Binding proteins specific for RAS neoantigens and uses thereof

Patent metadata

Field	Value
Publication number	US-11382954-B2
Application number	US-202117408340-A
Country	US
Kind code	B2
Filing date	Aug 20, 2021
Priority date	Feb 20, 2019
Publication date	Jul 12, 2022
Grant date	Jul 12, 2022

Abstract

The present disclosure provides compositions and methods for targeting a Ras antigen to, for example, treat or prevent cancer. Disclosed embodiments include binding proteins, such as a T cell receptor or a chimeric antigen receptor, that bind to a Ras antigen:HLA complex. Polynucleotides encoding such binding protein can introduced into a host cell, such as a T cell, and the cell can be used in immunotherapy for treating various cancers. Also provided are immunogenic polypeptides that can be useful to, for example, induce an immune response against a mutated Ras or to identify a binding protein that binds to a Ras antigen.

First claim

What is claimed is:

1. A method of treating a disease or disorder or preventing a relapse of a disease or disorder associated with a G12-mutant KRAS, NRAS, or HRAS mutation in a subject in need thereof, comprising
administering to said subject an effective amount of a cell population comprising a T cell comprising a membrane protein with a human or humanized extracellular binding domain that is configured to bind to a peptide:HLA complex comprising a G12-mutant KRAS, NRAS, or HRAS peptide, wherein said peptide:HLA complex is HLA-A*11 serotype restricted,
wherein said extracellular binding domain comprises a framework region derived from a human TRBV, TRBD, TRBJ, TRAV, or TRAJ gene segment,
wherein said extracellular binding domain comprises a sequence derived from any one of:
(i) V28-01*01, D1*01F, J1-6*01F, V19*01F, or J6*01F;
(ii) V9-01*01F, D2*02F, J2-3*01F, V17*01F, or J45*01F;
(iii) V25-01*01F, D1*01F, J2-1*01F, V12-3*01F, or J17*01F;
(iv) V25-01*01F, D2*01F, J2-1*01F, V12-3*01F, or J17*01F;
(v) V12-04*01F, D1*01F, J2-3*01F, V29/DV5*01F, or J43*01F;
(vi) V12-04*01F, D2*02F, J2-1*01F, V2*01F, or J30*01F;
(vii) V11-02*01F, D2*02F, J2-3*01F, V26-1*01F, or J29*01F;
(viii) V7-09*01F, D2*01F, J2-4*01, V1-1*01F, J12*01F;
(ix) V25-01*01F, D1*01F, J2-1*01F, V12-3*01F, or J39*01F;
(x) V10-01*01F, D1*01F, J2-7*01F, V27*01F, or J52*01F; or
(xi) V30* 02 F, D1*01F, J1-5*01F, V12-2*01F, or J39*01F.

2. The method of claim 1 , wherein said T cell is configured to undergo an antigen-specific T-cell response to said peptide:HLA complex.

3. The method of claim 2 , wherein said T cell is configured to produce IFN-γ when in the presence of said peptide:HLA complex.

4. The method of claim 2 , wherein said T cell is configured to have elevated CD137 expression when in the presence of said peptide:HLA complex as compared to CD137 expression in a T cell not expressing said membrane protein.

5. The method of claim 1 , wherein said T cell does not substantially produce IFN-γ when in the absence of said peptide:HLA complex.

6. The method of claim 1 , wherein said G12-mutant KRAS, NRAS, or HRAS peptide comprises any one of

(i)

(SEQ ID NO.: 2)

VVVGAVGVGK;

(ii)

(SEQ ID NO.: 3)

VVGAVGVGK;

(iii)

(SEQ ID NO.: 5)

VVVGADGVGK;

or

(iv)

(SEQ ID NO.: 4)

VVGADGVGK.

7. The method of claim 1 , wherein said membrane protein does not comprise a cytoplasmic signaling domain fused thereto.

8. The method of claim 1 , wherein said membrane protein has a log 10 EC50 for the peptide of less than −8.0, optionally about −8.5 or less, further optionally about −8.5, about −8.6, about −8.7, about −8.8, about −8.9, about −9, about −9.1, or about −9.2.

9. The method of claim 1 , wherein said T cell is a CD8+ T cell, a CD4− CD8− double negative T cell, a γδ T cell, or a natural killer T cell.

10. The method of claim 1 , wherein said extracellular binding domain comprises a CDR3α and a CDR3β sequence according to:
(i) SEQ ID NOs.:618 or 617;
(ii) SEQ ID NOs.:624 or 623;
(iii) SEQ ID NOs.:636 or 635;
(iv) SEQ ID NOs.:642 or 641;
(v) SEQ ID NOs.:648 or 647;
(vi) SEQ ID NOs.:654 or 653;
(vii) SEQ ID NOs.:660 or 659;
(viii) SEQ ID NOs.:672 or 671;
(ix) SEQ ID NOs.:666 or 665;
(x) SEQ ID NOs.:678 or 677; or
(xi) SEQ ID NOs.:684 or 683.

11. The method of claim 8 , wherein said extracellular binding domain comprises a CDR1α and a CDR1β sequence according to
(i) SEQ ID NOs.:614 or 613;
(ii) SEQ ID NOs.:620 or 619;
(iii) SEQ ID NOs.:632 or 631;
(iv) SEQ ID NOs.:638 or 637;
(v) SEQ ID NOs.:644 or 643;
(vi) SEQ ID NOs.:650 or 649;
(vii) SEQ ID NOs.:656 or 655;
(viii) SEQ ID NOs.:668 or 667;
(ix) SEQ ID NOs.:662 or 661;
(x) SEQ ID NOs.:674 or 673; or
(xi) SEQ ID NOs.:680 or 679.

12. The method of claim 1 , wherein said extracellular binding domain comprises a Vα or a Vβ region having at least 90% identity to any one of
(i) SEQ ID NOs.:62 or 61;
(ii) SEQ ID NOs.:64 or 63;
(iii) SEQ ID NOs.:68 or 67;
(iv) SEQ ID NOs.:70 or 69;
(v) SEQ ID NOs.:72 or 71;
(vi) SEQ ID NOs.:74 or 73;
(vii) SEQ ID NOs.:76 or 75;
(viii) SEQ ID NOs.:80 or 79;
(ix) SEQ ID NOs.:78 or 77;
(x) SEQ ID NOs.:82 or 81; or
(xi) SEQ ID NOs.:84 or 83.

13. The method of claim 12 , wherein said T cell comprises a heterologous polynucleotide sequence encoding said Vα and Vβ region separated by a sequence encoding a self-cleaving peptide.

14. The method of claim 13 , wherein said self-cleaving peptide is a P2A, T2A, F2A, E2A peptide, or any combination thereof.

15. The method of claim 1 , wherein said subject is HLA-A*11:01 positive.

16. The method of claim 1 , further comprising determining a HLA genotype of said subject prior to said administering.

17. The method of claim 1 , wherein said cell population comprises CD8+ or CD4+ T cells comprising said membrane protein.

18. The method of claim 1 , wherein said disease or disorder comprises a cancer.

19. The method of claim 18 , wherein said cancer comprises a solid cancer.

20. The method of claim 18 , wherein said cancer comprises a hematological malignancy.

21. The method of claim 19 , wherein said solid cancer comprises a pancreatic, lung, or colorectal cancer.

22. The method of claim 18 , wherein said cancer is positive for G12-mutant KRAS, NRAS, or HRAS.

23. The method of claim 16 , further comprising determining the presence of said G12-mutant KRAS, NRAS, or HRAS mutation in said subject prior to said administering.

24. The method of claim 1 , wherein said T cell is autologous to said subject.

25. The method of claim 1 , wherein said T cell is allogeneic to said subject.

26. The method of claim 1 , wherein said effective amount of said cell population is from about 10 4 cells/kg to about 10 11 cells/kg.

27. The method of claim 1 , wherein said subject has received lymphodepleting chemotherapy prior to said administration.

28. A method of treating a disease or disorder or preventing a relapse of a disease or disorder associated with a G12-mutant KRAS, NRAS, or HRAS mut

Assignees

• Fred Hutchinson Cancer Center

Inventors

• Perret Rachel
• Greenberg Philip D
• Schmitt Thomas M
• Chapuis Aude G
• Stromnes Ingunn M
• Martinov Tijana

Classifications

• C07K2319/03

  containing a transmembrane segment · CPC title

• C07K14/7051 Primary

  T-cell receptor (TcR)-CD3 complex · CPC title

• A61K40/4253

  GTPases, e.g. Ras or Rho · CPC title

• A61K40/32

  T-cell receptors [TCR] · CPC title

• A61K40/11

  T-cells, e.g. tumour infiltrating lymphocytes [TIL] or regulatory T [Treg] cells; Lymphokine-activated killer [LAK] cells · CPC title