Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in lewy body diseases

ABSTRACT: Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in lewy body diseases

PROVIDER: PRJNA737467 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14808200.fastq.gz	Fastqsanger.gz
	SRR14808201.fastq.gz	Fastqsanger.gz
	SRR14808202.fastq.gz	Fastqsanger.gz
	SRR14808203.fastq.gz	Fastqsanger.gz
	SRR14808204.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 28

Similar Datasets

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in lewy body diseases

Project description:Parkinson’s disease (PD), Parkinson’s disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of diseasemodifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular “window” of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.

2021-08-15 | GSE178146 | GEO

Cross-platform transcriptional profiling identifies common and distinct molecular pathologies in Lewy body diseases.

Project description:Parkinson's disease (PD), Parkinson's disease with dementia (PDD) and dementia with Lewy bodies (DLB) are three clinically, genetically and neuropathologically overlapping neurodegenerative diseases collectively known as the Lewy body diseases (LBDs). A variety of molecular mechanisms have been implicated in PD pathogenesis, but the mechanisms underlying PDD and DLB remain largely unknown, a knowledge gap that presents an impediment to the discovery of disease-modifying therapies. Transcriptomic profiling can contribute to addressing this gap, but remains limited in the LBDs. Here, we applied paired bulk-tissue and single-nucleus RNA-sequencing to anterior cingulate cortex samples derived from 28 individuals, including healthy controls, PD, PDD and DLB cases (n = 7 per group), to transcriptomically profile the LBDs. Using this approach, we (i) found transcriptional alterations in multiple cell types across the LBDs; (ii) discovered evidence for widespread dysregulation of RNA splicing, particularly in PDD and DLB; (iii) identified potential splicing factors, with links to other dementia-related neurodegenerative diseases, coordinating this dysregulation; and (iv) identified transcriptomic commonalities and distinctions between the LBDs that inform understanding of the relationships between these three clinical disorders. Together, these findings have important implications for the design of RNA-targeted therapies for these diseases and highlight a potential molecular "window" of therapeutic opportunity between the initial onset of PD and subsequent development of Lewy body dementia.

| S-EPMC8357687 | biostudies-literature

CD4+ T cells contribute to neurodgeneration in Lewy Body dementia

Project description:Recent studies indicate a role of the adaptive immune system in Lewy body dementia (LBD). However, the mechanisms regulating T cell brain homing in LBD remain unknown. Here, we demonstrate interaction of T cells with Lewy bodies and with dopaminergic neurons in post-mortem LBD brains. Single cell RNA sequencing of cerebrospinal fluid (CSF) cells identified upregulated expression of C-X-C Motif Chemokine Receptor 4 (CXCR4) in CD4+ T cells in LBD. CSF protein levels of the CXCR4 ligand, C-X-C Motif Chemokine Ligand 12 (CXCL12) were associated with neuroaxonal damage in LBD. Finally, we demonstrate clonal expansion and upregulated Interleukin 17A by CD4+ T cells stimulated with phosphorylated α-synuclein. Cumulatively, these results indicate CXCR4-CXCL12 signaling as a mechanistic target for inhibiting pathological T cell trafficking in LBD.

2021-09-14 | GSE161192 | GEO

Proteomic Profiling of the Substantia Nigra to Identify Determinants of Lewy Body Pathology and Dopaminergic Neuronal Loss

Project description:Proteinaceous aggregates containing alpha-synuclein protein called Lewy bodies in the substantia nigra is a hallmark of Parkinson's disease. The molecular mechanisms of Lewy body formation and associated neuronal loss remain largely unknown. To gain insights on proteins and pathways associated with Lewy body pathology, we performed quantitative profiling of the proteome. We analyzed substantia nigra tissue from 51 subjects arranged into three groups: cases with Lewy body pathology, Lewy body-negative controls with matching neuronal loss and controls with no neuronal loss. Using label-free LC-MS/MS approach we quantified the 2,963 most abundant proteins. Statistical testing for differential protein abundance, followed by pathway enrichment and Bayesian learning of the causal network structure were performed to identify likely drivers of Lewy body formation and dopaminergic neuronal loss. The identified pathways include (1) Arp2/3 complex-mediated actin nucleation; (2) synaptic function; (3) poly(A) RNA binding; (4) basement membrane and endothelium; and (5) hydrogen peroxide metabolic process. According to the data, the endothelial/basement membrane pathway is tightly connected with both pathologies and likely to be one of the drivers of the neuronal loss. The poly(A) RNA-binding proteins, including the ones relevant to other neurodegenerative disorders (e.g. TDP-43 and FUS) have strong inverse correlation with Lewy bodies and may reflect alternative mechanism of nigral neurodegeneration.

2022-08-11 | PXD019279 | 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.

2022-10-28 | GSE216281 | GEO

CD4+ T cells contribute to neurodegeneration in Lewy body dementia [CSF_and_PBMCs_Healthy and LBD]

Project description:Recent studies indicate that the adaptive immune system plays a role in Lewy body dementia (LBD). However, the mechanism regulating T cell brain homing in LBD is unknown. Here, we observed T cells adjacent to Lewy bodies and dopaminergic neurons in post-mortem LBD brains. Single-cell RNA sequencing of cerebrospinal fluid (CSF) identified upregulated expression of C-X-C Motif Chemokine Receptor 4 (CXCR4) in CD4+ T cells in LBD. CSF protein levels of the CXCR4 ligand, C-X-C Motif Chemokine Ligand 12 (CXCL12) were associated with neuroaxonal damage in LBD. Furthermore, we observed clonal expansion and upregulated Interleukin 17A expression by CD4+ T cells stimulated with a phosphorylated α-synuclein epitope. Thus, CXCR4-CXCL12 signaling may represent a mechanistic target for inhibiting pathological interleukin-17-producing T cell trafficking in LBD.

2021-09-14 | GSE141578 | GEO

Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases

Project description:Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases

| PRJNA453994 | ENA

Epigenome-wide association study of human frontal cortex identifies differential methylation in Lewy body pathology

Project description:The goal of the study was to investigate if DNA methylation is associated with Lewy body pathology in human brain tissue. The Illumina Infinium MethylationEPIC Beadchip was used to obtain DNA methylation profiles across approximately 850,000 CpGs in postmortem human frontal cortex samples from European donors in the Netherlands Brain Bank. Following quality checks, sample filtering and normalization, association between CpG methylation and Braak alpha-synuclein stage was assessed using linear models.

2022-07-20 | GSE203332 | GEO

Subtyping Lewy body disorders using proteomics

Project description:Lewy body disorders (LBD), characterized by the deposition of misfolded α-synuclein (α-Syn), are clinically heterogeneous. We hypothesized that this heterogeneity might reflect α-Syn molecular diversity, between both patients and different brain regions. Using an ultra-sensitive assay, we evaluated α-Syn seeding from 30 LBD patients with different clinical phenotypes and disease durations. Interestingly, α-Syn from patients with rapid disease progression (<3 years) had a higher nigral seeding capacity than the rest of the patients included. We performed a proteomic-wide profiling of the substantia nigra from 5 high and 5 low seeder patients. The proteomic data suggests a significant disruption in mitochondrial function and lipid metabolism in high seeder cases compared to the low seeders.

2022-07-20 | PXD034441 | Pride

CD4+ T cells contribute to neurodgeneration in Lewy Body dementia

Project description:CD4+ T cells contribute to neurodgeneration in Lewy Body dementia

| PRJNA675845 | ENA