15 SP -mature IL-15 -CD8 hinge -CD8α TM with 3 intracellular aa) SEQ ID NO: 10 Secreting IL15 armored BCMA CAR (CD8α SP –VHH1 –VHH2 –CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζ intracellular –P2A -secreting IL15 with IL15 SP) SEQ ID NO: 11 IL15-IL15Rα TM armored BCMA CAR (CD8α SP –VHH1 –VHH2 –CD8 hinge -CD8αTM –4-1BB co-stim –CD3ζ intracellular –P2A –IgE SP –IL15 –linker –IL15Rα without intracellular domain) SEQ ID NO: 12 GS linker 1 SEQ ID NO: 13 GS linker 2 SEQ ID NO: 14 IL15Rα SEQ ID NO: 15 IL15Rα TM SEQ ID NO: 16 DAP12 SP SEQ ID NO: 17 DAP12 (SP is squared; TM is bolded) SEQ ID NO: 18 DAP12 TM SEQ ID NO: 19 CD8α SP SEQ ID NO: 20 CD8α SEQ ID NO: 21 CD8 Hinge SEQ ID NO: 22 CD8α TM SEQ ID NO: 23 CD137 co-stimulatory signaling domain SEQ ID NO: 24 CD3ζ primary intracellular signaling domain SEQ ID NO: 25 IL-15 SP SEQ ID NO: 26 linker 3 SEQ ID NO: 27 IL15Rα without intracellular domain SEQ ID NO: 28 IL15 propeptide SEQ ID NO: 29 mature IL-15 -CD8 H -DAP12 TM with 2 intracellular aa SEQ ID NO: 30 IgE leader SEQ ID NO: 31 BCMA CAR (VHH1 –VHH2 –CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζintracellular) SEQ ID NO: 32 DAP12 TM with two intracellular AA SEQ ID NO: 33 BCMA 269A37948 VHH (BCMA VHH 1) SEQ ID NO: 34 BCMA 269A37948 VHH CDR1 (BCMA 1 CDR-H1) SEQ ID NO: 35 BCMA 269A37948 VHH CDR2 (BCMA 1 CDR-H2) SEQ ID NO: 36 BCMA 269A37948 VHH CDR3 (BCMA 1 CDR-H3) SEQ ID NO: 37 BCMA 269AS34822 VHH (BCMA VHH 2) SEQ ID NO: 38 BCMA 269AS34822 VHH CDR1 (BCMA 2 CDR-H1) SEQ ID NO: 39 BCMA 269AS34822 VHH CDR2 (BCMA 2 CDR-H2) SEQ ID NO: 40 BCMA 269AS34822 VHH CDR3 (BCMA 2 CDR-H3) SEQ ID NO: 41 CD8α TM with 3 intracellular aa SEQ ID NO: 42 IL-15 SP -mature IL-15 -CD8 H -CD8α TM SEQ ID NO: 43 mature IL-15 -CD8 H -CD8α TM SEQ ID NO: 44 IL-15 SP -IL-15-CD8h-CD8α TM armored BCMA CAR (CD8α SP –VHH1 –VHH2 –CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζ intracellular –P2A –IL-15 SP -mature IL-15 -CD8 hinge -CD8α TM) SEQ ID NO: 45 DAP12 SP –mature IL-15 -CD8 H -DAP12 TM SEQ ID NO: 46 mature IL-15 -CD8 H -DAP12 TM SEQ ID NO: 47 DAP12 SP -IL-15 -CD8 H -DAP12 TM armored BCMA CAR (CD8α SP –VHH1 –VHH2 – CD8 hinge -CD8α TM –4-1BB co-stim –CD3ζ intracellular –P2A -DAP12 SP –mature IL-15 -CD8 hinge -DAP12 TM) SEQ ID NO: 48 hIL-15 (N72D) SEQ ID NO: 49 DAP12 intracellular domain SEQ ID NO: 50 Mutein 1 (m1) SEQ ID NO: 51 Mutein 2 (m2) SEQ ID NO: 52 Mutein 3 (m3) SEQ ID NO: 53 Mutein 4 (m4) SEQ ID NO: 54 Mutein 5 (m5) SEQ ID NO: 55 Mutein 6 (m6) SEQ ID NO: 56 Mutein 7 (m7) SEQ ID NO: 57 Mutein 8 (m8) SEQ ID NO: 58 Mutein 9 (m9) SEQ ID NO: 59 Mutein 10 (m10) SEQ ID NO: 60 Mutein 11 (m11) SEQ ID NO: 61 Mutein 12 (m12) SEQ ID NO: 62 Mutein 13 (m13) SEQ ID NO: 63 Mutein 14 (m14) SEQ ID NO: 64 Mutein 15 (m15) SEQ ID NO: 65 Mutein 16 (m16) SEQ ID NO: 66 Mutein 17 (m17) SEQ ID NO: 67 Mutein 18 (m18) SEQ ID NO: 68 (GxS) n linker SEQ ID NO: 69 linker
Claims
1.An engineered immune cell comprising an IL-15 construct, wherein the IL-15 construct comprises an IL-15 moiety and a transmembrane domain derived from DAP12.2.The engineered immune cell of claim 1, wherein the IL-15 moiety is derived from a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1.3.The engineered immune cell of claim 2, wherein the IL-15 moiety is a mature wildtype human IL-15 polypeptide comprising the amino acid sequence of SEQ ID NO: 1.4.The engineered immune cell of claim 2, wherein the IL-15 moiety is a functional fragment of the mature wildtype human IL-15 polypeptide.5.The engineered immune cell of claim 2, wherein the IL-15 moiety is a functional variant of the mature wildtype human IL-15 polypeptide.6.The engineered immune cell of any one of claims 1-5, wherein the transmembrane domain is derived from a wildtype human DAP12 polypeptide comprising the amino acid sequence of SEQ ID NO: 17.7.The engineered immune cell of claim 6, wherein the transmembrane domain comprises the amino acid sequence of SEQ ID NO: 18.8.The engineered immune cell of claim 6, wherein the transmembrane domain is a functional variant of the transmembrane domain comprising the amino acid sequence of SEQ ID NO:18.9.The engineered immune cell of any one of claims 1-8, wherein the IL-15 construct further comprises a hinge domain between the IL-15 moiety and the transmembrane domain derived from DAP12.10.The engineered immune cell of claim 9, wherein the hinge domain is derived from CD8.11.The engineered immune cell of claim 10, wherein the hinge domain comprises the amino acid sequence of SEQ ID NO: 21.12.The engineered immune cell of any one of claims 1-11, wherein the IL-15 construct does not comprise a functional intracellular signaling domain.13.The engineered immune cell of any one of claims 1-12, wherein the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 29 or 46.14.The engineered immune cell of any one of claims 1-13, wherein the IL-15 construct further comprises a signal peptide at the N-terminus.15.The engineered immune cell of claim 14, wherein the signal peptide is derived from DAP12.16.The engineered immune cell of claim 15, wherein the IL-15 construct comprises the amino acid sequence of SEQ ID NO: 2 or 45.17.The engineered immune cell of any one of claims 1-16, further comprising a chimeric receptor.18.The engineered immune cell of claim 17, wherein the chimeric receptor is selected from the group consisting of an engineered T cell receptor (TCR) , a chimeric antigen receptor (CAR) , a chimeric TCR (cTCR) , a T cell antigen coupler (TAC) , and a TAC-like engineered receptor.19.The engineered immune cell of claim 18, wherein the chimeric receptor is a CAR comprising an extracellular antigen binding domain, a transmembrane domain, and a primary intracellular signaling domain.20.The engineered immune cell of claim 19, wherein the extracellular antigen binding domain comprises an antigen-binding moiety specifically recognizing a target antigen.21.The engineered immune cell of claim 20, wherein the antigen-binding moiety is an sdAb.22.The engineered immune cell of claim 20 or claim 21, wherein the target antigen is BCMA.23.The engineered immune cell of any one of claims 19-22, wherein the transmembrane domain of the CAR is not derived from DAP12.24.The engineered immune cell of claim 23, wherein the transmembrane domain of the CAR is derived from CD8.25.The engineered immune cell of any one of claims 19-24, wherein the CAR further comprises a hinge domain between the extracellular antigen binding domain and the transmembrane domain.26.The engineered immune cell of claim 25, wherein the hinge domain of the CAR is derived from CD8.27.The engineered immune cell of any one of claims 19-26, wherein the primary intracellular signaling domain is derived from CD3ζ.28.The engineered immune cell of any one of claims 19-27, wherein the CAR further comprises a costimulatory intracellular signaling domain.29.The engineered immune cell of claim 28, wherein the costimulatory intracellular signaling domain is derived from 4-1BB.30.The engineered immune cell of any one of claims 19-29, wherein the CAR comprises the amino acid sequence of SEQ ID NO: 31.31.The engineered immune cell of any one of claims 17-30, wherein the IL-15 construct is encoded by a first nucleic acid, wherein the chimeric receptor is encoded by a second nucleic acid, and optionally wherein the first nucleic acid and the second nucleic acid are present on a single vector.32.The engineered immune cell of claim 31, wherein the first nucleic acid and the second nucleic acid are operably linked to a single promoter.33.The engineered immune cell of claim 32, wherein the first nucleic acid and the second nucleic acid are connected by a linking sequence.34.The engineered immune cell of any one of claims 31-33, wherein the single vector encodes the amino acid sequence of SEQ ID NO: 8 or 47.35.An IL-15 construct comprising an IL-15 moiety and a transmembrane domain derived from DAP12.36.The IL-15 construct of claim 35, wherein the IL-15 construct further comprises a hinge domain between the IL-15 moiety and the transmembrane domain derived from DAP12.37.The IL-15 construct of claim 36, wherein the hinge domain is derived from CD8.38.The IL-15 construct of any one of claims 35-37, wherein the IL-15 construct comprises the amino acid sequence of any of SEQ ID NOs: 2, 29, 45, and 46.39.An isolated nucleic acid encoding the IL-15 construct of any one of claims 35-38.40.A vector comprising the isolated nucleic acid of claim 39.41.The vector of claim 40, which is a viral vector.42.The vector of claim 40 or claim 41, wherein the vector further comprises a second nucleic acid encoding a chimeric receptor.43.The vector of claim 42, wherein the chimeric receptor is a CAR comprising an extracellular antigen binding domain, a transmembrane domain, and a primary intracellular signaling domain.44.The vector of claim 42 or claim 43, wherein the nucleic acid encoding the IL-15 construct and the second nucleic acid are operably linked to a single promoter and are connected by a linking sequence.45.The vector of claim 44, wherein the linking sequence encodes a 2A self-cleaving peptide.46.The vector of any one of claims 43-45, wherein the vector encodes the amino acid sequence of SEQ ID NO: 8 or 47.47.An engineered immune cell expressing the IL-15 construct of any one of claims 35-38, or comprising the isolated nucleic acid of claim 39 or the vector of any one of claims 40-46.48.The engineered immune cell of any one of claims 1-34 and 47, wherein the engineered immune cell is selected from the group consisting of: T cell, NK cell, NKT cell, peripheral blood mononuclear cell (PBMC) , macrophage, and monocyte.49.The engineered immune cell of claim 48, wherein the engineered immune cell is an NK cell.50.The engineered immune cell of claim 49, wherein the NK cell is further modified to:(i) reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules; and / or(ii) increase the expression and / or function of one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9.51.A pharmaceutical composition comprising the engineered immune cell of any one of claims 1-34 and 47-50, the isolated nucleic acid of claim 39, or the vector of claim 40-46.52.A method of treating a disease or condition in an individual, comprising administering to the individual an effective amount of the engineered immune cell of any one of claims 1-34 and 47-50, or the pharmaceutical composition of claim 51.53.The method of claim 52, wherein the disease or condition is cancer, an autoimmune disorder, or an infection.54.The method of claim 53, wherein the disease or condition is an autoimmune disorder.55.The method of any one of claims 52-54, wherein the engineered immune cell is allogeneic.56.The method of any one of claims 52-55, wherein the individual is a human.57.A method of making the engineered immune cell of any one of claims 1-34 and 47-50, comprising introducing into an immune cell the isolated nucleic acid of claim 39 or the vector of any one of claims 40-46.58.A method of promoting persistence and / or expansion of an immune cell, comprising introducing into the immune cell the isolated nucleic acid of claim 39 or the vector of any one of claims 40-46.59.The method of claim 57 or 58, further comprising introducing into the immune cell a second nucleic acid encoding a chimeric receptor.60.The method of claim 57 or 58, wherein the immune cell expresses a chimeric receptor.61.The method of claim 59 or 60, wherein the chimeric receptor is a CAR.62.The method of any one of claims 57-61, wherein the immune cell is selected from the group consisting of: T cell, NK cell, NKT cell, PBMC, macrophage, and monocyte.63.The method of claim 62, wherein the immune cell is an NK cell.64.The method of claim 63, further comprising modifying the NK cell to:(i) reduce the expression and / or function of one or more endogenous MHC Class I and / or endogenous MHC Class II molecules; and / or(ii) increase the expression and / or function of one or more tolerogenic factors selected from the group consisting of HLA-E, CD43, CD47, CD24, CD26, CD27, CD31, CD35, CD200, HLA-C, HLA-G, PD-L1, IDO1, CTLA4-Ig, C1-inhibitor, IL-10, IL-35, FASL, DUX4, CCL21, MFGE8, and SERPINB9.
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