基于TCGA数据库筛选与三阴型乳腺癌预后相关的miRNAs及其基因网络

Screening of miRNAs related to prognosis of triple-negative breast cancer and its gene network based on TCGA Database

摘要

目的 筛选与三阴型乳腺癌（TNBC）预后相关的关键微小RNA（miRNAs）及其靶基因，探讨其参与调控的生物学功能和信号通路，为TNBC患者预后标志物的筛选提供理论依据。 方法 基于癌症基因组图谱（TCGA）数据库筛选TNBC患者与非TNBC患者差异表达miRNAs，通过生存分析明确与患者预后相关的miRNAs。利用miRDB和miRWalk3.0在线数据库筛选miRNAs的靶基因，Cytoscape 3.8.2软件明确miRNA-信使核糖核酸（mRNA）调控网络，利用R软件limma数据包筛选TNBC患者与非TNBC患者差异表达miRNAs，利用R软件clusterProfiler包分析靶基因参与的生物学功能和通路。 结果 生存分析，miR-9、miR-17、miR-31、miR-146a、miR-188和miR-190b与TNBC患者的预后有关，且上述miRNAs表达量越低，TNBC患者预后越差。筛选出受这6种miRNAs调控的靶基因224个。基因本体论（GO）功能富集分析，靶基因主要参与乳腺腺泡的发育、DNA转录的正向调控以及血管生成等功能；京都基因与基因组百科全书（KEGG）信号通路富集分析，靶基因主要富集在细胞因子-细胞因子受体相互作用以及胰岛素分泌信号等通路。网络分析，miR-9、miR-17、溶质载体家族24成员2（SLC24A2）、vav鸟苷酸交换因子3 （VAV3）、三部结构域含有36（TRIM36）、突触标记素1（SYT1）、 富勒林和Sec7结构域含有3（PSD3）、过氧化物酶体增殖物活化受体α（PPARA）、RNA聚合酶Ⅲ亚基G（POLR3G）、多形性腺瘤基因1（PLAG1）、泛素相关和SH3结构域含有B（UBASH3B）及SH3结构域和四重肽重复2（SH3TC2）是调控网络中的关键基因，其中miR-9-SYT1、miR-9-KIF13B、miR-9-KITLG、miR-17-SLC24A2、miR-31-SLC24A2、miR-146a-SYT1、miR-146a-KIF13B、miR-188-SLC24A2和miR-188-SLC24A2的miRNA-mRNA相互作用最为密切。 结论 miR-9、miR-17、miR-31、miR-146a、miR-188和miR-190b及其靶基因参与乳腺腺泡发育和血管生成等生理过程，与TNBC患者的不良预后密切相关。

Abstract

Objective To identify the key microRNAs （miRNAs） and their target genes associated with the prognosis of triple-negative breast cancer （TNBC） and to discuss their roles in regulatory biological functions and signaling pathways， and to provide the theoretical basis for the selection of prognostic biomarkers for the patients with TNBC. Methods The differentially expressed miRNAs between the TNBC patients and non-TNBC patients were selected based on The Cancer Genome Atlas （TCGA） Database； survival analysis was used to clarify the miRNAs related to the prognosis of the patients；miRDB and miRWalk3.0 online Databases were used to screen for the miRNA target gene； Cytoscape 3.8.2 software was used to elucidate the miRNA-messenger RNA （mRNA） regulatory network；the limma package in R software was used to screen the differentially expressed miRNAs of the TNBC patients and non-TNBC patients； the clusterProfiler package in R software was used to analyze the biological functions and pathways involved by the target genes. Results The survival analysis results showed that miR-9， miR-17， miR-31， miR-146a， miR-188， and miR-190b were associated with the prognosis of the TNBC patients， and low expression levels of these miRNAs were correlated with the poorer prognosis of the patients. A total of 224 target genes regulated by these six miRNAs were identified. The Gene Ontology （GO） functional enrichment analysis results showed that the target genes were primarily involved in the development of mammary alveoli， positive regulation of DNA transcription， and angiogenesis.The Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analysis results showed that the target genes were mainly enriched in cytokine-cytokine receptor interaction and insulin secretion signaling pathways. The network analysis results identified the key genes in the regulatory network， including solute carrier family 24 member 2 （SLC24A2）， vav guanine nucleotide exchange factor 3 （VAV3）， tripartite motif containing 36 （TRIM36）， synaptotagmin 1 （SYT1）， pleckstrin and Sec7 domain containing 3 （PSD3）， peroxisome proliferator-activated receptor α （PPARA）， RNA polymerase Ⅲ subunit G （POLR3G）， pleomorphic adenoma gene 1 （PLAG1）， ubiquitin associated and SH3 domain containing B （UBASH3B）， and SH3 domain and tetramerization domain containing 2 （SH3TC2）； the interactions of miRNA-mRNA of miR-9-SYT1， miR-9-KIF13B， miR-9-KITLG， miR-17-SLC24A2， miR-31-SLC24A2，miR-146a-SYT1， miR-146a-KIF13B， miR-188-SLC24A2， and miR-188-SLC24A2 were the closest. Conclusion MiR-9， miR-17， miR-31， miR-146a， miR-188， miR-190b and their target genes are involved in physiological processes such as mammary alveolar development and angiogenesis， which are closely associated with the poor prognosis of the patients with TNBC.

关键词

三阴型乳腺癌 / 微小核糖核酸 / 预后 / 调控网络 / 靶基因

Key words

Triple negative breast cancer / MicroRNA / Prognosis / Regulatory network / Target gene

Author summay

宋玥莹（1998－），女，吉林省长春市人，医师，主要从事分子流行病学方面的研究。