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

基本信息

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
项目类别：
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&apos 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

项目摘要

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的表观遗传过程可能在易感性和认知能力下降和与年龄相关的神经退行性疾病（例如阿尔茨海默病）的进展。脱氧核糖核酸修饰，主要是胞嘧啶碱基甲基化和羟甲基化（分别为 mC 和 hmC） DNA 可及性和基因调控/表达的基本调节因子，对基因具有不同的影响表达取决于修饰 (mC/hmC)、背景 CG/非 CG（也称为 CH）和基因组地点。理解表观遗传机制在大脑衰老和 DNA 中的作用的进展障碍特别是修改，缺乏特定细胞中定量准确的全基因组数据类型。如果不了解随衰老而改变的修饰的特定基因组位置，不可能设计合理化的机制研究来揭示表观遗传的功能效应重新配置。因此，该领域关键的下一步是生成 mC 和的全基因组数据。 hmC 在整个生命周期中两性特定细胞类型的 CG 和 CH 环境中。为了解决这个关键问题我们开发了细胞类型特异性、他莫昔芬诱导型 Cre、转基因 NuTRAP 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）。在目标 1 中，细胞类型特异性通过全基因组氧化亚硫酸氢盐测序检查海马 mC/hmC 随衰老的变化 (WGoxBS) 在小胶质细胞、星形胶质细胞和神经元中。来自同一组的配对表观基因组和转录组数据动物将被用来：1）以细胞类型特定的方式用“表观遗传时钟”评估衰老，2）确定改变的修饰模式在与年龄相关的基因表达变化中的作用，3) 确定基因组调控区域的差异修饰，以及 4) 识别表观基因组的基因座编辑。在之前的研究中，我们已经确定可以通过以下方法来预防与年龄相关的 DNA 修饰变化：热量限制。在目标 2 中，我们将测试异时性联体共生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 NuTRAP 模型中。使用所有公开可用的独特数据库，带注释的人类甲基化数据，我们将验证我们在人类中的发现的各个方面。在目标 3 中，我们将检查将 mC/hmC 的变化引导至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的 DNA 修饰模式的关键基因组区域，这些区域可以在未来的介入研究中进行操纵。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，以维持衰老过程中的大脑功能并预防与年龄相关的疾病神经变性。