Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses

Fernandes, Hugo J. R.; Patikas, Nikolaos; Foskolou, Stefanie; Field, Sarah; Park, Jong-Eun; Byrne, Meg L; Bassett, Andrew; Metzakopian, Emmanouil

doi:10.1016/j.celrep.2020.108263

Cited by 90 publications

(98 citation statements)

References 64 publications

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“…We harvested more than 10,000 hKO1-positive cells from a single brain, which are su cient for most downstream analyses such as RNA-seq, bisul te sequencing, and ChIP-sequencing. Single-cell RNA-seq (scRNA-seq) has recently been used to obtain transcriptome pro ling of small cell populations, including neurons 23,24,26,39 . Although scRNA-seq provides a great platform for pro ling individual cells, technical issues such as high noise, low capture e ciency, and substantial cost remain.…”

Section: Discussionmentioning

confidence: 99%

“…Apart from the PD model study, our reporter mice and neuron isolation protocol also offer other applications. For instance, it can be applied in the analysis of DA neuron subtypes, which show distinct expression patterns in marker genes 23,26,30,39 . Although scRNA-seq and immunohistochemical analyses demonstrate the heterogeneity of DA subpopulations in the brain, their speci c function is still unclear.…”

Section: Discussionmentioning

confidence: 99%

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Establishment of dopaminergic neuron purification system in mice for the Parkinson’s disease study

Sheng

Hayakawa

Baba

et al. 2021

Preprint

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Parkinson’s disease (PD) is a progressive neurodegenerative disorder characterized by the degeneration of dopaminergic (DA) neurons. The key neuropathological hallmarks in the brain of patients with PD are Lewy body (LB) inclusions, consisting of misfolded α-synuclein proteins. Despite extensive efforts, the molecular link between LB inclusions and DA neurodegeneration remains elusive because of the lack of a suitable approach. Here, we aimed to establish a novel dopa-decarboxylase (Ddc) fluorescent reporter mouse model that allows the identification and collection of DA neurons using a fluorescence-activated cell sorter. Successful enrichment of Ddc-expressing cells was validated by RNA-sequencing analysis. This approach allowed us to analyze the effect of α-synuclein accumulation on the DA neuron’s transcriptome prior to neurodegeneration occurrence. We found that lipid-related process genes, followed by protein modification and degradation-related process genes, were upregulated in the α-synuclein-injected DA neurons. The activation of fatty acid-binding protein 1 (Fabp1) was particularly evident and confirmed by immunohistochemistry. Thus, our mouse model system and datasets provide a new method and insights into molecular mechanisms in PD.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Establishment of dopaminergic neuron purification system in mice for the Parkinson’s disease study

Sheng

Hayakawa

Baba

et al. 2021

Preprint

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“…Hubs, or highly connected neurons, are a common feature of complex networks 42,43,[47][48][49] , but dopaminergic networks have yet to be tested empirically for the existence of hub neurons. Consistently, many investigations describe the substantia nigra pars compacta dopaminergic network as more vulnerable than the adjacent ventral tegmental area, albeit with a less understood mechanism 30,[50][51][52][53][54][55][56][57] . While the origin of these regional differences has remained nebulous, network analysis can provide clues to how functional network organization of these regions may contribute to resilience or failure within the network that ultimately lead to neurocognitive and behavioral dysfunction.…”

Section: Introductionmentioning

confidence: 95%

Dopamine transporter is a master regulator of dopaminergic neural network connectivity

Miller

Guenther

Maurer

et al. 2021

Preprint

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Dopaminergic neurons of the substantia nigra (SNC) and ventral tegmental area (VTA) exhibit spontaneous firing activity. The dopaminergic neurons in these regions have been shown to exhibit differential sensitivity to neuronal loss and psychostimulants targeting dopamine transporter. However, it remains unclear whether these regional differences scale beyond individual neuronal activity to regional neuronal networks. Here we utilized live-cell calcium imaging to show that network connectivity greatly differs between SNC and VTA regions with higher incidence of hub-like neurons in the VTA. Specifically, the frequency of hub-like neurons was significantly lower in SNC dopamine neurons than in the adjacent VTA, consistent with the interpretation of a lower network resilience to SNC neuronal loss. We tested this hypothesis when activity of an individual dopaminergic neuron is suppressed, through whole-cell patch clamp electrophysiology, in either SNC, or VTA networks. Neuronal loss in the SNC decreased network clustering, whereas the larger number of hub-neurons in the VTA overcompensated by increasing network clustering in the VTA. We further show that network properties are regulatable via a dopamine transporter but not a D2 receptor dependent mechanism. Our results demonstrate novel regulatory mechanisms of functional network topology in dopaminergic brain regions.

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“…Approaches that nominate enrichment in specific cell types have been useful in identifying likely genes as most tissues have heterogeneous cellular composition. Several approaches have nominated dopamine neurons (4)(5)(6)(7), which are principal cell types lost in PD, as mediators of neurodegeneration, although other studies have identified non-neuronal cells including oligodendrocytes and oligodendrocyte precursor cells (4,8) as contributing to disease risk. Such approaches rely on the presumed mechanism that non-coding variants affect gene expression, which can be inferred by mapping expression quantitative trait loci (eQTL).…”

Section: Introductionmentioning

confidence: 99%

Association of a Common Genetic Variant with Parkinson’s Disease is Propagated through Microglia

Langston

Beilina

Reed

et al. 2021

Preprint

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Studies of the genetic basis of Parkinson’s disease (PD) have identified many disease-associated genetic variants, but the mechanisms linking variants to pathogenicity are largely unknown. PD risk is attributed to both coding mutations in the Leucine-rich repeat kinase 2 (LRRK2) gene and to common non-coding variation upstream of the LRRK2 locus. Here we show that the influence of genotype at non-coding variant rs76904798 on LRRK2 expression is propagated specifically through microglia, in contrast to evaluations based on general rather than genotype-dependent expression. We find evidence of microglia-specific regulatory regions that may modulate LRRK2 expression using single nuclei sequencing analyses of human frontal cortex and confirm these results in a human induced pluripotent stem cell-derived microglia model. Our study demonstrates that cell type is an important consideration in interrogation of the role of non-coding variation in disease pathogenesis.

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Single-Cell Transcriptomics of Parkinson’s Disease Human In Vitro Models Reveals Dopamine Neuron-Specific Stress Responses

Cited by 90 publications

References 64 publications

Establishment of dopaminergic neuron purification system in mice for the Parkinson’s disease study

Establishment of dopaminergic neuron purification system in mice for the Parkinson’s disease study

Dopamine transporter is a master regulator of dopaminergic neural network connectivity

Association of a Common Genetic Variant with Parkinson’s Disease is Propagated through Microglia

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