Differential DNA Methylation Correlates with Differential Expression of Angiogenic Factors in Human Heart Failure

Epigenetic mechanisms such as microRNA and histone modification are crucially responsible for dysregulated gene expression in heart failure. In contrast, the role of DNA methylation, another well-characterized epigenetic mark, is unknown. In order to examine whether human cardiomyopathy of different etiologies are connected by a unifying pattern of DNA methylation pattern, we undertook profiling with ischaemic and idiopathic end-stage cardiomyopathic left ventricular (LV) explants from patients who had undergone cardiac transplantation compared to normal control. We performed a preliminary analysis using methylated-DNA immunoprecipitation-chip (MeDIP-chip), validated differential methylation loci by bisulfite-(BS) PCR and high throughput sequencing, and identified 3 angiogenesis-related genetic loci that were differentially methylated. Using quantitative RT-PCR, we found that the expression of these genes differed significantly between CM hearts and normal control (p<0.01). Moreover, for each individual LV tissue, differential methylation showed a predicted correlation to differential expression of the corresponding gene. Thus, differential DNA methylation exists in human cardiomyopathy. In this series of heterogenous cardiomyopathic LV explants, differential DNA methylation was found in at least 3 angiogenesis-related genes. While in other systems, changes in DNA methylation at specific genomic loci usually precede changes in the expression of corresponding genes, our current findings in cardiomyopathy merit further investigation to determine whether DNA methylation changes play a causative role in the progression of heart failure.

表观遗传机制（Epigenetic mechanisms）如微小RNA（microRNA）与组蛋白修饰（histone modification），是心力衰竭（heart failure）中基因表达失调的关键诱因。与之相对，另一类已被充分表征的表观遗传标记——DNA甲基化（DNA methylation）的作用尚不明确。为探究不同病因的人类心肌病（cardiomyopathy）是否存在统一的DNA甲基化模式，我们对接受心脏移植的缺血性（ischaemic）与特发性（idiopathic）终末期心肌病左心室（LV）移植外植体进行了图谱分析，并以正常组织作为对照。我们采用甲基化DNA免疫沉淀芯片（MeDIP-chip）开展初步分析，通过亚硫酸氢盐（BS）PCR与高通量测序验证了差异甲基化位点，并鉴定出3个存在差异甲基化的血管生成相关基因位点。借助定量实时逆转录聚合酶链反应（quantitative RT-PCR），我们发现这些基因在心肌病（CM）心脏与正常对照组织中的表达存在显著差异（p<0.01）。此外，对于每一例左心室组织样本，差异甲基化水平与对应基因的差异表达均呈现出预期的相关性。由此可见，人类心肌病中存在DNA甲基化差异。在本系列异质性心肌病左心室移植外植体研究中，我们至少发现了3个存在差异甲基化的血管生成相关基因。尽管在其他研究体系中，特定基因组位点的DNA甲基化改变通常先于对应基因的表达变化，但我们在心肌病中的这一发现仍需进一步研究，以明确DNA甲基化改变是否在心力衰竭进展中发挥致病作用。