Patent Publication Number: US-2020291125-A1

Title: Chimeric antigen receptors, compositions, and methods

Description:
CROSS-REFERENCE TO RELATED APPLICATION 
     This application is a continuation application of U.S. patent application Ser. No. 15/546,177, filed Jul. 25, 2017, which is a National Stage application under 35 U.S.C. § 371 of International Application No. PCT/US2016/015351 having an International Filing Date of Jan. 28, 2016, which claims the benefit of U.S. Patent Application No. 62/109,281, filed on Jan. 29, 2015, which are incorporated herein by reference. 
    
    
     SUMMARY 
     This disclosure describes, in one aspect, a chimeric antigen receptor for expression in a Natural Killer (NK) cell. Generally, the chimeric antigen receptor includes an ectodomain that includes an antigen recognition region, a transmembrane domain linked to the ectodomain, and an endodomain linked to the transmembrane domain. The endodomain can include a signaling peptide that activates an NK cell. 
     In some embodiments, the antigen recognition domain can specifically bind an antigen associated with a disease. 
     In some embodiments, the antigen recognition domain can specifically bind a tumor antigen. 
     In some embodiments, the ectodomain can further include a signal peptide or leader sequence and/or a spacer. 
     In some embodiments, the endodomain can include a signaling domain of and NK cell membrane-bound signaling adaptor protein such as, for example, 2B4, DAP10, DAP12, IL21R, CD137 (41BB), or CD3ζ. 
     In some embodiments, the transmembrane domain can include a transmembrane region of a natural cytotoxicity receptor expressed in NK cells such as, for example, CD16, NKp44, NKp46, or NKG2D. 
     In another aspect, this disclosure describes a pharmaceutical composition that includes an NK cell (and/or iPSCs) modified to express any embodiment of chimeric antigen receptor summarized above. 
     In another aspect, this disclosure describes a method of providing immunotherapy to a subject having a condition. Generally, the method includes administering to the subject the therapeutic composition summarized above in which the antigen recognition region of the chimeric antigen receptor specifically binds to an antigen associated with the condition. 
     The above summary is not intended to describe each disclosed embodiment or every implementation of the present invention. The description that follows more particularly exemplifies illustrative embodiments. In several places throughout the application, guidance is provided through lists of examples, which examples can be used in various combinations. In each instance, the recited list serves only as a representative group and should not be interpreted as an exclusive list. 
    
    
     
       BRIEF DESCRIPTION OF THE FIGURES 
         FIG. 1 . (A) Exemplary natural cytotoxicity receptors and the effect of binding those receptors with their ligands on NK cell degranulation and polarization and target cell killing. (B) Representative examples of natural cytotoxicity receptors and their corresponding signaling adaptors. (C) Third generation chimeric T cell antigen receptor construct used in iPSC-derived NK cells. 
         FIG. 2 . (A) A generalized schematic illustration of an NK-activating CAR. (B) Schematic of novel chimeric antigen receptor constructs. Chimeric antigen receptors were cloned into a pkt2 vector containing an IR/DR for use with SB100X transposase, a mCAGs promoter, chimeric antigen receptor (CAR) sequence, Internal ribosomal entry site (IRES), and GFP:Zeo selection marker. Chimeric antigen receptor fragments were obtained from UniProt and assembled through gBlock synthesis and traditional restriction enzyme cloning (IDT). 
         FIG. 3 . Surface expression of chimeric antigen receptors in NK92 and iPS cells. NK92 cells or iPS cells were transfected using the Sleeping Beauty transposon system using SB100X. Cells were then selected using Zeocin and flow cytometry was performed to assess cell surface expression of the various chimeric antigen receptors. Expression was assessed using a biotin-conjugated polyclonal goat anti-mouse antibody recognizing the mouse IgG F(ab′)2 fragment (Jackson ImmunoResearch Laboratories, Inc., West Grove, Pa., cat #115-065-072). Bound antibody was detected using strepavadin conjugated to a fluorescent dye. 
         FIG. 4 . CD107A release and IFN-γ production in NK92 Cells. NK92 cell degranulation and cytokine production were evaluated by flow cytometry. NK92 cells were mixed 1:1 with mesothelin negative (MA148), mesothelin positive (A1847) ovarian cancer target cells, or Protein A beads with or without conjugation to a mesothelin/Fc chimeric protein. Cells were stained for CD107a and intracellular staining was performed for IFN-γ production. 
         FIG. 5 . Cr-51 release assay using NK92 cells. NK92, NK92/28/41BB/CD3, or NK92/CAR4 cells were incubated for 4 hours at the indicated ratios with K562, K562 mesothelin+, MA148, or A1847 cells. Cr-51 release was then detected to evaluate cell killing. This experiment performed as in Woll et al., 2009 , Blood  113(24):6094-6101, except that iPSC-derived NK cells were used in place of hESC-derived NK cells. 
         FIG. 6 . Exemplary additional NK-activating chimeric antigen receptors. 
         FIG. 7 . Schematic illustration comparing a 3 rd  Generation T cell CAR with exemplary NK CAR constructs reflected in  FIG. 2 . 
         FIG. 8 . Schematic illustration of exemplary NK CAR constructs. 
         FIG. 9 . Schematic illustration of exemplary NK CAR constructs. 
         FIG. 10 . Data showing cytotoxicity of NK CARs against K562 cells 
         FIG. 11 . Data showing cytotoxicity of NK CARs against two ovarian cancer cell lines. 
         FIG. 12 . Data showing expression of an exemplary NK CAR by induced pluripotent stem cells. 
         FIG. 13 . Data showing surface expression of an exemplary CAR by iPSC-derived NK cells expressing. 
         FIG. 14 . An exemplary generalized NK CAR vector construct. 
         FIG. 15 . An exemplary generalized NK CAR vector construct. Tandem cHS4 insulators can inhibit silencing of the CAR vector and, therefore, improve expression of the CAR in NK cells and iPSCs. 
     
    
    
     DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS 
     This disclosure describes chimeric antigen receptors designed to specifically incorporate NK cell activation domains. Chimeric antigen receptors can incorporate intracellular and/or transmembrane regions including, for example, intracellular and/or transmembrane regions from CD16, NKp44, NKp46, and/or NKG2D, linked to co-activation or signaling domains from, for example, 2B4 (CD244), CD137 (41BB), IL21, DAP10, DAP12, and/or CD3ζ. 
     Chimeric antigen receptors (CARs) are engineered artificial receptors that can provide an engineered specificity to an immune cell that expresses the CAR. Generally, an immune cell population can be collected from a subject that has a particular form of cancer. The collected immune cells can be modified to express a chimeric antigen receptor that specifically binds to antigens expressed by tumor cells, then reintroduced into the subject. The modified immune cells that express the chimeric antigen receptor are better able to recognize and kill tumor cells that express the antigen(s) specifically recognized by the chimeric antigen receptor. 
     Chimeric antigen receptors have been designed to activate T cells for the treatment of refractory ALL (targeting CD19), pancreatic cancer (targeting mesothelin), and other malignancies. Several chimeric antigen receptors constructs exist, but most were designed to activate T cells. 
     In contrast, the chimeric antigen receptors described herein are designed to be expressed in induced pluripotent stem cells (iPSCs), which can then be differentiated into NK cells. They also can be expressed directly into peripheral blood (PB)-NK cells, NK-92 cells, or another suitable NK cell line. NK-92 cells or other NK cell lines have been used in clinical studies for anti-cancer therapy. NK cells that express the chimeric antigen receptor can then be used as an immunotherapy for the treatment of multiple cancers. The chimeric antigen receptors described herein can include a signaling domain that could be used with antigen-recognition portions of various targeting antibodies. Specifically, this disclosure describes exemplary embodiments that reflect mesothelin-targeted chimeric antigen receptors for the treatment of ovarian cancer. The described embodiments can have broader utility, however, since mesothelin is expressed on many adenocarcinomas. Moreover, the described mesothelin targeting domain is merely exemplary; other single chain variable fragments (scFVs) can be engineered into the NK-specific chimeric antigen receptor (NK-CAR) signaling constructs to target essentially any malignancy. 
     One feature of the NK cell chimeric antigen receptors described herein is that one can bypass the adaptor molecules/accessory proteins that natural cytotoxicity receptors need to initiate signal transduction. Alternatively, or additionally, including the transmembrane domain of receptors that typically associate with an adaptor molecule/accessory protein can allow accessory proteins to bind as well, making signal transduction more likely to be initiated. The NK cell chimeric antigen receptors designed to include, for example, CD3ζ can allow bypassing other natural cytotoxicity receptors. Incorporating the transmembrane domains and other intracellular domains can allow these NK cell chimeric antigen receptors to associate with adaptor proteins and provide improved signaling over CD3ζ alone through activation of multiple pathways. 
     While some T cell chimeric antigen receptor constructs can activate NK cells to some degree due to shared signaling domains, the chimeric antigen receptors described herein are specifically designed to activate NK cells. Chimeric antigen receptors designed to specifically activate NK cells can improve NK function and receptor utility in NK cell immunotherapy such as, for example, cell-mediated killing of refractory tumors. 
     A chimeric antigen receptor typically includes an ectodomain, a transmembrane domain, and an endodomain. The endodomain typically resides in the cytoplasm of the cell. Once an antigen is recognized by the ectodomain, the endodomain transmits an activation signal to the NK cell that induces the NK cell to destroy the targeted tumor cell. Exemplary signaling endodomains include, for example, the signaling domains of membrane-bound signaling adaptor proteins, including, for example, 2B4 (CD244), CD137 (41BB), IL21, DAP10, DAP12, and/or CD3ζ, or a portion thereof including, for example, an immunoreceptor tyrosine-based activation motif (ITAMs), a YxxM motif, a TxYxxV/I motif, FcRγ, NKp80 (signaling through an atypical hemi-ITAM), and/or DNAM, etc. 
     The transmembrane domain traverses the plasma membrane and links the endodomain to the ectodomain. Exemplary transmembrane domains include, for example, the intracellular and/or transmembrane domains of natural cytotoxicity receptors (NCRs) including for example, CD16, NKp44, NKp46, NKG2D, NKp30, NKp80, and/or DNAM-1, or a portions thereof including, for example, one or more charged amino acids. In some embodiments, the charged amino acid can be a lysine and/or an arginine residue. In some cases, a transmembrane region may be from a transmembrane protein, meaning that it natively has an extracellular C-terminal rather than an extracellular N-terminal. In such cases, one can reverse the orientation of the transmembrane region, indicated in, for example,  FIG. 6  as “Rev TM” so that the chimeric antigen receptor orients properly in the NK cell membrane. 
     The ectodomain generally includes a signal peptide and an antigen recognition region. In many embodiments, the ectodomain also can include a spacer. The signal peptide directs the nascent polypeptide into the endoplasmic reticulum so that it can be properly glycosylated and anchored into the plasma membrane. Generally, any eukaryotic signal peptide can be used so long as it directs the protein to the endoplasmic reticulum. One exemplary signal peptide includes the CD8α leader sequence, but other signal peptide sequences may be suitable. The spacer, when present, links the antigen recognition domain to the transmembrane domain. The spacer typically offers flexibility so that antigen recognition region is free to orient in different directions, thereby allowing the antigen recognition region to bind to antigen targets. One exemplary spacer includes the CD8α hinge sequence, but other Ig hinge regions may be suitable. The antigen recognition region can include any peptide sequence that is capable of specifically binding to a designated target. As used herein, “specifically bind” and variatons thereof refer to having a differential or a non-general affinity, to any degree, for a particular target. Thus, the antigen recognition region can include a fragment of an antibody such as, for example, an scFv or a Fab that specifically binds to a particular antigen such as, for example, a tumor antigen, a viral antigen, a modified self-antigen, etc. In some embodiments, the scFv can be from a monoclonal antibody. A chimeric antigen receptor can be designed to include an antigen recognition region that can specifically bind to any designated target. Thus, while  FIG. 2 ,  FIG. 6 ,  FIG. 7 , and  FIG. 8  show embodiments that are designed to specifically bind to mesothelin, an NK-activating chimeric antigen receptor can be designed to specifically bind, and therefore target, any antigen associated with cells that are intended to be the target of NK cell-mediated killing including, for example, tumorigenic or virally infected cells. For example, NK cells and/or CARs have demonstrated activity against diverse solid tumors and virally-infected cells including but limited to HIV (human immunodeficiency virus), hepatitis B, hepatitis C, CMV (cytomegalovirus), EBV (Epstein-Barr virus), HPV (human papilloma virus), and others. 
     So, for example, to better mediate NK cell cytotoxicity against tumors that include cells that express mesothelin (e.g., ovarian cancers, pancreatic cancers, lung cancers, colon adenocarcinomas, mesotheliomas, and other adenocarcinomas that express mesothelin), a chimeric antigen receptor such as ones shown in  FIG. 2 ,  FIG. 6 ,  FIG. 7 , and  FIG. 8  may be designed and expressed in NK cells. The illustrated chimeric antigen receptor constructs contain an NK cell-specific transmembrane domain and activating domains, and was capable of being expressed in the NK cell tumor line, NK92. Transmembrane and intracellular regions were taken from CD16, NKp44, NKp46, and/or NKG2D, while the activating domains of 2B4, DAP10, DAP12, and/or CD3 were combined in a fashion intended to maximally activate NK cells.  FIG. 3  shows that NK92 and iPS cells expressed the chimeric antigen receptors shown in  FIG. 2 . 
     To assess the function of the chimeric antigen receptors, NK cells expressing the chimeric antigen receptors were tested against antigen-coated beads and mesothelin-expressing cell lines.  FIG. 4  shows that the chimeric antigen receptors of  FIG. 2  enhanced degranulation and cytokine production of NK cells when NK cells expressing the chimeric antigen receptors were mixed with mesothelin-positive targets. 
       FIG. 5  shows that NK92 cells expressing an NK-specific chimeric antigen receptor as described herein improved in vitro killing of mesothelin-positive target cells compared to a third generation T cell-specific chimeric antigen receptor (NK92/28/41BB/CD3ζ) or non-transfected NK92 cells. 
       FIG. 9  shows cytotoxicity of exemplary NK CARs against K562 cells (upper left panel) and K562 cells expressing mesothelin (upper right panel) that is target for the CARs. These results show markedly improved killing in a mesothelin-specific fashion, most notably for CAR7 and CAR9. The lower panel is a summary of the results expressed in lytic units (Bryant et al., 1992 , J immunol Methods  146(1):91-103). CAR 7 and CAR 9 exhibit markedly greater cytotoxicity than the 3 rd  generation T cell CAR used in previous studies (NK92 meso 3 rd ). Cytotoxicity was measured using a Cr-51 release assay as previously described (Knorr et al., 2013 , Stem Cells Transl Med  2(4):274-283; Woll et al., 2009 , Blood  113(24):3094-6101; Woll et al., 2005 , J Immunol  175(8):5095-5103).  FIG. 10  shows similar results using two ovarian cancer cell lines that are meso-high (A1497) and meso-low (MA148). NK92 cells with different NK cell-based anti-meso CARs kill in a meso-specific fashion. The bottom panel against reflects a summary expressed in lytic units. Moreover, the NK CARs mediate increased expression of CD107a and/or IFN-γ when stimulated with targets as in  FIG. 9  and  FIG. 10  (data not shown). 
     In some embodiments, an NK-specific chimeric antigen receptor as described herein can be expressed in iPSCs, which can then be differentiated into NK cells. The iPSCs may be differentiated as described in Knorr et al., 2013 , Stem Cells Transl Med.  2(4):274-283 or Ni et al., 2014 , Stem Cells  32(4):1021-1031.  FIG. 11  shows expression of an exemplary NK CAR by induced pluripotent stem cells (iPSCs), as shown by production of CD45+CD56+ cells (top row, 5 th  panel).  FIG. 12  shows CAR surface expression by iPSC-derived NK cells. The bottom three rows of  FIG. 12  show CAR expression only on the surface of iPSC-CAR4v2 (4 th  column, bottom three rows) compared to the PB-NK cells and iPSC-NK cells that don&#39;t express CARs (unmodified control cells, 4 th  column, row 4 and row 5). Other panels in  FIG. 11  and  FIG. 12  show other typical NK cell surface antigens/receptors on the iPSC-CAR4v2 are similar to those found on the unmodified control cells. These results indicate that iPSC-derived NK cells can exhibit the same target-specific cytotoxicity as the mesothelin-targeted-CAR-expressing NK cells in  FIG. 9  and  FIG. 10 . 
     A polynucleotide that encodes an NK CAR construct may be introduced into an NK cell or iPSC using conventional transfection method. Thus, while described herein in the context of an exemplary embodiment in which a polynucleotide encoding the CAR is transfected into cells using a Sleeping Beauty transposon system, NK cells (and/or iPSCs) may be modified using any suitable transfection method.  FIG. 14  illustrates an exemplary vector construct that may be used to modify NK cells (and/or iPSCs) to express a chimeric antigen receptor.  FIG. 15  illustrates the construction of an alternative exemplary vector that further includes tandem cHS4 insulators (Aker et al., 2007 , Hum Gene Ther  18(4):333-343), which can inhibit silencing of the CAR vector and, therefore, improve expression of the CAR in NK cells and iPSCs. 
     NK cells and/or iPSCs modified to express a chimeric antigen receptor described herein may be formulated into a pharmaceutical composition along with a “carrier” for delivery to a subject having a condition at least partially characterized by cells that can be targets of NK cytotoxicity. As used herein, “carrier” includes any solvent, dispersion medium, vehicle, coating, diluent, antibacterial, and/or antifungal agent, isotonic agent, absorption delaying agent, buffer, carrier solution, suspension, colloid, and the like. The use of such media and/or agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients also can be incorporated into the compositions. 
     By “pharmaceutically acceptable” is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to an individual along with NK cells (and/or iPSCs) modified to express a chimeric antigen receptor without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. 
     The pharmaceutical composition may be formulated in a variety of forms adapted to a preferred route of administration. Thus, a composition can be administered via known routes including, for example, parenteral (e.g., intradermal, transcutaneous, subcutaneous, intramuscular, intravenous, intraperitoneal, etc.) or topical (e.g., intratracheal, intrapulmonary, etc.). A composition also can be administered via a sustained or delayed release. 
     A formulation may be conveniently presented in unit dosage form and may be prepared by methods well known in the art of pharmacy. Methods of preparing a composition with a pharmaceutically acceptable carrier include the step of bringing NK cells (and/or iPSCs) modified to express a chimeric antigen receptor into association with a carrier that constitutes one or more accessory ingredients. In general, a formulation may be prepared by uniformly and/or intimately bringing the NK cells (and/or iPSCs) into association with, for example, a liquid carrier. 
     A pharmaceutical composition that includes NK cells (and/or iPSCs) modified to express a chimeric antigen receptor may be provided in any suitable form including but not limited to a solution, a suspension, an emulsion, a spray, an aerosol, or any form of mixture. The composition may be delivered in formulation with any pharmaceutically acceptable excipient, carrier, or vehicle. 
     The amount of NK cells (and/or iPSCs) modified to express a chimeric antigen receptor that is administered to a subject can vary depending on various factors including, but not limited to, the weight, physical condition, and/or age of the subject, whether one or more chimeric antigen receptors are being administered, and/or the route of administration. Thus, the absolute amount of NK cells (and/or iPSCs) included in a given unit dosage form can vary widely, and depends upon factors such as the species, age, weight and physical condition of the subject, as well as the method of administration. Accordingly, it is not practical to set forth generally the amount that constitutes an amount of NK cells (and/or iPSCs) modified to express a chimeric antigen receptor that is effective for each and/or all possible applications. Those of ordinary skill in the art, however, can readily determine the appropriate amount with due consideration of such factors. 
     In some embodiments, the method can include administering a sufficient number of NK cells (and/or iPSCs) modified to express a chimeric antigen receptor to provide a dose of, for example, from about 10 5  cells/kg to about 10 10  cells/kg to the subject, although in some embodiments the methods may be performed by administering an amount of NK cells (and/or iPSCs) in a dose outside this range. In some of these embodiments, the method includes administering sufficient NK cells (and/or iPSCs) modified to express a chimeric antigen receptor to provide a dose of from about 10 7  cells/kg to about 10 8  cells/kg to the subject, for example, a dose of from about 1×10 7  cells/kg to about 8×10 7  cells/kg. 
     Alternatively, the dose may be calculated using actual body weight obtained just prior to the beginning of a treatment course. For the dosages calculated in this way, body surface area (m 2 ) is calculated prior to the beginning of the treatment course using the Dubois method: m 2 =(wt kg 0.425 ×height cm 0.725 )×0.007184. 
     In some embodiments, the pharmaceutical composition that includes NK cells (and/or iPSCs) modified to express a chimeric antigen receptor may be administered, for example, from a single dose to multiple doses per week, although in some embodiments the method can be performed by administering the pharmaceutical composition at a frequency outside this range. In certain embodiments, the pharmaceutical composition may be administered from about once per month to about five times per week. 
     Generally, the pharmaceutical composition is administered to a subject in an amount, and in a dosing regimen effective to reduce, limit the progression of, ameliorate, or resolve, to any extent, the symptoms or clinical signs of the condition. As used herein, “ameliorate” refers to any reduction in the extent, severity, frequency, and/or likelihood of a symptom or clinical sign characteristic of a particular condition. “Symptom” refers to any subjective evidence of disease or of a patient&#39;s condition. “Sign” or “clinical sign” refers to an objective physical finding relating to a particular condition capable of being found by one other than the patient. 
     In the preceding description, particular embodiments may be described in isolation for clarity. Unless otherwise expressly specified that the features of a particular embodiment are incompatible with the features of another embodiment, certain embodiments can include a combination of compatible features described herein in connection with one or more embodiments. 
     For any method disclosed herein that includes discrete steps, the steps may be conducted in any feasible order. And, as appropriate, any combination of two or more steps may be conducted simultaneously. 
     The present invention is illustrated by the exemplary embodiments described above. It is to be understood that the particular examples, materials, amounts, and procedures are to be interpreted broadly in accordance with the scope and spirit of the invention as set forth herein. 
     As used herein, the term “and/or” means one or all of the listed elements or a combination of any two or more of the listed elements; the terms “comprises” and variations thereof do not have a limiting meaning where these terms appear in the description and claims; unless otherwise specified, “a,” “an,” “the,” and “at least one” are used interchangeably and mean one or more than one; and the recitations of numerical ranges by endpoints include all numbers subsumed within that range (e.g., 1 to 5 includes 1, 1.5, 2, 2.75, 3, 3.80, 4, 5, etc.). 
     The complete disclosure of all patents, patent applications, and publications, and electronically available material (including, for instance, nucleotide sequence submissions in, e.g., GenBank and RefSeq, and amino acid sequence submissions in, e.g., SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq) cited herein are incorporated by reference in their entirety. In the event that any inconsistency exists between the disclosure of the present application and the disclosure(s) of any document incorporated herein by reference, the disclosure of the present application shall govern. The foregoing detailed description and examples have been given for clarity of understanding only. No unnecessary limitations are to be understood therefrom. The invention is not limited to the exact details shown and described, for variations obvious to one skilled in the art will be included within the invention defined by the claims. 
     Unless otherwise indicated, all numbers expressing quantities of components, molecular weights, and so forth used in the specification and claims are to be understood as being modified in all instances by the term “about.” Accordingly, unless otherwise indicated to the contrary, the numerical parameters set forth in the specification and claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques. 
     Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. All numerical values, however, inherently contain a range necessarily resulting from the standard deviation found in their respective testing measurements. 
     All headings are for the convenience of the reader and should not be used to limit the meaning of the text that follows the heading, unless so specified.