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

项目总结 阿尔茨海默病(AD)是一种毁灭性的神经退行性疾病，估计有1600万人受到影响 到2050年美国人。AD是一种混合性蛋白病变(例如，淀粉样蛋白-β(Aβ)聚集，tau神经原纤维缠结， 和TDP-43包涵体)，并选择性地影响大脑的某些区域(例如，新皮质和海马体) 有着复杂的病理生理学。 以及对特定的 尽管多项研究都集中在阿尔茨海默病的遗传因素上，但 神经细胞和神经胶质细胞群对蛋白质病的易感性增加 广告仍不为人所知。我们的团队已经证明了单细胞/核多组学(SnRNA-seq/SnATAC- SEQ)可用于研究人类神经细胞和神经胶质细胞亚群的“正常”和“病理” 我们还建立了一个大型人脑生物库，具有多种蛋白质病变 (包括Aβ、Tau、TDP-43等)。此外，我们还演示了如何针对特定的蛋白质病 网络，如乙酰化Tau和由Tau和Aβ共享的协同蛋白质病网络，可以识别 AD的可重复用途治疗(如西地那非和地氟尼沙)。我们初步的SnRNA-seq和SnATACT-seq 7例人死后小脑区分析(n=4[AD]和n=3例痴呆) 与传统技术相比，揭示了独特的神经元和神经胶质细胞群体和基因/网络 来自大脑皮层和海马区的SnRNA-seq数据。我们的综合SnRNA-seq数据分析也确定了 与疾病相关的小胶质细胞亚型，包括含有淀粉样蛋白b/磷酸-tau的小胶质细胞以及小胶质细胞 利用深层生殖模型，丰富了促炎标志物的表达。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基因组数据 易受AD蛋白病变影响的细胞。我们将使用样本池SnRNA-seq/SnATAC-seq技术来 分析死后患有不同程度蛋白质病的人的新皮质、海马体和小脑 严重程度(淀粉样蛋白-b、β-tau和TDP-43)和年龄、性别和载脂蛋白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，我们将检验神经元的假设 和/或神经胶质细胞特有的基因组/表观基因组特征和网络识别脑出血的分子机制(S) AD中的脆弱性和复原力。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成为靶点的假设 通过药物治疗延缓动物模型中AD样疾病的进展。成功完成 我们的项目将确定针对特定神经元和/或神经胶质细胞的新治疗机会。 风险/复原力基因和网络使阿尔茨海默病和其他痴呆症易受蛋白质病的影响。

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.