基因组转录调控元件内单核苷酸多态性调控基因表达介导扩张型心肌病

Single Nucleotide Polymorphisms in Transcriptional Regulatory Elements Mediates Dilated Cardiomyopathy

目的探究人类基因组转录调控元件区域单核苷酸多态性与扩张型心肌病发病之间的关联及潜在的致病机制。方法利用心脏组织表达数量性状基因座(expression quantitative trait locus,eQTL)数据与50例扩张型心肌病患者的H3K27ac组蛋白修饰的ChIP-seq数据进行联合分析,筛选出扩张型心肌病患者基因组转录调控元件内的单核苷酸突变。基于筛选出的单核苷酸突变,鉴定关联的表达水平发生改变的基因,进而探究扩张型心肌病潜在的致病基因并构建基因功能网络。结果心脏组织eQTL数据库与扩张型心肌病患者H3K27ac组蛋白修饰的ChIP-seq数据取交集后,在患者基因组启动子区域筛选到317个单核苷酸突变位点,增强子区域筛选到239个单核苷酸突变位点。通过eQTL数据库预测共得到556个基因在位点突变后表达水平发生改变,基因功能分析显示这些基因与内皮细胞迁移、组蛋白乙酰化修饰、肌动蛋白细胞骨架重组、皮层微管组织等生物学过程显著相关。通过对比扩张型心肌病患者与健康对照组RNA-seq数据,发现启动子区域单核苷酸突变关联的基因TMEM30B、AEBP1、SCARA3、HSH2D、DACT2、EGR3、AC108448.2、RP11-338N10.2表达水平显著上调,HRCT1显著下调;增强子区域单核苷酸突变关联的基因ATP1B2、SKAP1表达水平显著上调,FER1L6、SLGLEC14、RP11-231C14.6显著下调(Padj<0.01,|Log2FoldChange|>1)。结合KEGG通路分析,在启动子区域筛选到核心关联基因:PIK3CD、SREBF1、SOS1、SEH1L、WDR24、NPRL3、RPS6,在增强子区域筛选到核心关联基因:TRPV4、EZR、EFNB2、ANXA1,这些基因参与多个生物学过程或信号通路。结论单核苷酸突变与扩张型心肌病相关,且在基因组启动子和增强子区域等基因组转录调控元件内广泛分布。单核苷酸突变可能引起关联基因表达水平改变,进而导致参与的生物学过程和信号通路失调,最终介导扩张型心肌病的发生和进展。预测得到的基因表达水平改变的关联基因和核心关联基因可作为扩张型心肌病潜在的生物标志物和治疗靶点。

Objective To explore the association between single nucleotide polymorphisms in transcriptional regulatory elements of human genome and the pathogenesis of dilated cardiomyopathy(DCM)as well as the potential pathogenic mechanism.Methods The expression quantitative trait locus(eQTL)data of cardiac tissue was combined with the H3K27ac histone⁃modified ChIP⁃seq data of 50 DCM patients to identify single nucleotide mutations located in transcriptional regulatory elements.Based on the selected single nucleotide mutations,the associated genes with altered expression levels were identified,and the potential pathogenic genes of DCM were further explored.Finally,the gene functional network was constructed.Results After intersection of heart tissue eQTL database with H3K27ac ChIP⁃seq data of patients with DCM,317 single nucleotide mutation sites located in the promoter regions of the patient genome and 239 single nucleotide mutation sites located in the enhancer regions were identified.A total of 556 genes associated with these mutations were predicted by the eQTL database to have altered expression levels upon occurrence of these single nucleotide mutations.Gene function analysis showed that these genes were significantly enriched in many biological processes such as endothelial cell migration,histone acetylation modification,actin cytoskeleton recombination,and cortical microtubule organization.By comparing the RNA⁃seq data of patients with DCM and healthy controls,we found that the expression levels of genes associated with single nucleotide mutations in the promoter region including TMEM30B,AEBP1,SCARA3,HSH2D,DACT2,EGR3,AC108448.2 and RP11⁃338N10.2 were significantly up⁃regulated,while HRCT1 was significantly down⁃regulated.The genes associated with single nucleotide mutation in enhancer region including ATP1B2 and SKAP1 were significantly up⁃regulated,while FER1L6,SLGLEC14 and RP11⁃231C14.6 were significantly down⁃regulated(Padj<0.01,|Log2FoldChange|>1).Combined with KEGG pathway analysis,core genes possess mutations in promoters and involves in many pathways were found which included PIK3CD,SREBF1,SOS1,SEH1L,WDR24,NPRL3 and RPS6.Core genes possess mutations in enhancers were also found which included TRPV4,EZR,EFNB2 and ANXA1.These genes were involved in multiple biological processes or signaling pathways.Conclusion Single nucleotide mutations are associated with DCM and are broadly distributed in promoter and enhancer regions of the genome.Single nucleotide mutations may lead to changes in the expression level of associated genes,which in turn lead to dysregulation of participating biological processes and signaling pathways,and ultimately mediate the occurrence and progression of dilated cardiomyopathy.The associated genes and core associated genes predicted to change the gene expression level can be used as potential biomarkers and therapeutic targets for dilated cardiomyopathy.