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.

项目摘要/摘要 DNA甲基化有助于许多重要生物过程的表观遗传调节。盛行 教条是DNA甲基化几乎完全发生在真核生物中胞嘧啶（5MC）的第五位。 在过去的五年中，该教条已修订，因为多项研究报告了N6-的存在 跨真核生物包括小鼠和人类基因组在内的甲基趋化（6mA）。一些研究发现 证据表明潜水功能6MA在哺乳动物中的作用。一些研究也报道了 在某些神经元细胞和社会压力下增加了6MA水平，表明6MA可能起重要作用 在健康和疾病中。但是，一些研究挑战了哺乳动物中6mA的存在 基因组，突出了多种混杂因素来源。积极的辩论创造了不寻常的 表观遗传社区的混乱。然而，数十个研究继续报告了有关6MA的新发现 人类基因组在备受瞩目的期刊上包括一些论文。一些正在进行的研究设定了 检查6MA在脑细胞和脑疾病中的功能作用，尤其是在阿尔茨海默氏病中。 要明确评估人类基因组中6MA的抽象和流行率，必须 采用可靠且敏感的6MA映射方法。但是，过去和正在进行的研究主要使用 基于抗体的方法，与非特异性相关。虽然单分子实时 测序（SMRT-SEQ）已被广泛用于在细菌的基础分辨率下绘制6MA，我们最近的工作 其他人发现，现有方法对低6mA的真核基因组不够敏感 抽象。为了解决这一基本技术差距，我们将基于我们在SMRT-的> 10年经验的基础 SEQ开发了一种新的敏感6MA检测方法，并采用中性视角进行批判性检查 人类基因组中的6MA和来自阿尔茨海默氏病（AD）患者的脑组织中的6MA 相关的tauopathy（部分，另一种类型的痴呆症）和对照。这个项目很重要，非常及时 因为（1）如果新方法支持人类基因组中6MA的存在，则将提供持续的 以及急需的工具，未来的研究在某些细胞类型和阿尔茨海默氏病中检测6MA； （2）如果 这种新方法不支持所报道的显着水平的6MA，它将作为急需的直接 阐明当前辩论的证据。