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域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（MESA）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整体DNA甲基化模式。DNA和RNA将从大样本（n=1600） MESA受试者（44-85岁，40%白人，27%黑人和21%西班牙裔）的血液样本中分离的单核细胞中纯化，这些受试者没有临床动脉粥样硬化性心血管疾病（ASCVD），并计划在MESA检查5（2010-2011）中进行颈动脉内膜-内侧厚度（IMT）的定量超声评估和计算机断层扫描确定的钙化冠状动脉斑块。DNA样本将被用于确定随机1/2（800）名参与者的全基因组DNA甲基化谱。商业平台将用于检测大约27,000个CpG位点的甲基化，覆盖超过14,000个良好注释的基因和基因组中的大多数cgi。来自相同单核细胞的RNA将用于执行约25,000个基因的表达谱分析，其中超过12,700个基因也存在于甲基化分析中。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被确定。将进行综合分析，以阐明DNA甲基化标记物与同源基因的细胞mRNA表达之间的联系。后续研究将在剩余队列中对这些基因的亚群进行，以验证DNA甲基化/mRNA转录的关系及其与亚临床动脉粥样硬化的关联。随后，将使用540名具有极端IMT表型的MESA受试者（从1600名MESA参与者中选择）对代表已证实关联的基因组区域进行调查，以揭示功能影响。利用这一独特且具有良好特征的人群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中的作用的理解。所获得的知识将为ASCVD诊断提供新的生物标志物，并为未来的靶向干预发现独特的治疗靶点。

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.