Proteogenomic studies to understand mechanisms and drivers of resistance to immunotherapies

Project Summary/Abstract Melanoma is the deadliest form of skin cancer. Its incidence is on the rise with 106,000 new cases expected in the U.S. in 2021. Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of early and advanced melanoma, with concurrent anti-CTLA-4 and anti-PD-1 monoclonal antibodies demonstrating a response in ~50% of patients, including highly durable responses. Unfortunately, there are no adequate biomarkers to predict response to single agent or combination ICI, and dual checkpoint blockade is associated with significant grade 3/4 immune-related adverse events (irAEs) in ~55% of patients. The goals of our PTRC are designed to address two unmet clinical needs: (i) improve our understanding of mechanisms of resistance to ICIs to design more effective immunotherapies and combinations, and (ii) identify potential biomarkers to select patients appropriately for single agent vs combination immunotherapies and to predict and monitor irAEs. In our Preclinical Arm, we will perform integrated proteogenomic analysis of clinically annotated, pre-treatment biopsies from melanoma patients who received ICI. The data will be analyzed in the context of clinical annotations to refine an existing signature of melanoma ICI response identified by our team and to further elucidate mechanisms of ICI response/resistance and signatures associated with irAEs. In our Clinical Arm, we will analyze clinical trial biospecimens using MRM-based assays to confirm & extend findings generated in the Preclinical Arm.