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DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

ABSTRACT: People with ataxia-telangiectasia (A-T) display clinical variability, yet molecular profiles associated with distinct A-T phenotypes remain undefined. We report transcriptional and DNA methylation signatures that inform the regulatory networks underlying A-T phenotypes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE142843 | GEO | 2020/05/04

REPOSITORIES: GEO

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DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [gene expression/RNA-seq]

Project description:People with ataxia-telangiectasia (A-T) display clinical variability, yet molecular profiles associated with distinct A-T phenotypes remain undefined. We report transcriptional and DNA methylation signatures that inform the regulatory networks underlying A-T phenotypes.

2020-05-04 | GSE142842 | GEO

Ataxia-telangiectasia cerebellar cortex expression

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

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

Project description:DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype [DNA methylation/RRBS]

| PRJNA598602 | ENA

Transcription profiling of ATM +/+, ATM +/- and ATM -/- human lymphoblastoid cell lines exposed to 5 Gy IR at 0, 4 and 24 hours to identify expression phenotypes in Ataxia Telangiectasia carriers and patients

Project description:Transcription profiling of ATM (Ataxia Telangiectasia Mutated) +/+ (Control), ATM +/- (AT Carrier) and ATM -/- (AT patient) human lymphoblastoid cell lines exposed to 5 Gy IR at 0, 4 and 24 hours to identify expression phenotypes in Ataxia Telangiectasia carriers and patients

2008-07-29 | E-TABM-321 | biostudies-arrayexpress

Ataxia-telangiectasia cerebellar cortex expression

2015-10-30 | GSE61019 | GEO

Increased X-ray sensitivity and sustained chromosomal stability in Ataxia Telangiectasia-derived induced pluripotent stem (AT-iPS) cells

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

Increased X-ray sensitivity and sustained chromosomal stability in Ataxia Telangiectasia-derived induced pluripotent stem (AT-iPS) cells

2013-06-22 | E-GEOD-47498 | biostudies-arrayexpress

DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

Project description:DNA methylation and gene expression signatures are associated with ataxia-telangiectasia phenotype

| PRJNA598592 | ENA

SMRT compounds abrogate cellular phenotypes of Ataxia Telangiectasia in neural derivatives of patient specific hiPSCs

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

SMRT compounds abrogate cellular phenotypes of Ataxia Telangiectasia in neural derivatives of patient specific hiPSCs

2013-04-01 | E-GEOD-45030 | biostudies-arrayexpress

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