PD-L1-binding molecules comprising Shiga toxin a subunit scaffolds
Provided herein are PD-L1 binding molecules comprising or conjugated to a toxin, e.g. a Shiga toxin A Subunit derived polypeptide. In some embodiments, the PD-L1 binding molecules are cytotoxic. In some embodiments, the PD-L1 binding molecules are capable of delivering a CD8+ T-cell epitope to an MHC class molecule inside a PD-L1 positive cell. The PD-L1 binding molecules described herein have uses for selectively killing specific cells (e.g., PD-L1 positive tumor cells and/or immune cells); for selectively delivering cargos to specific cells (e.g., PD-L1 positive tumor cells or immune cells), and as therapeutic and/or diagnostic molecules for treating and diagnosing a variety of conditions, including cancers and tumors involving PD-L1 expressing cells (e.g., PD-L1 positive tumor cells or immune cells).
1. A method of treating cancer in a human subject in need thereof, the method comprising administering to the subject a therapeutically effective amount of a PD-L1 binding molecule comprising a Shiga toxin effector polypeptide and a binding region capable of specifically binding an extracellular part of PD-L1;
wherein the binding region comprises:
(a) a heavy chain variable region (V H ) comprising:
(i) a CDR1 comprising the amino acid sequence EYTMH (SEQ ID NO:27),
(ii) a CDR2 comprising the amino acid sequence GINPNNGGTWYNQKFKG (SEQ ID NO:29), and
(iii) a CDR3 comprising the amino acid sequence PYYYGSREDYFDY (SEQ ID NO:32); and
(b) a light chain variable region (V L ) comprising:
(i) a CDR1 comprising the amino acid sequence SASSSVSYMY (SEQ ID NO:19),
(ii) a CDR2 comprising the amino acid sequence LTSNLAS (SEQ ID NO:20), and
(iii) a CDR3 comprising the amino acid sequence QQWSSNPPT (SEQ ID NO:26); and
wherein the subject has the cancer, and wherein the cancer comprises PD-L1 expressing tumor cells.
2. The method of claim 1 , wherein the Shiga toxin effector polypeptide comprises the sequence of SEQ ID NO: 41, or a sequence at least 90% identical thereto.
3. The method of claim 1 , wherein the V H comprises the sequence of SEQ ID NO: 34.
4. The method of claim 1 , wherein the V L comprises the sequence of SEQ ID NO: 35.
5. The method of claim 1 , wherein the V H comprises the sequence of SEQ ID NO: 34 and the V L comprises the sequence of SEQ ID NO: 35.
6. The method of claim 1 , wherein the binding region comprises a scFv linker that links the V H and the V L .
7. The method of claim 6 , wherein the scFv linker comprises the sequence of SEQ ID NO: 72.
8. The method of claim 1 , wherein the binding region is a single chain variable fragment (scFv).
9. The method of claim 1 , wherein the binding region comprises the sequence of SEQ ID NO: 106, or a sequence at least 90% identical thereto.
10. The method of claim 1 , wherein the PD-L1 binding molecule comprises a binding domain linker which links the Shiga toxin effector polypeptide and the binding region.
11. The method of claim 10 , wherein the binding domain linker comprises the sequence of SEQ ID NO: 73.
12. The method of claim 10 , wherein the PD-L1 binding molecule comprises, from N-terminus to C-terminus, the Shiga toxin effector polypeptide, the binding domain linker, the V H , and the V L .
13. The method of claim 1 , wherein the PD-L1 binding molecule comprises a CD8+ T-cell epitope that is heterologous to Shiga toxin A subunits.
14. The method of claim 13 , wherein the CD8+ T-cell epitope comprises the sequence NLVPMVATV (SEQ ID NO: 78).
15. The method of claim 13 , wherein the CD8+ T-cell epitope is linked to the binding region via a spacer.
16. The method of claim 15 , wherein the spacer has the sequence HHAA (SEQ ID NO: 265).
17. The method of claim 13 , wherein the PD-L1 binding molecule comprises, from N-terminus to C-terminus, the Shiga toxin effector polypeptide, a binding domain linker, the V H , an scFv linker, the V L , and the CD8+ T-cell epitope.
18. The method of claim 1 , wherein the PD-L1 binding molecule comprises the sequence of SEQ ID NO: 128, or a sequence at least 95% identical thereto.
19. The method of claim 1 , wherein the PD-L1 binding molecule is a single continuous polypeptide.
20. The method of claim 1 , wherein the PD-L1 binding molecule comprises two polypeptides.
21. The method of claim 20 , wherein each of the two polypeptides comprises the sequence of SEQ ID NO: 128.
22. The method of claim 20 , wherein the two polypeptides are non-covalently linked to each other.
23. The method of claim 20 , wherein the two polypeptides are non-covalently linked to each other via the binding region.
24. The method of claim 1 , wherein the PD-L1 binding molecule is cytotoxic.
25. The method of claim 1 , wherein the PD-L1 binding molecule is non-cytotoxic.
26. The method of claim 1 , wherein the cancer is characterized by a high mutational burden and/or a high frequency of indels.
27. The method of claim 1 , wherein the cancer is a solid tumor.
28. The method of claim 1 , wherein the cancer is bladder cancer, breast cancer, colon cancer, endometrial cancer, esophageal cancer, fallopian tube cancer, gastrointestinal cancer, glioma, head and neck cancer, kidney cancer, liver cancer, lung cancer, lymphoma, Merkel cell carcinoma, mesothelioma, myeloma, nasopharyngeal neoplasm, ovarian cancer, pancreatic cancer, peritoneal neoplasm, prostate cancer, skin cancer, transitional cell carcinoma, or urothelial cancer.
29. The method of claim 1 , wherein the cancer is bladder cancer, and the bladder cancer is urothelial carcinoma.
30. The method of claim 1 , wherein the cancer is breast cancer, and the breast cancer is HER2 positive breast cancer or triple negative breast cancer.
31. The method of claim 1 , wherein the cancer is colon cancer, and the colon cancer is colorectal cancer.
32. The method of claim 1 , wherein the cancer is gastrointestinal cancer, and the gastrointestinal cancer is gastric cancer, biliary tract neoplasm, or gastroesophageal junction cancer.
33. The method of claim 1 , wherein the cancer is glioma, and the glioma is glioblastoma.
34. The method of claim 1 , wherein the cancer is head and neck cancer, and the head and neck cancer is squamous cell carcinoma of the head and neck.
35. The method of claim 1 , wherein the cancer is kidney cancer, and the kidney cancer is renal cell carcinoma.
36. The method of claim 1 , wherein the cancer is liver cancer, and the liver cancer is hepatocellular carcinoma.
37. The method of claim 1 , wherein the cancer is lung cancer, and the lung cancer is non-small cell lung cancer or small-cell lung cancer.
38. The method of claim 1 , wherein the cancer is lymphoma, and the lymphoma is Hodgkin lymphoma, non-Hodgkin lymphoma, primary mediastinal large B-cell lymphoma, or diffuse large B-cell lymphoma.
39. The method of claim 1 , wherein the cancer is mesothelioma, and the mesothelioma is pleural mesothelioma.
40. The method of claim 1 , wherein the cancer is myeloma, and the myeloma is multiple myeloma.
41. The method of claim 1 , wherein the cancer is skin cancer, and the skin cancer is squamous cell cancer of the skin or melanoma.
42. The method of claim 1 , wherein the cancer is relapsed or refractory to treatment with at least one of ipilimumab, nivolumab, pembrolizumab, atezolizumab, durvalumab, avelumab, tremelimumab and cemiplimab.
43. The method of claim 1 , wherein the cancer is metastatic.