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 recombinant polynucleotide comprising a coding sequence encoding a binding protein comprising a T cell receptor (TCR) α-chain variable (Vα) domain and a TCR β-chain variable (Vβ) domain, wherein the encoded binding protein is capable of binding to a mutant KRAS peptide/HLA complex, the mutant KRAS peptide comprises the amino acid sequence of any one of SEQ ID NOs.:2-5, the HLA comprises an HLA-A*11, and:
the Vα or the Vβ domain comprises an amino acid sequence having at least 90% identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 72, 75, 521, and 561.
2. The recombinant polynucleotide of claim 1 , wherein
(i) the Vα domain comprises or consists of an amino acid sequence having at least 90% identity to the amino acid sequence set forth in SEQ ID NO.: 72; and
(ii) the Vβ domain comprises or consists of an amino acid sequence having at least 92% identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 75, 521, and 561.
3. The recombinant polynucleotide of claim 2 , wherein the encoded binding protein comprises:
(a) the CDR1α amino acid sequence according to SEQ ID NO.: 513 and the CDR2α amino acid sequence according to SEQ ID NO.: 514; or
(b) the CDR1β amino acid sequence according to SEQ ID NO.: 516 and the CDR2β amino acid sequence according to SEQ ID NO.: 517.
4. The recombinant polynucleotide of claim 1 , further comprising a heterologous expression control element operatively linked to the coding sequence.
5. The recombinant polynucleotide of claim 4 , wherein the expression control element is not a human expression control element.
6. The recombinant polynucleotide of claim 4 , wherein the expression control element comprises a promoter, wherein the promoter is heterologous to the sequence encoding a binding protein.
7. The recombinant polynucleotide of claim 1 , wherein the encoded binding protein comprises:
(a) the CDR1α amino acid sequence according to SEQ ID NO.: 513 and the CDR2α amino acid sequence according to SEQ ID NO.: 514; or
(b) the CDR1β amino acid sequence according to SEQ ID NO.: 516 and the CDR2β amino acid sequence according to SEQ ID NO.: 517.
8. The recombinant polynucleotide of claim 1 , wherein the Vβ domain amino acid sequence has at least 90% identity to the amino acid sequence according to any one of SEQ ID NOs.: 521, 75, and 561.
9. The recombinant polynucleotide of claim 8 , wherein the encoded binding comprises:
(a) the CDR1α amino acid sequence according to SEQ ID NO.: 513 and the CDR2α amino acid sequence according to SEQ ID NO.: 514; or
(b) the CDR1β amino acid sequence according to SEQ ID NO.: 516 and the CDR2β amino acid sequence according to SEQ ID NO.: 517.
10. The recombinant polynucleotide of claim 1 , wherein the Vβ domain has at least 92% identity to the amino acid sequence according to any one of SEQ ID NOs.: 521, 75, and 561.
11. The recombinant polynucleotide of claim 1 , wherein the encoded binding protein further comprises a TCR α-chain constant (Cα) domain and/or a TCRβ-chain constant (Cβ) domain.
12. The recombinant polynucleotide of claim 11 , wherein:
(a) the Cα domain comprises an amino acid sequence having at least 90% identity to the amino acid sequence according to SEQ ID NO.: 85 or 86; and/or
(b) the Cβ domain comprises an amino acid sequence having at least 90% identity to the amino acid sequence according to SEQ ID NO.: 87 or 99.
13. The recombinant polynucleotide of claim 1 , wherein the encoded binding protein comprises a TCR.
14. The recombinant polynucleotide of claim 1 , wherein the encoded binding protein comprises a chimeric antigen receptor (CAR).
15. The recombinant polynucleotide of claim 1 , wherein the encoded binding protein comprises a TCR α-chain and a TCR β-chain, wherein the polynucleotide comprises a polynucleotide encoding a self-cleaving peptide disposed between the polynucleotide encoding a TCR α-chain and the polynucleotide encoding a TCR β-chain.
16. The recombinant polynucleotide of claim 1 , which is a polynucleotide sequence that is codon-optimized for expression in a host cell, wherein the host cell is a human T cell.
17. A recombinant expression vector comprising a polynucleotide encoding a binding protein comprising a T cell receptor (TCR) α-chain variable (Vα) domain and a TCR β-chain variable (Vβ) domain, wherein the encoded binding protein is capable of binding to a mutant KRAS peptide/HLA complex, the mutant KRAS peptide comprises the amino acid sequence of any one of SEQ ID NOs.:2-5, the HLA comprises an HLA-A*11, and:
the Vα or the Vβ domain comprises an amino acid sequence having at least 90% identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 72, 75, 521, and 561.
18. The recombinant expression vector of claim 17 , wherein
(i) the Vα domain comprises or consists of an amino acid sequence having at least 90% identity to the amino acid sequence set forth in SEQ ID NO.: 72; and
(ii) the Vβ domain comprises or consists of an amino acid sequence having at least 92% identity to the amino acid sequence set forth in any one of SEQ ID NOs.: 75, 521, and 561.
19. The recombinant expression vector of claim 17 , wherein the encoded binding protein comprises:
(a) the CDR1α amino acid sequence according to SEQ ID NO.: 513 and the CDR2α amino acid sequence according to SEQ ID NO.: 514; or
(b) the CDR1β amino acid sequence according to SEQ ID NO.: 516 and the CDR2β amino acid sequence according to SEQ ID NO.: 517.
20. The recombinant expression vector of claim 19 , wherein the Vβ domain amino acid sequence has at least 90% identity to any one of SEQ ID NOs.: 521, 75, and 561.
21. The recombinant expression vector of claim 20 , wherein the Vβ domain has at least 92% identity to the amino acid sequence according to any one of SEQ ID NOs.: 521, 75, and 561.
22. The recombinant expression vector of claim 21 , wherein the encoded binding protein comprises:
(a) the CDR1α amino acid sequence according to SEQ ID NO.: 513 and the CDR2α amino acid sequence according to SEQ ID NO.: 514; or
(b) the CDR1β amino acid sequence according to SEQ ID NO.: 516 and the CDR2β amino acid sequence according to SEQ ID NO.: 517.
23. The recombinant expression vector of claim 17 , wherein the encoded binding protein further comprises a TCR α-chain constant (Cα) domain and/or a TCR β-chain constant (Cβ) domain.
24. The recombinant expression vector of claim 23 , wherein:
(a) the Cα domain comprises an amino acid sequence having at least 90% identity to the amino acid sequence according to SEQ ID NO: 85 or 86; or
(b) the Cβ domain comprises an amino acid sequence having at least 90% identity to the amino acid sequence according to SEQ ID NO: 87 or 99.
25. The recombinant expression vector of claim 17 , wherein the encoded binding protein comprises a TCR or a chimeric antigen receptor (CAR).
26. The recombinant expression vector of claim 17 , wherein the vector comprises a viral vector.
27. The recombinant expression vector of claim 26 , wherein the viral vector comprises a γ-retroviral vector or a lentiviral vector.
28. The recombinant expression vector of claim 17 , wherein the vector is capable of delivering the polynucleotide to a host cell.
29. The recombinant expression vector of claim 28 , wherein the host cell is a hematopoietic progenitor cell or a human immune system cell.
30. The recombinant expression vector of claim 29 , wherein the human immune system cell is a CD4 + T cell, a CD8 + T cell, a CD4 − CD8 − double negative T cell, a γδ T cell, a natural killer cell, a natural killer T cell, a macrophage, a monocyte, a dendritic cell, or any combination thereof.