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Gene expressioin signatures at basal level in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes

ABSTRACT: Transcriptional profiling of human lymphoblastoid cell lines with different ATM genotypes at basal level was compared to extract gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients.

ORGANISM(S): Homo sapiens

PROVIDER: GSE45848 | GEO | 2013/04/09

SECONDARY ACCESSION(S): PRJNA196588

REPOSITORIES: GEO

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Gene expressioin signatures at basal level in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes

Project description:Transcriptional profiling of human lymphoblastoid cell lines with different ATM genotypes at basal level was compared to extract gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients. Biological replicates: 4; Technical replicates: 2 with C3 and C5 dye swap.

2013-04-09 | E-GEOD-45848 | biostudies-arrayexpress

Gene expressioin signatures in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes post sham- or IR-treatment

Project description:Transcriptional profiling of human lymphoblastoid cell lines with different ATM genotypes 6h post sham- or 1.5 Gy IR-treatmentl was compared to extract IR-related gene expression signatures that can identify ataxia telangiectasia (AT) carries from non AT carries and AT patients.

2013-04-09 | GSE45849 | GEO

Gene expressioin signatures in human lymphoblastoid cell lines with different ataxia telangiectasia-mutated (ATM) genotypes post sham- or IR-treatment

2013-04-09 | E-GEOD-45849 | biostudies-arrayexpress

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

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

Ataxia-telangiectasia mutated (Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy

Project description:Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by inactivating p53 mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress, presenting therapeutic opportunities. We used RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce K27M in the native H3f3a allele in a lineage- and spatially-directed manner, yielding primary mouse DMGs. Disruption of the DNA damage response kinase Ataxia-telangiectasia mutated (Atm) enhanced the efficacy of focal brain irradiation, extending mouse survival. This finding suggests that targeting ATM will enhance the efficacy of radiation therapy for p53-mutant DMG but not p53-wildtype DMG. We used spatial in situ transcriptomics and an allelic series of primary murine DMG models to identify transactivation-independent p53 activity as the key mediator of such radiosensitivity.

2023-11-04 | GSE246584 | GEO

Ataxia-telangiectasia cerebellar cortex expression

2015-10-30 | GSE61019 | GEO

EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia

Project description:The symptoms of ataxia-telangiectasia (A-T) include a progressive neurodegeneration caused by ATM protein deficiency. We previously found that nuclear accumulation of histone deacetylase-4, HDAC4, contributes to this degeneration; we now report that increased histone H3K27 trimethylation (H3K27me3) mediated by polycomb repressive complex 2 (PRC2) also plays an important role in the A-T phenotype. Enhancer of zeste homolog 2 (EZH2), a core catalytic component of PRC2, is identified as a new ATM kinase target, and its S734 phosphorylation reduces protein stability. Thus, PRC2 formation is elevated along with H3K27me3in ATM deficiency. ChIP-sequencing shows a significant increase in H3K27me3 ‘marks’ and a dramatic shift in their location. The change of H3K27me3 chromatin-binding pattern is directly related to cell cycle re-entry and cell death of ATM-deficient neurons. Lentiviral knockdown of EZH2 rescues Purkinje cell degeneration and behavioral abnormalities in Atm / mice, demonstrating that EZH2-mediated H3K27me3 is another key factor in A-T neurodegeneration. Two samples each were run of brain total RNA from Atm+/+ and Atm-/- mice.

2013-10-25 | E-GEOD-50951 | biostudies-arrayexpress

EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia

2013-10-25 | GSE50951 | GEO

Genomic profiling of Acute Lymphoblastic Leukemia in Ataxia Telangiectasia patients reveals tight link between ATM mutations and chromothripsis

Project description:Recent developments in sequencing technologies led to the discovery of a novel form of genomic instability, termed chromothripsis. This catastrophic genomic event, involved in tumorigenesis, is characterized by tens to hundreds of simultaneously acquired locally clustered rearrangements on one chromosome. We hypothesized that leukemias developing in individuals with Ataxia Telangiectasia, who are born with two mutated copies of the ATM gene, an essential guardian of genome stability, would show a higher prevalence of chromothripsis due to the associated defect in DNA double-strand break repair. Using whole-genome sequencing, fluorescence in situ hybridization and RNA sequencing, we characterized the genomic landscape of Acute Lymphoblastic Leukemia (ALL) arising in patients with Ataxia Telangiectasia. We detected a high frequency of chromothriptic events in these tumors, specifically on acrocentric chromosomes, as compared to tumors from individuals with other types of DNA repair syndromes (27 cases total, 10 with Ataxia Telangiectasia). Our data suggest that the genomic landscape of Ataxia Telangiectasia ALL is clearly distinct from that of sporadic ALL. Mechanistically, short telomeres and compromised DNA damage response in cells of Ataxia Telangiectasia patients may be linked with frequent chromothripsis. Furthermore, we show that ATM loss is associated with increased chromothripsis prevalence in additional tumor entities.

| EGAS00001002270 | EGA

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