Multi-omics and machine learning refine HCC molecular subtypes and prognosis based on liquid-liquid phase separation related genes.

Accumulating evidence has demonstrated that biological processes associated with liquid-liquid phase separation (LLPS) play a critical role in cancer development. However, the effect of LLPS on hepatocellular carcinoma (HCC) remains largely unknown. In this study, we integrated consensus clustering with an ensemble machine learning framework to establish robust LLPS-related molecular subtypes and a consensus machine learning-driven LLPS-related signature (CMLLS) for HCC. The consensus clustering robustly identified three fundamental LLPS-driven subtypes (LS1-LS3), and the subsequent machine learning integration, which encompassed 101 algorithm combinations, objectively identified the most generalizable prognostic signature from multiple candidate genes. Our analysis revealed that LS3 exhibits the worst prognosis, significant upregulation of cell cycle and epithelial-mesenchymal transition (EMT)-related pathways, and enhanced immune resistance. Conversely, LS2 displays the best prognosis, enrichment in metabolism-related pathways, and increased sensitivity to immunotherapy. The CMLLS demonstrated robust predictive performance in prognostic stratification and effectively distinguished patients who would benefit from immunotherapy. This study provides novel insights into HCC heterogeneity at the LLPS level and offers a powerful tool for individualized treatment decision-making.