染色质开放状态对结肠癌相关功能通路影响的生物信息学分析

Effect of chromatin opening state on colon cancer-related functional pathways:a bioinformatics analysis

目的利用癌症基因组图谱(TCGA)数据库的染色质开放性高通量测序(ATAC-seq)数据和转录组测序(RNA-seq)数据,探索染色质开放状态对结肠癌相关功能通路的影响。方法从TCGA数据库下载结肠癌ATAC-seq数据和RNA-seq数据,使用R 3.5.3软件对ATAC-seq数据进行质量控制。对全部样本ATAC-seq数据峰值(peaks)进行基因注释,对所注释基因进行基因本体(GO)功能富集分析和京都基因与基因组百科全书(KEGG)通路富集分析。选择结肠癌关键基因肿瘤抑制基因APC(APC)、Kirsten大鼠肉瘤病毒癌基因(KRAS)、v-raf小鼠肉瘤病毒癌基因同源物B1(BRAF),对3个基因的启动子区ATAC-seq数据peaks与RNA-seq的每千个碱基的转录每百万映射读取的片段数(FPKM)进行Pearson相关性分析。对TNM分期Ⅲ+Ⅳ期和Ⅰ+Ⅱ期的组织样本进行差异ATAC-seq数据peaks分析,并对上调和下调peaks注释基因进行KEGG通路富集分析。结果结肠癌ATAC-seq数据peaks在染色体分布均匀,大多数分布于启动子区(距离转录起始位点≤1 kb、>1~2 kb、>2~3 kb者分别占30.17%、5.42%、3.88%)和远端基因间区(26.17%),符合染色质开放区2种主要类型的分布。GO功能和KEGG通路富集分析结果显示,结肠癌ATAC-seq数据peaks注释基因显著富集于癌症相关功能和通路,如Wnt信号通路的细胞间信号转导、表皮生长因子受体(ErbB)信号通路等。结肠癌关键基因APC、KRAS、BRAF启动子区ATAC-seq数据peaks与其RNA-seq的FPKM呈正相关。TNM分期Ⅲ+Ⅳ期相对Ⅰ+Ⅱ期患者上调peaks注释基因显著富集于ErbB信号通路、Wnt信号通路、PI3K-Akt信号通路、P53信号通路等增殖、侵袭和转移相关信号通路,下调peaks注释基因显著富集于T细胞受体信号通路、B细胞受体信号通路、细胞黏附分子信号通路等免疫识别相关信号通路。结论染色质开放状态对结肠癌相关功能通路调控起着重要作用。

Objective To explore the effect of open chromatin state on functional pathways related to colon cancer using the data of assay for transposase-accessible chromatin using sequencing(ATAC-seq)and RNA sequencing(RNAseq)from The Cancer Genome Atlas(TCGA)database.Methods ATAC-seq and RNA-seq data of colon cancer were downloaded from TCGA,and the quality of ATAC-seq data was controlled using R 3.5.3 software.The ATAC-seq peaks of all samples were annotated,and the Gene Ontology(GO)function and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analyses were carried out.The key genes of colon cancer,including APC regulator of Wnt signaling pathway(APC),Kirsten rat sarcoma viral oncogene(KRAS)and v-raf murine sarcoma viral oncogene homolog B1(BRAF),were selected to analyze the correlation between ATAC-seq peaks of the 3 genes and the fragments per kilobase of exon model per million mapped fragments(FPKMs)of RNA-seq.The tissue samples of TNM stage Ⅲ+Ⅳ and Ⅰ+Ⅱ were selected to analyze the differential ATAC-seq peaks,and KEGG pathway enrichment analysis was performed for up-regulated and downregulated peaks annotated genes.Results The ATAC-seq peaks of colon cancer were evenly distributed in the chromosome,and most of them were located in promoter region(30.17%,5.42% and 3.88% in the distance from transcription initiation site ≤1 kb,>1-2 kb and>2-3 kb,respectively)and distal intergenic region(26.17%),which were consistent with 2 main types of chromatin open region.GO function and KEGG pathway enrichment analyses showed that the peaks annotated genes in ATAC-seq data of colon cancer were significantly enriched in cancer-related functions and pathways,such as intercellular signaling conduction of Wnt signaling pathway and epidermal growth factor receptor(ErbB)signaling pathway.The RNA-seq FPKMs of APC,KRAS and BRAF were positively correlated with ATAC-seq peaks in promoter region.The up-regulated peaks annotated genes were significantly enriched in ErbB signal pathway,Wnt signal pathway,PI3K-Akt signal pathway,p53 signal pathway and other signal pathways related to proliferation,invasion and metastasis,while down-regulated peaks annotated genes were significantly enriched in T cell receptor signaling pathway,B cell receptor signaling pathway,cell adhesion molecule signaling pathway and other immune recognition related signaling pathways in patients at TNM stage Ⅲ+Ⅳ than at stage Ⅰ+Ⅱ.Conclusion Open chromatin plays an important role in the functional pathways related to colon cancer.