E-MTAB-9950
Ontology highlight
ABSTRACT:
DISEASE(S): Parkinson's Disease,Normal
PROVIDER: E-MTAB-9950 | ExpressionAtlas | 2021-01-15
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:mRNA expression profiling of mitochondrial subunits in subjects with Parkinson’s disease
| PRJEB42212 | ENA
Project description:Introduction: Parkinson's disease (PD), typically developing between the ages of 55 and 65 years, is a common neurodegenerative disorder caused by a progressive loss of dopaminergic neurons due to the accumulation of α-synuclein in the substantia nigra. Mitochondria are known to play a key role in cell respiratory function and bioenergetic. Indeed, mitochondrial dysfunction causes an insufficient energy production required to satisfy the needs of several organs, especially the nervous system. Material and methods: The present study explored the mRNA expression of mitochondrial DNA (mtDNA) encoded respiratory chain (RC) subunits in PD patients by using the next generation sequencing analysis (NGS) and the quantitative real-time PCR (qRT-PCR) assay for the confirmation of the NGS results. Results: All tested mitochondrial RC subunits was significantly over-expressed in subjects with PD compared to normal controls . In qRT-PCR the mean expression of all mitochondrial subunits had an expression level of at least 7 times compared to controls. Conclusion: The over-expression of mitochondrial subunits in PD subjects might be secondary to a degeneration-related alteration of the mitochondrial structure or dynamics or to the occurrence of a compensatory mechanism. The study of specific mRNA by peripheral blood mononuclear cells (PBMCs) may provide a better diagnostic frame to early detect PD cases.
2022-01-01 | E-MTAB-9950 | biostudies-arrayexpress
Project description:Homo sapiens Raw sequence reads of Mitochondrial subunits expression in Parkinson disease
| PRJNA680218 | ENA
Project description:mTRAN proteins are components of the plant mitochondrial small subunits, thought to bind the mRNA 5' regions to initiate translation. This experiment was designed to identify the mTRAN1 binding regions on the plant mitochondrial mRNAs
2023-09-01 | E-MTAB-13060 | biostudies-arrayexpress
Project description:Chronic alcohol consumption may alter mRNA transcriptomic changes in reward-related brain regions, leading to neuroadaptations and thus increased risk of AUD. We used the Affymetrix Clariom™ D Assay Array to map mRNA transcriptome profiles in six reward-related regions of postmortem brains of AUD and control subjects and identified differentially expressed mRNAs.
2021-10-13 | GSE180722 | GEO
Project description:RNA stabilizing reagents have been developed to ensure that transcription profiles of whole blood samples reflect the physiological state at the time of the blood drawn. Ability to preserve and maintain the in vivo gene expression status ex vivo is essential for gene expression profiling and biomarker discovery from clinical sample material. We compared transcriptional profiles obtained from samples collected using two established peripheral blood RNA collection systems, TEMPUS™ and PAXgene™. We demonstrated that TEMPUS™ and PAXgene™ systems can be used in combination with RiboAmp® mRNA amplification without a need for a separate globin reduction step. However, use of samples collected through different blood collection methods in the same experiment should be avoided.
2012-11-05 | GSE29487 | GEO
Project description:Blood was sampled from severe burns patients over time as well as healthy subjects. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™. The Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program Blood was sampled from 244 severe burns patients over time as well as 35 healthy subjects who consented to blood sampling. Study subjects were treated under standard operating procedures to minimize treatment variations. Patients had burns covering >20% of the total body surface area and were admitted within 96 hours of injury. Genome-wide expression analyses were conducted using the Affymetrix U133 plus 2.0 GeneChip™.
2013-02-12 | E-GEOD-37069 | biostudies-arrayexpress
Project description:Background: Transcription control of mitochondrial metabolism is essential for cellular function. A better understanding of this process will aid the elucidation of mitochondrial disorders, in particular of the many genetically unsolved cases of oxidative phosphorylation (OXPHOS) deficiency. Yet, to date only few studies have investigated nuclear gene regulation in the context of OXPHOS deficiency. In this study, we combined RNA sequencing of human complex I-deficient patient cells across 32 conditions of perturbed mitochondrial metabolism, with a comprehensive analysis of gene expression patterns, co-expression calculations and transcription factor binding sites. Results: Our analysis shows that OXPHOS genes have a significantly higher co-expression with each other than with other genes, including mitochondrial genes. We found no evidence for complex-specific mRNA expression regulation in the tested cell types and conditions: subunits of different OXPHOS complexes are similarly (co-)expressed and regulated by a common set of transcription factors. However, we did observe significant differences between the expression of OXPHOS complex subunits compared to assembly factors, suggesting divergent transcription programs. Furthermore, complex I co-expression calculations identified 684 genes with a likely role in OXPHOS biogenesis and function. Analysis of evolutionarily conserved transcription factor binding sites in the promoters of these genes revealed almost all known OXPHOS regulators (including GABP, NRF1/2, SP1, YY1, E-box factors) and a set of six yet uncharacterized candidate transcription factors (ELK1, KLF7, SP4, EHF, ZNF143, and EL2). Conclusions: OXPHOS genes share an expression program distinct from other mitochondrial genes, indicative of targeted regulation of this mitochondrial sub-process. Within the subset of OXPHOS genes we established a difference in expression between subunits and assembly factors. Most transcription regulators of genes that co-express with complex I are well-established factors for OXPHOS biogenesis. For the remaining six factors we here suggest for the first time a link with transcription regulation in OXPHOS deficiency. RNA-SEQ of whole cell RNA in 2 control and 2 complex I deficient patient fibroblast cell lines treated with 4 compounds in duplicate, resulting in a total of 2x2x4x2=32 samples
2015-08-31 | E-GEOD-65634 | biostudies-arrayexpress
Project description:Several proteins have been linked to neurodegenerative disorders (NDDs), but their molecular function is not completely understood. Here, we used quantitative interaction proteomics to identify binding partners of Amyloid beta precursor protein (APP) and Presenilin-1 (PSEN1) for Alzheimer’s disease (AD), Huntingtin (HTT) for Huntington’s disease, Parkin-2 (PARK-2) for Parkinson’s disease and Ataxin-1 (ATXN-1) for spinocerebellar ataxia type 1. Our network reveals common signatures of protein degradation and misfolding and recapitulates known biology. Toxicity modifier screens and comparison to genome-wide association studies show that interaction partners are significantly linked to disease phenotypes in vivo. Direct comparison of wild-type proteins and disease-associated variants identified binders involved in pathogenesis, highlighting the value of differential interactome mapping. Finally, we show that the mitochondrial protein LRPPRC interacts preferentially with an early onset AD variant of APP. This interaction appears to induce mitochondrial dysfunction, which is an early phenotype of AD.
2015-09-22 | PXD001942 | Pride
Project description:Primary mitochondrial respiratory chain (RC) diseases are heterogeneous in etiology and manifestations but collectively impair cellular energy metabolism. To identify a common cellular response to RC disease, systems biology level transcriptome investigations were performed in human RC disease skeletal muscle and fibroblasts. Global transcriptional and post-transcriptional dysregulation in a tissue-specific fashion was identified across diverse RC complex and genetic etiologies. RC disease muscle was characterized by decreased transcription of cytosolic ribosomal proteins to reduce energy-intensive anabolic processes, increased transcription of mitochondrial ribosomal proteins, shortened 5'-UTRs to improve translational efficiency, and stabilization of 3'-UTRs containing AU-rich elements. These same modifications in a reversed direction typified RC disease fibroblasts. RC disease also dysregulated transcriptional networks related to basic nutrient-sensing signaling pathways, which collectively mediate many aspects of tissue-specific cellular responses to primary RC disease. These findings support the utility of a systems biology approach to improve mechanistic understanding of mitochondrial RC disease. To identify a common cellular response to primary RC that might improve mechanistic understanding and lead to targeted therapies for human RC disease, we performed collective transcriptome profiling in skeletal muscle biopsy specimens and fibroblast cell lines (FCLs) of a diverse cohort of human mitochondrial disease subjects relative to controls. Systems biology investigations of common cellular responses to primary RC disease revealed a collective pattern of transcriptional, post-transcriptional and translational dysregulation occurring in a highly tissue-specific fashion. Affymetrix Human Exon 1.0ST microarray analysis was performed on 29 skeletal muscle samples and Fibroblast cell lines from mitochondrial disease patients and age- and gender-matched controls.
2013-07-01 | E-GEOD-42986 | biostudies-arrayexpress