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

人类 AD 大脑 DNA 6mA 甲基化组的全基因组作图和综合分析

• 批准号: 10404653
• 负责人: DAVID ALAN BENNETT
• 金额: $ 71.38万
• 依托单位: UNIVERSITY OF FLORIDA
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10404653
• 关键词: 3-Dimensional; Adenine; Affect; Aging; Alzheimer' s Disease; Alzheimer' s disease brain; Alzheimer' s disease pathology; Alzheimer' s disease patient; Amyloid; Attention; Autopsy; Bioinformatics; Biological; Biological Process; Brain; Brain Mapping; Candidate Disease Gene; Chemicals; Clinical; Communities; Cytosine; DNA; DNA Methylation; DNA Modification Process; DNA analysis; Data; Data Set; Dementia; Development; Dimensions; Disease; Elderly; Epigenetic Process; Etiology; Exons; Freezing; Gene Expression; Genes; Genetic; Genetic Variation; Genomics; Goals; Histone Acetylation; Human; Intercistronic Region; Introns; Joints; Lead; Link; Maps; Measures; Memory; Mental Depression; Meta-Analysis; Methylation; MicroRNAs; Modification; Molecular; Molecular Target; Mus; Neurofibrillary Tangles; Organoids; Participant; Pathogenesis; Pathway interactions; Pattern; Persons; Phenotype; Play; Population; Positioning Attribute; Prefrontal Cortex; Prosencephalon; Quantitative Trait Loci; Research; Role; Sampling; Senile Plaques; Site; Stress; System; Testing; Tissue Sample; Tissues; Validation; Variant; Work; aging brain; base; brain tissue; cell type; cohort; design; effective therapy; epigenetic marker; epigenetic regulation; frontier; genetic epidemiology; genome wide association study; genome-wide; genomic locus; induced pluripotent stem cell; innovation; insight; knock-down; mammalian genome; methylation pattern; methylome; multidisciplinary; multiple omics; neuropathology; novel; novel diagnostics; novel therapeutic intervention; novel therapeutics; overexpression; population based; promoter; religious order study; tool; transcriptome; transcriptome sequencing

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.

项目摘要 阿尔茨海默氏病（AD）是老年人中最常见的痴呆症，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诊断方法的必要条件。 和治疗策略。DNA的化学修饰，如甲基化， 调节基因表达和许多其他关键的生物过程，改变DNA甲基化模式， 与大脑老化和AD有关虽然很多注意力都集中在第五代DNA甲基化上， 最近的研究发现，在胞嘧啶（5 mC）的第六个位置上， 腺嘌呤（6 mA）在哺乳动物的大脑。然而，关于它的存在、基因组分布和 人类大脑中可能的功能以及与AD的相关性。我们在小鼠和人脑中的初步数据 表明6 mA对环境应激具有动态响应，并在人AD脑中积累。 我们的中心假设是，6 mA修饰的改变信号与AD有因果关系 神经病理学该项目的目标是生成第一个详细的大脑6 mA甲基化图谱 并鉴定携带与定量神经病理学相关的异常6 mA改变的致病基因， AD病理学早期特征的测量（例如，淀粉样斑块、神经纤维缠结）。为了实现这一点， 我们提出了三个具体的目标：（1）全基因组定位脑DNA 6 mA甲基化组，以确定 与AD病理学相关的差异甲基化基因/区域， 由两个大型社区人口老龄化队列收集的1，200份死后脑组织样本 和痴呆症。(2)综合多组学分析，以阐明6 mA改变在细胞凋亡中的潜在机制作用。 AD病理学;和（3）在3D脑类器官中排名靠前的候选基因的功能验证 从人类的iPSCs。这个创新的项目利用了丰富的深度临床和神经病理学 表型沿着丰富的组学数据，包括遗传（GWAS，WGS），表观遗传（5 mC，5 hmC，6 mA， H3 K9 Ac）和转录组（RNA-seq）在同一前额叶皮层上的分布，并将提供前所未有的 发现AD病理学中涉及的新分子机制的机会。我们的提议带来了 我们拥有一支非常强大和独特的多学科团队，在遗传学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氏症研究。 提出的工作代表了AD和组学研究之间的接口的前沿。调查结果 这些研究将为AD发病机制提供新机制，并有可能发现新的分子 具有重要临床和转化意义的靶点。