Binding proteins specific for RAS neoantigens and uses thereof
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.
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 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 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.
29. 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 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.
30. The method of claim 29 , wherein the Vα and the Vβ region comprise the amino acid sequences of:
(i) SEQ ID NOs.:62 and 61, respectively;
(ii) SEQ ID NOs.:64 and 63, respectively;
(iii) SEQ ID NOs.:68 and 67, respectively;
(iv) SEQ ID NOs.:70 and 69, respectively;
(v) SEQ ID NOs.:72 and 71, respectively;
(vi) SEQ ID NOs.:74 and 73, respectively;
(vii) SEQ ID NOs.:76 and 75, respectively;
(viii) SEQ ID NOs.:80 and 79, respectively;
(ix) SEQ ID NOs.:78 and 77, respectively;
(x) SEQ ID NOs.:82 and 81, respectively; or
(xi) SEQ ID NOs.:84 and 83, respectively.