Biomarkers for cancer treatment
阅读说明：本技术 用于癌症治疗的生物标志物 (Biomarkers for cancer treatment ) 是由 詹尼弗·洛兰·甘塞特 亚伯拉罕·安东尼奥·安德森 凯文·古尔斯基 于 2018-04-27 设计创作，主要内容包括：提供了可用于鉴定多种癌症的生物标志物,所述癌症对用包含派姆单抗、派姆单抗变体或其抗原结合片段与塔利拉维(talimogene laherparepvec)的组合治疗进行的治疗有响应。提供了治疗对用派姆单抗、派姆单抗变体或其抗原结合片段进行的单药治疗具有抗性的癌症的方法。还提供了在患有肿瘤的对象中治疗癌症的方法,所述肿瘤具有低CD8+密度、低或阴性干扰素γ特征和/或低或阴性PD-L1状态。(Biomarkers are provided that can be used to identify a variety of cancers that respond to treatment with a combination therapy comprising pembrolizumab, a pembrolizumab variant, or an antigen binding fragment thereof, and taliomogene laherervec. Methods of treating cancer that is resistant to monotherapy with pembrolizumab, pembrolizumab variants, or antigen binding fragments thereof are provided. Also provided are methods of treating cancer in a subject having a tumor with low CD8+ density, low or negative interferon gamma signature, and/or low or negative PD-L1 status.)
1. A method of treating a tumor in a subject, comprising:
selecting a subject having a tumor comprising less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density;
administering to the subject talimogene laherparepvec; and
administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject.
2. The method of claim 1, wherein the tumor expresses lower levels of two, three, four, or five interferon gamma (IFN γ) signature genes prior to administration as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, signal transducer and activator of transcription 1(STAT1), C-C chemokine receptor type 5 (CCR5), chemokine (C-X-C motif) ligand 9(CXCL9), perforin 1(PRF1), HLA-DRA, chemokine (C-X-C motif) ligand 10(CXCL10), chemokine (C-X-C motif) ligand 11(CXCL11), indoleamine 2, 3-dioxygenase 1(IDO1), and granzyme A (GZMA).
3. The method of claim 1, wherein the tumor does not express an IFN γ signature gene prior to administration of the talipraza and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
4. The method of claim 1, wherein the tumor has a programmed death ligand 1(PD-L1) status of less than about 50% prior to administration of the talipraz and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
5. The method of claim 1, wherein the tumor has a PD-L1 status of less than about 1% prior to administration of the talipraz and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
6. The method of claim 1, wherein the talilavine is administered to the subject prior to administering the pembrolizumab or antigen-binding fragment thereof.
7. The method of claim 1, wherein the subject has a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
8. The method of claim 7, wherein:
the melanoma is cutaneous melanoma, metastatic melanoma, or uveal melanoma;
the breast cancer is HER2+ breast cancer, HER2-HR + breast cancer, or triple negative breast cancer;
the prostate cancer is castration-resistant prostate cancer;
the bladder cancer is transitional cell carcinoma or urothelial cancer;
the head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma; and/or
The sarcoma is soft tissue sarcoma or osteosarcoma.
9. The method of claim 1, wherein the tumor comprises less than about 1000 cells/mm2CD8 (1)+T cell infiltration density.
10. A method of treating a tumor that responds poorly or non-responds to monotherapy with pembrolizumab, a pembrolizumab variant, or an antigen binding fragment thereof in a subject, comprising:
administering talliravine to the subject; and
administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject.
11. The method of claim 10, wherein:
prior to administration, the tumor comprises less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density;
the tumor expresses lower levels of two, three, four or five interferon gamma (IFN γ) signature genes prior to administration compared to a pre-specified threshold for a control group of signature genes selected from: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA; and/or
The tumor has a PD-L1 status of less than about 50% prior to administration of the talipraza and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
12. A method of treating a tumor in a subject that has progressed during monotherapy with pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, comprising:
administering talliravine to the subject; and
administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject.
13. The method of claim 12, wherein:
prior to administration, the tumor comprises less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density;
the tumor expresses lower levels of two, three, four or five interferon gamma (IFN γ) signature genes prior to administration compared to a pre-specified threshold for a control group of signature genes selected from: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL1l, IDO1 and GZMA; and/or
The tumor has a PD-L1 status of less than about 50% prior to administration of the talipraza and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
14. A method of treating a tumor comprising contacting the tumor with talisman and pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof, said tumor having less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density.
15. The method of claim 14, wherein the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
16. The method of claim 15, wherein:
the melanoma is cutaneous melanoma, metastatic melanoma, or uveal melanoma; and/or
The head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma.
17. The method of claim 14, wherein the tumor expresses lower levels of two, three, four, or five interferon gamma (IFN γ) signature genes prior to contact as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
18. The method of claim 14, wherein the tumor has a PD-L1 of less than about 50% prior to contacting the talipraz and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
19. A method of treating a tumor comprising contacting the tumor with talisman and pembrolizumab, pembrolizumab variant, or an antigen binding fragment thereof, said tumor expressing a lower level of two, three, four, or five interferon gamma (IFN γ) signature genes prior to treatment as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCLl0, CXCL11, IDO1 and GZMA.
20. The method of claim 19, wherein the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
21. The method of claim 20, wherein:
the melanoma is cutaneous melanoma, metastatic melanoma, or uveal melanoma; and/or
The head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma.
22. The method of claim 19, wherein prior to contacting, the tumor has less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density.
23. The method of claim 19, wherein the tumor has a PD-L1 status of less than about 50% prior to contact with the taliprazole and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
24. A method of treating a tumor comprising contacting the tumor with talisman and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, said tumor having a PD-L1 status of less than about 50% prior to treatment.
25. The method of claim 24, wherein the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
26. The method of claim 25, wherein:
the melanoma is cutaneous melanoma, metastatic melanoma, or uveal melanoma; and/or
The head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma.
27. The method of claim 24, wherein prior to contacting, the tumor has less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density.
28. The method of claim 24, wherein the tumor expresses lower levels of two, three, four, or five interferon gamma (IFN γ) signature genes prior to contact as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
29. A method of treating a tumor comprising contacting the tumor with talisman and pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof, said tumor having less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density and express lower levels of five or fewer interferon gamma (IFN γ) signature genes prior to treatment compared to pre-specified thresholds for a control group of signature genes selected from: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
30. The method of claim 29, wherein the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
31. The method of claim 30, wherein:
the melanoma is cutaneous melanoma, metastatic melanoma, or uveal melanoma; and/or
The head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma.
32. The method of claim 29, wherein the tumor has a PD-L1 status of less than about 50% prior to contact with the taliprazole and the pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
33. A method of treating a tumor that was previously resistant to pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof in a subject subsequently exposed to taliravine, comprising administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject.
34. The method of claim 33, wherein the subject has a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
35. The method of claim 34, wherein:
the melanoma is cutaneous melanoma, metastatic melanoma, or uveal melanoma; and/or
The head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma.
36. A method of sensitizing a tumor that is resistant to monotherapy with pembrolizumab, a pembrolizumab variant, or an antigen binding fragment thereof to pembrolizumab, a pembrolizumab variant, or an antigen binding fragment thereof in a subject comprising contacting the tumor with talilavine.
37. The method of claim 36, wherein a sample of the tumor taken from the subject after contacting the tumor with taliravine has an increased level of one or any combination of CD8+ T cells, CD4+ T cells, IFN γ, CD20+ B cells, memory T cells, regulatory T cells, and CD56+ cells relative to a sample of the tumor taken prior to contacting the tumor with taliravine.
38. The method of claim 36, wherein the tumor has greater than 1000 cells/mm after contact with taliravine2CD8 (1)+T cell infiltration density.
39. A method of treating a tumor in a subject, comprising:
selecting a subject having a tumor comprising less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density;
intratumorally administering to the subject taliravir as an initial dose followed by one or more secondary doses; and
systemically administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject as an initial dose followed by one or more second doses.
Technical Field
The present invention relates to the field of cancer therapy. In particular, the present invention relates to biomarkers useful for identifying a variety of cancers that can be treated with a combination therapy comprising pembrolizumab, pembrolizumab variants, and/or antigen binding fragments thereof, and talimogenlaeparvec.
Background
Treatment with anti-PD-1 or anti-PD-L1 antibodies results in a long-term anti-tumor response in patients with a variety of cancers, and is becoming The standard of care treatment for patients with metastatic melanoma, head and neck, lung, kidney and bladder cancers, as well as Merkel cell carcinosoma and Hodgkin's disease (Sharma, p., and Allison, J.P. (2015). The future of immune checkpoint heat. science 348, 56-61). However, in all of these indications, only a small group of patients responded to treatment, with the majority of patients being predominantly resistant to PD-1 blockade. Therefore, there is a need for new cancer treatments that target cancers that are resistant to PD-1 blockade.
Disclosure of Invention
The present disclosure is based on the discovery of biomarkers (e.g., intratumoral biomarkers) that can be used to identify tumors that respond to combination therapy with pembrolizumab, pembrolizumab variants, or antigen-binding fragments thereof, and taliravine. The invention is particularly useful for treating tumors in a subject that were previously not treatable or not adequately treatable with a monotherapy, i.e., with a checkpoint inhibitor (e.g., treatment with anti-PD-L1 or anti-PD-1 treatment (e.g., pembrolizumab variants, or antigen-binding fragments thereof))). Intratumoral administration of the oncolytic virus taliravir, a herpes
In one aspect, there is provided a method of treating a tumor in a subject, comprising: selecting a subject having a tumor comprising less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8+ T cell infiltration density (infiltration density) of (a); administering talliravine to the subject; and administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject.
In certain embodiments, the tumor expresses lower levels of two, three, four, or five interferon gamma (IFN γ) signature genes prior to administration as compared to a pre-specified threshold for a control group of signature genes selected from: IFN gamma, signaling and activator of transcription 1 (STAT 1), C-C chemokine receptor type 5 (C-
In certain embodiments, the tumor has less than about 50% programmed death-ligand 1 (PD-L1) status prior to administration of the talisman and pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof. In certain embodiments, the tumor has a PD-L1 status of less than about 1% prior to administration of talira and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof.
In certain embodiments, the taliravioli is administered intratumorally to the subject and/or pembrolizumab, or an antigen-binding fragment thereof, is administered systemically to the subject.
In certain embodiments, the talilavine is administered to the subject prior to administering pembrolizumab, or an antigen-binding fragment thereof.
In certain embodiments, the reduction in size of the injected tumor and/or the reduction in size of the non-injected tumor occurs after administration of talira and pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof.
In certain embodiments, the CD8+ T cell infiltration density in the tumor increases after administration of talilavir. In certain embodiments, following administration of talira and pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof, circulating, dividing CD8 in a subject+T cells increase.
In certain embodiments, the subject has a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer. In certain embodiments, the melanoma is cutaneous, metastatic, or uveal melanoma, the breast cancer is HER2+ breast cancer, HER2-HR + breast cancer, or triple negative breast cancer, the prostate cancer is castration-resistant prostate cancer (castration-resistant prostate cancer), the bladder cancer is transitional cell cancer or urothelial cancer, the head and neck cancer is recurrent or metastatic head and neck squamous cell carcinoma, and/or the sarcoma is soft tissue sarcoma or osteosarcoma.
In certain embodiments, the tumor comprises less than about 1000 cells/mm2CD8 (1)+T cell infiltration density.
In one aspect, a method of treating a tumor in a subject that responds poorly or non-responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or antigen-binding fragment thereof)) is provided, comprising administering to the subject taliravir, and administering to the subject pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof.
In certain embodiments, prior to administration, the tumor comprises less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density; two, three, four or five interferon gamma (IFN γ) signature genes were expressed by the tumor at lower levels prior to administration compared to pre-specified thresholds for a control group of signature genes selected from: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA; and/or the tumor has a PD-L1 status of less than about 50% prior to administration of talira and pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof.
In one aspect, a method of treating a tumor that has progressed during monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or an antigen-binding fragment thereof)) in a subject is provided, comprising administering to the subject taliravir, and administering to the subject pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof.
In certain embodiments, prior to administration, the tumor comprises less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density; two, three, four or five IFN γ signature genes were expressed at lower levels by the tumor prior to administration compared to pre-specified thresholds for a control group of signature genes selected from: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA; and/or the tumor has a PD-L1 status of less than about 50% prior to administration of talira and pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof.
In certain embodiments, taliravir is administered sequentially as an initial dose followed by one or more secondary doses. In certain embodiments, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is administered sequentially as an initial dose followed by one or more second doses. In certain embodiments, the taliravine is administered sequentially as an initial dose followed by one or more second doses, and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is administered sequentially and concomitantly with the one or more second doses of taliravine.
In certain embodiments, the tarlivisfate is administered intratumorally, and wherein pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is administered systemically. In certain embodiments, the talicharide and pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof is administered intratumorally.
In one aspect, there is provided a method of treating a tumor comprising contacting the tumor with tarila and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, said tumor having less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density.
In certain embodiments, the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer. In certain embodiments, the cancer is cutaneous melanoma. In certain embodiments, the cancer is recurrent or metastatic head and neck squamous cell carcinoma.
In certain embodiments, the tumor expresses lower levels of two, three, four, or five IFN γ signature genes prior to contact as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
In certain embodiments, the tumor has less than about 50% PD-L1 prior to contacting with taliprazole and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof.
In one aspect, there is provided a method of treating a tumor comprising contacting the tumor with talia and pembrolizumab, pembrolizumab variant, or an antigen binding fragment thereof, said tumor expressing lower levels of two, three, four, or five IFN γ signature genes prior to treatment as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
In certain embodiments, the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer. In certain embodiments, the cancer is melanoma (e.g., cutaneous melanoma). In certain embodiments, the cancer is a head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma).
In certain embodiments, prior to contacting, the tumor has less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density.
In certain embodiments, the tumor has a PD-L1 status of less than about 50% prior to contact with taliprazole and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof.
In one aspect, a method of treating a tumor is provided, comprising contacting the tumor with talisman and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, the tumor having a PD-L1 status of less than about 50% prior to treatment.
In certain embodiments, the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer. In certain embodiments, the cancer is melanoma (e.g., cutaneous melanoma). In certain embodiments, the cancer is a head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma).
In certain embodiments, prior to contacting, the tumor has less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density.
In certain embodiments, the tumor expresses lower levels of two, three, four, or five IFN γ signature genes prior to contact as compared to a pre-specified threshold for a control group of signature genes selected from the group consisting of: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
In one aspect, there is provided a method of treating a tumor comprising contacting the tumor with tarila and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, said tumor having less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+T cell infiltration density and express lower levels of five or fewer IFN γ signature genes prior to treatment compared to pre-specified thresholds for a control group of signature genes selected from: IFN gamma, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, IDO1 and GZMA.
In certain embodiments, the tumor is from a subject having a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer. In certain embodiments, the cancer is melanoma (e.g., cutaneous melanoma). In certain embodiments, the cancer is a head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma).
In certain embodiments, the tumor has a PD-L1 status of less than about 50% prior to contact with taliprazole and pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof.
In one aspect, a method of treating a tumor previously resistant to pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof in a subject subsequently exposed to taliravine is provided, comprising administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject.
In certain embodiments, the subject has a cancer selected from the group consisting of: melanoma, non-small cell lung cancer, head and neck cancer, colorectal cancer, breast cancer, ovarian cancer, bladder cancer, prostate cancer, sarcoma, renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer. In certain embodiments, the cancer is melanoma (e.g., cutaneous melanoma). In certain embodiments, the cancer is a head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma).
In one aspect, a method of sensitizing a tumor that is resistant to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or an antigen-binding fragment thereof)) to pembrolizumab, pembrolizumab variant, or an antigen-binding fragment thereof in a subject is provided, comprising contacting the tumor with taliravine.
In certain embodiments, the sample of the tumor taken from the subject after contacting the tumor with taliravine has an increased level of one or any combination of CD8+ T cells, CD4+ T cells, IFN γ, CD20+ B cells, memory T cells, regulatory T cells, and CD56+ cells relative to the sample of the tumor taken prior to contacting the tumor with taliravine.
In certain embodiments, the tumor has greater than 1000 cells/mm after contact with taliravine2CD8 (1)+T cell infiltration density.
In certain embodiments, the blood sample taken from the subject after contacting the tumor with taliravine has an increased level of CD8+ T cells and/or CD4+ T cells compared to the blood sample taken from the subject prior to the contacting, optionally wherein the CD8+ T cells are dividing CD8+ T cells.
In one aspect, a method of treating a tumor in a subject is provided, comprising selecting a subject having a tumor comprising less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/mm2CD8 (1)+(ii) a T cell infiltration density; intratumorally administering taliravine to the subject as an initial dose followed by one or more second doses; and systemically administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof to the subject as an initial dose followed by one or more second doses.
In certain embodiments, the second dose is administered every two weeks (Q2W). In certain embodiments, the initial dose of taliravine is administered on
In certain embodiments, 10 is used6An initial dose of talalavir was administered at a dose of plaque forming units (pfu)/mL, and was 108A second dose of talalavir was administered at a dose of pfu/mL.
In certain embodiments, an initial dose of pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is administered at a dose of 200mg, and a second dose of pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is administered at a dose of 200 mg.
The summary of the disclosure described above is non-limiting and other features and advantages of the disclosed biomarkers and methods will be apparent from the following drawings, detailed description of the disclosure, and claims.
Drawings
Figure 1 depicts melanoma study design and clinical response to a combination of talipraza and pembrolizumab. (A) Phase 1b study design is shown. Asterisks indicate time of scheduled tumor biopsy. (B) Computed tomography scans of two patients responsive to combination therapy are depicted. Melanoma metastases were marked at baseline with blue arrows. (C) A waterfall plot of the best response change in tumor burden from baseline is depicted. Patients were asked to include baseline and > 1 post-baseline tumor assessments. (D) The change in tumor burden over time is depicted. (E) A Kaplan-Meier analysis of progression free survival is described. (F) Kaplan-Meier analysis of overall survival is depicted.
Figure 2 shows that the combination of taliprazole and pembrolizumab was effective in patients with low tumor CD8 density. (A) Baseline CD8 density in tumor biopsies as a function of response rate is depicted. The amplitude of the bars represents the baseline tumor CD8 density in the baseline biopsy of each patient, and the best overall response is indicated on the x-axis and by the color of the bars. Red: complete Response (CR); pink color: partial Response (PR), black: progressive Disease (PD). (B) The baseline PD-L1 (1% cutoff) by IHC status and interferon gamma signature score by NanoString analysis are shown below the CD8 results for each patient. For each investigator, the best overall response was shown with an expiration date of 2016 and 8 months. n.a. ═ results are not available.
Figure 3 shows that taliravir increases tumor CD8 density in patients who responded to a combination of talira and pembrolizumab. (A) Examples of the pre (week 1) and post (week 6) talrivavir and the CD8+ T cell density of talrivavirenzumab (week 30) in tumor biopsies are depicted: visualization of cells stained with CD8 antibody with red chromogen. Staining was quantified for tissue regions of interest, including CD8 density in tumors, as shown for talalavir-injected tumors. Depicted are (B) CD8 density and (C) granzyme-B H-score, shown for baseline and post-baseline biopsies. The left side of each figure shows post-baseline results from injected lesions, and the right side of each figure shows results from non-injected lesions. Open circles represent results from tumor biopsies depleted of melanoma cells but with pathological features (e.g., melanin deposition) that have previously been infiltrated by melanoma cells. For each researcher, the responses were color coded for the best overall response: full or partial response is red and no response is blue. Depicted are (D) CD8 α and (E) interferon γ normalized mRNA transcript counts measured in NanoString Pan Cancer imaging Panel.
Figure 4 shows that talilavir increases tumor infiltrating lymphocyte density and PD-L1expression in tumors. Ten-color immunofluorescent staining was performed on a single slide from tumor biopsies before and after paired talilavine from each of 13 patients. Markers evaluated included S100 (as melanoma differentiation marker), CD3, CD4, CD8, PD-1, PD-L1, CTLA-4, CD45RO, Foxp3, CD56, CD68, and
Figure 5 depicts circulating T cell subpopulations and activation marker expression. Peripheral blood cells obtained from baseline,
Fig. 6 depicts biopsy availability for treatment and biomarker testing of patients enrolled in the study.
Figure 7 depicts changes in tumor burden at the lesion level. (A) Injected lesion response is depicted. (B) Non-injected non-visceral focal responses are depicted. (C) Non-injected visceral lesion responses are depicted.
Figure 8 shows that the density of CD8 in the injected lesion increased in responders after administration of talilavine. Changes in CD8 density measured by IHC after talliravine treatment but before the start of combination treatment (W6) versus baseline (BL, week 1) were plotted for responders and non-responders, respectively. Based on the fold change scale, the left graph shows the change in injected lesions (Inj) and the right graph shows the change in non-injected lesions (Not Inj). For each investigator, the response was defined as the best overall response for CR or PR, and the no response was PD or SD. Tumor depleted samples are indicated by open circles. Median fold changes are indicated by horizontal lines (solid lines for all samples, dashed lines for those with only tumor present).
Figure 9 shows that talilava reduces the Treg fraction of CD 4T cells in tumors. Ten-color immunofluorescent staining was performed on single slides from paired tumor biopsies before and after talilavine from each of 13 patients. Markers evaluated included S100 (as a melanoma division marker), CD3, CD4, CD8, PD-1, PD-L1, CTLA-4, CD45RO, Foxp3, CD56, CD68, and
FIG. 10 depicts additional multi-parameter imaging (MultiOmyx) from a patient with partial response to treatmentTMPlatform) example for (a) the combination of S100, CD8, and PD-L1 (0.6 mm) at baseline (week 1), after injection of taliravine at
Figure 11 depicts an IFN- γ gene profile according to certain embodiments of the present invention.
Figure 12 depicts a schematic of a
Detailed Description
It has been determined that high levels of CD8+ T cell infiltration, high levels of PD-L1, and/or positive IFN γ gene profiles in tumors are required for successful tumor treatment using PD-1/PD-L1 antagonists. Indeed, current cancer treatments targeting programmed death-1 (PD-1) receptors have been shown to have unprecedented persistent clinical response rates in patients with multiple cancer types, including tumor regression following therapeutic PD-1 blockade, with such outcomes requiring high levels of pre-existing CD8+ T cells (Tumeh et al (2014) Nature 515: 568-571). anti-PD-L1 antibodies were determined to be effective in treating a variety of cancer types in patients with tumors that express high levels of PD-L1 (Herbst et al (2014) Nature 515: 563-7). Furthermore, the presence of high interferon gamma (IFN γ) gene signature in tumors correlates with the ability to treat tumors with PD-1 antagonists (WO 2015/094992; Applicant, Merck Sharp & Dohme Corporation).
Surprisingly, and in complete contrast to accepted dogma (high CD8+ T cell infiltration levels, high PD-L1 levels, and/or positive IFN γ gene profiles are essential for successful tumor treatment with PD-1 antagonists), it has been found that tumors with low CD8+ T cell infiltration levels, low or negative PD-L1 states, and/or low or negative IFN γ gene profiles can be effectively treated with the PD-1 antagonist pembrolizumab using a combination therapy with taliravir. This finding represents the first clinical demonstration that taliravine can trigger an immune response in vivo in a tumor sufficient to target the PD-1 antagonist pembrolizumab to that tumor with high efficiency.
It has also been found that intratumoral administration of talilavir favorably alters the tumor microenvironment of the injected lesion by, for example, increasing CD8+ T cell infiltration, increasing PD-L1expression, and/or producing a more positive IFN γ gene signature, thus rendering the tumor cells more susceptible to anti-PD-1 therapy. The expression of PD-L1 increased after treatment with talilavine, but was offset in the case of pembrolizumab due to subsequent PD-1 blockade. After injection of talilava into the lesion, tumor antigen-specific CD8+ T cells were transported to and infiltrated by local lesions as well as distant metastatic lesions. anti-PD-1 blockade checkpoint protein-mediated inhibition to counteract immune responses using combined treatment of pembrolizumab and talilavine.
Thus, administration of oncolytic viruses makes such tumors more susceptible to pembrolizumab blocking therapy by converting a "cold" (cold) "tumor (i.e., a tumor that exhibits low levels of immunoinfiltration (e.g., by CD8+ T cells), negative IFN γ gene signature, and/or low PD-L1 status) to a" hot "(hot)" tumor (i.e., a tumor that exhibits high levels of immunoinfiltration (e.g., by CD8+ T cells), positive IFN γ gene signature, and/or high PD-L1 status). Thus, tumors that previously had a very low response or no response to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab or a variant or antigen-binding fragment thereof)) can be sensitized to treatment with pembrolizumab or a variant or antigen-binding fragment thereof.
Thus, in one embodiment, the combination of pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof, and taliravine is used to increase the magnitude of a tumor-specific T cell response in a patient compared to pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof alone. This effect is particularly observed for previously untreated, unresectable, stable IIIb-IV melanoma. The combination of pembrolizumab, pembrolizumab variant, or antigen binding fragment thereof, and talilavine is intended to enhance the systemic anti-tumor response against tumor antigens after lytic replication of talilavine in tumors. Thus, combination therapy can lead to enhanced destruction of injected tumors as well as non-injected/distal tumors (including micrometastatic disease) to improve the proportion of overall tumor response and the duration of the response. Collectively, these effects can contribute to an improvement in overall survival, particularly when compared to monotherapy with checkpoint inhibitors (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variants, or antigen-binding fragments thereof)). The use of taliravir in combination with pembrolizumab, pembrolizumab variants, or antigen binding fragments thereof is aimed at enhancing T cell activation by different mechanisms, increasing dendritic cell-mediated tumor antigen presentation after release of tumor antigens by lytic viral replication (Kaufman et al, Ann surginnocol, 17 (3): 718-.
In certain embodiments, a cold tumor-associated cancer is treated with a combination of pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof, and talliravine, having less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2CD8+ T cell infiltration density, low or negative PD-L1 status, and/or negative IFN γ gene signature of the sample (or/1 mL sample). Such tumors include, but are not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell cancer, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, and pancreatic cancer.
In other embodiments, a thermal tumor (or a cancer associated with a thermal tumor) that is responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or antigen-binding fragment thereof)) is treated with a combination of pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof, and taliravine (i.e., with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Cancer unrelated to one or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and/or low IFN γ gene signature expression level of the sample (or/1 mL sample). Such cancers include, but are not limited to: black colourMelanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer), nasopharyngeal cancer, thyroid cancer, salivary gland cancer (salivary cancer), esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular carcinoma, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, Hodgkin's lymphoma), and mesothelioma.
Definition of
Certain technical and scientific terms are specifically defined below so that the present invention may be more readily understood. Unless specifically defined elsewhere in this document, all other technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs.
As used herein (including the appended claims), the terms "a", "an", and "the" mean "includes one and/or more than one unless the context clearly dictates otherwise.
"about" when used to modify a numerically defined parameter (e.g., the genetic signature score of a genetic signature discussed herein, or the dosage of pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof, or talilavine, or the treatment duration of pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof, or talilavine) means that the parameter can vary by as much as 10% above or below the specified value for the parameter. For example, a gene signature consisting of about 10 genes may have 9 to 11 genes.
"administration" and "treatment," when applied to an animal, human, subject, cell, tissue, organ, or biological fluid, means that an exogenous pharmaceutical, therapeutic, diagnostic agent or composition is in contact with the animal, human, subject, cell, tissue, organ, or biological fluid. Treatment of a cell encompasses contact of an agent with a cell, and contact of an agent with a fluid, wherein the fluid is in contact with the cell. "administration" and "treatment" also mean in vitro and ex vivo treatment, such as in vitro and ex vivo treatment of cells by reagents, diagnostics, binding compounds, or by other cells.
The term "antibody" as used herein refers to any form of antibody that exhibits a desired biological or binding activity. It is therefore used in its broadest sense and specifically includes, but is not limited to: monoclonal antibodies (including full length monoclonal antibodies), polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), humanized antibodies, fully human antibodies, chimeric antibodies, and camelized single domain antibodies. A "parent antibody" is an antibody obtained by exposing the immune system to an antigen prior to modifying the antibody for its intended use (e.g., humanizing the antibody for use as a human therapeutic).
In general, the basic antibody building block comprises a tetramer. Each tetramer comprises two identical pairs of polypeptide chains, each pair having one "light" (about 25kDa) and one "heavy" chain (about 50 to 70 kDa). The amino-terminal portion of each chain comprises a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The carboxy-terminal portion of the heavy chain may define a constant region primarily responsible for effector function. Generally, human light chains are classified as kappa and lambda light chains. Furthermore, human heavy chains are generally classified as μ, δ, γ, α or ε, and the isotype of antibodies is defined as IgM, IgD, IgG, IgA, and IgE, respectively. In both light and heavy chains, the variable and constant regions are connected by a "J" region of about 12 or more amino acids, wherein the heavy chain also comprises a "D" region of about 10 more amino acids. See generally Fundamental Immunology ch.7(Paul, w., ed., 2nd ed. raven Press, n.y. (1989)).
The variable regions of each light/heavy chain pair form the antibody binding site. Thus, in general, an intact antibody has two binding sites. Generally, the two binding sites are identical, except in bifunctional or bispecific antibodies.
Generally, the variable domains of both the heavy and light chains comprise three hypervariable regions, also known as Complementarity Determining Regions (CDRs), which are located within relatively conserved Framework Regions (FRs). CDRs are typically arranged through framework regions to enable binding to a particular epitope. In general, from N-terminus to C-terminus, both light and heavy chain variable domains comprise FR1, CDR1, FR2, CDR2, FR3, CDR3 and
The term "hypervariable region" as used herein refers to the amino acid residues of an antibody which are responsible for antigen binding. The hypervariable regions comprise amino acid residues from the "complementarity determining regions" or "CDRs" (i.e., LCDR1, LCDR2 and LCDR3 in the light chain variable domain and HCDR1, HCDR2 and HCDR3 in the heavy chain variable domain). See Kabat et al (1991) Sequences of proteins of Immunological Interest, 5th Ed. public Health Service, national institutes of Health, Bethesda, Md. (CDR regions of antibodies are defined by sequence); see also Chothia and Lesk (1987) j.mol.biol.196: 901-917 (CDR regions of the antibody are defined by structure). The term "framework" or "FR" residues as used herein refers to those variable domain residues other than the hypervariable region residues defined herein as CDR residues.
As used herein, unless otherwise specified, "antibody fragment" or "antigen-binding fragment" refers to an antigen-binding fragment of an antibody, i.e., an antibody fragment that retains the ability to specifically bind to an antigen to which a full-length antibody binds, e.g., a fragment that retains one or more CDR regions. Some examples of antibody binding fragments include, but are not limited to, Fab ', F (ab') 2, and Fv fragments; a diabody; a linear antibody; single chain antibody molecules (e.g., sc-Fv); nanobodies and multispecific antibodies formed from antibody fragments.
An antibody that "specifically binds" to a particular target protein is one that exhibits preferential binding to the target compared to other proteins, but such specificity does not require absolute binding specificity. An antibody is considered "specific" for its intended target if its binding determines the presence of the target protein in the sample (e.g., does not produce an undesirable result, such as a false positive). Antibodies or binding fragments thereof useful in the present invention will bind to a target protein with an affinity that is at least 2-fold higher, preferably at least 10-fold higher, more preferably at least 20-fold higher, and most preferably at least 100-fold higher than the affinity for a non-target protein. As used herein, an antibody is considered to specifically bind to a polypeptide comprising a given amino acid sequence (e.g., the amino acid sequence of mature human PD-1 or human PD-L1 molecule) if the antibody binds to a polypeptide comprising that sequence but does not bind to a protein lacking that sequence.
"chimeric antibody" refers to an antibody in which a portion of the heavy and/or light chain is identical to or homologous to corresponding sequences in antibodies derived from a particular species (e.g., human) or belonging to a particular antibody class or subclass, while the remainder of the chain is identical to or homologous to corresponding sequences in antibodies derived from other species (e.g., mouse) or belonging to other antibody classes or subclasses, as well as fragments of such antibodies, so long as they exhibit the desired biological activity.
"human antibody" refers to an antibody comprising only human immunoglobulin sequences. A human antibody may comprise a murine carbohydrate chain if produced in a mouse, a mouse cell, or a hybridoma derived from a mouse cell. Similarly, "mouse antibody" or "rat antibody" refers to an antibody comprising only mouse or rat immunoglobulin sequences, respectively.
"humanized antibody" refers to a form of antibody that comprises sequences from non-human (e.g., murine) antibodies as well as human antibodies. Such antibodies comprise very small sequences derived from non-human immunoglobulins. In general, the humanized antibody will comprise substantially all of at least one and typically two variable domains, wherein all or substantially all of the hypervariable loops correspond to those of a non-human immunoglobulin and all or substantially all of the FR regions are those of a human immunoglobulin sequence. The humanized antibody optionally will also comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin. When necessary, the prefixes "hum", "hu", or "h" are added to the antibody clone names to distinguish the humanized antibody from the parent rodent antibody. Humanized versions of a rodent antibody will typically comprise the same CDR sequences of the parent rodent antibody, but may comprise certain amino acid substitutions to improve affinity, to improve stability of the humanized antibody, or for other reasons.
By "biotherapeutic agent" is meant a biological molecule, such as an antibody, that blocks ligand/receptor signaling and/or recruits CD8+ T cell infiltration to a tumor in any biological pathway that supports tumor maintenance and/or growth or inhibits an anti-tumor immune response.
The terms "cancer," "cancerous," or "malignant" refer to or describe the physiological condition in mammals that is typically characterized by unregulated cell growth. And less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Some examples of cancers associated with one or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and/or low IFN γ gene signature expression levels of a sample (or/1 mL sample) include, but are not limited to: epithelial cancer (carcinoma), lymphoma, leukemia, blastoma, and sarcoma.
And less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Some examples of specific cancers associated with one or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and/or low IFN γ gene signature expression levels of a sample (or/1 mL sample) include, but are not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell carcinoma, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinomaGastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer or pancreatic cancer.
May be combined with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Some examples of specific cancers that are associated or unrelated in one or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and/or negative IFN γ gene signature of the sample (or/1 mL sample), responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variants, or antigen binding fragments thereof)) include, but are not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer, nasopharyngeal cancer, thyroid cancer, salivary gland cancer, esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular carcinoma, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma. In certain embodiments, a particular cancer type may have one or more thermal subsets (i.e., it may have less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm)2One or more of the CD8+ T cell infiltration density, low or negative PD-L1 status, and/or negative IFN γ gene signature of the sample (or/1 mL sample) and one or more cold subsets (i.e., it is associated with less than 1000 cells/1 mm)2One or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and/or negative IFN γ gene signature of the sample (or/1 mL sample) are correlated).
Particularly preferred cancers that may be treated according to the invention include those characterized by one or any combination of the following: low CD8+ T cell density; low or negative interferon gamma characteristics; and a low or negative PD-L1 status. In certain embodiments, the cancer is "cold," which refers to exhibiting low levelsCancers that are immune-infiltrated (e.g., by CD8+ T cells) are often susceptible to anti-PD-1 blocking therapy by converting such tumors to "hot" tumors. In certain embodiments, the cold tumor has less than or equal to about 3000, e.g., less than about 3000, about 2900, about 2800, about 2700, about 2600, about 2500, about 2400, about 2300, about 2200, about 2100, about 2000, about 1900, about 1800, about 1700, about 1600, about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Or 1mL (i.e., 1 cm)3) CD8+ T cell density of the sample.
As used herein, a "hot" tumor is a tumor that exhibits a higher level of immune infiltration (by, e.g., CD8+ T cells) than a cold tumor. In certain embodiments, a thermal tumor has greater than about 3000 cells, e.g., greater than about 4000 cells or greater than about 5000 cells/1 mm2CD8+ T cell density of the sample.
CD8+ (cytotoxic) T cells are produced in the thymus and express T cell receptors. CD8+ T cells express the dimeric co-receptor CD8, which is typically composed of one CD8 α chain and one CD8 β chain. CD8+ T cells recognize peptides presented by MHC class I molecules found on all nucleated cells. The CD8 heterodimer binds to a conserved portion of MHC class I (the
High tumor-infiltrating CD8+ T cell densities are often associated with favorable clinical outcomes in a very large Cancer spectrum in the field and are indicative of ongoing host immune responses, and the prognostic value of high tumor-infiltrating lymphocyte densities to clinical outcomes has been evaluated in a variety of Cancer entities (Zhang et al (2003) NEJM 348: 203-13; Galon et al (2006) Science 313: 1960-64; Gao et al (2007) J Clin oncol.25: 2586-93; Gooden et al (2011) Br J Cancer 105: 93-103).
The terms "
As used herein, unless otherwise indicated, "CDR" means the complementarity determining region in an immunoglobulin variable region defined using the Kabat numbering system.
By "checkpoint inhibitor" is meant a molecule that reduces, inhibits, interferes with, or modulates, in whole or in part, one or more checkpoint proteins. Checkpoint proteins regulate T cell activation or function. A number of checkpoint proteins are known, for example CTLA-4 and its ligands CD80 and CD 86; and PD1 and its ligands PDL1 and PDL2(Pardol (2012) Nature Reviews Cancer 12: 252-. These proteins are responsible for either co-stimulatory or inhibitory interactions of T cell responses. Checkpoint proteins regulate and maintain self-tolerance and the duration and magnitude of physiological immune responses. In certain embodiments, the checkpoint inhibitor comprises an antibody or is derivable from an antibody.
A "chemotherapeutic agent" is a compound useful for the treatment of cancer. Classes of chemotherapeutic agents include, but are not limited to: alkylating agents, antimetabolites, kinase inhibitors, spindle poison plant alkaloids, cytotoxic/antitumor antibiotics, topoisomerase inhibitors, photosensitizers, antiestrogens and Selective Estrogen Receptor Modulators (SERMs), antiprogestins, estrogen receptor down-regulators (ERDs), estrogen receptor antagonists, luteinizing hormone-releasing hormone agonists, antiandrogens, aromatase inhibitors, EGFR inhibitors, VEGF inhibitors, antisense oligonucleotides that inhibit the expression of genes involved in abnormal cell proliferation or tumor growth. Chemotherapeutic agents useful in the treatment methods of the invention include cytostatic and/or cytotoxic agents.
As used herein, "Clothia" means Al-Lazikani et Al, JMB 273: 927-948 (1997).
"conservatively modified variant" or "conservative substitution" refers to the replacement of an amino acid in a protein with another amino acid having similar characteristics (e.g., charge, side chain size, hydrophobicity/hydrophilicity, backbone conformation, and rigidity, etc.) such that changes can generally be made without altering (or substantially altering) the biological activity or other desired property of the protein, such as antigen affinity and/or specificity. One skilled in The art recognizes that, in general, a single amino acid substitution in a non-essential region of a polypeptide does not substantially alter biological activity (see, e.g., Watson et al (1987) Molecular Biology of The Gene, The Benjamin/Cummings pub. Co., p.224(4th Ed.). Furthermore, substitutions of structurally or functionally similar amino acids are unlikely to destroy biological activity.
Unless the context requires otherwise due to express language or necessary implication, "comprise/comprising" or variations thereof is used in an inclusive sense throughout the specification and claims, i.e., to specify the presence of the stated features but not to preclude the presence or addition of further features that may materially enhance the operation or utility of any embodiment of the invention.
As used throughout the specification and claims, the word "consisting essentially of, and variations thereof, means including any recited element or group of elements, and optionally including other elements of similar or different nature than the recited element which do not materially alter the basic or novel characteristics of the specified dosage regimen, method or composition. As one non-limiting example, if a gene signature score is defined as a composite RNA expression score for a set of genes consisting of a list of specified genes, the skilled person will appreciate that the gene signature score may comprise RNA expression levels determined for one or more additional genes, preferably no more than three additional genes, if such inclusion does not substantially affect the predictive power.
As used herein, "framework region" or "FR" means immunoglobulin variable regions other than CDR regions.
"homology" refers to sequence similarity between two polypeptide sequences when they are optimally aligned. When a position in both of the two compared sequences is occupied by the same amino acid monomer subunit, e.g., if a position in the light chain CDRs of two different abs is occupied by alanine, then the two abs are homologous at that position. Percent homology is the number of homologous positions shared by two sequences divided by the total number of positions compared x 100. For example, two sequences are 80% homologous if 8 of 10 positions in the two sequences match or are homologous when the sequences are optimally aligned. Typically, comparisons are made when aligning two sequences to give the maximum percent homology. For example, the comparison can be made by the BLAST algorithm, where the parameters of the algorithm are selected to give the maximum match between the respective sequences over the entire length of the respective reference sequences.
The following references refer to the BLAST algorithm often used for sequence analysis: BLAST ALGORITHMS: altschul, s.f., et al, (1990) j.mol.biol.215: 403-; gish, w., et al., (1993) naturegene.3: 266-272; madden, t.l., et al, (1996) meth.enzymol.266: 131-141; altschul, s.f., et al., (1997) Nucleic Acids res.25: 3389 and 3402; zhang, j., et al., (1997) genomer res.7: 649-; wootton, j.c., et al, (1993) comput.chem.17: 149-163; hancock, j.m.et., (1994) comput.appl.biosci.10: 67 to 70; ALIGNMENT SCORING SYSTEMS: dayhoff, m.o., et al, "a model of evolution change in proteins," in Atlas of protein sequence and Structure, (1978) vol.5, suppl.3.m.o.dayhoff (ed.), pp.345-352, natl.biomed.res.foundation, Washington, d.c.; schwartz, r.m., et al, "materials for detecting distances," in Atlas of Protein sequences and structures, (1978) vol.5, suppl.3.m.o.dayhoff (ed.), pp.353-358, natl.biomed.res.foundation, Washington, d.c.; altschul, s.f. (1991) j.mol.biol.219: 555-565; states, d.j., et., (1991) Methods 3: 66 to 70; henikoff, s., et al., (1992) proc.natl.acad.sci.usa 89: 10915-; altschul, s.f., et al., (1993) j.mol.evol.36: 290-300; ALIGNMENTSTATISTICS: karlin, s., et al., (1990) proc.natl.acad.sci.usa 87: 2264-2268; karlin, s., et al, (1993) proc.natl.acad.sci.usa 90: 5873-5877; dembo, a., et a1., (1994) ann.prob.22: 2022-2039; and Altschul, S.F. "Evaluating the statistical of statistical variations such as" in the Theoretical and quantitative Methods in Genome Research (S.Suhai, ed.), (1997) pp.1-14, Plenum, N.Y..
"isolated antibody" and "isolated antibody fragment" refer to the purified state, and in such context means that the specified molecule is substantially free of other biomolecules, such as nucleic acids, proteins, lipids, carbohydrates, or other substances (e.g., cell debris and growth media). In general, the term "isolated" is not intended to refer to the complete absence of such material or the absence of water, buffer, or salts, unless present in an amount that significantly interferes with the experimental or therapeutic use of the binding compounds described herein.
"Kabat" as used herein means the immunoglobulin alignment and numbering system advocated by Elvin A.Kabat ((1991) Sequences of Proteins of immunological Interest, 5th Ed. public Health Service, National institutes of Health, Bethesda, Md.).
As used herein, a "monoclonal antibody" or "mAb" refers to a population of substantially homogeneous antibodies, i.e., the antibody molecules comprising the population are identical in amino acid sequence except for possible naturally occurring mutations that may be present in minor amounts. In contrast, conventional (polyclonal) antibody preparations typically comprise a plurality of different antibodies, typically specific for different epitopes, having different amino acid sequences in their variable domains, in particular in their CDRs. The modifier "monoclonal" indicates the character of the antibody as obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method. For example, monoclonal antibodies for use according to the invention can be identified by the methods described by Kohler et al (1975) Nature 256: 495 or may be prepared by recombinant DNA methods (see, e.g., U.S. patent No.4,816,567). For example, Clackson et al (1991) Nature 352: 624-: the technique described in 581-597 isolates "monoclonal antibodies" from phage antibody libraries. See also Presta (2005) j. 731.
"interferon γ" and "IFN γ" (also known as immune or type II interferons) refer to pleiotropic cytokines involved in regulating almost all stages of the immune and inflammatory responses, including activation, growth and differentiation of T cells, B cells, macrophages, NK cells and other cell types such as endothelial cells and fibroblasts. IFN γ enhances MHC expression on antigen presenting cells and also plays an important role in activating lymphocytes to enhance antitumor effects.
IFN γ can help to restrict tumor progression and growth by increasing tumor antigen presentation to tumor-specific T cells and increasing susceptibility to NK cytotoxicity. In addition to promoting an immune response against a tumor, IFN- γ can also induce the expression of tumor suppressor factors.
As used herein, "genetically modified oncolytic virus" refers to an oncolytic virus that has been modified compared to the wild-type form of the virus, typically for the removal and/or insertion of one or more genes. A preferred genetically modified oncolytic virus of the invention is taliravir, also known as Tallowra
Talilavir, HSV-1 (strain JS1) ICP34.5-/ICP47-/hGM-CSF (formerly OncoVex)GM-CSF) An intratumorally delivered oncolytic immunotherapeutic comprising an immunopotentiating HSV-1 that selectively replicates in solid tumors. (Lui et al, Gene Therapy, 10: 292-. HSV-1 is derived from strain JS1 deposited with the european collection of cell cultures (ECAAC) under accession number 01010209. In talilavine, the HSV-1 viral gene encoding ICP34.5 has been functionally deleted. Functional deletion of ICP34.5, which acts as a virulence factor during HSV infection, limits replication in non-dividing cells and renders the virus non-pathogenic. Furthermore, in talilavine, the HSV-1 viral gene encoding ICP47 (which blocks viral antigen presentation to major histocompatibility complex class I and class II molecules) has been functionally deleted. Functional deletion of ICP47 also leads to premature expression of US11, a gene that promotes viral growth in tumor cells without reducing tumor selectivity, US 11. Finally, the coding sequence of human GM-CSF (a cytokine involved in stimulating the immune response) has been inserted into the viral genome of talilavir. Insertion of the gene encoding human GM-CSF so that it replaces almost all of the ICP34.5 gene ensures any potential between Tarila and wild-type virusThe recombination event in question may result in the production of only the disabled non-pathogenic virus and not in the wild-type virus carrying the human GM-CSF gene. The HSV Thymidine Kinase (TK) gene remains intact in talilavine, which makes the virus sensitive to antiviral agents such as acyclovir (acyclovir). Thus, acyclovir can be used to block talavir replication if necessary.
Intratumoral injection of talavium into melanoma metastases improved the persistent Response Rate compared to subcutaneous GM-CSF in Patients With advanced melanoma in
TalilavirApproved as monotherapy for metastatic melanoma in the united states, the european union and australia in 2015. In a
Furthermore, the safety of HSV with functional deletions of ICP34.5 has been shown in a number of clinical studies (MacKie et al, Lancet 357: 525-.
Talilava produces direct oncolytic effects by virus replication in tumors and enhances induction of anti-tumor immune responses by local expression of GM-CSF. Expected clinical effects include, but are not limited to: destruction of injected tumors; destroying local, local-regional and distal non-injected tumors; reduce the occurrence of new metastases; reducing the overall rate of progression; and extending overall survival.
The efficacy of taliravine has been tested in a variety of in vitro (cell lines) and in vivo murine tumor models, and has been shown to eradicate tumors or substantially inhibit their growth at doses comparable to those used in clinical studies. Non-clinical evaluation has also demonstrated that GM-CSF enhances the immune response generated, thereby enhancing injected and non-injected tumor responses, and that elevated surface levels of MHC class I molecules are caused by the absence of ICP 47. Talilava has been injected into normal and tumor-bearing mice to assess its safety. In general, viruses are well tolerated and are as high as 1 × 108The dose of PFU/dose has not given any indication of safety issues. (see, e.g., Liu et al, Gene Ther 10: 292-.
Clinical studies have been or are being conducted in several advanced tumor types (advanced solid tumors, melanoma, head and neck squamous cell carcinoma and pancreatic cancer), with more than 400 subjects being treated with talalavin (see, e.g., Hu et al, ClinCan Res 12: 6737-.
"oligonucleotide" refers to a nucleic acid that is typically 5 to 100 consecutive bases in length, and most commonly 10 to 50, 10 to 40, 10 to 30, 10 to 25, 10 to 20, 15 to 50, 15 to 40, 15 to 30, 15 to 25, 15 to 20, 20 to 50, 20 to 40, 20 to 30, or 20 to 25 consecutive bases in length.
By "patient" or "subject" is meant any individual subject for whom treatment or participation in clinical trials, epidemiological studies, or for use as a control is desired, including humans, non-human primates, mammalian veterinary patients such as cows, horses, dogs, cats, etc., and research animals such as non-human primates, rats, mice, dogs, rabbits, etc.
Pembrolizumab is a humanized monoclonal antibody directed to bind to and block PD-1. Pembrolizumab works by: by blocking the interaction between PD-1 and its ligands PD-L1 and PD-L2, and thereby activating T lymphocytes that can affect both tumor and healthy cells, the body's immune system is enhanced in its ability to help detect and fight tumor cells.
Pembrolizumab monotherapy is known to treat melanoma, non-small cell lung cancer, and head and neck squamous cell carcinoma in affected individuals with higher baseline CD8+ T cell infiltration density, IFN γ gene signature, and PD-L1expression, as compared to levels found in non-responsive individuals. This is understood by those of skill in the art to limit the utility of pembrolizumab in individuals with low CD8+ T cell density, negative IFN γ gene signature, and/or low or negative PD-L1 status.
"pembrolizumab" as used herein refers to the proprietary name
Pembrolizumab may comprise a heavy chain sequence as shown below:
(SEQ ID NO: 1), and the light chain sequence shown below:
(SEQ ID NO：2)。
pembrolizumab may comprise a heavy chain Variable (VH) domain sequence as shown below:
(SEQ ID NO: 3), and the light chain Variable (VL) domain as shown below:
(SEQ ID NO：4)。
pembrolizumab may comprise the following heavy chain complementary-determining regions (HCDRs): NYMY (HCDR1, SEQ ID NO: 5); GINPSNGGTNFN (HCDR2, SEQ ID NO: 6); and RDYRFDMGFDY (HCDR3, SEQ ID NO: 7).
Pembrolizumab may comprise the following light chain complementary-determining regions (LCDRs): RASKGVSTSGYSYLH (LCDR1, SEQ ID NO: 8); LASYLES (LCDR2, SEQ ID NO: 9); and QHSRDLPLT (LCDR3, SEQ ID NO: 10).
In certain embodiments, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is provided comprising a heavy chain CDR SEQ ID NO: 5. 6 and 7, and SEQ ID NO: 8. 9 and 10 light chain CDRs.
In other embodiments, provided is pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, comprising a sequence derived from SEQ ID NO: 3 and SEQ ID NO: 4, and the heavy and light chain CDR sequences of the VH/VL sequence pair.
In other preferred embodiments, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is provided, comprising a peptide comprising SEQ ID NO: 3 or a variant thereof and/or a light chain variable region comprising SEQ ID NO: 4 or a variant thereof. In other embodiments, the pembrolizumab variant or antigen-binding fragment thereof comprises: a heavy chain variable region comprising a sequence identical to SEQ ID NO: 3 (e.g., 80%, 85%, 90%, 95%, 98%, or 99%) sequence homology or identity of at least 80%; and/or a light chain variable region comprising a sequence identical to SEQ ID NO: 4 (e.g., 80%, 85%, 90%, 95%, 98%, or 99%) of at least 80% sequence homology or identity.
As used herein, a "variant of a heavy chain variable region sequence" is a sequence that is identical to a reference sequence, except that it has up to 17 conservative amino acid substitutions in the framework regions (i.e., outside the CDRs) and preferably has fewer than ten, nine, eight, seven, six, or five conservative amino acid substitutions in the framework regions. As used herein, a "variant of a light chain variable region sequence" is a sequence that is identical to a reference sequence, except that it has up to five conservative amino acid substitutions in the framework regions (i.e., outside the CDRs) and preferably has fewer than four, three, or two conservative amino acid substitutions in the framework regions.
In other embodiments, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is provided comprising a peptide comprising SEQ ID NO: 1 or a variant thereof and/or a light chain comprising SEQ ID NO: 2 or a variant thereof. In other embodiments, the pembrolizumab variant or antigen-binding fragment thereof comprises: a heavy chain comprising a sequence identical to SEQ ID NO: 1 (e.g., 80%, 85%, 90%, 95%, 98%, or 99%) sequence homology or identity of at least 80%; and/or a light chain comprising a heavy chain sequence identical to SEQ ID NO: 2 (e.g., 80%, 85%, 90%, 95%, 98%, or 99%) of at least 80% sequence homology or identity.
As used herein, "pembrolizumab variant" refers to a monoclonal antibody comprising heavy and light chain sequences identical to those of pembrolizumab except having up to five conservative amino acid substitutions in the framework region (i.e., outside the CDRs) and preferably having less than four, three, or two conservative amino acid substitutions in the framework region; and up to 17 conservative amino acid substitutions in the framework region (i.e., outside the CDRs) and preferably less than ten, nine, eight, seven, six, or five conservative amino acid substitutions in the framework region, and preferably less than four, three, or two conservative amino acid substitutions in the framework region. In other words, pembrolizumab and pembrolizumab variants comprise the same CDR sequences, but differ from each other by having conservative amino acid substitutions in no more than three or six other positions in their full-length light and heavy chain sequences, respectively. Pembrolizumab variants are substantially the same or better than pembrolizumab with respect to the following properties: binding affinity and neutralizing effect on PD-1 in vivo.
In certain embodiments, a biological analog of pembrolizumab (biosimilar) is provided. The term "biosimilar" as used herein is used in a manner consistent with the working definition promulgated by the U.S. food and Drug Administration, which defines a biosimilar product as one that is "highly similar" (despite minor differences in clinically inactive components) to a reference product. In practice, there are no clinically meaningful differences between the reference product and the bio-analogue product in terms of safety, purity and efficacy (Public Health Service (PHS) Act 262). In certain embodiments, a double-blind, single dose comparative Pharmacokinetic (PK) cross-study is performed to compare pembrolizumab to candidate bioanalog antibodies to determine comparable bioavailability.
The term "reference product" as used herein is used to refer to commercially available pembrolizumab.
The PD-1 receptor (also known as CD279) is expressed on the surface of activated T cells. The ligands PD-L1 (B7-H1; CD274) and PD-L2 (B7-DC; CD273) are usually expressed on the surface of dendritic cells or macrophages. PD1 and PD-L1/PD-L2 belong to a family of immune checkpoint proteins that act as co-suppressors that can stop or limit the occurrence of T cell responses. The PD1/PD-L1 interaction ensures that the immune system is activated only at the appropriate time to minimize the likelihood of chronic autoimmune inflammation. When PD-L1 binds to PD-1, an inhibitory signal is transmitted into T cells, which reduces cytokine production and inhibits T cell proliferation. Tumor cells utilize this immune checkpoint pathway as a mechanism to evade detection and suppress immune responses.
PD-L1 is typically overexpressed on tumor cells or on non-transformed cells in the tumor microenvironment. PD-L1 expressed on tumor cells binds to PD-1 receptors on activated T cells, which results in the inhibition of cytotoxic T cells. These deactivated T cells remain inhibited in the tumor microenvironment. The PD1/PD-L1 pathway represents an adaptive immune resistance mechanism exerted by tumor cells in response to endogenous anti-tumor activity.
As used herein, "PD-L1 status" or "PD-L1 expression status" refers to the level of PD-L1 present in a sample (e.g., in a tumor sample). In certain embodiments, the PD-L1 status is expressed as "tumor proportion score (tumor score)" or "TPS," which refers to the percentage of tumor cells in a sample that express detectable levels of PD-L1. (see, Garon et al (2015) NEJM 372: 2018-28.). A PD-L1 status is "under-expressed" or "reduced" or "low" if PD-L1 is expressed in about 1% to about 49% of the tumor cells in the sample, i.e., a PD-L1 status of about 1% to about 49%. The PD-L1 status is "negative" if PD-L1 is expressed in less than about 1% of the tumor cells in the sample, i.e., the PD-L1 status is less than about 1%. The PD-L1 status is "high" if PD-L1 is expressed in about 50% or more of the tumor cells in the sample, i.e., the PD-L1 status is about 50% or more.
In some preferred embodiments, the low expression, reduction or low PD-L1 status is less than about 50%, or is about 49%, about 48%, about 47%, about 46%, about 45%, about 44%, about 43%, about 42%, about 41%, about 40%, about 39%, about 38%, about 37%, about 36%, about 35%, about 34%, about 33%, about 32%, about 31%, about 30%, about 29%, about 28%, about 27%, about 26%, about 25%, about 24%, about 23%, about 22%, about 21%, about 20%, about 19% about 18%, about 17%, about 16%, about 15%, about 14%, about 13%, about 12%, about 11%, about 10%, about 9%, about 8%, about 7%, about 6%, about 5%, about 4%, about 3%, about 2%, or about 1%. In some particularly preferred embodiments, the low expression, reduced or low PD-L1 status is about 10%, about 9%, about 8%, about 7%, about 6%, about 5%, about 4%, about 3%, about 2% or about 1%. In some preferred embodiments, the low expression, reduced or low PD-L1 status is about 1% to about 10%, about 1% to about 9%, about 1% to about 8%, about 1% to about 7%, about 1% to about 6%, about 1% to about 5%, about 1% to about 4%, about 1% to about 3%, about 1% to about 2%, about 2% to about 6%, about 3% to about 7%, about 4% to about 8%, or about 5% to about 9%.
In some preferred embodiments, the negative PD-L1 status is less than about 1%, or is about 0.9%, about 0.8%, about 0.7%, about 0.6%, about 0.5%, about 0.4%, about 0.3%, about 0.2%, about 0.1%, about 0.05%, about 0.01%, about 0.005%, about 001%, or about 0% (i.e., no tumor cells have detectable levels of PD-L1).
In some preferred embodiments, the high PD-L1 status is about 50% or higher, e.g., about 55%, about 60%, about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95%, about 96%, about 97%, about 98%, about 99%, or about 100% (i.e., all tumor cells have detectable levels of PD-L1).
In certain preferred embodiments, PD-L1expression is detected in an IHC assay of FFPE or frozen tissue sections of tumor samples removed from a subject using a diagnostic anti-human PD-L1 antibody or antigen binding fragment thereof. In certain embodiments, PD-L1expression may be assessed in a sample (e.g., a tumor sample) using a PD-L1 IHC 22C3 pharmDx immunohistochemistry assay (Dako North America, Carpinteria, CA). (see Daud, A.I., Wolchok, J.D., Robert, C., Hwu, W.J., Weber, J.S., Ribas, A., Hodi, F.S., Joshua, A.M., Kefford, R., Hersey, P., et al (2016) (Programmed Death-Ligand 1Expression and Response to the Anti-Programmed Death 1Antibody Pembrolizumab in Melanoma.J. Clin Oncol34, 4102-
As used herein, "pembrolizumab primary antibody" and "pembrolizumab variant primary antibody" refer to an antibody that specifically binds to PD-L1 in tissue sections and is typically used as the primary antibody in IHC assays for PD-L1expression in tumor samples. In one embodiment, the primary antibody is the only antibody used in the IHC assay.
As used herein, "secondary antibody" refers to an antibody that specifically binds to pembrolizumab, or pembrolizumab variant, primary antibody, thereby forming a bridge between the primary antibody and subsequent detection reagents (if any). The secondary antibody is typically the secondary antibody used in IHC assays for PD-L1expression in tumor samples.
As used herein, a "patient" refers to a subject having a cancer that is treated by a combination of pembrolizumab, pembrolizumab variant, or antigen-binding fragment thereof, and taliravine.
In certain embodiments, the patient has less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Cancer associated with one or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and low IFN γ gene signature levels of the sample (or/1 mL sample), including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., melanoma), ovarian cancer, bladder cancer, prostate cancerE.g., transitional cell carcinoma, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, or pancreatic cancer.
In other embodiments, the patient has a cancer that is responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or an antigen-binding fragment thereof)), which may optionally be combined with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2One or more of CD8+ T cell infiltration density, low or negative PD-L1 status, and low IFN γ gene signature levels of the sample (or/1 mL sample) are correlated, including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer, nasopharyngeal cancer, thyroid cancer, salivary gland cancer, esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular carcinoma, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma.
As used herein, a "probe" refers to an oligonucleotide that is capable of specifically hybridizing under stringent hybridization conditions to a transcript expressed by a gene of interest and, in some preferred embodiments, to a particular transcript of the gene of interest under stringent hybridization conditions.
As used herein, "RECIST 1.1 response criteria" means Eisenhauer et al, e.a.et al, eur.j Cancer 45: 228-.
As used herein, "reference IFN- γ gene signature score" means a score of an IFN- γ gene signature that has been determined to separate at least a majority of responders from at least a majority of non-responders in a reference population of subjects who have the same tumor type as the subject and have been treated with pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof, in combination with taliveride. Preferably, 60%, 70%, 80%, or 90% (at least any one) of the responders in the reference population will have an IFN- γ gene signature score (i.e., a negative IFN γ gene signature) that is lower than a selected reference score (e.g., a pre-specified threshold for the control group), while 60%, 70%, 80%, 90%, or 95% (at least any one) of the non-responders in the reference population will have an IFN- γ gene signature that is greater than the selected reference score (i.e., a positive IFN γ gene signature). In some preferred embodiments, responders in the reference population are defined as subjects achieving Partial Response (PR) or Complete Response (CR) as measured by RECIST 1.1 criteria, and non-responders are defined as not achieving any RECIST 1.1 clinical response.
When referring to a specific anti-tumor response to treatment with a combination therapy as described herein, a "responder patient" means a patient exhibiting an anti-tumor response.
When referring to a tumor or any other biological material as referred to herein, a "sample" means a sample that has been taken from a subject.
By "sustained response" is meant a sustained therapeutic effect following discontinuation of treatment with a therapeutic agent or combination therapy as described herein. In some embodiments, the duration of the sustained response is at least the same as the duration of treatment, or at least 1.5, 2.0, 2.5, or 3 times as long as the duration of treatment.
"tissue section" refers to a single portion or piece of a tissue sample, such as a thin section of tissue cut from a normal tissue sample or a tumor sample.
As used herein, "treating" cancer means administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, with talliravine and/or other therapeutic agent to a subject having or diagnosed with cancer to achieve at least one positive therapeutic effect, e.g., a reduction in cancer cell number, a reduction in tumor size, a reduction in the rate of cancer cell infiltration into peripheral organsLow, or a reduced rate of tumor metastasis or tumor growth. Positive treatment effects in cancer can be measured in a variety of ways (see, w.a. weber, j.null. med.50: 1S-10S (2009); Eisenhauer et al, supra). In some preferred embodiments, RECIST 1.1 criteria are used to assess response to pembrolizumab, pembrolizumab variants and/or antigen-binding fragments thereof, and/or taliravine. In some embodiments, the treatment effected by the therapeutically effective amount is any of Partial Response (PR), Complete Response (CR), Progression Free Survival (PFS), Disease Free Survival (DFS), Objective Response (OR), OR Overall Survival (OS). In some preferred embodiments, the CD8+ cell density, gene signature biomarker, and/or low or negative PD-L1 status of the invention predict whether a subject with a solid tumor is likely to achieve PR or CR. The dosage regimen of the treatments described herein effective to treat a cancer patient may vary depending on factors such as: the disease state, age and weight of the patient, and the ability of the treatment to elicit an anti-cancer response in the subject. Although embodiments of the methods of treatment, medicaments and uses of the invention may not be effective in achieving a positive therapeutic effect in every subject, as by any statistical test known in the art (e.g., t-test (Student's t-test), chi-square test (chi)2-test), as determined by the U test of Mann and Whitney, the Kruskal-Wallis test (H test), the Jonckheere-Terpsra test and the Wilcoxon test), which should be so in a statistically significant number of subjects.
When "tumor" is applied to a subject diagnosed with or suspected of having cancer, it refers to a malignant or potentially malignant neoplasm or mass of tissue of any size and includes both primary tumors and secondary neoplasms. A solid tumor is an abnormal growth or mass of tissue that generally does not contain cysts or fluid areas. Different types of solid tumors are named for the type of cells that form them. Some examples of solid tumors are sarcomas, epithelial carcinomas, and lymphomas. Leukemia (blood Cancer) does not usually form solid tumors (National Cancer Institute, Dictionary of Cancer Terms).
"tumor burden," also referred to as "tumor burden," refers to the total amount of tumor mass distributed throughout the body. Tumor burden refers to the total number of cancer cells or the total size of the tumor throughout the body, including lymph nodes and bone marrow. Tumor burden can be determined by a variety of methods known in the art, such as by measuring the size of the tumor after removal from the subject, for example, using calipers, or while in vivo using imaging techniques (e.g., ultrasound, bone scan, Computed Tomography (CT), or Magnetic Resonance Imaging (MRI) scan).
The term "tumor size" refers to the total size of a tumor that can be measured as the length and width of the tumor. Tumor size can be determined by a variety of methods known in the art, such as by measuring the size of the tumor after removal from the subject, for example, using calipers, or while in vivo using imaging techniques (e.g., bone scan, ultrasound, CT, or MRI scan).
As used herein, "variable region" or "V region" means a segment of an IgG chain that is variable in sequence between different antibodies. It extends to Kabat residue 109 in the light chain and Kabat residue 113 in the heavy chain.
In some embodiments of the inventive methods, medicaments, and uses disclosed herein, the subject is a human, and the cancer is associated with a low or negative PD-L1 status and/or a low or negative CD8+ T cell density, including but not limited to: melanoma (high T cell infiltration generally% PD-L1 +; subgroup PD-L1/TIL low, Tumeh et al Nature 2014; Daud, JCO 2016); non-small cell lung cancer (some high% PD-L1 +; subgroup PD-L1/TIL low, Topalian NEJM 2012; Garon etalNEJM 2015; Arneratunga PlosOne 2016); recurrent or metastatic head and neck squamous cell carcinoma; HPV-positive or HPV-negative Head and Neck cancer (usually high T-cell infiltration high% PD-L1 +; subgroup PD-L1/TIL low, evident for both HPV + and HPV-Head and Neck cancer, Lyford-Pyke CanRes 2013; Malm Head cock 2015; Mandal et al JCI 2016); colorectal cancer (mismatch repair-deficient CRC/Lynch syndrome high PD-L1+ TIL infiltration; MSI stable CRC is usually a cold tumor, Le et al NEJM 2015; Maby CanRes 2015); HER2+ breast cancer (CD8+ high (61%) Foxp3Treg high; lymphodominant breast cancer (16%), Stanton JAMA (2016)); HER2- (HR +) breast cancer (lower Foxp3Treg in CD8+ (43%); lymphodominant breast cancer (6%), Stanton JAMA (2016)); triple negative breast cancer (CD8+ high (60%) Foxp3Treg high; lymphodominant breast cancer (20%), Stanton JAMA (2016)); ovarian cancer (prognostic data around TIL is similar to melanoma; response rate in Hamanishi JCO is 15% to 40%, Hamanishi JCO, 2015; Mandai IJCO 2016); bladder cancer (associated with PD-L1; possible TIL bladder cancer association for checkpoint inhibitors, Powles Nature 2014 (Atezo); Kim ICU 2016); uveal melanoma (bmx data provided by pip-Neumann ASCO 2016, uveal melanoma); castration-resistant Prostate Cancer (disease of PD-L1expression in Prostate Cancer: inactive and adaptive immune response, Martin Prostate Cancer and pathological Diseases 2015Kim ICU 2016); soft tissue or osteosarcoma (moderate response rate; prognostic PD-L1/TIL data are available, or need to be mined to look for Clinical data of TIL versus checkpoint inhibitor response-l.paoluzzi Clinical Sarcoma Research 2016; D' Angelo SP Human path 2015); and renal cell carcinoma (pembrolizumab is used mainly in combination in RCC: Ipi, axitinib, anti-VEGF, etc., generally high T cell infiltration by% PD-L1 +; subgroup PD-L1/TIL low, Taube Clin Can Res 2014).
In other embodiments of the inventive methods, medicaments and uses disclosed herein, the individual is a human and the cancer is associated with low or negative IFN γ mRNA signature, including but not limited to: melanoma (ORR/PFS associated with IFN γ characteristics, eyers et al JITC 2015); head and neck cancer ("inflammatory phenotype" characteristic is a powerful predictor of clinical benefit from anti-PD-1 treatment against HNSCC, even in a patient group that has been considered PD-L1 +; clinical trial information: NCT01848834, SeiwaaASCO et al JITC); gastric cancer (PFS is associated with IFN γ signature, eyers et alJITC 2015); esophageal cancer (overall, those with higher feature scores experienced a more robust response to pembrolizumab and progressed significantly delayed; in non-inflammatory, low scoring cohorts, ORR 11%, Doi et al GCS 2016; this RNA profile dataset from 5 cancers increased more and more evidence that tumor infiltration of activated T cells is a prerequisite to response to PD-1 checkpoint blockade and that T cell inflammatory gene expression was characterized as a pan-cancer predictor from clinical benefit of anti-PD-1 treatment, Piha-Paulet al. Anal canal cancer (according to Piha-Paul et al. Biliary cancer (according to Piha-paule al. Colorectal cancer (according to Piha-Paul et al. Ovarian cancer (according to Piha-Paulet al. And transitional cell carcinoma (similar to melanoma, SCCHN and gastric cancer in terms of predictive value of IFN γ signature).
In other embodiments of the above methods of treatment, medicaments and uses, the individual is a human and the cancer is associated with low or negative PD-L1 mRNA expression, including but not limited to: pancreatic cancer (4% PD-L1+, Ayers et al AACR 2015); prostate cancer (14% PD-L1+, supra); triple negative breast cancer (29% PD-L1+, supra); melanoma (41% PD-L1+, supra); non-small cell lung cancer (42% PD-L1+, supra); urothelial cancer (42% PD-L1+, supra); and head and neck cancer (59% PD-L1+, supra) (e.g., recurrent or metastatic head and neck squamous cell carcinoma).
Methods, uses and medicaments
In one aspect, the invention relates to a method for treating cancer in an individual comprising administering to the individual a combination therapy comprising pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof, and taliravine.
The combination therapy may further comprise one or more additional therapeutic agents. Additional therapeutic agents can be, for example, chemotherapeutic agents, biotherapeutic agents, immunogenic agents (e.g., attenuated cancer cells, tumor antigens, antigen presenting cells (e.g., dendritic cells pulsed with tumor-derived antigens or nucleic acids), immunostimulatory cytokines (e.g., IL-2,
Some examples of chemotherapeutic agents include: alkylating agents, such as thiotepa and cyclophosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzotepa (benzodopa), carboquone (carboquone), metotepipa (meturedpa) and uredepa (uredpa); ethyleneimine and methylmelamine including altretamine, triethylenemelamine, triethylenephosphoramide, triethylenethiophosphoramide, and trimethlamelamine; annonaceous acetogenins (especially bullatacin and bullatacin); camptothecin (camptothecin) (including the synthetic analogue topotecan); bryostatin; caristatin (cally statin); CC-1065 (including its adozelesin (adozelesin), carvelesin (carzelesin), and bizelesin (bizelesin) synthetic analogs); cryptophycins (especially cryptophycin 1 and cryptophycin 8); dolastatin (dolastatin); duocarmycins (duocarmycins) (including the synthetic analogs KW-2189 and CBI-TMI); eiscosahol (eleutherobin); coprinus atrata base (pancrati statin); sarcandra glabra alcohol (sarcodictyin); spongistatin (spongistatin); nitrogen mustards (nitrosgen mustards), such as chlorambucil (chlorambucil), chlorambucil (chlorenaphazine), cholorophosphamide (cholorophosphamide), estramustine (estramustine), ifosfamide (ifosfamide), mechlorethamine (mechlorethamine), mechlorethamine hydrochloride (mechlorethamine oxide hydrochloride), melphalan, neomustard (novembichin), benzene mustard cholesterol (phenyleneterestine), prednimustine (prednimustine), triamcinolone (fosfamide), uracil mustard (uracil mustard); nitroureas such as carmustine (carmustine), chlorouretocin (chlorozotocin), fotemustine (fotemustine), lomustine (lomustine), nimustine (nimustine), ranimustine (ranimustine); antibiotics, e.g. enediynes (enediynes) antibiotics (e.g. calicheamicin), especially calicheamicinIt is calicheamicin gamma ll (calicheamicin gamma) and calicheamicin
Each therapeutic agent in the combination therapy of the present invention may be administered alone or in a medicament (also referred to herein as a pharmaceutical composition) comprising the therapeutic agent and one or more pharmaceutically acceptable carriers, excipients and diluents according to standard pharmaceutical practice.
Each therapeutic agent in the combination therapy of the present invention may be administered simultaneously (i.e., in the same drug), simultaneously (i.e., in separate drugs administered one after the other in any order), or sequentially in any order. Sequential administration is particularly useful when the therapeutic agents in the combination therapy are in different dosage forms (one agent is a tablet or capsule and the other agent is a sterile liquid) and/or are administered on different dosing schedules (e.g., the chemotherapeutic agent is administered at least daily and the biologic therapeutic agent is administered less frequently (e.g., once per week, once every two weeks, or once every three weeks)) and/or are administered to different parts of the body (e.g., intratumoral administration of one therapeutic agent and systemic administration of one therapeutic agent).
In some particularly preferred embodiments, the taliprazole is administered prior to administering pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof. In other embodiments, the taliravir is administered after the pembrolizumab, the pembrolizumab variant, or the antigen-binding fragment thereof. In another embodiment, the talilavine is administered simultaneously with pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof.
In some embodiments, at least one therapeutic agent in the combination therapy is administered using the same dosage regimen (dose, frequency and duration of treatment) that is typically employed when the agents are used as monotherapy to treat the same cancer. In other embodiments, the patient receives a lower total amount of the at least one therapeutic agent in the combination therapy, e.g., a smaller dose, a less frequent dose, and/or a shorter duration of treatment, than when the agents are used as monotherapy.
In certain embodiments, the taliravine is administered intratumorally. In certain embodiments, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is administered parenterally.
The combination therapy of the present invention may be used before or after surgical removal of the tumor and may be used before, during or after radiation therapy.
In some embodiments, the combination therapy of the present invention is administered to a patient that has not been previously treated with a biologic therapeutic or a chemotherapeutic agent (i.e., not treated for cancer). In other embodiments, the combination therapy is administered to a patient who failed to achieve a sustained response after a prior treatment (e.g., after treatment with a checkpoint inhibitor (e.g., treatment with anti-PD-L1 or anti-PD-1 (e.g., pembrolizumab variant, or antigen-binding fragment thereof)) or chemotherapy treatment failed or failed, i.e., underwent cancer therapy).
The combination therapy of the present invention is typically used to treat tumors that are large enough to be found by palpation or by imaging techniques well known in the art (e.g., MRI, ultrasound, or CAT scan).
The combination therapy of the invention is preferably administered to human patients suffering from cancer with low CD8+ T cell density, negative IFN γ gene signature and/or with low or negative PD-L1 status.
The selection of the dosage regimen (also referred to herein as an administration regimen) for the combination therapy of the invention depends on several factors, including the serum or tissue turnover rate of the entity, the level of symptoms, the immunogenicity of the entity, and the accessibility of the target cells, tissues or organs in the individual being treated. Preferably, the dosage regimen maximizes the amount of each therapeutic agent delivered to the patient consistent with an acceptable level of side effects. Thus, the dosage and frequency of administration of each of the biotherapeutic agents and chemotherapeutic agents in the combination will depend, in part, on the particular therapeutic agent, the severity of the cancer being treated and the patient characteristics. Guidelines are available for selecting appropriate doses of antibodies, cytokines, and small molecules. See, e.g., Wawrzynczak (1996) Antibody Therapy, Bios Scientific pub. ltd, Oxfordshire, UK; kresina (ed.) (1991) monoclonal antibodies, Cytokines and Arthritis, Marcel Dekker, New York, NY; bach (ed.) (1993) Monoclonal Antibodies and Peptide Therapy in Autoimmune Diseases, Marcel Dekker, New York, NY; baert et al, (2003) New engl.j.med.348: 601-608; milgrom et al (1999) New engl.j.med.341: 1966-; slamon et al (2001) New Engl.J.Med.344: 783-792; beniamovitz et al, (2000) New engl.j.med.342: 613-619; ghosh et al, (2003) New engl.j.med.348: 24-32; lipsky et al, (2000) New engl.j.med.343: 1594-; physicians 'Desk Reference 2003 (Physicians' Desk Reference, 57th Ed); medical Economics Company; ISBN: 1563634457, respectively; 57th edition (11 months 2002). Determination of an appropriate dosage regimen can be made by a clinician, for example, using parameters or factors known or suspected in the art to affect treatment or to predict the effect on treatment, and will depend on, for example, the clinical history of the patient (e.g., previous treatment), the type and stage of cancer to be treated, and biomarkers responsive to one or more therapeutic agents in the combination therapy. The optimal dose of pembrolizumab combined with taliravone may be determined by dose escalation or dose decrementing of one or both of these agents.
The invention also provides a medicament comprising pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof, as described above, and a pharmaceutically acceptable excipient. Pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof can be produced in CHO cells using conventional cell culture and recovery/purification techniques.
In some embodiments, the medicament comprising pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof, may be provided as a liquid formulation or prepared by reconstituting a lyophilized powder with sterile water for injection prior to use. WO 2012/135408 describes the preparation of liquid and lyophilized medicaments comprising pembrolizumab suitable for use in the present invention. In some embodiments, a medicament comprising pembrolizumab, comprising about 100mg of pembrolizumab in 4ml of solution, is provided in a glass vial. Each 1mL solution contained 25mg pembrolizumab and was formulated in: l-histidine (1.55mg), polysorbate 80(0.2mg), sucrose (70mg) and water for injection, USP. The solution needs to be diluted for IV infusion.
The biotherapeutic agents in the combination therapy of the present invention may be administered by continuous infusion or by dosing, e.g., at intervals daily, every other day, three times a week, or once a week, once every two weeks, once every three weeks, once a month, once every two months, etc. The total weekly dose is typically at least 0.05. mu.g/kg, 0.2. mu.g/kg, 0.5. mu.g/kg, 1. mu.g/kg, 10. mu.g/kg, 100. mu.g/kg, 0.2mg/kg, 1.0mg/kg, 2.0mg/kg, 10mg/kg, 25mg/kg, 50mg/kg body weight or more. See, e.g., Yang et al (2003) New engl.j.med.349: 427-434; herold et al (2002) new engl.j.med.346: 1692 and 1698; liu et al, (1999) j.neurol.neurosurg.psych.67: 451-456; portaleji et al (20003) Cancer immunol.immunother.52: 133-144.
In certain embodiments using pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof, a dosing regimen will comprise administering pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof at a dose of 1, 2,3, 5, or 10mg/kg at intervals of about 14 days (+ -2 days) or about 21 days (+ -2 days) or about 30 days (+ -2 days) throughout the course of treatment. In a preferred embodiment, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is used at a dose of 2mg/kg every 3 weeks (e.g., for melanoma). In another preferred embodiment, pembrolizumab, a pembrolizumab variant, or an antigen-binding fragment thereof is used at a dose of 200mg (fixed) every 3 weeks (e.g., for non-small cell lung cancer, head and neck squamous cell carcinoma, and/or hodgkin's lymphoma).
In other embodiments where pembrolizumab, pembrolizumab variant, and/or an antigen-binding fragment thereof is used in a combination therapy, a dosing regimen will comprise administering pembrolizumab, pembrolizumab variant, and/or an antigen-binding fragment thereof at a dose of about 0.005mg/kg to about 10mg/kg with up-dosing in the patient. In other incremental dose embodiments, the interval between doses will be progressively shorter, e.g., about 30 days (+ -2 days) between the first and second doses and about 14 days (+ -2 days) between the second and third doses. In certain embodiments, for doses subsequent to the second dose, the dosing interval will be about 14 days (± 2 days).
In certain embodiments, the subject will be administered a parenteral administration, such as an Intravenous (IV) infusion, of a medicament comprising any of pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof.
In a preferred embodiment of the invention, pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof is administered as a liquid medicament at a dose selected from the group consisting of: 1mg/kg biweekly (Q2W), 2mg/kg Q2W, 3mg/kg Q2W, 5mg/kg Q2W, 10mg Q2W, 1mg/kg every 3 weeks (Q3W), 2mg/kg Q3W, 3mg/kg Q3W, 5mg/kg Q3W, 10mg Q3W and a flat dose equivalent of any of these doses, i.e., e.g., 200mg Q3W. In some embodiments, pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof is provided as a liquid medicament comprising 25mg/ml pembrolizumab, 7% (w/v) sucrose, 0.02% (w/v)
In some embodiments, the selected dose of pembrolizumab, pembrolizumab variant, and/or an antigen-binding fragment thereof is administered by IV infusion. In one embodiment, the selected dose of pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof is administered by IV infusion over a period of 25 to 40 minutes, or about 30 minutes.
The invention also provides a medicament comprising talitra and pharmaceutically acceptable excipients. Talilavir can be suspended in physiological buffer for intratumoral injection.
In certain embodiments, up to 4.0
TABLE 1 Talilavir injection volume guidelines based on tumor size
All lesions that can be reasonably injected (skin, subcutaneous and nodular diseases that can be injected with or without ultrasound guidance) should be injected at the maximum volume of administration available with single administration. On each treatment day, the following prioritizations of injections are recommended: any new injectable tumors that appeared since the last injection; by tumor size, starting with the largest tumor; any tumor that was previously not injectable and is now injectable. The composition may comprise one or more substances selected from: buffers, antioxidants such as ascorbic acid, low molecular weight polypeptides (e.g., those having less than 10 amino acids), proteins, amino acids, carbohydrates such as glucose, sucrose, or dextrins, chelating agents such as EDTA, glutathione, stabilizers, and excipients. Neutral buffered saline or saline mixed with specific serum albumin are some examples of suitable diluents. Preservatives such as benzyl alcohol may also be added according to appropriate industry standards. The composition can be formulated as a lyophilizate using a suitable excipient solution (e.g., sucrose) as a diluent. Suitable components are nontoxic to recipients at the dosages and concentrations employed.
In some embodiments, if a patient is as follows, then the patient is selected for treatment with a combination therapy of the invention: (1) has less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2CD8+ T cell infiltration density, low or negative PD-L1 status, and/or negative IFN γ gene signature of the sample (or/1 mL sample); (2) has been diagnosed with melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell cancer, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, or pancreatic cancer.
In other embodiments, a patient is selected for treatment with a combination therapy of the invention if the patient is: (1) having a cancer that responds to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or an antigen-binding fragment thereof)); (2) the cancer may optionally be associated with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2(ii) the CD8+ T cell infiltration density, low or negative PD-L1 status, and negative IFN γ gene signature of the sample (or/1 mL sample) are correlated; and (3) has been diagnosed with melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer, nasopharyngeal cancer, thyroid cancer, salivary gland cancer, esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, inflammatory breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular carcinoma, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma.
The medicaments described herein may be provided as a kit comprising a first container and a second container and a packaging insert. The first container comprises at least one dose of a medicament comprising pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof, and the second container comprises at least one dose of taliravine. The kit may optionally comprise a package insert or label comprising instructions for using the drug to treat cancer in a patient. The first and second containers may be constructed of the same or different shapes (e.g., vials, syringes, and bottles) and/or materials (e.g., plastic or glass). The kit may further comprise other materials useful for administering drugs, such as diluents, filters, IV bags and lines, needles and syringes. In some preferred embodiments of the kit, the instructions state that the medicament is intended for treating a patient having a cancer with less than 1,000 cells/mm2CD8+ T cell density, negative IFN γ gene signature, and/or low or negative PD-L1 status.
Pharmaceutical composition
The invention relates to the use of the above-mentioned agents for prophylactic and/or therapeutic treatment, as described below. Accordingly, pembrolizumab variants, and/or antigen-binding fragments thereof, and/or talilavine of the present invention may be incorporated into a pharmaceutical composition suitable for administration. Such compositions typically comprise pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof, or talilavine and a pharmaceutically acceptable carrier. The language "pharmaceutically acceptable carrier" as used herein is intended to include any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like, compatible with pharmaceutical administration. The use of such media and agents for pharmaceutically active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active compound, its use in the compositions is contemplated. Supplementary active compounds may also be incorporated into the compositions.
The pharmaceutical compositions of the present invention are formulated to be compatible with their intended route of administration. Some examples of routes of administration include: parenteral (e.g., intravenous, intradermal, subcutaneous, intraperitoneal, intramuscular, transdermal (topical), and transmucosal) administration). Solutions or suspensions for parenteral, intradermal, or subcutaneous application may comprise the following components: sterile diluents such as water for injection, saline solution, fixed oils, polyethylene glycols, glycerin, propylene glycol or other synthetic solvents; antibacterial agents such as benzyl alcohol or methyl paraben; antioxidants such as ascorbic acid or sodium bisulfite; chelating agents such as ethylenediaminetetraacetic acid; buffers such as acetates, citrates or phosphates and agents for adjusting tonicity (tonality) such as sodium chloride or dextrose (dextrose). The pH can be adjusted with an acid or base (e.g., hydrochloric acid or sodium hydroxide). The parenteral formulations may be enclosed in ampoules, disposable syringes or multiple dose vials made of glass or plastic.
Pharmaceutical compositions suitable for injectable use include sterile aqueous solutions (where water soluble) or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. For intravenous, IS, ICV and/or IT administration, suitable carriers include saline, bacteriostatic water, Cremophor ELTM (BASF, Parsippany, n.j.) or Phosphate Buffered Saline (PBS). In all cases, the composition must be sterile and fluid to the extent that ease of injection exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), and suitable mixtures thereof. For example, proper fluidity can be maintained, for example, by the use of a coating (e.g., lecithin), by the maintenance of the required particle size in the case of dispersions, and by the use of surfactants. Prevention of the action of microorganisms can be achieved by various antibacterial and antifungal agents (e.g., parabens, chlorobutanol, phenol, ascorbic acid, thimerosal, and the like). In many cases, it will be preferable to include isotonic agents, for example, sugars, polyalcohols (e.g., mannitol, sorbitol), sodium chloride in the composition. Prolonged absorption of the injectable compositions can be brought about by including in the composition an agent which delays absorption, for example, aluminum monostearate and gelatin.
Sterile injectable solutions can be prepared by incorporating the active compound in the required amount in a suitable solvent with one or a combination of ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the active compound into a sterile vehicle which contains a base dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum drying and freeze-drying which yields a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.
Systemic administration may be by transmucosal or transdermal means. For transmucosal or transdermal administration, penetrants appropriate to the barrier to be permeated are used in the formulation. Such penetrants are generally known in the art, and include, for example, for transmucosal administration, detergents, bile salts, and fusidic acid (fusidic acid) derivatives. Transmucosal administration can be accomplished through the use of nasal sprays or suppositories. For transdermal administration, the active compounds are formulated as ointments, salves (salves), gels, or creams, as is well known in the art.
In one embodiment, pembrolizumab variants, and/or antigen-binding fragments thereof, or talipezil is prepared with a carrier that will protect the compound from rapid elimination from the body, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable biocompatible polymers may be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Methods for preparing such formulations will be apparent to those skilled in the art. Materials are also commercially available from Alza Corporation and Nova Pharmaceuticals, Inc. Liposomal suspensions (including liposomes targeted to infect cells with monoclonal antibodies against viral antigens) can also be used as pharmaceutically acceptable carriers. These can be prepared according to methods known to those skilled in the art (e.g., as described in U.S. Pat. No.4,522,811).
Formulating parenteral compositions in dosage unit form is particularly advantageous for ease of administration and uniformity of dosage. Dosage unit form as used herein refers to physically discrete units suitable as unitary dosages for the subject to be treated; each unit containing a predetermined quantity of active compound calculated to produce the desired therapeutic effect in association with the required pharmaceutical carrier. The specification for the dosage unit forms of the invention is determined by and directly depends on: the unique characteristics of the active compounds and the particular therapeutic effect to be achieved, as well as the inherent limitations in the art of compounding such active compounds for individual treatment.
The pharmaceutical composition may be contained in a container, package or dispenser together with optional instructions for administration.
The pharmaceutical compositions of the present invention may be administered in a variety of ways depending on whether local or systemic treatment is desired and on the area to be treated. Administration may be intratumoral or parenteral. Parenteral administration includes intravenous drip, subcutaneous, intraperitoneal or intramuscular injection, intrathecal or intraventricular administration.
Formulations for parenteral administration may include sterile aqueous solutions, which may also contain buffers, diluents, and other suitable additives. An intra-ventricular injection may be facilitated by, for example, an intra-ventricular catheter attached to a reservoir. For intravenous use, the total concentration of solutes should be controlled to make the formulation isotonic.
Types of pharmaceutically acceptable excipients that may be used as carriers include: stabilizers such as Human Serum Albumin (HSA), bulking agents such as carbohydrates, amino acids, and polypeptides; a pH adjusting or buffering agent; salts such as sodium chloride; and the like. These carriers may be in crystalline or amorphous form, or may be a mixture of both.
Particularly valuable bulking agents include compatible carbohydrates, polypeptides, amino acids, or combinations thereof. Suitable carbohydrates include: monosaccharides such as galactose, D-mannose, sorbose, and the like; disaccharides such as lactose, trehalose, and the like; cyclodextrins, such as 2-hydroxypropyl- β -cyclodextrin; and polysaccharides such as raffinose, maltodextrin, dextran, etc.; sugar alcohols such as mannitol, xylitol and the like. A preferred group of carbohydrates includes lactose, trehalose, raffinose, maltodextrins and mannitol. Suitable polypeptides include aspartame. The amino acids include alanine and glycine, with glycine being preferred.
Suitable pH adjusting agents or buffers include organic salts prepared from organic acids and bases, such as sodium citrate, sodium ascorbate, and the like; sodium citrate is preferred.
In one embodiment, a unit dose or measured dose of a composition comprising pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof, or talilavine is dispensed by an implanted device. The device may include a sensor that monitors a parameter within the subject. For example, the device may include a pump (e.g., an osmotic pump) and optionally associated electronics.
Biomarker testing
Biomarker expression scores (e.g., IFN- γ gene signature scores and/or PD-L1 status) may be determined in tumor tissue samples taken from subjects. The tumor may be primary or recurrent, and may be of any type (as described above), any stage (e.g., stage I, II, III, or IV or equivalent of other staging systems), and/or any histology. The subject may be of any age, gender, history of treatment and/or extent and duration of remission.
Tumor samples can be obtained by a variety of methods including, but not limited to, surgical resection, aspiration, or biopsy. Tissue samples can be sectioned and assayed as fresh specimens. Alternatively, the tissue sample may be frozen for further sectioning. In some preferred embodiments, the tissue sample is preserved by fixing and embedding in paraffin or the like.
Tumor tissue samples can be fixed by conventional methods, wherein the length of fixation depends on the size of the tissue sample and the fixative used. Neutral buffered formalin, glutaraldehyde, buuin's, and paraformaldehyde are some non-limiting examples of fixatives. In some preferred embodiments, the tissue sample is fixed with formalin. In some embodiments, the fixed tissue sample is also embedded in paraffin to prepare a formalin-fixed paraffin-embedded (FFPE) tissue sample.
Generally, tissue samples are fixed and dehydrated through a series of gradient alcohols, infiltrated with paraffin or other sectioning media and embedded so that the tissue sample can be sectioned. Alternatively, the tumor tissue sample is first sectioned and then the individual sections are fixed.
In some preferred embodiments, FFPE tissue sections of about 3 to 5 microns, and preferably 4 or 5 microns, mounted on microscope slides and dried are used to determine biomarker expression scores for tumors.
Diagnostic test for IFN-gamma gene signature score and/or PD-L1 status
In one embodiment, the tumor sample tested is from a tumor associated with a low or negative PD-L1 status and/or a negative IFN γ gene signature and optionally less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2CD8+ T cell infiltration density-related cancers for the sample (or/1 mL sample), including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell cancer, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, or pancreatic cancer.
In another embodiment, the tumor sample tested is from a cancer that is responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or antigen binding fragment thereof)), which may optionally be with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2The CD8+ T cell infiltration density, low or negative PD-L1 status, and negative IFN γ gene signature of the sample (or/1 mL sample) are correlated, including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal black)Melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer, nasopharyngeal cancer, thyroid cancer, salivary gland cancer, esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular cancer, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma.
Once a suitable tumor tissue sample is obtained, it can be analyzed to quantify the level of expression of each of the genes comprising the particular IFN- γ gene signature to be scored (e.g., one or any combination of IFN γ, STAT1, CCR5, CXCL9, PRF1, HLA-DRA, CXCL10, CXCL11, ID01, and GZMA), or the mRNA level of PD-L1. The phrase "determining the expression level of a gene" as used herein refers to the detection and quantification of RNA transcribed from the gene or protein translated from such RNA. The term "RNA transcript" includes mRNA transcribed from a gene, and/or specific splice variants thereof, and/or fragments of such mRNA and splice variants. In some preferred embodiments, the RNA transcript for which expression is measured is the transcript in figure 11 and/or the PD-L1 transcript.
One skilled in the art will appreciate that many methods can be used to isolate RNA from a tissue sample for analysis. For example, RNA can be isolated from frozen tissue samples by homogenization in guanidinium isothiocyanate and acidic phenol-chloroform extraction. Commercial kits are available for isolating RNA from FFPE samples.
The skilled artisan is also aware of several methods that can be used to detect and quantify the level of RNA transcripts in isolated RNA or whole cell lysates. Quantitative detection methods include, but are not limited to: arrays (i.e., microarrays), quantitative real-time PCR (RT-PCR), multiplex assays, nuclease protection assays, and Northern blot analysis. Generally, such methods use labeled probes that are complementary to a portion of each transcript to be detected. Probes for these methods can be readily designed based on the known sequence of the gene and the transcript expressed thereby. In some preferred embodiments, the probes are designed to hybridize to each of the gene signature transcripts identified in FIG. 11. Suitable labels for the probes are well known and include, for example, fluorescent labels, chemiluminescent labels and radioactive labels.
In some embodiments, the real-time detection and quantification of RNA levels using Nucleic Acid Sequence Based Amplification (NASBA) in combination with molecular beacon detection molecules is employed for gene characterization tumor samples of the invention. NASBA is described, for example, in comptonj, Nature 350 (6313): 91-92 (1991). NASBA is a single-step isothermal RNA-specific amplification method. Generally, the method comprises the steps of: providing an RNA template to the reaction mixture, wherein the first primer is attached to its complementary site at the 3' end of the template; reverse transcriptase synthesizes the opposite complementary DNA strands; rnase H destroys the RNA template (rnase H only destroys RNA in RNA-DNA hybrids, but does not destroy single-stranded RNA); the second primer is attached to the 3' end of the DNA strand and the reverse transcriptase synthesizes a second DNA strand; and T7 RNA polymerase binds to double stranded DNA and produces a complementary RNA strand that can be reused in
In other embodiments, the assay format is a flap endonuclease (flap endonuclease) -based format, such as an InvaderTMAssay (Third Wave Technologies). In the case of using the invader method, an invader probe comprising a sequence specific to a region 3 'to the target site, and an initial probe (primaryprobe) comprising a sequence specific to a region 5' to the target site of the template and an unrelated flanking sequence (flap sequence) are prepared. The lyase is then allowed to act in the presence of these probes, the target molecule, and a FRET probe comprising a sequence complementary to the flanking sequence and an auto-complementary sequence labeled with both a fluorescent dye and a quencher. When the initial probe is hybridized to the template, the 3' end of the invader probe penetrates the target site and the structure is cleaved by the lyase, resulting in dissociation of the flap. The flap binds to the FRET probe and the fluorescent dye moiety is cleaved by the cleaving enzyme, resulting in emission of fluorescence.
In othersIn embodiments, the assay format employs direct mRNA capture with branched DNA (QuantiGene)TMPanomics) or Hybrid CaptureTM(Digene)。
An example of an array technique suitable for measuring the expression of genes in IFN- γ gene profiles or for measuring the expression of PD-L1 is ArrayPlateTMAssay techniques, marketed by HTG Molecular, Tucson AZ. and described in Martel, r.r., et al, Assay and Drug Development Technologies 1 (1): 61-71, 2002. Briefly, this technique combines a nuclease protection assay with array detection. Nuclease protection assays were performed on cells in microplate wells. The cells are lysed in the presence of a probe that binds to the targeted mRNA species. After addition of S1 nuclease, excess probe and unhybridized mRNA were degraded, leaving only mRNA: a probe duplex. Basic hydrolysis destroys the mRNA component of the duplex, leaving the probe intact. After addition of the neutralization solution, the contents of the treated cell culture plate are transferred to another ArrayPlateTMIt is called a programmed ArrayPlateTM。ArrayPlateTMA16-element array (16-element array) was included at the bottom of each well. Each array unit comprises position-specific anchor oligonucleotides, which remain the same between assays. The binding specificity of each of the 16 anchors is modified with an oligonucleotide, called a programming adapter oligonucleotide, which is complementary to the anchor at one end and to the nuclease protection probe at the other end. During the hybridization reaction, the probes transferred from the culture plate are captured by the immobilized programming linker. The captured probes are labeled by hybridization with a detector adapter oligonucleotide, which is in turn labeled with a detection conjugate that incorporates peroxidase. A chemiluminescent substrate is supplied to the enzyme and light produced by the enzyme is captured in a digital image. The light intensity at the array element is a measure of the amount of the corresponding target mRNA present in the original cell.
As another example, DNA microarrays can be used to measure gene expression. Briefly, DNA microarrays (also called DNA chips) are microscopic arrays of DNA fragments (e.g., synthetic oligonucleotides) disposed in a defined pattern on a solid support, where they can be analyzed by standard hybridization methods (see Schena, BioEssays 18: 427 (1996)). Exemplary microarrays and methods of making and using the same are described in t.r. hughes et al, Nature Biotechnology 9: 342-347 (2001). Many different microarray configurations and methods of their production are known to those skilled in the art and are disclosed in the following: U.S. patent nos. 5,242,974; 5,384,261; 5,405,783; 5,412,087; 5,424,186; 5,429,807, respectively; 5,436,327, respectively; 5,445,934; 5,556,752, respectively; 5,405,783; 5,412,087; 5,424,186; 5,429,807, respectively; 5,436,327, respectively; 5,472,672, respectively; 5,527,681, respectively; 5,529,756, respectively; 5,545,531, respectively; 5,554,501, respectively; 5,561,071, respectively; 5,571,639, respectively; 5,593,839; 5,624,711, respectively; 5,700,637, respectively; 5,744,305; 5,770,456, respectively; 5,770,722, respectively; 5,837,832; 5,856,101, respectively; 5,874,219; 5,885,837, respectively; 5,919,523, respectively; 6,022,963; 6,077,674, respectively; and U.S. Pat. Nos. 6,156,501; shena, et al, Tibtech 6: 301-306, 1998; duggan, et al, nat. genet.2: 10-14, 1999; bowtell, et al, nat. genet.21: 25-32, 1999; lipshutz, et al, nat. genet.21: 20-24, 1999; blanchard, et al, Biosensors and Bioelectronics 77: 687-90, 1996; maskos, et al, Nucleic Acids Res.2: 4663-69, 1993; and Hughes, et al, nat. biotechnol.79: 342-347, 2001. Patents describing methods of using arrays in a variety of applications include: U.S. Pat. Nos. 5,143,854; 5,288,644, respectively; 5,324,633, respectively; 5,432,049, respectively; 5,470,710, respectively; 5,492,806, respectively; 5,503,980, respectively; 5,510,270, respectively; 5,525,464, respectively; 5,547,839, respectively; 5,580,732, respectively; 5,661,028, respectively; 5,848,659, respectively; and 5,874,219; the disclosure of which is incorporated herein by reference in its entirety for all purposes.
In one embodiment, the array of oligonucleotides may be synthesized on a solid support. Exemplary solid supports include glass, plastic, polymer, metal, metalloid, ceramic, organic, and the like. Using chip masking techniques and photo-protection chemistry, ordered arrays of nucleic acid probes can be generated. These arrays (which are known, for example, as "DNA chips" or very large-scale immobilized polymer arrays: (
To compare expression levels, labeled nucleic acids can be contacted with the array under conditions sufficient for binding between the target nucleic acids and the probes on the array. In one embodiment, hybridization conditions can be selected to provide a desired level of hybridization specificity; i.e., conditions sufficient for hybridization to occur between the labeled nucleic acids and the probes on the microarray.
Hybridization can be performed under conditions that allow for substantially specific hybridization. The length and GC content of the nucleic acid will determine the thermal melting point and thus the hybridization conditions necessary to obtain specific hybridization of the probe to the target nucleic acid. These factors are well known to those skilled in the art and can also be tested in assays. Extensive guidance to Nucleic Acid Hybridization can be found in Tijssen, et al (Laboratory Techniques in Biochemistry and Molecular Biology, Vol.24: Hybridization With Nucleic Acid Probes, P.Tijssen, ed.; Elsevier, N.Y. (1993)). The above methods will result in a hybridization pattern of labeled target nucleic acids on the array surface. The resulting hybridization pattern of labeled nucleic acids can be visualized or detected in a variety of ways, with the particular mode of detection being selected based on the particular label of the target nucleic acid. Representative detection methods include scintillation counting, autoradiography, fluorescence measurements, calorimetric measurements, light emission measurements, light scattering, and the like.
One such detection method utilizes a commercially available array scanner (Affymetrix, Santa Clara, CA), for example,
One preferred assay method for measuring the abundance of biomarker transcripts comprises the use of
The absolute expression of each gene in the tumor sample is compared to a control when measuring the expression of the genes in the IFN- γ gene signature or to determine the PD-L1 status as described herein. For example, the control may be the average expression level of each gene in the subject pool. However, in order to improve the sensitivity of comparison, the expression level values are preferably converted in various ways.
For example, the expression level of each gene in a gene signature can be normalized by the average expression level of all genes or the total expression level of all genes determining the expression level, or by the average expression level of a set of control genes. Thus, in one embodiment, the genes are represented by a set of genes, and the expression level of each gene is normalized by the average or median expression level of all genes represented (including any genes that are not part of the gene signature of interest). In one embodiment, normalization is performed by dividing by the median or average expression level of all genes on the microarray. In another embodiment, the expression level of the signature gene is normalized by the mean or median expression level of a set of control genes. In a specific embodiment, the control gene comprises a housekeeping gene. In another embodiment, normalization is accomplished by dividing by the median or average expression level of the control gene.
The sensitivity of the gene signature scoring will also be improved if the expression level of an individual gene in the gene signature is compared to the expression of the same gene in a pool of tumor samples. Preferably, the comparison is to the mean or median expression level of each signature gene in the sample pool. Such comparison may be achieved, for example, by dividing the expression level of each gene in the subject sample of interest by the average or median expression level of each gene of the library. This has the effect of highlighting the relative differences in expression between the genes in the sample and the genes in the pool as a whole, making it more sensitive and more likely to produce meaningful results than using absolute expression levels alone. The expression level data may be converted in any convenient manner. Preferably, the expression level data for all genes is logarithmically transformed before taking the mean or median value.
In performing the comparison with the library, two methods may be used. First, the expression levels of characteristic genes in a sample can be compared to the expression levels of those genes in a library, where nucleic acids from the sample and nucleic acids from the library hybridize during the course of a single experiment. Such methods require the generation of a new nucleic acid pool for each comparison or a limited number of comparisons and are therefore limited by the amount of nucleic acid available. Alternatively and preferably, the expression levels in the library, whether normalized and/or transformed, are stored on a computer or computer readable medium for comparison with individual expression level data (i.e., single channel data) from the sample.
When a tumor sample from a subject is compared to a standard or control, the expression value of a particular gene in the sample is compared to the expression value of that gene in the standard or control. For each gene in the gene signature of the invention, a log is generated for expression values in a single sample relative to a standard or control10A ratio. The score for IFN- γ gene signature or PD-L1expression was calculated by determining the mean log (10) ratio of the genes in the signature. A sample is considered positive for an IFN- γ gene signature biomarker if the gene signature score of the test sample is above a predetermined threshold for the gene signature. In one embodiment of the invention, the predetermined threshold is set at any value from 2.17 to 2.69 (i.e., 2.18, 2.19, 2.20 … 2.66, 2.67, 2.68). The predetermined threshold may also be the mean, median or percentile of the scores of the gene signature in the sample set or pooled samples used as standards or controls.
One skilled in the art will recognize that other differential expression values besides log (10) ratios may be used to calculate the feature score, so long as the value represents an objective measure of transcript abundance of the gene. Some examples include, but are not limited to: xdev, error weighted log (ratio), and mean minus log (intensity).
In a preferred embodiment, the raw expression values are normalized by performing quantile normalization with respect to a reference distribution and subsequent log 10-transformation. When in use bySold by NanoStringtechnologies
In some preferred embodiments, the reference distribution is generated from raw expression counts for a normalized set of genes consisting essentially of each gene in the set of 400 genes listed in fig. 11, or a subset thereof. The subset may consist of at least any of 25, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, or any integer from 25 to 400.
Obtaining a tissue sample, preparing one or more tissue sections therefrom for each of the steps of gene signature biomarker determination, performing the determination, and scoring the results may be performed by an independent individual/entity at an independent location. For example, a surgeon may obtain a tissue sample from a tumor of a cancer patient by biopsy and then send the tissue sample to a pathology laboratory, which may fix the tissue sample and then prepare one or more slides (each with a single tissue section) for assay. The slides may be assayed shortly after preparation or stored for future assays. The laboratory that prepared the tissue sections can perform the assays or the slides can be sent to a different laboratory for the assays. A pathologist or trained professional scoring the slides for IFN- γ gene signature may be a diagnostic laboratory task, or may be an independent contractor. Alternatively, a diagnostic laboratory obtains a tissue sample from the subject's physician or surgeon and then performs all of the steps involved in preparing a tissue section, assaying a slide, and calculating a genetic signature score for the tissue section.
In some embodiments, the individual involved in preparing the tissue section and determining its genetic signature biomarkers is not aware of the identity of the subject the sample is being tested for; that is, samples received by a laboratory are processed anonymously in some manner before being sent to the laboratory. For example, the sample may be identified by a number or some other code ("sample ID") alone, and the result of the assay reported to the party requiring the test using the sample ID. In some preferred embodiments, the association between the identity of the subject and the tissue sample of the subject is known only to the individual or to the individual's physician.
In some embodiments, after test results have been obtained, the diagnostic laboratory generates a test report, which may include either or both of the following results: the tissue sample is positive or negative for the biomarker, the gene signature score for the tumor sample, and a reference score for the gene signature. The test report may also contain a list of genes whose expression was analyzed in the assay.
In other embodiments, the test report may further comprise guidance on how to interpret the results for predicting whether the subject is likely to respond to pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof/talilavine combination therapy. For example, in one embodiment, the tumor sample tested is from a cancer, including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell cancer, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, or pancreatic cancer, and having a negative IFN- γ gene signature score and/or a low or negative PD-L1 status score, the test report may indicate that the subject has a score that is responsive or better correlated with treatment with pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof/taliravir combination therapy, whereas if the CD8+ T cell density score and/or IFN- γ gene signature score is above a threshold, and/or the PD-L1 status score is high, the test report indicates that the patient has a score associated with no response or poor response to treatment with pembrolizumab, pembrolizumab variants, and/or antigen binding fragments thereof/talilavine combination therapy.
In another embodiment, the tumor sample tested is from a cancer that is responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or antigen binding fragment thereof)), which may optionally be with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2The CD8+ T cell infiltration density, low or negative PD-L1 status, and negative IFN γ gene signature of the sample (or/1 mL sample) are correlated, including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer, nasopharyngeal cancer, thyroid cancer, salivary gland cancer, esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular carcinoma, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma.
In some embodiments, the test report is a written file prepared by a diagnostic laboratory and sent to the patient or the patient's physician as a hard copy or by email. In other embodiments, the test report is generated by a computer program and displayed on a video monitor at the doctor's office. The test report may also include an authorized employee who verbally communicates the test results directly to the patient or to the patient's doctor or doctor's office. Similarly, the test report may include a record of the test results made by the physician in the patient file.
Detection of the presence or absence of a marker of the invention may be carried out using kits specifically designed for this purpose. In one embodiment, the kit comprises a set of oligonucleotide probes capable of hybridizing to a target transcript in a gene signature. The kit may also comprise oligonucleotide probes capable of detecting transcripts of other genes, such as control genes or genes for normalization purposes. The set of oligonucleotide probes can comprise an ordered array of oligonucleotides on a solid surface, such as a microchip, silica beads (e.g., the bead array technology from Illumina, San Diego, Calif) or a glass slide (see, e.g., WO 98/20020 and WO 98/20019). In some embodiments, the oligonucleotide probes are provided in one or more compositions in liquid or dry form.
Immunohistochemistry (IHC)
IHC assays generally begin with antigen retrieval (antigen retrieval), which can vary in reagents and methods. The antigen retrieval process may involve pressure cooking, protease treatment, microwave treatment, or heating of tissue sections in a bath of a suitable buffer, with the standard goal of exposing antigens hidden by formalin crosslinking or other fixation. (see, e.g., Leong et al. appl. Immunohistochem.4 (3): 201 (1996))
Two general IHC methods can be used: direct assay and indirect assay. In the direct IHC assay, the binding of the antibody to the target antigen is determined directly. This direct assay uses a labeled reagent, such as a fluorescent label or an enzyme-labeled primary antibody, which can be visualized without further antibody interaction. In a typical indirect assay, unconjugated primary antibody binds to the antigen, and subsequently a labeled secondary antibody binds to the primary antibody. When the secondary antibody is conjugated to an enzyme label, a chromogenic or fluorogenic substrate is added to provide visualization of the antigen. Signal amplification occurs because several secondary antibodies can react with different epitopes on the primary antibody.
The primary and/or secondary antibodies used for immunohistochemistry will typically be labeled with a detectable moiety. Many markers are available, which can be generally classified into the following categories: (a) Radioisotopes, e.g.35S、14C、131I、3H and123i (antibodies can be labeled with radioisotopes using techniques such as those described in Current Protocols in Immunology,
A variety of enzyme-substrate labels are available (see U.S. Pat. No.4,275,149). Enzymes typically catalyze chemical alteration of a chromogenic substrate, which can be measured using a variety of techniques. For example, the enzyme may catalyze a color change in the substrate, which can be measured spectrophotometrically. Alternatively, the enzyme may alter the fluorescence or chemiluminescence of the substrate. Techniques for quantifying changes in fluorescence are described above. The chemiluminescent substrate becomes electronically excited by a chemical reaction and can then emit measurable light (e.g., using a chemiluminometer) or contribute energy to a fluorogenic receptor.
Some examples of enzyme labels include: luciferases (e.g., firefly and bacterial luciferases; U.S. Pat. No.4,737,456), luciferin, 2, 3-dihydrophthalazinediones, malate dehydrogenase, urease, peroxidase (e.g., horseradish peroxidase (HRPO)), alkaline phosphatase, beta-galactosidase, glucoamylase, lysozyme, carbohydrate oxidases (e.g., glucose oxidase, galactose oxidase, and glucose-6-phosphate dehydrogenase), heterocyclic oxidases (e.g., uricase and xanthine oxidase), lactoperoxidase, microperoxidase, and the like. Techniques for conjugating enzymes to antibodies are described in O' sublivan et al, Methods for the Preparation of Enzyme-Antibody Conjugates for use in Enzyme Immunoassay, Methods in Enzyme, (edj. langbne & h. van vunaks), Academic press, New York, 73: 147, 166 (1981).
Many enzyme-substrate combinations are available to those skilled in the art. For a general review of these, see U.S. Pat. Nos. 4,275,149 and 4,318,980. Some examples of enzyme-substrate combinations are: (i) horseradish peroxidase (HRP) and catalase as substrates, wherein the catalase oxidizes dye precursors such as: 3, 3' Diaminobenzidine (DAB), which produces a brown end product; 3-amino-9-ethylcarbazole (AEC), which forms a rose-red end product after oxidation; 4-chloro-1-naphthol (CN), which precipitates as a blue end product; and p-phenylenediamine dihydrochloride/catechol, which yields a bluish-black product; ortho-phenylene diamine (OPD) and 3, 3 ', 5, 5' -tetramethylbenzidine hydrochloride (TMB); (ii) alkaline Phosphatase (AP) with p-nitrophenyl phosphate, naphthol AS-MX phosphate, Fast Red TR and Fast Blue BB, naphthol AS-BI phosphate, naphthol AS-TR phosphate, 5-bromo-4-chloro-3-indolyl phosphate (5-bromo-4-chloro-3-indoxyl phosphate, BCIP), Fast Red LB, Fast GarnetGBC, nitroblue Tetrazolium (NBT), and iodonitrotetrazolium violet (INT); and (iii) β -D-galactosidase (β -D-Gal) with either a chromogenic substrate (e.g., P-nitrophenyl-P-D-galactosidase) or a fluorescent substrate (e.g., 4-methylumbelliferyl-P-D-galactosidase).
Any method known in the art for conjugating antibody molecules to various moieties can be used, including Hunter, et al, (1962) Nature 144: 945; david, et al, (1974) Biochemistry 13: 1014; pain, et al, (1981) j.immunol.meth.40: 219; and Nygren, j., (1982) histochem.andcechem.30: 407, respectively.
In some embodiments, the label is indirectly conjugated to the antibody. The skilled person will be aware of a number of techniques for achieving this. For example, the antibody may be conjugated to biotin and any of the four broad classes of labels described above may be conjugated to avidin, or vice versa. Biotin binds selectively to avidin and thus, the label can be conjugated to the antibody in this indirect manner. Alternatively, to achieve indirect conjugation of the label to the antibody, the antibody is conjugated to a small hapten and one of the different types of labels described above is conjugated to an anti-hapten antibody. Thus, indirect conjugation of the label to the antibody can be achieved.
Following the antigen retrieval and optional blocking steps, the tissue sections are exposed to pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof as a primary antibody for a sufficient time and under suitable conditions to allow the primary antibody to bind to PD-L1 protein in the tissue sections. Suitable conditions for achieving this can be determined by routine experimentation. The slides were then washed to remove unbound and excess primary antibody.
In some embodiments, the primary antibody is linked to a detectable label, such as a paramagnetic ion, radioisotope, fluorescent pigment, and the like, and the slide is evaluated for PD-L1 staining using a suitable imaging device.
In other embodiments, an immune complex between PD-L1 and a primary antibody can be detected using a second binding agent linked to a detectable label. The second binding agent is preferably a secondary antibody that is applied to the slide at a concentration and for a time sufficient to allow formation of a second immune complex. The slide is then typically washed to remove any non-specifically bound secondary antibodies and to detect the label in the secondary immune complexes.
The secondary antibody may be labeled with avidin, streptavidin, or biotin, which is independently labeled with a detectable moiety, such as a fluorescent dye (stain), luminescent dye, or non-fluorescent dye. In principle, any enzyme may be used which may be conjugated to the secondary antibody or which may indirectly bind thereto (e.g. via conjugated avidin, streptavidin, biotin). The enzyme used may be, for example, Alkaline Phosphatase (AP), horseradish peroxidase (HRP), beta-galactosidase and/or glucose oxidase. The enzyme may also be directed to catalyze a luminescent reaction of a substrate, such as, but not limited to luciferase and aequorin, which has a substantially insoluble reaction product capable of luminescence or capable of directing a second reaction of a second substrate, such as, but not limited to, luciferin and ATP, or coelenterazine and Ca2+It has a luminescent product. Finally, a detection reagent is applied, which includes a chromogen (chromogen) or a fluorescently labeled molecule to visualize the localization of the immune complex.
IHC assays can be performed using an automated pathology system, which may include automated staining (conventional staining, histochemical techniques, immunostaining machines (immunostainers)); an automated in situ hybridization system; automatic slide preparation (coverslip, slide drying) and integrated slide and cassette labeling, as described in Roja et al, Review of imaging solutions for integrated, quantitative immunological in the Pathology study, Folia histochemistry et Cytobiologica, Vol.47, No. 3, 349-354, 2009.
In certain exemplary embodiments, the IHC assay employs a commercially available Dako EnVisionTMFLEX detection system, which is intended for use with Dako automated stainers (Dako, Agilent Technologies Company, Glostrup, Denmark). These agents can be supplied off-the-shelf for other automatic dyeing machines or for dyeing performed manually (without automatic dyeing machines).
Sample Collection and preparation of tissue sections
Tumor tissue samples for preparing stained tissue sections to score PD-L1expression may be collected from a subject before and/or after exposure of the subject to one or more therapeutic agents (e.g., pembrolizumab variants and/or antigen-binding fragments thereof, talilavine, and/or chemotherapeutic agents). Thus, a tumor sample may be collected from a subject over a period of time. Tumor samples can be obtained by a variety of methods including, but not limited to, surgical resection, aspiration, or biopsy. Tissue samples can be sectioned and examined as fresh specimens for PD-L1. In other embodiments, the tissue sample is frozen for further sectioning. In other embodiments, the tissue sample is preserved by fixing and embedding in paraffin or the like.
The tissue sample may be fixed by conventional methods, wherein the length of fixation depends on the size of the tissue sample and the fixative used. Neutral buffered formalin, glutaraldehyde, bubon's fixative or paraformaldehyde are some non-limiting examples of fixatives. In some preferred embodiments, the tissue sample is fixed with formalin. In some embodiments, the fixed tissue sample is also embedded in paraffin to prepare a Formalin Fixed and Paraffin Embedded (FFPE) tissue sample. Some examples of paraffin waxes include, but are not limited to, Paraplast, Broloid, and tissue.
Generally, tissue samples are fixed and dehydrated through a series of gradient alcohols, infiltrated with paraffin or other sectioning media and embedded so that the tissue sample can be sectioned. Alternatively, the tumor tissue sample is first sectioned and then the individual sections are fixed.
In some embodiments, the scoring process of the present invention is performed on FFPE tissue sections of about 3 to 4mm and preferably 4 microns that are mounted on microscope slides and dried.
Pembrolizumab and pembrolizumab variant antibodies
The primary antibody described herein for use in IHC assays is pembrolizumab, a pembrolizumab variant, and/or an antigen-binding fragment thereof, which binds to the mature form of PD-L1 (lacking a pre-secretory leader sequence, also known as a leader peptide) expressed on the surface of certain mammalian cells. The terms "PD-L1" and "mature PD-L1" are used interchangeably herein and are understood to mean the same molecule unless otherwise indicated or apparent from the context. Anti-human PD-L1 antibody or anti-hPD-L1 antibody as used herein refers to an antibody that specifically binds to mature human PD-L1, e.g., pembrolizumab variants, and/or antigen-binding fragments thereof. The mature human PD-L1 molecule consists of amino acids 19 to 290 of the following sequence:
an antibody that "specifically binds to human PD-L1" or an antibody that "specifically binds to a polypeptide comprising the amino acid sequence of human PD-L1" is an antibody that exhibits preferential binding to human PD-L1 over other antigens, but such specificity does not require absolute binding specificity. An anti-hPD-L1 antibody is considered "specific" for human PD-L1 if the binding of the anti-hPD-L1 antibody determines the presence of human PD-L1 in the sample, e.g., in cases that do not produce an undesirable result (e.g., a false positive in an IHC diagnostic assay). An antibody or binding fragment thereof that can be used as a primary antibody in the processes and methods of the invention will bind to human PD-L1 with an affinity that is at least 2-fold higher, preferably at least 10-fold higher, more preferably at least 20-fold higher, and most preferably at least 100-fold higher than the affinity for any non-PD-L1 protein. As used herein, an antibody is considered to specifically bind to a polypeptide comprising a given sequence (e.g., mature human PD-L1) if it binds to the polypeptide but does not bind to a protein lacking that sequence. Tissue sections from tumor samples from human subjects may be scored for PD-L1expression using pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof.
Diagnostic test for PD-L1expression
In one embodiment, the tumor sample tested is from a low or negative PD-L1 state and optionally less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2CD8+ T cell infiltration density and/or low or negative PD-L1 state-related cancers of the sample (or/1 mL sample) and are from melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), colorectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell carcinoma, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, or pancreatic cancer.
In another embodiment, the tumor sample being tested is responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or an antigen-binding fragment thereof)) and may optionally be less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2The CD8+ T cell infiltration density, low or negative PD-L1 status, and negative IFN γ gene signature of the sample (or/1 mL sample) are correlated, including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma, nasopharyngeal carcinoma, thyroid carcinoma, salivary gland carcinoma, esophageal carcinoma), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urinary bladder cancer)Epithelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular cancer, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma.
The steps of obtaining a tissue sample, preparing one or more tissue sections therefrom for IHC determination, performing IHC staining, and scoring the results may be performed by separate individuals/entities at the same or separate locations. For example, a surgeon may obtain a tissue sample from a tumor of a cancer patient by biopsy and then send the tissue sample to a pathology laboratory that may fix the tissue sample and then prepare one or more slides (each with a single tissue section) for IHC determination. Slides may be analyzed by IHC shortly after preparation or stored for future assays. The laboratory that prepares the tissue sections for the IHC assay may perform the assay or send the slides to a different laboratory for assay. A pathologist or trained professional scoring a stained slide for PD-L1 staining may be a diagnostic laboratory task, or may be an independent contractor. Alternatively, a diagnostic laboratory obtains a tissue sample from the subject's doctor or surgeon and then performs all of the steps involved in preparing a tissue section, staining the slide, and scoring PD-L1expression in the stained tissue section or sending the stained slide to a trained professional for PD-L1 scoring.
In some embodiments, the individuals involved in preparing tissue sections and analyzing them by IHC assays are unaware of the identity of the subject the sample is being tested for, i.e., the sample received at the laboratory is treated in some way anonymously before being sent to the laboratory. For example, the sample may be identified by a number or some other code ("sample ID") only, and the result of the IHC assay reported to the party requiring the test using the sample ID. In some preferred embodiments, the association between the identity of the subject and the tissue sample of the subject is known only to the individual or to the individual's physician.
In some embodiments, after the test results have been obtained, the diagnostic laboratory generates a test report that may include the results of the tissue sample being positive or negative for PD-L1 expression. The test report may also include guidance on how to interpret the results for predicting whether the subject is likely to respond to pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof/talilavine combination therapy. For example, in one embodiment, the test report may indicate that the patient has a PD-L1expression score that correlates with a response or better response to treatment with pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof/talilavine combination therapy if the patient's tumor is below a pre-specified threshold, and a PD-L1expression score that correlates with no response or poor response to treatment with pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof/talilavine combination therapy if the PD-L1expression score is at or above the pre-specified threshold.
In some embodiments, the test report is a written file prepared by a diagnostic laboratory and sent to the patient or the patient's physician as a hard copy or by email. In other embodiments, the test report is generated by a computer program and displayed on a video monitor at the doctor's office. The test report may also include direct verbal delivery of the test results to the patient or to the patient's doctor or to an authorized employee in the doctor's office. Similarly, the test report may include a record of the test results made by the physician in the patient file.
Method for quantifying lymphocytes
Flow cytometry
Lymphocyte subpopulations are typically measured by immunofluorescent labeling of cells with fluorochromes conjugated with specific monoclonal antibodies and quantifying the proportion of specifically labeled cells by flow cytometry. Manual alternatives to flow cytometry can also be used to quantify CD4 cells. They are simple light or fluorescence microscopy methods that require only cell counting.
In flow cytometry, specific monoclonal antibodies prepared against specific CD antigens present on cells are labeled with fluorescent dyes. Labeled monoclonal antibodies are reacted with mononuclear cells (lymphocytes and monocytes), and the reacted cells can be classified into subpopulations by flow cytometry depending on which antibody they bind. Flow cytometry typically gives the percentage of CD4+ or CD8+ cells. To obtain absolute cell counts, a dual platform technique and a single platform technique were used. The dual platform technology employs a flow cytometer and a hematology analyzer. The absolute count of CD4 using the dual platform method is the product of three measurements: white blood cell count, percentage of white blood cell count as lymphocytes (difference), and percentage of lymphocytes as CD4 cells (determined by flow cytometry). If a single platform technique is used, the absolute count of lymphocyte subpopulations is measured in a single tube by a single instrument. This is usually done by spiking a fixed volume of sample with a known number of fluorescent beads (bead-based systems) or by accurately recording the volume of sample analyzed. Recent proposals indicate that the single platform technology should be the gold standard for absolute counts of
Several flow cytometers are available, of which facscalibur (becton dickinson) and EPICS XL (Beckman Coulter) are the most popular. These instruments provide high sample throughput, automated workflow management and simple software applications. Both instruments can detect four colors and measure relative cell size and cell complexity. The system is designed to use whole blood collected in liquid EDTA. In addition to using traditional flow cytometers (open platforms that can employ dual platform or single platform technology), a simplified proprietary platform for CD4+ T cell counting was developed. Commercially available proprietary platforms include FACSCount (Becton Dickinson), CyFLow Counter (Partec), and Guava Auto CD4/
Artificial method for quantifying lymphocytes
Manual alternatives to flow cytometry available on the market are: Cyto-Spheres (Coulter corporation, USA) and Dynabeads (Dynal AS, Norway). Dynal T4 kit (Dynabeads) was used to manually count CD4 cells under a microscope in a cell counting chamber. The method measures the absolute count of
It will be apparent to those skilled in the art that other suitable modifications and adaptations to the methods described herein may be made using suitable equivalents without departing from the scope of the embodiments disclosed herein. Having now described certain embodiments in detail, these embodiments will be more clearly understood by reference to the following examples, which are included merely for purposes of illustration and are not intended to be limiting.
Diagnostic test for CD8+ expression
In one embodiment, the tumor sample tested is from less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2Cancers associated with CD8+ T cell infiltration density of the sample (or/1 mL sample), optionally with low or negative PD-L1 status and/or negative IFN γ gene signature, include but are not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), non-small cell lung cancer, head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell carcinoma), nodulesRectal cancer, breast cancer (e.g., HER2+ breast cancer, HER2- (HR +) breast cancer, triple negative breast cancer), ovarian cancer, bladder cancer (e.g., transitional cell carcinoma, urothelial cancer), prostate cancer (e.g., castration-resistant prostate cancer), sarcoma (e.g., soft tissue sarcoma, osteosarcoma), renal cell carcinoma, gastric cancer, esophageal cancer, anal canal cancer, biliary tract cancer, or pancreatic cancer.
In one embodiment, the tumor sample tested is from a cancer that is responsive to monotherapy with a checkpoint inhibitor (e.g., with anti-PD-L1 therapy or anti-PD-1 therapy (e.g., pembrolizumab variant, or antigen-binding fragment thereof)), which may optionally be with less than about 1500, about 1400, about 1300, about 1200, about 1100, about 1000, about 900, about 800, about 700, about 600, or about 500 cells/1 mm2The CD8+ T cell infiltration density, low or negative PD-L1 status, and negative IFN γ gene signature of the sample (or/1 mL sample) are correlated, including but not limited to: melanoma (e.g., cutaneous melanoma, metastatic melanoma, uveal melanoma), lung cancer (e.g., non-small cell lung cancer, small cell lung cancer), head and neck cancer (e.g., recurrent or metastatic head and neck squamous cell cancer, nasopharyngeal cancer, thyroid cancer, salivary gland cancer, esophageal cancer), breast cancer (e.g., ER +/HER 2-breast cancer, triple negative breast cancer), ovarian cancer, cervical cancer, bladder cancer (e.g., urothelial cancer), renal cell cancer, gastrointestinal cancer (e.g., hepatocellular carcinoma, colorectal cancer, anal cancer), biliary tract cancer, multiple myeloma, lymphoma (e.g., mediastinal large B-cell lymphoma, hodgkin's lymphoma), or mesothelioma.
Each of the steps of obtaining a sample, preparing a sample for flow cytometry, performing flow cytometry, and scoring the results may be performed by separate individuals/entities at the same or separate locations. For example, a surgeon may obtain a sample from a cancer patient by biopsy and then send the sample to a pathology laboratory, which may prepare the sample for flow cytometry. Slides may be analyzed by IHC shortly after preparation or stored for future assays. The laboratory that prepares the sample for flow cytometry can perform the assay or send the slide to a different laboratory for assaying. A pathologist or trained professional performing flow cytometry may be a diagnostic laboratory work, or may be an independent contractor. Alternatively, a diagnostic laboratory obtains a sample from the subject's doctor or surgeon and then performs all of the steps involved in preparing the sample and scoring CD8+ in the sample or sending the sample to a trained professional for CD8+ scoring.
In some embodiments, the individuals involved in preparing the sample and analyzing it by flow cytometry are unaware of the identity of the subject the sample is being tested for, i.e., the sample received by the laboratory is treated in some way anonymously before being sent to the laboratory. For example, the sample may be identified by a number or some other code ("sample ID") alone, and the sample ID used to report the results of the flow cytometry assay to the party requiring the test. In some preferred embodiments, the association between the identity of the subject and the tissue sample of the subject is known only to the individual or to the individual's physician.
In some embodiments, after test results have been obtained, the diagnostic laboratory generates a test report that may include guidance on how to interpret the results for predicting whether the subject is likely to respond to pembrolizumab, pembrolizumab variants, and/or antigen-binding fragments thereof/talilavine combination therapy. For example, in one embodiment, if the patient's tumor is below a pre-specified threshold, the test report may indicate that the patient has a CD8+ expression score that correlates with a response or better response to treatment with pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof/talilavine combination therapy, while if the CD8+ expression score is at or above the pre-specified threshold, the CD8+ expression score correlates with no response or poor response to treatment with pembrolizumab, pembrolizumab variant, and/or antigen-binding fragment thereof/talilavine combination therapy.
In some embodiments, the test report is a written file prepared by a diagnostic laboratory and sent to the patient or the patient's physician as a hard copy or by email. In other embodiments, the test report is generated by a computer program and displayed on a video monitor at the doctor's office. The test report may also include an authorized employee who verbally communicates the test results directly to the patient or to the patient's doctor or doctor's office. Similarly, the test report may contain a record of the test results made by the physician in the patient file.
It will be apparent to those skilled in the art that other suitable modifications and adaptations to the methods described herein may be made using suitable equivalents without departing from the scope of the embodiments disclosed herein. Having now described certain embodiments in detail, these embodiments will be more clearly understood by reference to the following examples, which are included merely for purposes of illustration and are not intended to be limiting. All patents, patent applications, and references described herein are incorporated by reference in their entirety for all purposes.
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