The Enhancer Code of AD-A Genetic Approach

项目摘要 遗传和全基因组关联研究(GWAS)已经确定了大量的基因和危险等位基因 提示阿尔茨海默病的细胞自主和非细胞自主机制 (Ad)。除了神经元表达的基因外，观察到几个风险等位基因，如TREM2， 都是专门或主要在小胶质细胞中表达的，这使得人们更加努力地了解 小胶质细胞在AD病理中的作用。重要的是，GWAS确定的大多数风险变量都存在于非编码中 基因组的某些区域，这意味着其中一些区域会改变基因的表达。我们最近对神经元的比较 通过对AD患者和年龄匹配的对照组的成纤维细胞转分化获得的结果显示 AD神经元基因表达的变化。同时，我们最近的全球分析能力 人小胶质细胞的转录本和增强子图谱显示出显著的个体差异 阿尔茨海默病相关免疫基因的表达。总体而言，这些发现表明 阿尔茨海默病易感性基因表达的改变与世代无关 β淀粉样蛋白。增强剂已经成为细胞内和细胞外信号整合的主要点 与发育、动态平衡和疾病相关，导致特定背景的转录输出。 通过定义细胞的增强子环境，可以推断细胞所处的环境信号 接收并解释其后续的基因表达程序。在本应用程序中，我们建议定义 ‘增强阿尔茨海默氏病的密码’，以定性地促进我们对细胞自主和 驱动基因表达致病程序的非细胞自主因素。在具体目标1中，我们将 定义从神经细胞和小胶质细胞分离的细胞核的转录本和增强子图谱 散发性和遗传性阿尔茨海默病大脑和年龄和性别匹配的对照组大脑。这些研究将使 对完整衰老和阿尔茨海默病患者神经元和小胶质细胞调控格局的前所未有的分析 大脑。在特定的目标2中，我们将通过直接验证和解释神经元的AD特异性增强子编码 来自散发性和遗传性AD患者和年龄/性别匹配的对照组的成纤维细胞的重新编程。在……里面 具体目标3，我们将定义小胶质细胞的细胞自主AD特异性增强子编码，通过 对照和AD受试者的IPSCs和单核细胞的重新编程。这些研究将建立在我们最近 显示显著水平的人类小胶质细胞转录本和增强子景观的特征 与AD风险相关的基因表达的个体差异。在具体目标4中，我们将界定 神经元-小胶质细胞相互作用对每种细胞类型的转录本和表观基因组的影响。通过 利用现有的资源和数据集，这些研究将定义转录网络 阿尔茨海默病中神经元和小胶质细胞的异常调节，为确定阿尔茨海默病的发病机制提供了概念证据 遗传形式的阿尔茨海默病，并提出进一步研究的其他途径。

Project Summary Genetic and genome wide association studies (GWAS) have identified numerous genes and risk alleles that indicate both cell autonomous and non-cell autonomous mechanisms contributing to Alzheimer's Disease (AD). In addition to genes expressed by neurons, the observation that several risk alleles, such as TREM2, are exclusively or mainly expressed in microglia, has led to increased efforts to understand the roles of microglia in AD pathology. Importantly, the majority of risk variants identified by GWAS reside in non-coding regions of the genome, implying that some act to alter gene expression. Our recent comparisons of neurons derived by trans-differentiation of fibroblasts from AD subjects and age matched controls demonstrate marked changes in gene expression in AD neurons. In parallel, our recent ability to globally analyze the transcriptomes and enhancer atlases of human microglia demonstrated marked individual variation in expression of immune genes associated with AD risk alleles. Collectively, these findings suggest widespread alterations in the expression of genes that may contribute to susceptibility of AD independent of the generation of βamyloid. Enhancers have emerged as major points of integration of intra and extra-cellular signals associated with development, homeostasis and disease, resulting in context-specific transcriptional outputs. By defining a cell's enhancer landscape, it is possible to both infer the environmental signals the cell is receiving and explain its consequent program of gene expression. In this application, we propose to define the `Enhancer codes of Alzheimer's Disease' to qualitatively advance our understanding of cell autonomous and non-cell autonomous factors that drive pathogenic programs of gene expression. In Specific Aim 1, we will define transcriptomes and enhancer landscapes of nuclei isolated from neurons and microglia derived from sporadic and genetic AD brains and brains from age and sex-matched controls. These studies will enable an unprecedented analysis of the regulatory landscapes of neurons and microglia in the intact aging and AD brain. In Specific Aim 2, we will validate and explain AD-specific enhancer codes of neurons by direct reprogramming of fibroblasts from sporadic and genetic AD patients and age/sex-matched control subjects. In Specific aim 3, we will define cell autonomous AD-specific enhancer codes of microglia obtained by reprograming of iPSCs and monocytes from control and AD subjects. These studies will build upon our recent characterization of human microglia transcriptomes and enhancer landscapes that demonstrate striking levels of individual variation in the expression of genes linked to risk of AD. In Specific Aim 4, we will define consequences of neuron-microglia interactions on the transcriptomes and epigenomes of each cell type. By leveraging existing resources and data sets, these studies will define transcriptional networks that are dysregulated in neurons and microglia in AD, provide proof of concept for defining the mechanistic basis of inherited forms of AD, and nominate additional pathways for further investigation.