Genome-wide mapping and integrative analysis of DNA 6mA methylome in human AD brain

项目摘要 阿尔茨海默病(AD)是老年人中最常见的一种痴呆症，无法治愈或有效 治疗。为了发现新的诊断方法，需要对其分子机制有深入的了解 以及针对AD的治疗策略。DNA的化学修饰，如甲基化，在 调节基因表达和许多其他关键生物学过程，并改变DNA甲基化模式 与脑老化和阿尔茨海默病有关。虽然人们的注意力都集中在DNA甲基化上 关于胞嘧啶(5mC)的位置，最近的研究发现了一种新的DNA修饰形式，位于 哺乳动物大脑中的腺嘌呤(6 MA)。然而，人们对它的存在、基因组分布和 人脑的可能功能及其与阿尔茨海默病的相关性。我们在小鼠和人脑中的初步数据 提示6 mA对环境应激有动态反应，并在人AD脑内蓄积。 我们的中心假设是6 mA修饰的签名改变与AD有因果关系 神经病理学。这个项目的目标是生成第一张详细的大脑6 mA甲基组图谱 并确定与定量神经病理相关的含有异常6 mA变化的致病基因 AD病理早期特征(如淀粉样斑块、神经原纤维缠结)的测量。为了实现这一目标， 我们提出了三个具体目标：(1)脑DNA 6 mA甲基组的全基因组作图以识别 与AD病理相关的差异甲基化基因/区域含有改变的6 mA位点(D6AMR) 由两个大型社区老年人群队列收集的1200个死后脑组织样本 和痴呆症。(2)整合多组学分析阐明6 mA改变在脑出血中的潜在作用机制 AD病理学；以及(3)3D脑器官衍生的顶级候选基因的功能验证 来自人类的ipscs。这一创新项目充分利用了丰富的临床和神经病理学知识 表型和丰富的组学数据，包括遗传(Gwas，WGS)，表观遗传(5mC，5hmC，6 mA， H3K9Ac)和转录组(RNA-seq)在同一前额叶皮质上表达，并将提供前所未有的 发现AD病理中涉及的新的分子机制的机会。我们的建议带来了 汇聚在一起的是一个非常强大和独特的多学科团队，在遗传学方面具有互补的专业知识 流行病学、统计遗传学、生物信息学、分子和神经表观遗传学，以及阿尔茨海默氏症研究。 所提出的工作代表了AD和组学研究之间的接口的前沿。这方面的发现 这项研究将为AD的发病机制提供新的见解，并可能发现新的分子 具有重要临床和翻译意义的靶点。

Project Summary Alzheimer’s disease (AD) is the most common form of dementia among older people with no cure or effective treatment. A thorough understanding of its molecular mechanisms is required for discovering novel diagnostic and therapeutic strategies against AD. Chemical modifications of DNA such as methylation play critical roles in regulating gene expression and many other key biological processes, and altered DNA methylation pattern has been implicated in brain aging and AD. While much attention has focused on DNA methylation at the fifth position on cytosine (5mC), recent research identified a new form of DNA modification at the sixth position on adenine (6mA) in mammalian brains. However, little is known about its presence, genomic distribution, and possible functions in human brain and relevance to AD. Our preliminary data in mouse and human brain indicated that 6mA is dynamically responsive to environmental stress and accumulates in human AD brain. Our central hypothesis is that altered signature of 6mA modification is causally associated with AD neuropathology. The objectives of this project are to generate the first detailed map of brain 6mA methylome and identify causative genes harboring aberrant 6mA alterations associated with quantitative neuropathological measures for early features of AD pathology (e.g., amyloid plaques, neurofibrillary tangles). To achieve this, we propose three specific aims: (1) Genome-wide mapping of brain DNA 6mA methylome to identify differentially methylated genes/regions harboring altered 6mA sites (D6AMRs) associated with AD pathology in 1,200 postmortem brain tissue samples collected by two large, community-based population cohorts of aging and dementia. (2) Integrated multiomics analysis to elucidate the potential mechanistic role of 6mA alteration in AD pathology; and (3) Functionally validation of top-ranked candidate genes in 3D brain organoids derived from human iPSCs. This innovative project leverages the wealth of deep clinical and neuropathological phenotypes along with rich omics data including genetic (GWAS, WGS), epigenetic (5mC, 5hmC, 6mA, H3K9Ac), and transcriptome (RNA-seq) profiled on the same prefrontal cortex, and will provide unprecedented opportunities to uncover novel molecular mechanisms implicated in AD pathology. Our proposal brings together an exceptionally strong and unique multidisciplinary team with complementary expertise in genetic epidemiology, statistical genetics, bioinformatics, molecular and neuroepigenetics, and Alzheimer’s research. The work proposed represents the frontier in the interface between AD and omics research. Findings of this study will provide novel mechanistic insight into AD pathogenesis, and are likely to discover new molecular targets with important clinical and translational implications.