Screening Differentially Expressed Genes For Basal-like Breast Cancer Based On Bioinformatics

Objective:Basal-like breast cancer?BLBC?is the most aggressive subtype of breast cancer and is associated with poor outcomes.BLBC has a triple negative phenotype,and the molecular mechanism has not been fully discovered,therefore BLBC lacks effective treatment.This study intends to screen the differentially expressed genes?DEGs?of BLBC through bioinformatics analysis,analyze the DEGs,explore the potential gene characteristics of BLBC,and provide ideas for the further study of BLBC.Methods:1.Analysis of microarray data sets?GSE25066?for basal and non-basal breast cancers?nBLBC?downloaded from the gene expression database?GEO?of the national center for biotechnology information?NCBI?.After evaluating the data quality of gene chip,using R language and Bioconductor packages,DEGs were screened by setting screening conditions P<0.01 and differential expression multiple?log₂FC?>1 or<-1.The ClusterProfiler package of R software and KOBAS 3.0 online database were used to conduct enrichment analysis of related gene function and signal pathway of DEGs.Meanwhile,the protein-protein interaction network?PPI?was constructed through the STRING online database,and the results were imported into Cytoscape software.MCODE plug-in was used to build the model,and finally the key genes were screened out and visualizing.2.The paraffin-embedded tissues of normal breast tissu,BLBC and nBLBC were collected for immunohistochemical analysis to verify the expression of screened DLGAP5 gene in these three tissues.Results:1.After analysising of BLBC and nBLBC tissue chips,a total of395 DEGs were screened,among which 193 were up-regulated differentially expressed genes and 202 were down-regulated differentially expressed genes.GO function enrichment analysis was conducted on up-regulated and down-regulated differentially expressed genes respectively.The up-regulated differentially expressed genes of biological processes mainly involved in gland development,sister chromatid separation,microtubule cytoskeleton organization involved in mitosis,regulation of mitotic metaphase/anaphase transition,mitotic spindle assembly checkpoint,mitotic spindle assembly checkpoint and spindle assembly,etc;cellular components in extracellular matrix,and centromeres region,etc;molecular functions in G protein-coupled receptor binding,serine-type endopeptidase activity,and cadherin binding,etc.Then,the down-regulated differentially expressed genes of biological processes mainly involved in gland development,monosaccharide metabolic process,cell maturation and regulation of lipid metabolic process,etc;cellular components in apical plasma membrane and apical part of cell;molecular functions in insulin-like growth factor I binding,sulfur compound transmembrane transporter activity and steroid binding.The up-regulated differentially expressed genes were mainly enriched in the cell cycle,metabolic pathway,p53signaling pathway,wnt signaling pathway,PI3K-Akt signaling pathway,and signaling pathway regulating pluripotency of stem cells.Down-regulated differentially expressed genes were mainly enriched in the metabolic pathways,PI3K-Akt signaling pathway,MicroRNAs in cancer,and AMPK signaling pathway.DEGs was imported into STRING database to construct protein-protein interaction network?PPI?,and 13 key genes including EZH2CDC20 FOXM1 MYBL2 TYMS CCNB2 BUB1 CENPE MCM4 MCM5 TTK DLGAP5 and TPX2 were finally found through Cytoscape analysis.The key genes are of biological processes mainly involved in cell cycle regulation,and sister chromatids are separated,spindles are assembled,telomere regions are composed,spindles constitute spindles,spindles constitute spindles,constitute DNA replication,and cell cycle oocytes reduce the signaling pathways such as division and DNA replication.2.Immunohistochemical experiments showed that the expression levels of DLGAP5 in normal breast tissue,BLBC and nBLBC tissues were significantly different,P<0.05.The positive expression rate of DLGAP5 in invasive breast cancer was higher than that in normal breast cancer tissues,and the positive expression rate of DLGAP5 in BLBC was higher than that in nBLBC.The results of immunohistochemistry were consistent with the results of bioinformatics analysis,which further verified the high expression of DLGAP5 in BLBC.It was speculated that the high expression of DLGAP5might influence the process of chromosome separation and chromosomal instability?CIN?of BLBC.To some extent,it also indicates that this method can be used to identify potential target genes based on the existing research database.Conclusion:1.There are differentially expressed genes in basal breast cancer and non-basal breast cancer tissues.2.Thirteen key genes,including EZH2,CDC20,FOXM1,MYBL2,TYMS,CCNB2,BUB1,CENPE,MCM4,MCM5,TTK,DLGAP5 and TPX2 are highly expressed in basal-like breast cancer and may be involved in the development of basal-like breast cancer.3.The expression of DLGAP5 gene in invasive breast cancer was higher than that in normal breast tissue,and the expression of DLGAP5 gene in basal-like breast cancer was higher than that in non-basal-like breast cancer.