Sex divergence and cell specificity of age-related hippocampal DNA modifications

年龄相关海马 DNA 修饰的性别差异和细胞特异性

• 批准号: 10615662
• 负责人: WILLARD M FREEMAN
• 金额: $ 53.55万
• 依托单位: OKLAHOMA MEDICAL RESEARCH FOUNDATION
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-07-01 至 2025-03-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10615662
• 关键词: Address; Age; Aging; Alleles; Alzheimer' s Disease; Animal Model; Animals; Astrocytes; Biochemical; Bioinformatics; Biological; Biological Assay; Brain; Caloric Restriction; Cells; Central Nervous System; Chromatin; Clinical; Cognition; Correlative Study; Cytosine; DNA; DNA Methylation; DNA Modification Process; DNA analysis; Data; Databases; Elderly; Enhancers; Enterobacteria phage P1 Cre recombinase; Entropy; Enzymes; Epigenetic Process; Female; Future; Gene Expression; Gene Expression Regulation; Genome; Genomic Segment; Genomics; Goals; Hippocampus; Human; Impaired cognition; Intervention; Intervention Studies; Knowledge; Longevity; Mass Spectrum Analysis; Messenger RNA; Methylation; Microglia; Mitotic; Modeling; Modification; Morbidity - disease rate; Mus; Nerve Degeneration; Neurobiology; Neurodegenerative Disorders; Neurons; Nucleic Acid Regulatory Sequences; Nucleic Acids; Oklahoma; Parabiosis; Pathway interactions; Pattern; Play; Population; Predisposition; Prevention; Process; Proteins; Proteomics; RNA; Rationalization; Regulation; Rejuvenation; Research; Role; Sex Differences; Shock; Site; Site-Directed Mutagenesis; Specificity; Stimulus; Tamoxifen; Testing; Tissues; Transgenic Organisms; Visualization; age related; age related neurodegeneration; aged; aging brain; base; bisulfite sequencing; candidate identification; cell type; conflict resolution; design; epigenome; epigenome editing; epigenomics; experience; genome-wide; genomic locus; human old age (65+); improved; inducible Cre; insight; male; methylation pattern; middle age; mortality; mouse model; neurogenesis; novel; prevent; programs; protein expression; response; sex; tool; transcription factor; transcriptome; transcriptomics; whole genome

Abstract Epigenetic processes in the central nervous system may play a mechanistic role in susceptibility to and progression of cognitive decline and age-related neurodegenerative diseases, such as Alzheimer's. DNA modifications, principally cytosine base methylation and hydroxymethylation (mC and hmC respectively), are fundamental regulators of DNA accessibility and gene regulation/expression with differential effects on gene expression depending on the modification (mC/hmC), context CG/non-CG (also known as CH), and genomic location. A barrier to progress in understanding the role of epigenetic mechanisms in brain aging and DNA modifications in particular, has been the lack of quantitatively accurate, genome-wide data in specific cell types. Without the knowledge of the specific genomic locations of altered modifications with aging it is impossible to design well-rationalized, mechanistic studies that unravel the functional effects of epigenetic reconfiguration. Therefore, the critical next step for the field is to generate this genome-wide data of mC and hmC in CG and CH contexts in specific cell types from both sexes across the lifespan. To address this critical issue we have developed cell-type specific, tamoxifen-inducible Cre, transgenic NuTRAP models to allow isolation of nucleic acids (DNA & RNA) from microglia, astrocytes, and neurons. In Aim 1, cell type-specific hippocampal changes in mC/hmC with aging will be examined by whole genome oxidative bisulfite sequencing (WGoxBS) in microglia, astrocytes, and neurons. Paired epigenomic and transcriptomic data from the same animals will be used to: 1) assess aging with `epigenetic clocks' in a cell-type specific fashion, 2) determine the role of altered modification patterns in age-related changes in gene expression, 3) determine enrichment of differential modifications in regulatory regions of the genome, and 4) identify genomic loci for epigenome editing. In prior studies we have determined that age-related DNA modification changes can be prevented by caloric restriction. In Aim 2 we will test whether heterochronic parabiosis can reverse age-related changes once extant in the same Cre-inducible, NuTRAP models. Using a unique database of all publicly available, annotated human methylation data we will validate aspects of our findings in humans. In Aim 3 we will examine the targeting mechanisms that direct changes in mC/hmC to specific genomic regions. These studies will allow the determination of critical genomic regions with altered DNA modification patterns that can be manipulated in future interventional studies. The ultimate goal of the research is to develop clinical interventions that target the epigenome to maintain brain function with aging and prevent age-related neurodegeneration.

抽象的 中枢神经系统中的表观遗传过程可能在易感性和 认知能力下降和与年龄有关的神经退行性疾病的进展，例如阿尔茨海默氏症。脱氧核糖核酸 修饰，主要是胞嘧啶碱基甲基化和羟甲基（分别为MC和HMC），是 DNA可及性和基因调节/表达的基本调节剂对基因的影响有所不同 表达取决于修饰（MC/HMC），上下文CG/NON-CG（也称为CH）和基因组 地点。在理解表观遗传机制在大脑衰老和DNA中的作用方面进步的障碍 尤其是修改是缺乏特定细胞中定量准确的全基因组数据 类型。在不了解随着衰老改变改变的特定基因组位置，就是 不可能设计良好的机械研究，以揭示表观遗传的功能效应 重新配置。因此，该领域的关键下一步是生成MC和MC的全基因组数据 CG和CH上下文中的HMC在整个生命周期中的两个性别中的特定细胞类型中。解决这个关键 问题我们开发了细胞类型的特异性，他莫昔芬可诱导的CRE，转基因营养模型，以允许 从小胶质细胞，星形胶质细胞和神经元中分离核酸（DNA和RNA）。在AIM 1中，特定于细胞类型 整个基因组氧化亚硫酸盐测序将检查MC/HMC的海马变化 （WGOXB）在小胶质细胞，星形胶质细胞和神经元中。来自相同的表观基因组和转录组数据 动物将用于：1）以细胞类型的方式评估“表观遗传钟”的衰老，2）确定 修饰模式改变在基因表达与年龄相关的变化中的作用，3）确定富集 基因组调节区域的差异修饰，4）鉴定表观基因组的基因组基因座 编辑。在先前的研究中，我们确定与年龄相关的DNA修饰变化可以通过 热量限制。在AIM 2中，我们将测试异核抛物线是否可以逆转与年龄相关的变化 曾经存在于相同的CRE诱导型营养模型中。使用所有公开可用的唯一数据库 注释的人类甲基化数据我们将验证人类发现的各个方面。在目标3中，我们将 检查将MC/HMC直接变化为特定基因组区域的靶向机制。这些研究 将允许确定具有改变DNA修饰模式的关键基因组区域 在以后的介入研究中操纵。该研究的最终目标是开发临床 针对表观基因组的干预措施以保持衰老并预防与年龄有关的干预措施 神经变性。