基于生物信息学筛选食管鳞状细胞癌生物标志物
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国家自然科学基金资助项目(81800434);四川省科技计划联合创新专项(2022YFS0627);西南医科大学附属医院博士科研启动基金项目(21037)


screening of biomarkers for esophageal squamous cell carcinoma based on bioinformatics
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    目的 应用生物信息学筛选食管鳞状细胞癌(ESCC)组织中差异表达的microRNA (miRNA)并预测其靶基因,分析生物学功能。方法 收集西南医科大学附属医院2021年6月—2022年2月期间的20对食管鳞状细胞癌癌组织和癌旁正常配对组织标本。通过GEO数据库下载ESCC miRNA表达谱芯片数据,利用R软件limma包进行归一化,筛选差异表达miRNA;利用在线工具Kaplan-meier Plotter对差异表达miRNA进行生存分析。通过qRT-PCR验证与生存率相关的差异miRNA在ESCC组织中的表达;利用TargetScan和miRDB预测靶基因,应用DAVID对靶基因进行GO功能注释和KEGG通路富集分析;通过STRING和Cytoscape构建PPI网络鉴定核心基因并构建miRNA-mRNA网络图;最后利用UALCAN评估核心基因在食管癌中的表达。结果 与癌旁正常组织相比,hsa-miR-93、hsa-miR-130b、hsa-miR-18a、hsa-miR-23b在ESCC组织中表达上调;而hsa-miR-1、hsa-miR-133b、hsa-miR-378a在ESCC组织中表达下调。其中3种下调miRNA在ESCC组织中的表达较癌旁正常组织有显著差异(P<0.01)。核心基因HNRNPK、HNRNPU、DHX15、MATR3、HNRNPA3在食管癌中的表达明显上调,且与hsa-miR-1密切相关。结论 ESCC癌组织中miRNA存在差异表达,miRNA可能通过作用靶基因间接参与调控相关的生物功能和通路,从而影响ESCC的发生发展

    Abstract:

    Objective Bioinformatics was applied to screen differentially expressed microRNAs (miRNAs) in esophageal squamous cell carcinoma(ESCC) and predict their target genes and analyze the biological functions.Methods Twenty,pairs of esophageal squamous cell carcinoma tissues and normal paired tissues adjacent to the carcinoma were collected from June 2021 to February 2022, Southwest Medical University Hospital. The miRNA expression profile microarray data of ESCC was downloaded from the GEO database and normalized using the R software limma package to screen for differentially expressed miRNAs. The survival analysis of differentially expressed miRNAs was performed using the online tool Kaplan-meier Plotter. The expression of differential miRNAs associated with survival was verified in ESCC tissues by qRT-PCR; targetScan and miRDB were used to predict target genes, and DAVID was used to annotate GO functions and KEGG pathway enrichment analysis of target genes. The PPI network was constructed by STRING and Cytoscape to identify core genes. The cytoscape was used to construct miRNA-mRNA network diagrams. UALCAN was used to evaluate the expression of core genes in esophageal cancer. Results Compared with normal tissues, hsa-miR-93, hsa-miR-130b, hsa-miR-18a, and hsa-miR-23b were expressed up-regulated in ESCC tissues; while hsa-miR-1, hsa-miR-133b, and hsa-miR-378a were expressed down-regulated in ESCC tissues. Three of these down-regulated miRNAs were significantly differentially expressed in ESCC tissues compared with normal tissues. The expressions of core genes HNRNPK, HNRNPU, DHX15, MATR3 and HNRNPA3 were significantly increased in esophageal cancer, and these core genes are closely related to hsa-miR-1. Conclusion The miRNAs are differentially expressed in ESCC tissues. The miRNAs may be involved in regulating relevant biological functions and pathways through target genes, thus affecting the occurrence and development of ESCC

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  • 在线发布日期: 2024-07-18
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