MicroRNA dysregulation in Ataxia Telangiectasia
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ABSTRACT:
PROVIDER: PRJNA1107187 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28878530.fastq.gz | Fastqsanger.gz | |||
| SRR28878531.fastq.gz | Fastqsanger.gz | |||
| SRR28878532.fastq.gz | Fastqsanger.gz | |||
| SRR28878533.fastq.gz | Fastqsanger.gz | |||
| SRR28878534.fastq.gz | Fastqsanger.gz |
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Project description:Ataxia Telangiectasia (AT) is a rare disorder characterized by neurodegeneration, combined immunodeficiency, predisposition to malignancies and high clinical variability. MicroRNAs (miRNAs) profiling may provide information on the pathophysiology of complex rare human diseases as they are involved in numerous biological functions including proliferation, differentiation, and DNA repair. To investigate the differential expression of miRNAs in AT patient samples with the aim of identifying miRNA signatures and correlate these patterns with disease pathogenesis. Twenty AT patients (mean age 17.7 + 9.6 years) were enrolled in the study. Clinical and genetic data were collected. We performed a small RNA-seq analysis in PBMCs and fibroblasts to compare miRNA expression profiles in AT patients and controls, and to identify specific expression signatures for AT. We found 42 differentially expressed (DE)-miRNAs in blood samples and 26 in fibroblasts samples. Three DE-miRNAs, miR-342-3p, miR-30a-5p, and miR-195-5p were validated in further AT samples and their dysregulation was confirmed.We identified for the first time, an AT-associated miRNA signature in blood cells and fibroblast samples obtained from a cohort of AT patients. Several pathways were predicted commonly deregulated, mainly involved in cancer. miRNAs may provide information on AT pathophysiology and tumorigenesis.
2024-10-01 | GSE266440 | GEO
Project description:Analysis of microRNA levels in fibroblast of Ataxia Telangiectasia
| PRJNA1107119 | ENA
Project description:Cerebellar cortex expression in ataxia-telangiectasia patients and normal controls. The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-deficiency. Here, we present that 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic marker found at high levels in neurons, is substantially reduced in human A-T and Atm-/- mouse cerebellar PCs. TET1, an enzyme that converts 5mC to 5hmC, responds to DNA damage. Manipulation of TET1 activity directly affects neuronal cell cycle reentry and cell death after the induction of DNA damage. Quantitative, genome-wide analysis of 5hmC of samples from human cerebellum showed that in ATM-deficiency there is a remarkable genome-wide reduction of 5hmC enrichment at both proximal and distal regulatory elements. These results reveal a role of TET1-mediated 5hmC in DNA damage response, and provide insights into the basis of a PC-specific DNA demethylation alteration in ATM-deficiency. Human frozen tissue was obtained from the NICHD Brain and Tissue Bank of Developmental Disorders at the University of Maryland, Baltimore, MD. RNA was prepared and run on an Illumina Human HT-12 v4 microarray. 3 ataxia-telangiectasia (A-T) cases and 4 normal controls.
2015-10-30 | E-GEOD-61019 | biostudies-arrayexpress
Project description:Previous studies have demonstrated the possible roles of dysregulation of endogenous retroelements in the pathogenesis of neurodegenerative diseases. In our study, we demonstrated that the activation and upregulation of endogenous retroelement LINE-1 in the cerebellum can induce the cerebellar ataxia phenotype in vivo using mouse model. While there has been reports demonstrating that ATM gene, whose mutations are causative of Ataxia Telangiectasia (A-T) in humans, regulates LINE-1, and suggesting that the LINE-1 dysregulation caused by its mutation plays a role in the pathogenesis of ataxia phenotype in A-T, little is known about the transcriptome of the A-T patients’ cerebellum. This is the first detailed analysis of the cellular and retroelement transcriptome in A-T patient’s cerebellum, and the result of this analysis, together with the transcriptomic analysis in our LINE-1 activation mice, collectively suggests the profound roles of LINE-1 dysregulation in the development as well as the progression of ataxia in A-T patients.
2022-09-06 | GSE175776 | GEO
Project description:Cerebellar cortex expression in ataxia-telangiectasia patients and normal controls. The neurodegenerative disease known as ataxia-telangiectasia (A-T) is caused by the absence of the ATM (A-T mutated) protein. A long-standing mystery surrounding A-T is why cerebellar Purkinje cells (PCs) appear uniquely vulnerable to ATM-deficiency. Here, we present that 5-hydroxymethylcytosine (5hmC), a newly recognized epigenetic marker found at high levels in neurons, is substantially reduced in human A-T and Atm-/- mouse cerebellar PCs. TET1, an enzyme that converts 5mC to 5hmC, responds to DNA damage. Manipulation of TET1 activity directly affects neuronal cell cycle reentry and cell death after the induction of DNA damage. Quantitative, genome-wide analysis of 5hmC of samples from human cerebellum showed that in ATM-deficiency there is a remarkable genome-wide reduction of 5hmC enrichment at both proximal and distal regulatory elements. These results reveal a role of TET1-mediated 5hmC in DNA damage response, and provide insights into the basis of a PC-specific DNA demethylation alteration in ATM-deficiency.
2015-10-30 | GSE61019 | GEO
Project description:Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. In this study, we generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells), a neurodegenerative, inherited disease with chromosomal instability and hypersensitivity to ionizing radiation. AT-iPS cells exhibited hypersensitivity to X-ray irradiation, one of the characteristics of the disease. Surprisingly, while parental ataxia telangiectasia cells exhibited significant chromosomal abnormalities, AT-iPS cells did not show any chromosomal instability in vitro, i.e. maintenance of intact chromosomes at least by 80 passages (560 days) probably due to robust stability of pluripotent stem cells such as iPS cells and embryonic stem cells. The whole exome analysis also showed comparable nucleotide substitution speed in AT-iPS cells. Interestingly, after longer period of AT-iPS implantation into immunodeficient mice, teratoma generated by AT-iPS cells exhibited telangiectasia and carcinogenesis that are two characteristic symptoms of ataxia telangiectasia. Taken together, AT-iPS cells would be a good model for ataxia telangiectasia to clarify pathogenesis of the disease, and may allow us to facilitate development of drugs that inhibit ataxia and hypersensitivity to ionizing radiation for therapeutic application.
2013-06-22 | GSE47498 | GEO
Project description:IntroductionAtaxia telangiectasia (AT) is a rare disorder characterized by neurodegeneration, combined immunodeficiency, a predisposition to malignancies, and high clinical variability. Profiling of microRNAs (miRNAs) may offer insights into the underlying mechanisms of complex rare human diseases, as miRNAs play a role in various biological functions including proliferation, differentiation, and DNA repair. In this study, we investigate the differential expression of miRNAs in samples from AT patients to identify miRNA patterns and analyze how these patterns are related to the disease.MethodsWe enrolled 20 AT patients (mean age 17.7 ± 9.6 years old) and collected clinical and genetic data. We performed short non-coding RNA-seq analysis on peripheral blood mononuclear cells (PBMCs) and fibroblasts to compare the miRNA expression profile between AT patients and controls.ResultsWe observed 42 differentially expressed (DE)-miRNAs in blood samples and 26 in fibroblast samples. Among these, three DE-miRNAs, miR-342-3p, miR-30a-5p, and miR-195-5p, were further validated in additional AT samples, confirming their dysregulation.DiscussionWe identified an AT-related miRNA signature in blood cells and fibroblast samples collected from a group of AT patients. We also predicted several dysregulated pathways, primarily related to cancer, immune system control, or inflammatory processes. The findings suggest that miRNAs may provide insights into the pathophysiology and tumorigenesis of AT and have the potential to serve as useful biomarkers in cancer research.
| S-EPMC11366618 | biostudies-literature
Project description:Ataxia Telangiectasia (AT) is a rare disorder characterized by neurodegeneration, combined immunodeficiency, a predisposition to malignancies and high clinical variability. Profiling of microRNAs (miRNAs) may offer insights into the underlying mechanisms of complex rare human diseases, as miRNA play a role in various biological functions including proliferation, differentiation, and DNA repair. To investigate the differential expression of miRNAs in samples from AT patients with the aim of identifying miRNA patterns and to investigate how these patterns are related to the disease. We performed short a small RNA-seq analysis on fibroblasts to compare the miRNA expression profile between AT patients and controls. We identified, an AT-related miRNA signature in blood cells and fibroblast samples collected from a group of AT patients. We also predicted several dysregulated pathways, primarily related to cancer, immune system control or inflammatory processes. The findings suggest that miRNAs may provide insights into the pathophysiology and tumorigenesis of AT and have the potential to serve as useful biomarkers in cancer research.
2024-10-01 | GSE266411 | GEO
Project description:Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. In this study, we generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells), a neurodegenerative, inherited disease with chromosomal instability and hypersensitivity to ionizing radiation. AT-iPS cells exhibited hypersensitivity to X-ray irradiation, one of the characteristics of the disease. Surprisingly, while parental ataxia telangiectasia cells exhibited significant chromosomal abnormalities, AT-iPS cells did not show any chromosomal instability in vitro, i.e. maintenance of intact chromosomes at least by 80 passages (560 days) probably due to robust stability of pluripotent stem cells such as iPS cells and embryonic stem cells. The whole exome analysis also showed comparable nucleotide substitution speed in AT-iPS cells. Interestingly, after longer period of AT-iPS implantation into immunodeficient mice, teratoma generated by AT-iPS cells exhibited telangiectasia and carcinogenesis that are two characteristic symptoms of ataxia telangiectasia. Taken together, AT-iPS cells would be a good model for ataxia telangiectasia to clarify pathogenesis of the disease, and may allow us to facilitate development of drugs that inhibit ataxia and hypersensitivity to ionizing radiation for therapeutic application. The parental AT1OS fibroblast cells and four independent AT-iPS clones were subjected to Illumina HumanCytoSNP-12 v2.1 BeadChip analysis.
2013-06-22 | E-GEOD-47498 | biostudies-arrayexpress
Project description:gene expression profiling of WT fibroblasts, hiPSCs, and NPCs compared to the same cell types isolated from patients with Ataxia Telangiectasia gene expression profiling was carried out with Affymetrix Hg133 2.0 plus chips
2013-04-01 | GSE45030 | GEO