Compositions and methods for identification, assessment, prevention, and treatment of T-cell exhaustion using CD39 biomarkers and modulators

1. A method of detecting terminally exhausted CD8+ T cells, the method comprising detecting the presence or a significant increase in the copy number, amount, and/or activity of CD39 in Eomesodermin+ CD8+ T cells in a biological sample comprising CD8+ T cells relative to a control, optionally wherein

i) the biological sample is selected from the group consisting of cells, cell lines, histological slides, paraffin embedded tissue, fresh frozen tissue, fresh tissue, biopsies, blood, plasma, serum, buccal scrape, saliva, cerebrospinal fluid, urine, stool, mucus, bone marrow, and samples obtained from a subject;

ii) the presence of CD39 or copy number of CD39 is assessed by whole exome sequencing, microarray, quantitative PCR (qPCR), high-throughput sequencing, comparative genomic hybridization (CGH), or fluorescent in situ hybridization (FISH);

iii) the amount of CD39 is assessed by detecting the presence of a polynucleotide molecule encoding the biomarker or a portion of said polynucleotide molecule;

iv) the amount of CD39 is assessed by annealing a nucleic acid probe of the polynucleotide encoding CD39 or a portion of said polynucleotide molecule under stringent hybridization conditions;

v) the amount of CD39 is assessed by detecting the presence of CD39 polypeptide;

vi) the activity of CD39 is assessed by determining the magnitude of enzymatic activity, cellular proliferation, cell death, or cytokine production;

vii) the control is a sample comprising CD8+ T cells obtained from a subject not afflicted with a chronic immune condition; and/or

viii) the control is a copy number, amount, and/or activity value determined from a population of CD8+ T cells not afflicted with a chronic immune condition or obtained with a subject not afflicted with a chronic immune condition.

2. The method of claim 1 , further comprising

i) detecting the presence or a significant increase in the copy number, amount, and/or activity of at least one T cell exhaustion biomarker in the CD8+ T cells in the biological sample comprising CD8+ T cells relative to a control; and/or

ii) determining responsiveness of the subject from which the biological samples was obtained to anti-chronic immune condition therapy measured by at least one criteria selected from the group consisting of clinical benefit rate, survival until mortality, pathological complete response, semi-quantitative measures of pathologic response, clinical complete remission, clinical partial remission, clinical stable disease, recurrence-free survival, metastasis free survival, disease free survival, circulating tumor cell decrease, circulating marker response, and RECIST criteria.

3. The method of claim 2 , wherein the T cell exhaustion biomarker is selected from the group consisting of inhibitory receptors, T-bet, and combinations thereof.

4. The method of claim 1 , wherein

a) the polynucleotide molecule in iii) is a mRNA, cDNA, or functional variants or fragments thereof;

b) the method further comprises amplifying the polynucleotide molecule;

c) the presence of CD39 polypeptide is detected using a reagent which specifically binds with said polypeptide, optionally wherein the reagent is selected from the group consisting of an antibody, an antibody derivative, and an antibody fragment; and/or

d) the subject is mammal, preferably a chronic immune disorder animal model or a human.

5. The method of claim 4 , wherein

i) the reagent in c) is selected from the group consisting of an antibody, an antibody derivative, and an antibody fragment; and/or

ii) the chronic immune disorder in d) is a chronic infection or cancer.

6. The method of claim 5 , wherein

a) the chronic infection in ii) is caused by an agent selected from the group consisting of human immunodeficiency virus (HIV), hepatitis C virus (HCV), hepatitis B virus (HBV), adenovirus, cytomegalovirus, Epstein-Barr virus, herpes simplex virus 1, herpes simplex virus 2, human herpesvirus 6, varicella-zoster virus, hepatitis B virus, hepatitis D virus, papilloma virus, parvovirus B19, polyoma virus BK, polyoma virus JC, measles virus, rubella virus, human T cell leukemia virus I, human T cell leukemia virus II, Leishmania, Toxoplasma, Trypanosoma, Plasmodium, Schistosoma , and Encephalitozoon;

b) the chronic infection in ii) is not a latent infection; and/or

c) the cancer in ii) is a hematological cancer or a solid cancer.

7. The method of claim 6 , wherein the solid cancer in c) is selected from the group consisting of lung cancer, non-small cell lung cancer (NSCLC), skin cancer, melanoma, cervical cancer, uterine cancer, ovarian cancer, breast cancer, pancreatic cancer, stomach cancer, esophageal cancer, colorectal cancer, liver cancer, prostate cancer, kidney cancer, bladder cancer, head and neck cancer, sarcoma, lymphoma, and brain cancer.