Understanding the protective and neuroinflammatory role of human brain immune cells in Alzheimer Disease

了解人脑免疫细胞在阿尔茨海默病中的保护和神经炎症作用

• 批准号: 10362719
• 负责人: VAHRAM HAROUTUNIAN
• 金额: $ 151.36万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-02-15 至 2025-01-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10362719
• 关键词: ATAC-seq; Address; Affect; Age; Aging; Alzheimer' s Disease; Alzheimer' s disease model; Alzheimer' s disease risk; Animals; Brain; CRISPR/Cas technology; Cell Nucleus; Cells; Clinical; Communities; DNA; Data; Data Set; Development; Disease; Fluorescence-Activated Cell Sorting; Freezing; Functional disorder; Future; Gene Expression; Gene Proteins; Generations; Genes; Genome; Genomic approach; Genomics; Goals; HLA-DRB1; Haplotypes; Human; Immune; Innate Immune System; Joints; Light; Measurement; Methods; Microglia; Molecular; Molecular Profiling; Multiomic Data; Mus; Myelogenous; Nerve Degeneration; Neurobiology; PTPRC gene; Pathogenesis; Pathway interactions; Phenotype; Population; Proteome; Proteomics; Quantitative Trait Loci; Research; Resolution; Resources; Risk Factors; Role; Site; System; TREM2 gene; TYROBP gene; Taxonomy; Testing; Transcriptional Regulation; Untranslated RNA; Work; base; brain cell; brain tissue; case control; cell type; chromosome conformation capture; cost; design; epigenetic variation; epigenome; gene regulatory network; genetic association; genetic variant; genome sequencing; high dimensionality; human tissue; human very old age (85+); immunological diversity; induced pluripotent stem cell; innovation; insight; mouse model; multidimensional data; multiscale data; neuroinflammation; neuropathology; novel; protein expression; risk variant; selective expression; single cell analysis; single-cell RNA sequencing; transcriptome sequencing; whole genome

PROJECT SUMMARY Despite extensive clinical and genomic studies, the mechanisms of development and progression of Alzheimer's disease (AD) remain elusive. Microglia and other myeloid origin cells (collectively called human brain immune cells, or HBICs) have recently emerged as crucial players in the pathogenesis of AD. This is supported through genetic association studies, where many of the common and rare risk loci affect genes that are preferentially or selectively expressed in HBICs, emphasizing the pivotal role of the innate immune system in AD. In addition, single cell RNA sequencing analysis in mouse models of AD has identified a microglia subpopulation that is present at sites of neurodegeneration. It is unclear if HBICs assume a protective or damaging role, but that might vary depending on the stage and progression of AD. Therefore, further analysis of microglia and other immune cells purified from human brains is needed to understand the state of HBIC activity in human AD at different stages of disease. As HBICs constitute a small proportion of total brain cells, homogenate-based studies in human brain tissue are unlikely to capture the full spectrum of HBIC molecular signatures, especially in light of the growing appreciation for the diversity of HBICs in the brain. The proposed work addresses some of the limitations of previous research and is focused on: (1) cell type specific and single cell studies in immune cells isolated from human brain tissue; and (2) a systematic study of the regulatory effects of non-coding DNA on gene and protein expression, which is necessary given that the majority of common risk variants are situated in non-coding regions of the genome. More specifically, our application is uniquely designed to: (1) apply innovative genomic approaches and generate multi-omics data from HBICs isolated from 300 donors, including whole genome sequencing, RNAseq, ATACseq, HiC chromosome conformation capture and proteomics; (2) perform state-of-the-art single cell analysis that will allow us to assess the diversity of HBIC subpopulations, as well as detect those that are associated with AD; (3) connect AD risk loci with changes in the regulatory mechanisms of gene and protein expression in HBICs; and (4) organize HBIC multiscale data in functional networks and identify key drivers for AD. Our overall hypothesis is that HBIC subpopulations assume a neuroprotective role during aging and early stages of AD, but as disease progresses, specific HBIC subpopulations transform to neuroinflammatory phenotype(s). This conversion is partially driven by AD risk genetic variants, which affect regulatory mechanisms of genes that are key drivers of neuroinflammatory HBIC subpopulations. Successful completion of the proposed studies will provide: (1) an increased mechanistic understanding of dysfunction in AD risk loci; (2) prioritization of significant loci and genes for future mechanistic studies; and (3) access to large-scale, multidimensional datasets, together with systems level analyses of these datasets for transcriptional regulation in HBICs, which is an urgently needed (and currently missing) resource.

项目概要 尽管进行了广泛的临床和基因组研究，但其发展和进展的机制 阿尔茨海默病（AD）仍然难以捉摸。小胶质细胞和其他骨髓来源细胞（统称为人类 脑免疫细胞（HBIC）最近已成为 AD 发病机制的关键参与者。这是 通过遗传关联研究得到支持，其中许多常见和罕见的风险位点影响基因 在 HBIC 中优先或选择性表达，强调先天免疫系统的关键作用 在公元。此外，AD 小鼠模型中的单细胞 RNA 测序分析发现了一种小胶质细胞 存在于神经变性部位的亚群。目前尚不清楚 HBIC 是否具有保护性或保护性 具有破坏性作用，但这可能会根据 AD 的阶段和进展而有所不同。因此，进一步分析 需要从人脑中纯化的小胶质细胞和其他免疫细胞来了解 HBIC 的状态 人类 AD 在疾病不同阶段的活性。由于 HBIC 只占脑细胞总数的一小部分， 基于人脑组织匀浆的研究不太可能捕获 HBIC 分子的全谱 签名，特别是考虑到人们对大脑中 HBIC 多样性的日益重视。拟议的 工作解决了先前研究的一些局限性，重点是：（1）细胞类型特异性和单一 从人脑组织中分离出的免疫细胞的细胞研究； (2) 对监管的系统研究 非编码 DNA 对基因和蛋白质表达的影响，这是必要的，因为大多数 常见的风险变异位于基因组的非编码区域。更具体地说，我们的应用程序是 独特的设计目的是：(1) 应用创新的基因组方法并从 HBIC 生成多组学数据 从 300 名捐赠者中分离，包括全基因组测序、RNAseq、ATACseq、HiC 染色体 构象捕获和蛋白质组学； (2) 进行最先进的单细胞分析，使我们能够 评估 HBIC 亚群的多样性，并检测与 AD 相关的亚群； (3)连接 HBIC 中基因和蛋白表达调控机制发生变化的 AD 风险位点；和（4） 在功能网络中组织 HBIC 多尺度数据并确定 AD 的关键驱动因素。我们的总体假设是 HBIC 亚群在衰老和 AD 早期阶段发挥神经保护作用，但随着疾病的发展 随着进展，特定的 HBIC 亚群转变为神经炎症表型。这个转换是 部分由 AD 风险基因变异驱动，这些变异影响基因的调节机制，而基因是 AD 风险的关键驱动因素。 神经炎症 HBIC 亚群。成功完成拟议的研究将提供：（1） 增加对 AD 风险位点功能障碍的机制理解； (2) 重要位点的优先顺序和 用于未来机制研究的基因； (3) 访问大规模、多维数据集，以及 对这些数据集进行系统级分析以进行 HBIC 转录调控，这是迫切需要的 （目前缺少）资源。