Epigenetic markers for newborn congenital heart defect (CHD)

<i>Objective</i>: Our objective was to determine whether there were significant differences in genome-wide DNA methylation in newborns with major congenital heart defect (CHD) compared to controls. We also evaluated methylation of cytosines in CpG motifs for the detection of these CHDs. <i>Methods</i>: Genome-wide DNA methylation analysis was performed on DNA from 60 newborns with various CHDs, including hypoplastic left heart syndrome, ventricular septal deficit, atrial septal defect, pulmonary stenosis, coarctation of the aorta and Tetralogy of Fallot, and 32 controls. <i>Results</i>: Highly significant differences in cytosine methylation were seen in a large number of genes throughout the genome for all CHD categories. Gene ontology analysis of CHD overall indicated over-represented biological processes involving cell development and differentiation, and anatomical structure morphogenesis. Methylation of individual cytosines in CpG motifs had high diagnostic accuracy for the detection of CHD. For example, for coarctation one predictive model based on levels of particular cytosine nucleotides achieved a sensitivity of 100% and specificity of 93.8% (AUC = 0.974, <i>p</i> <i>Conclusion</i>: Profound differences in cytosine methylation were observed in hundreds of genes in newborns with different types of CHD. There appears to be the potential for development of accurate genetic biomarkers for CHD detection in newborns.

<i>研究目标</i>：本研究旨在探究重症先天性心脏病（Congenital Heart Defect, CHD）新生儿与健康对照新生儿之间，全基因组DNA甲基化（genome-wide DNA methylation）水平是否存在显著差异；同时评估CpG基序（CpG motif）内胞嘧啶（cytosine）的甲基化特征，以实现该类先天性心脏病的检测。<i>研究方法</i>：本研究对60名罹患各类先天性心脏病的新生儿的DNA开展全基因组DNA甲基化分析，涉及的心脏病亚型包括左心发育不良综合征、室间隔缺损、房间隔缺损、肺动脉狭窄、主动脉缩窄及法洛四联症；同时纳入32名健康新生儿作为对照。<i>研究结果</i>：针对所有先天性心脏病亚型，全基因组范围内大量基因的胞嘧啶甲基化水平均呈现出高度显著的组间差异。对全部先天性心脏病样本进行的基因本体（Gene Ontology, GO）富集分析显示，富集度显著偏高的生物学过程主要涵盖细胞发育与分化、解剖结构形态发生。CpG基序中单个胞嘧啶的甲基化水平对先天性心脏病具有较高的诊断效能。例如，针对主动脉缩窄，基于特定胞嘧啶核苷酸水平构建的预测模型灵敏度达100%、特异度达93.8%（曲线下面积AUC=0.974，<i>p</i>）。<i>研究结论</i>：本研究证实，罹患不同类型先天性心脏病的新生儿，其体内数百个基因的胞嘧啶甲基化水平存在显著差异。这提示开发用于新生儿先天性心脏病检测的精准遗传生物标志物具备潜在可行性。