In the present study, we explored a total of 116 common DEGs comprising 27 up-regulated and 89 down-regulated DEGs. Then, DAVID together with KOBAS was used to analyze GO and KEGG pathways, and PPIs of these DEGs were visualized with Cytoscape. The PPI network complex of 78 nodes and 209 edges was constructed. According to the results of Cytotype MCODE, 15 up-regulated genes were identified from the PPI network complex. We found that CDK1, PRC1, NEK2, DTL, ANLN, PBK, RACGAP1, CDKN3, ECT2, HMMR, CCNB1, RRM2, BUB1B, TOP2A, and ASPM had a significantly worse survival rate and high expression in the HCC samples. Furthermore, KEGG pathway enrichment re-analysis results of the 15 selected genes indicated that CCNB1, CDK1, and RRM2 were significantly enriched in the p53 signaling pathway. In GSEA analysis, highly-expressed samples of three core genes were enriched in the p53 signaling pathway in the validation dataset. Our bioinformatics analysis results predicted that CCNB1, CDK1, and RRM2 may be closely related to the development of HBV-related HCC. The verification results in liver cancer tissues and cells showed that expression of the core genes was higher than in the normal tissues and cells, while transfection of si-p53, and knockdown of p53 led to lower expression, indicating that three core genes in the p53 signaling pathway may play a significant role in the occurrence and development of HBV-related HCC. Finally, five lncRNA (NEAT1, MALAT1, XIST, AC021078.1, and SNHG16) were identified with close interactions by predicting the ceRNA network of the core genes.
CCNB1, G2/Mitotic-specific cyclin B1, was shown to play an important role in the occurrence and development of tumors. Mussnich reported that down-regulation of CCNB1 could reduce cell proliferation [34]. Zhao[35] reported that up-regulation of CCNB1 played a part in the pathology of pituitary adenomas in the cell cycle. CDK1, cyclin-dependent kinases A was suggested to play a role in the development of HCC. Some results strongly suggested that CDK1 acts as a tumor-specific mediator, affecting apoptin-induced cytotoxicity in HCC cells. CDK1 could be an important factor in cell division [36], and several CDK1 substrates, such as histone H1 and PI3K/AKT, play crucial roles in cell cycle modulation [37, 38]. RRM2 ribonucleotide reductase regulatory subunit M2, is one of the protein genes encoding ribonucleoreductase (RR) [39]. RRM2 can be used as a prognostic biomarker for a variety of cancer types, such as colon cancer, breast cancer [40–42], and overexpression of RRM2 also stimulates the migration, invasion, and proliferation of many other solid tumor cells. A previous study showed that RRM2 is directly regulated by p53 to supply nucleotides to repair damaged DNA [43]. A study also showed that p53R2-dependent DNA synthesis plays a pivotal role in cell survival by repairing damaged DNA in the nucleus and that dysfunction of this pathway might result in activation of p53-dependent apoptosis to eliminate dangerous cells[44]. Small-interfering RNA-mediated knockdown of RRM2 can depress HCC cell proliferation [45]. Furthermore, Lee [46] indicated that high expression of RRM2 could be a useful marker to predict early recurrence of HCC following curative hepatectomy.
Moreover, the p53 signaling pathway was a potent barrier for tumor progression and it plays important roles in hepatocarcinogenesis [47–50]. Tu[51] found that the activation of F-box and WD repeat domain-containing 7 (Fbxw7) via adenoviral delivery of p53 caused increased proteasomal degradation of cyclin E and c-Myc, thus recombinant human adenovirus-p53 injection could be a possible therapeutic agent for HCC.
Non-coding RNAs (ncRNAs), which cannot code proteins, were originally believed to be “junk RNAs” [52]. However, recently ncRNA was believed to play a vital role in HCC. Many of the lncRNAs were frequently dysregulated in both HBV-related HCC tissues and HBV-/HBx-expressing cell lines. Most studies mention the underlying mechanisms of lncRNAs in HCC progression are the alterations of lncRNA expression that may result in altered proliferative capacities and colony formation abilities of HCC cells. Some results suggested dysregulation of lncRNAs was related to migration, invasion, and metastasis of HCC cells by regulating the cell cycle, thus contributing to the proliferation of HCC cells [53–56]. In our study, NEAT1, MALAT1, XIST, AC021078.1, and SNHG16 were identified to have close interactions with three core genes from the CeRNA network, thus suggesting dynamic changes in these competing endogenous RNA activities and they may play important roles in regulating the expression and function of core genes associated with the occurrence and progression of HBV-HCC.