基于TCGA数据库分析参与结肠癌进展的关键基因

Screen of key genes involved in colon cancer progression based on TCGA database

目的通过生物信息学方法与实验验证挖掘结肠癌发生发展中的关键基因,预测可用于诊断结肠癌(colorectal cancer,CRC)的生物标志物。方法从TCGA数据库中获取结肠癌转录组数据,用edgR,Deseq2和limma3个R包分析癌组织与癌旁组织的差异性,将得到的差异基因进行Gene Ontology(GO)和Kyoto Encyclopedia of Genes and Genomes(KEGG)分析。通过STRING数据库构建蛋白-蛋白互作网络后,置于Cytoscape软件中进行可视化及核心基因筛选。利用R包对核心基因进行Kaplan-Meier单因素生存分析,通过qRT-PCR对13对结肠癌及配对癌旁组织中各核心基因的表达进行检测。结果研究共获得1645个差异基因,其中712个上调,933个下调。上调基因主要富集在类风湿性关节炎、IL-17信号通路、细胞因子-细胞因子受体相互作用、Wnt信号通路、Hippo信号通路。下调基因主要富集在矿物质吸收、神经活性配体-受体相互作用、CAMP信号通路、胆汁分泌、碳酸氢盐在肾单位近曲小管重吸收等通路。研究共获得10个核心基因:CXCL8、CXCL1、CXCL12、CXCL5、CSF2、CXCL2、CXCL3、CXCL11、CCL19和CCL13。生存分析显示CXCL8、CXCL5、CSF2、CCL13、CCL19、CXCL12与结肠癌预后相关,qRT-PCR检测结果证实CXCL8、CXCL5和CSF2结肠癌及癌旁组织中的表达有明显差异。结论结肠癌发生发展过程中CXCL8、CXCL5和CSF2基因存在表达变化,可能在结肠癌的发生发展中起关键作用。

Objective Bioinformatics methods and experimental validation were co-used to predict the biomarkers that can be used to diagnose colorectal cancer(CRC).Methods Transcriptome data of colon cancer were obtained from TCGA database,and genes differenly expressed in cancer tissues and paracancer tissues were analyzed by three R packages,edgR,Deseq2 and limma,and the obtained differential genes were subjected to Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis.The protein-protein interaction network was constructed by STRING database,and then put into Cytoscape software for visualization and core gene screening.Kaplan-Meier one-way survival analysis was performed on the core genes using the R package,and the expression of each core gene in 13 pairs of colon cancers and paired paracancerous tissues was examined by qRTPCR.Results A total of 1645 differential genes were obtained in this study,of which 712 were up-regulated and 933 were down-regulated.The up-regulated genes were mainly enriched in rheumatoid arthritis,IL-17 signaling pathway,cytokine-cytokine receptor interaction,Wnt signaling pathway,and Hippo signaling pathway.Downregulated genes were mainly enriched in mineral absorption,neuroactive ligand-receptor interaction,CAMP signaling pathway,bile secretion,and bicarbonate reabsorption in the proximal tubule.A total of 10 core genes:CXCL8,CXCL1,CXCL12,CXCL5,CSF2,CXCL2,CXCL3,CXCL11,CCL19,and CCL13 were obtained.Survival analyses showed that CXCL8,CXCL5,CSF2,CCL13,CCL19,and CXCL12 were correlated with the prognosis of colon cancer,and the qRT-PCR test results confirmed that the expression of CXCL8,CXCL5 and CSF2 in colorectal cancer and paracancerous tissues were significantly different.Conclusion The expression of CXCL8,CXCL5 and CSF2 genes changes during the development of colorectal cancer,which may play a key role in the development of colorectal cancer.