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预防医学  2022, Vol. 34 Issue (9): 906-913    DOI: 10.19485/j.cnki.issn2096-5087.2022.09.009
  疾病控制 本期目录 | 过刊浏览 | 高级检索 |
应用生物信息学方法鉴定食管鳞状细胞癌生物标志物
张玉俊1, 王岩2, 地力亚尔·吾斯曼江1, 刘广超1, 聂艳武1, 朱琳2
1.新疆医科大学公共卫生学院,新疆 乌鲁木齐 830054;
2.新疆医科大学附属肿瘤医院,新疆 乌鲁木齐 830011
Identification of biomarkers for esophageal squamous cell carcinoma based on bioinformatics
ZHANG Yujun1, WANG Yan2, Diliyaer Wusimanjiang1, LIU Guangchao1, NIE Yanwu1, ZHU Lin2
1. School of Public Health, Xinjiang Medical University, Urumqi, Xinjiang 830054, China;
2. Affiliated Cancer Hospital of Xinjiang Medical University, Urumqi, Xinjiang 830011, China
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摘要 目的 采用生物信息学方法鉴定与食管鳞状细胞癌(ESCC)相关的生物标志物,为ESCC诊断和靶向治疗提供依据。方法 从GEO数据库筛选并下载基因芯片数据集GSE23400、GSE45670、GSE20347和GSE17351,使用在线分析工具GEO2R筛选ESCC的差异表达基因(DEGs),并采用韦恩图确定4个数据集共同的DEGs。通过DAVID数据库对DEGs进行基因本体论(GO)功能注释和京都基因与基因组百科全书(KEGG)通路分析;采用STRING数据库进行蛋白相互作用(PPI)分析,采用Cytoscape软件的MCODE插件识别关键模块;采用CytoHubba插件筛选连接度最高的关键基因,并通过UALCAN平台进行表达验证;采用Kaplan-Meier plotter数据库对关键基因进行生存分析。结果 共获得146个共同DEGs,包括102个上调基因和44个下调基因。GO功能注释分析显示,共同DEGs主要参与细胞周期过程、有丝分裂后期姐妹染色单体分离和细胞周期调控过程,存在于纺锤体、中心体细胞组分,发挥酶结合和腺苷三磷酸(ATP)结合的分子功能。KEGG通路分析显示基因显著富集于细胞周期、ECM-受体相互作用和卵母细胞减数分裂。筛选出10个关键基因,经基因表达水平验证和生存分析,有7个基因与ESCC预后有关,分别为CCNB1、CDK1、BUB1B、ZWINT、AURKA、MAD2L1和MCM4,且均在ESCC组织中表达升高。结论 通过生物信息学方法鉴定获得ESCC的7个关键基因,可作为ESCC潜在生物标志物和治疗靶点。
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张玉俊
王岩
地力亚尔·吾斯曼江
刘广超
聂艳武
朱琳
关键词 食管鳞状细胞癌生物信息学生物标志物差异表达基因    
AbstractObjective To identify biomarkers for esophageal squamous cell carcinoma (ESCC) using bioinformatics tools, so as to provide insights into diagnosis and targeted therapy of ESCC. Methods The gene expression datasets GSE23400, GSE45670, GSE20347 and GSE17351 were screened and downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) of ESCC were screened using the online tool GEO2R, and the common DEGs among the four datasets were determined using Venn diagram. Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the DAVID database, and protein-protein interaction (PPI) analysis was performed using the STRING database. The key modules were identified using molecular complex detection (MCODE) plugin in the Cytoscape software, and hub genes with the highest connectivity degree were identified using the CytoHubba plugin, and the gene expression was validated on the UALCAN platform. Survival analysis of hub genes was performed using the Kaplan-Meier plotter database. Results Totally 146 common DEGs were screened, including 102 up-regulated genes and 44 down-regulated genes. GO annotation analysis showed that the common DEGs were mainly enriched in biological processes of cell cycle, sister chromatid separation in the late mitotic phase and cell cycle regulation, enriched in cellular components of spindle and centrosome, and molecular functions of enzyme binding and ATP binding. KEGG pathway analysis showed that DEGs was significantly enriched in cell cycle, extracellular matrix (ECM)-receptor interactions and oocyte meiosis. A total of 10 hub genes were screened, and gene expression validation and survival analysis identified 7 genes associated with prognosis of ESCC, including CCNB1, CDK1, BUB1B, ZWINT, AURKA, MAD2L1 and MCM4, which were all highly expressed in ESCC specimens. Conclusion Seven hub genes of ESCC are identified based on bioinformatics, which may serve as biomarkers and therapeutic targets for ESCC.
Key wordsesophageal squamous cell carcinoma    bioinformaticr    biomarker    differentially expressed gene
收稿日期: 2022-03-24      修回日期: 2022-06-25     
中图分类号:  R735.1  
基金资助:省部共建中亚高发病成因与防治国家重点实验室开放课题项目(SKL-HIDCA-2020-ER3,SKL-HIDCA-2020-33); 新疆维吾尔自治区自然科学基金项目(2021D01C379)
通信作者: 朱琳,E-mail:476674539@qq.com   
作者简介: 张玉俊,硕士研究生在读
引用本文:   
张玉俊, 王岩, 地力亚尔·吾斯曼江, 刘广超, 聂艳武, 朱琳. 应用生物信息学方法鉴定食管鳞状细胞癌生物标志物[J]. 预防医学, 2022, 34(9): 906-913.
ZHANG Yujun, WANG Yan, Diliyaer Wusimanjiang, LIU Guangchao, NIE Yanwu, ZHU Lin. Identification of biomarkers for esophageal squamous cell carcinoma based on bioinformatics. Preventive Medicine, 2022, 34(9): 906-913.
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http://www.zjyfyxzz.com/CN/10.19485/j.cnki.issn2096-5087.2022.09.009      或      http://www.zjyfyxzz.com/CN/Y2022/V34/I9/906
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