Single-Cell Transcriptomics of Human Substantia Nigra in Parkinson's Disease

Parkinson’s disease (PD) is the most common neurodegenerative movement disorder with unknown etiology. Loss of neuromelanin-containing dopaminergic (DA) neurons in the substanstia nigra (SN) is the hallmark of PD neuropathology. Here we performed single-nucleus RNA sequencing (snRNA-seq) of nuclei from the postmortem SN of control and idiopathic PD patients across various disease stages. The resulting transcriptomic atlas revealed a landscape of cellular alterations associated with disease progression in PD. Overall design: The SN from postmortem brains of 32 donors, including 21 idiopathic PD, 1 LBD and 9 controls, were requested from NIH Neurobiobank (www.neurobiobank.nih.gov) and fulfilled by Brain Endowment Bank at Miller School of Medicine, University of Miami. Specifically, frozen punches of substantia nigra were obtained and then pulverized in a liquid-nitrogen-chilled mortar and aliquoted. Approximately 50mg tissues were used for snRNA-seq. Single nucleus gene expression sequencing was performed on the samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the Next GEM Single cell 3’GEX Reagent kit, and an input of ~10,000 nuclei from a debris-free suspension.

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