Single-cell sequencing of human midbrain reveals glial activation and a Parkinson-specific neuronal state

Abstract

Idiopathic Parkinson’s disease is characterized by a progressive loss of dopaminergic neurons, but the exact disease etiology remains largely unknown. To date, Parkinson’s disease research has mainly focused on nigral dopaminergic neurons, although recent studies suggest disease-related changes also in non-neuronal cells and in midbrain regions beyond the substantia nigra. While there is some evidence for glial involvement in Parkinson’s disease, the molecular mechanisms remain poorly understood. The aim of this study was to characterize the contribution of all cell types of the midbrain to Parkinson’s disease pathology by single-nuclei RNA sequencing and to assess the cell type-specific risk for Parkinson’s disease employing the latest genome-wide association study. We profiled >41 000 single-nuclei transcriptomes of postmortem midbrain from six idiopathic Parkinson’s disease patients and five age-/sex-matched controls. To validate our findings in a spatial context, we utilized immunolabeling of the same tissues. Moreover, we analyzed Parkinson’s disease-associated risk enrichment in genes with cell type-specific expression patterns. We discovered a neuronal cell cluster characterized by CADPS2 overexpression and low TH levels, which was exclusively present in IPD midbrains. Validation analyses in laser-microdissected neurons suggest that this cluster represents dysfunctional dopaminergic neurons. With regard to glial cells, we observed an increase in nigral microglia in Parkinson’s disease patients. Moreover, nigral idiopathic Parkinson’s disease microglia were more amoeboid, indicating an activated state. We also discovered a reduction in idiopathic Parkinson’s disease oligodendrocyte numbers with the remaining cells being characterized by a stress-induced upregulation of S100B. Parkinson’s disease risk variants were associated with glia- and neuron-specific gene expression patterns in idiopathic Parkinson’s disease cases. Furthermore, astrocytes and microglia presented idiopathic Parkinson’s disease-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signaling. While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson’s disease-microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B, GPNMB, and HSP90AA1. Taken together, we generated the first single-nuclei RNA sequencing dataset from the idiopathic Parkinson’s disease midbrain, which highlights a disease-specific neuronal cell cluster as well as ‘pan-glial’ activation as a central mechanism in the pathology of the movement disorder. This finding warrants further research into inflammatory signaling and immunomodulatory treatments in Parkinson’s disease.

Single-nuclei paired multiomic analysis of young, aged, and Parkinson’s disease human midbrain reveals age- and disease-associated glial changes and their contribution to Parkinson’s disease

“…3e). We also noticed a distinct polarization in expression of several genes including OPALIN and RBFOX1, as previously reported 14 (Extended Data Fig. 3c).…”

“…Of particular note, CARNS1, which encodes carnosine synthase1, has been previously suggested to have a protective role in neurodegenerative conditions 34, 35 . Next, we applied our cPP pipeline to analyze the control and PD midbrain dataset published by Smajić et al 14 to see if we could find the same disease-associated population in another single-cell study. We found a population of disease-associated ODC exhibiting similar differential expression of disease-associated genes, supporting our result that identifies differentially affected subpopulations of cells in PD (Extended Data Fig.…”

Defining specific cell states of MPTP-induced Parkinson’s disease by single-nucleus RNA sequencing

“…Evidence suggests that glutamate excitotoxicity may also play roles in the neurotoxicity of MPTP 62 . We also found heatshock proteins (HSPs, Hspa1a) overexpressed in AST1 of PD, which is consistent with PD-specific microglia in PD human midbrain 8 . HSPs have been shown to be protective toward each of the hypothesized mechanisms of MPTP toxicity 62 .…”

“…Single cell/nucleus RNA sequencing (sc/snRNA-seq) technology has emerged as the most powerful instrumental for assessing cell type heterogeneity 4 , and this technique has been widely used in neuroscience. Currently, the majority of previous sc/snRNA-seq studies on PD were focused on iPSC-derived dopamine neurons 5,6 and mutant mouse (LRRK2, SNCA) postmortems brain [7][8][9] . However, most PD cases are sporadic, and up to 15% of PD cases are related to genetic mutations, but various environmental factors can also induce PD-like symptoms, including the exposure to pesticides or biotoxins.…”

Single-cell transcriptomic atlas of the human substantia nigra in Parkinson’s disease

“…Their results suggested an association of common risk for PD with DA neuron-specific expression 13, 14 . A recent study further examined PD midbrains by snRNAseq and reported a disease-specific DA neuron cluster and “pan-glial” activation 15 . However, the subtypes or classification of DA neurons from the human SN remains uncharacterized 16 .…”