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

Abstract

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 in <i>NFKBIE</i>, a negative regulator of <i>NFkB</i>, were found exclusively in the responders. Mutations in <i>NKBIE</i>-related genes were also enriched in the responder group compared to the non-responders. Patients that harbored <i>NFKBIE</i>-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 the <i>TNFalpha</i> signaling via <i>NFkB</i> pathway was one of the top pathways with differential expression in responders vs. non-responders. In vitro <i>NFkB</i> activity assays indicated that the G34E variant caused loss-of-function of <i>NFKBIE</i>, and resulted in activation of <i>NFkB</i> signaling. Flow cytometry assays indicated that G34E variant was associated with upregulation of CD83 in human melanoma cell lines. These results suggest that <i>NFkB</i> activation and signaling in tumor cells contributes to a favorable anti-PD1 treatment response, and clinical screening to include aberrations in <i>NFkB</i>-related genes should be considered.