Dynamics of the brain epigenome with aging

通过表观遗传过程调节大脑衰老是目前最具挑衅性的衰老领域之一 研究。中枢神经系统中的表观遗传过程可能在易感性中发挥机械作用 认知衰退和阿尔茨海默病等与年龄相关的神经退行性疾病的进展 以及其他痴呆症患者。DNA修饰，主要是胞嘧啶的甲基化和羟甲基化(MC和 HMC)，是DNA可及性和基因调控/表达的基本调节者 对基因表达的不同影响取决于修饰(MC/HMC)、上下文CG/CH和基因组 地点。在理解表观遗传机制在脑老化和DNA中的作用方面的进展障碍 特别是修改，一直缺乏定量准确的全基因组数据。如果没有 随着年龄的增长，改变的修饰的特定基因组位置的知识是不可能设计的 理性化、机械化的研究，揭示表观遗传变化的功能效应。因此， 该领域的关键下一步是在CG和CH上下文中生成MC和HMC的全基因组数据 特定的细胞类型，在男性和女性中。为了解决这一阻碍进步的障碍，我们制定了 创新的方法来分析整个基因组的MC和HMC水平，并在一个碱基上进行绝对定量- 和特定于链的方式。使用这些新的工具，我们发现与 在海马区MC和HMC的模式中，这些变化主要是性别特异性的，并且它们 与基因表达的改变相对应。有趣的是，我们还发现非CpG甲基化是 随着年龄的增长而改变的原发甲基化形式和雄性特有的动物间差异增加(甲基化 随着海马体中的衰老，基因组中的所有基因都发生了变化。这些发现提出了一些重要的问题 必须解决这一问题，以便将该领域转移到机械学研究。神经表观基因组是否发生了类似的或 不同类型的中枢神经系统细胞和不同性别之间的差异？年龄相关的变化会不会发生在 神经表观基因组可以预防吗？表观基因组编辑应该针对基因组的哪些区域 测试大脑老化能否通过保持或恢复“青春”来预防或逆转的方法 DNA修饰模式？在目标1中，男性和男性中枢神经系统MC/HMC的细胞类型特异性变化随着年龄的增长而变化 雌性小鼠将接受全基因组测序(WGoxBS)。小胶质细胞、星形胶质细胞和神经元 通过细胞表面标记和NuTRAP技术从海马区分离出来的细胞将被检测。年青的 (3M)、成年(12M)和老年(24M)C57BL6雄性和雌性小鼠将被检查，MC/HMC数据将被 与配对的RNA-Seq数据连接。然后将使用生物信息学方法来确定 改变修饰模式中与年龄相关的基因表达的变化，分化丰富 基因组调节区的修饰，以及确定表观基因组编辑的基因组位置。在AIM 2 限制热量摄入防止年龄相关的DNA甲基化和羟甲基化改变的能力 维持年轻的神经表观基因组将在神经元、星形胶质细胞和小胶质细胞中确定。在组织上 我们发现，在男性中，通过限制热量摄入可以防止与年龄相关的表观基因组变化，但 对分离的细胞群体和雌性细胞的影响尚不清楚。使用所有公共可用数据的唯一数据库， 经过注释的人类甲基化数据，我们将在人类身上验证我们的发现的各个方面。这些研究将允许 通过改变DNA修饰模式确定关键基因组区域，这些DNA修饰模式可以在 未来的干预研究。这项研究的最终目标是针对 表观基因组在退伍军人中随着年龄的增长维持大脑功能和预防与年龄相关的神经疾病。

Regulation of brain aging through epigenetic processes is currently one of the most provocative areas of aging research. Epigenetic processes in the central nervous system may play a mechanistic role in susceptibility to and progression of cognitive decline and age-related neurodegenerative disease such as Alzheimer’s disease and other dementias. DNA modifications, principally methylation and hydroxymethylation of cytosines (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/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. Without the knowledge of the specific genomic locations of altered modifications with aging and it is impossible to design well-rationalized, mechanistic studies that unravel the functional effects of epigenetic changes. 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 and in both males and females. To address this barrier to progress we have developed innovative methods to analyze mC and hmC levels across the genome with absolute quantitation in a base- and strand-specific manner. Using these novel tools, we have found that there are significant changes with aging in the patterns of hippocampal mC and hmC, that these changes are principally sex-specific, and they correspond to altered gene expression. Intriguingly, we have also identified non-CpG methylation as the primary form of altered methylation with aging and a male-specific increased inter-animal variance (methylation entropy) across the genome with aging in the hippocampus. These findings raise significant questions that must be addressed to move the field to mechanistic studies. Is the neuroepigenome altered in a similar or dissimilar manner across CNS cell types and between sexes? Can age-related changes in the neuroepigenome be prevented? What regions of the genome should be targeted by epigenome editing approaches to test whether brain aging can be prevented or reversed by maintaining or restoring a ‘youthful’ DNA modification pattern? In Aim 1, cell type-specific changes in mC/hmC with aging in the CNS of male and female mice will be examined by whole genome sequencing (WGoxBS). Microglia, astrocytes, and neurons isolated from the hippocampus by both cell surface markers and NuTRAP technology will be examined. Young (3M), Adult (12M), and Aged (24M) C57Bl6 male and female mice will be examined and mC/hmC data will be concatenated with paired RNA-Seq data. Bioinformatic approaches will then be used to determine the role of altered modification patterns in age-related changes in gene expression, enrichment of differential modifications in regulatory regions of the genome, and to identify genomic loci for epigenome editing. In Aim 2 the ability of caloric restriction to prevent age-related changes in DNA methylation and hydroxymethylation and maintain a ‘young’ neuroepigenome will be determined in neurons, astrocytes, and microglia. At the tissue level, we have found prevention of age-related epigenomic changes by caloric restriction in males but the effects on isolated cell populations and females are unknown. Using a unique database of all publicly available, annotated human methylation data we will validate aspects of our finding in humans. 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 being clinical interventions that target the epigenome to maintain brain function with aging and prevent age-related neurological disease in Veterans.