Integrated analysis of ATM mediated gene and protein expression impacting cellular metabolism

Journal of Proteome Research

Volumn 10, Issue 5, 2011, Pages 2651-2657

  Cheema, Amrita K ^a   Timofeeva, Olga ^a   Varghese, Rency ^a   Dimtchev, Alexandre ^a   Shiekh, Kathryn ^a   Shulaev, Vladimir ^b   Suy, Simeng ^a   Collins, Sean ^a   Ressom, Habtom ^a   Jung, Mira ^a   Dritschilo, Anatoly ^a  

^a GEORGETOWN UNIVERSITY   (United States)

^b VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

integromics; metabolomics; systems biology; transcriptomics

Indexed keywords

ADENYLATE KINASE; ATM PROTEIN; PURINE; PYRIMIDINE;

ARTICLE; ATM GENE; CELL FUNCTION; CELL METABOLISM; ENERGY BALANCE; FEASIBILITY STUDY; GENE; GENE EXPRESSION; METABOLITE; METABOLOMICS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEOMICS; SENSOR; TRANSCRIPTOMICS; UREA CYCLE;

ADENOSINE MONOPHOSPHATE; AMP-ACTIVATED PROTEIN KINASES; BLOTTING, WESTERN; CELL CYCLE PROTEINS; CELL LINE; CELL SURVIVAL; CHROMATOGRAPHY, LIQUID; DNA-BINDING PROTEINS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ENERGY METABOLISM; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, ENZYMOLOGIC; HOMEOSTASIS; HUMANS; MASS SPECTROMETRY; METABOLOMICS; MICROARRAY ANALYSIS; PROTEIN-SERINE-THREONINE KINASES; PROTEOMICS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA INTERFERENCE; SYSTEMS BIOLOGY; TUMOR SUPPRESSOR PROTEINS;

ATAXIA TELANGIECTASIA;

EID: 79955797346     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr101243j     Document Type: Article

References (29)

1. Dieterle, F.; Riefke, B.; Schlotterbeck, G.; Ross, A.; Senn, H.; Amberg, A. NMR and MS methods for metabonomics Methods Mol. Biol. 2011, 691, 385-415
2. Mamas, M.; Dunn, W. B.; Neyses, L.; Goodacre, R. The role of metabolites and metabolomics in clinically applicable biomarkers of disease Arch Toxicol. 2011, 85, 5-17
3. Kell, D. B. Metabolomics and systems biology: making sense of the soup Curr. Opin. Microbiol. 2004, 7 (3) 296-307 (Pubitemid 38765114)
4. Fukushima, A.; Kusano, M.; Redestig, H.; Arita, M.; Saito, K. Integrated omics approaches in plant systems biology Curr. Opin. Chem. Biol. 2009, 13 (5-6) 532-8
5. Kell, D. B. Systems biology, metabolic modelling and metabolomics in drug discovery and development Drug Discovery Today 2006, 11 (23-24) 1085-92 (Pubitemid 44810914)
6. del Sol, A.; Balling, R.; Hood, L.; Galas, D. Diseases as network perturbations Curr Opin Biotechnol. 2010, 21 (4) 566-71
7. Reaves, M. L.; Rabinowitz, J. D. Metabolomics in systems microbiology Curr Opin Biotechnol. 2010,; DOI:10.1016/j.copbio.2010.10.001
8. Boder, E., Ataxia-Telangiectasia: An Overview. In Ataxia-Telangiectasia: Genetics, Neuropathology and Immunology of a degenerative Disease of Childhood; Richard, A.; Gatti, M. S. L., Ed.; New York, 1985; pp 1 - 63.
9. Cunliffe, P. N.; Mann, J. R.; Cameron, A. H.; Roberts, K. D.; Ward, H. W. C. Radiosensitivity in ataxia-telangiectasia Br. J. Radiol. 1975, 48 (569) 374-76
10. Taylor, A.; Metcalfe, J.; Thick, J.; Mak, Y. Leukemia and lymphoma in ataxia telangiectasia Blood 1996, 87 (2) 423-38 (Pubitemid 26030297)
11. Swift, M.; Morrell, D.; Massey, R. B.; Chase, C. L. Incidence of cancer in 161 families affected by ataxia-telangiectasia N. Engl. J. Med. 1991, 325 (26) 1831-6
12. Savitsky, K.; Bar-Shira, A.; Gilad, S.; Rotman, G.; Ziv, Y.; Vanagaite, L.; Tagle, D. A.; Smith, S.; Uziel, T.; Sfez, S.; Ashkenazi, M.; Pecker, I.; Frydman, M.; Harnik, R.; Patanjali, S. R.; Simmons, A.; Clines, G. A.; Sartiel, A.; Gatti, R. A.; Chessa, L.; Sanal, O.; Lavin, M. F.; Jaspers, N. G.; Taylor, A. M.; Arlett, C. F.; Miki, T.; Weissman, S. M.; Lovett, M.; Collins, F. S.; Shiloh, Y. A single ataxia telangiectasia gene with a product similar to PI-3 kinase Science 1995, 268 (5218) 1749-53
13. Lavin, M. F. Ataxia-telangiectasia: from a rare disorder to a paradigm for cell signalling and cancer Nat. Rev. Mol. Cell Biol. 2008, 9 (10) 759
14. Bakkenist, C. J.; Kastan, M. B. DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation Nature 2003, 421 (6922) 499-506 (Pubitemid 36168436)
15. Zhan, H.; Suzuki, T.; Aizawa, K.; Miyagawa, K.; Nagai, R. Ataxia telangiectasia mutated (ATM)-mediated DNA damage response in oxidative stress-induced vascular endothelial cell senescence J Biol Chem 2010, 285 (38) 29662-70
16. Varghese, R. S.; Cheema, A.; Cheema, P.; Bourbeau, M.; Tuli, L.; Zhou, B.; Jung, M.; Dritschilo, A.; Ressom, H. W. Analysis of LC-MS data for characterizing the metabolic changes in response to radiation J. Proteome Res. 2010, 9 (5) 2786-93
17. Jung, M.; Zhang, Y.; Lee, S.; Dritschilo, A. Correction of radiation sensitivity in ataxia telangiectasia cells by a truncated I kappa B-alpha Science 1995, 268 (5217) 1619-21
18. Dennis, G., Jr.; Sherman, B. T.; Hosack, D. A.; Yang, J.; Gao, W.; Lane, H. C.; Lempicki, R. A. DAVID: Database for Annotation, Visualization, and Integrated Discovery Genome Biol. 2003, 4 (5) 3
19. Kathryn Sheikh, S. W. B.; Fornace, A. J., Jr.; Cheema, A. K. Small molecule metabolite extraction strategy for improving LC/MS detection of cancer cell metabolome. J. Biomol. Tech. 2011, in press.
20. Lee, S. J.; Dimtchev, A.; Lavin, M. F.; Dritschilo, A.; Jung, M. A novel ionizing radiation-induced signaling pathway that activates the transcription factor NF-kappaB Oncogene 1998, 17 (14) 1821-6 (Pubitemid 28482785)
21. Breiman, L. Random Forests Machine Learning 2001, 45, 5-32 (Pubitemid 32933532)
22. Colon, M.; Hernandez, F.; Lopez, K.; Quezada, H.; Gonzalez, J.; Lopez, G.; Aranda, C.; Gonzalez, A. Saccharomyces cerevisiae Bat1 and Bat2 Aminotransferases Have Functionally Diverged from the Ancestral-Like Kluyveromyces lactis Orthologous Enzyme PLoS ONE 2010, 6 (1) e16099
23. Goshima, G.; Mayer, M.; Zhang, N.; Stuurman, N.; Vale, R. D. Augmin: a protein complex required for centrosome-independent microtubule generation within the spindle J. Cell Biol. 2008, 181 (3) 421-9 (Pubitemid 351645032)
24. Dote, H.; Burgan, W. E.; Camphausen, K.; Tofilon, P. J. Inhibition of hsp90 compromises the DNA damage response to radiation Cancer Res. 2006, 66 (18) 9211-20 (Pubitemid 44521142)
25. Hubner, R. H.; Schwartz, J. D.; De Bishnu, P.; Ferris, B.; Omberg, L.; Mezey, J. G.; Hackett, N. R.; Crystal, R. G. Coordinate control of expression of Nrf2-modulated genes in the human small airway epithelium is highly responsive to cigarette smoking Mol. Med. 2009, 15 (7-8) 203-19
26. Barzilai, A.; Rotman, G.; Shiloh, Y. ATM deficiency and oxidative stress: a new dimension of defective response to DNA damage DNA Repair (Amst) 2002, 1 (1) 3-25 (Pubitemid 34475690)
27. Hardie, D. G. AMP-activated/SNF1 protein kinases: conserved guardians of cellular energy Nat. Rev. Mol. Cell Biol. 2007, 8 (10) 774-85 (Pubitemid 47462132)
28. Hardie, D. G. AMPK: a key regulator of energy balance in the single cell and the whole organism Int. J. Obes. (London) 2008, 32 (Suppl 4) S7-12
29. Carling, D.; Sanders, M. J.; Woods, A. The regulation of AMP-activated protein kinase by upstream kinases Int. J. Obes. (London) 2008, 32 (Suppl 4) S55-9