Melanoma cell states define therapeutic vulnerabilities in a multimodal single-cell atlas

PURPOSE: High-dimensional tumor profiling has the potential to refine therapeutic decisions in metastatic melanoma, especially in the beyond-standard-of-care setting, but its clinical utility remains uncertain. The Tumor Profiler Study prospectively integrated multi-platform molecular, single-cell, spatial, and functional analyses into a 4-week clinical workflow. We report the biological and clinically actionable findings from the melanoma cohort. METHODS: Tumor and blood samples from 116 patients (126 tumors) underwent comprehensive profiling including CyTOF, single-cell RNA and DNA sequencing, imaging mass cytometry, proteotyping, bulk RNA/DNA sequencing, and two ex vivo drug-response platforms. Cross-modal integration defined melanoma phenotypes and identified treatment-relevant features. RESULTS: Single-cell protein profiling of 1.7 million melanoma cells identified six recurrent melanoma phenotypes present across melanoma subtypes and oncogenic drivers. Resulting tumor phenotypes stratified patients into six CyTOF-derived groups with distinct molecular characteristics and significantly different ex vivo responses to FDA-approved therapies. TYRP1-high classical melanocytic tumors showed broad drug resistance but reproducible sensitivity to cisplatin plus vindesine, consistent with elevated p53-associated DNA damage response pathways. Conversely, melanomas with heightened unfolded-protein-response activity exhibited marked sensitivity to proteasome inhibitors, supported by transcriptomic, proteomic, and functional readouts. CONCLUSION: This study establishes a clinically annotated, single-cell–resolved multi-omic atlas of advanced melanoma that links tumor phenotypes to actionable drug vulnerabilities. These findings provide a biological rationale for biomarker-driven, phenotype-guided interventional trials aimed at improving therapeutic outcomes in metastatic melanoma.