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王晨峰,卢旭华*.基于基因表达汇编数据库的外周血中脊柱椎间盘退行性变诊断标志物的生物信息学分析[J].脊柱外科杂志,2022,20(5):322-326,333.
基于基因表达汇编数据库的外周血中脊柱椎间盘退行性变诊断标志物的生物信息学分析     点此下载全文 (Fulltext)
王晨峰  卢旭华*
海军军医大学长征医院骨科, 上海 200003
基金项目:国家自然科学基金面上项目(81071507,81572201)
DOI:10.3969/j.issn.1672-2957.2022.05.007
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摘要:
      目的 通过生物信息学分析椎间盘退行性变(IDD)相关的差异表达基因(DEG),寻找疾病的新型诊断标志物。方法 通过基因表达汇编(GEO)数据库GSE124272、GSE150408数据集下载IDD相关的外周血样本芯片数据,筛选出IDD组和正常组之间的DEG。使用DAVID在线数据库对DEG进行基因本体(GO)功能富集和京都基因与基因组百科全书(KEGG)信号通路富集,然后利用STRING在线数据库和Cytoscape软件构建蛋白质-蛋白质相互作用(PPI)网络并获取关键基因,并利用GSE23130数据集中的纤维环样本芯片数据进行验证。利用GSE124272、GSE150408数据集中的数据,采用受试者工作特征(ROC)曲线评估外周血中关键基因的诊断效能。结果 联合分析后筛选出597个DEG,包含363个上调基因和234个下调基因。GO功能富集分析发现DEG主要参与细胞黏附、细胞凋亡、趋化作用和细胞迁移等功能,KEGG分析发现DEG主要参与细胞外基质受体相互作用和癌症中的信号通路。PPI网络分析筛选出17个关键基因,经验证获得RBMX、EEF1A1、SSR1和POLR2C这4个基因,ROC曲线分析显示这4个基因对IDD诊断效能显著,曲线下面积分别为0.763、0.741、0.710、0.702。结论 RBMX、EEF1A1、SSR1和POLR2C或可成为IDD的新型诊断标志物,为该病进一步的功能研究提供理论依据。
关键词:脊柱  椎间盘退行性变  基因表达  病因学
Bioinformatics analysis of diagnostic blood biomarkers for intervertebral disc degeneration based on Gene Expression Omnibus database    Fulltext
Wang Chenfeng  Lu Xuhua*
Department of Orthopaedics, Changzheng Hospital, Naval Medical University, Shanghai 200003, China
Fund Project:
Abstract:
      Objective To explore the differentially expressed genes(DEG) related to intervertebral disc degeneration(IDD) through bioinformatics analysis methods,and to find new diagnostic biomarkers of the disease.Methods The chip data of peripheral blood samples related to IDD were downloaded from GSE124272 and GSE150408 of the Gene Expression Omnibus(GEO) database,and the DEG were identified between the IDD patients and the normal.The online database DAVID was utilized to complete the gene ontology(GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes(KEGG) signaling pathway enrichment.The database STRING and Cytoscape software were applied to construct a protein-protein(PPI) network to obtain hub genes,and the annulus fibrosus sample chip data in GSE23130 dataset was used for verification.The data of GSE124272 and GSE150408 datasets were used to evaluate the diagnostic efficacy of hub genes in peripheral blood.Results After conjoint analysis,597 DEG were screened out,including 363 up-regulated genes and 234 down-regulated genes.GO functional enrichment analysis demonstrated that DEG were mainly involved in cell adhesion,cell apoptosis,chemotaxis and cell migration;and KEGG analysis showed that DEG were mainly involved in extracellular matrix receptor interactions and signaling pathways in cancers.Seventeen hub genes were screened out based on the PPI network analysis,and RBMX,EEF1A1,SSR1 and POLR2C were verified.Receiver operating characteristic(ROC) curve analysis showed that the 4 genes had significant diagnostic efficiency for IDD,and the areas under curve were 0.763,0.741,0.710 and 0.702 respectively.Conclusion RBMX,EEF1A,SSR1,and POLR2C may be new diagnostic markers related to IDD in peripheral blood species,which provides a theoretical basis for further functional studies of the disease.
Keywords:Spine  Intervertebral disc degeneration  Gene expression  Etiology
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