Single-nucleus transcriptome profiling across multiple brain regions in Parkinson's Disease

考虑到细胞异质性和细胞类型组成随疾病进展的变化，在人脑中进行的大量组织研究无法完全捕获帕金森病（PD）的分子变化。为了解决这个与PD对大脑的影响有关的关键问题，需要在单细胞水平上进行全面的组织表征。这包括鉴定新的稀有细胞类型，富集关键细胞群，以及鉴定与发病机制相关的细胞回路。我们的提案汇集了一个多学科团队，拥有所需的资源、高质量人脑组织的可用性和专业知识，以实现本资助机会公告中描述的目标。我们建议的总体目标是在120名PD患者的死后脑组织中进行单核RNA测序和全基因组测序，这些患者代表了PD的早期，中期和晚期，以及30名年龄，性别，pH值，死后间隔和种族匹配的对照组。我们将利用高质量的脑组织，对已知受PD不同阶段病理影响的四个大脑区域（背侧运动X核、黑质、丘脑中背侧和前扣带皮层）和一个已知相对不受影响的区域（初级视觉皮层）进行测序。所有单核RNA测序和全基因组测序、人口统计学、临床和神经病理学数据将通过加速帕金森病知识门户与研究界广泛共享。通过确定在受影响和未受影响的大脑区域的特定细胞类型中发生的精确分子变化，该项目可以作为PD基因表达变化的全脑分期的起点，类似于神经病理学分期的Braak分期。此外，通过关注病理发病前后的基因表达结果，我们希望创建一种资源，可以为PD的起源和进展提供机制见解，有可能在PD相关病理积累之前识别细胞类型特异性基因通路的破坏。

Molecular changes in Parkinson's disease (PD) cannot be fully captured with bulk tissue studies in the human brain given the cellular heterogeneity and changes in the cell type composition with disease progression. To address this key vexing question related to effects of PD on the brain, comprehensive tissue characterization at the single-cell level is needed. This includes the identification of novel rare cell types, enrichment of key cellular populations, and identification of cellular circuits tied to pathogenesis. Our proposal brings together a multidisciplinary team with the required resources, availability of high-quality human brain tissue and expertise to accomplish the goals described in this Funding Opportunity Announcement. The overarching goal of our proposal is to generate single nucleus RNA sequencing and whole genome sequencing in postmortem brain tissue from 120 patients with PD that represent early, middle, and late stages of PD and 30 age-, gender-, pH-, postmortem interval- and ethnicity-matched controls. We will utilize high quality brain tissue and perform sequencing in four brain regions known to be affected by different stages of PD pathology (dorsal motor X nucleus, substantia nigra, mediodorsal thalamus and anterior cingulate cortex) and one region known to be relatively unaffected (primary visual cortex). All single nucleus RNA sequencing and whole genome sequencing, demographics, clinical and neuropathological data will be broadly shared with the research community through the Accelerating Medicine Partnership in Parkinson's Disease Knowledge Portal. By establishing the precise molecular changes that occur within specific cell types from affected and unaffected brain regions, this project can act as a starting point for brain-wide staging of gene expression changes with PD analogous to the Braak stages used for neuropathology staging. Moreover, by focusing on gene expression outcomes around the onset of pathology, we expect to create a resource that could provide mechanistic insight into the origin and progression of PD, potentially identifying cell type-specific disruption of gene pathways prior to accumulation of PD-related pathology.