Methods of identifying and treating patient populations amenable to cancer immunotherapy

A method of treating cancer in a human subject having cancer comprising:

• (a) generating a first scaffold map from a first population of blood leukocytes isolated from the human subject having cancer, wherein the cancer is melanoma, and a second scaffold map from a second population of blood leukocytes isolated from a control, wherein the control is the human subject having cancer at an earlier time, a distinct human subject having cancer that is unresponsive to anti-cancer immunotherapy, or a healthy human subject, wherein the cancer is melanoma;
• (b) generating a first cell population expression profile from the first scaffold map, and a second cell population expression profile from the second scaffold map;
• (c) comparing the first cell population expression profile and the second cell population expression profile to determine expression level of CD127low PD-1low T cells in the human subject having cancer and the control;
• (d) administering a therapeutically effective amount of a composition comprising an immune checkpoint inhibitor, wherein the immune checkpoint inhibitor is ipilumimab, to the human subject having cancer, if the expression level of CD127low PD-1low T cells in the human subject having cancer is greater than the expression level of CD127low PD-1low T cells in the control, thereby treating the cancer in the human subject having cancer.