Prognostic value of PRAME gene promoter methylation and expression in hepatocellular carcinoma

BACKGROUND: PRAME is a member of the cancer-testis antigen family and exhibits abnormally high expression in various solid tumors. Epigenetic regulation plays a critical role in the development and progression of hepatocellular carcinoma (HCC). Alterations in promoter methylation of specific genes have been widely recognized as valuable biomarkers for predicting cancer risk and assessing prognosis. OBJECTIVE: This study systematically investigated the biological function and clinical relevance of PRAME promoter methylation in HCC. METHODS: Using data from The Cancer Genome Atlas (TCGA) cohort, we identified methylation-associated prognostic genes and examined the association between PRAME promoter methylation, its mRNA expression levels, overall survival (OS), and clinicopathologic characteristics. We then validated these findings in an independent HCC cohort from Shulan (Hangzhou) Hospital using MethylTarget multiplex gene methylation detection technology. To investigate the potential role of PRAME in vascular invasion and metastasis, we conducted Gene Ontology (GO) enrichment analysis and Gene Set Enrichment Analysis (GSEA) at both histological and cellular levels. RESULTS: Analyses across three HCC cohorts consistently showed that the PRAME promoter is generally hypomethylated in tumor tissues, and this hypomethylation was significantly correlated with elevated PRAME mRNA expression. In both the TCGA and Shulan (Hangzhou) Hospital cohorts, PRAME promoter hypomethylation was associated with more advanced clinicopathologic features and shorter OS. Moreover, PRAME promoter methylation status was strongly linked to vascular invasion and distant metastasis in HCC. Further functional analyses revealed significant upregulation of Wnt signaling and cell adhesion-related pathways in tissues with high PRAME expression, a finding corroborated by single-cell RNA sequencing data. CONCLUSION: Hypomethylation of the PRAME promoter is closely associated with poor overall survival, adverse clinicopathologic features, vascular invasion, and metastasis in HCC patients. It plays a pivotal role in regulating gene expression and promoting tumor invasiveness. These findings suggest that PRAME promoter methylation may serve as a promising epigenetic biomarker for prognostic evaluation in HCC.