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Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors

ABSTRACT: Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors

PROVIDER: PRJNA353643 | ENA |

REPOSITORIES: ENA

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Single-Cell Atlas of Neuroglial Dynamics in SNCA-A53T Parkinson's Disease Model

Project description:Single-cell sequencing reveals that activation of the neuroinflammatory axis triggered by mutations in the SNCA gene A53T and dysregulation of the transcriptional regulatory network in Parkinson's disease (PD) combine to shape a cell-specific pathological picture of the substantia nigra-striatal pathway

2025-09-01 | GSE306642 | GEO

Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-11-16 | GSE89886 | GEO

Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors [genotype]

Project description:We have generated human induced Pluripotent Stem cells (hiPSc) using Sendai virus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation and downstream assays. Excess α-synuclein compromises phagocytosis in iPSC-derived macrophages.

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Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors [gene expression]

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Single-Cell Atlas of Neuroglial Dynamics in SNCA-A53T Parkinson's Disease Model

Project description:Single-Cell Atlas of Neuroglial Dynamics in SNCA-A53T Parkinson's Disease Model

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Proteome of the cortex of old Pink1-SNCA A53T double mutant Parkinson mice

Project description:Parkinson's Disease (PD) is primarily caused by aggregates of alpha synuclein (SNCA) in dopaminergic neurons of the substantia nigra, but PD is a systemic disease and may lead to PD-associated dementia complex. PD-associated encephalopathy is a late manifestation in PD patients at risk for example owing to mutations of the lysosomal enzyme glucocerebrosidase. Defects of lysosomal waste removal and aggregation of mutant alpha synuclein (SNCA) impacts of the proteome. Here, we studied the proteome of the prefrontal cortex in Pink1-/-SNCA A53T double mutant mice in comparison with their wildtype controls. Pink1-/-SNCA A53T mice carry a loss of function knock-in mutation of PTEN induced kinase (Pink1), plus the human A53T mutation of alpha synuclein (SNCA-A53T) [1, 2]. Homozygous Pink1-/-SNCA A53T double mutant mice were generated by crossing Pink1-/- mice (background: 129/SvEv) with A53T-SNCA-overexpressing PrPmtA mice (background: FVB/N) and then, interbreeding the littermates. Wildtype (WT) control mice are hybrids from a crossbreeding of 129/SvEv and FVB/N mice, which were descended from littermates of the respective single mutant animals. Pink1-/-SNCA A53T mice develop spontaneous motor symptoms at advanced ages, with a progressive incidence above 15 months of age. The phenotype of Pink1-/-SNCA A53T and wildtype control mice was observed during aging. Mice were euthanized at an age of 1-1.5 years (matched with the controls). The cortices were rapidly removed and frozen in liquid nitrogen and processed for label free proteomic analyses.

2025-10-21 | PXD039172 | Pride

Brain transcriptomic analysis in Parkinson's disease patients stratified by Braak Lewy body stage / Sex differences in Parkinson's disease brain transcriptome

Project description:To investigate transcriptomic changes associated with Parkinson's disease development we compared frontal cortex gene expression across four Braak Lewy body stage groups. Additionally we investigated sex-specific gene expression differences in neuropathologically healthy donors and Parkinson's disease patients at Braak Lewy body stage 5. We investigated sex-specific gene expression differences in neuropathologically healthy donors and Parkinson's disease patients at Braak Lewy body stage 5.

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The Parkinson's Disease Variant rs356182 Regulates Neuronal Differentiation Independently from Alpha-Synuclein

Project description:One of the most significant risk variants for Parkinson's disease (PD), rs356182, is located at the PD-associated locus near the alpha-synuclein (α-syn) encoding gene, SNCA. SNCA-proximal variants, including rs356182, are thought to function in PD risk through enhancers via allele-specific regulatory effects on SNCA expression. However, this interpretation discounts the complex activity of genetic enhancers and possible nonconical functions of α-syn. Here we investigated a novel risk mechanism for rs356182. We use CRISPR-Cas9 in LUHMES cells, a model for dopaminergic midbrain neurons, to generate precise hemizygous lesions at rs356182. The PD-protective (A/-), PD-risk (G/-), and wildtype (A/G) clones were neuronally differentiated and then compared transcriptionally and morphologically. Among the affected genes was SNCA, whose expression was promoted by the PD-protective allele (A) and repressed in its absence. In addition to SNCA, hundreds of genes were differentially expressed and associated with neurogenesis and axonogenesis- an effect not typically ascribed to α-syn. We also found that the transcription factor FOXO3 specifically binds to the rs356182 A-allele in differentiated LUHMES cells. Finally, we compared the results from the rs356182-edited cells to our previously published knockouts of SNCA and found only minimal overlap between the sets of significant differentially expressed genes. Together, the data implicate a risk mechanism for rs356182 in which the risk-allele (G) is associated with abnormal neuron development, independent of SNCA expression. We speculate that these pathological effects manifest as a diminished population of dopaminergic neurons during development leading to the predisposition for PD later in life.

2025-09-01 | GSE212535 | GEO

Vimentin network dysregulation mediates neurite deficits in SNCA duplication Parkinson’s patient-derived midbrain neurons

Project description:Duplication of the SNCA gene (SNCADupl), linked to elevated levels of alpha-synuclein (aSyn), is a genetic cause of Parkinson's disease (PD). Our prior work with human-induced pluripotent stem cell (hiPSC)-derived midbrain neurons generated from PD SNCADupl patients identified neuritic deficits, accompanied by decreased levels of cytoskeletal element b-tubulin-III (bTubIII). To explore mechanisms underlying these effects in SNCADupl neurons, we employed CRISPR/Cas9 to generate isogenic control hiPSCs. Isogenic correction of SNCA dosage restored SNCADupl-induced neurite defects and bTubIII levels. Multi-omics analyses revealed SNCADupl-induced alterations in neuronal differentiation, with a notable downregulation of PAX6. Moreover, SNCADupl induced an upregulation of vimentin. Further characterization revealed heightened vimentin truncation, associated with altered distribution and organization. Similar changes in vimentin levels and truncation were observed in post-mortem putamen tissue from sporadic PD patients. Notably, targeting vimentin with okadaic acid and withaferin A restored bTubIII- and neurite-associated defects, suggesting its potential to prevent aSyn-mediated neuritic degeneration.

2025-07-16 | PXD063433 | Pride

Parkinson's Disease Risk Enhancers in Microglia [ATAC-seq]

Project description:Genome-wide association studies (GWAS) have uncovered thousands of single nucleotide polymorphisms (SNPs) that are associated with Parkinson's disease (PD) risk. The functions of most of these SNPs, including the cell type they influence, and how they affect PD etiology remain largely unknown. To identify functional SNPs, we aligned PD risk SNPs within active regulatory regions of DNA in microglia, a cell type implicated in PD development. Out of 6,749 ‘SNPs of interest’ from the most recent PD GWAS metanalysis, 73 were located in open regulatory chromatin as determined by both ATAC-seq and H3K27ac ChIP-seq. We identified an active enhancer in microglia in intron two of SNCA that overlaps two PD risk SNPs, rs2737004 and rs2619356. In iPSC-derived microglia, CRISPR/Cas9 deletion of the open chromatin encompassing these SNPs caused reduced expression of multiple genes including SNCA and the adjacent gene MMRN1. Loss of the enhancer also led to upregulation of genes involved in glucose metabolism, a process that is known to be altered in PD patients. Our work expands the role of SNCA in Parkinson’s Disease and provides a connection between PD-associated genetic variants and underlying biology that points to a risk mechanism in microglia.

2024-01-21 | GSE245522 | GEO

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