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.

项目总结/摘要 DNA甲基化有助于许多重要生物过程的表观遗传调控。现行 在真核生物中，DNA甲基化几乎只发生在胞嘧啶的第五位（5 mC）。 在过去的五年里，随着多项研究报告了N6- 甲基腺嘌呤（6 mA）在包括小鼠和人类基因组的真核生物中的表达。一些研究发现， 证据表明，6 mA在哺乳动物中发挥着多种功能。一些研究还报告说， 在某些神经元细胞和社会压力下，6 mA水平增加，表明6 mA可能起重要作用 健康和疾病。然而，一些研究已经挑战了哺乳动物中6 mA的存在， 基因组，突出混杂因素的多种来源。这场激烈的辩论创造了不同寻常的 表观遗传学界的困惑然而，数十项研究继续报告了关于6 mA的新发现， 人类基因组，包括一些在知名期刊上发表的论文。一些正在进行的研究已经建立了 旨在研究6 mA在脑细胞和脑部疾病（特别是阿尔茨海默病）中的功能作用。 为了明确评估6 mA在人类基因组中的丰度和流行率，必须 采用可靠且灵敏的6 mA标测方法。然而，过去和正在进行的研究大多采用 基于抗体的方法，这与非特异性有关。单分子实时 测序（SMRT-seq）已被广泛用于在细菌中以碱基分辨率定位6 mA，我们最近的工作 其他人发现，现有的方法对于低6 mA的真核基因组不够灵敏， 丰饶。为了解决这一根本性的技术差距，我们将建立在我们在SMRT超过10年的经验， seq开发了一种新的方法，用于灵敏的6 mA检测，并采取中立的观点来批判性地检查 6 mA在人类基因组和阿尔茨海默病（AD）患者的脑组织中， 相关的tau蛋白病（PART，另一种类型的痴呆症）和对照组。这个项目意义重大，非常及时 因为（1）如果新方法支持人类基因组中存在6 mA，它将提供正在进行的 和未来的研究与急需的工具，以检测6 mA在某些细胞类型和阿尔茨海默病;（2）如果 该新方法不支持所报道的6 mA的显著水平，它将作为急需的直接 以澄清当前的争论。