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

项目概要 阿尔茨海默病 (AD) 是老年人中最常见的痴呆症，无法治愈或有效 治疗。发现新的诊断方法需要彻底了解其分子机制 以及针对 AD 的治疗策略。 DNA 的化学修饰（例如甲基化）在 调节基因表达和许多其他关键生物过程，并改变 DNA 甲基化模式 与大脑衰老和AD有关。虽然很多注意力都集中在第五次DNA甲基化上 胞嘧啶 (5mC) 上的位置，最近的研究在胞嘧啶 (5mC) 的第六位上发现了一种新形式的 DNA 修饰 哺乳动物大脑中的腺嘌呤 (6mA)。然而，人们对其存在、基因组分布和作用知之甚少。 人脑中可能的功能及其与 AD 的相关性。我们在小鼠和人脑中的初步数据 表明 6mA 对环境压力动态响应并在人类 AD 大脑中积累。 我们的中心假设是 6mA 修饰的改变特征与 AD 存在因果关系 神经病理学。该项目的目标是生成大脑 6mA 甲基化组的第一个详细图谱 并识别含有与定量神经病理学相关的异常 6mA 改变的致病基因 AD 病理学早期特征（例如淀粉样蛋白斑、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）大脑 DNA 6mA 甲基化组的全基因组图谱，以识别 差异甲基化基因/区域含有与 AD 病理相关的改变的 6mA 位点 (D6AMR) 由两个大型社区老龄人口队列收集的 1,200 个死后脑组织样本 和痴呆症。 (2) 综合多组学分析阐明 6mA 改变的潜在机制作用 AD病理学； (3) 3D 脑类器官中排名靠前的候选基因的功能验证 来自人类 iPSC。这个创新项目利用了丰富的深度临床和神经病理学知识 表型以及丰富的组学数据，包括遗传（GWAS、WGS）、表观遗传（5mC、5hmC、6mA、 H3K9Ac）和转录组（RNA-seq）在同一前额皮质上进行分析，并将提供前所未有的 揭示 AD 病理学中涉及的新分子机制的机会。我们的建议带来 汇集了一支异常强大且独特的多学科团队，在遗传领域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病研究。 所提出的工作代表了 AD 和组学研究之间的前沿。本次调查结果 研究将为 AD 发病机制提供新的机制见解，并可能发现新的分子 具有重要临床和转化意义的目标。

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.