Our findings demonstrated that epigenetic regulations, including DNA methylation of RPL30, ALDOB, IGF2, and TIMP1, led to changes in the DNA methylation profiles of RPL30 (p value ≤ 1.00 × 10−3), ALDOB (p value ≤ 0.83), IGF2 (p value ≤ 1.00 × 10−3), and TIMP1 (p value ≤ 1.00 × 10−3), which contributed to the significant changes in the gene expression profiles of RPL30 (p value ≤ 1.00 × 10−3), ALDOB (p value ≤ 7.2 × 10−2), IGF2 (p value ≤ 1.1 × 10−2), and TIMP1 (p value ≤ 1.00 × 10−3) to progress from PBC&PSC to HCC, as shown in Figure 7. This evidence concerns the gene TIMP1 and hepatocellular carcinoma.