Genome-wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development-associated genes in fetuses with cardiac defects.
Genome-wide methylation analysis reveals differentially methylated CpG sites and altered expression of heart development-associated genes in fetuses with cardiac defects.
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全基因组甲基化分析揭示了心脏缺陷胎儿中差异甲基化的 CpG 位点和心脏发育相关基因的表达改变
DOI：
10.3892/etm.2021.10464
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发表时间：
2021-09
影响因子：
2.7
通讯作者：
Li X
中科院分区：
文献类型：
--
作者：
Zhou J;Xiong Y;Dong X;Wang H;Qian Y;Ma D;Li X
DNA甲基化作为一种表观遗传机制，在心脏发育过程中起着至关重要的作用。越来越多的研究调查了来自先天性心脏病(CHD)患者的儿童或成人心脏样本中异常的DNA甲基化。胎盘组织、脐带血或新生儿血也被用来检测CHD的DNA甲基化生物标志物。然而，很少有研究将患有心脏缺陷的胎儿心脏组织中的甲基化水平与正常对照组进行比较。本研究采用甲基化DNA免疫沉淀微阵列和Massarray EpiTYPER分析方法，对17例孤立性心脏缺陷、14例非孤立性心脏缺陷和22例正常心脏的胎心标本进行了全基因组和CpG位点特异性DNA甲基化分析。RT-qPCR和免疫印迹分析检测差异甲基化区(DMRS)附近基因的表达。结果显示，心脏缺陷的胎儿表现为整体低甲基化。基因组分析显示，部分DMR位于外显子(12.4%)、远端基因间隔区(11.14%)和内含子(8.97%)。只有55.7%的DMR位于启动子区域。对这些DMR邻近基因的功能富集度分析表明，低甲基化基因参与了胚胎心管的形态发生和免疫相关的调节功能。EGFR和溶质载体家族19成员1(SLC19A1)基因间高甲基化和NOTCH1基因内低甲基化在心脏缺陷胎儿组织中得到证实。只有SLC19A1在mRNA水平上显著降低，而EGFR、NOTCH1和SLC19A1在蛋白水平上均显著降低。总之，本研究表明，胎儿心脏缺陷可能与启动子区外的区域和单个CpG位点甲基化改变有关，导致与心脏发育相关的相应基因的差异表达。这些结果为研究心脏发育异常的表观遗传学机制提供了新的见解。
DNA methylation, as an epigenetic mechanism, has a vital role in heart development. An increasing number of studies have investigated aberrant DNA methylation in pediatric or adult heart samples from patients with congenital heart defects (CHD). Placenta tissue, umbilical cord blood, or newborn blood have also been used to detect DNA methylation biomarkers for CHD. However, few studies have compared the methylation levels in fetal heart tissue with cardiac defects with that in normal controls. The present study conducted an integrative whole-genome and CpG site-specific DNA methylation analysis of fetal heart samples from 17 isolated cardiac defect cases, 14 non-isolated cardiac defect cases, and 22 controls with normal hearts, using methylated DNA immunoprecipitation microarray and MassARRAY EpiTYPER assays. Expression of genes adjacent to differentially methylated regions (DMRs) was measured by RT-qPCR and western blot analysis. The results revealed that fetuses with cardiac defects presented global hypomethylation. Genomic analysis of DMRs revealed that a proportion of DMRs were located in exons (12.4%), distal intergenic regions (11.14%), and introns (8.97%). Only 55.7% of DMRs were observed at promoter regions. Functional enrichment analysis for genes adjacent to these DMRs revealed that hypomethylated genes were involved in embryonic heart tube morphogenesis and immune-related regulation functions. Intergenic hypermethylation of EGFR and solute carrier family 19 member 1 (SLC19A1), and intragenic hypomethylation of NOTCH1 were validated in fetal heart tissues with cardiac defects. Only SLC19A1 expression was significantly decreased at the mRNA level, while EGFR, NOTCH1, and SLC19A1 expression were all significantly decreased at the protein level. In conclusion, the present study demonstrated that fetal cardiac defects may be associated with alterations in regional and single CpG site methylation outside of promoter regions, resulting in differentiated expression of corresponding genes associated with heart development. These results present new insights into the epigenetic mechanisms underlying abnormal heart development.
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DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
3.7
作者：
Serra-Juhé C;Cuscó I;Homs A;Flores R;Torán N;Pérez-Jurado LA
通讯作者：
Pérez-Jurado LA
影响因子：
14.9
作者：
Ritchie ME;Phipson B;Wu D;Hu Y;Law CW;Shi W;Smyth GK
通讯作者：
Smyth GK
影响因子：
64.8
作者：
Schultz, Matthew D.;He, Yupeng;Whitaker, John W.;Hariharan, Manoj;Mukamel, Eran A.;Leung, Danny;Rajagopal, Nisha;Nery, Joseph R.;Urich, Mark A.;Chen, Huaming;Lin, Shin;Lin, Yiing;Jung, Inkyung;Schmitt, Anthony D.;Selvaraj, Siddarth;Ren, Bing;Sejnowski, Terrence J.;Wang, Wei;Ecker, Joseph R.
通讯作者：
Ecker, Joseph R.
影响因子：
64.8
作者：
Neri, Francesco;Rapelli, Stefania;Oliviero, Salvatore
通讯作者：
Oliviero, Salvatore