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US-12624082-B2 - T cell receptors and methods of use thereof

US12624082B2US 12624082 B2US12624082 B2US 12624082B2US-12624082-B2

Abstract

The present disclosure is directed recombinant T cell receptors capable of binding a MUC5AC epitope and nucleic acid molecules encoding the same. In some aspects, the nucleic acid molecules further comprise a second nucleotide sequence, wherein the second nucleotide sequence or the polypeptide encoded by the second nucleotide sequence inhibits the expression of an endogenous TCR. Other aspects of the disclosure are directed to vectors comprising the nucleic acid molecule and cells comprising the recombinant TCR, the nucleic acid molecule, or the vector. Still other aspects of the disclosure are directed to methods of using the same. In some aspects, the methods comprise treating a cancer in a subject in need thereof.

Inventors

  • Naoto Hirano
  • Kenji SUGATA
  • Kayoko SASO

Assignees

  • UNIVERSITY HEALTH NETWORK

Dates

Publication Date
20260512
Application Date
20200729

Claims (19)

  1. 1 . A nucleic acid molecule comprising: (a) a first nucleotide sequence encoding a recombinant T cell receptor (TCR) or an antigen binding portion thereof that specifically binds an epitope of MUC5AC human mucin 5AC (MUC5AC) (“anti-MUC5AC TCR”), wherein the epitope comprises the amino acid sequence set forth in SEQ ID NO: 13, which is complexed with an HLA class II molecule HLA-DP4 allele; and (b) a second nucleotide sequence, wherein the second nucleotide sequence or the polypeptide encoded by the second nucleotide sequence inhibits the expression of an endogenous TCR, wherein the anti-MUC5AC TCR comprises an alpha chain variable domain comprising an alpha chain CDR1, an alpha chain CDR2, and an alpha chain CDR3; and a beta chain variable domain comprising a beta chain CDR1, a beta chain CDR2, and a beta chain CDR3; wherein: (i) the beta chain CDR3 of the anti-MUC5AC TCR comprises the amino acid sequence set forth in SEQ ID NO: 10; (ii) the beta chain CDR2 of the anti-MUC5AC TCR comprises the amino acid sequence set forth in SEQ ID NO: 9; (iii) the beta chain CDR1 of the anti-MUCSAC TCR comprises the amino acid sequence set forth in SEQ ID NO: 8; (iv) the alpha chain CDR3 of the anti-MUC5AC TCR comprises the amino acid sequence set forth in SEQ ID NO: 7; (v) the alpha chain CDR2 of the anti-MUC5AC TCR comprises the amino acid sequence set forth in SEQ ID NO: 6; and (vi) the alpha chain CDR1 of the anti-MUC5AC TCR comprises the amino acid sequence set forth in SEQ ID NO: 5.
  2. 2 . The nucleic acid molecule of claim 1 , wherein (i) the alpha chain variable domain of the anti-MUC5AC TCR comprises the amino acid sequence of a variable domain present in the amino acid sequence set forth in SEQ ID NO: 1; ii) the beta chain variable domain of the anti-MUC5AC TCR comprises the amino acid sequence of a variable domain present in the amino acid sequence set forth in SEQ ID NO: 2; or (ii) both (i) and (ii).
  3. 3 . The nucleic acid molecule of claim 1 , wherein: (a) the anti-MUC 5 AC TCR further comprises an alpha chain constant region, wherein the alpha chain constant region is different from a constant region of an endogenous alpha chain, and wherein (i) the alpha chain constant region comprises an amino acid sequence having at least about 85% sequence identity to a constant region present in the amino acid sequence set forth in SEQ ID NO: 1; or (ii) the alpha chain constant region comprises an amino acid sequence comprising at least 1 amino acid substitution relative to a constant region present in the amino acid sequence set forth in SEQ ID NO: 1; (b) the anti-MUC5AC TCR further comprises a beta chain constant region, wherein the beta chain constant region is different from a constant region of an endogenous beta chainp, and wherein (i) the beta chain constant region comprises an amino acid sequence having at least about 85% sequence identity to a constant region present in the amino acid sequence set forth in SEQ ID NO: 2; or (ii) the beta chain constant region comprises an amino acid sequence comprising at least 1 amino acid substitution relative to a constant region present in the amino acid sequence set forth in SEQ ID NO: 2; or (c) both (a) and (b).
  4. 4 . The nucleic acid molecule of claim 1 , wherein the second nucleotide sequence is one or more siRNAs that reduce the expression of endogenous TCRs, wherein the one or more siRNAs are complementary to a target sequence within a nucleotide sequence encoding a constant region of the endogenous TCRs.
  5. 5 . A vector comprising the nucleic acid molecule of claim 1 .
  6. 6 . A cell comprising the nucleic acid molecule of claim 1 .
  7. 7 . The cell of claim 6 , which further expresses CD3.
  8. 8 . The cell of claim 6 , which is a T cell.
  9. 9 . The cell of claim 6 , which is a natural killer (NK) cell, a natural killer T (NKT) cell, or an ILC cell.
  10. 10 . The nucleic acid molecule of claim 1 , wherein the anti-MUC5AC TCR comprises an alpha chain comprising the amino acid sequence set forth in SEQ ID NO: 1 and a beta chain comprising the amino acid sequence set forth in SEQ ID NO: 2.
  11. 11 . A cell comprising the nucleic acid molecule of claim 10 .
  12. 12 . The cell of claim 11 , which further expresses CD3.
  13. 13 . The cell of claim 11 , which is a T cell.
  14. 14 . The cell of claim 11 , which is an NK cell, a natural killer T (NKT) cell, or an ILC cell.
  15. 15 . A method of treating a cancer in a subject in need thereof, comprising administering to the subject the cell of claim 6 .
  16. 16 . The method of claim 15 , wherein the cancer comprises melanoma, bone cancer, pancreatic cancer, skin cancer, cancer of the head or neck, 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 (NHL), primary mediastinal large B cell lymphoma (PMBC), diffuse large B cell lymphoma (DLBCL), follicular lymphoma (FL), transformed follicular lymphoma, splenic marginal zone lymphoma (SMZL), cancer of the esophagus, cancer of the small intestine, 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, chronic or acute leukemia, acute myeloid leukemia, chronic myeloid leukemia, acute lymphoblastic leukemia (ALL) (including non T cell ALL), chronic lymphocytic leukemia (CLL), solid tumors of childhood, lymphocytic lymphoma, 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 including those induced by asbestos, other B cell malignancies, or a combination of one or more of said cancers.
  17. 17 . The method of claim 15 , wherein the cancer is locally advanced, advanced, or metastatic.
  18. 18 . The method of claim 15 , wherein the cancer is relapsed or refractory.
  19. 19 . A method of engineering an antigen-targeting cell, comprising transducing a cell collected from a subject in need of a T cell therapy with the nucleic acid molecule of claim 1 .

Description

CROSS REFERENCE TO RELATED APPLICATIONS This PCT application claims the priority benefit of U.S. Provisional Application No. 62/880,505, filed Jul. 30, 2019, which is incorporated herein by reference in its entirety. REFERENCE TO SEQUENCE LISTING SUBMITTED ELECTRONICALLY VIA EFS-WEB The content of the electronically submitted sequence listing (Name: 4285_014PC01_Seqlisting_ST25.txt, Size: 70,689 bytes; and Date of Creation: Jul. 28, 2020) is incorporated herein by reference in its entirety. FIELD OF THE DISCLOSURE The present disclosure provides recombinant T cell receptors (“TCRs”) that specifically bind human Mucin 5AC (MUC5AC) and uses thereof. BACKGROUND OF THE DISCLOSURE Immunotherapy has emerged as a critical tool in the battle against a variety of diseases, including cancer. T cell therapies are at the forefront of immunotherapeutic development, and adoptive transfer of antitumor T cells has been shown to induce clinical responses in cancer patients. Though many T cell therapies target mutated tumor antigens, the vast majority of neoantigens are not shared and are unique to each patient. Potential non-mutated antigens outnumber mutated antigens by multiple orders of magnitude. The elucidation of T cell epitopes derived from shared antigens may facilitate the robust development of efficacious and safe adoptive T cell therapies that are readily available to a larger cohort of cancer patients. However, the sheer number of non-mutated antigens and the high polymorphism of HLA genes may have hampered comprehensive analyses of the specificity of antitumor T cell responses toward non-mutated antigens. SUMMARY OF THE DISCLOSURE Certain aspects of the present disclosure are directed to a nucleic acid molecule comprising (i) a first nucleotide sequence encoding a recombinant T cell receptor (TCR) or an antigen binding portion thereof that specifically binds human mucin 5AC (MUC5AC) (“anti-MUC5AC TCR”); and (ii) a second nucleotide sequence, wherein the second nucleotide sequence or the polypeptide encoded by the second nucleotide sequence inhibits the expression of an endogenous TCR, wherein the anti-MUC5AC TCR cross competes for binding to human MUC5AC with a reference TCR, which comprises an alpha chain and a beta chain, and wherein the alpha chain comprises an amino acid sequence as set forth in SEQ ID NO: 1 and the beta chain comprises an amino acid sequence as set forth in SEQ ID NO: 2. Certain aspects of the present disclosure are directed to a nucleic acid molecule comprising (i) a first nucleotide sequence encoding a recombinant T cell receptor (TCR) or an antigen binding portion thereof that specifically binds human MUC5AC (“anti-MUC5AC TCR”); and (ii) a second nucleotide sequence, wherein the second nucleotide sequence or the polypeptide encoded by the second nucleotide sequence inhibits the expression of an endogenous TCR, wherein the anti-MUC5AC TCR binds the same epitope or an overlapping epitope of human MUC5AC as a reference TCR, which comprises an alpha chain and a beta chain, wherein the alpha chain comprises an amino acid sequence as set forth in SEQ ID NO: 1 and the beta chain comprises an amino acid sequence as set forth in SEQ ID NO: 2. In some aspects, the anti-MUC5AC TCR binds to an epitope of MUC5AC consisting of an amino acid sequence as set forth in SEQ ID NO: 13. In some aspects, the epitope is complexed with an HLA class II molecule. In some aspects, the HLA class II molecule is an HLA-DP, HLA-DQ, or HLA-DR allele, or any combination thereof. In some aspects, the HLA class II molecule is an HLA-DP allele. In some aspects, the HLA class II molecule is an HLA-DP4 allele. In some aspects, the anti-MUC5AC TCR comprises an alpha chain and a beta chain, wherein the alpha chain comprises a variable region comprising an alpha chain CDR1, an alpha chain CDR2, and an alpha chain CDR3; and wherein the beta chain comprises variable domain comprising a beta chain CDR1, a beta chain CDR2, and a beta chain CDR3; wherein the alpha chain CDR3 comprises an amino acid sequence as set forth in SEQ ID NO: 7. In some aspects, the beta chain CDR3 of the anti-MUC5AC TCR comprises an amino acid sequence as set forth in SEQ ID NO: 10. In some aspects, the anti-MUC5AC TCR comprises an alpha chain and a beta chain, wherein the alpha chain comprises a variable region comprising an alpha chain CDR1, an alpha chain CDR2, and an alpha chain CDR3; and wherein the beta chain comprises variable domain comprising a beta chain CDR1, a beta chain CDR2, and a beta chain CDR3; wherein the beta chain CDR3 of the anti-MUC5AC TCR comprises an amino acid sequence as set forth in SEQ ID NO: 10. In some aspects, the alpha chain CDR3 of the anti-MUC5AC TCR comprises an amino acid sequence as set forth in SEQ ID NO: 7. In some aspects, the alpha chain CDR1 of the anti-MUC5AC TCR comprises an amino acid sequence as set forth in SEQ ID NO: 5. In some aspects, the beta chain CDR1 of the anti-MUC5AC TCR comprises an amino acid sequen