天津医药

天津医药 ›› 2018, Vol. 46 ›› Issue (5): 504-508.doi: 10.11958/20171099

• 细胞与分子生物学 • 上一篇    下一篇

基于mRNA和miRNA表达谱及基因甲基化谱的直肠腺癌发生相关分子标志物的研究

秦海1， 2 ， 华扬2 ， 石洋2 ， 李鹏2   

  1. 1天津医科大学 （邮编300070）； 2天津市人民医院肛肠科
  • 收稿日期:2017-10-16 修回日期:2018-02-11 出版日期:2018-05-15 发布日期:2018-05-15
  • 通讯作者: 秦海 E-mail:yunshanyi11@sina.com

Screening critical genes for rectal adenocarcinoma using combined mRNA, microRNA alteration and aberrant DNA methylation patterns

QIN Hai 1,2 , HUA Yang2 , SHI Yang2 , LI Peng2   

  1. 1 Tianjin Medical University, Tianjin 300070, China； 2 Department of Anorectal Surgery, Tianjin Union Medical Center
  • Received:2017-10-16 Revised:2018-02-11 Published:2018-05-15 Online:2018-05-15

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摘要： 摘要： 目的 通过综合分析高通量miRNA/mRNA的表达数据及DNA甲基化数据， 研究直肠腺癌 （READ） 潜在的发病机制。方法 从癌症基因组图谱 （TCGA） 数据库中下载miRNA/mRNA表达数据及DNA甲基化数据。利用 DESeq2软件包筛选差异表达的miRNA （DEmiRNAs）、 mRNA （DEmRNAs）， 利用COHCAP软件包筛选差异甲基化位点（DMSs）。采用生物信息学方法分别构建DEmiRNAs与DEmRNAs的调控网络和DNA甲基化与DEmRNAs调控网络，获得DEmiRNAs与DEmRNAs负调控关系对 （DEmiRNA-DEmRNA）， 以及DNA甲基化与DEmRNAs的负调控关系对（DNAmethylation-DEmRNA）。利用KEGG分析得到异常甲基化的DEmRNAs富集的通路。最后通过实时定量聚合酶链式反应 （qRT-PCR） 验证其中差异显著的DEmRNAs的表达水平。结果 在数据中筛选到了1 192个DEmRNAs， 27个DEmiRNAs， 通过靶基因筛选， 获得1 987个miRNA-mRNA调控关系对。得到446个甲基化异常的基因， 6 403 个异常甲基化的CpG位点。通过对446个异常甲基化基因和668个DEmRNAs的关联性分析， 发现50个DEmRNAs （39个下调和11个上调） 伴有高甲基化， 同时受到DEmiRNAs的负调控。这50个DEmRNAs显著富集于cAMP、 昼夜节律和谷氨酸等信号通路。qRT-PCR结果显示DEmRNAs表达结果与预测结果一致。结论 受到DEmiRNAs负调控的7个高甲基化基因 （SORCS1、 PDZRN4、 LONRF2、 CNGA3、 HAND2、 RSPO2和GNAO1） 可能促进了READ的发生。

关键词: 直肠肿瘤, 腺癌, 微RNAs, RNA, 信使, DNA甲基化, 基因表达谱, 计算生物学

Abstract: Abstract: Objective To study the underlying pathogenesis of rectal adenocarcinoma (READ) by analyzing the expression data of high throughput miRNA / mRNA and DNA methylation. Methods The miRNA/ mRNA expression profiling and corresponding DNA methylation data were downloaded from the Cancer Genome Atlas (TCGA) database. The differentially expressed mRNAs (DEmRNA)/miRNAs (DEmiRNAs)/methylated regions were identified in READ. The negatively correlation of DEmiRNA-DEmRNAs and DNA methylation-DEmRNAs were obtained. DEmRNA expression was validated through quantitative real-time polymerase chain reaction (qRT-PCR) analyses. Results A total of 1 192 DEmRNAs and 27 DEmiRNAs were screened in the data. And 1 987 miRNA-mRNA regulatory relationships were obtained by screening target genes. In this study, 446 genes with aberrant methylation were annotated, and 6 403 aberrant methylation CpG sites were screened in READ compared to normal controls. Eventually, 50 DEmRNAs (39 down-regulated and 11 up- regulated DEmRNAs) with hyper methylation and synchronously negatively targeted by DEmiRNAs, were identified through the correlation analysis among 446 genes with aberrant methylation and 668 DEmRNAs. The 50 DEmRNAs were significantly enriched in cAMP signaling pathway, circadian entrainment and glutamatergic synapse. Results of qRT-PCR showed that the validation results of expression levels of DEmRNAs were compatible with our study. Conclusion Seven hypermethylation genes (SORCS1, PDZRN4, LONRF2, CNGA3, HAND2, RSPO2 and GNAO1) that are negatively regulated by DEmiRNAs may promote the occurrence of READ.

Key words: rectal neoplasms, adenocarcinoma, microRNAs, RNA, messenger, DNA methylation, gene expression profiling, computational biology