Multi-omics integration and machine learning define robust molecular subtypes and prognostic signatures in hepatocellular carcinoma

BACKGROUND: Hepatocellular carcinoma (HCC) exhibits high aggressiveness and substantial molecular heterogeneity, yet precise and individualized therapeutic strategies remain limited. Comprehensive multi-omics integration and machine learning-driven modeling hold promise for refining molecular subtyping and improving prognostic prediction in HCC. METHODS: We developed a computational framework integrating multi-omics datasets from HCC patients. Ten clustering algorithms were combined to perform integrative multi-omics clustering and identify molecular subtypes. Ten machine learning algorithms were subsequently applied to construct a consensus prognostic signature. The clinical relevance of subtypes and risk groups was assessed through survival analysis, immunotherapy response prediction, and tumor immune microenvironment profiling. Single-cell RNA sequencing and spatial transcriptomics data were incorporated to determine the cellular origins and spatial expression patterns of key genes. RESULTS: Integrative multi-omics analysis identified four prognostically distinct cancer subtypes (CS1-CS4), with CS4 exhibiting the most favorable clinical outcomes. Five key genes were selected to build a robust prognostic model. Patients in the low-risk group demonstrated significantly better survival, an enhanced response to immunotherapy, and a higher probability of exhibiting a "hot tumor" phenotype. Conversely, the high-risk group showed poorer prognosis and reduced immunotherapy benefit. Single-cell and spatial transcriptomics analyses revealed that the key genes are predominantly enriched in malignant hepatocytes and display spatial patterns suggestive of tumor regional heterogeneity. CONCLUSIONS: This study provides a refined molecular classification of HCC through integrative multi-omics analysis and establishes a machine learning-driven prognostic model with potential utility in early prognosis prediction and immunotherapy stratification. The dual-dimensional single-cell and spatial transcriptomic analyses further illuminate the cellular and spatial features associated with key prognostic genes. Prospective clinical validation is required to confirm the model's predictive performance.