Single-cell transcriptomic landscape deciphers intratumoral heterogeneity and subtypes of acral and mucosal melanoma.
Li Y., Cui Z., Song X., Chen Y., Li C., Shi J., Qian W., Ren G., Zhou J., Li C., Ma X., Chen Y., Jia D., Zhang Y., Zhang Z., Zhang R., Zhang Z., Chen Y., Xu Z., Chen W., Miao X., Yu H., Chen J., Wang K., Goding CR., Wei Z., Li T., Cui R.
PURPOSE: To identify the specific intratumoral and microenvironmental heterogeneity of acral (AM) and mucosal melanoma (MM), we aimed to delineate their distinct cellular compositions, evolutionary trajectories, and subtype-specific therapeutic strategies. EXPERIMENTAL DESIGN: Single-cell transcriptomic and genomic landscapes were analyzed across 42 melanoma samples (28 AM, 11 MM, and 3 non-acral cutaneous melanoma [CM]), supplemented by in vitro and in vivo validation. Tumor and stromal cells were profiled using scRNA-seq, whole-exome sequencing, and functional assays, including transwell migration, co-culture systems, and xenograft models. RESULTS: Tumor cells exhibited divergent evolutionary routes, with MM dominated by MGP⁺/PCOLCE⁺ subpopulations showing high epithelial-to-mesenchymal transition (EMT) potential. MM displayed elevated neutrophil infiltration and CXCL3⁺ tumor-associated macrophages, while AM was enriched with PI16⁺ cancer-associated fibroblasts (CAFs) promoting tumor proliferation. Molecular classification revealed MM subtypes: an antigen-presenting subtype linked to favorable outcomes and a proliferative subtype associated with recurrence. TIGIT⁺ Treg cells were enriched in AM, suggesting targeted inhibition potential. Genomic analysis connected BRAF/NRAS mutations to ALDOA⁺ stem-like tumor cells and identified PTGDS as a therapeutic target in triple-WT melanomas. CONCLUSIONS: Our study provides a comprehensive comparison of AM and MM, uncovering subtype-specific stromal-immune interactions and molecular programs. The findings highlight actionable targets (e.g., TIGIT in AM, CXCL3⁺ macrophages in MM) and propose a framework for precision therapies, biomarker-driven trials, and risk stratification to improve outcomes in these aggressive melanomas.