Epigenome-Wide Association Study of DNA Methylation and Atherosclerosis

描述（由申请人提供）：表观遗传修饰，特别是基因启动子区DNA甲基化的改变，越来越多地被认为是各种复杂疾病发病机制的关键因素。我们建议在多种族动脉粥样硬化研究（梅萨）中研究循环单核细胞中与动脉粥样硬化和单核细胞基因表达谱相关的全球DNA甲基化模式。将从梅萨受试者的大样本（n=1600）血液样本中分离的单核细胞中纯化DNA和RNA（44-85岁，40%白人，27%黑人，和21%的西班牙裔），他们没有临床动脉粥样硬化性心血管疾病（ASCVD），并计划接受颈动脉内膜中层厚度（IMT）的定量超声评估和计算机断层扫描-在梅萨检查5（2010-2011年）中确定钙化冠状动脉斑块。DNA样本将用于确定随机1/2（800）参与者的全基因组DNA甲基化谱。商业平台将用于检测约27，000个CpG位点的甲基化，涵盖基因组中超过14，000个注释良好的基因和大多数CGI。来自相同单核细胞的RNA将用于对约25，000个基因进行表达谱分析，其中超过12，700个基因也存在于甲基化试验中。将确定DNA甲基化模式与颈动脉IMT测量的动脉粥样硬化程度之间的关联。将进行综合分析，以阐明DNA甲基化标志物和同源基因的细胞mRNA表达之间的联系。将对剩余队列中这些基因的子集进行随访研究，以验证DNA甲基化/mRNA转录本关系及其与亚临床动脉粥样硬化的相关性。随后将使用540名具有极端IMT表型的梅萨受试者（从1600名梅萨参与者中选择）研究代表已确认关联的基因组区域，以揭示功能意义。利用这一独特且充分表征的人群进行的拟议研究将改变对表观基因组学和DNA甲基化在动脉粥样硬化和ASCVD中作用的理解。所获得的知识应该产生新的ASCVD诊断生物标志物，并为未来的靶向干预发现独特的治疗靶点。公共卫生相关性：动脉粥样硬化性心血管疾病（ASCVD）仍然是全球发病率和死亡率的主要原因之一。我们建议通过绘制单核细胞DNA甲基化图谱来研究ASCVD的表观基因组学。这种跨学科的合作工作将改变我们对ASCVD病因和严重程度的理解。

DESCRIPTION (provided by applicant): Epigenetic modifications, especially alterations in DNA methylation in promoter regions of genes, are increasingly being recognized as key factors in the pathogenesis of a wide variety of complex disorders. We propose to investigate the association of global DNA methylation patterns in circulating monocytes in relation to atherosclerosis and monocyte gene expression profiles in the Multi-Ethnic Study of Atherosclerosis (MESA). DNA and RNA will be purified from monocytes isolated from blood samples of a large sample (n=1600) of MESA subjects (44-85 year old, 40% Whites, 27% Blacks, and 21% Hispanics) who are free of clinical atherosclerotic cardiovascular disease (ASCVD) and scheduled to undergo quantitative ultrasound assessment of carotid artery intimal-medial thickness (IMT) and computed tomography-determined calcified coronary plaque at MESA exam 5 (in 2010-2011). The DNA samples will be used to determine genome-wide DNA methylation profiles in a random 1/2 (800) of the participants. Commercial platforms will be used to assay methylation of approximately 27,000 CpG sites covering more than 14,000 well-annotated genes and most CGIs in the genome. RNA from the same monocytes will be used to perform expression profiling of ~25,000 genes, of which more than 12,700 are also present on the methylation assay. Associations between DNA methylation patterns and the extent of atherosclerosis measured by carotid IMT will be determined. Integrative analyses will be performed to elucidate the connections between DNA methylation markers and cellular mRNA expression of cognate genes. Follow-up studies will be performed on subsets of these genes in the remaining cohort to verify DNA methylation/mRNA transcript relationships and their associations with subclinical atherosclerosis. Genomic regions representing confirmed associations will be subsequently investigated using 540 MESA subjects (selected from the 1600 MESA participants) with extremes of IMT phenotypes to reveal functional implications. The proposed studies utilizing this unique and well characterized population will transform the understanding of the role of epigenomics and DNA methylation in relation to atherosclerosis and ASCVD. The knowledge obtained should yield new biomarkers for ASCVD diagnosis and uncover unique therapeutic targets for future targeted interventions. Public Health Relevance: Atherosclerotic cardiovascular disease (ASCVD) remains one of the leading causes of morbidity and mortality world-wide. We propose to investigate the epigenomics of ASCVD through mapping of monocytic DNA methylation profiles. This interdisciplinary, cooperative work will transform our understanding of the etiology and severity of ASCVD.