Fig. 1

Comparison of DNA methylation patterns in liver tissues using MeD-seq. The volcano plot depicted DNA methylation scores for statistically significant (DESeq2 analysis, FDR < 0.01) hypermethylated (red) and hypomethylated (cyan) DMRs across transcriptional start site (TSS), CpG islands (CpG), and gene bodies (GB) regions. A In liver tissues, cirrhotic HCC (n = 6) exhibited distinct DNA methylation patterns compared to cirrhotic controls (n = 15), demonstrated through both differentially methylation analysis on either the three mentioned regions (TSS, CpG islands and gene bodies) and the full genome-wide analysis which also contains intergenic DMRs (heatmap). B Principal component analysis on DMRs of the three mentioned regions (TSS, CpG islands and gene bodies) revealed DNA methylation profiles for each liver sample of cirrhotic HCC and cirrhosis. C The comparison of DNA methylation between livers from patients with cirrhosis and non-cirrhotic liver disease (NCLD, n = 10) or benign hepatic lesions (BHL, n = 7) yielded significantly fewer DMRs than the comparison between liver samples from cirrhotic HCC and non-cirrhotic controls. D The comparison of DNA methylation from livers of non-cirrhotic HCC patients (n = 8) and non-cirrhotic controls (n = 17) exhibited a higher number of DMRs than the comparison between BHL and NCLD. DMRs located on the X- and Y-chromosome were removed to avoid gender-related effects