High affinity merkel cell polyomavirus T antigen-specific TCRS and uses thereof

Patent metadata

Field	Value
Publication number	US-11534461-B2
Application number	US-201716348378-A
Country	US
Kind code	B2
Filing date	Nov 14, 2017
Priority date	Nov 14, 2016
Publication date	Dec 27, 2022
Grant date	Dec 27, 2022

Abstract

The present disclosure provides binding proteins and TCRs with high affinity and specificity against Merkel cell polyomavirus T antigen epitopes or peptides, T cells expressing such high affinity Merkel cell polyomavirus T antigen specific TCRs, nucleic acids encoding the same, and compositions for use in treating Merkel cell carcinoma.

First claim

What is claimed is:

1. An expression vector comprising a polynucleotide encoding a binding protein, wherein the binding protein comprises:
(a) a T cell receptor (TCR) α-chain variable (Vα) domain having a CDR3 amino acid sequence of any one of SEQ ID NOS.:13, 44 and 355-364; and
(b) a TCR β-chain variable (Vβ) domain having a CDR3 amino acid sequence of any one of SEQ ID NOS.:14, 69 and 365-374.

2. The expression vector of claim 1 , wherein the binding protein is capable of specifically binding to a Merkel cell polyomavirus T antigen peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8.

3. The expression vector according to claim 1 , wherein the binding protein is capable of specifically binding to a KLLEIAPNC (SEQ ID NO.:17):human leukocyte antigen (HLA) complex or a KLLEIAPNA (SEQ ID NO.:37):human leukocyte antigen (HLA) complex with a K d less than or equal to about 10 −8 M.

4. The expression vector according to claim 1 , wherein the binding protein specifically binds to a KLLEIAPNC (SEQ ID NO.:17):HLA-A*02:01 complex or a KLLEIAPNA (SEQ ID NO.:37):HLA-A*02:01 complex.

5. The expression vector according to claim 1 , wherein the
Vα domain is at least about 90% identical to the Vα amino acid sequence set forth in
MDKILGASFLVLWLQLCWVSGQQKEKSDQQQVKQSPQSLIVQKGGISIINCAYE NTAFDYFPWYQQFPGKGPALLIAIRPDVSEKKEGRFTISFNKSAKQFSLHIMDSQP GDSATYFCAVPNTGNQFYFGTGTSLTVIP (SEQ ID NO.: 428); and/or

the Vβ domain is at least about 90% identical to the V β amino acid sequence set forth in
MGTRLLCWVVLGFLGTDHTGAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFW YQQALGQGPEFLTYFQNEAQLDKSGLPSDRFFAERPEGSVSTLKIQRTQQEDSAV YLCASSLIAGLSYEQYFGPGTRLTVT (SEQ ID NO.: 429).

6. The expression vector according to claim 1 , wherein the
Vα domain comprises the Vα amino acid sequence set forth in
MDKILGASFLVLWLQLCWVSGQQKEKSDQQQVKQSPQSLIVQKGGISIINCAYE NTAFDYFPWYQQFPGKGPALLIAIRPDVSEKKEGRFTISFNKSAKQFSLHIMDSQP GDSATYFCAVPNTGNQFYFGTGTSLTVIP (SEQ ID NO.: 428); and/or

the Vβ domain comprises the Vβ amino acid sequence set forth in
MGTRLLCWVVLGFLGTDHTGAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFW YQQALGQGPEFLTYFQNEAQLDKSGLPSDRFFAERPEGSVSTLKIQRTQQEDSAV YLCASSLIAGLSYEQYFGPGTRLTVT (SEQ ID NO.: 429).

7. The expression vector according claim 1 , wherein the binding protein further comprises a TCR α-chain constant domain (Cα) having at least 90% sequence identity to the amino acid sequence of SEQ ID NO.:2, and/or wherein the binding protein further comprises a TCR β-chain constant domain (Cβ) having at least 90% sequence identity to the amino acid sequence of SEQ ID NO.:4.

8. The expression vector according claim 1 , wherein:
the Vα domain comprises the Vα amino acid sequence set forth in

MDKILGASFLVLWLQLCWVSGQQKEKSDQQQVKQSPQSLIVQKGGISIINCAYENTAFD YFPWYQQFPGKGPALLIAIRPDVSEKKEGRFTISFNKSAKQFSLHIMDSQPGDSATYFCA VPNTGNQFYFGTGTSLTVIP (SEQ ID NO.: 428); and
the Vβ domain comprises the Vβ amino acid sequence set forth in

MGTRLLCWVVLGFLGTDHTGAGVSQSPRYKVAKRGQDVALRCDPISGHVSLFWYQQA LGQGPEFLTYFQNEAQLDKSGLPSDRFFAERPEGSVSTLKIQRTQQEDSAVYLCASSLIA GLSYEQYFGPGTRLTVT (SEQ ID NO.: 429); and
wherein the binding protein further comprises a TCR α-chain constant domain (Cα) comprising the amino acid sequence of SEQ ID NO.:2; and a TCR β-chain constant domain (Cβ) comprising the amino acid sequence of SEQ ID NO.:4,
wherein the Vα and the Cα are comprised in a TCRα chain and wherein the Vβ and the Cβ are comprised in a TCRβ chain.

9. The expression vector according to claim 1 , wherein the binding protein is a T cell receptor (TCR), an antigen-binding fragment of a TCR, or a chimeric antigen receptor.

10. The expression vector according to claim 9 , wherein the TCR, the chimeric antigen receptor, or the antigen-binding fragment of the TCR is chimeric, humanized or human.

11. The expression vector according to claim 9 , wherein the antigen-binding fragment of the TCR comprises a single chain TCR (scTCR).

12. A composition comprising the expression vector according to claim 1 and a pharmaceutically acceptable carrier, diluent, or excipient.

13. The expression vector of claim 1 , wherein the polynucleotide is operably linked to an expression control sequence.

14. A genetically engineered host cell, comprising the expression vector of claim 1 and expressing the binding protein on its cell surface.

15. The genetically engineered host cell of claim 14 , wherein:
(a) the host cell is a hematopoietic progenitor cell or a human immune system cell;
(b) the host cell is an immune system cell selected from the group consisting of: a CD4+ T cell, a CD8+ T cell, a CD4−CD8− double negative T cell, a γδ T cell, a natural killer cell, and a dendritic cell;
(c) the host cell is a T cell; or
(d) the host cell is a T cell selected from the group consisting of: a naïve T cell, a central memory T cell, and an effector memory T cell.

16. An adoptive immunotherapy method for treating a subject having a Merkel cell carcinoma, comprising administering to the subject an effective amount of a genetically engineered host cell according to claim 15 .

17. A unit dose form comprising a genetically engineered host cell according to claim 15 .

18. An adoptive immunotherapy method for treating a subject having a Merkel cell carcinoma, comprising administering to the subject an effective amount of a genetically engineered host cell according to claim 14 .

19. A unit dose form comprising a genetically engineered host cell according to claim 14 .

20. A host cell comprising a heterologous polynucleotide encoding a binding protein that is capable of specifically binding to a Merkel cell polyomavirus T antigen peptide:HLA complex, wherein the binding protein comprises:
(a) a T cell receptor (TCR) α chain variable (Vα) domain having a CDR3 amino acid sequence of any one of SEQ ID NOS.:13, 44, and 355-364, and
(b) a TCR β chain variable (Vβ) domain having a CDR3 amino acid sequence of any one of SEQ ID NOS.:14, 69, and 365-374.

21. The host cell of claim 20 , wherein the host cell comprises a CD4+ T cell, a CD8+ T cell, a CD4−CD8− double negative T cell, a γδ T cell, a naïve T cell, a central memory T cell, an effector memory T cell, a natural killer cell, a dendritic cell, or any combination thereof.

22. A method of treating a Merkel cell carcinoma, comprising administering a therapeutically effective amount of the host cell according to claim 20 to a subject having or at risk of having Merkel cell carcinoma.

23. The host cell according to claim 20 , wherein the binding protein comprises a TCR.

24. The host cell according to claim 20 , wherein the host cell comprises a CD4+ T cell and further comprises a heterologous polynucleotide encoding a CD8 co-receptor molecule.

25. The host cell according to claim 20 , wherein the binding protein is capable of specifically binding to a Merkel cell polyomavirus T antigen peptide:HLA complex on a cell surface independent of CD8 or in the absence of CD8.

26. The host cell according to claim 20 , wherein the binding protein is capable of specifically binding to a KLLEIAPNC (SEQ ID NO.:17):human leukocyte antigen (HLA) complex and/or a KLLEIAPNA (SEQ ID NO.:37):human leukocyte antigen (HLA) complex, with a K d less than or equal to about 10 −8 M.

27. The host cell according to claim 20 , wherein the binding protein is capable of specifically binding to a KLLEIAPNC (SEQ ID NO.:17):HLA-A*02:01 complex and/or a KLLEI

Assignees

• Fred Hutchinson Cancer Center
• Univ Washington

Inventors

• Chapuis Aude G
• Nghiem Paul T
• Mcafee Megan S
• Miller Natalie J
• Paulson Kelly Garneski
• Koelle David Martin
• Schmitt Thomas M
• Church Candice

Classifications

• C07K2317/24

  containing regions, domains or residues from different species, e.g. chimeric, humanized or veneered · CPC title

• A61P35/00 Primary

  Antineoplastic agents · CPC title

• A61K38/2013

  IL-2 · CPC title

• C07K16/2818

  against CD28 or CD152 · CPC title

• C07K2317/21

  from primates, e.g. man · CPC title