基于乳腺癌ChIP-seq数据的p53抑癌机制研究

Molecular mechanism of p53-mediatedtumor suppressionin p53-WT breast cancerusing Ch IP-seq data

采用生物信息学方法分析野生型p53乳腺癌MCF7细胞的Ch IP-seq(染色质免疫共沉淀-测序)数据,以揭示p53的抑癌分子机制。从NCBI下载的编号为GSE47041的Ch IP-seq数据来源于三组试验,分别为:未经处理的乳腺癌MCF7细胞对照(NS_input),Nutlin-3a(一种MDM2拮抗剂)处理的MCF7细胞对照(S_input)和Nutlin-3a刺激MCF7细胞后加入p53抗体的实验组(S_p53)。Ch IP获得的DNA数据的测序平台为Illumina Hi Seq 2000。利用Bowtie参照人基因组hg19进行序列比对;利用MACS进行峰信号检测,并利用自定义软件筛选p53可能的靶基因;利用DAVID在线工具对靶基因进行通路富集分析;最后利用STRING构建蛋白互作网络。研究共得到50个p53的靶基因,其中8个靶基因(CDKN1A、BBC3、BAX、DDB2、MDM2、CCNG1、XPC和PCNA)分别富集到p53信号转导通路和核苷酸切除修复通路两个通路上。在得到的由19个靶基因构成的蛋白质相互作用网络中,连通度最高的前5个基因分别是PCNA、MDM2、REV3L、CDKN1A和BAX。研究中采用的分析Ch IP-seq数据的方法能有效揭示野生型p53乳腺癌MCF7细胞中Nutlin-3a激活的p53的抑癌分子机制。

To unveilthe molecular mechanism of p53-mediated tumor suppression in p53-WT breast cancervia analyzing Ch IP-seq（ chromatin immunoprecipitation-sequencing） data by bioinformatics methods. Ch IP-Seq dataset GSE47041 was downloaded from Gene Expression Omnibus,which includes three groups of samples： untreated MCF-7 cells（ NS_input）,MCF-7 cells treated with a Mdm2 antagonist Nutlin-3a（ S_input）,Nutlin-3a-treated MCF-7 cells plus p53 antibody treatment（ S_p53）. The obtained DNA fragments were sequenced using the Illumina Hi Seq 2000 platform. Sequence alignment was performed with reference to hg19 using Bowtie; peak calling was performed using MACS; a selfprogrammed software was used to detect p53 target genes. A total of 50 p53 target genes were predicted. Among them,eight（ CDKN1 A,BBC3,BAX,DDB2,MDM2,CCNG1,XPC and PCNA） were enriched in p53 signaling transduction pathway and nucleotide excision repairing pathways respectively. A protein-protein interaction network consisting of 19 target genes was obtained; PCNA,MDM2,REV3 L,CDKN1A and BAX were the top five genes with the highest degrees of connection. The methods recruited to investigate the molecular mechanism underlying p53-mediated tumor suppression in p53-WT MCF-7 breast cancer cells based on Ch IP-seq data are proven feasible and reliable.