Proteomic and T cell biomarkers identify sensitivity and resistance to immunotherapy in cancer patients

Abstract

Background: Immune checkpoint inhibitors are approved for a variety of malignancies but optimal patient selection remains challenging. Materials and Methods: Matrix-assisted laser desorption/ionization (MALDI) mass spectra were generated for pretreatment serum from 119 melanoma patients treated with nivolumab. A protein classifier development platform was employed to create a test that identifies patients with particularly good outcomes. Difference in outcomes between patients classified as group 1 and group 2 were assessed using log-rank p values and Cox proportional hazard ratios (HRs). We also identified pre-treatment peripheral blood T regulatory cell parameters by flow cytometry associated with outcome. Results: Of the 119 patients used in mass spec test development, 34 (29%) were classified as group 1. Group 1 had better survival (OS) and progression-free survival (p=0.002, p=0.014 respectively),. Thirteen patients (43%) from a Yale cohort and eleven patients (44%) from aMGH cohort were classified as Group 1. In the combined analysis of validation cohorts receiving anti-PD-1 agents, patients classified as Group 1 had better OS than Group 2 (p<0.0001, HR=0.162). For patients receiving combination PD-1/CTLA-4 blockade, 13 (62%) were classified as Group 1. Flow cytometry analyses suggested that decreased suppressive function of, and pSTAT3 signaling in T regulatory cells induced with PD-1 blockade was associated with a favorable outcome and prolonged survival. Conclusions: A serum proteomic test, and flow-based assays of T regulatory cells identify patients with long survival on anti-PD-1. The test has potential utility in identifying patients who derive benefit from anti-PD-1 and might gain little benefit from the addition of anti-CTLA-4. High levels of T regulatory cells that have intact suppressive function and low pSTAT3 signaling in patients resistant to PD-1 blockade suggest new strategies to eliminate T regulatory cells to overcome PD-1 resistance.