Clonorchis sinensis infection alters the methylation and hydroxymethylation of hepatocellular carcinoma

Clonorchis sinensis (Cs) infection is prevalent in Southeast Asia and has been classified as a Group I carcinogen by the International Agency for Research on Cancer, posing significant risks to the human liver and biliary system. While recent studies have linked Cs infection to poorer outcomes in hepatocellular carcinoma (HCC) patients, the precise molecular mechanisms underlying its effect on HCC remain to be fully elucidated. This study investigates the epigenetic changes in Cs-infected HCC using whole-genome bisulfite sequencing and whole-genome oxidative bisulfite sequencing to map 5-methylcytosine and 5-hydroxymethylcytosine profiles at single-nucleotide resolution. We identified 29 differentially methylated regions and 13 differentially hydroxymethylated regions in Cs-infected HCC, which were associated with 28 differentially methylated/hydroxymethylated-associated genes (DAGs/DhAGs). The methylation levels of four promoter CpG sites of DAGs/DhAGs were found to correlate with prognosis in Cs-infected HCC, while two key DMR/DhMR-associated genes, DHDH and KCNQ3, were significantly linked to overall survival. Our study provides the first detailed epigenetic map of Cs-associated HCC, uncovering novel insights into potential biomarkers and therapeutic targets that could enhance prognostic predictions and inform treatment strategies for patients affected by this condition.