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.