Deciphering dysregulation and CpG methylation in hepatocellular carcinoma using multi-omics and machine learning.

This study investigates the altered expression and CpG methylation patterns of histone demethylase in hepatocellular carcinoma (HCC), aiming to uncover insights and promising diagnostics biomarkers. Leveraging TCGA-LIHC multi-omics data, we employed R/Bioconductor libraries and Cytoscape to analyze and construct a gene correlation network, and LASSO regression to develop an HCC-predictive model. In HCC, downregulation is correlated with CpGs hypermethylation. Differential gene correlation analysis unveiled a liver carcinoma-associated network marked by increased cell division and compromised liver-specific functions. The LASSO regression identified a highly accurate HCC prediction signature, prominently featuring CpG methylation at cg02871891. Our study uncovers CpG hypermethylation at cg02871891, possibly influencing downregulation in HCC, suggesting these as promising biomarkers and targets.