基于生物信息学分析肾透明细胞癌预后相关关键基因

doi:10.24920/003651

摘要/Abstract

摘要：

目的识别与肾透明细胞癌预后相关的关键基因。
方法基于生物信息学分析技术对GEO数据库中的62个肾透明细胞癌样本和54个正常肾组织的数据集（GSE12606,GSE36895和GSE66272）进行分析。首先在GEO2R和J Venn网站上获取差异表达基因基因,之后采用GO和KEGG对基因进行功能注释;在使用STRING网站构建PPI网络后,采用Cytoscape软件的MCODE App对核心基因进行筛选;最后利用GEPIA网站分析与生存率有关的核心基因。
结果我们共发现648个差异表达基因,包括222个上调表达基因和426个下调表达基因。PPI蛋白网络分析共发现28个表达上调的核心基因,其中7个核心基因（CCNE2,CDK1,CDC6,CCNB2,BUB1,TTK和PTTG1）富集于细胞周期,4个（CCNE2,CDK1,CCNB2和RRM2）富集于p53信号通路。GEPIA生存率分析发现：CDK1,CCNB2,RRM2,BUB1,PTTG1与肾透明细胞癌患者的生存率密切相关。肾透明细胞癌患者BUB1,CCNB2,PTTG1和RRM2等4个关键基因的表达量高于正常人群（P<0.05）。
结论 BUB1、CCNB2、PTTG1、RRM2等4个上调差异表达基因可能是肾透明细胞癌患者预后关键预测基因。

关键词: 肾透明细胞癌, 生物信息学分析, 差异表达基因

Abstract:

Objective To identify new genes that correlate with prognosis of clear-cell renal cell carcinoma (ccRCC) via bioinformatics analysis.
Methods The gene expression profiles of 62 ccRCC and 54 normal kidney tissues were available from the Gene Expression Omnibus database: GSE12606, GSE36895 and GSE66272. The differentially expressed genes were screened with GEO2R and J Venn online tools. Functional annotation including Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was applied to identify the possible function of the hub genes involved in prognosis of ccRCC. In protein protein interaction network (PPI network), the STRING online tool was used to visualize the network of the differentially expressed genes, and the core gene was selected by MCODE App in Cytoscape software. Finally, GEPIA Survival Plot was performed to assess genes associated with worse survival.
Results We totally found 648 differentially expressed genes, including 222 up-regulated genes and 426 down-regulated genes. PPI network showed that in 28 up-regulated genes 7 (CCNE2, CDK1, CDC6, CCNB2, BUB1, TTK and PTTG1) enriched in cell cycle and 4 genes (CCNE2, CDK1, CCNB2 and RRM2) enriched in p53 signaling pathway. GEPIA Survival Plot assay revealed that ccRCC patients carrying CDK1, CCNB2, RRM2, BUB1, and PTTG1 had a worse survival. GEPIA Box Plot showed that BUB1, CCNB2, PTTG1, and RRM2 were over expressed in the ccRCC tissues in contrast to the normal tissues (P<0.05).
Conclusion ccRCC patients with the four up-regulated differentially expressed genes including BUB1,CCNB2,PTTG1, and RRM2might manifest a poor prognosis.

Key words: clear-cell renal cell carcinoma, bioinformatical analysis, differentially expressed genes

Ping Jiang, Taotao Sun, Cunwu Chen, Renshu Huang, Zhimei Zhong, Xinjian Lou, Gang Liu, Lin Wang, Ruihua Zuo. Identification of Prognostic Related Hub Genes in Clear-Cell Renal Cell Carcinoma via Bioinformatical Analysis[J].Chinese Medical Sciences Journal, 2021, 36(2): 127-134.

图/表 7

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