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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.

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

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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

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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.

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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.

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Ataxia-telangiectasia cerebellar cortex expression

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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.

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EZH2-mediated H3K27 trimethylation mediates neurodegeneration in ataxia-telangiectasia

2013-10-25 | GSE50951 | GEO

ATM-knockout on total and phosphorylation proteomes of cortical brain organoids

Project description:ATM (ataxia telangiectasia mutated) kinase is crucial to a wide range of human developmental disorders and adult/pediatric malignancies. Its mutations are causally tied to ataxia telangiectasia, a multi-systemic congenital disorder mainly affecting brain and blood systems. We generated 4 separate ATM-knockout human pluripotent stem cell lines and differentiated them to form 3-dimensional brain cortical brain organoids. Brain cortical organoids are an excellent model of human developing cortex. Using these analyses, we identified ATM-dependent phosphorylation predominantly influences factors in neurogenesis, neuronal differentiation, cell morphogenesis, and microtubule cytoskeleton as well as kinases involved in ATM, BNDF, and WNT signaling, G2/M checkpoint, and p53 regulation. These findings have broad implications about diseases associated with ATM, including ataxia telangiectasia.

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