Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy

Immunotherapy, such as anti-PD1, has improved the survival of patients with metastatic melanoma. However, predicting which patients will respond to immunotherapy remains a significant knowledge gap. In this study we analyzed pre-immunotherapy treated tumors from 52 patients with metastatic melanoma and monitored their response based on RECIST 1.1 criteria. The responders group contained 21 patients that had a complete or partial response, while the 31 non-responders had stable or progressive disease. Whole exome sequencing (WES) was used to identify biomarkers of anti-PD1 response from somatic mutations between the two groups. Variants in codons G34 and G41 inNFKBIE, a negative regulator ofNFkB, were found exclusively in the responders. Mutations inNKBIE-related genes were also enriched in the responder group compared to the non-responders. Patients that harboredNFKBIE-related gene mutations also had a higher mutational burden, decreased tumor volume with treatment, and increased progression-free survival. RNA sequencing on a subset of tumor samples identified that CD83 was highly expressed in our responder group. Additionally, Gene Set Enrichment Analysis showed that theTNFalphasignaling viaNFkBpathway was one of the top pathways with differential expression in responders vs. non-responders. In vitroNFkBactivity assays indicated that the G34E variant caused loss-of-function ofNFKBIE, and resulted in activation ofNFkBsignaling. Flow cytometry assays indicated that G34E variant was associated with upregulation of CD83 in human melanoma cell lines. These results suggest thatNFkBactivation and signaling in tumor cells contributes to a favorable anti-PD1 treatment response, and clinical screening to include aberrations inNFkB-related genes should be considered.