Screening Of Differentially Expressed Genes In Triple-Negative Cancer Based On Bioinformatics

objective:Analyzing the triple-negative breast cancer and non-triple negative breast cancer related gene microarray by bioinformatics to screen differentially expressed genes（DEGs）of them.And then analyzing their functional annotation,signal pathway analysis,and protein-protein interaction network for further study.Meanwhile,Exploring tumor development related genes from the molecular level and looking for triple-negative breast cancer related genes provide a partial theoretical basis for better study of triple-negative breast cancer.Methods:1.The expression of triple-negative breast cancer and non-triple-negative breast cancer gene microarray data were extracted from Gene Expression Omnibus（GEO）database.The differentially expressed genes（DEGs）of TNBC and nTNBC were screened out with R language and Biocondctor packages according the setting conditions.The GO functional enrichment analysis and KEGG signal pathway of related genes was conducted with DAVID online analysis software.Subsequently,the protein-protein interaction（PPI）network was constructed using String software,and then,the data of PPI was imported into Cytoscape software to analyze the network modules with close interactions and screen the important nodes in whole network by MCODE plugin.2.Collecting paraffin-embedded tissues of TNBC,nTNBC and adjacent normal tissues to verify the genes obtained by using immunohistochemistry.Results:A total of 298 DEGs were screened out,including 121 upregulated and 177 downregulated ones（|log₂FC|>1.0,P<0.05）.GO functional annotation found upregulated differentially expressed genes of biological processes involved mainly in the mitotic nuclear division,cell proliferation,cell division,positive regulation of cell proliferation,sister chromatid cohesion and chromosome segregation;cellular components in cytoplasm;and molecular function in structural constituent of cytoskeleton.Then,downregulated differentially expressed genes of biological processes involved mainly in negative regulation of platelet-derived growth factor receptor signaling pathway,vesicle fusion,negative regulation of cell proliferation,glucose metabolic process,negative regulation of smooth muscle cell proliferation,brown fat cell differentiation,regulation of calcium ion-dependent exocytosis,positive regulation of cell differentiation,and axonogenesis;cellular components in extracellular space,extracellular exosomes,receptor complex,extracellular region,and proteinaceous extracellular matrix;and molecular functions in protein homodimerization activity,receptor binding,calcium-dependent phospholipid binding,heme binding,epidermal growth factor receptor binding,calcium ion binding,and enzyme binding.At the same time,the signal pathways involved in upregulation DEGS are cell cycle and Wnt signaling pathway while the downregulated DEGs are PPAR signaling pathway.The STRING online database was used to construct the protein-protein interaction network of differentially expressed genes.The Cytoscape software analyzed the network,and obtained 9 identified significant genes:CDC20,MELK,TPX2,CEP55,ASPM,NDC80,BUB1B,TTK,and DLGAP5,all of which are upregulated genes.The biological function of them involved in mitotic nuclear division,cell division,cell proliferation,sister chromatid cohesion,kinetochore and spindle.2.We verified the expression of some genes by immunohistochemistry experiments,the expression of NDC80 protein in breast cancer tissues was significantly higher than that in normal tissues adjacent to breast cancer,and the expression was also different between triple negative breast cancer tissues and non-negative breast cancer tissues.Conclusion:1.There are differences in gene expression between triple negative breast cancer and non-triple negative breast cancer;2.The expression of genes CDC20,MELK,TPX2,CEP55,ASPM,BUB1B,TTK,DLGAP5 and NDC80 were upregulated in triple-negative breast cancer;3.Protein NDC80 is highly expressed in triple negative breast cancer.