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Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients

ABSTRACT: Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients

PROVIDER: PRJNA414616 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6182240.fastq.gz	Fastqsanger.gz
	SRR6182250.fastq.gz	Fastqsanger.gz
	SRR6182260.fastq.gz	Fastqsanger.gz
	SRR6182270.fastq.gz	Fastqsanger.gz
	SRR6182280.fastq.gz	Fastqsanger.gz

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Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients

Project description:Friedreich’s ataxia (FRDA; OMIM 229300), an autosomal recessive neurodegenerative mitochondrial disease, is the most prevalent hereditary ataxia. In addition, FRDA patients showed additional non-neurological features such as scoliosis, diabetes and cardiac complications. Hypertrophic cardiomyopathy, which is found in two thirds of patients at the time of diagnosis, is the primary cause of death in these patients. In this data set, using small RNA-sequencing of small RNA purified from plasma samples of FRDA patients and controls we identified differential expression of miRNAs (hsa-miR-128-3p, hsa-miR-625-3p, hsa-miR-130b-5p, hsa-miR-151a-5p, hsa-miR-330-3p, hsa-miR-323a-3p, and hsa-miR-142-3p) between both groups. In addition, we found that miR-323a-3p can be used as a biomarker for differentiation of FRDA patients with cardiac problems. Identification of miRNA signatures could therefore provide new molecular explanation for pathological mechanisms occurring during the natural history of the FRDA. Since miRNA levels change with disease progression and pharmacological interventions, miRNAs will contribute to design new therapeutic strategies and improve clinical decisions. Plama miRNA profiles of 25 Friedreich's ataxia patients and 17 healthy subjects were generated by deep sequencing using Illumina HiScan SQ.

2017-10-18 | E-GEOD-105052 | biostudies-arrayexpress

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients

2017-10-18 | GSE105052 | GEO

Small RNA-seq analysis of circulating miRNAs to identify phenotypic variability in Friedreich's ataxia patients.

Project description:Friedreich's ataxia (FRDA; OMIM 229300), an autosomal recessive neurodegenerative mitochondrial disease, is the most prevalent hereditary ataxia. In addition, FRDA patients have shown additional non-neurological features such as scoliosis, diabetes, and cardiac complications. Hypertrophic cardiomyopathy, which is found in two thirds of patients at the time of diagnosis, is the primary cause of death in these patients. Here, we used small RNA-seq of microRNAs (miRNAs) purified from plasma samples of FRDA patients and controls. Furthermore, we present the rationale, experimental methodology, and analytical procedures for dataset analysis. This dataset will facilitate the identification of miRNA signatures and provide new molecular explanation for pathological mechanisms occurring during the natural history of FRDA. Since miRNA levels change with disease progression and pharmacological interventions, miRNAs will contribute to the design of new therapeutic strategies and will improve clinical decisions.

| S-EPMC5839159 | biostudies-literature

Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich's Ataxia

Project description:RNA sequencing of skeletal muscle biopsies from healthy controls and Friedreich's Ataxia (FRDA) patients before and after treatment with recombinant human erythropoietin (rhuEPO) to dissect the mechanisms of disease.

2023-04-01 | GSE226646 | GEO

Tunable phenotypic variability through an autoregulatory alternative sigma factor circuit

Project description:Genetically identical individuals in bacterial populations can display significant phenotypic variability. This variability can be functional, for example by allowing a fraction of stress prepared cells to survive an otherwise lethal stress. The optimal fraction of stress prepared cells depends on environmental conditions. However, how bacterial populations modulate their level of phenotypic variability remains unclear. Here we show that the alternative sigma factor σV circuit in B. subtilis generates functional phenotypic variability that can be tuned by stress level, environmental history, and genetic perturbations. Using single-cell time-lapse microscopy and microfluidics, we find the fraction of cells that immediately activate σV under lysozyme stress depends on stress level and on a transcriptional memory of previous stress. Iteration between model and experiment reveals that this tunability can be explained by the autoregulatory feedback structure of the sigV operon. As predicted by the model, genetic perturbations to the operon also modulate the response variability. The conserved sigma-anti-sigma autoregulation motif is thus a simple mechanism for bacterial populations to modulate their heterogeneity based on their environment.

2021-04-10 | GSE171761 | GEO

Genomic basis of phenotypic variability of complex disorders

Project description:Genomic basis of phenotypic variability of complex disorders

| PRJNA734669 | ENA

Genomic basis of phenotypic variability of complex disorders

Project description:Genomic basis of phenotypic variability of complex disorders

| PRJNA734670 | ENA

Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich's Ataxia

Project description:Skeletal muscle transcriptomics dissects the pathogenesis of Friedreich's Ataxia

| PRJNA940990 | ENA

Sensory ataxia and cardiac hypertrophy caused by neurovascular oxidative stress

Project description:In our chemogenetic neurovacular mouse model, DRGs transcriptomic analysis was performed by RNA-seq; Oxidative stress is associated with cardiovascular and neurodegenerative disease. We created transgenic chemogenetic mouse lines expressing yeast D-amino oxidase (DAAO) in endothelial cells and neurons. DAAO generates hydrogen peroxide (H2O2) in target tissues when mice are provided with D-amino acids, causing oxidative stress. DAAO-TGCdh5 transgenic mice express DAAO under control of the putatively endothelial-specific Cdh5 promoter. We provided these mice with D-alanine¬– expecting a vascular phenotype– but found that the mice develop sensory ataxia and neurodegeneration in dorsal root ganglia (DRG), associated with transgene expression within DRG neurons; electron microscopy revealed distorted mitochondria. DAAO-TGCdh5 mice also develop cardiac hypertrophy in response to chemogenetic oxidative stress, and we discovered transgene expression in parasympathetic nodose ganglia innervating the heart. We developed and characterized another transgenic line expressing DAAO under control of a different endothelial cell-specific Tie2 promoter. DAAO-TGTie2 mice express the transgene in endothelium but not neurons, and develop neither ataxia nor cardiac hypertrophy. The combination of ataxia, mitochondrial dysfunction, and cardiac hypertrophy is similar to findings in patients with Friedreich's Ataxia. Our observations confirm that neurovascular oxidative stress is sufficient to cause sensory ataxia and cardiac hypertrophy, and identify the DAAO-TGCdh5 mouse as a potentially informative animal model for Friedreich’s Ataxia.

2023-05-01 | GSE229143 | GEO

Altered gene expression and DNA damage in peripheral blood cells from Friedreich's ataxia patients

Project description:Frataxin, a conserved mitochondrial protein involved in iron homeostasis, is reduced in patients with Friedreich’s ataxia (FRDA). Transcription profiling and DNA damage assays were performed on blood cells from FRDA patients. Altered expression patterns pertained to immune response, signaling pathways, transcription, apoptosis, and genotoxic stress response pathways. FRDA patients had significantly more mitochondrial and nuclear DNA damage than a control population. Frataxin mRNA levels correlated with age of onset and displayed unique sets of gene alterations involved in oxidative phosphorylation and protein synthesis. Thus analysis of blood in FRDA patients yields insight into the nature and progression of the disease, as well as potential therapeutic approaches. Keywords: Friedreich's ataxia; frataxin; mitochondrial DNA damage; nuclear DNA damage; genotoxic stress

2009-12-08 | GSE11204 | GEO

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