Analysis Of Key Genes In Esophageal Squamous Cell Carcinoma Based On GEO Database And Bioinformatics Methods And Preliminary Verification

Objective:To provide the theoretical basis for the diagnosis and treatment of esophageal squamous cell carcinoma(ESCC),bioinformatics methods were used to identify the key genes related to ESCC which biological functions were analyzed and verified by experiments.Methods:1.ESCC-related microarray data sets were downloaded from the gene expression database—Gene Expression Omnibus(GEO).The differentially expressed genes(DEGs)in ESCC and normal esophageal tissues were screened by Venn Diagram.GO enrichment and KEGG pathway analysis of differential genes were analyzed by DAVID online tools.And then,the STRING database and Cytoscape software were used to discover the key genes of ESCC.Finally,we performed the expression validation and overall survival(OS)analysis of key genes in the GEPIA and Kaplan Meier Plotter databases.2.The expression of TTK and CDKN3 in ESCC was detected by immunohistochemical method.The relationship between the two proteins and the clinicopathological features of ESCC were analyzed.And the SPSS software Kaplan Meier was used to analyze the survival of patients.Results:1.A total of 512 common DEGs were screened from the four ESCC-related gene chips,of which 508 genes had the same expression trend,including 248 up-regulated genes and 260 down-regulated genes.2.The protein-protein interaction(PPI)network of DEGs was built by STRING online analysis platform.The MOCODE plug-in of Cytoscape software was used to analyze the PPI network and construct the core module,which contained 46 genes;The MCC algorithm of the cytoHubba plug-in rankedthe key genes and obtained the top 20 genes with the highest connectivity:ASPM,AURKA,AURKB,BUB1,BUB1B,CDC6,CDC45,CDK1,CDKN3,CENPF,KIF4A,MAD2L1,NDC80,PBK,RRM2,TOP2A,TPX2,TRIP13,TTK,UBE2C,PRC1.3.GO enrichment analysis suggested that key genes were mainly involved in molecular biological processes,including cell division,mitotic nuclear division,DNA replication,G1/S conversion of the mitotic cell cycle,sister chromatid condensation,and initiation of DNA replication;KEGG pathway analysis suggested that key genes were mainly enriched in signaling pathways such as cell cycle,DNA replication,oocyte meiosis,p53 signaling pathway,and progesterone-mediated oocyte maturation.4.After further expression validation and clinical prognosis analysis,13 key ESCC genes,including AURKA,BUB1,BUB1B,CDC6,CDC45,CDK1,CDKN3,CENPF,MAD2L1,PBK,TOP2A,TPX2,TTK,were found to be highly expressed in esophageal squamous cell carcinoma tissues.All of them may be associated with the prognosis of ESCC.5.The results of immunohistochemical method showed that TTK and CDKN3 were highly expressed in 212 ESCC tissues and 88 squamous intraepithelial neoplasia tissues.They were little or no expression in 70 cases of normal esophageal mucosa tissues.The difference was statistically significant(P<0.05).6.In ESCC tissues,TTK protein was positively correlated with CDKN3(rs=0.312).But their expression was not significantly associated with clinical characteristics of patients such as gender,age,tumor location,gross type,histological grade and lymph node metastasis(P>0.05).7.Over survival of 91 patients analysed by the SPSS software Kaplan Meier suggested that TTK and CDKN3 was associated with the prognosis of ESCC.CDKN3 was a risk factor for ESCC.Conclusions:1.Based on the GEO database,we preliminarily discussed the potential of 13 genes AURKA,BUB1,BUB1B,CDC6,CDC45,CDK1,CDKN3,CENPF,MAD2L1,PBK,TOP2A,TPX2 and TTK as the key genes in the diagnosis and prognosis of ESCC.It provided a theoretical basis for studying the pathogenesis of ESCC and finding potential therapeutic targets.However,the specific mechanisms and roles of these key genes in the development of ESCC need to be verified at the functional level through further molecular biology experiments.2.The overexpression of TTK and CDKN3 was related to occurrence and progression of ESCC and they may be potential therapeutic targets for ESCC.3.The overexpression of TTK and CDKN3 was associated with the prognosis,and CDKN3 was a risk factor for ESCC.4.The overexpression of TTK and CDKN3 in ESCC was positively correlated,and they may play a role in the occurrence and progression of ESCC through the common regulation mechanism.