Ataxia telangiectasia (AT) is a rare autosomal recessive disease caused by mutations in the ataxia telangiectasia-mutated gene (ATM). AT carriers with one mutant ATM allele are usually not severely affected although they carry an increased risk of developing cancer. There has not been an easy and reliable diagnostic method to identify AT carriers. Cell cycle checkpoint functions upon ionizing radiation (IR)-induced DNA damage and gene expression signatures were analyzed in the current study to t ...[more]
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.
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
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. Biological replicates: 6 or 4; Technical replicates: 2 with C3 and C5 dye swap.
Project description:Maintenance of genomic stability depends on the DNA damage response (DDR), a biological barrier in early stages of cancer development. Failure of this response results in genomic instability and high predisposition toward lymphoma, as seen in patients with ataxia-telangiectasia mutated (ATM) dysfunction. ATM activates multiple cell cycle checkpoints and DNA repair following DNA damage, but its influence on posttranscriptional gene expression has not been examined on a global level. We show that ionizing radiation (IR) modulates the dynamic association of the RNA-binding protein HuR with target mRNAs in an ATM-dependent manner, potentially coordinating the genotoxic response as an RNA operon. Pharmacologic ATM inhibition and use of ATM-null cells revealed a critical role for ATM in this process. Numerous mRNAs encoding cancer-related proteins were differentially associated with HuR depending on the functional state of ATM, in turn affecting expression of encoded proteins. The findings presented here reveal a previously unidentified role of ATM in controlling gene expression post-transcriptionally. Dysregulation of this DDR RNA operon is likely relevant to lymphoma development in ataxia-telangiectasia individuals. These novel RNA regulatory modules and genetic networks provide critical insight into the function of ATM in oncogenesis. Overall design: B-lymphocyte cell lines GM02184 (wild type, ATM +/+) and GM03332 (AT, ATM -/-) were either untreated or exposed to 1 Gy of IR. 6 h later cells were harvested and used for immunoprecipitation (IP) in the presence of HuR antibody (Santa Cruz Biotech.). RNA from IP material was extracted and used for microarray analysis.
Project description:Whole seedlings of wild type (4d) and atm mutants (4d) have been analyzed after a gamma ray irradiation of 0.75h, 1.5h, 3h & 5h (time course). Roots of wt (4d), atm (3d) and atr (4d) mutants have been analyzed after a 1h irradiation.<br><br> Ataxia Telangiectasia Mutated (ATM), encodes a large protein with a phosphatidylinositol 3-kinase (PI3K)-like domain at the C terminus (reviewed by Rotman and Shiloh, 1998). PI3K-related proteins make up a large family of Ser-Thr protein kinases, numerous members of which are involved in the regulation of cell cycle progression, responses to DNA damage, and the maintenance of genomic stability (Hoekstra, 1997). AtATM plays an essential role in meiosis and in the somatic response to DNA damage in plants, similar to the function of ATM in mammals and other eukaryotes.<br>Ataxia telangiectasia-mutated and Rad3-related (ATR) plays a central role in cell-cycle regulation, transmitting DNA damage signals to downstream effectors of cell-cycle progression.
Project description:Transcriptional profiling of A. nidulans comparing starvation for 0 (reference), 12 and 24 h. The main objective was to identify genes specifically regulated during starvation by atmA and xprG. The results of the experiment were further validated by real-time PCR. Overall design: Experimental procedure: Three A. nidulans strains were used in this study: WT, delta atmA and delta xprG. Strains were grown on minimal medium for 24 h (0 h starvation reference), then exposed to 12 and 24 h starvation. atmA: ATM, Ataxia-Telangiectasia mutated; Malavazi, I., Savoldi, M., Da Silva Ferreira, M. E., Soriani, F. M., Bonato, P. S., De Souza Goldman, M. H. and Goldman, G. H. (2007), Transcriptome analysis of the Aspergillus nidulans AtmA (ATM, Ataxia-Telangiectasia mutated) null mutant. Molecular Microbiology, 66: 74-99 (PMID 17880424). xprG: extracellular protease; Margaret E. Katz, Karen-Ann Gray, Brian F. Cheetham, (2006) The Aspergillus nidulans xprG (phoG) gene encodes a putative transcriptional activator involved in the response to nutrient limitation, Fungal Genetics and Biology, 43, 190-199 (PMID 16464624).
Project description:The ataxia telangiectasia-mutated (ATM) gene is a moderate-risk breast cancer susceptibility gene; germline loss-of-function variants are found in up to 3% of hereditary breast and ovarian cancer (HBOC) families who undergo genetic testing. So far, no clear molecular features of breast tumors occuring in ATM deleterious variant carriers have been described, but identification of an ATM-associated tumors signature may help patients' management. To characterize hallmarks of ATM-associated tumors, absolute copy number variation and loss of heterozygosity profiles were obtained from the OncoScan SNP array. Overall design: Copy number analysis of Affymetrix OncoScan HD arrays was performed on 23 formamid-fixed paraffin-embedded breast tumors. Tumors were developed by carriers of one or two mutated copies of ATM.
Project description:Ataxia-telangiectasia mutated (ATM) protein kinase regulates the DNA damage response and is associated with cancer suppression. Here, we used microarray to study global transcriptomic expression to identify tumor-promoting functions of ATM. Human breast cancer MDA-MB-231 cells were transfected with siATM, sip53 or control siRNA followed by RNA extraction and hybridization on Affymetrix GeneChip Human Gene 2.0 ST array.
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.