METHODS OF PRODUCING ENRICHED POPULATIONS OF TUMOR-REACTIVE T CELLS FROM TUMOR

• US 20160010058A1
• Filed: 04/30/2013
• Published: 01/14/2016
• Est. Priority Date: 03/01/2013
• Status: Abandoned Application

• Current Assignee: United States Department Of Health And Human Services
• Original Assignee: The United States of America As Represented By The Secretary of Agriculture
• Inventors: Gros, Alena, Rosenberg, Steven A.
• Application Number:
  US14/771,615
• Publication Number:
  US 20160010058A1
• Time in Patent Office: Days
• US Class Current: 1/1
• CPC Class Codes: A61K 2039/5158 Antigen-pulsed cells, e.g. T-cells
• CPC Class Codes: A61K 2239/51 Stomach
• CPC Class Codes: A61K 2239/57 Skin; melanoma
• 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 39/0011 Cancer antigens
• 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 39/464402 Receptors, cell surface antigens or cell surface determinants
• CPC Class Codes: A61K 39/464411 Immunoglobulin superfamily
• CPC Class Codes: A61K 39/464417 Receptors for tumor necrosis factors [TNF], e.g. lymphotoxin receptor [LTR], CD30
• CPC Class Codes: A61K 39/464491 Melan-A/MART
• CPC Class Codes: A61P 35/00 Antineoplastic agents
• CPC Class Codes: A61P 35/02 specific for leukemia
• CPC Class Codes: C12N 5/0636 T lymphocytes
• CPC Class Codes: C12N 5/0638 Cytotoxic T lymphocytes [CTL] or lymphokine activated killer cells [LAK]

Abstract

Methods of obtaining a cell population enriched for tumor-reactive T cells, the method comprising: (a) obtaining a bulk population of T cells from a tumor sample; (b) specifically selecting CD8⁺ T cells that express any one or more of TIM-3, LAG-3, 4-1BB, and PD-1 from the bulk population; and (c) separating the cells selected in (b) from unselected cells to obtain a cell population enriched for tumor-reactive T cells are disclosed. Related methods of administering a cell population enriched for tumor-reactive T cells to a mammal, methods of obtaining a pharmaceutical composition comprising a cell population enriched for tumor-reactive T cells, and isolated or purified cell populations are also disclosed.

Claims

1. A method of obtaining a cell population enriched for tumor-reactive T-cells, the method comprising:

(a) obtaining a bulk population of T cells from a tumor sample;

(b) specifically selecting CD8⁺ T cells that express any one or more of TIM-3. LAG-3, 4-1BB, and PD-1 from the bulk population; and

(c) separating the cells selected in (h) from unselected cells to obtain a cell population enriched for tumor-reactive T cells.

3. The method of claim 1, wherein (b) comprises specifically selecting CD8 ⁺ T cells that express TIM-3 from the bulk population.

4. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that express LAG-3 from the bulk population.

5. The method of claim 1, wherein (b) comprises specifically selecting CD8 ⁺ T cells that express 4-1BB from the bulk population.

6. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that express PD-1 from the bulk population.

7. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) 4-1BB⁺/PD-1⁺, (ii) 4-1BB⁻

/PD-1⁺, and/or (iii) 4-1BB³⁰ /PD-1⁻

from the bulk population.

8. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) LAG-3⁺/PD-1⁺, (ii) LAG-3⁻

/PD-1⁺, and/or (iii) LAG-3⁺/PD-1⁻

from the bulk population.

9. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) TIM-3⁺/PD-1⁺, (ii) TIM-3⁻

/PD-1⁺, or (iii) TIM-3⁺/PD-1⁻

from the bulk population.

10. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) TIM-3⁺/LAG-3⁺, (ii) TIM-3⁻

/LAG-3⁺, or (iii) TIM-3⁺/LAG-3⁻

from the bulk population.

11. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) 4-1BB⁺/LAG-3⁺, (ii) 4-1BB⁻

/LAG-3⁺, or (iii) 4-1BB⁺/LAG-3⁻

from the bulk population.

12. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) 4-1BB⁺/TIM-3⁺, (ii) 4-1BW/TIM-3^÷

, or (iii) 4-1BB⁺/TIM-3⁻

from the bulk population.

13. The method of claim 1, wherein the cell population enriched for tumor-reactive T cells is obtained without screening for autologous tumor recognition.

14. The method of claim 1, wherein the bulk population of T cells is not non-specifically stimulated prior to (b).

15. The method of claim 1, further comprising expanding the numbers of T cells in the enriched cell population obtained in (c).

16. The method of claim 1, further comprising culturing the enriched cell population obtained in (c) in the presence of any one or more of TWS 119, interleukin (IL-21), IL-12, IL-15, IL-7, transforming growth factor (TGF) beta, and AKT inhibitor (AKTi).

17. The method of claim 1, further comprising stimulating the enriched cell population obtained in (c) with a cancer antigen and/or with autologous tumor cells.

18. The method of claim 1, further comprising transducing or transfecting the cells of the enriched population obtained in (c) with a nucleotide sequence encoding any one or more of IL-12, IL-7, IL-15, IL-2, IL-21, mir155, and anti-PD-1 siRNA.

19. An isolated or purified cell population enriched for tumor-reactive T cells obtained by the method of claim 1.

39. A method of treating or preventing cancer in a mammal, the method comprising obtaining a cell population enriched for tumor-reactive T cells by the method claimed in claim 1, and administering the cell population to the mammal in an amount effective to treat or prevent cancer in the mammal.

40. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that express two or more of TIM-3, LAG-3, and PD-1 from the bulk population.

41. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are LAG-3⁺/PD-1⁺ or TIM-3⁺/PD-1⁺ from the bulk population.

42. The method of claim 1, wherein (b) comprises specifically selecting CD8⁺ T cells that are 4-1BB⁻

/PD-1⁺, 4-1BB⁻

/LAG-3⁺, or 4-1BB⁻

/TIM3⁺.

2. A method of obtaining a pharmaceutical composition comprising a cell population enriched for tumor-reactive T cells, the method comprising:

(a) obtaining a bulk population of T cells from a tumor sample;

(b) specifically selecting CD8⁺ T cells that express any one or more of TIM-3, LAG-3, 4-1BB, and PD-1 from the bulk population;

(c) separating the cells selected in (b) from unselected cells to obtain a cell population enriched for tumor-reactive T cells; and

(d) combining the cell population enriched for tumor-reactive T cells with a pharmaceutically acceptable carrier to obtain a pharmaceutical composition comprising a cell population enriched for tumor-reactive T cells.

20. An isolated or purified cell population comprising any one or more of:

(a) CD8⁺/4-1BB⁺/PD-1⁺ T cells,

(b) CD8⁺/4-1BB³¹ /PD-1⁺ T cells,

(c) CD8⁺/4-1BB⁺/PD-1⁻

T cells,

(d) CD8⁺/LAG-3⁺/PD-1⁺ T cells,

(e) CD8⁺/LAG-3³¹ /PD-1⁺ T cells,

(f) CD8⁺/LAG-3⁺/PD-1⁻

T cells,

(g) CD8⁺/TIM-3⁺/PD-1⁺ T cells,

(h) CD8⁺/TIM-3⁻

/PD-1⁺ T cells,

(i) CD8⁺/TIM-3⁺/PD-1⁻

T cells,

(j) CD8⁺/TIM-3⁺/LAG-3⁺ T cells,

(k) CD8⁺/TIM-3⁻

/LAG-3⁺ T cells,

(l) CD8⁺/TIM-3⁺/LAG-3⁻

T cells,

(m) CD8⁺/4-1BB⁺/LAG-3⁺ T cells,

(n) CD8⁺/4-1BB⁻

/LAG-3⁺ T cells,

(o) CD8⁺/4-1BB⁺, LAG-3⁻

T cells,

(p) CD8⁺/4-1BB⁺/TIM-3⁺ T cells,

(q) CD8⁺/4-1BB⁻

/TIM-3⁺ T cells, and

(r) CD8⁺/4-1BB⁺/TIM-3⁻

T cells,

wherein the cell population is enriched for tumor-rcactive T cells.

21. The isolated or purified cell population of claim 20 comprising:

(a) CD8⁺/4-1BB⁺/PD-1⁺ T cells,

(b) CD8⁺/4-1BB³¹ /PD-1⁺ T cells,

(c) CD8⁺/4-1BB⁺/PD-1⁻

T cells,

(d) CD8⁺/LAG-3⁺/PD-1⁺ T cells,

(e) CD8⁺/LAG-3⁻

/PD-1³⁰ T cells,

(f) CD8⁺/LAG-3⁺/PD-1⁻

T cells,

(g) CD8⁺/TIM-3⁺/PD-1⁺ T cells,

(h) CD8⁺/TIM-3⁻

/PD-1⁺ T cells,

(i) CD8⁺/TIM-3³⁰ /PD-1⁻

T cells,

(j) CD8⁺/TIM-3⁺/LAG-3⁺ T cells,

(k) CD8⁺/TIM-3⁻

/LAG-3⁺ T cells,

(l) CD8⁺/TIM-3⁺/LAG-3⁻

T cells,

(m) CD8⁺/4BB⁺/LAG-3⁺ T cells,

(n) CD8⁺/4-1BB⁻

/LAG-3⁺ T cells,

(o) CD8⁺/4-1BB⁺/LAG-3⁻

T cells,

(p) CD8⁺/4-1BB⁺/TIM-3⁺ T cells,

(q) CD8⁺/4-1BB⁻

/TIM-3⁺ T cells, or

(r) CD8⁺/4-BB⁺/TIM-3⁻

T cells.

43. The isolated or purified cell population of claim 20 comprising:

(a) CD8⁺/LAG-3⁺/PD-1⁺ T cells, or

(b) CD8⁺/TIM-3⁺/PD-1⁺ T cells.

44. The isolated or purified cell population of claim 20 comprising:

(a) CD8⁺/4-1BB⁻

/PD-1⁺ T cells,

(b) CD8⁺/4-1BB⁻

/LAG-3⁺ T cells, or

(c) CD8⁺/4-1BB⁻

/TIM3⁺ T cells.

22. A method of administering a cell population enriched for tumor-reactive T cells to a mammal, the method comprising:

(a) obtaining a bulk population of T cells from a tumor sample;

(b) specifically selecting CD8⁺ T cells that express any one or more of TIM-3, LAG-3, 4-1BB, and PD-1 from the bulk population;

(c) separating the cells selected in (b) from unselected cells to obtain a cell population enriched for tumor-reactive T cells; and

administering the cell population enriched for tumor-reactive T cells to the mammal.

23. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that express TIM-3 from the bulk population.

24. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that express LAG-3 from the bulk population.

25. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that express 4-1BB from the bulk population.

26. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that express PD-1 from the bulk population.

27. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) 4-1BB⁺/PD-1⁺, (ii) 4-1BB⁻

/PD-1⁺, and/or (iii) 4-1BB⁺/PD-1⁻

from the bulk population.

28. The method, of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) LAG-3⁺/PD-1⁺, (ii) LAG-3⁻

/PD-1⁺, and/or (iii) LAG-3⁺/PD-1⁻

from the bulk population.

29. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) TIM-3⁺/PD-1⁺, (ii) TIM-3⁻

/PD-1⁺, or (iii) TIM-3⁺/PD-1⁻

from the bulk population.

30. The method of claim 22, wherein (b) comprises specifically selecting CD8³⁰ T cells that are (i) TIM-3⁺/LAG-3⁺, (ii) TIM-3⁻

/LAG-3⁺, or (iii) TIM-3⁺/LAG-3⁻

from the bulk population.

31. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) 4-1BB⁺/LAG-3⁺, (ii) 4-1BB⁻

/LAG-3⁺, or (iii) 4-1BB⁺/LAG-3⁻

from the bulk population.

32. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are (i) 4-1BB⁺TIM-3⁺, (ii) 4-1BB⁻

/TIM-3⁺, or (iii) 4-1BB⁺/TIM-3⁻

from the bulk population.

33. The method of claim 22, wherein the cell population enriched for tumor-reactive T cells is obtained without screening for autologous tumor recognition.

34. The method of claim 22, wherein the bulk population of T cells is not non-specifically stimulated prior to (b).

35. The method of claim 22, further comprising expanding the numbers of T cells in the enriched cell population obtained in (c).

36. The method of claim 22, further comprising culturing the enriched cell population obtained in (c) in the presence of any one or more of TWS119, interleukin (IL-21), IL-12, IL-15, IL-7, transforming growth factor (TGF) beta, and AKT inhibitor (AKTi).

37. The method of claim 22, further comprising stimulating the enriched cell population obtained in (c) with a tumor antigen and/or with autologous tumor T cells.

38. The method of claim 22, further comprising transducing or transfecting the cells of the enriched population obtained in (c) with a nucleotide sequence encoding any one or more of IL-12, IL-7, IL-15, IL-2, IL-21, mir155, and anti-PD-1 siRNA.

45. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that express two or more of TIM-3, LAG-3, and PD-1 from the bulk population.

46. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are LAG-3⁺/PD-1⁺ or TIM-3⁺/PD-1⁺ from the bulk population.

47. The method of claim 22, wherein (b) comprises specifically selecting CD8⁺ T cells that are 4-1BB⁻

/PD-1⁺, 4-1BB⁻

/LAG-3⁺, or 4-1BB⁻

/TIM3⁺.