NZ779633B2

NZ779633B2 - T cell receptors recognizing hla-cw8 restricted mutated kras

Info

Publication number: NZ779633B2
Application number: NZ779633A
Authority: NZ
Inventors: Yong Chen Lu; Steven A Rosenberg; Eric Tran
Original assignee: The United States Of America As Represented By The Secretary Department Of Health And Human Services
Filing date: 2016-09-09
Publication date: 2025-05-01

Abstract

Disclosed is an isolated or purified T cell receptor (TCR) having antigenic specificity for mutated Kirsten rat sarcoma viral oncogene homolog (KRAS) presented in the context of an HLA-Cw*0802 molecule. Related polypeptides and proteins, as well as related nucleic acids, recombinant expression vectors, host cells, populations of cells, and pharmaceutical compositions are also provided. Also disclosed are methods of detecting the presence of cancer in a mammal and methods of treating or preventing cancer in a mammal.

Claims

CLAIM (S):

1. An in vitro or ex-vivo method of producing an engineered population of human cells, the method comprising: introducing a recombinant expression vector to a population of human cells, wherein the recombinant expression vector comprises a nucleotide sequence encoding a T cell receptor (TCR) comprising: (a) an a chain complementarity determining region (CDR) 1 comprising the amino acid sequence of SEQ ID NO: 3, an a chain CDR2 comprising the amino acid sequence of SEQ ID NO: 4, and an a chain CDR3 comprising the amino acid sequence of SEQ ID NO: 5; (b) a ß chain CDR1 comprising the amino acid sequence of SEQ ID NO: 6, a ß chain CDR2 comprising the amino acid sequence of SEQ ID NO: 7, and a ß chain CDR3 comprising the amino acid sequence of SEQ ID NO: 8.

2. The method of claim 1, wherein the TCR has antigenic specificity for the mutated KRAS amino acid sequence of GADGVGKSA (SEQ ID NO: 18) presented in a human leukocyte antigen (HLA)-Cw8 molecule.

3. The method of claim 2, wherein the HLA-Cw8 molecule is HLA-Cw*0802.

4. The method of any one of claims 1-3, wherein the recombinant expression vector comprises a nucleotide sequence encoding: (a) an a chain variable region comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 9; (b) a ß chain variable region comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 10; or (c) both (a) and (b).

5. The method of any one of claims 1-3, wherein the recombinant expression vector comprises a nucleotide sequence encoding: (a) an a chain variable region comprising the amino acid sequence of SEQ ID NO: 9; (b) a ß chain variable region comprising the amino acid sequence of SEQ ID NO: 10; (c) both (a) and (b).

6. The method of any one of claims 1-3, wherein the recombinant expression vector comprises a nucleotide sequence encoding: (a) an a chain constant region comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 11, wherein: (i) X at position 48 of SEQ ID NO: 11 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 11 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 11 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 115 of SEQ ID NO: 11 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a ß chain constant region comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 12, wherein X at position 57 of SEQ ID NO: 12 is Ser or Cys; or (c) both (a) and (b).

7. The method of any one of claims 1-3, wherein the recombinant expression vector comprises a nucleotide sequence encoding: (a) an a chain constant region comprising the amino acid sequence of SEQ ID NO: 11, wherein: (i) X at position 48 of SEQ ID NO: 11 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 11 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 11 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 115 of SEQ ID NO: 11 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a ß chain constant region comprising the amino acid sequence of SEQ ID NO: 12, wherein X at position 57 of SEQ ID NO: 12 is Ser or Cys; or (c) both (a) and (b).

8. The method of any one of claims 1-3, wherein the recombinant expression vector comprises a nucleotide sequence encoding: (a) an a chain comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a ß chain comprising an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; or (c) both (a) and (b).

9. The method of any one of claims 1-3, wherein the recombinant expression vector comprises a nucleotide sequence encoding: (a) an a chain comprising the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; and (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) a ß chain comprising the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; or (c) both (a) and (b).

10. An in vitro or ex-vivo method of producing an engineered population of human cells, the method comprising: introducing a recombinant expression vector to a population of human cells, wherein the recombinant expression vector comprises a nucleotide sequence encoding a polypeptide comprising a functional portion of a TCR as defined in any one of claims 1-9, wherein the functional portion comprises the amino acid sequences of: SEQ ID NOs: 3-8.

11. The method of claim 10, wherein the polypeptide comprises: (a) an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 9; (b) an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 10; or (c) both (a) and (b).

12. The method of claim 10, wherein the polypeptide comprises: (a) the amino acid sequence of SEQ ID NO: 9; (b) the amino acid sequence of SEQ ID NO: 10; or (c) both (a) and (b).

13. The method of any one of claims 10-12, wherein the polypeptide further comprises: (a) an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 11, wherein: (i) X at position 48 of SEQ ID NO: 11 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 11 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 11 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 115 of SEQ ID NO: 11 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 12, wherein X at position 57 of SEQ ID NO: 12 is Ser or Cys; or (c) both (a) and (b).

14. The method of any one of claims 10-12, wherein the polypeptide further comprises: (a) the amino acid sequence of SEQ ID NO: 11, wherein: (i) X at position 48 of SEQ ID NO: 11 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 11 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 11 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 115 of SEQ ID NO: 11 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the amino acid sequence of SEQ ID NO: 12, wherein X at position 57 of SEQ ID NO: 12 is Ser or Cys; or (c) both (a) and (b).

15. The method of any one of claims 10-12, wherein the polypeptide further comprises: (a) an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; or (c) both (a) and (b).

16. The method of any one of claims 10-12, wherein the polypeptide further comprises: (a) the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; or (c) both (a) and (b).

17. An in vitro or ex-vivo method of producing an engineered population of human cells, the method comprising: introducing a recombinant expression vector to a population of human cells, wherein the recombinant expression vector comprises a nucleotide sequence encoding a protein comprising the functional portion of a TCR as defined in any one of claims 1-9, wherein the functional portion comprises the amino acid sequences SEQ ID NOs: 3-8, and wherein the protein comprises a first polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 3-5 and a second polypeptide chain comprising the amino acid sequences of SEQ ID NOs: 6-8.

18. The method of claim 17, wherein: (a) the first polypeptide chain comprises an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 9; (b) the second polypeptide chain comprises an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 10; or (c) both (a) and (b).

19. The method of claim 17, wherein: (a) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 9; (b) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 10; or (c) both (a) and (b).

20. The method of any one of claims 17-19, wherein: (a) the first polypeptide chain comprises an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 11, wherein: (i) X at position 48 of SEQ ID NO: 11 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 11 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 11 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 115 of SEQ ID NO: 11 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the second polypeptide chain comprises an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 12, wherein X at position 57 of SEQ ID NO: 12 is Ser or Cys; or (c) both (a) and (b).

21. The method of any one of claims 17-19, wherein: (a) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 11, wherein: (i) X at position 48 of SEQ ID NO: 11 is Thr or Cys; (ii) X at position 112 of SEQ ID NO: 11 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 114 of SEQ ID NO: 11 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 115 of SEQ ID NO: 11 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 12, wherein X at position 57 of SEQ ID NO: 12 is Ser or Cys; or (c) both (a) and (b).

22. The method of any one of claims 17-19, wherein: (a) the first polypeptide chain comprises an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the second polypeptide chain comprises an amino acid sequence at least 99% identical to the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; or (c) both (a) and (b).

23. The method of any one of claims 17-19, wherein: (a) the first polypeptide chain comprises the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (b) the second polypeptide chain comprises the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; or (c) both (a) and (b).

24. An isolated or purified TCR comprising an a chain variable region comprising the amino acid sequences of SEQ ID NO: 3-5 and a ß chain variable region comprising the amino acid sequences of SEQ ID NO: 6-8, wherein: (a) the a chain variable region comprises an amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO: 9; (b) the ß chain variable region comprises an amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO: 10; (c) the a chain variable region comprises an amino acid sequence at least 95% identical to amino acids 20-129 of SEQ ID NO: 9; (d) the ß chain variable region comprises an amino acid sequence at least 95% identical to amino acids 22-132 of SEQ ID NO: 10; (e) the a chain comprises an amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (f) the ß chain comprises an amino acid sequence at least 95% identical to the amino acid sequence of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or (g) the a chain comprises an amino acid sequence at least 95% identical to amino acids 20-266 of SEQ ID NO: 13, wherein: (i) X at position 177 of SEQ ID NO: 13 is Thr or Cys; (ii) X at position 241 of SEQ ID NO: 13 is Ser, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (iii) X at position 243 of SEQ ID NO: 13 is Met, Ala, Val, Leu, Ile, Pro, Phe, or Trp; (iv) X at position 244 of SEQ ID NO: 13 is Gly, Ala, Val, Leu, Ile, Pro, Phe, Met, or Trp; (h) the ß chain comprises an amino acid sequence at least 95% identical to amino acids 22-305 of SEQ ID NO: 14, wherein X at position 189 of SEQ ID NO: 14 is Ser or Cys; (i) both (a) and (b), both (a) and (d), both (b) and (c), both (c) and (d), both (e) and (f), both (e) and (h), both (f) and (g), or both (g) and (h).

25. An isolated or purified polypeptide comprising a functional portion of the TCR of claim

26. An isolated or purified protein comprising a functional portion of the TCR of claim 24, wherein the protein comprises a first polypeptide chain comprising the a chain variable region and a second polypeptide chain comprising the ß chain variable region.

27. An isolated or purified protein comprising a functional portion of the TCR of claim 24, wherein the protein comprises a first polypeptide chain comprising the a chain and a second polypeptide chain comprising the ß chain.

28. An isolated or purified nucleic acid which encodes the TCR of claim 24, the polypeptide of claim 25, or the protein of claim 26 or 27.

29. A recombinant expression vector comprising the nucleic acid of claim 28.

30. An isolated or purified host cell comprising the recombinant expression vector of claim

31. An isolated population of cells comprising at least two isolated or purified host cells of claim 30.

32. A pharmaceutical composition comprising the TCR of claim 24, the polypeptide of claim 25, or the protein of claim 26 or 27, the nucleic acid of claim 28, the recombinant expression vector of claim 29, the host cell of claim 30, or the population of host cells of claim 31, and a pharmaceutically acceptable carrier.

33. A method of detecting the presence of cancer in a mammal, the method comprising: (a) contacting a sample obtained from said mammal, wherein said sample comprises cells of the cancer, with the TCR of claim 24, the polypeptide of claim 25, or the protein of claim 26 or 27, the nucleic acid of claim 28, the recombinant expression vector of claim 29, the host cell of claim 30, the population of host cells of claim 31, or the pharmaceutical composition of claim 32, thereby forming a complex; and (b) detecting the complex, wherein detection of the complex is indicative of the presence of cancer in the mammal.

34. The method of claim 33, wherein the cancer is pancreatic, colorectal, lung, endometrial, ovarian, or prostate cancer.

35. Use of the TCR of claim 24, the polypeptide of claim 25, or the protein of claim 26 or 27, the nucleic acid of claim 28, the recombinant expression vector of claim 29, the host cell of claim 30, the population of host cells of claim 31, or the pharmaceutical composition of claim 32, in the manufacture of a medicament for the treatment or prevention of cancer in a human.

36. The use of claim 35, wherein the cancer is pancreatic, colorectal, lung, endometrial, ovarian, or prostate cancer.

37. A method as claimed in any one of claims 1-23, 33 and 34; an isolated or purified TCR as claimed in claim 24; an isolated or purified polypeptide as claimed in claim 25; an isolated or purified protein as claimed in claim 26 or 27; an isolated or purified nucleic acid as claimed in claim 28; a recombinant expression vector as claimed in claim 29; an isolated or purified host cell as claimed in claim 30; an isolated or purified population of cells as claimed in claim 31; a pharmaceutical composition as claimed in claim 32; or a use as claimed in claim 35 or 36, substantially as described herein and with reference to any example thereof.