Genome-wide Profiling of Brain DNA Hydroxymethylome in Alzheimer?sDisease

项目摘要 阿尔茨海默病（AD）是一种毁灭性的神经退行性疾病，目前尚无治愈或有效的治疗方法。 治疗深入了解其分子机制是发现新的 AD的诊断和治疗策略胞嘧啶第五位（5 mC）的DNA甲基化是 一种被广泛研究的与AD有关的表观遗传标记新发现的5-羟甲基胞嘧啶（5 hmC） 是5 mC的氧化产物，对DNA去甲基化至关重要。5 hmC特别富集在 大脑，随着年龄的增长而积累，并受到生活经验的动态调节。5 hmC展品 与5 mC相比，不同的基因组分布，改变的5 hmC影响基因表达。这些 研究结果表明，5 hmC代表了大脑功能表观遗传调控的一个新维度， 神经变性然而，很少有研究检查人类5 hmC的全基因组模式 大脑及其在人群中AD中的作用。基于我们之前在人脑和动物模型方面的工作， 我们假设异常的5 hmC修饰与AD病理学有因果关系。我们的目标是 鉴定与早期特征定量神经病理学测量相关的致病性5 hmC改变 AD病理学（例如，淀粉样斑块、神经纤维缠结）。为此，我们提出四个具体目标： (1)通过全基因组分析确定与AD病理学相关的差异羟甲基化区域 5 hmC在740死后的大脑收集了两个大的，以社区为基础的人口研究老化和 痴呆：宗教秩序研究（发现样本）和拉什记忆和衰老项目（复制 样品）。由于传统方法无法区分5 mC和5 hmC，我们将进行5 hmC捕获 测序，然后使用我们小组开发的新技术进行TET辅助亚硫酸氢盐测序， 合作者(2)进行靶向甲基化测序，以确定其他AD相关5 mC 由于有限的分辨率和基因组，我们以前的EWAS可能错过了一些改变。 Illumina平台的覆盖范围。(3)使用以下方法对目标1和2中鉴定的推定基因进行功能验证 来自相同大脑皮层的现有RNA-seq数据和AD的苍蝇模型。(4)执行综合“组学” 分析以测试多层“组学”标志物对AD病理学的联合和交互作用。这一创新 该项目利用了丰富的深度临床和神经病理学表型以及多层次“组学”数据集 在相同的脑组织中产生，并提供了前所未有的机会来发现新的分子 AD病理学的潜在机制。我们的建议汇集了一个非常强大和独特的多- 专业团队与互补的专业知识需要实现我们的目标。拟议的工作代表了 AD和“组学”研究之间的界面前沿。这项研究将提供重要的 对疾病病因学的机械见解，并极有可能导致发现新的战略， AD的早期发现、预防和治疗干预。

Project Summary Alzheimer's disease (AD) is a devastating neurodegenerative disorder for which there is no cure or effective treatment. A thorough understanding of its molecular mechanisms is a prerequisite for discovering novel diagnostic and therapeutic strategies against AD. DNA methylation at the fifth position of cytosine (5mC) is a well-studied epigenetic mark that is implicated in AD. The newly discovered 5-hydroxymethylcytosine (5hmC) is an oxidative product of 5mC that is essential for DNA demethylation. 5hmC is particularly enriched in the brain, accumulates with aging process, and is dynamically regulated by life experiences. 5hmC exhibits distinctive genomic distribution as compared to 5mC, and altered 5hmC influences gene expression. These findings suggest that 5hmC represents a new dimension of epigenetic regulation for brain function and neurodegeneration. However, there is little research examining the genome-wide pattern of 5hmC in human brain and its role in AD in human populations. Building on our prior work in human brain and animal models, we hypothesize that aberrant 5hmC modification is causally associated with AD pathology. Our goal is to identify causative 5hmC alterations associated with quantitative neuropathological measures for early features of AD pathology (e.g., amyloid plaques, neurofibrillary tangles). To achieve this, we propose four specific aims: (1) Identify differentially hydroxymethylated regions associated with AD pathology by genome-wide profiling of 5hmC in 740 postmortem brains collected by two large, community-based population studies of aging and dementia: the Religious Order Study (discovery sample) and the Rush Memory and Aging Project (replication sample). As traditional methods cannot discriminate between 5mC and 5hmC, we will perform 5hmC-capture sequencing, followed by TET-assisted bisulfite sequencing using novel techniques developed by our group and collaborators. (2) Conduct targeted methylation sequencing to identify additional AD-associated 5mC alterations that may have been missed by our previous EWAS as a result of the limited resolution and genome coverage of the Illumina platform. (3) Functionally validate the putative genes identified in Aims 1 and 2 using existing RNA-seq data from the same brain cortex and a fly model for AD. (4) Perform integrative `omics' analyses to test the joint and interactive effects of multi-layer `omics' markers on AD pathology. This innovative project leverages the wealth of deep clinical and neuropathological phenotypes and multi-level `omics' datasets generated in the same brain tissue, and provides unprecedented opportunities to uncover novel molecular mechanisms underlying AD pathology. Our proposal brings together an exceptionally strong and unique multi- disciplinary team with complementary expertise needed to achieve our goal. The work proposed represents the frontier in the interface between AD and `omics' research. Findings of this study will provide important mechanistic insights into disease etiology, and are highly likely to lead to the discovery of novel strategies for early detection, prevention and therapeutic intervention of AD.