Targeted DNA Sequencing of Cutaneous Melanoma Identifies Prognostic and Predictive Alterations

Abstract

Importance: Cutaneous melanoma (CM) can be molecularly classified into four groups: BRAF mutant, NRAS mutant, NF1 loss, and triple wild type (TWT) tumors lacking these three alterations, yet their clinical significance remains unclear. Here, we integrate targeted DNA sequencing with comprehensive clinical followup in CM patients. Objective: To explore how molecular features and tumor mutational burden (TMB) impact outcomes in CM patients Design: Retrospective cohort study that assessed clinical and molecular features from patients with CM who underwent targeted next-generation sequencing as part of routine clinical care. Setting: Tertiary referral, comprehensive NCI cancer center from 2013 to 2023. Participants: A total of 254 patients with CM who had a CLIA certified targeted sequencing assay performed on their tumor tissue were included Exposure: A CLIA certified targeted sequencing assay was performed as standard of care on 254 patients with CM treated at a single institution. Main Outcome: NRAS mutation correlated with significantly worse overall survival compared to other TCGA driver groups. Elevated TMB correlated with improved progression-free survival on combination checkpoint inhibition (anti-PD1 plus anti-CTLA4). Results: Of 254 patients with cutaneous melanoma, 77 were BRAF mutant (30.3%), 77 were NRAS mutant (30.3%), 47 were NF1 mutant (18.5%), 33 were TWT (13.0%) and the remaining 20 (7.9%) carried mutations in multiple driver genes (BRAF/NRAS/NF1 co-mutated), most commonly in NF1 (n=19 or 90%). Consistently, NF1 mutant tumors harbored numerous significantly co-altered genes compared to BRAF or NRAS mutant tumors. Most TWT tumors (n=29, 87.9%) harbored a known pathogenic Ras/MAPK mutation. NRAS mutant melanoma demonstrated significantly decreased overall survival (HR for death 2.95, 95% CI 1.13 to 7.69, p=0.027, log rank test). Of the 154 cases with available TMB data, the median TMB was 20 (range 0.7 to 266 mutations/Mb). Elevated TMB was associated with significantly longer progression-free survival following dual agent ICI (HR 0.26, 95% CI 0.07 to 0.90, p=0.033, log-rank test). Conclusions and Relevance: NRAS mutation in CMs correlated with significantly worse overall survival. Elevated TMB was associated with increased progression-free survival for patients treated with combination dual ICI, supporting the potential utility of TMB as a predictive biomarker for ICI response in melanoma.