Immune biomarkers and assays predictive of clinical response to immunotherapy for cancer

1. A method of identifying and treating a subject with non-small cell lung cancer (NSCLC) comprising a (sex determining region Y)-box 2-positive (SOX2-positive) T-cell, the method comprising:

assaying a reaction system comprising a biological sample from the NSCLC subject, wherein the biological sample comprises a T cell from the subject, and a set of overlapping peptides that span a SOX2 protein region selected from the group consisting of: (a) amino acids 1-89 of SEQ ID NO:134; (b) amino acids 79-171 of SEQ ID NO:134; (c) amino acids 161-246 of SEQ ID NO:134; and (d) amino acids 236-321 of SEQ ID NO:134;

for: (i) at least one T cell response biomarker generated by the T cell in response to the set of overlapping peptides, wherein the at least one T cell biomarker is at least one selected from the group consisting of IFN-γ and IP10, or (ii) proliferation of the T cell in response to the set of overlapping peptides,

wherein:

when in (i) the amount of the at least one T cell response biomarker in the reaction system is higher than in an otherwise identical control reaction system that lacks the set of overlapping peptides or in (ii) proliferation of the T cell in the reaction mixture is higher than in an otherwise identical control reaction system that lacks the set of overlapping peptides, the biological sample from the subject comprises a SOX2-positive T cell,

and,

administering to the subject immunotherapy for cancer, wherein the immunotherapy comprises at least one selected from the group consisting of a PD1 blockade immunotherapy and a CTLA-4 blockade immunotherapy, wherein the PD1 blockade immunotherapy comprises at least one selected from the group consisting of AMP224, BMS936558, GSK2661380, ONO4538, CT011, MK3475, MEDI4736, BMS936559, RG7446, MPDL3280A, and MDX1105.

2. The method of claim 1 , wherein the assaying comprises at least one assay selected from the group consisting of flow cytometry, immunocytochemistry, immunohistochemistry, ELISPOT, ELISA and variations thereof.

3. The method of claim 1 , wherein the set of overlapping peptides is selected from the group consisting of:

(a) a mixture of each SOX2 fragment from the group consisting of SEQ ID NOs:1-22, which spans the SOX2 protein region corresponding to amino acids 1-89 of SEQ ID NO:134;

(b) a mixture of each SOX2 fragment from the group consisting of SEQ ID NOs:23-44, which spans the SOX2 protein region corresponding to amino acids 79-171 of SEQ ID NO:134;

(c) a mixture of each SOX2 fragment from the group consisting of SEQ ID NOs:45-66, which spans the SOX2 protein region corresponding to amino acids 161-246 of SEQ ID NO:134; and

(d) a mixture of each SOX2 fragment from the group consisting of SEQ ID NOs:67-86, which spans the SOX2 protein region corresponding to amino acids 236-321 of SEQ ID NO:134.

4. The method of claim 1 , wherein the at least one biomarker is detected and the at least one biomarker's level is quantified.

5. The method of claim 1 , wherein in (i) the amount of the at least one T cell response biomarker in the reaction system is higher than in an otherwise identical control reaction system that lacks the set of overlapping peptides, or in (ii) proliferation of the T cell in the reaction mixture is higher than in an otherwise identical control reaction system that lacks the set of overlapping peptides, by at least 10%, by at least 20%, by at least 30%, by at least 40%, by at least 50%, by at least 60%, by at least 70%, by at least 80%, by at least 90%, by at least 100%, by at least 125%, by at least 150%, by at least 175%, by at least 200%, by at least 250%, by at least 300%, by at least 400%, or by at least 500%.

6. The method of claim 1 , wherein the biological sample is at least one selected from the group consisting of blood, serum, plasma, lymph and tumor tissue.

7. The method of claim 1 , wherein the biological sample comprises at least one selected from the group consisting of peripheral blood lymphocyte and peripheral blood mononuclear cell.

8. The method of claim 1 , wherein the at least one T cell response biomarker is detected using an antibody or antibody fragment that specifically binds to the at least one T cell response biomarker.