Genomic and Proteomic Architecture of Atherosclerosis

描述(由申请人提供)：我们的目标是确定人类基因组中的变异和动脉蛋白质组中与过早动脉粥样硬化相关的相应变化。为了实现这一目标，我们计划对青年动脉粥样硬化病理生物学决定因素(PDAY)库中受试者的动脉组织进行详细的分子表征。我们将整合来自PDAY样本的基因组和蛋白质组数据，并使用其他系统生物学工具和来自NIH资助的其他基因组资源的数据来优化对早期疾病的分子相关性的搜索。我们的具体目标是：目的1.确定与PDAY早期动脉粥样硬化相关的遗传变异，包括：a.通过PDAY病例对照外显子和启动子测序确定的基因中罕见的变异，以及b.通过(先前进行的)PDAY Gwas鉴定的常见变异。名义上有意义的外显子组测序和GWAS结果将与来自ESP早发性心肌梗死项目(N=2,400)和MIGen联盟(N=6,402)的类似测序和GWAS数据结合起来，使用荟萃分析来精炼用于蛋白质验证的候选基因产物列表。(目标3)目标2.使用统计方法扩展目标1的候选蛋白质列表并对其进行优先排序，以结合来自SNPs、稀有变体和结构变体的证据、基于基因网络先验知识的基因途径浓缩技术(例如。KEGG、Invenity、PPI、GO等)，以及使用Polyphen-2和相关工具对特定遗传标记进行功能评估。目的3.测量AIMS 1和AIMS 2中鉴定的动脉壁蛋白质浓度的病例对照差异。为此，我们将利用一种新的定量质谱学方法--多反应监测(MRM)的多重能力，评估所有1,100名PDAY病例对照受试者的~150个动脉壁蛋白质。目的4.利用基因分型、特异性蛋白定量和补充免疫组织化学分析，进一步评估广泛动脉粥样硬化患者(N=150)和非广泛动脉粥样硬化患者(N=150)死后动脉标本中具有最有说服力证据的遗传变异和蛋白。目标5.为来自具体目标1-4的数据提供统一的命名和注释，并通过适当的可供公众查阅的NCBI数据库与科学界共享整个数据集。这种高度特异和精确的组织病理学表型与最先进的分子和分析方法相结合，为构建过早动脉粥样硬化的基因组和蛋白质组结构创造了前所未有的机会，并将从根本上增加关于动脉壁基因组和蛋白质组之间联系的新知识。

DESCRIPTION (provided by applicant): Our goal is to identify variants in the human genome and corresponding changes in the arterial proteome that are correlated with premature atherosclerosis. To accomplish this goal we plan detailed molecular characterization of arterial tissue from subjects in the Pathobiologic Determinants of Atherosclerosis in Youth (PDAY) repository. We will integrate genomic and proteomic data from the PDAY samples and use additional systems biology tools and data from other NIH funded genomic resources to optimize the search for molecular correlates of early disease. Our specific aims are: Aim 1. To identify genetic variants associated with premature atherosclerosis in PDAY, including: a. rare variants in genes identified through PDAY case-control exome and promoter sequencing, and b. common variants identified through a (previously conducted) PDAY GWAS. Nominally significant exome sequencing and GWAS results will be combined with similar sequencing and GWAS data from the ESP Early Onset MI Project (N=2,400) and the MIGen Consortium (N=6,402) using meta- analysis to refine the list of candidate gene products for protein validation. (Aim 3) Aim 2. To expand and prioritize the list of candidate proteins from Aim 1 using statistical methods to combining evidence from SNPs, rare variants and structural variants, gene-pathway enrichment techniques based on a priori knowledge of gene networks (eg. KEGG, Ingenuity, PPI, GO, etc.), and functional evaluation of specific genetic markers using Polyphen-2 and related tools. Aim 3. To measure case-control differences in arterial wall concentration of proteins identified in Aims 1 and 2. For this aim we will exploit the multiplex capability of a new quantitative mass-spectrometry method, multiple reaction monitoring (MRM), to evaluate ~150 arterial wall proteins in all 1,100 PDAY case-control subjects. Aim 4. To further evaluate genetic variants and proteins with the most compelling evidence for association using genotyping, specific protein quantitation and complementary immunohistochemical analyses in de-novo post-mortem arterial specimens from subjects with and without extensive atherosclerosis (N=150). Aim 5. To provide harmonized nomenclature and annotation for the data from Specific Aims 1-4 and share the entire data set with the scientific community through the appropriate publically accessible NCBI databases. This combination of highly specific and precise histopathologic phenotyping with state-of-the-art molecular and analytic methods creates an unprecedented opportunity to construct the genomic and proteomic architecture of premature atherosclerosis and will add fundamentally new knowledge about the linkage between genome and proteome in the artery wall.