Dissecting cellular heterogeneity across two ocular melanoma subtypes by single-cell RNA sequencing

Ocular melanoma, the most common primary ocular malignancy in adults, is a rare subtype of melanoma characterized by high malignancy and poor prognosis. The aim of this study is to investigate the tumor cells and microenvironmental heterogeneity in two ocular melanoma subtypes at the single-cell level. We performed single-cell analysis across 28 ocular melanoma samples, including 14 uveal melanoma and 14 conjunctival melanoma (CoM) samples. Tumor cells and immune cells were analyzed to investigate the heterogeneous cellular composition in the tumor microenvironment. We compared the transcriptome profile of uveal melanoma and CoM to uncover subtype-specific biological signatures and molecular programs. Compared with uveal melanoma, CoM exhibited significantly higher immune cell infiltration. Tumor cells from the two subtypes displayed distinct transcriptional states and functional pathway activities. CoM was enriched for melanoma subpopulations characterized by epithelial–mesenchymal transition-related and stemness-associated transcriptional programs, together with relatively higher copy number variation scores, suggesting transcriptional and genomic features previously associated with more aggressive tumor behavior. While uveal melanoma was characterized by CD8 + T cells with relatively higher cytotoxicity- and terminal exhaustion-associated activities, CoM exhibited comparatively lower cytotoxicity and terminal exhaustion signatures but higher progenitor-like and exhausted-like effector features. CoM also showed increased infiltration of monocytes and CXCL3+ tumor-associated macrophages with elevated M2-associated signature activity. Our study provides a comprehensive comparison between two ocular melanoma subtypes at the single-cell level, revealing distinct cellular compositions, transcriptional state distributions, and molecular programs of tumor cells, as well as immune microenvironmental features.