Binding proteins specific for ras neoantigens and uses thereof

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.

1 - 30 . (canceled) 
     
     
         31 . 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 comprising a T-cell receptor Vα and Vβ region 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 subject is HLA-A*11:01 positive.   
     
     
         32 . The method of  claim 31 , wherein said disease or disorder is positive for G12-mutant KRAS, NRAS, or HRAS. 
     
     
         33 . The method of  claim 32 , wherein said disease or disorder is positive for G12 mutant KRAS. 
     
     
         34 . The method of  claim 33 , wherein said disease or disorder is positive for G12V mutant KRAS. 
     
     
         35 . The method of  claim 31 , wherein said cell population further comprises both CD4+ and CD8+ T cells comprising said membrane protein. 
     
     
         36 . The method of  claim 31 , wherein said cell population further comprises T cells comprising said membrane protein and (i) a transgenic polynucleotide encoding a polypeptide that comprises an extracellular portion of a CD8 co-receptor α chain; (ii) a transgenic polynucleotide encoding a polypeptide that comprises an extracellular portion of a CD8 co-receptor β chain; or (iii) a transgenic polynucleotide encoding (1) a polypeptide that comprises an extracellular portion of a CD8 co-receptor α chain and (2) a polypeptide that comprises an extracellular portion of a CD8 co-receptor β chain. 
     
     
         37 . The method of  claim 31 , wherein said cell population further comprises T cells comprising said membrane protein and a chromosomal gene knockout of a TCR constant region. 
     
     
         38 . The method of  claim 31 , wherein a presence of said G12-mutant KRAS, NRAS, or HRAS mutation has been determined in said subject prior to said administering. 
     
     
         39 . The method of  claim 31 , wherein said T cell is configured to undergo an antigen-specific T-cell response to said peptide:HLA complex. 
     
     
         40 . The method of  claim 31 , wherein said T cell is configured to produce IFN-γ when in the presence of said peptide:HLA complex. 
     
     
         41 . The method of  claim 31 , 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. 
     
     
         42 . The method of  claim 31 , wherein the T cell does not substantially produce IFN-γ when in the absence of said peptide:HLA complex. 
     
     
         43 . The method of  claim 31 , wherein said extracellular binding domain comprises a framework region derived from a human TRBV, TRBD, TRBJ, TRAV, or TRAJ gene segment. 
     
     
         44 . The method of  claim 31 , wherein said membrane protein does not comprise a cytoplasmic signaling domain fused thereto. 
     
     
         45 . The method of  claim 31 , 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 
     
     
         46 . The method of  claim 31 , 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. 
     
     
         47 . The method of  claim 31 , wherein said T cell comprises a heterologous polynucleotide sequence encoding a TCR α chain and a TCR β chain separated by a sequence encoding a self-cleaving peptide. 
     
     
         48 . The method of  claim 47 , wherein said self-cleaving peptide is a P2A, T2A, F2A, or E2A peptide, or any combination thereof. 
     
     
         49 . The method of  claim 31 , further comprising determining the HLA genotype of said subject prior to said administering. 
     
     
         50 . The method of  claim 31 , wherein said cell population comprises CD8+ or CD4+ T cells comprising said membrane protein. 
     
     
         51 . The method of  claim 31 , wherein said disease or disorder comprises a cancer. 
     
     
         52 . The method of  claim 51 , wherein said cancer comprises a solid cancer. 
     
     
         53 . The method of  claim 51 , wherein said cancer comprises a hematological malignancy. 
     
     
         54 . the method of  claim 52 , wherein said solid cancer comprises a pancreatic, lung, or colorectal cancer. 
     
     
         55 . The method of  claim 31 , wherein said T cell is autologous to said subject. 
     
     
         56 . The method of  claim 31 , wherein said T cell is allogenic to said subject. 
     
     
         57 . The method of  claim 31 , wherein said effective amount of said cell population is from about 10 4  cells/kg to about 10 11  cells/kg. 
     
     
         58 . The method of  claim 31 , wherein said subject has received lymphodepleting chemotherapy prior to said administration. 
     
     
         59 . 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 cell population further comprises T cells comprising said membrane protein and (i) a transgenic polynucleotide encoding a polypeptide that comprises an extracellular portion of a CD8 co-receptor α chain; (ii) a transgenic polynucleotide encoding a polypeptide that comprises an extracellular portion of a CD8 co-receptor β chain; or (iii) a transgenic polynucleotide encoding (1) a polypeptide that comprises an extracellular portion of a CD8 co-receptor α chain and (2) a polypeptide that comprises an extracellular portion of a CD8 co-receptor β chain.   
     
     
         60 . The method of  claim 59 , wherein said disease or disorder is positive for G12 mutant KRAS. 
     
     
         61 . The method of  claim 60 , wherein said disease or disorder is positive for G12V mutant KRAS. 
     
     
         62 . The method of  claim 59 , wherein said cell population further comprises both CD4+ and CD8+ T cells comprising said membrane protein. 
     
     
         63 . The method of  claim 59 , wherein said cell population further comprises T cells comprising said membrane protein and a chromosomal gene knockout of a TCR constant region. 
     
     
         64 . The method of  claim 59 , wherein a presence of said G12-mutant KRAS, NRAS, or HRAS mutation has been determined in said subject prior to said administering. 
     
     
         65 . The method of  claim 59 , wherein said extracellular binding domain comprises a T-cell receptor Vα and Vβ region. 
     
     
         66 . The method of  claim 59 , wherein said T cell comprises a heterologous polynucleotide sequence encoding a T-cell receptor α chain and a T-cell receptor β chain separated by a sequence encoding a self-cleaving peptide. 
     
     
         67 . The method of  claim 66 , wherein said self-cleaving peptide is a P2A, T2A, F2A, or E2A peptide, or any combination thereof. 
     
     
         68 . The method of  claim 59 , wherein said subject is HLA-A*11:01 positive. 
     
     
         69 . 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 cell population further comprises both CD4+ and CD8+ T cells comprising said membrane protein.   
     
     
         70 . The method of  claim 69 , wherein said disease or disorder is positive for G12 mutant KRAS. 
     
     
         71 . The method of  claim 70 , wherein said disease or disorder is positive for G12V mutant KRAS. 
     
     
         72 . The method of  claim 69 , wherein a presence of said G12-mutant KRAS, NRAS, or HRAS mutation has been determined in said subject prior to said administering. 
     
     
         73 . The method of  claim 69 , wherein said extracellular binding domain comprises a T-cell receptor Vα and Vβ region. 
     
     
         74 . The method of  claim 69 , wherein said T cell comprises a heterologous polynucleotide sequence encoding a T-cell receptor α chain and a T-cell receptor β chain separated by a sequence encoding a self-cleaving peptide. 
     
     
         75 . The method of  claim 74 , wherein said self-cleaving peptide is a P2A, T2A, F2A, or E2A peptide, or any combination thereof. 
     
     
         76 . The method of  claim 69 , wherein said subject is HLA-A*11:01 positive. 
     
     
         77 . The method of  claim 69 , further comprising administering a cell population comprising about a 1:1 ratio of CD4+ to CD8+ cells comprising said membrane protein.