Characterize neuronal and glial cell-specific vulnerability to proteinopathies in Alzheimer's disease using multimodal single-nuclei genomic and epigenomic approaches

使用多模式单核基因组和表观基因组方法表征阿尔茨海默病中神经元和神经胶质细胞对蛋白质病的特异性脆弱性

• 批准号: 10666954
• 负责人: Borna Bonakdarpour
• 金额: $ 81.16万
• 依托单位: CLEVELAND CLINIC LERNER COM-CWRU
• 依托单位国家: 美国
• 财政年份: 2023
• 资助国家: 美国
• 起止时间: 2023-09-01 至 2028-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10666954
• 关键词: ATAC-seq; Acetylation; Affect; Age; Alzheimer' s Disease; Alzheimer' s disease model; Alzheimer' s disease related dementia; American; Amyloid beta-Protein; Animal Model; Astrocytes; Autopsy; Biological; Brain; Brain region; Cause of Death; Cell Nucleus; Cells; Cerebellum; Clinical; Clinical Data; Cognitive; Complex; Data; Data Analyses; Data Analytics; Dementia; Diflunisal; Disease; Disease Progression; Disease associated microglia; Drug Modulation; Drug Targeting; Drug usage; Freezing; Frontotemporal Dementia; Functional disorder; Funding; Genes; Genetic; Genomics; Heterogeneity; Hippocampus; Human; Individual; Inflammation; Investigation; Knowledge Portal; Laboratories; Link; Medicine; Microglia; Modeling; Molecular; Nature; Neocortex; Nerve Degeneration; Neuroglia; Neurons; Outcome; Pathogenesis; Pathologic; Pathway interactions; Patients; Persons; Pharmaceutical Preparations; Pharmacological Treatment; Population; Preclinical Testing; Process; Quantitative Trait Loci; Reproducibility; Research; Risk; Sampling; Severities; Systems Biology; Technology; Testing; Transgenic Mice; United States; Universities; Vulnerable Populations; abeta accumulation; biobank; brain cell; cell type; cohort; cost effective; drug development; drug repurposing; effective therapy; epigenome; epigenomics; ethnic diversity; functional genomics; gene regulatory network; genetic signature; genome sequencing; genome wide association study; genomic data; human data; human disease; induced pluripotent stem cell; inflammatory marker; intercellular communication; mouse model; multimodal data; multimodality; multiple omics; neocortical; neuropathology; novel; preclinical efficacy; protein TDP-43; resilience; risk variant; sex; sildenafil; single nucleus RNA-sequencing; stem cell model; tau Proteins; tau aggregation; tau-1; transcriptome; treatment response; whole genome

PROJECT SUMMARY Alzheimer’s disease (AD) is a devastating neurodegenerative condition that it is estimated to affect 16 million Americans by 2050. AD is mixed proteinopathies (e.g., amyloid-β (Aβ) aggregation, tau neurofibrillary tangles, and TDP-43 inclusions) and selectively affect certain regions of the brain (e.g., neocortex and hippocampus) with complex pathophysiology. and characterization of specific Although multiple studies have focused on genetic factors for AD, the delineation neuronal and glial cell populations with enriched vulnerability to proteinopathy in AD remains unknown. Our team has demonstrated that single-cell/nucleus multi-omics (snRNA-seq/snATAC- seq) can be used to investigate both “normal” and “pathological” neuronal and glial subpopulations from human post-mortem brains and we have also established a large human brain biobank with diverse proteinopathies (including Aβ, tau, TDP-43 and others). Moreover, we have demonstrated how targeting proteinopathy-specific networks, such as acetylated Tau and synergistic proteinopathy networks shared by Tau and Aβ, can identify repurposable treatments (e.g., sildenafil and diflunisal) for AD. Our preliminary snRNA-seq and snATACT-seq analyses of human post-mortem cerebellum regions from 7 individuals (n=4 [AD] and n=3 other dementia cases) have revealed unique neuronal and glial cell populations and genes/networks when comparing to traditional snRNA-seq data from neocortex and hippocampus. Our integrative snRNA-seq data analysis has also identified disease-relevant microglial subtypes, including microglia containing amyloid-b/phosphor-tau, as well as microglia enriched in expression of pro-inflammatory markers, using deep generative models. We therefore hypothesize that comprehensive characterization of human neuronal and glial cell genomic and epigenomic signatures and networks that are vulnerable to proteinopathies will help to identify novel mechanistic pathways and disease- modifying treatments. In Aim 1, we will generate comprehensive multi-ome data of human neuronal and glial cells vulnerable to AD proteinopathies. We will use a sample pooling snRNA-seq/snATAC-seq technology to analyze human post-mortem neocortex, hippocampus, and cerebellum with varying degrees of proteinopathy severity (amyloid-b, p-tau and TDP-43) and age-, sex- and APOE-matched cognitive healthy controls available from the Northwestern Alzheimer’s Disease Research Center. In Aim 2, we will test the hypothesis that neuronal and/or glial cell-specific genomic/epigenomic signatures and networks identify the molecular mechanism(s) of vulnerability and resilience in AD. These multimodal data analyses will integrate large snRNA-seq/snATAC-seq profiles with existing whole genome-sequencing data from the Alzheimer’s disease sequencing project (ADSP). In Aim 3, we will test the hypothesis that selective cellular vulnerability linked to genes/networks can be targeted via pharmacologic treatment to slow progression of AD-like disease in animal models. Successful completion of our project will identify new treatment opportunities that target specific neuronal and/or glial cell-specific risk/resilience genes and networks that confer vulnerability to proteinopathies in AD and other dementias.

项目摘要 阿尔茨海默氏病（AD）是一种破坏性的神经退行性疾病，估计影响1600万人 2050年的美国人AD是混合性蛋白病（例如，β淀粉样蛋白（Aβ）聚集，tau神经元缠结， 和TDP-43内含物）并选择性地影响脑的某些区域（例如，新皮层和海马） 复杂的病理生理学 和具体的特征 尽管多项研究都集中在AD的遗传因素上， 神经元和神经胶质细胞群体对蛋白质病的易感性增加， AD仍然未知。我们的团队已经证明，单细胞/细胞核多组学（snRNA-seq/snATAC- SEQ）可用于研究来自人类的“正常”和“病理性”神经元和神经胶质亚群 我们还建立了一个大型的人脑生物库， （包括Aβ、tau、TDP-43等）。此外，我们已经证明了靶向蛋白质病变特异性 网络，如乙酰化Tau和Tau和Aβ共享的协同蛋白病网络，可以识别 可再利用的治疗（例如，西地那非和二氟尼柳）治疗AD。我们初步的snRNA-seq和snATACT-seq 对7名个体（n=4 [AD]和n=3例其他痴呆病例）的人死后小脑区域的分析 揭示了独特的神经元和神经胶质细胞群和基因/网络，当与传统相比， 来自新皮层和海马的snRNA-seq数据。我们的综合snRNA-seq数据分析还确定了 疾病相关的小胶质细胞亚型，包括含有淀粉样蛋白-b/磷酸化-tau的小胶质细胞，以及 富含促炎标志物的表达，使用深层生成模型。因此我们假设 人类神经元和神经胶质细胞基因组和表观基因组特征的全面表征， 易受蛋白质病影响的网络将有助于识别新的机制途径和疾病- 修改治疗方法。在目标1中，我们将生成人类神经元和神经胶质细胞的综合多组数据， 易受AD蛋白质病影响的细胞。我们将使用样本池snRNA-seq/snATAC-seq技术， 分析人类死后新皮层、海马和小脑不同程度的蛋白质病变 严重程度（淀粉样蛋白-b、p-tau和TDP-43）以及年龄、性别和APOE匹配的认知健康对照 来自西北阿尔茨海默病研究中心在目标2中，我们将检验神经元 和/或神经胶质细胞特异性基因组/表观基因组标记和网络鉴定了 脆弱性和复原力。这些多模式数据分析将整合大型snRNA-seq/snATAC-seq 与阿尔茨海默病测序项目（ADSP）现有的全基因组测序数据进行比较。 在目标3中，我们将测试与基因/网络相关的选择性细胞脆弱性可以被靶向的假设。 通过药物治疗来减缓动物模型中AD样疾病的进展。成功完成 我们的项目将确定新的治疗机会，针对特定的神经元和/或神经胶质细胞特异性 风险/弹性基因和网络，赋予易受AD和其他痴呆症的蛋白质病。