Integrated Biology Analysis Reveal Distinct Gene Classes And Regulatory Networks In Hepatocellular Carcinoma

Hepatocellular carcinoma is one of the highly malignant and lethal cancers in the world. Its complex process of molecular pathogenesis indicated that HCC is caused by multiple etiological factors with the involvement of multiple types of genes during its development and progression.We have performed microarray analysis of mRNA and microRNA (miRNA) to measure the comparative levels of mRNAs and miRNAs in HCC (C), non-cancerous liver (P) and normal liver (N) tissues. After integrating all these results with the information from Database of Gene Ontology (biological process) and KEGG Pathway, we analyzed the possible interaction among different genes and among miRs and genes, and further constructed the interaction network.Based on the analysis of differences in expression of genes, their relevant biological pathways, the core regulators and effectors in the complex network, we can categorize all these alterations into 3 classes of gene profilings.Class I:Altered expression of genes, biological pathways and their core regulator and effectors enriched in non-cancerous liver.The alterations included up-regulated immune response pathway and down-regulated metabolic pathways. Relevant to such changes, genes for regulation of cell proliferation, apoptosis, defense and immune response were up-regulated; while genes responsible for carbohydrate transport, sterol and androgen biosynthesis, and bile acid synthesis were down-regulated. The core regulators were TNXB and COL1A1; while the effector was ITGB7. These changes might implicate the biological consequences of inflammation, relevant cell death and regeneration as well as some damages of hepatic function present in the non-cancerous liver possibly attributed to chronic hepatitis or cirrhosis.Class II:Altered expression of genes, biological pathways and their core regulator and effectors enriched in both HCC and non-cancerous liver versus normal liver tissues.These change included up-regulated pathways of immune response, neuroactive ligand-receptor interaction, and extensively down-regulated metabolic pathways of androgen, estrogen, bile acid, fatty acid, glycerol-lipid, amino acid, glycolysis/gluconeogenesis and PPAR signaling pathway. The relevant changes in gene expressions involved up-regulated expression of genes for cell mobility, integrin-mediated signaling pathway, negative regulation of apoptosis, positive regulation of immune response and down-regulated expression of genes for metabolism related to above-mentioned pathways. The core regulators and effectors included RFX5, COL4A1, SPP1 and CD74, ACTB, TGFB1, SDC3 respectively.Class III:Altered expression of genes, biological pathways and their core regulators and effectors enriched in HCC only, as compared with non-cancerous and normal liver.These changes covered up-regulated biological pathways in cell proliferation, anaerobic glycolysis, DNA repair, DNA replication, DNA recombination, protein folding, spliceosome assembly and snRNP biogenesis etc; and the down-regulated pathways of metabolism of amino acid, lipoprotein, metal response, lipid as well as those in negative regulation of fibrinolysis, blood coagulation and proteolysis. The relevant gene expression changes were evident in the up-regulated expression of genes for cell cycle, DNA replication, ECM-receptor interaction, focal adhesion and Jak-STAT signaling pathway, as well as in the down-regulated expression of genes related to axon guidance, cytokine-cytokine receptor interaction and metabolism of amino acid, fatty acid and others. The core regulator in the network included 4 collagen-related genes,3 laminin-related genes, THBS1, THBS2 and RFXANK; while the key effectors were PLG and PIK3R3.The above global transcriptomic network analysis may provide us following implications:Firstly, the class I profile might putatively represent the early events of hepatocarcinogenesis, i.e. the alteration only present in the liver which bears the HCC, but not in the tumor. One of the interpretations of the absence of such expression abnormality in HCC is the alteration of gene expression present at the initial stage subsided once the cancer developed, though many alterations may persist and even further intensify along with cancer progression. Alternatively, these gene alterations are attributed to chronic hepatitis and/or cirrhosis; therefore, they would not be observed in cancer nodules.Secondly, the class II profile indicates that the dramatic alterations in non-cancerous liver even comparable to those in HCC itself may represent the precancerous status, including cell anti-apoptosis, metabolic disorder and immune abnormality.Thirdly, the class III profile may represent the alterations unique for cancer, including abnormality in cancer cells as well as their microenvrioment.Besides, we found hsa-mir-29c, hsa-mir-424, hsa-mir-370, hsa-mir-198 all downergulated in HCC. These miRNAs should be classified into Class III genes. Notably, all these miRNAs are core regulators in the regulatory network.Furthermore, we have constructed 6 classifiers based on gene (mRNAs) and miRNAs. These classifiers can remarkably differentiate HCC versus non-cancerous liver. Moreovers, these classifiers are intimately correlated to presence or absence of metastasis and recurrence. Therefore, our results would be important for development of biomarkers for differential diagnosis, prediction of HCC clinical behaviors and personalized HCC treatment.Taken together, our studies may put some insight into better understanding of the progressive alteration in genome-wide network during the course of hepatocarcinogenesis and HCC progression as well as developing novel biomarkers for predictive and personalized medicine.