Critical assessment of DNA adenine methylation in brain cells from healthy aging and Alzheimer's disease

健康老龄化和阿尔茨海默病脑细胞 DNA 腺嘌呤甲基化的批判性评估

• 批准号: 10365337
• 负责人: Kristen Jennifer Brennand
• 金额: $ 74.57万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10365337
• 关键词: Address; Adenine; Age; Alzheimer' s Disease; Antibodies; Autopsy; Bacteria; Bacterial DNA; Benchmarking; Binding Sites; Biological Process; Brain; Brain Diseases; CRISPR/Cas technology; Cells; Cognitive; Communities; Complex; Confusion; Cytosine; DNA; DNA Methylation; DNA Modification Process; DNA-Directed DNA Polymerase; Data; Data Set; Dementia; Detection; Disease; Enzymes; Epigenetic Process; Eukaryota; Future; Genes; Genome; Genome engineering; Genomics; Health; Histones; Human; Human Characteristics; Human Development; Human Genome; Induced pluripotent stem cell derived neurons; Informatics; Journals; Kinetics; Knowledge; Link; Location; Mammals; Maps; Methods; Methylation; Methyltransferase; Mitochondrial DNA; Mus; Neuroglia; Neurons; Nucleotides; Paper; Patients; Play; Positioning Attribute; Prevalence; Process; RNA; Reader; Regulation; Reporting; Resolution; Risk Factors; Role; Sensitivity and Specificity; Side; Source; Specificity; Tauopathies; Technology; Time; Validation; Work; age related; base; brain cell; brain tissue; cell type; deep sequencing; design; detection method; epigenetic regulation; experience; genome-wide; healthy aging; human disease; improved; induced pluripotent stem cell; mammalian genome; mouse genome; mutant; nanopore; nerve stem cell; novel; pathogen; research study; risk mitigation; single molecule; single molecule real time sequencing; social; social stress; tau Proteins; tool

PROJECT SUMMARY/ABSTRACT DNA methylation contributes to epigenetic regulation of many important biological processes. The prevailing dogma is that DNA methylation almost exclusively occurs at the fifth position of cytosine (5mC) in eukaryotes. This dogma has been revised in the past five years as multiple studies reported the existence of N6- methyladenine (6mA) across eukaryotes including the mouse and human genome. A few studies have found evidence that suggests the diverse functions 6mA plays in mammals. Some studies have also reported increased 6mA level in certain neuronal cells and upon social stress, suggesting 6mA may play important roles in health and diseases. However, several studies have challenged the presence of 6mA in mammalian genomes, highlighting multiple sources of confounding factors. The active debate has created unusual confusions in the epigenetic community. Yet, tens of studies continued to report new discoveries about 6mA in the human genome including some papers at high-profile journals. A few ongoing research studies have set out to examine the functional roles of 6mA in brain cells and brain disorders, especially in Alzheimer’s disease. To unambiguously assess the abundance and prevalence of 6mA in the human genome, it is imperative to employ a reliable and sensitive 6mA mapping method. However, past and ongoing studies mostly employ antibody-based methods, which are associated with non-specificity. Although Single Molecule Real-Time sequencing (SMRT-seq) has been widely used to map 6mA at base resolution in bacteria, recent work by us and others have found that existing methods are not sensitive enough for eukaryotic genomes with low 6mA abundance. To address this fundamental technological gap, we will build on our >10-yr experience in SMRT- seq to develop a new method for sensitive 6mA detection, and take a neutral perspective to critically examine 6mA in the human genome and in brain tissues from patients with Alzheimer’s disease (AD), Primary age- related tauopathy (PART, another type of dementia) and controls. This project is significant and very timely because (1) if the novel method supports the existence of 6mA in the human genome, it will provide ongoing and future studies with a much-needed tool to detect 6mA in certain cell types and Alzheimer’s diseases; (2) if the novel method does not support a significant level of 6mA as reported, it will serve as a much-needed direct evidence to clarify the current debate.

项目概要/摘要 DNA 甲基化有助于许多重要生物过程的表观遗传调控。 众所周知，真核生物中 DNA 甲基化几乎只发生在胞嘧啶的第五位 (5mC)。 随着多项研究报告 N6- 的存在，这一教条在过去五年中得到了修订。 一些研究发现，甲基腺嘌呤 (6mA) 存在于真核生物中，包括小鼠和人类基因组。 一些研究还报道了表明 6mA 在哺乳动物中发挥多种功能的证据。 某些神经元细胞和社会压力下 6mA 水平增加，表明 6mA 可能发挥重要作用 然而，一些研究对哺乳动物体内 6mA 的存在提出了质疑。 基因组，强调了混杂因素的多种来源，激烈的争论创造了不同寻常的结果。 然而，数十项研究继续报告了有关 6mA 的新发现。 人类基因组，包括一些知名期刊上的论文。 旨在检查 6mA 在脑细胞和脑部疾病（尤其是阿尔茨海默病）中的功能作用。 为了明确评估人类基因组中 6mA 的丰度和普遍性，必须 采用可靠且灵敏的 6mA 映射方法然而，过去和正在进行的研究大多采用。 基于抗体的方法，尽管是单分子实时的，但具有非特异性。 测序 (SMRT-seq) 已广泛用于在细菌中以碱基分辨率绘制 6mA 的图谱，这是我们最近的工作 等人发现现有方法对于低 6mA 的真核基因组不够灵敏 为了解决这一根本性的技术差距，我们将利用我们在 SMRT 领域超过 10 年的经验。 seq开发灵敏6mA检测新方法，并以中立角度批判性审视 人类基因组和阿尔茨海默病 (AD) 患者脑组织中的 6mA，主要年龄- 相关的 tau 病（PART，另一种类型的痴呆）和控制该项目意义重大且非常及时。 因为 (1) 如果新方法支持人类基因组中存在 6mA，它将提供持续的 以及未来的研究，使用急需的工具来检测某些细胞类型和阿尔茨海默病中的 6mA（2）； 该新颖方法不支持所报道的 6mA 的显着水平，它将作为急需的直接方法 澄清当前争论的证据。