Methods of determining patient populations amenable to immunomodulatory treatment of cancer

Abstract

The disclosure provides methods of determining patient populations amenable or suitable for immunomodulatory treatment of disease such as cancer by measuring the relative or absolute levels of T-cell sub-populations correlated with disease such as cancer.

Claims

1. A method of treating cancer in a human subject having cancer by determining if the subject is amenable to treatment with ipilimumab and administering to the subject determined to be amenable to treatment with ipilimumab an effective amount of ipilimumab to treat the cancer in the subject, said method comprising: (a) isolating a population of peripheral blood mononuclear cells (PBMCs) from the subject having cancer and a population of PBMCs from a cancer-free human subject; (b) quantifying the percentages of CD4.sup.+CD3.sup.+ FoxP3.sup.− T effector (T.sub.eff) cells expressing PD1, PD-L1, and/or CTLA-4 in each of said populations; (c) comparing the percentages of T.sub.eff cells expressing PD1, PD-L1, and/or CTLA-4 in the population of PBMCs from the subject having cancer and the percentages of T.sub.eff cells expressing PD1, PD-L1, and/or CTLA-4 in the population of PBMCs from the cancer-free subject; (d) determining that the subject having cancer is amenable to treatment with ipilimumab if: (1) the percentage of T.sub.eff cells expressing PD-1 in the population of PBMCs from the subject having cancer is lower than the percentage of T.sub.eff cells expressing PD-1 in the population of PBMCs from the cancer-free subject; (2) the percentage of T.sub.eff cells expressing PD-L1 in the population of PBMCs from the subject having cancer is lower than the percentage of T.sub.eff cells expressing PD-L1 in the population of PBMCs from the cancer-free subject; and (3) the percentage of T.sub.eff cells expressing CTLA-4 in the population of PBMCs from the subject having cancer is higher than the percentage of T.sub.eff cells expressing CTLA-4 in the population of PBMCs from the cancer-free subject; and (e) if the subject having cancer is determined to be amenable to treatment with ipilimumab, administering to the subject an effective amount of ipilimumab to treat the cancer in the subject.

2. The method of claim 1, wherein the cancer is an adenocarcinoma, a castration-resistant prostate cancer, a melanoma, a Head-and-Neck cancer, a lung cancer, a kidney cancer, a bladder cancer, a gastric cancer, a colorectal cancer, an ovarian cancer, a hepatocellular cancer, a hepatobiliary cancer, a breast cancer, or a blood cancer.

3. A method of inhibiting growth of cancer in a human subject having cancer by determining if the subject is amenable to treatment with ipilimumab and administering to the subject determined to be amenable to treatment with ipilimumab an effective amount of ipilimumab to inhibit growth of the cancer in the subject, said method comprising: (a) isolating a population of peripheral blood mononuclear cells (PBMCs) from the subject having cancer and a population of PBMCs from a cancer-free human subject; (b) quantifying the percentages of CD4.sup.+CD3.sup.+ FoxP3.sup.−T effector (T.sub.eff) cells expressing PD1, PD-L1, and/or CTLA-4 in each of said populations; (c) comparing the percentages of T.sub.eff cells expressing PD1, PD-L1, and/or CTLA-4 in the population of PBMCs from the subject having cancer and the percentages of T.sub.eff cells expressing PD1, PD-L1, and/or CTLA-4 in the population of PBMCs from the cancer-free subject; (d) determining that the subject having cancer is amenable to treatment with ipilimumab if: (1) the percentage of T.sub.eff cells expressing PD-1 in the population of PBMCs from the subject having cancer is lower than the percentage of T.sub.eff cells expressing PD-1 in the population of PBMCs from the cancer-free subject; (2) the percentage of T.sub.eff cells expressing PD-L1 in the population of PBMCs from the subject having cancer is lower than the percentage of T.sub.eff cells expressing PD-L1 in the population of PBMCs from the cancer-free subject; and (3) the percentage of T.sub.eff cells expressing CTLA-4 in the population of PBMCs from the subject having cancer is higher than the percentage of T.sub.eff cells expressing CTLA-4 in the population of PBMCs from the cancer-free subject; and (e) if the subject having cancer is determined to be amenable to treatment with ipilimumab, administering to the subject an effective amount of ipilimumab to inhibit growth of the cancer in the subject.

4. The method of claim 3, wherein the cancer is an adenocarcinoma, a castration-resistant prostate cancer, a melanoma, a Head-and-Neck cancer, a lung cancer, a kidney cancer, a bladder cancer, a gastric cancer, a colorectal cancer, an ovarian cancer, a hepatocellular cancer, a hepatobiliary cancer, a breast cancer, or a blood cancer.

5. A method of treating cancer in a human subject having cancer by determining if the subject is amenable to treatment with ipilimumab and administering to the subject determined to be amenable to treatment with ipilimumab an effective amount of ipilimumab to treat the cancer in the subject, said method comprising: (a) isolating a population of peripheral blood mononuclear cells (PBMCs) from the subject having cancer and a population of PBMCs from a cancer-free human subject; (b) quantifying the percentages of total CD4.sup.+ cells expressing PD1, PD-L1, and/or CTLA-4 in each of said populations; (c) comparing the percentages of total CD4.sup.+ cells expressing PD1, PD-L1, and/or CTLA-4 in the population of PBMCs from the subject having cancer and the percentages of total CD4.sup.+ cells expressing PD1, PD-L1, and/or CTLA-4 in the population of PBMCs from the cancer-free subject; (d) determining that the subject having cancer is amenable to treatment with ipilimumab if: (1) the percentage of total CD4.sup.+ cells expressing PD-1 in the population of PBMCs from the subject having cancer is lower than the percentage of total CD4.sup.+ cells expressing PD-1 in the population of PBMCs from the cancer-free subject; (2) the percentage of total CD4.sup.+ cells expressing PD-L1 in the population of PBMCs from the subject having cancer is lower than the percentage of total CD4.sup.+ cells expressing PD-L1 in the population of PBMCs from the cancer-free subject; and (3) the percentage of total CD4.sup.+ cells expressing CTLA-4 in the population of PBMCs from the subject having cancer is higher than the percentage of total CD4.sup.+ cells expressing CTLA-4 in the population of PBMCs from the cancer-free subject; and (e) if the subject having cancer is determined to be amenable to treatment with ipilimumab, administering to the subject an effective amount of ipilimumab to treat the cancer in the subject.

6. The method of claim 3, wherein the cancer is an adenocarcinoma, a castration-resistant prostate cancer, a melanoma, a Head-and-Neck cancer, a lung cancer, a kidney cancer, a bladder cancer, a gastric cancer, a colorectal cancer, an ovarian cancer, a hepatocellular cancer, a hepatobiliary cancer, a breast cancer, or a blood cancer.

Description

BRIEF DESCRIPTION OF THE DRAWING

(1) FIG. 1. Ipilimumab (anti-CTLA-4) treatment schedule. A, Metastatic castration resistant prostate cancer (mCRPC) patients were treated every 4 weeks with anti-CTLA-4 administered on day 1 of every cycle and GM-CSF administered at 250 μg/m2/dose from day 1 to day 14 daily of every cycle. Escalating doses were given to each cohort with an expansion cohort at 3 mg/kg/dose. B, Metastatic melanoma patients were treated every 3 weeks with anti-CTLA-4 administered at 10 mg/kg/dose on day 1 of every cycle and GM-CSF administered at 125 μg/m2/dose from day 1 to day 14 daily of every cycle.

(2) FIG. 2. Clinical outcomes of 42 metastatic castration resistant prostate cancer (mCRPC) patients in a Phase Ib ipilimumab (anti-CTLA-4) and GM-CSF clinical trial. A, Waterfall plot of the maximum percentage change in PSA from baseline of each patient until nadir or off study. Dashed line shows 50% decline in PSA. B, Spider plot shows change in PSA with time from baseline of each patient until nadir or off study. Dashed line shows 50% decline in PSA. C, Graph showing the duration of study treatment, duration of response, time to disease progression, and time to at least 50% decline in PSA for each patient. D, Overall survival curve for all patients as of analysis on the censor date. Dotted lines below and above the survival curve (solid line) show lower and upper 95% confidence intervals (CI) respectively. Vertical tick marks indicate OS of patients who were still alive as of the censor date.

(3) FIG. 3. Clinical outcomes of 21 metastatic melanoma patients in a Phase II ipilimumab (anti-CTLA-4) and GM-CSF clinical trial. A, Overall survival curve for all patients as of analysis on the censor date. Dotted lines below and above the survival curve (solid line) show lower and upper 95% confidence intervals (CI) respectively. Vertical tick marks indicate OS of patients who were still alive as of the censor date. B, Kaplan-Meier plots of treated melanoma patients separated by presence of complete response (CR) plus partial response (PR) plus stable disease (SD) compared to patients with progressive disease (PD). Sum of patients with CR, PR or SD are hence denoted as responders (R) and sum of patients with PD are hence denoted as non-responders (NR).

(4) FIG. 4. Surface PD-1 expression of CD4 T.sub.eff cells and CD8 T cells for mCRPC patients. A, Flow cytometry was used to assess PD-1 expression by CD4 T.sub.eff cells and CD8 T cells. Percentage of PD-1 positive cells in antibody-stained sample was gated based on isotype-containing controls. Shaded histograms denote isotype controls; open histograms denote stained samples. B and C, Time course of percentage of CD4 T.sub.eff and CD8 T cells that express PD-1 respectively. Connected dots show time course of the same patient. D and E, Time course of absolute counts of CD4 T.sub.eff and CD8 T cells that express PD-1 respectively. F and G, Box plots of percentage of CD4 T.sub.eff and CD8 T cells that express PD-1 respectively for long-term (L) and short-term (S) survivors at each time point. H and I, Box plots of absolute counts of CD4 T.sub.eff and CD8 T cells that express PD-1 respectively for long-term (L) and short-term (S) survivors at each time point. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001.

(5) FIG. 5. Total CTLA-4.sup.+ expression in total CD4 and CD8 T cells for mCRPC patients. A, Flow cytometry was used to assess CTLA-4 expression by CD4 T cells and CD8 T cells. Percentage of CTLA-4 positive cells in antibody-stained sample was gated based on isotype-containing controls. Shaded histograms denote isotype controls; open histograms denote stained samples. B and C, Time course of percentage of CD4 T and CD8 T cells that express CTLA-4 respectively. Connected dots show time course of the same patient. D and E, Time course of absolute counts of CD4 T and CD8 T cells that express CTLA-4 respectively. F and G, Box plots of percentage of CD4 T and CD8 T cells that express CTLA-4 respectively for long-term (L) and short-term (S) survivors at each time point. H and I, Box plots of absolute counts of CD4 T and CD8 T cells that express CTLA-4 respectively for long-term (L) and short-term (S) survivors at each time point. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001.

(6) FIG. 6. Surface PD-L1 expression of CD4 cells and CD8 T cells for metastatic melanoma patients. A, Flow cytometry was used to assess PD-L1 expression by CD4 T cells and CD8 T cells. Percentage of PD-L1 positive cells in antibody-stained sample was gated based on isotype-containing controls. Shaded histograms denote isotype controls; open histograms denote stained samples. B and C, Time course of percentage of CD8 T and CD4 T cells that express PD-L1 respectively. Connected dots show time course of the same patient. D and E, Time course of absolute counts of CD8 T and CD4 T cells that express PD-L1 respectively. F and G, Box plots of percentage of CD4 T and CD8 T cells that express PD-L1 respectively for responders (R) and non-responders (NR) at each time point. H and I, Box plots of absolute counts of CD8 T and CD4 T cells that express PD-L1 respectively for responders (R) and non-responders (NR) at each time point. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001, **** p-value <0.0001.

(7) FIG. 7. Levels of circulating lymphocytes, CD4 T.sub.eff cells and CD8 T cells with treatment for mCRPC patients. A, Time course of absolute lymphocyte counts for assessed patients at week 0 (pre-treatment), week 4 (cycle 1), and week 8 (cycle 2) of treatment. Connected dots show time course of the same patient. B, Box plots of absolute lymphocyte counts for long-term (L) and short-term (S) survivors at each time point. C and G, Time course of percentage of CD4 T.sub.eff cells and CD8 T cells of total lymphocytes, respectively. Connected dots show time course of the same patient. E and I, Time course of absolute counts of CD4 T.sub.eff cells and CD8 T cells respectively. D and H, Box plots of percentage of CD4 T.sub.eff cells and CD8 T cells of total lymphocytes respectively for long-term (L) and short-term (S) survivors at each time point. F and J, Box plots of absolute counts of CD4 T.sub.eff cells and CD8 T cells respectively for long-term (L) and short-term (S) survivors at each time point. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001.

(8) FIG. 8. Levels of circulating lymphocytes, CD4 T cells and CD8 T cells with treatment for metastatic melanoma patients. A, Time course of absolute lymphocyte counts for assessed patients at week 0 (pre-treatment), week 3 (cycle 1), and week 6 (cycle 2) of treatment. Connected dots show time course of the same patient. B, Box plots of absolute lymphocyte counts for responders plus SD (R) and non-responders (N) at each time point. C and G, Time course of percentage of CD4 T cells and CD8 T cells of total lymphocytes respectively. Connected dots show time course of the same patient. E and I, Time course of absolute counts of CD4 T cells and CD8 T cells respectively. D and H, Box plots of percentage of CD4 T cells and CD8 T cells of total lymphocytes respectively for responders plus SD (R) and non-responders (N) at each time point. F and J, Box plots of absolute counts of CD4 T cells and CD8 T cells respectively for responders plus SD (R) and non-responders (N) at each time point. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001.

(9) FIG. 9. Comparison of PD-1, CTLA-4 and PD-L1 expression levels between cancer-free controls and cancer patients at baseline. A, Box plots of percentage of CD4 T.sub.eff cells that express PD-1 for cancer-free controls (Controls), long-term (L) and short-term (S) survivors for mCRPC. B, Box plots of percentage of total CD4 T cells that express CTLA-4 for cancer-free controls (Controls), long-term (L) and short-term (S) survivors for mCRPC. C, Box plots of percentage of CD4 T.sub.eff cells that express PD-1 for cancer-free controls (Controls), responders (R) and non-responders (N) for metastatic melanoma. D, Box plots of percentage of total CD4 T cells that express PD-L1 for cancer-free controls (Controls), responders (R) and non-responders (N) for metastatic melanoma. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001.

(10) FIG. 10. Comparison of overall survival of patients separated by levels of immune subsets a designated in the legend. A and B, Kaplan-Meier plots of percentage of CD4 T.sub.eff cells that expressed PD-1 and absolute counts of PD-1.sup.+ CD4 T.sub.eff cells respectively, separated by cutoff levels designated in the legend. C and D, Kaplan-Meier plots of percentage of CD4 T cells that expressed CTLA-4 and absolute counts of CTLA-4.sup.+ CD4 T cells respectively, separated by cutoff levels designated in the legend. E and F, Kaplan-Meier plots of percentage of CD4 T cells that expressed PD-L1 and absolute counts of PD-L1.sup.+ CD4 T cells respectively, separated by cutoff levels designated in the legend.

(11) FIG. 11. A, Cytokine expression and surface markers of PD-1.sup.+ and PD-1.sup.− CD4 T cells. Representative flow cytometry diagrams showing percentages of IFNγ, IL-4, granzyme B, CD49b, and Lag-3 expression in PD-1.sup.+ and PD-1.sup.− CD4 T cells for one out of three healthy donors and one out of six mCRPC patients. Pre-treatment PBMC from cancer patients were used. B, Cytokine expressions and surface markers of PD-1.sup.+ and PD-1.sup.− CD8 T cells. Representative flow cytometry diagrams showing percentages of IFNγ, IL-4, granzyme B, CD49b, and Lag-3 expression in PD-1.sup.+ and PD-1.sup.− CD8 T cells for one out of three healthy donors and one out of six mCRPC patients. Pre-treatment PBMC from cancer patients were used. For IFNγ and IL-4 staining, PBMC were stimulated with PMA and ionomycin for 4 hours in culture at 37° C. with Brefeldin A added at the last 2 hours of incubation. For granzyme B, CD49b, and Lag-3 staining, unstimulated PBMC were used.

(12) FIG. 12. Baseline characteristics for mCRPC patients. A, B, C, and D, Box plots of age, baseline PSA levels, LDH levels, and months on study respectively for long-term (L) and short-term (S) survivors. Whiskers show minimum and maximum levels. E, F, G, H, I, and J, Bar graphs showing the number of patients with the attributes designated in the legends for ECOG, Gleason score, prior RP, prior radiation, subsequent therapies, and clinical responses, respectively, for long-term (L) and short-term (S) survivors.

(13) FIG. 13. Baseline characteristics for metastatic melanoma patients. A, Box plot of age for responders (R) and non-responders (NR). Whiskers show minimum and maximum levels. B, C, D, E, and F, Bar graphs showing the number of patients with the attributes designated in the legends for sex, tumor stage, prior therapy, immune adverse events, and prior systemic therapy respectively for responders (R) and non-responders (NR).

(14) FIG. 14. Surface PD-1 expression of CD4 T.sub.eff cells and CD8 T cells for metastatic melanoma patients. A, Flow cytometry was used to assess PD-1 expression by CD4 T.sub.eff cells and CD8 T cells. Percentage of PD-1-positive cells in antibody-stained sample was gated based on isotype-containing controls. Shaded histograms denote isotype controls; open histograms denote stained samples. B and C, Time course of percentage of CD4 T.sub.eff and CD8 T cells that express PD-1, respectively. Connected dots show time course of the same patient. D and E, Time course of absolute counts of CD4 T.sub.eff and CD8 T cells that express PD-1, respectively. F and G, Box plots of percentage of CD4 T.sub.eff and CD8 T cells that express PD-1, respectively, for responders (R) and non-responders (NR) at each time point. H and I, Box plots of absolute counts of CD4 T.sub.eff and CD8 T cells that express PD-1, respectively, for responders (R) and non-responders (NR) at each time point. Whiskers show minimum and maximum levels. * p-value <0.05, ** p-value <0.01, *** p-value <0.001.

DETAILED DESCRIPTION

(15) Cytotoxic T-Lymphocyte-associated antigen 4 (CTLA-4) blockade can induce tumor regression and improve survival in cancer patients. This treatment can enhance adaptive immune responses without an exogenous vaccine, but the immunologic parameters associated with improved clinical outcome in prostate cancer patients are not established. Ipilimumab is a fully humanized monoclonal antibody targeting CTLA-4 that is FDA approved for the treatment of melanoma. In two phase III studies in advanced melanoma, ipilimumab was shown to significantly prolong overall survival (OS) (3) (4). In the pivotal trial, melanoma patients were treated with ipilimumab plus gp100 (a melanoma peptide vaccine), ipilimumab alone or gp100 alone (3). The median overall survivals were 10.0, 10.1, and 6.4 months respectively. Althoμgh improvement in median overall survival was modest, a subset of patients was observed in these and other melanoma clinical trials to have durable long-term survival benefit (5) (6). Notably, long-term survival can happen without accompanying objective response. Additionally, treatment with ipilimumab plus sargramostim (GM-CSF) resulted in improved median OS and lower toxicity compared to ipilimumab alone (17.5 months versus 12.7 months) in a phase II clinical trial with unresectable melanoma (7).

(16) A phase III clinical trial for metastatic castration resistant prostate cancer (mCRPC) treated with ipilimumab versus placebo after radiotherapy reported no significant difference in OS between the two groups (8). Median OS was 11.2 months for the ipilimumab treated group and 10.0 months for the placebo group. However, it was observed that the hazard ratio (HR) decreased over time, showing that ipilimumab associated with better survival at later time points. HR for 0-5 months was 1.46 (95% CI 1.10-1.95) and for beyond 12 months was 0.6 (95% CI 0.43-0.86). Treatment with ipilimumab also improved progression-free survival compared to placebo (median 4.0 versus 3.1 months; HR 0.70; p-value less than 0.001). Post hoc analysis showed that patients who have no visceral metastases benefited more from ipilimumab treatment than those that do have visceral metastases (HR 1.64; p-value=0.0056).

(17) Disclosed herein is an up-dated long-term follow-up of a phase Ib dose escalation trial in patients with metastatic, castration resistant prostate cancer (mCRPC) was performed combining ipilimumab (anti-CTLA-4) and sargramostim (GM-CSF). Patients were followed clinically for response and overall survival, and for immunomodulation of circulating T cells. Of the 42 mCRPC enrolled patients, five patients had PSA declines of at least 50% with associated radiographic responses in two patients from the groups treated with at least 3 mg/kg of ipilimumab. Long-term follow-up demonstrated that 16 patients (38%) had overall survival of greater than 30 months, of whom four patients had PSA declines of at least 50% or objective responses. The combination of GM-CSF and ipilimumab can induce prolonged survival in a subset of patients who did not have PSA or objective responses. Clinical responses were both immediate and delayed. Two patients were still alive with overall survivals of 4.8 and 7 years as of censored date on Oct. 21, 2014. One of these patients had a continued PSA response without additional therapy.

(18) Disclosed herein are the clinical results of a phase II trial in patients with metastatic melanoma was performed combining ipilimumab (anti-CTLA-4) and sargramostim (GM-CSF). Of the 22 metastatic melanoma patients, one patient received only 1 cycle of ipilimumab and sargramostim and was not included in subsequent analysis. Of the 21 remaining patients, one patient had complete response (CR), 6 patients had partial response (PR), 1 patient had stable disease (SD), and 13 patients had progressive disease (PD). These clinical responses were found to associate with overall survival. As of censored date on Feb. 12, 2015, 10 patients were still alive.

(19) Immune subsets in peripheral blood mononuclear cells (PBMC) were evaluated for 23 out of 42 mCRPC patients whom were treated with ipilimumab at 3 mg/kg/dose or greater and sargramostim at 250 μg/m.sup.2/dose. Immune subsets were examined in PBMC from baseline, after cycle 1 and after cycle 2 of treatment with flow cytometry. As the number of clinical responses observed were low, comparison of immune subsets were made between patients who had overall survival greater than the median (23.6 months) for the group (long-term survivors, LTS, OS range: 25.4 months-99.7 months) (n=11)) versus patients who had overall survival less than the median for the group (short-term survivors, STS, OS range: 1.9 months-22.4 months) (n=12)).

(20) Immune subsets in PBMC were evaluated for all 21 metastatic melanoma patients who were treated with ipilimumab at 10 mg/kg/dose and sargramostim at 125 μg/m.sup.2/dose. Immune subsets were examined in PBMC from baseline, after cycle 1 and after cycle 2 of treatment with flow cytometry. As the number of patients who were alive is almost half of all the patients, comparison of immune subsets were made between patients with complete response, partial response and stable disease (responders, R, n=8) versus patients who had progressive disease (non-responder, NR, n=13)

(21) Disclosed herein are the results that pre-treatment clinical characteristics of patients where applicable, such as age, LDH levels, Eastern Cooperative Oncology group (ECOG) performance status, Gleason score of tumors, metastatic stages, prior treatments, and subsequent therapies after leaving clinical trial did not relate with survival for mCRPC patients and clinical responses for metastatic prostate cancer patients.

(22) It has been shown that the absolute lymphocyte counts after two ipilimumab treatments correlate significantly with clinical benefit and OS in a clinical trial for melanoma. Disclosed herein are the results that for our clinical trials, the levels of absolute lymphocyte counts of patients at pre-treatment or after cycle 1 and cycle 2 of treatment did not relate with survival for mCRPC patients and clinical responses for metastatic prostate cancer patients.

(23) Disclosed herein are the results that lower pre-treatment levels of PD-1.sup.+ CD4 T.sub.eff cells and higher pre-treatment levels of CTLA-4.sup.+ CD4 T cells, were each significantly associated with better overall survival for mCRPC patients. The levels of these same immune subsets examined after cycle 1 and cycle 2 did not relate with survival. The levels of the parent subsets, total CD4 T cells, CD4 T.sub.eff cells, and CD8 T cells did not relate with survival at pre-treatment or after cycle 1 and cycle 2 of treatment.

(24) Disclosed herein are the results that lower pre-treatment levels of PD-L1.sup.+ CD4 T cells and PD-1.sup.+ CD4 T.sub.eff cells were significantly associated with clinical responses for metastatic melanoma patients. The levels of PD-L1.sup.+ CD4 T cells and PD-1.sup.+ CD4 T.sub.eff cells also relate with survival after cycle 2 but not after cycle 1 of treatment. The levels of total CD4 T cells also relate with responses at pre-treatment, after cycle 1 and cycle 2 of treatment.

(25) Disclosed herein are the results that mCRPC patients with poorer survival have significantly higher pre-treatment levels of PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls, whereas patients with better survival have similar pre-treatment levels of PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls.

(26) Disclosed herein are the results that mCRPC patients with poorer survival have similar or slightly higher pre-treatment levels of CTLA-4.sup.+ CD4 T cells compared to cancer-free controls, whereas patients with better survival have significantly higher pre-treatment levels of CTLA-4.sup.+ CD4 T cells compared to cancer-free controls.

(27) Disclosed herein are the results that metastatic melanoma patients with progressive disease have significantly higher pre-treatment levels of PD-L1.sup.+ CD4 T cells and PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls, whereas patients with clinical responses or stable disease have similar pre-treatment levels of PD-L1.sup.+ CD4 T cells and PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls.

(28) Disclosed herein are the results that a proportion of these PD-1.sup.+ CD4 T.sub.eff cells express granzyme B without activation and IFNγ upon PMA/ionomycin activation, which is consistent with an effector T cell phenotype.

(29) Without wishing to be bound by theory, a potential explanation for the association of PD-1.sup.+ and PD-L1.sup.+ CD4 T cells with poorer survival is that CTLA-4 blockade with ipilimumab treatment removes inhibition on T cells that express CTLA-4, but tolerance to tumor antigens maintained by PD-1.sup.+ or PD-L1.sup.+ CD4 T cells persists and results in poorer survival. In addition it may also explain the increased effectiveness of combined CTLA-4 and PD-1 blockade therapies (10), especially as CTLA-4 blockade also increased the levels of PD-1.sup.+ CD4 effector T cells during treatment. It is expected that low PD-1 and/or low PD-L1 but high CTLA-4 levels in CD4 T cells will be useful as biomarkers for improved survival following CTLA-4 blockade immunotherapy and it is expected that high PD-1 but low CTLA-4 levels will characterize patients suitable for combination immunotherapy with anti-PD-1 and anti-CTLA-4 immunotherapeutics.

(30) The following examples illustrate embodiments of the disclosure.

Example 1

(31) Materials and Methods

(32) Clinical Trial

(33) For mCRPC, the results for the lower dose levels up to 3 mg/kg/dose for this phase Ib trial have been previously described (13). Briefly, patients had histologically proven metastatic castration resistant adenocarcinoma of the prostate with progression as defined by the PSA Working Group Consensus Criteria (14). Patients had received no prior steroids, chemotherapy or immunotherapy treatment. Patients received escalating doses of ipilimumab (Bristol-Myers Squibb) with a fixed dose of sargramostim (Sanofi). The initial design included dose escalation of ipilimumab from 0.5 mg/kg to 3 mg/kg (0.5, 1.5, and 3) every 4 weeks for 4 doses (13). The study was subsequently modified to include 5 and 10 mg/kg dose levels, as well as an expansion cohort of 6 patients at 3 mg/kg/dose (cohort 5A) (Table 1). Sargramostim at 250 μg/m2/dose on days 1-14 of 28 days cycles was administered subcutaneously and continued until disease progression or grade 3 or 4 treatment-related toxicity.

(34) For mCRPC, the primary endpoint of safety was graded according to National Cancer Institute (NCI) Common Terminology Criteria for Adverse Events version 3.0. Dose-limiting toxicity (DLT) included grade 3 or 4 treatment-related toxicity but excluded grade 3 immune-related adverse events (unless ocular) that did not require the use of steroids. Exploratory endpoints included T-cell activation, objective tumor responses (decrease in tumor size and/or lesions) as defined by Response Evaluation Criteria in Solid Tumors (RECIST) (15), and PSA declines of ≥50% in PSA levels confirmed 4 weeks later defined by the PSA Working Group Consensus Criteria. Progression is defined as a 50% rise in PSA above the nadir or back to baseline, whichever is lower, on at least two consecutive measurements at least two weeks apart; or the appearance of one or more new lesions occurring more than one month after the initiation of therapy. Bone scans (and CT scans if abnormal) were repeated every 12 weeks and at the time of PSA progression. Best PSA decline was the maximum percentage (%) decline from initial PSA levels before treatment. Overall survival (OS) was calculated from date of first treatment to date of death (n=40) or censor date of trial on Oct. 21, 2014 (n=2).

(35) For metastatic melanoma, inclusion criteria were histologically confirmed, surgically incurable or unresectable, Stage III or IV metastatic melanoma. Patients must have had disease progression following 1 systemic therapy for metastatic disease, a minimum of 1 measurable lesion according to irRC criteria, ECOG performance status of 0-2, and LDH ≤4× upper limit of normal (ULN). Patients had no uncontrolled brain metastasis, no history of autoimmune disease, and no prior immunotherapy treatments. Patients were treated with treated with 4 courses of GM-CSF and ipilimumab administered every 3 weeks. GM-CSF will be administered subcutaneously daily in a dose of 125 μg/m.sup.2 beginning on day 1 to day 14 of each 21-day cycle and ipilimumab will be administered intravenously in a dose of 10 mg/kg on day 1 of each cycle. After the initial 3 months (4 cycles) of treatment, GM-CSF administration continued for 4 additional cycles on the same schedule and dose without ipilimumab for 14 days every 21 days until month 6. Maintenance therapy began at month 6 and consisted of ipilimumab in the same dose combined with 14 days of GM-CSF. Administration of this combination was repeated every 3 months for up to 2 years or until disease progression, whichever occurred first.

(36) For metastatic melanoma, primary end point is disease control rate at 24 weeks. Secondary endpoints are assessment of immune activation, duration of disease control, overall survival, objective response rate using the immune related Response Criteria (irRC) (11), time to objective response, duration of objective response (CR or PR), and safety of the combination as defined by the NCI CTCAE criteria Version 4.0. Disease assessments will be performed using CT scans of the chest, abdomen, and pelvis and MRI scan of the brain at screening and every 3 months. OS was calculated from date of first treatment to date of death (n=11) or censor date of trial on Feb. 12, 2015 (n=10).

(37) Flow Cytometry

(38) Staining for flow cytometry was carried out on cryopreserved peripheral blood mononuclear cells (PBMC). In addition to study participants, PBMC were also obtained from men undergoing prostate cancer screening without a subsequent diagnosis of cancer (cancer-free male controls). Cell surface staining was performed in FACS buffer for 30 min at 4° C. Intracellular FoxP3, CTLA-4, and Ki67 staining was performed using the FoxP3 fix/perm buffer set (Biolegend, Inc., 421403) according to the manufacturers' protocol. CD49b, granzyme B, and Lag-3 were stained using the intracellular fixation and permeabilization buffer set (eBioscience, Inc., 88-8824). Intracellular IFNγ and IL-4 were stained suing the Foxp3 staining buffer set (eBioscience, Inc., 00-5523) after PBMC were activated with 50 ng/ml PMA and 1 μg/ml ionomycin for four hours at 37° C. in the presence of 5 μg/ml of Brefeldin A for the last two hours of activation. The following anti-human antibodies were used: (A700)-CD3 (Biolegend, Inc., 300324), (BV570)-CD4 (Biolegend, Inc., 300533), (PerCP/Cy5.5)-CD8 (Biolegend, Inc., 301032), (BV650)-CD25 (Biolegend, Inc., 302633), (FITC)-CD49b (Biolegend, Inc., 359306), (A647)-CD127 (Biolegend, Inc., 351318), (PE)-CTLA-4 (Biolegend, Inc., 349906), (A488)-FoxP3 (Biolegend, Inc., 320112), (PE)-Granzyme B (BD Biosciences, 561142), (BV650)-IFNγ (Biolegend, Inc., 502537), (A647)-IL-4 (Biolegend, Inc., 500712), (APC)-Lag-3 (eBioscience, Inc., 3DS223H), (BV421)-PD-1 (Biolegend, Inc., 329920), and (PE-Cy7)-PD-L1 (BD Biosciences, 558017). Stained cells were analyzed with an LSRII (BD Biosciences) flow cytometer. Data analysis was performed with Flowjo software (Treestar). Percentage (%) of positive cells was gated based on appropriate isotype control. Absolute count for each immune subset is calculated by multiplying the percentage of each subset with the preceding parent subset and with the absolute lymphocyte count quantitated on the day of blood drawn for that sample.

(39) Statistical Analysis

(40) Distributions of percentage of paired immune subsets at pre-treatment (week 0) were compared with cycle 1 (week 4 for mCRPC patients; week 3 for metastatic melanoma patients) or with cycle 2 (week 8 for mCRPC patients; week 6 for metastatic melanoma patients) using Wilcoxon matched-pairs signed rank test using Prism (GraphPad) software. The number of patients with PBMC at the various time points differed based on availability.

(41) Distributions of categorical patient characteristics such as ECOG status, Gleason score, prior radical prostatectomy, prior radiation, subsequent therapies, and clinical responses for mCRPC patients, sex, tumor stage, presence of immune adverse related events, prior therapy, and prior systemic therapy for metastatic melanoma patients were compared using Fisher's exact test with Prism (Graphpad) software.

(42) Distributions of continuous patient characteristics where applicable, such as age, baseline PSA levels, lactate dehydrogenase (LDH) levels, months on study, percentage or absolute counts of immune subsets between long-term survivors (LTS) and short-term survivors (STS), and percentage or absolute counts of immune subsets between responders (R) and non-responders (NR). Percentage of immune subsets between cancer-free male controls and LTS or STS or R or NR were similarly compared using Mann-Whitney U-test.

(43) Comparison of overall survival of cancer patients divided into two groups based on cutoff levels of immune subsets were carried out by plotting Kaplan-Meier curves for each group and carrying out log-rank test.

(44) Statistical significance was declared based on alpha level of 0.05 with Bonferroni correction to adjust for multiple testing as needed. Due to the small sample size, all significant outcomes should be considered as hypothesis generating and confirmation with a larger sample size are needed.

Example 2

(45) Patient Characteristics

(46) TABLE-US-00001 TABLE 1 Patient Characteristics for mCRPC N = 42 Median (range) Age (years) 72.5 (52-82) ECOG PS (n) 0 31 1 11 Gleason score ≤6 8 7 11 ≥8 21 Baseline PSA (ng/mL) 37.5 (6.7-435) LDH (U/L) 172 (136-557) Alkaline phosphatase (U/L) 92 (28-1725) Metastases Bone 25 Soft tissue 5 Both 12

(47) TABLE-US-00002 TABLE 2 Patient Characteristics for metastatic melanoma N = 22 Percentage (range) Age, median (range), years 65 (41-85) Sex Men 12 (54.5)  Women 10 (45.5)  Metastatic Stage Unresectable III 1 (4.55) M1a 1 (4.55) M1b 5 (22.7) M1c 15 (68.2)  Sites of Metastasis Lymph Nodes 14 (63.6)  Lung 14 (63.6)  Liver 10 (45.5)  Bone 7 (31.8) Subcutaneous tissue 6 (27.3) CNS 4 (18.2) Skin 3 (13.6) Adrenal 3 (13.6) Intestine 1 (4.55) Spleen 1 (4.55) Retroperitoneum 1 (4.55) Received prior systemic therapy No 15 (68.2)  Yes 7 (31.8) Prior Therapy Radiation 9 (40.9) Systemic, Chemo 4 (18.2) Adjuvant 3 (13.6) Systemic, Non-Chemo 2 (9.1)  Localized 1 (4.5) 

Example 3

(48) Clinical Outcomes

(49) A waterfall plot of nadir PSA values (FIG. 2A) demonstrates that 23 out of 42 patients (54%) had some decline in PSA. Five of 42 patients (11.9%) experienced a 50% or greater decline in PSA (Table 1). The median time to PSA nadir was 5.9 weeks (range 1.9-39.1 weeks) for patients with any PSA decline and 15.9 weeks (range 11.9-39.1 weeks) for patients with at least a 50% PSA decline (FIG. 2B). Objective tumor response and at least a 50% PSA decline was not observed in cohorts treated at less than 3 mg/kg/dose level. Three out of 12 patients treated at 3 mg/kg/dose experienced at least a 50% PSA decline, of whom two had objective responses with regression of liver metastasis in one patient and bone metastasis in another (cohort 5). One patient in the expansion cohort at 3 mg/kg experienced a 49% decline (cohort 5A). In the cohort treated at 5 mg/kg/dose, none of 6 patients demonstrated at least a 50% PSA decline or objective tumor response. Of the 6 patients treated at the 10 mg/kg, two had at least a 50% PSA decline. No accompanying objective tumor response was seen.

(50) As of censor date of the trial, all patients had come off study. One patient came off treatment by patient's choice. 13 patients came off treatment for PSA progression prior to the first set of scans, 16 patients came off treatment with PSA progression following the first set of scans, 6 patients came off treatment for tumor progression by scans, and 6 patients came off treatment for immune-related adverse toxicities. However, two patients from the 3 mg/kg/dose group whom came off treatment due to immune-related toxicities demonstrated durable responses with their PSA levels remaining less than 50% of their pre-treatment levels for 19 and 85 months after being off treatment without any new treatment (FIG. 2C). One patient from the 5 mg/kg/dose group came off treatment due to an initial disease progression, but a delayed response was observed with his PSA decline attaining 50% at 7 months without any new treatment.

(51) As this is a Phase Ib study, survival analysis was not specified in the protocol. As immunotherapies can induce improvements in overall survival without conventional progression, survival analysis was carried out post-hoc. The median OS for all the patients (n=42) is 23.6 months (95% confidence limits {CI}={116.2, 39.3}) (FIG. 2D).

(52) TABLE-US-00003 TABLE 3 Clinical Responses for mCRPC ≥50% PSA Median Response Overall (Best Objective TTP.sup.c Survival Dose Level.sup.a decline %) Response.sup.b (months) (months) 1 0/3 0/3 25 (0.5 mg/kg x 4) 2 0/7 0/7 26 (1.5 mg/kg x 1, 0.5 mg/kg x 3) 3 0/5 0/5 28 (1.5 mg/kg x 4) 4 0/3 0/3 12 (3 mg/kg x 1, 1.5 mg/kg x 3) 5 3/6 2/6 20, 25.75, 56 (3 mg/kg x 4) (79, 95, 97) 89.25 6 0/6 0/6 13 (5 mg/kg x 4) 7 2/6 0/6 9.75, 18 19 (10 mg/kg x 4) (50, 80) 5A 0/6 0/6 20 (3 mg/kg x 4) Cumulative  5/42  2/42 20 (median) 23.6 .sup.aDosage of ipilimumab and the number of doses are given in brackets ( ); .sup.bObjective tumor response defined by RECIST; .sup.cTTP is time to progression calculated from the time of initial response.

(53) Clinical outcomes for metastatic melanoma: Out of 21 patients who had received at least 2 cycles of treatment, 1 patient had CR, 6 patients had PR, 1 patient had SD, and 13 patients had PD. The median OS for all the treated patients (n=22) was 21.4 months (FIG. 3A). Overall survival associated significantly with clinical responses (CR+PR) plus SD (FIG. 3B) (p-value=0.005).

Example 4

(54) Toxicity

(55) Consistent with the known toxicity profile of ipilimumab, toxicity was primarily immune in nature.

(56) TABLE-US-00004 TABLE 4 Adverse events for mCRPC Dose Level All adverse events.sup.a Dose-Limiting Toxicities 1 1/3 0/3 grade 1: nausea (1) 2 1/7 1/7 grade 3: CVA (1) grade 3: CVA 3 2/5 1/5 grade 3: fatigue (1), rash (1) grade 3: rash requiring steroids 4 0/3 0/3 5 4/6 1/6 grade 2: muscle spasms (1) grade 4: CVA grade 3: angina (1), temporal arteritis (1), diarrhea (1), panhypopituitarism (1) grade 4: CVA (1) 6 5/6 1/6 grade 1: fatigue (1), muscle spasms (1), grade 5: PE diarrhea (2) grade 2: wheezing (1), hot flashes (1), fatigue (1), pruritus (2), rash (3) grade 3: fatigue (1), atrial fibrillation (1) grade 5: PE (1) 7 6/6 1/6 grade 1: diarrhea (1), rash (1) grade 3: rash requiring steroids grade 2: vomiting (1), dehydration (1), pruritus (3), fatigue (1), erythema (1), adrenal insufficiency (2) grade 3: fatigue (2), diarrhea (2), rash (3) grade 4: elevated troponin (1) 5A.sup.b 4/4 1/4 grade 1: increased LFT (1) grade 3: diarrhea requiring steroids grade 2: adrenal insufficiency (1), pneumonitis (1) grade 3: atrial fibrillation (1), DVT (1), diarrhea (1) grade 4: fatigue (1) .sup.aImmune-related adverse events are in bold. The fraction of patients with any adverse event is presented per cohort. The number of patients with each adverse event is listed in brackets ( ). As a patient might have experienced more than one adverse event, the sum of all adverse events may be greater than the number of patients in each cohort; .sup.bInformation for adverse events was available only for four out of six patients in this cohort; CVA, cerebrovascular accidents; DVT, deep venous thrombosis; LFT, liver function test; PE, pulmonary embolism.

(57) TABLE-US-00005 TABLE 5 Adverse events for metastatic melanoma % % Grades Grades Toxicity 1-2 3-4 Fatigue 50 6.25 Injection Site Reaction 43.75 6.25 Infusion Reaction 12.5 6.25 Fever 12.5 0 Flu-like symptoms 6.25 0 Irritability 6.25 0 Flushing 6.25 0 Gastrointestinal 50 37.5 Diarrhea 18.75 12.5 Nausea 31.25 0 Colitis 0 18.75 Colon Perforation 0 6.25 Skin and Subcutaneous 81.25 6.25 Rash 31.25 6.25 Pruritis 31.25 0 Urticaria 12.5 0 Hyperhidrosis 6.25 0 Anorexia 37.5 6.25 Investigational 25 6.25 Weight loss 12.5 0 Decreased ACTH 0 6.25 Increased AST 6.25 0 Increased ALT 6.25 0 Nervous System 25 0 Headache 12.5 0 Tremor 6.25 0 Dysgeusia 6.25 0 Cardiac 12.5 6.25 Palpitations 6.25 0 Atrial fibrillation 0 6.25 Pericarditis 6.25 0 Endocrine 6.25 6.25 Hyperthyroidism 6.25 6.25 Musculoskeletal 12.5 0 Myalgias 6.25 0 Arthalgias 6.25 0 Infection 6.25 0 Phayrngitis 6.25 0

Example 5

(58) Patients' Baseline Characteristics Did not Relate with Survival for mCRPC Patients or Clinical Responses for Metastatic Melanoma Patients.

(59) For mCRPC patients, age, baseline PSA levels, LDH levels, months on study, did not relate with OS (p-values=0.193, 0.311, 0.277, and 0.100 respectively). The number of patients with ECOG status of 0 or 1, Gleason scores grouped as 3 to 6, or 7 to 9, prior radical prostatectomy, and prior radiation, were not significantly different between the two groups (p-values=1.00, 0.90, 1.00, and 0.67 respectively). The number of patients with clinical responses as described above and the number of patients who went on to subsequent therapies also did not correlate with OS (p-values=0.16 and 0.38 respectively) (FIG. 11).

(60) For metastatic melanoma, age, sex, tumor stage, prior therapy, immune adverse events, and prior systemic therapy did not relate significantly with either responders (R) or non-responders (NR) (p-values=0.23, 0.66, 0.71, 0.67, 0.39, and 0.40 respectively) (FIG. 12).

Example 6

(61) Absolute Lymphocyte Counts Did not Associate with Survival for mCRPC Patients or Clinical Responses for Metastatic Melanoma Patients

(62) For mCRPC patients, the absolute lymphocyte counts were significantly higher compared to pre-treatment levels after cycle 1 but not after cycle 2 of treatment (p-values=0.002 and 0.119 respectively) (FIG. 7A). The distribution of the absolute lymphocyte counts however did not differ between LTS and STS at pre-treatment (p-value=0.201), after cycle 1 (p-value=0.670), and after cycle 2 of treatment (p-value=0.779) (FIG. 7B).

(63) For metastatic melanoma patients, the absolute lymphocyte counts were significantly higher compared to pre-treatment levels after cycle 1 and after cycle 2 of treatment (p-values=0.0002 and <0.0001 respectively) (FIG. 8A). The distribution of the absolute lymphocyte counts however did not differ between R and NR at pre-treatment (p-value=0.753), after cycle 1 (p-value=0.983), and after cycle 2 of treatment (p-value=0.126) (FIG. 8B).

Example 7

(64) Relationship of CD4 T.sub.eff Cells, Total CD4 T Cells and CD8 T Cells with Survival or Clinical Responses.

(65) For mCRPC, the percentages of total lymphocytes and absolute counts of CD4 T.sub.eff cells (CD4.sup.+CD3.sup.+ FoxP3.sup.−) were significantly higher after one cycle of treatment (FIGS. 7C and E). However, for CD8 T cells, only the absolute counts and not the percentage of total lymphocytes, were significantly higher after one cycle of treatment (FIGS. 7G and I). This difference could be due to the higher levels of absolute lymphocyte counts after one cycle of treatment as described above.

(66) For mCRPC patients, the distribution of the percentages of total lymphocytes and absolute counts of CD4 T.sub.eff cells did not differ between LTS and STS at pre-treatment (p-values=0.263 and 0.841 respectively), after cycle 1 (p-values=0.805 and 0.745 respectively), and after cycle 2 of treatment (p-values=0.920 and 0.845 respectively) (FIG. 7D, F). The percentages of total lymphocytes and absolute counts of CD8 T cells also did not relate with survival at pre-treatment (p-values=0.461 and 0.304 respectively), after cycle 1 (p-values=0.555 and 0.670 respectively), and after cycle 2 of treatment (p-values=0.671 and 0.835 respectively) (FIG. 7H, J).

(67) For metastatic melanoma patients, the percentages of total lymphocytes and absolute counts of total CD4 T cells (CD8.sup.− CD3.sup.+) were significantly higher after 1 and 2 cycles of treatment (FIGS. 8C and E). The percentages of total lymphocytes and absolute counts of total CD8 T cells (CD8.sup.+ CD3.sup.+) were significantly higher after 1 and 2 cycles of treatment (FIGS. 8G and I).

(68) The distribution of the percentages of total lymphocytes but not the absolute count of CD4 T cells did not differ between R and NR at pre-treatment (p-values=0.025 and 0.064 respectively), was significantly different for percentages but not absolute counts after cycle 1 (p-values=0.008 and 0.076 respectively), and was significantly different for both percentages and absolute counts after cycle 2 of treatment (p-values=0.033 and 0.026, respectively) (FIG. 8D, F). The percentages of total lymphocytes and absolute counts of CD8 T cells did not relate with clinical responses at pre-treatment (p-values=0.053 and 0.886). The percentages of total lymphocytes and absolute counts of CD8 T cells after cycle 1 did not correlate with clinical responses (p-values=0.053 and 0.074, respectively). The percentages of total lymphocyte but not the absolute counts of CD8 T cells related significantly with clinical responses after cycle 2 of treatment (p-values=0.035 and 0.372, respectively) (FIG. 8H, J).

Example 8

(69) Lower Pre-Treatment Levels of PD-1.sup.+ CD4 Effector T Cells Associate with Longer Survival for mCRPC Patients and with Clinical Responses for Metastatic Melanoma Patients

(70) For mCRPC patients, the percentages of CD4 T.sub.eff cells that express surface PD-1 were significantly higher after cycle 1 (p-value=0.0001) and continued to be significantly higher after cycle 2 compared to pre-treatment levels (p-value=0.0002) (FIG. 4A, B, D). The absolute counts of PD-1+CD4 T.sub.eff cells were also significantly higher after both cycles (p-values=0.0001 and 0.0002 respectively). The percentages of CD8 T cells that express PD-1 were also significantly higher from pre-treatment levels after cycle 1 (p-value=0.004) and after cycle 2 of treatment (p-value=0.005) (FIG. 4A, C, E). The absolute counts of PD-1.sup.+ CD8 T cells were also significantly higher after both cycles (p-values=0.005 and 0.022 respectively).

(71) For mCRPC patients, the distribution of the percentages of surface PD-1+ on CD4 T.sub.eff cells and absolute counts of PD-1.sup.+ CD4 T.sub.eff at pre-treatment was significantly lower in LTS compared to STS (p-values=0.0007 and 0.003 respectively) (FIG. 4F, H). After treatment, the distribution of the percentages of surface PD-1.sup.+ on CD4 T.sub.eff cells and absolute counts of PD-1.sup.+ CD4 T.sub.eff were not significantly different between STS or LTS after cycle 1 (p-values=0.055 and 0.090 respectively) and after cycle 2 (p-values=0.054 and 0.150 respectively) (FIG. 4F, H). The distributions of the percentages and absolute counts of surface PD-1.sup.+ CD8 T cells between STS and LTS did not differ at pre-treatment (p-value=0.246 and >0.999 respectively) or at any time point after treatment (FIG. 4A, G, I).

(72) For metastatic melanoma patients, the percentages of CD4 T.sub.eff cells that express surface PD-1 similarly increased after cycle 1 and cycle 2 (p-values=<0.0001 for both). The absolute counts of PD-1.sup.+ CD4 T.sub.eff cells were similarly higher after both cycles (p-values=<0.0001 and 0.0001 respectively). The percentages of CD8 T cells that express PD-1 were also significantly higher from pre-treatment levels after cycle 1 (p-value=0.001) and after cycle 2 of treatment (p-value=0.003). The absolute counts of PD-1.sup.+ CD8 T cells were also significantly higher after both cycles (p-values=<0.0001 for both) (FIG. 14).

(73) For metastatic melanoma patients, the distribution of the percentages of surface PD-1+ on CD4 T.sub.eff cells but not the absolute counts of PD-1.sup.+ CD4 T.sub.eff at pre-treatment was significantly lower in R compared to NR (p-values=0.017 and 0.887, respectively). The distribution of the percentages of surface PD-1+ on CD4 T.sub.eff cells but not the absolute counts of PD-1.sup.+ CD4 T.sub.eff after cycle 2 was significantly lower in R compared to NR (p-values=0.040 and 0.946 respectively). The distributions of the percentages and absolute counts of surface PD-1.sup.+ CD8 T cells between R and NR did not differ at pre-treatment (p-values=0.453 and 0.744 respectively) or at any time point after treatment (cycle 1 percentage and absolute count p-values=0.543 and 0.441; cycle 2 percentage and absolute count p-values=0.229 and 0.118).

Example 9

(74) High Pre-Treatment Levels of CLTA-4.sup.+ CD4 T Cells Associate with Improved Survival

(75) For mCRPC patients, the percentages of CTLA-4.sup.+ of CD4 T cells increased significantly after cycle 1 (p-value=0.0078) and after cycle 2 (p-value=0.016) of treatment (FIGS. 5A, and B). The absolute counts of CTLA-4.sup.+ CD4 T cells also increased significantly after cycle 1 (p-value=0.0078) and after cycle 2 (p-value=0.016) of treatment (FIG. 5D). The percentages of CTLA-4.sup.+ of CD8 T cells increased significantly after cycle 1 (p-value=0.0078) and after cycle 2 (p-value=0.016) of treatment (FIGS. 5A, and C). The absolute counts of CTLA-4.sup.+ CD8 T cells also increased significantly after cycle 1 (p-value=0.0078) and after cycle 2 (p-value=0.016) of treatment (FIG. 5E).

(76) For mCRPC patients, higher pre-treatment percentages of CTLA-4.sup.+ of CD4 T cells at pre-treatment related with long-term survivors (p-value=0.030) but not after cycle 1 or cycle 2 of treatment (p-values=0.524 and >0.999 respectively) (FIG. 5F). The pre-treatment absolute CTLA-4.sup.+ CD4 T cell count was also significantly different between LTS and STS at pre-treatment (p-value=0.0411) (FIG. 5H) but not after cycle 1 or cycle 2 of treatment (p-values=0.111 for both). The distribution of the percentages of CTLA-4.sup.+ of CD8 T cells at pre-treatment or after cycles 1 or 2 did not relate with long-term survivors (p-values=0.788, 0.508, and 0.683 respectively) (FIG. 5G). The pre-treatment absolute CTLA-4.sup.+ CD8 T cell count was also not significantly different between LTS and STS at pre-treatment or after cycles 1 or 2 (p-values=>0.999, 0.83, and >0.999 respectively) (FIG. 5I).

Example 10

(77) Lower Pre-Treatment Levels of PD-L1.sup.+ CD4 Effector T Cells Associate with Clinical Responses for Metastatic Melanoma Patients

(78) For metastatic melanoma patients, the percentages of PD-L1.sup.+ of CD4 T cells did not increased significantly after cycle 1 (p-value=0.058) but increased significantly after cycle 2 (p-value=0.004) of treatment (FIGS. 6A, and B). The absolute counts of PD-L1.sup.+ CD4 T cells increased significantly after cycle 1 (p-value=<0.0001) and after cycle 2 (p-value=0.0004) of treatment (FIG. 6D). The percentages of PD-L1.sup.+ of CD8 T cells did not increased significantly after cycle 1 (p-value=0.202) and after cycle 2 (p-value=0.562) of treatment (FIGS. 6A, and C). The absolute counts of PD-L1.sup.+ CD8 T cells increased significantly after cycle 1 (p-value=0.012) and after cycle 2 (p-value=0.001) of treatment (FIG. 6E).

(79) For metastatic melanoma patients, lower pre-treatment percentages of PD-L1.sup.+ of CD4 T cells at pre-treatment and after cycle 2 related with clinical responses (p-values=0.006 and 0.007 respectively) but not after cycle 1 of treatment (p-value=0.087) (FIG. 6F). The pre-treatment absolute PD-L1.sup.+ CD4 T cell count was not significantly different between R and NR at pre-treatment (p-value=0.268) (FIG. 6H) or after cycle 1 or cycle 2 of treatment (p-values=0.065 and 0.111 respectively). The distribution of the percentages of PD-L1.sup.+ of CD8 T cells at pre-treatment or after cycles 1 or 2 did not relate with clinical responses (p-values=0.727, 0.962, and 0.643 respectively) (FIG. 6G). The pre-treatment absolute PD-L1.sup.+ CD8 T cell count was also not significantly different between R and NR at pre-treatment or after cycles 1 or 2 (p-values=0.244, 0.399, and 0.181 respectively) (FIG. 6I).

Example 11

(80) Comparison with Cancer-Free Controls

(81) mCRPC patients with poorer survival have significantly higher pre-treatment levels of PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls (p-value=0.001), whereas patients with better survival have similar pre-treatment levels of PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls (FIG. 9A).

(82) mCRPC patients with poorer survival have similar or slightly higher pre-treatment levels of CTLA-4.sup.+ CD4 T cells compared to cancer-free controls, whereas patients with better survival have significantly higher pre-treatment levels of CTLA-4.sup.+ CD4 T cells compared to cancer-free controls (p-value=0.001) (FIG. 9B).

(83) Metastatic melanoma patients with progressive disease have significantly higher pre-treatment levels of PD-1.sup.+ CD4 T.sub.eff cells compared to cancer-free controls (p-value=0.0002), whereas patients with clinical responses or stable disease have similar pre-treatment levels of PD-L1.sup.+ CD4 T cells compared to cancer-free controls (FIG. 9C).

(84) Metastatic melanoma patients with progressive disease have significantly higher pre-treatment levels of PD-L1.sup.+ CD4 T cells compared to cancer-free controls (p-value=0.047), whereas patients with clinical responses or stable disease have similar pre-treatment levels of PD-L1.sup.+ CD4 T cells compared to cancer-free controls (FIG. 9D).

Example 12

(85) Summary of Significance Values

(86) Percentages of Immune Subsets

(87) TABLE-US-00006 TABLE 6 Comparison of pre-treatment T cell subsets LTS (n = 8) STS (n = 12) mCRPC patients Median.sup.a (Range.sup.b) Median.sup.a (Range.sup.b) p-value.sup.c Total CD4 T cells (CD4.sup.+CD3.sup.+) 41.0 (32.8-59.6) 48.3 (33.6-71.8) 0.203 CD4 T.sub.eff cells (CD4.sup.+CD3.sup.+FoxP3.sup.−) 38.9 (30.1-56.2) 45.2 (30.4-66.8) 0.263 PD-1.sup.+CD4.sup.+CD3.sup.+FoxP3.sup.− 10.1 (5.4-14.5)  22.0 (12.8-42.3) 0.0007 Total CD8 T cells (CD4.sup.−CD3.sup.+) 24.5 (5.0-42.2)  18.3 (6.7-50.7)  0.461 PD-1.sup.+CD4.sup.−CD3.sup.+ 15.0 (5.3-28.0)  22.2 (8.4-33.0)  0.246 LTS (n = 6) STS (n = 6) mCRPC patients Median.sup.a (Range.sup.b) Median.sup.a (Range.sup.b) p-value.sup.c Total CD4 T cells (CD8.sup.−CD3.sup.+) 43.0 (35.2-58.9) 51.7 (40.6-61.9) 0.305 CTLA-4.sup.+CD8.sup.−CD3.sup.+ 18.7 (14.2-21.6) 13.7 (9.4-19.9)  0.030 Total CD8 T cells (CD8.sup.+CD3.sup.+) 10.8 (4.2-25.0)  12.9 (5.4-24.5)  0.675 CTLA-4.sup.+CD8.sup.+CD3.sup.+ 6.2 (2.1-12.2) 5.5 (3.7-12.0) 0.788 R (n = 8) NR (n = 13) Metastatic melanoma patients Median.sup.a (Range.sup.b) Median.sup.a (Range.sup.b) p-value.sup.c CD4 T.sub.eff cells (CD4.sup.+CD3.sup.+FoxP3.sup.−) 46.9 (24.3-58.9) 38.2 (19.1-53.6) 0.104 PD-1.sup.+CD4.sup.+CD3.sup.+FoxP3.sup.− 14.6 (11.5-33.9) 30.2 (15.4-43.8) 0.017 Total CD8 T cells (CD4.sup.−CD3.sup.+) 18.9 (13.3-39.6) 29.8 (16.4-64.4) 0.157 PD-1.sup.+CD4.sup.−CD3.sup.+ 31.2 (19.2-53.4) 28.5 (9.3-56.9)  0.453 Total CD4 T cells (CD8.sup.−CD3.sup.+) 56.1 (37.4-69.1) 43.0 (20.4-61.6) 0.025 PD-L1.sup.+CD8.sup.−CD3.sup.+ 15.1 (9.2-24.7)  24.4 (18.1-38.1) 0.006 Total CD8 T cells (CD8.sup.+CD3.sup.+) 13.7 (6.1-27.3)  23.7 (4.5-63.4)  0.053 PD-L1.sup.+CD8.sup.+CD3.sup.+ 7.0 (3.9-19.4) 6.7 (3.8-10.3) 0.727 .sup.aMedian values of parent gates are % of total lymphocytes and median values of immune checkpoint markers are % of the respective parent gate; .sup.bValues in brackets ( ) are range of each data set; .sup.cMann-Whitney test; Bold-faced characters highlight p-value ≤ 0.05; LTS, long-term survivors; STS, short-term survivors; R, clinical responders; NR, non-responders.
Absolute Counts of Immune Subsets

(88) TABLE-US-00007 TABLE 7 Comparison of pre-treatment absolute counts of T cell subsets LTS (n = 8) STS (n = 12) mCRPC patients Median.sup.a (Range.sup.b) Median.sup.a (Range.sup.b) p-value.sup.c Total CD4 T cells (CD4.sup.+CD3.sup.+) 0.80 (0.48-0.99) 0.64 (0.33-1.15) 0.841 CD4 T.sub.eff cells (CD4.sup.+CD3.sup.+FoxP3.sup.−) 0.74 (0.45-0.91) 0.61 (0.27-1.07) 0.841 PD-1.sup.+CD4.sup.+CD3.sup.+FoxP3.sup.− 0.07 (0.04-0.10) 0.12 (0.07-0.30) 0.003 Total CD8 T cells (CD4.sup.−CD3.sup.+) 0.44 (0.05-0.79) 0.22 (0.09-1.17) 0.304 PD-1.sup.+CD4.sup.−CD3.sup.+ 0.05 (0.01-0.10) 0.03 (0.02-0.37) >0.999 LTS (n = 6) STS (n = 6) mCRPC patients Median.sup.a (Range.sup.b) Median.sup.a (Range.sup.b) p-value.sup.c Total CD4 T cells (CD8.sup.−CD3.sup.+) 1.02 (0.62-1.25) 0.65 (0.60-1.03) 0.387 CTLA-4.sup.+CD8.sup.−CD3.sup.+ 0.19 (0.09-0.23) 0.09 (0.06-0.20) 0.041 Total CD8 T cells (CD8.sup.+CD3.sup.+) 0.24 (0.03-0.67) 0.19 (0.07-0.32) 0.788 CTLA-4.sup.+CD8.sup.+CD3.sup.+  0.01 (0.003-0.05) 0.009 (0.005-0.04) >0.999 R (n = 8) NR (n = 13) Metastatic melanoma patients Median.sup.a (Range.sup.b) Median.sup.a (Range.sup.b) p-value.sup.c CD4 T.sub.eff cells (CD4.sup.+CD3.sup.+FoxP3.sup.−) 0.80 (0.13-1.31) 0.40 (0.12-1.08) 0.064 PD-1.sup.+CD4.sup.+CD3.sup.+FoxP3.sup.− 0.12 (0.06-0.25) 0.11 (0.04-0.31) 0.886 Total CD8 T cells (CD4.sup.−CD3.sup.+) 0.35 (0.10-0.75) 0.26 (0.15-1.22) 0.744 PD-1.sup.+CD4.sup.−CD3.sup.+ 0.10 (0.03-0.20) 0.09 (0.03-27)   0.744 Total CD4 T cells (CD8.sup.−CD3.sup.+) 1.01 (0.20-1.61) 0.46 (0.12-1.17) 0.064 PD-L1.sup.+CD8.sup.−CD3.sup.+ 0.11 (0.03-0.17) 0.12 (0.05-0.38) 0.268 Total CD8 T cells (CD8.sup.+CD3.sup.+) 0.20 (0.03-0.52) 0.19 (0.06-1.21) 0.886 PD-L1.sup.+CD8.sup.+CD3.sup.+  0.02 (0.008-0.06)  0.01 (0.002-0.04) 0.244 .sup.aMedian absolute counts of T cell subsets; .sup.bValues in brackets ( ) are range of each data set; .sup.cMann-Whitney test; Bold-faced characters highlight p-value ≤ 0.05; LTS, long-term survivors; STS, short-term survivors; R, clinical responders; NR, non-responders.
Comparison with Cancer-Free Controls

(89) TABLE-US-00008 TABLE 8 Comparison of pre-treatment T cell subsets between cancer-free controls and cancer patients Groups Median.sup.d (Range.sup.e) p-value.sup.f mCRPC patients.sup.a PD-1.sup.+ CD4 T.sub.eff cells Cancer-free controls 11.7 (6.7-14.3) {close oversize brace} 0.456 LTS week 0  10.1 (5.4-14.5) {close oversize brace} 0.002 {close oversize brace} 0.0007 STS week 0 22.2 (8.4-33.0) PD-1.sup.+ CD8 T cells Cancer-free controls 13.7 (8.7-27.5) {close oversize brace} 0.931 LTS week 0  15.0 (5.3-28.0) {close oversize brace} 0.117 {close oversize brace} 0.246 STS week 0 22.2 (8.4-33.0) mCRPC patients.sup.b CTLA-4.sup.+ CD4 T cells Cancer-free controls   8.8 (6.1-13.4) {close oversize brace} 0.001 LTS week 0 .sup. 18.7 (14.2-21.6) {close oversize brace} 0.022 {close oversize brace} 0.030 STS week 0 13.7 (9.4-19.9) CTLA-4.sup.+ CD8 T cells Cancer-free controls   3.1 (3.0-10.6) {close oversize brace} 0.363 LTS week 0 .sup. 6.2 (2.1-12.2) {close oversize brace} 0.138 {close oversize brace} 0.788 STS week 0   5.5 (3.7-12.0) Metastatic melanoma patients.sup.c PD-1.sup.+ CD4 T.sub.eff cells Cancer-free controls   13.3 (11.3-21.1) {close oversize brace} 0.379 R week 0 .sup. 14.6 (11.5-33.9) {close oversize brace} 0.0002 {close oversize brace} 0.017 NR week 0   30.2 (15.4-43.8) PD-1.sup.+ CD8 T cells Cancer-free controls 15.6 (9.2-26.8) {close oversize brace} 0.009 R week 0 .sup. 31.2 (19.2-53.4) {close oversize brace} 0.058 {close oversize brace} 0.246 NR week 0 28.5 (9.3-56.9) PD-L1.sup.+ CD4 T cells Cancer-free controls 11.1 (3.6-32.5) {close oversize brace} 0.495 R week 0  15.1 (9.2-24.7) {close oversize brace} 0.047 {close oversize brace} 0.006 NR week 0   24.4 (18.1-38.1) PD-L1.sup.+ CD8 T cells Cancer-free controls 2.9 (1.9-4.6) {close oversize brace} 0.010 R week 0 .sup. 5.0 (2.8-14.6) {close oversize brace} 0.002 {close oversize brace} 0.341 NR week 0 4.6 (2.7-6.0) .sup.acancer-free controls, n = 7, LTS, n = 8; STS, n = 12; .sup.bcancer-free controls, n = 7, LTS, n = 6, STS, n—6; .sup.ccancer-free controls, n = 8, R, n = 8, NR, n = 13; .sup.dMedian values of immune checkpoint markers are % of the respective parent gate; .sup.eValues in brackets ( ) are range of each data set; .sup.fMann-Whitney test; Bold-faced characters highlight p-value ≤ 0.05; LTS, long-term survivors; STS, short-term survivors; R, clinical responders; NR, non-responders.

Example 13

(90) Establishing Optimal Cutoff Levels of Immune Subsets with Kaplan-Meier Plots and Log-Rank Test

(91) Overall survival of mCRPC patients with ≤21% of PD-1.sup.+ of CD4 T.sub.eff cells was significantly different from overall survival of patients with >21% of PD-1.sup.+ of CD4 T.sub.eff cells (p-value=0.0027, FIG. 10). Overall survival of mCRPC patients with ≤106 cells/μl of PD-1.sup.+ CD4 T.sub.eff cells was significantly different from overall survival of patients with >106 cells/μl of PD-1.sup.+ CD4 T.sub.eff cells (p-value=0.026, FIG. 10).

(92) Overall survival of mCRPC patients with >15.6% of CTLA-4.sup.+ of CD4 T cells was significantly different from overall survival of patients with ≤15.6% of CTLA-4.sup.+ of CD4 T cells (p-value=0.012, FIG. 10). Overall survival of mCRPC patients with >99 cells/μl of CTLA-4.sup.+ CD4 T cells was significantly different from overall survival of patients with ≤99 cells/μl of CTLA-4.sup.+ CD4 T cells (p-value=0.012, FIG. 10).

(93) Overall survival of metastatic melanoma patients with ≤23.5% of PD-L1.sup.+ of CD4 T cells was significantly different from overall survival of patients with >23.5% of PD-L1.sup.+ of CD4 T cells (p-value=0.027, FIG. 10).

Example 14

(94) Intracellular Cytokine Expression of PD-1.sup.+ CD4 T.sub.eff Cells

(95) Cytokine expression patterns of PD-1.sup.+ and PD-1.sup.−CD4 and CD8 T cells of pre-treatment PBMC from mCRPC patients were compared to PBMC from healthy donors (FIG. 11). Freshly thawed PBMC were stimulated with PMA and ionomycin for 4 hours in culture at 37° C., and intracellularly stained for IFNγ and IL-4. About 40% of PD-1.sup.+CD4 T cells expressed IFNγ compared to 5% of PD-1.sup.−CD4 T cells. On the other hand, almost 90% of PD-1.sup.+CD8 T cells expressed IFNγ, compared to 30 to 50% of PD-1.sup.−CD8 T cells. The ratio of PD-1.sup.+to PD-1.sup.− T cells expressing IFNγ is significantly greater for CD4 than for CD8 T cells. More PD-1.sup.+ than PD-1.sup.−CD4 T cells expressed IL-4 although the levels were low. CD8 T cells did not express IL-4. The percentages of IFNγ and IL-4-expressing PD-1.sup.+ and PD-1.sup.−CD4 T cells from cancer patients were comparable to healthy donors.

(96) Unstimulated pre-treatment PBMC from mCRPC patients and unstimulated PBMC from healthy donors were also stained for surface CD49b and Lag-3, and for intracellular granzyme B (FIG. 11). More PD-1.sup.+ CD4 T cells expressed CD49b, Lag-3, and granzyme B than PD-1.sup.− CD4 T cells. The percentages of Lag-3 expression were similar for cancer patients and healthy donors. However, the percentages of granzyme B and CD49b-expressing PD-1.sup.+ CD4 T cells were higher in cancer patients than in healthy donors. Granzyme B-expressing PD-1.sup.− CD4 T cells were also greater in cancer patients than in healthy donors, whereas CD49b-expressing PD-1.sup.− CD4 were similar for cancer patients and healthy donors. CD8 T cells displayed a different pattern of expression of granzyme B compared to CD4 T cells. Similar percentages of PD-1.sup.+ and PD-1.sup.− CD8 T cells from cancer patients expressed granzyme B, and both levels were higher than those from healthy donors. More PD-1.sup.+ than PD-1.sup.− CD8 T cells from healthy donors expressed granzyme B. Expressions of Lag-3 and CD49b were low and did not differ for PD-1.sup.+ and PD-1.sup.− CD8 T cells, or for cancer patients and healthy donors.

(97) Each of the references cited below is incorporated by reference herein in its entirety, or in relevant part, as would be apparent from context. The references are cited throughout this disclosure using superscripted numbers corresponding to the following numbered reference list.

REFERENCES

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(99) The disclosed subject matter has been described with reference to various specific and preferred embodiments and techniques. It should be understood, however, that many variations and modifications may be made while remaining within the spirit and scope of the disclosed subject matter.