Study On Genes Related To Hepatocarcinogenesis And Its Clinical Significance Based On Bioinformatics

Objective: In this study,based on bioinformatics study of hepatocarcinogenesis-related genes and their clinical significance,we aim to enrich the study of hepatocarcinogenesis-related genes and do some useful work for finding biomarkers that are helpful for the early diagnosis and prognostic evaluation of liver cancer as well as new drug targets for liver cancer treatment.Research methods: Hepatocellular carcinoma gene chip GSE40367,GSE41804,GSE101685,GSE112790 were downloaded from the GEO database,the above four gene chip data were analyzed using the Limma R package to obtain differentially expressed genes,the above differentially expressed genes were further integrated and analyzed using Robust Rank Aggreg to obtain the final differentially expressed genes;Cluster Profiler and Org using the R language.Hs.Eg.Sb,Enrichplot and Ggplot2 package GO and KEGG analysis of the above differentially expressed genes obtained after Robust Rank Aggreg treatment;then the differentially expressed genes were plotted into protein interaction network maps by STRING online analysis database and visualized using Cytoscape software,hub genes were selected according to the arrangement of the number of nodes,and then the intersection of PPI network hub genes with the top 20 up-regulated and top 20 down-regulated differentially expressed genes was obtained by Wayne online drawing website,from which NUF2 gene,which is currently poorly studied,was determined as the target gene for the next study,Oncomine database was applied to analyze the expression of NUF2 gene in different liver cancer research chips in the next step,and Firebrowse was used to analyze the expression of NUF2 in most human cancers;then Kaplan-Meier survival analysis curve was drawn using Oncolnc data.Finally,the hepatic stellate cell line LX-2 and three hepatoma cell lines Hep G2,Hep3 B,and Huh-7 were cultured for q PCR experiments to verify the differential expression levels of NUF2 gene in the normal hepatic stellate cell line LX-2 and three hepatoma cell lines Hep G2,Hep3 B,and Huh-7.Results: 338 differentially expressed genes were finally obtained from the four gene chip data,and GO analysis results showed that the biological processes involved in differentially expressed genes mainly involved organelle fission,mitosis,and small molecule catabolic processes;their changes affecting cellular components mainly focused on spindles,intermediates,and chromosomal centromere regions;their molecular functions were mainly manifested in iron ion binding,heme binding,and tetrapyrrole binding,while KEGG results showed that differentially expressed genes were mainly enriched in chemical carcinogenesis,retinol metabolism,cell cycle,drug metabolism-cytochrome P450,and exogenous substances metabolized through cytochrome P450.The 30 hub genes selected by the protein interaction network map were intersected with the top 20 up-regulated and top 20 down-regulated differentially expressed genes to obtain 10 genes: KIF20 A,RRM2,CCNB1,NUF2,TOP2 A,MELK,ASPM,DLGAP5,KIF4 A,and TTK.The results of Oncomine's analysis showed that NUF2 gene was relatively highly expressed in liver cancer,and the boxplot of Firebrowse showed that NUF2 expression was generally higher in most human cancers including liver cancer than in normal tissues.However,Kaplan-Meier survival analysis curves depicted according to the data of Oncolnc showed that HCC patients with lower NUF2 expression had a better prognosis than those with higher NUF2 expression(P = 0.000461).The results of the final q PCR experiments indicated that the expression levels of NUF2 gene in the three hepatoma cell lines,Hep G2,Hep3 B,and Huh-7,were significantly higher than their expression levels in the control hepatic stellate cell line LX-2,and the differences were statistically significant.Conclusion:(1)Chemical carcinogenesis,retinol metabolism,cell cycle,drug metabolism-abnormal activation of cytochrome P450 as well as xenobiotics through cytochrome P450 metabolism and other pathways are closely related to hepatocarcinogenesis.(2)KIF20A,RRM2,CCNB1,NUF2,TOP2 A,MELK,ASPM,DLGAP5,KIF4 A,and TTK may be closely related to hepatocarcinogenesis,in which NUF2 gene expression is increased in hepatoma cell lines,and may be associated with poor prognosis of liver cancer.