基于癌症基因组图谱数据分析筛选结肠癌预后相关长链非编码RNA  

Analysis and screening of long non-coding RNAs associated with colon cancer prognosis utilizing TCGA data

作　　者：闫军浩 郭魁元[1] 吴万庆[1] 罗昭峰 杨战锋[1] 王冬阳[2] 王争[2] Yan Junhao;Guo Kuiyuan;Wu Wanqing;Luo Zhaofeng;Yang Zhanfeng;Wang Dongyang;Wang Zheng(Department of Gastrointestinal and Thyroid Surgery,the Fifth Affiliated Hospital of Zhengzhou University,Henan Zhengzhou 450052,China;Department of Gastrointestinal Surgery,Renji Hospital,Shanghai Jiaotong University School of Medicine,Shanghai 200001,China)

机构地区：[1]郑州大学第五附属医院胃肠甲状腺外科,河南郑州450052 [2]上海交通大学附属仁济医院胃肠外科,上海200001

出　　处：《现代肿瘤医学》2020年第17期3004-3008,共5页Journal of Modern Oncology

基　　金：上海市科学技术委员会科研计划项目(编号:19140903002)。

摘　　要：目的:通过分析癌症基因组图谱(TCGA)数据库中有关结肠癌的转录组测序数据,筛选结肠癌预后相关长链非编码RNA(lncRNA),寻找新的lncRNA结肠癌分子标志物。方法:下载TCGA数据库中结肠癌转录组测序数据及结肠癌患者临床资料,利用R语言进行数据整理。采用edgeR包筛选差异表达lncRNA,采用单因素Cox回归模型对差异表达lncRNA进行生存分析。提取与这些lncRNA共表达的编码基因,行京都基因与基因组百科全书(KEGG)分析。结果:差异表达分析共筛选出227个在肿瘤各TNM分期中均异常表达的lncRNA,其中表达上调169个,表达下调58个。生存分析鉴定出15个差异表达lncRNA与预后显著相关(P<0.05),其中2个为保护因素,13个为危险因素。KEGG分析发现,这些预后相关lncRNA的共表达基因主要富集在核糖体生物合成、mRNA监视通路等。结论:通过挖掘TCGA结肠癌数据集,发现了一些具有预后意义的异常表达lncRNA,为后续深入研究其功能奠定了基础,这些lncRNA有望成为新的结肠癌诊断或治疗分子标志物。Objective:To screen long non-coding RNAs(lncRNAs)associated with colon cancer prognosis and to identify novel lncRNAs as colon cancer biomarkers by analyzing the transcriptome sequencing data in The Cancer Genome Atlas(TCGA)database.Methods:The transcriptome sequencing data and patient clinical materials of colon cancer were downloaded from TCGA database and analyzed by R language.Differentially expressed lncRNAs between colon cancer tissues and adjacent normal tissues were screened using edgeR package and survival analysis of these lncRNAs was performed by univariate Cox regression model.The coding genes co-expressed with the prognostic lncRNAs were identified and extracted,and subjected to Kyoto Encyclopedia of Genes and Genomes(KEGG)analysis.Results:The differential expression analysis screened out 227 lncRNAs that were aberrantly expressed across all TNM stages of colon cancer.Among these lncRNAs,169 lncRNAs were upregulated and 58 lncRNAs were downregulated.Survival analysis identified 15 differentially expressed lncRNAs that were significantly associated with patient survival(P<0.05).Among the prognostic lncRNAs,2 lncRNAs were correlated with favorable prognosis and 13 lncRNAs were correlated with poor prognosis.KEGG analysis found that the coding genes co-expressed with the prognostic lncRNAs were mainly enriched in ribosome biogenesis,mRNA surveillance pathway,etc.Conclusion:A group of aberrantly expressed lncRNAs with prognostic significance were identified by mining the colon cancer dataset in TCGA database,which laid the foundation for further exploring their function in the future.These lncRNAs were expected to be novel diagnostic or therapeutic biomarkers for colon cancer.

关 键 词：结肠癌 长链非编码RNA 生存 预后 

分 类 号：R735.3[医药卫生—肿瘤]