Binding proteins specific for RAS neoantigens and uses thereof

Patent metadata

Field	Value
Publication number	US-11458191-B2
Application number	US-202117643410-A
Country	US
Kind code	B2
Filing date	Dec 8, 2021
Priority date	Feb 20, 2019
Publication date	Oct 4, 2022
Grant date	Oct 4, 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 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 ce

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

• A61P35/00

  Antineoplastic agents · CPC title

• C12N2510/00

  Genetically modified cells · CPC title

• C07K14/705

  Receptors; Cell surface antigens; Cell surface determinants {(tumour specific antigens C07K14/4748)} · CPC title