乳腺癌中基于开放染色质的环状RNA互作网络构建及功能分析

Construction and functional analysis of circular RNA interaction network based on open chromatin in breast cancer

目的发现乳腺癌中重要的环状RNA(circular RNA,circRNA)及其参与的分子生物处理过程。方法全基因组范围内分析3种乳腺癌细胞系:MCF-7、T-47D、MDA-MB-231的脱氧核苷酸酶Ⅰ超敏感位点高通测序数据(DNaseⅠhypersensitive sites sequencing,DNase-seq)和转座酶可接近性染色质高通测序数据(assay for transposase accessible chromatin with high-throughput sequencing,ATAC-seq),筛选出捕获的基因编码序列上对应的活化circRNA,然后基于KEGG pathway对活化circRNA基因进行富集筛选,在此结果中选取3个细胞系共有的活化circRNA基因,依据Gene Ontology的分子生物过程构建乳腺癌活化circRNA基因互作网络。结果表达调控网络识别出111个关键功能模块,主要分为调控类和反应类,此外还包括一些重要的信号通路。将活化circRNA基因互作网络中,连接度大于50的活化circRNA基因定义为hub基因,hub基因对应的circRNA定义为hub circRNA,它们是:PTK2B、PDCD6IP、ABL1、EGFR、RHOA、MTOR、NRP1、ATR、CTNNB1、ILK、NF1、PRKCA、HNRNPK、MEF2C、PMAIP1、LYN、NR4A3、SRF、AREG、PML、PTK2、ROCK2、TGFBR2、VEGFA、DLG1、HRAS、ITGA2、CREB1、STAT3、RUNX2和TIAM1。结论乳腺癌细胞染色质中处于活化状态的circRNA,其参与的生物过程主要是正、负调控细胞周期、凋亡、增生、分化等重要的细胞生物过程,因此表明circRNA在乳腺癌的发生发展过程中起到重要作用。

Objective To identify some important circular RNAs(circRNAs)in breast cancer and the molecular biological processes in which they participate.Methods Genome-wide analysis of three breast cancer cell lines:DnaseⅠhypersensitive sites sequencing data(DNase-seq)and assay for transposase accessible chromatin with high-throughput sequencing data,(ATAC-seq)of MCF-7,T-47D,MDA-MB-231,and screening out the corresponding activated circRNA on the sequence of the captured gene encoding were done.Then the activated circRNA gene was enriched and screened based on KEGG pathway.In this result,the activated circRNA gene shared in three cell lines was selected,and the interaction network of activated circRNA gene in breast cancer was constructed according to the molecular biological process of Gene Ontology.Results The expression regulatory network identified 111 key functional modules,which were mainly divided into regulation and response categories,and included some important signaling pathways.In the active circRNA gene interaction network,the activated circRNA gene with connectivity greater than 50 was defined as hub gene,and the corresponding circRNA of hub gene was defined as hub circRNA,including PTK2B,PDCD6IP,ABL1,EGFR,RHOA,MTOR,NRP1,ATR,CTNNB1,ILK,NF1,PRKCA,HNRNPK,MEF2C,PMAIP1,LYN,NR4A3,SRF,AREG,PML,PTK2,ROCK2,TGFBR2,VEGFA,DLG1,HRAS,ITGA2,CREB1,STAT3,RUNX2 and TIAM1.Conclusion Activated circRNA in the chromatin of breast cancer cells is mainly involved in positive and negative regulation of cell cycle,apoptosis,proliferation,differentiation and other important cellular biological processes,which indicates that circRNA plays an important role in the occurrence and development of breast cancer.