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: 10304120
• 负责人: Tushar Vinod Kamath
• 金额: $ 3.81万
• 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/10304120
• 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; mouse model; novel; response; single cell sequencing; single cell technology; single molecule; tau Proteins; tau-1; tool; transcriptome sequencing

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)仍然是前十大死因中唯一一种没有疾病修饰的疾病 提供治疗方法。在很大程度上，缺乏适当的治疗方法是由于我们对 大脑中特定的分子通路如何导致认知能力下降和记忆丧失。最新基因 研究表明，大脑中的多个神经免疫群体在阿尔茨海默病的发病机制中发挥了核心作用。 然而，这些细胞类型的确切分子作用在很大程度上仍不清楚。单细胞技术的进展 已经开启了强有力地分析复杂组织中细胞状态的能力，包括人脑。这个 测量活着的大脑中精确的细胞状态的能力是理解微妙的神经免疫细胞的关键 可能导致阿尔茨海默病的转录改变类型。鉴定人类这些细胞的分子变化 在脑组织中，我们已经使用了单核rna测序(snrna-seq)来分析额叶皮质。 疑似特发性正常压力性脑积水(INPH)和共病AD患者的活检。 这些活组织检查是测量与AD相关的转录变化的独特机会 没有受到死后伪影的困扰，可能在疾病末期之前。到目前为止，我有 成功获得了18个个体的815,843个单核图谱，其中6个人同时患有淀粉样蛋白和 7例有淀粉样斑块，5例无病理改变。在这里，我建议使用SnRNA-seq 和总计62例额叶皮质活检的幻灯片序列，涉及一系列APOE和淀粉样蛋白/tau状态，以 发现与阿尔茨海默病相关的分子改变。一开始，我会确定哪些细胞群 在AD病理中显著富含或缺失，并与APOE状态相关，识别转录 所有细胞类型的改变，并确定哪些人群的阿尔茨海默病的遗传风险丰富。使用Slide- 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病理的关系。最后，使用新的计算积分方法，我将基准 在阿尔茨海默病小鼠模型中看到的转录变化与我在人类特征分析工作中获得的转录变化， 为场提供了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AD死亡前的全面视图，提名新的细胞状态变化和 与阿尔茨海默病发病相关的转录途径。