Unravelling cell type specific response to Parkinson’s Disease at single cell resolution

Parkinson’s Disease (PD) is the second most common neurodegenerative disorder. The pathological hallmark of PD is loss of dopaminergic neurons and the presence of aggregated α-synuclein, primarily in the substantia nigra pars compacta (SNpc) of the midbrain. However, the molecular mechanisms that underlie the pathology in different cell types is not currently understood. Here, we present a single nuclei transcriptomic analysis of human post-mortem in substantia nigra pars compacta (SNpc) tissue from 15 sporadic Parkinson’s Disease (PD) cases and 14 Controls. Our dataset comprised of ∼80K nuclei, representing all major cell types of the brain and allowed us to obtain a transcriptome-level characterization of these cell types. Importantly, we identified multiple subpopulations for each cell type and described subpopulation-specific gene sets that provide insights into the differing roles of these subpopulations. Our findings revealed a significant decrease in neuronal cells in PD samples, accompanied by an increase in glial cells and T cells. Subpopulation analyses demonstrated a significant depletion of tyrosine hydroxylase (TH)-positive astrocyte, microglia, and oligodendrocyte populations, along with the TH-expressing neurons in PD samples, which were also depleted. Moreover, marker gene analysis of the depleted subpopulations identified 28 overlapping genes including those associated with dopamine metabolism (e.g., ALDH1A1, SLC6A3 & SLC18A2). Overall, our study provides a valuable resource for understanding the molecular mechanisms involved in dopaminergic neuron degeneration and glial responses in PD, highlighting the existence of novel subpopulations and cell type-specific gene sets. We present a large-scale single nuclei RNA-seq dataset of 29 post-mortems human brains collected from substantia nigra pars compacta (SNpc) of 15 sporadic PD and 14 control samples obtained from Oregon Brain Bank. The Ethics Committee of UZ Leuven/KU Leuven approved the current study under the S-number S64182. H&E-guided 2 mm biopsy punches were collected from the SNpc of selected samples, nuclei were isolated and sequencing libraries were prepared using the Chromium Single Cell 3 Reagent Kits v.3 according to the manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced using a NovaSeq6000 system: 1% PhiX, paired-end sequencing with 10X v3 parameters (28-8-0-91 cycles). 13 libraries having a saturation rate lower than 60% were re-sequenced with the same 10x parameters to obtain more reads and improve the quality of the database. Combining reads from both runs giving a >40% saturation rate for all the samples was achieved. In total >170K nuclei was sequenced.