Whole transcriptome and proteome analyses identify ncRNAs and mRNAs to predict competing endogenous RNA networks in hepatitis B virus-induced hepatocellular carcinoma

The presence of the Hepatitis B virus (HBV) is considered as a valuable risk factor of hepatocellular carcinoma (HCC). To more deeply comprehend the molecular mechanism and transcriptome of HBV-induced HCC, we utilized tandem mass tagging (TMT)-based quantitative proteomics analysis and whole-transcriptome sequencing to analyze three sets of matched HepG2 hepatoma cells and HBV-positive HepAD38 cells. The differentially expressed (DE) proteins (1596), mRNAs (5263), miRNAs (581), lncRNAs (2672) and circRNAs (222) were subjected to differential expression and enrichment analyses in order to thoroughly assess the gene-regulatory circuits of HBV-induced HCC. Subsequently, the amounts of 321 DEproteins-DEmRNAs with common alterations were confirmed. According to functional pathway analysis, the DEproteins-DEmRNAs were primarily linked to signaling pathways, amino acid metabolism, and cellular function. Furthermore, the viability and significance of the ceRNA regulatory networks, LOC105377730/miR-4726-5p/FHL2 and hsa_circ_0001098/miR-2110/IGF2BP1, were randomly chosen and confirmed. Our work provides a valuable asset in terms of understanding regulatory activities at the RNA level, and might reveal fresh information about the fundamental mechanism and potential therapeutic targets of HBV-induced HCC.