Single-Cell Analysis of Aging-Associated 4D Nucleome in the Human Hippocampus

项目概要/摘要 与年龄相关的认知能力下降是美国的一个重要问题，因为大约20%的人 预计到2030年，美国人口将达到65岁或以上。了解分子机制 因此，随着人口老龄化，大脑老化以延长健康的认知功能变得越来越重要， 老年人仍在工作。脑细胞在衰老过程中表现出深刻和异质性的变化， 分子和细胞水平。体育锻炼的简单干预已经成为一个重大的积极因素 衰老中认知功能的调节剂。为了响应RFA-RM-20-005，我们成立了一个跨学科的 一个在单细胞基因组学、神经回路和衰老方面具有专业知识的团队，调查年龄和身体活动， 死后人脑海马细胞4D核组在整个生命周期中的相关变化 细胞分辨率我们假设，细胞类型特异性重组的核组发生在人类 海马脑区在衰老和体力活动。核组的变化反过来控制大脑 表观基因组和转录组，调节神经回路功能。“甲基-HiC”，一种新的方法， 在单个细胞中进行DNA甲基化和染色质接触的联合分析，结合“Paired-seq”，一种超 用于开放染色质和转录组单细胞联合分析的高通量方法将用于 询问染色质结构沿着DNA甲基化、染色质可及性和基因表达 在人类的海马体中。在目标1中，我们将确定死后主要细胞类型的核组变化， 人海马体在4个年龄范围（20-39岁、40-59岁、60-79岁和80-99岁）的整个生命周期中的变化。我们 将进一步将核组中的这些变化与每种细胞类型中的表观基因组和转录组相关联， 衰老过程中脆弱的细胞类型，并揭示可能受到 衰老在目标2中，我们将确定身体活动如何修改和恢复特定人类的核组， 海马细胞类型。我们将研究两个年龄匹配的认知健康队列（70-99岁）， 高水平或低水平的身体活动，如可穿戴活动监测器所测量的。我们会把恢复性的 表观基因组和转录组对核组的影响。在目标3中，我们将绘制衰老和锻炼如何改变 在小鼠中具有高度受控的可量化的身体活动的特定海马细胞类型中的核组 与人类数据进行比较。这些小鼠研究允许对运动变量进行研究， 与可能影响海马核组的其他生活方式因素的影响隔离，这是不可能的， 人类实验对象拟议的研究将有助于改变我们理解的机制， 人类大脑老化背景下的染色质组织和功能。

Project Summary / Abstract Age-related cognitive decline is an important concern in the United States, as approximately 20% of the US population is expected to be age 65 or older by year 2030. Understanding the molecular mechansims of brain aging to prolong healthy cognitive function is therefore increasingly important as the population ages and older people remain in the work force. Brain cells exhibit profound and heterogeneous changes during aging at molecular and cellular levels. The simple intervention of physical exercise has emerged as a major positive modulator of cognitive function in aging. In response to RFA-RM-20-005, we have formed an interdisciplinary team with expertise in single-cell genomics, neural circuitry, and aging, to investigate age- and physical activity- related changes of 4D nucleome in post-mortem human brain hippocampus cells across the lifespan with single- cell resolution. We hypothesize that cell-type-specific re-organization of nucleome occurs in the human hippocampal brain region during aging and with physical activity. The changes in nucleome in turn control brain epigenome and transcriptome, modulating neural circuit functionality. The “Methyl-HiC”, a new approach for joint profiling of DNA methylation and chromatin contacts in single cells, combined with “Paired-seq”, an ultra- high-throughput method for single-cell joint analysis of open chromatin and transcriptome, will be used to interrogate the chromatin architecture along with DNA methylation, chromatin accessibility and gene expression in the human hippocampus. In Aim 1, we will determine changes in nucleome in major cell types of post-mortem human hippocampus across the life-span with 4 age ranges (20–39, 40–59, 60–79, and 80–99 years old). We will further correlate these changes in nucleome with epigenome and transcriptome in each cell type, to identify vulnerable cell types during aging, and uncover potential gene regulatory programs that could be impacted by aging. In Aim 2, we will determine how physical activity modifies and restores nucleome in specific human hippocampal cell types. We will study two age-matched cognitively–healthy cohorts (70-99 years old) with either high level or low level physical activity, as measured by wearable activity monitors. We will correlate restorative effects on nucleome with epigenome and transcriptome. In Aim 3, we will map how aging and exercise alter nucleome in specific hippocampal cell types with highly controlled quantifiable physical activity in the mouse model, for comparison with human data. These mouse studies allow the exercise variable to be investigated in isolation from effects of other lifestyle factors that can affect hippocampal nucleome, which is not possible with human subjects. The proposed research will help to transform our ability to understand the mechanisms of chromatin organization and function in the context of human brain aging.