Characterizing the landscape of cell-type specific changes associated with Alzheimer's disease before death with single-cell genomics

用单细胞基因组学描述死亡前与阿尔茨海默病相关的细胞类型特异性变化的情况

• 批准号: 10680438
• 负责人: Tushar Vinod Kamath
• 金额: $ 5.04万
• 依托单位: HARVARD MEDICAL SCHOOL
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-09-01 至 2024-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10680438
• 关键词: Alleles; Alzheimer' s Disease; Alzheimer' s disease brain; Alzheimer' s disease model; Alzheimer' s disease pathology; Alzheimer' s disease risk; Amyloid; Autopsy; Benchmarking; Biopsy; Biopsy Specimen; Brain; Brain Pathology; Cause of Death; Cell Nucleus; Cells; Cellular Assay; Cessation of life; Complex; Data Set; Disease; Fluorescent in Situ Hybridization; Freezing; Gene Expression; Genetic Transcription; Genetic study; Genomics; Heritability; Human; Immunohistochemistry; Impaired cognition; In Situ; Individual; Location; Measures; Memory Loss; Methods; Modeling; Molecular; Molecular Profiling; Morphologic artifacts; Neurofibrillary Tangles; Neuroimmune; Normal Pressure Hydrocephalus; Pathogenesis; Pathologic; Pathology; Pathway interactions; Patients; Population; Process; Protocols documentation; Regression Analysis; Research; Resolution; Resources; Role; Sampling; Senile Plaques; Signal Transduction; Slice; Slide; Techniques; Technology; Tissues; Transcription Alteration; Transgenic Mice; Variant; Work; brain tissue; cell type; cohort; comorbidity; computer framework; differential expression; end stage disease; experimental study; familial Alzheimer disease; frontal lobe; genome-wide; human tissue; insight; meter; mouse model; novel; response; single cell sequencing; single cell technology; single molecule; single nucleus RNA-sequencing; tau Proteins; tau-1; tool

Project Summary Alzheimer’s disease (AD) remains the only illness in the top 10 causes of death with no disease-modifying treatments available. In large part, the dearth of adequate therapies is due to our incomplete understanding of how specific molecular pathways in the brain result in cognitive decline and memory loss. Recent genetic studies implicate multiple neuroimmune populations in the brain as central players in the pathogenesis of AD, yet the precise molecular roles of these cell types remain largely unclear. Advances in single-cell technology have opened up the ability to robustly assay cell states within complex tissues, including the human brain. The ability to measure the precise cellular states in the living brain is key to understanding subtle neuroimmune cell type transcriptional changes that may give rise to AD. To identify molecular changes in these cells in human AD brain tissue, we have deployed single-nuclei RNA-sequencing (snRNA-seq) to profile frontal cortex biopsies from patients with suspected idiopathic normal pressure hydrocephalus (iNPH) and co-morbid AD. These biopsies represent a unique opportunity to measure transcriptional changes associated with AD unconfounded by postmortem artifact and, potentially, prior to the end stage of disease. To date, I have successfully obtained 815,843 single-nuclei profiles from 18 individuals, six of whom have both amyloid and tau pathology, seven with amyloid plaques, and five with no pathology. Here, I propose to employ snRNA-seq and Slide-seq on a total of 62 frontal cortex biopsies, across a range of APOE and amyloid/tau statuses, to uncover molecular alterations specifically associated with AD. Initially, I will determine which cell populations are significantly enriched or depleted in AD pathology and associated with APOE status, identify transcriptional alterations in all cell types, and determine which populations are enriched for heritable risk of AD. With Slide- seq, I will determine how cellular states and transcriptional changes are influenced by the spatial location in relation to amyloid and tau pathology. Finally, using novel computational integration methods, I will benchmark the transcriptional changes seen in a mouse model of AD with those obtained from my human profiling efforts, providing the field a resource of cellular state changes that are recapitulated in this model. If successful, these experiments will provide a comprehensive view of AD before death, nominating new cell state changes and transcriptional pathways associated with the pathogenesis of AD.

项目摘要 阿尔茨海默病（AD）仍然是十大死亡原因中唯一没有疾病修饰的疾病 可用的治疗。在很大程度上，缺乏适当的治疗方法是由于我们对 大脑中的特定分子通路如何导致认知能力下降和记忆丧失。最近的基因 研究表明脑中的多种神经免疫群体是AD发病机制的中心参与者， 然而，这些细胞类型的精确分子作用仍然很不清楚。单细胞技术的进展 已经开启了在复杂组织（包括人脑）内稳健地测定细胞状态的能力。的 测量活体大脑中精确细胞状态的能力是理解微妙神经免疫细胞的关键 类型的转录变化，可能会导致AD。为了确定这些细胞在人类中的分子变化， AD脑组织，我们已经部署了单核RNA测序（snRNA-seq）来描绘额叶皮层 疑似特发性正常压力脑积水（iNPH）和共病AD患者的活检。 这些活检代表了一个独特的机会，以衡量转录的变化与AD 不受死后伪影的干扰，并且可能在疾病的终末期之前。到目前为止， 成功地从18个个体中获得了815，843个单细胞核谱，其中6个人同时患有淀粉样蛋白和 tau病理，7例有淀粉样斑块，5例无病理。在这里，我建议使用snRNA-seq 和Slide-seq对总共62个额叶皮质活检，在一系列APOE和淀粉样蛋白/tau状态下， 揭示与AD特异性相关的分子改变。首先，我将确定哪些细胞群 在AD病理学中显著富集或耗尽，并与APOE状态相关， 所有细胞类型的改变，并确定哪些人群富含AD的遗传风险。与幻灯片- seq，我将确定细胞状态和转录变化如何受到空间位置的影响， 与淀粉样蛋白和tau病理学的关系。最后，使用新的计算积分方法，我将基准 在AD小鼠模型中观察到的转录变化与从我的人类分析工作中获得的那些转录变化， 为该场提供在该模型中概括的蜂窝状态变化的资源。如果成功，这些 实验将提供死亡前AD的全面视图，提名新的细胞状态变化， 与AD发病机制相关的转录途径。