Mitochondrial DNA allelic substitutions in Parkinson’s disease
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ABSTRACT:
PROVIDER: PRJNA453701 | ENA |
REPOSITORIES: ENA
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Project description:Mitochondrial DNA (mtDNA) damage is considered as a possible primary cause of Parkinson’s disease (PD). To explore the issue, mtDNA sequences from whole blood were analyzed in PD patients and controls using a resequencing chip and allelic substitutions were estimated for each nucleotide position (np) along the entire mtDNA sequence. Overall, 58 np showed a different allelic distribution in the two groups; of these, 81% showed an increase of non-reference alleles in PD patients, similar to findings reported in patients with Alzheimer’s disease, albeit in reduced proportion. These results suggest that age-related neurodegenerative diseases could share a mechanism involving mtDNA.
2019-05-21 | GSE113704 | GEO
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:mRNA expression profiling of mitochondrial subunits in subjects with Parkinson’s disease
| PRJEB42212 | ENA
Project description:Parkinson’s disease (PD) is the most common movement disorder in the aging population, with an estimated prevalence of 1% of people above 60 years old. More recently, PD risk genes, have been found to be regulated by the small non-coding RNAs, (microRNAs or miRNAs), and, as such, may contribute to PD development through a direct regulation on the mitochondrial and immune pathways. Many of these are influenced by epigenetic mechanisms, among which ones mediated by, miRNAs, that regulate gene expression at a post transcriptional level by binding to their 3′ un-translated region (3′ UTR) of target messenger RNAs (mRNAs) inducing mRNA degradation and translational repression. This study aimed to identify and characterize miRNA to evaluate their possible deregulation in PD patients compared to CRTL. In addition, we investigated how specific miRNAs are able to target genes and, thus, to modulate their functions in PD patient. Small RNA expression profiling was performed by next-generation sequencing in PD patients and CTRL after filtered out low-quality reads and trimming the adaptors. The obtained high-quality reads were aligned against the human genome reference.
2023-09-01 | E-MTAB-12087 | biostudies-arrayexpress
Project description:Neural stem cells of Parkinson’s disease patients exhibit aberrant mitochondrial morphology and functionality
| PRJNA526151 | ENA
Project description:Individual variation in complex traits results from allelic variants of multiple segregating genes, which are expressed as coregulated ensembles that are modulated by the environment. Coregulated transcriptional networks around focal genes, defined as their ‘transcriptional niches’, are sensitive to genetic and environmental perturbations. Understanding how single base pair substitutions affect this complex genotype-phenotype relationship by perturbing transcriptional niches is possible in Drosophila, which allows precise control of both the genetic background and the environment. We used a two-step CRISPR-Cas9 mediated gene deletion and reinsertion strategy to generate in a common genetic background five single nucleotide substitutions in the D. melanogaster Obp56h gene that correspond to naturally occurring allelic variants. Changes in single base pairs give rise to differential, sexually dimorphic effects on a plethora of fitness traits, including viability, sex ratio, feeding behavior, starvation resistance, recovery from a chill-induced coma, response to heat shock, activity, and sleep traits. These pleiotropic effects are accompanied by sexually dimorphic shifts in the transcriptional niche of Obp56h. Pairwise comparisons between the lines show common coregulated genes along with varying numbers of transcripts unique to one or few Obp56h alleles. Gene ontology enrichment analyses indicate that fundamental cellular processes for each sex underlie the phenotypic pleiotropy revealed by the Obp56h allelic series. Furthermore, different Obp56h alleles in a common genetic background give rise to allele-specific, sexually dimorphic microenvironmental variation. The reverse genetic engineering strategy, illustrated here, can be generally applied to other genes to dissect variation in the genotype-phenotype relationship at single base pair resolution.
2022-03-10 | GSE178635 | GEO
Project description:Emerging evidence suggest that Parkinson's disease (PD), besides being an age-associated disorder, might also have a neurodevelopment component. Disruption of mitochondrial homeostasis has been highlighted as a crucial cofactor in its etiology. Here, we show that PD patient-specific human neuroepithelial stem cells (NESCs) carrying the LRRK2-G2019S mutation recapitulate key mitochondrial defects previously described only in differentiated dopaminergic neurons. By combining high-content imaging approaches, 3D image analysis, and functional mitochondrial readouts we show that LRRK2-G2019S mutation caused aberrations in mitochondrial morphology and functionality compared to isogenic controls. LRRK2-G2019S NESCs displayed an increased number of mitochondria compared to isogenic control lines. However, these mitochondria were more fragmented and exhibited decreased membrane potential. Coherently, the release of total and mitochondrial redox oxidative species increased in LRRK2-G2019S NESC compared to controls. Functional alterations in LRRK2-G2019S cultures were also accompanied by a reduced mitophagic clearance via lysosomes. These findings support the hypothesis that preceding mitochondrial developmental defects contribute to the manifestation of the PD pathology later in life.
2019-03-09 | GSE128040 | GEO
Project description:Parkinson’s disease (PD) is the second most common neurodegenerative disorder, affecting ~2–3% of people over 65 years of age. Recent studies have revealed that the molecular pathogenesis of PD involves a series of pathways and neurobiological processes, such as protein degradation, mitochondrial dysfunction, oxidative stress, autophagy, calcium homeostasis, axonal transport, and neuroinflammation, all suggesting that both the onset and course of PD is a complex multilevel and systematic process. Accumulating evidence demonstrates that long non-coding RNAs (lncRNAs) affect the pathogenesis of several diseases, such as cancers, immunological diseases, and neurodegenerative disorders, including Alzheimer’s disease and PD. Next generation sequencing provides a high-throughput method for exploring the diverse polyadenylated RNA populations. This approach allows accurate identification and quantitation of mRNAs and other non-coding RNAs, such as lncRNAs. The present study explored mRNAs and lncRNAs expression by using the next generation sequencing analysis (NGS) and the quantitative real-time PCR (qRT-PCR) assay for the confirmation of the NGS results, followed by functional analysis of the results.
2023-01-16 | E-MTAB-11326 | biostudies-arrayexpress
Project description:In these studies, we used splice variant-specific microarrays manufactured by the ExonHit company ( www.exonhit.com) on the Affymetrix platform. The goal was to identify splice isoforms whose expression is altered in whole blood of early-stage Parkinson’s disease patients compared to healthy and neurodegenerative disease controls. The study included 19 cases of Parkinson’s disease (PD) samples, 4 of multiple system atrophy (MSA), 4 progressive supranuclear palsy (PSP) and 10 healthy controls. Thirteen splice variants were confirmed in quantitative polymerase chain reactions and used to classify blinded samples from Parkinson’s disease patients and controls with 90% accuracy and 94% sensitivity.
2012-12-01 | GSE34287 | GEO