Integrative genomics characterizes HCC eRNAs for prognosis and targeted therapy.

Hepatocellular carcinoma (HCC), a leading cause of cancer-related mortality globally, exhibits limited diagnostic and therapeutic biomarkers despite its clinical significance. Emerging evidence has positioned enhancer RNAs (eRNAs) as pivotal regulators in tumorigenesis, prompting this study to systematically identify HCC-specific eRNA signatures and elucidate their functional relevance. Through integrative analysis of three independent cohorts (n = 115 tumor-normal pairs), we identified three eRNA biomarkers-CAP2e, COLEC10e, and MARCOe-exhibiting significant differential expression between HCC and adjacent tissues, with validation in The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) dataset. Notably, these eRNAs demonstrated strong positive correlation with their host genes (r > 0.83, p < 0.05), suggesting co-regulatory mechanisms. Functional enrichment revealed their involvement in oncogenic pathways including MAPK signaling, with MARCOe emerging as a candidate therapeutic target due to its association with immune evasion pathways. Multi-omics characterization including survival analysis, immune infiltration profiling, and pan-cancer comparison further validated these eRNAs' diagnostic specificity and prognostic value. Critical experimental validation of MARCO was performed via immunohistochemistry (IHC) in 60 HCC tumor-normal paired samples, demonstrating significantly reduced MARCO protein expression in tumors (tumor vs. normal: 15% vs. 65% positivity, p < 0.001). MARCO overexpression experiments in HCC cells revealed significant alterations in MAPK pathway-related genes, suggesting potential therapeutic implications through pathway modulation. This investigation provides the first comprehensive identification of clinically relevant eRNA biomarkers for HCC, establishing their dual roles in disease progression and therapeutic targeting.