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Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains

ABSTRACT: Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains

PROVIDER: PRJNA835055 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19085687.fastq.gz	Fastqsanger.gz
	SRR19085688.fastq.gz	Fastqsanger.gz
	SRR19085689.fastq.gz	Fastqsanger.gz
	SRR19085690.fastq.gz	Fastqsanger.gz
	SRR19085691.fastq.gz	Fastqsanger.gz

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Single-cell transcriptomic and proteomic analysis of Parkinson’s disease brains

Project description:Parkinson’s disease (PD) is a prevalent neurodegenerative disorder where recent evidence suggests pathogenesis may be mediated by inflammatory processes. The molecular architecture of the disease remains to be fully elucidated. We performed single-nucleus transcriptomics and unbiased proteomics using postmortem tissue obtained from the prefrontal cortex of 12 individuals with late-stage PD and age-matched controls. We analyzed ~80,000 nuclei and identified eight major cell types, including brain-resident T cells, each with distinct transcriptional changes in line with the known genetics of PD. By analyzing Lewy body pathology in the same postmortem tissue, we found that α-synuclein pathology is inversely correlated with chaperone expression in excitatory neurons. Examining cell-cell interactions, we found a selective abatement of neuron-astrocyte interactions and enhanced neuroinflammation. Proteomic analyses of the same brains identified synaptic proteins in prefrontal cortex that were preferentially downregulated in PD. Strikingly, comparing this dataset to a regionally similar published analysis for Alzheimer’s disease (AD), we found no common differentially expressed genes in neurons, but identified many shared differentially expressed genes in glial cells, suggesting that disease etiology in PD and AD are likely distinct. These data are presented as a resource for interrogating the molecular and cellular basis of PD and other neurodegenerative diseases.

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Project description:Parkinson’s disease (PD) is a common neurodegenerative disorder where recent evidence suggests may be mediated by inflammatory processes. The molecular architecture of the disease remains to be elucidated. We performed single-nucleus transcriptomics and unbiased proteomics using postmortem tissue obtained from the prefrontal cortex of 12 individuals with late-stage PD and age-matched controls. We analyzed ~80,000 nuclei and identified eight major cell types, including brain-resident T cells, each with distinct transcriptional changes in line with the known genetics of PD. By analyzing Lewy body pathology in the same tissue, we determined that α-synuclein pathology is inversely correlated to chaperone expression in excitatory neurons. Examining cell-cell interactions, we found a selective abatement of neuron-astrocyte interactions and enhanced neuroinflammation. Proteomic analyses of the same brains identified synaptic proteins that were preferentially negatively impacted in PD. Strikingly, comparing this dataset to a similar published analysis for Alzheimer’s disease (AD), we found no common, differentially expressed genes in neurons, but identified many in glial cells, suggesting that disease etiology in PD and AD are distinct. These data are presented as a resource for interrogating the molecular and cellular basis of PD and other neurodegenerative diseases.

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