Clonorchis sinensis infection alters the methylation and hydroxymethylation of hepatocellular carcinoma

Background The molecular mechanisms contributing to the poor prognosis of Clonorchis sinensis ( Cs )-infected hepatocellular carcinoma (HCC) remain poorly understood, especially when it comes to DNA methylation. Methods Using parallel whole-genome bisulfite sequencing (WGBS) and whole-genome oxidative bisulfite sequencing (oxWGBS), we characterized the profiles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in Cs -infected HCC tumors and adjacent non-tumor tissues at single-nucleotide resolution. These profiles were compared with data from non- Cs -infected HCC available in the GEO database. Additionally, we investigated the impact of DNA methylation modifications on differential gene expression and prognosis in Cs -infected HCC by analyzing HCC related data from the TCGA database and RNA-seq data from previous studies. Results Here, we reported the methylation and hydroxymethylation landscapes of Cs -infected and Cs -non-infected HCC patients at single-nucleotide resolution by WGBS and oxWGBS, respectively. 29 differentially methylated regions (DMRs) and 13 differentially hydroxymethylated regions (DhMRs) were found in Cs -infected HCC tumor tissues compared to Cs -non-infected HCC tumor tissues. Following, we identified 28 differentially methylated/hydroxymethylated-associated genes (DAGs/DhAGs), two genes (DHDH and KCNQ3) of which were significantly correlated with the overall survival of HCC. Finally, we also revealed that four Cytosine-phosphate-Guanine sites in the promoter of DAGs/DhAGs certainly affect the survival outcomes of HCC. Conclusions This study provides the first comprehensive characterization of DNA methylome and hydroxymethylome landscapes in Cs -infected HCC, shedding light on the impact of on HCC methylation and offering new insights into the role of Cs in HCC progression. Our findings also highlight the key DMRs/DhMRs and DAGs/DhAGs in Cs -infected HCC tumors, which could serve as promising epigenetic biomarkers for predicting the prognosis and therapeutic targets of Cs -associated HCC.