Systematic tracking of disrupted modules identifies significant genes and pathways in hepatocellular carcinoma

Abstract

The objective of the present study is to identify significant genes and pathways associated with hepatocellular carcinoma (HCC) by systematically tracking the dysregulated modules of re-weighted protein-protein interaction (PPI) networks. Firstly, normal and HCC PPI networks were inferred and re-weighted based on Pearson correlation coefficient. Next, modules in the PPI networks were explored by a clique-merging algorithm, and disrupted modules were identified utilizing a maximum weight bipartite matching in non-increasing order. Then, the gene compositions of the disrupted modules were studied and compared with differentially expressed (DE) genes, and pathway enrichment analysis for these genes was performed based on Expression Analysis Systematic Explorer. Finally, validations of significant genes in HCC were conducted using reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis. The present study evaluated 394 disrupted module pairs, which comprised 236 dysregulated genes. When the dysregulated genes were compared with 211 DE genes, a total of 26 common genes [including phospholipase C beta 1, cytochrome P450 (CYP) 2C8 and CYP2B6] were obtained. Furthermore, 6 of these 26 common genes were validated by RT-qPCR. Pathway enrichment analysis of dysregulated genes demonstrated that neuroactive ligand-receptor interaction, purine and drug metabolism, and metabolism of xenobiotics mediated by CYP were significantly disrupted pathways. In conclusion, the present study greatly improved the understanding of HCC in a systematic manner and provided potential biomarkers for early detection and novel therapeutic methods.

Keywords: dysregulated gene; hepatocellular carcinoma; modules; pathway; protein-protein interaction network; reverse transcription-quantitative polymerase chain reaction.

Figure 1.

(A) Score-wise distribution of interactions. (B) Expression correlation-wise distribution of interactions in normal and hepatocellular carcinoma. HCC, hepatocellular carcinoma.

Figure 2.

Distribution of correlation density of modules in normal and hepatocellular carcinoma (inset, zoom into 0.3–0.5). HCC, hepatocellular carcinoma.

Figure 3.

Swapping behavior of disrupted modules. A swapping phenomenon means that novel genes replace existing genes, forming physical interactions with the remaining ones in these modules within a tumor. (A) A module in normal condition. (B) The paired disrupted module of (A) in hepatocellular carcinoma. (C) A normal module. (D) The paired disrupted module of (C). Relative to normal conditions, a novel gene CEBPZ in module (B) replaced the existing gene RRS1, and in module (D) a novel gene POLR2F replaced the existing gene GUCY2F. Furthermore, a new POLR2I gene was added. In addition, the interaction score changed. Nodes represent genes, while lines represent the interactions between these genes. The thickness of the lines represents the interaction score between two genes. PDCD11, programmed cell death 11; BYSL, bystin-like; NIP7, nucleolar pre-rRNA processing protein; WDR12, WD repeat domain 12; RRS1, ribosome biogenesis regulator homolog; DDX18, DEAD box protein 18; CEBPZ, CCAAT/enhancer binding protein (C/EBP), zeta; ENTPD1, ectonucleoside triphosphate diphosphohydrolase 1; POLR2C, polymerase (RNA) II (DNA directed) polypeptide C; NME4, NME/NM23 nucleoside diphosphate kinase 4; GUCY2D, guanylate cyclase 2D; POLR1B, polymerase (RNA) I polypeptide B; GUCY2F, guanylate cyclase 2F; POLR2F, polymerase (RNA) II (DNA directed) polypeptide F; POLR2E, polymerase (RNA) II (DNA directed) polypeptide E; POLR2I, polymerase (RNA) II (DNA directed) polypeptide I.

Figure 4.

Relative expression of PLCB1, CYP2C8, CYP2B6, CYP3A43, CYP2E19 and GMNN. The expression of one gene in HCC compared with normal controls was indicated by its P-value. All the six genes analyzed were significantly differently expressed in HCC (*P<0.001 vs. control). If a gene exhibited a P>0.05, it would be not significantly differently expressed; by contrast, a gene with P<0.05 was considered to be significantly differently expressed. PLCB1, phospholipase C beta 1; CYP, cytochrome P450; GMNN, geminin; HCC, hepatocellular carcinoma.