乳腺癌发生和转移相关差异基因GEO芯片分析

Analysis of differential genes for the occurrence and metastasis of breast cancer based on GEO microarray

目的乳腺癌是威胁女性健康的重大疾病,其发病率日益升高。本研究旨在筛选并验证与乳腺癌发生和转移相关的共同差异基因,并对差异基因进行生物信息学分析,对进一步筛选得出的差异基因进行表达水平验证。方法从基因表达综合(Gene Expression Omnibus,GEO)数据库中下载组织芯片数据GSE109169和GSE100534,用R语言软件筛选差异基因。运用Cytoscape3.6.0进行富集,筛选关键基因,运用STRING数据库对筛选出的共同差异基因进行蛋白互作网络分析,运用Kaplan-Meier Plotter绘制关键基因的生存曲线,运用实时荧光定量聚合酶链反应法(quantitative real-time polymerase chain reaction,qRT-PCR)验证关键基因的mRNA表达水平。结果筛选得到95个可能同时参与乳腺癌发生和转移过程的共同差异基因。共同差异基因主要富集于PI3K信号通路、p53通路、Jak-STAT信号通路、细胞-基质间黏附、细胞分化和胶原代谢过程等。关键蛋白互作网络由13个基因组成,将这13个基因与基因本体论(Gene Ontology,GO)和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)数据库分析得出的共同差异基因取交集,得到3个关键差异基因CDC6、ECT2和RRM2。生存分析表明,高表达这3个基因的患者预后差,总生存率低。qRT-PCR检测结果显示,与正常乳腺上皮细胞相比,这3个关键差异基因在乳腺癌细胞系中的表达升高,差异有统计学意义,P<0.05。结论 CDC6、ECT2和RRM2基因在乳腺癌中的表达高于其在正常乳腺上皮细胞中的表达,与乳腺癌者的预后密切相关。

OBJECTIVE Breast cancer,with the increasing mortality nowadays,is a major disease threatening women’s health.In present study,we aimed to screen and verify the co-differentially expressed genes(co-DEGs)relating to the pathogenesis and metastasis of breast cancer.METHODS Two different gene expression profiles GSE109169 and GSE100534 were obtained from Gene Expression Omnibus(GEO).Co-DEGs were analyzed by R project and enriched by Cytoscape3.6.0.The protein-protein interaction network was constructed by STRING.The survival curves of key DEGs were performed through Kaplan-Meier Plotter and their mRNA levels were tested by qRT-PCR.RESULTS Ninety-five co-DEGs genes with potential impact on the pathogenesis and metastasis of breast cancer were selected.They mainly enriched in PI3 K-Akt signaling pathway,p53 signaling pathway,Jak-STAT signaling pathway,cell-substrate adhesion,cell division and collagen metabolism.The main protein-protein interaction network were made up of 13 genes.Intersection elements of these 13 genes and the co-DEGs,CDC6,ECT2 and RRM2 was selected as key genes that may have specific effects on the pathogenesis and metastasis of breast cancer.Kaplan-Meier survival curve analysis revealed that high expression of CDC6,ECT2 and RRM2 resulted in a significant decrease in overall survival.Quantitative RT-PCR results revealed that CDC6,ECT2 and RRM2 were high expressed in breast cancer cells compared to normal breast epithelial cells(P<0.05).CONCLUSION The highly expressed genes,CDC6,ECT2 and RRM2,in breast cancer cells,may closely relate to the prognosis of breast cancer patients.