T cell receptors and engineered cells expressing same

• US 11,471,489 B2
• Filed: 04/03/2019
• Issued: 10/18/2022
• Est. Priority Date: 04/05/2018
• Status: Active Grant

• Current Assignee: Juno Therapeutics Incorporated (Bristol-Myers Squibb Company)
• Original Assignee: Juno Therapeutics Incorporated (Bristol-Myers Squibb Company)
• Inventors: Goldfless, Stephen Jacob, Belmont, Brian, Brandt, Cameron, Croft, Alexandra, Huss, David Jeffrey
• Primary Examiner(s): Hill, Kevin K
• Assistant Examiner(s): Roberts, Anjeanette
• Application Number:
  US16/374,729
• Publication Number:
  US 20190321401A1
• Time in Patent Office: 1,294 Days
• CPC Class Codes: A61K 2239/31 characterized by the route of administration
• CPC Class Codes: A61K 2239/38 characterised by the dose, timing or administration schedule
• CPC Class Codes: A61K 2239/46 characterised by the cancer treated
• CPC Class Codes: A61K 35/17 Lymphocytes; B-cells; T-cells; Natural killer cells; Interferon-activated or cytokine-activated lymphocytes when activated by a specific antigen A61K39/00
• CPC Class Codes: A61K 39/4611 T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
• CPC Class Codes: A61K 39/4632 T-cell receptors [TCR]; antibody T-cell receptor constructs
• CPC Class Codes: A61K 39/4644 Cancer antigens
• CPC Class Codes: A61K 39/464838 Viral antigens
• CPC Class Codes: A61P 31/20 for DNA viruses
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: C07K 14/025 Papovaviridae, e.g. papillomavirus, polyomavirus, SV40, BK virus, JC virus
• CPC Class Codes: C07K 14/7051 T-cell receptor (TcR)-CD3 complex
• CPC Class Codes: C07K 16/084 Papovaviridae, e.g. papillomavirus, polyomavirus, SV40, BK virus, JC virus
• CPC Class Codes: C07K 16/2833 against MHC-molecules, e.g. HLA-molecules
• CPC Class Codes: C12N 15/86 Viral vectors
• CPC Class Codes: C12N 5/0636 T lymphocytes

Abstract

Provided herein are binding molecules, such as those that recognize or bind a peptide epitope of a cancer antigen, such as expressed on a cancer cell, including cells infected with human papilloma virus (HPV) or that contain HPV DNA sequences and/or those that recognize or bind a peptide epitope of HPV 16 E6 or E7, in the context of a major histocompatibility complex (MHC) molecule. Among the provided binding molecules are T cell receptors (TCRs) or antibodies, including antigen-binding fragments thereof, that bind or recognize such peptide epitopes. The present disclosure further relates to engineered cells comprising such binding molecules, e.g., TCRs or antibodies (and chimeric antigen receptors containing the antibodies), and uses thereof in adoptive cell therapy.

Claims

1. A recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 in the context of an MHC molecule, comprising an alpha chain comprising a variable alpha (Vα

) region and a beta chain comprising a variable beta (Vβ

) region, wherein

the Vα

region comprises a complementarity determining region 1 (CDR-1), a complementarity determining region 2 (CDR-2), and a complementarity determining region 3 (CDR-3), comprising the amino acid sequences of SEQ ID NOs;

48, 49, and 50, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

61, 62, and 63, respectively.

2. The T cell receptor (TCR) or antigen-binding fragment thereof of claim 1, wherein

the Vα

region comprises the amino acid sequence set forth in SEQ ID NO;

47 or an amino acid sequence that has at least 90% sequence identity thereto, and the Vβ

region comprises the amino acid sequence set forth in SEQ ID NO;

60, or an amino acid sequence that has at least 90% sequence identity thereto.

3. The TCR or antigen-binding fragment thereof of claim 1, wherein the peptide epitope is or comprises E7(11-19) YMLDLQPET (SEQ ID NO:

271).

4. The TCR or antigen-binding fragment thereof of claim 1, wherein

the Vα

and Vβ

regions comprise the amino acid sequences of SEQ ID NOs;

47 and 60, respectively.

5. The TCR or antigen-binding fragment thereof of claim 1, wherein the alpha chain further comprises an alpha constant (Cα

) region and the beta chain further comprises a beta constant (Cβ

) region.

6. The TCR or antigen-binding fragment thereof of claim 5, wherein the Cα

and Cβ

regions are mouse constant regions.

7. The TCR or antigen-binding fragment thereof of claim 5, wherein the Cα

and Cβ

regions are human constant regions.

8. The TCR or antigen-binding fragment thereof of claim 5, wherein the Cα

and/or Cβ

regions comprise one or more amino acid replacements to introduce one or more cysteine residues capable of forming one or more non-native disulfide bridges between the alpha chain and beta chain.

9. The TCR or antigen-binding fragment thereof of claim 5, wherein

the alpha and beta chains comprise the amino acid sequences of SEQ ID NOs:

43 and 359, respectively.

10. The TCR or antigen-binding fragment thereof of claim 1, wherein the antigen-specificity is at least partially CD8-independent.

11. A nucleic acid molecule encoding the TCR or antigen-binding fragment thereof of claim 1, or an alpha or a beta chain thereof.

12. A vector comprising the nucleic acid of claim 11.

13. An isolated engineered cell comprising the nucleic acid molecule of claim 11.

14. An isolated engineered cell, comprising the TCR or antigen-binding fragment thereof of claim 1.

15. The isolated engineered cell of claim 14, wherein the cell is a T cell.

16. A method for producing a cell expressing a recombinant TCR or antigen-binding fragment thereof, comprising introducing the vector of claim 12 into a cell.

17. A composition comprising engineered cells of claim 14.

18. The composition of claim 17, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

19. A method of treatment, comprising administering the composition of claim 17 to a subject having a disease or disorder associated with HPV.

20. The isolated engineered cell of claim 15, comprising a genetic disruption of a T cell receptor alpha constant (TRAC) gene and/or a T cell receptor beta constant (TRBC) gene.

21. The isolated engineered cell of claim 20, wherein the genetic disruption comprises disruption of a T cell receptor alpha constant (TRAC) gene.

22. The TCR or antigen-binding fragment thereof of claim 5, wherein the Cα

region comprises the amino acid sequence of SEQ ID NO;

14, or an amino acid sequence having at least 90% sequence identity thereto; and

the Cβ

region comprises the amino acid sequence of SEQ ID NO;

350, or an amino acid sequence having at least 90% sequence identity thereto.

23. The TCR or antigen-binding fragment thereof of claim 5, wherein the Cα

region comprises the amino acid sequence of SEQ ID NO;

14, and the Cβ

region comprises the amino acid sequence of SEQ ID NO;

350.

24. The TCR or antigen-binding fragment thereof of claim 5, wherein the TCR or antigen-binding fragment thereof is encoded by a polynucleotide that encodes the amino acid sequence of SEQ ID NO:

362, or a sequence having at least 90% sequence identity thereto.

25. A nucleic acid molecule encoding the TCR or antigen-binding fragment thereof of claim 4, or an alpha or a beta chain thereof.

26. A vector comprising the nucleic acid of claim 25.

27. An isolated engineered cell comprising the nucleic acid molecule of claim 25.

28. An isolated engineered cell, comprising the TCR or antigen-binding fragment thereof of claim 4.

29. The isolated engineered cell of claim 28, wherein the cell is a T cell.

30. A method for producing a cell expressing a recombinant TCR or antigen-binding fragment thereof, comprising introducing the vector of claim 26 into a cell.

31. A composition comprising engineered cells of claim 28.

32. The composition of claim 31, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

33. A method of treatment, comprising administering the composition of claim 32 to a subject having a disease or disorder associated with HPV.

34. A nucleic acid molecule encoding the TCR or antigen-binding fragment thereof of claim 22, or an alpha or a beta chain thereof.

35. A vector comprising the nucleic acid of claim 34.

36. An isolated engineered cell comprising the nucleic acid molecule of claim 34.

37. An isolated engineered cell, comprising the TCR or antigen-binding fragment thereof of claim 22.

38. The isolated engineered cell of claim 37, wherein the cell is a T cell.

39. A method for producing a cell expressing a recombinant TCR or antigen-binding fragment thereof, comprising introducing the vector of claim 35 into a cell.

40. A composition comprising engineered cells of claim 37.

41. The composition of claim 40, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

42. A method of treatment, comprising administering the composition of claim 40 to a subject having a disease or disorder associated with HPV.

43. An isolated engineered T cell, comprising a recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 in the context of an MHC molecule,

wherein the TCR or antigen binding fragment thereof comprises an alpha chain comprising a variable alpha (Vα

) region and an alpha constant (Cα

) region, and a beta chain comprising a variable beta (Vβ

) region and a beta constant (Cβ

) region,

wherein the Vα

region comprises a complementarity determining region 1 (CDR-1), a complementarity determining region 2 (CDR-2), and a complementarity determining region 3 (CDR-3), comprising the amino acid sequences of SEQ ID NOs;

48, 49, and 50, respectively, and the Vβ

region comprises a CDR-1, a CDR-2, and a CDR-3, comprising the amino acid sequences of SEQ ID NOs;

61, 62, and 63, respectively; and

wherein the Cα

region comprises the amino acid sequence of SEQ ID NO;

14, and the Cβ

region comprises the amino acid sequence of SEQ ID NO;

350.

44. The isolated engineered cell of claim 43, comprising a genetic disruption of a T cell receptor alpha constant (TRAC) gene and/or a T cell receptor beta constant (TRBC) gene.

45. The isolated engineered cell of claim 44, wherein the genetic disruption comprises disruption of a T cell receptor alpha constant (TRAC) gene.

46. A composition comprising engineered cells of claim 43.

47. The composition of claim 46, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

48. A method of treatment, comprising administering the composition of claim 46 to a subject having a disease or disorder associated with HPV.

49. A composition comprising engineered cells of claim 44.

50. The composition of claim 49, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

51. A method of treatment, comprising administering the composition of claim 49 to a subject having a disease or disorder associated with HPV.

52. An isolated engineered T cell, comprising a recombinant T cell receptor (TCR) or antigen-binding fragment thereof that binds to or recognizes a peptide epitope of human papillomavirus (HPV) 16 E7 in the context of an MHC molecule,

wherein the TCR or antigen binding fragment thereof comprises an alpha chain comprising the amino acid sequence of SEQ ID NO:

43, and a beta chain comprising the amino acid sequence of SEQ ID NO;

359.

53. The isolated engineered cell of claim 52, comprising a genetic disruption of a T cell receptor alpha constant (TRAC) gene and/or a T cell receptor beta constant (TRBC) gene.

54. The isolated engineered cell of claim 53, wherein the genetic disruption comprises disruption of a T cell receptor alpha constant (TRAC) gene.

55. A composition comprising engineered cells of claim 52.

56. The composition of claim 55, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

57. A method of treatment, comprising administering the composition of claim 55 to a subject having a disease or disorder associated with HPV.

58. A composition comprising engineered cells of claim 53.

59. The composition of claim 58, wherein the composition comprises engineered CD8+ cells and engineered CD4+ cells.

60. A method of treatment, comprising administering the composition of claim 58 to a subject having a disease or disorder associated with HPV.