A Comprehensive Single Cell Atlas of Healthy Ocular Tissue and Uveal Melanoma Reveals Mutation- and Uveal Tract-Associated Cell States

Uveal melanoma is a rare but aggressive intraocular malignancy with limited therapeutic options and a high risk of metastatic relapse. Although its mutational landscape is well defined, how genetic factors, uveal location, and disease progression shape cell states and the tumor ecosystem remains poorly understood. We integrate single-cell RNA sequencing and spatial transcriptomics across a cohort spanning healthy uveal tissue, primary tumors, and metastases. We uncover a continuous shift in melanoma cell states during disease progression, from differentiated, pigmentation-associated programs toward stress- and epithelial-to-mesenchymal transition-associated states. This trajectory is modulated by uveal tract location, with iris tumors exhibiting a more differentiated phenotype and choroidal tumors enriched for stemness-associated features that localize to melanoma-rich regions correlating with genomic instability. In parallel, genetic background defines distinct melanoma cell states and tumor–immune interactions. Together, these findings define clinically relevant cellular states and provide a framework for understanding metastatic progression and therapeutic vulnerability.