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

Abstract

Parkinson′s disease (PD) is a common and complex neurodegenerative disorder. Loss of neuromelanin–containing dopaminergic (DA) neurons in the substantia nigra (SN) is a hallmark of PD neuropathology, however, the etiology of PD remains unclear. Single–cell (–nucleus) RNA sequencing (sc or snRNAseq) has significantly advanced our understanding of neurodegenerative diseases including Alzheimer′s, but limited progress has been made in PD. Here we generated by far the largest snRNAseq data of high–quality 315,867 nuclei from the human SN including 9 healthy controls and 23 idiopathic PD cases across different Braak stages. Clustering analysis identified major brain cell types including DA neurons, excitatory neurons, inhibitory neurons, glial cells, endothelial, pericytes, fibroblast and T-cells in the human SN. By combining immunostaining and validating against the datasets from independent cohorts, we identified three molecularly distinct subtypes of DA–related neurons, including a RIT2–enriched population, in human aged SN. All DA neuron subtypes degenerated in PD, whereas the composition of non-neuronal cell clusters including major glial types showed little change. Our study delineated cell–type–specific PD–linked gene expression in the SN and their alterations in PD. Examination of cell–type–based transcriptomic changes suggests the complexity and diversity of molecular mechanisms of PD. Analysis of the remaining DA neurons of the three subtypes from PD demonstrated alterations of common gene sets associated with neuroprotection. Our findings highlight the heterogeneity of DA neurons in the human SN and suggest molecular basis for vulnerability and resilience of human DA neurons in PD. Our cohort thus provides a valuable resource for dissecting detailed mechanisms of DA neuron degeneration and identifying new neuroprotective strategies for PD.

Prolonged Differentiation of Neuron-Astrocyte Co-Cultures Results in Emergence of Dopaminergic Neurons

“…Interestingly, the astrocytes in this model expressed high levels of VMAT2, which do not seem to be present in astrocytes in the SNpc [ 41 ], but only in the prefrontal cortex of mice and potentially humans [ 42 , 43 ]. This suggests that the culture might contain a population of astrocytes resembling the population the dopaminergic neurons project to, rather than the astrocytes in the SNpc.…”

Rit2 silencing in dopamine neurons drives a Parkinsonian phenotype

“…Rit2 was identified as a PD risk allele in multiple GWAS and, although critical SNPs have been identified, it was unknown whether decreased Rit2 expression itself is detrimental to DAN function and/or viability (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26). Rit2 mRNA is one of the more highly downregulated genes in postmortem PD patient substantia nigra (31), and defines a specific transcriptomic cluster in single-cell RNAseq studies from post-mortem patients (32). However, whether that diminished Rit2 levels is causal or consequential for PD progression has yet to be determined.…”

“…Genome-wide association studies (GWAS) link Rit2 genetic anomalies to PD (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26), as well as to other neuropsychiatric disorders including essential tremor (24), schizophrenia (24,27), autism spectrum disorder (28,29), bipolar disorder (24), and speech delay (30). Significant Rit2 mRNA decreases were reported in postmortem PD patient SNc (31), and a major transcriptomic cluster was recently identified in SNc DANs from PD subjects that exhibits striking Rit2 expression loss (32). Moreover, Rit2 overexpression is sufficient to rescue cellular and behavioral deficits in an a-synuclein (a-syn) mouse PD model (33).…”

Rit2 silencing in dopamine neurons drives a progressive Parkinsonian phenotype

“…Rit2 was identified as a PD risk allele in multiple GWAS and, although critical SNPs have been identified, it was unknown whether decreased Rit2 expression itself is detrimental to DAN function and/or viability (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26). Rit2 mRNA is one of the more highly downregulated genes in postmortem PD patient substantia nigra (31), and defines a specific transcriptomic cluster in single-cell RNAseq studies from post-mortem patients (32). However, whether that diminished Rit2 levels is causal or consequential for PD progression has yet to be determined.…”

“…Genome-wide association studies (GWAS) link Rit2 genetic anomalies to PD (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25)(26), as well as to other neuropsychiatric disorders including essential tremor (24), schizophrenia (24,27), autism spectrum disorder (28,29), bipolar disorder (24), and speech delay (30). Significant Rit2 mRNA decreases were reported in postmortem PD patient SNc (31), and a major transcriptomic cluster was recently identified in SNc DANs from PD subjects that exhibits striking Rit2 expression loss (32). Moreover, Rit2 overexpression is sufficient to rescue cellular and behavioral deficits in an a-synuclein (a-syn) mouse PD model(33).…”