Single-cell RNA sequencing and AlphaFold 3 insights into cytokine signaling and its role in uveal melanoma

Background Uveal melanoma (UVM) is a form of eye cancer with a poor prognosis, particularly in metastatic patients. This study aimed to elucidate the cellular heterogeneity within UVM and identify prognostic biomarkers.Methods We performed single-cell RNA sequencing (scRNA-seq) on primary and metastatic UVM samples. A UVM-specific gene signature was constructed using LASSO regression and validated via ROC curve analysis in the TCGA-UVM and GSE84976 cohorts. AlphaFold 3 was used to predict the 3D structures of key proteins. T-cell populations were analyzed using pseudotime trajectory mapping and interaction network visualization. CRISPR-Cas9 screening analysis was conducted to identify hub genes and cytokine pathways that may serve as therapeutic targets. Additionally, we constructed the Dictionary of Immune Responses to Cytokines at single-cell resolution to evaluate cytokine signatures.Results ScRNA-seq revealed five major cell types within UVMs and subdivided them into seven distinct subtypes. Cytokine signaling analysis revealed differential expression of cytokine signaling in immune-related genes (CSIRGs) across these subtypes in primary and metastatic tumors. The UVM-specific gene signature demonstrated high predictive accuracy in ROC curve analysis and was associated with overall survival in Kaplan-Meier survival analyses. Additionally, AlphaFold 3 predicted the 3D structures of key proteins with high confidence. T-cell population analysis revealed complex developmental pathways and interaction networks in UVM. Myeloid-derived suppressor cells (MDSCs) were found to be increased in metastatic UVM, correlating with the enrichment of GM-CSF. CRISPR-Cas9 screening analysis identified hub genes and cytokine pathways with low gene effect scores across cell lines, indicating their potential importance in UVM.Conclusion This study identified critical cellular subtypes and prognostic biomarkers in UVM, shedding light on targeted therapies. The insights into cytokine signaling and T-cell dynamics within the UVM microenvironment provide a foundation for developing personalized therapeutic strategies to improve patient outcomes.