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Redox Report
Communications in Free Radical Research
Volume 15, 2010 - Issue 3
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Review

Oxygenomics in environmental stress

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Pages 98-114 | Published online: 19 Jul 2013

References

  • Gibb S. Toxicity testing in the 21st century: a vision and a strategy. Reprod Toxicol 2008; 25: 136–138.
  • Woods CG, Heuvel JP, Rusyn I. Genomic profiling in nuclear receptor-mediated toxicity. Toxicol Pathol 2007; 35: 474–494.
  • Franco R, Panayiotidis MI. Environmental toxicity, oxidative stress, human disease and the ‘black box’ of their synergism: how much have we revealed? Mutat Res 2009; 674: 1–2.
  • Hansen JM, Zhang H, Jones DP. Differential oxidation of thioredoxin-1, thioredoxin-2, and glutathione by metal ions. Free Radic Biol Med 2006; 40: 138–145.
  • Valko M, Rhodes CJ, Moncol J, Izakovic M, Mazur M. Free radicals, metals and antioxidants in oxidative stress-induced cancer. Chem Biol Interact 2006; 160: 1–40.
  • Bau DT, Wang TS, Chung CH, Wang AS, Wang AS, Jan KY. Oxidative DNA adducts and DNA-protein cross-links are the major DNA lesions induced by arsenite. Environ Health Perspect 2002; 110 (Suppl 5): 753–756.
  • Kawai Y, Furuhata A, Toyokuni S, Aratani Y, Uchida K. Formation of acrolein-derived 2'-deoxyadenosine adduct in an iron-induced carcinogenesis model. J Biol Chem 2003; 278: 50346–50354.
  • Chiu HJ, Fischman DA, Hammerling U. Vitamin A depletion causes oxidative stress, mitochondrial dysfunction, and PARP-1-dependent energy deprivation. FASEB J2008; 22: 3878-3887.
  • Knott L, Hartridge T, Brown NL, Mansell JP, Sandy JR. Homocysteine oxidation and apoptosis: a potential cause of cleft palate. In Vitro Cell Dev Biol Anim 2003; 39: 98–105.
  • Nebert DW, Petersen DD, Fornace AJ Jr. Cellular responses to oxidative stress: the [Ah] gene battery as a paradigm. Environ Health Perspect 1990; 88: 13–25.
  • Cheng Y, Chang LW, Cheng LC, Tsai MH, Lin P. 4-Methoxyestradiol-induced oxidative injuries in human lung epithelial cells. Toxicol Appl Pharmacol 2007; 220: 271–277.
  • Mendrick DL. Genomic and genetic biomarkers of toxicity. Toxicology 2008; 245: 175–181.
  • Luhe A, Suter L, Ruepp S, Singer T, Weiser T, Albertini S. Toxicogenomics in the pharmaceutical industry: hollow promises or real benefit? Mutat Res 2005; 575: 102–115.
  • Wall ME, Dyck PA, Brettin TS. SVDMAN - singular value decomposition analysis of microarray data. Bioinformatics 2001; 17: 566–568.
  • Yeung KY, Ruzzo WL. Principal component analysis for clustering gene expression data. Bioinformatics 2001; 17: 763–774.
  • Portier CJ, Toyoshiba H, Sone H, Parham F, Irwin RD, Boorman GA. Comparative analysis of gene networks at multiple doses and time points in livers of rats exposed to acetaminophen. Altex 2006; 23 (Suppl): 380-384.
  • Toyoshiba H, Yamanaka T, Sone H et al. Gene interaction network suggests dioxin induces a significant linkage between aryl hydrocarbon receptor and retinoic acid receptor beta. Environ Health Perspect 2004; 112: 1217–1224.
  • Bumgamer RE, Yeung KY Methods for the inference of biological pathways and networks. Methods Mol Biol 2009; 541: 225–245.
  • Huang JC, Babak T, Corson TW et al. Using expression profiling data to identify human microRNA targets. Nat Methods 2007; 4: 1045–1049.
  • Li H, Lu L, Manly KF et al. Inferring gene transcriptional modulatory relations: a genetical genomics approach. Hum Mol Genet 2005; 14: 1119–1125.
  • Toyokuni S. Molecular mechanisms of oxidative stress-induced carcinogenesis: from epidemiology to oxygenomics. IUBMB Life 2008; 60: 441–447.
  • Kultz D. Molecular and evolutionary basis of the cellular stress response. Annu Rev Physiol 2005; 67: 225–257.
  • Hamilton ML, Van Remmen H, Drake JA et al. Does oxidative damage to DNA increase with age? Proc Natl Acad Sci USA 2001; 98: 10469–10474.
  • von Zglinicki T, Saretzki G, Ladhoff J, d'Adda di Fagagna F, Jackson SP. Human cell senescence as a DNA damage response. Mech Ageing Dev 2005; 126: 111–117.
  • Lambeth JD. Nox enzymes, ROS, and chronic disease: an example of antagonistic pleiotropy. Free Radic Biol Med 2007; 43: 332–347.
  • Collado M, Blasco MA, Serrano M. Cellular senescence in cancer and aging. Cell 2007; 130: 223–233.
  • Trachootham D, Alexandre J, Huang P. Targeting cancer cells by ROS-mediated mechanisms: a radical therapeutic approach? Nat Rev Drug Discov 2009; 8: 579–591.
  • Kimbro KS, Simons JW. Hypoxia-inducible factor-1 in human breast and prostate cancer. Endocr Relat Cancer 2006; 13: 739–749.
  • Kruse JP, Gu W Modes of p53 regulation. Cell 2009; 137: 609–622.
  • Benz CC, Yau C. Ageing, oxidative stress and cancer: paradigms in parallax. Nat Rev Cancer 2008; 8: 875–879.
  • Vousden KH, Ryan KM. p53 and metabolism. Nat Rev Cancer 2009; 9: 691–700.
  • Capri M, Salvioli S, Sevini F et al. The genetics of human longevity. Ann NY Acad Sci 2006; 1067: 252–263.
  • Sanchez-Capelo A. Dual role for TGF-betal in apoptosis. Cytokine Growth Factor Rev 2005; 16: 15–34.
  • Chalmers L, Kaskel FJ, Bamgbola O. The role of obesity and its bioclinical correlates in the progression of chronic kidney disease. Adv Chronic Kidney Dis 2006; 13: 352–364.
  • Eleuteri E, Magno F, Gnemmi I et al. Role of oxidative and nitrosative stress biomarkers in chronic heart failure. Front Biosci 2009; 14: 2230–2237.
  • Albano E. Oxidative mechanisms in the pathogenesis of alcoholic liver disease. Mol Aspects Med 2008; 29: 9–16.
  • Vogelstein B, Lane D, Levine AJ. Surfing the p53 network. Nature 2000; 408: 307–310.
  • Vousden KH, Lane DP. p53 in health and disease. Nat Rev Mol Cell Biol 2007; 8: 275–283.
  • Marchenko ND, Moll UM. The role of ubiquitination in the direct mitochondrial death program of p53. Cell Cycle 2007; 6: 1718–1723.
  • Chao C, Wu Z, Mazur SJ et al. Acetylation of mouse p53 at lysine 317 negatively regulates p53 apoptotic activities after DNA damage. Mol Cell Biol 2006; 26: 6859–6869.
  • Chao C, Herr D, Chun J, Xu Y. Ser18 and 23 phosphorylation is required for p53-dependent apoptosis and tumor suppression. EMBO J2006; 25: 2615-2622.
  • Blattner C, Tobiasch E, Litfen M, Rahmsdorf HJ, Herrlich P. DNA damage induced p53 stabilization: no indication for an involvement of p53 phosphorylation. Oncogene 1999; 18: 1723–1732.
  • Chao C, Hergenhahn M, Kaeser MD et al. Cell type- and promoter-specific roles of Ser18 phosphorylation in regulating p53 responses. J Biol Chem 2003; 278: 41028–41033.
  • Brooks CL, Gu W Ubiquitination, phosphorylation and acetylation: the molecular basis for p53 regulation. Curr Opin Cell Biol 2003; 15: 164–171.
  • Poyton RO, Ball KA, Castello PR. Mitochondrial generation of free radicals and hypoxic signaling. Trends Endocrinol Metab 2009; 20: 332–340.
  • van Faassen EE, Bahrami S, Feelisch M et al. Nitrite as regulator of hypoxic signaling in mammalian physiology. Med Res Rev 2009; 29: 683–741.
  • Taylor CT, Cummins EP. The role of NF-kappaB in hypoxia-induced gene expression. Ann NY Acad Sci 2009; 1177: 178–184.
  • Maziere C, Maziere JC. Activation of transcription factors and gene expression by oxidized low-density lipoprotein. Free Radic Biol Med 2009; 46: 127–137.
  • Bertout JA, Majmundar AJ, Gordan JD et al. HIF2alpha inhibition promotes p53 pathway activity, tumor cell death, and radiation responses. Proc Natl Acad Sci USA 2009; 106: 14391–14396.
  • Moriya J, Minamino T, Tateno K et al. Inhibition of semaphorin as a novel strategy for therapeutic angiogenesis. Circ Res 2010; 106: 391–398.
  • Fosslien E. Cancer morphogenesis: role of mitochondrial failure. Ann Clin Lab Sci 2008; 38: 307–329.
  • Koli K, Myllamiemi M, Keski-Oja J, Kinnula VL. Transforming growth factor-beta activation in the lung: focus on fibrosis and reactive oxygen species. Antioxid Redox Signal 2008; 10: 333–342.
  • Zhang H, Jiang Z, Chang J et al. Role of NAD(P)H oxidase in transforminggrowthfactor-betal-inducedmonocytechemoattractant protein-1 and interleukin-6 expression in rat renal tubular epithelial cells. Nephrology ( Carlton) 2009; 14: 302–310.
  • Chan DW, Liu VW, To RM et al. Overexpression of FOXG1 contributes to TGF-beta resistance through inhibition of p21WAF1/CIP1 expression in ovarian cancer. Br J Cancer 2009; 101: 1433–1443.
  • Tezel G. TNF-alpha signaling in glaucomatous neurodegeneration. Prog Brain Res 2008; 173: 409–421.
  • Aguilera-Aguirre L, Bacsi A, Saavedra-Molina A, Kurosky A, Sur S, Boldogh I. Mitochondrial dysfunction increases allergic airway inflammation. J Immunol 2009; 183: 5379–5387.
  • Bertram KM, Baglole CJ, Phipps RP, Libby RT. Molecular regulation of cigarette smoke induced-oxidative stress in human retinal pigment epithelial cells: implications for age-related macular degeneration. Am J Physiol 2009; 297: C1200–C1210.
  • Lal N, Kumar J, Erdahl WE et al. Differential effects of non-steroidal anti-inflammatory drugs on mitochondrial dysfunction during oxidative stress. Arch Biochem Biophys 2009; 490: 1–8.
  • Nelson GM, Ahlbom GJ, Allen JW et al. Transcriptional changes associated with reduced spontaneous liver tumor incidence in mice chronically exposed to high dose arsenic. Toxicology 2009; 266: 6–15.
  • Bailey SM. A review of the role of reactive oxygen and nitrogen species in alcohol-induced mitochondrial dysfunction. Free Radic Res 2003; 37: 585–596.
  • Kim GJ, Chandrasekaran K, Morgan WE Mitochondrial dysfunction, persistently elevated levels of reactive oxygen species and radiation-induced genomic instability: a review. Mutagenesis 2006; 21: 361–367.
  • Protti A, Singer M. Bench-to-bedside review: potential strategies to protect or reverse mitochondrial dysfunction in sepsis-induced organ failure. Crit Care 2006; 10: 228.
  • Shults CW. Mitochondrial dysfunction and possible treatments in Parkinson's disease - a review. Mitochondrion 2004; 4: 641–648.
  • Lee HK, Cho YM, Kwak SH, Lim S, Park KS, Shim EB. Mitochondrial dysfunction and metabolic syndrome-looking for environmental factors. Biochim Biophys Acta 2010; 1800: 282–289.
  • Almon RR, Lai W, DuBois DC, Jusko WJ. Corticosteroid-regulated genes in rat kidney: mining time series array data. Am J Physiol 2005; 289: E870–E882.
  • Jin JY, Almon RR, DuBois DC, Jusko WJ. Modeling of corticosteroid pharmacogenomics in rat liver using gene microarrays. J Pharmacol Exp Ther 2003; 307: 93–109.
  • Sullivan CJ, Teal TH, Luttrell IP, Tran KB, Peters MA, Wessells H. Microarray analysis reveals novel gene expression changes associated with erectile dysfunction in diabetic rats. Physiol Genomics 2005; 23: 192–205.
  • Lattanzi W, Bemardini C, Gangitano C, Michetti E Hypoxia-like transcriptional activation in TMT-induced degeneration: microarray expression analysis on PC12 cells. J Neurochem 2007; 100: 1688–1702.
  • Erlandsen SE, Fykse V, Waldum HL, Sandvik AK. Octreotide induces apoptosis in the oxyntic mucosa. Mol Cell Endocrinol 2007; 264: 188–196.
  • Chen H, Huang XN, Stewart AF, Sepulveda JL. Gene expression changes associated with fibronectin-induced cardiac myocyte hypertrophy. Physiol Genomics 2004; 18: 273–283.
  • Guan H, Arany E, van Beek JP et al. Adipose tissue gene expression profiling reveals distinct molecular pathways that define visceral adiposity in offspring of maternal protein-restricted rats. Am J Physiol 2005; 288: E663–E673.
  • Sakurai H, Bush KT, Nigam SK. Heregulin induces glial cell line-derived neurotrophic growth factor-independent, non-branching growth and differentiation of ureteric bud epithelia. J Biol Chem 2005; 280: 42181–42187.
  • Koh S, Chung H, Xia H, Mahadevia A, Song Y Environmental enrichment reverses the impaired exploratory behavior and altered gene expression induced by early-life seizures. J Child Neurol 2005; 20: 796–802.
  • Kubisch CH, Gukovsky I, Lugea A et al. Long-term ethanol consumption alters pancreatic gene expression in rats: a possible connection to pancreatic injury. Pancreas 2006; 33: 68–76.
  • Kodavanti UP, Schladweiler MC, Ledbetter AD et al. The spontaneously hypertensive rat: an experimental model of sulfur dioxide-induced airways disease. Toxicol Sci 2006; 94: 193–205.
  • Bruder ED, Lee JJ, Widmaier EP, Raff H. Microarray and real-time PCR analysis of adrenal gland gene expression in the 7-day-old rat: effects of hypoxia from birth. Physiol Genomics 2007; 29: 193–200.
  • Almon RR, DuBois DC, Yao Z, Hoffman EP, Ghimbovschi S, Jusko WJ. Microarray analysis of the temporal response of skeletal muscle to methylprednisolone: comparative analysis of two dosing regimens. Physiol Genomics 2007; 30: 282–299.
  • Chan MM, Lu X, Merchant FM, Iglehart JD, Miron PL. Gene expression profiling of NMU-induced rat mammary tumors: cross species comparison with human breast cancer. Carcinogenesis 2005; 26: 1343–1353.
  • Kendziorski C, Irizarry RA, Chen KS, Haag JD, Gould MN. On the utility of pooling biological samples in microarray experiments. Proc Natl Acad Sci USA. 2005; 102: 4252–4257.
  • Aplin AC, Gelati M, Fogel E, Carnevale E, Nicosia RE Angiopoietin-1 and vascular endothelial growth factor induce expression of inflammatory cytokines before angiogenesis. Physiol Genomics 2006; 27: 20–28.
  • Rampil IJ, Moller DH, Bell AH. Isoflurane modulates genomic expression in rat amygdala. Anesth Analg 2006; 102: 1431–1438.
  • Collins JF. Gene chip analyses reveal differential genetic responses to iron deficiency in rat duodenum and jejunum. Biol Res 2006; 39: 25–37.
  • Guzelian J, Barwick JL, Hunter L, Phang TL, Quattrochi LC, Guzelian PS. Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats. Toxicol Sci 2006; 94: 379–387.
  • Gebel S, Gerstmayer B, Kuhl P, Borlak J, Meurrens K, Muller T. The kinetics of transcriptomic changes induced by cigarette smoke in rat lungs reveals a specific program of defense, inflammation, and circadian clock gene expression. Toxicol Sci 2006; 93: 422–431.
  • Su Y, Simmen FA, Xiao R, Simmen RC. Expression profiling of rat mammary epithelial cells reveals candidate signaling pathways in dietary protection from mammary tumors. Physiol Genomics 2007; 30: 8–16.
  • Rowe WB, Blalock EM, Chen KC et al. Hippocampal expression analyses reveal selective association of immediate-early, neuroenergetic, and myelinogenic pathways with cognitive impairment in aged rats. J Neurosci 2007; 27: 3098–3110.
  • Volpicelli F, Caiazzo M, Greco D et al. Bdnf gene is a downstream target of Nurr 1 transcription factor in rat midbrain neurons in vitro. J Neurochem 2007; 102: 441–453.
  • Stemmer K, Ellinger-Ziegelbauer H, Ahr HJ, Dietrich DR. Carcinogen-specific gene expression profiles in short-term treated Eker and wild-type rats indicative of pathways involved in renal tumorigenesis. Cancer Res 2007; 67: 4052–4068.
  • Impey S, McCorkle SR, Cha-Molstad H et al. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell 2004; 119: 1041–1054.
  • Bush EW, Hood DB, Papst PJ et al. Canonical transient receptor potential channels promote cardiomyocyte hypertrophy through activation of calcineurin signaling. J Biol Chem 2006; 281: 33487–33496.
  • Zhou Z, Cornelius CP, Eichner M, Bornemann A. Reinnervation-induced alterations in rat skeletal muscle. Neurobiol Dis 2006; 23: 595–602.
  • Bursztyn M, Gross ML, Goltser-Dubner T, et al. Adult hypertension in intrauterine growth-restricted offspring of hyperinsulinemic rats: evidence of subtle renal damage. Hypertension 2006; 48: 717–723.
  • Thomas H, Senkel S, Erdmann S et al. Pattern of genes influenced by conditional expression of the transcription factors HNF6, HNF4alpha and HNF1 beta in a pancreatic beta-cell line. Nucleic Acids Res 2004; 32: e150.
  • Schumann A, Nutten S, Donnicola D et al. Neonatal antibiotic treatment alters gastrointestinal tract developmental gene expression and intestinal barrier transcriptome. Physiol Genomics 2005; 23: 235–245.
  • Roy S, Khanna S, Kuhn DE et al. Transcriptome analysis of the ischemia-reperfused remodeling myocardium: temporal changes in inflammation and extracellular matrix. Physiol Genomics. 2006; 25: 364–374.
  • Tugues S, Morales-Ruiz M, Fernandez-Varo G et al. Microarray analysis of endothelial differentially expressed genes in liver of cirrhotic rats. Gastroenterology 2005; 129: 1686–1695.
  • Akavia UD, Shur I, Rechavi G, Benayahu D. Transcriptional profiling of mesenchymal stromal cells from young and old rats in response to Dexamethasone. BMC Genomics 2006; 7: 95.
  • Zhou M, Roma A, Magi-Galluzzi C. The usefulness of immunohistochemical markers in the differential diagnosis of renal neoplasms. Clin Lab Med 2005; 25: 247–257.
  • Schiffer D, Giordana MT, Mauro A, Migheli A, Germano I, Giaccone G. Immunohistochemical demonstration of vimentin in human cerebral tumors. Acta Neuropathol 1986; 70: 209–219.
  • Niehans GA, Manivel JC, Copland GT, Scheithauer BW, Wick MR. Immunohistochemistry of germ cell and trophoblastic neoplasms. Cancer 1988; 62: 1113–1123.
  • Iwakuma T, Lozano G. Crippling p53 activities via knock-in mutations in mouse models. Oncogene 2007; 26: 2177–2184.
  • Marine JC, Jochemsen AG. Mdmx as an essential regulator of p53 activity. Biochem Biophys Res Commun 2005; 331: 750–760.
  • Tang Y, Zhao W, Chen Y, Zhao Y, Gu W Acetylation is indispensable for p53 activation. Cell 2008; 133: 612–626.
  • Gong X, Kole L, Iskander K, Jaiswal AK. NRH:quinone oxidoreductase 2 and NAD(P)H:quinone oxidoreductase 1 protect tumor suppressor p53 against 20s proteasomal degradation leading to stabilization and activation of p53. Cancer Res 2007; 67: 5380–5388.
  • Lai Z, Yang T, Kim YB et al. Differentiation of Hdm2-mediated p53 ubiquitination and Hdm2 autoubiquitination activity by small molecular weight inhibitors. Proc Natl Acad Sci USA 2002; 99: 14734–14739.
  • Wang W, Ho WC, Dicker DT et al. Acridine derivatives activate p53 and induce tumor cell death through Bax. Cancer Biol Ther 2005; 4: 893–898.
  • Kawata K, Yokoo H, Shimazaki R, Okabe S. Classification of heavy-metal toxicity by human DNA microarray analysis. Environ Sci Technol 2007; 41: 3769–3774.
  • Fry RC, Navasumrit P, Valiathan C et al. Activation of inflammation/NF-kappaB signaling in infants born to arsenic-exposed mothers. PLoS Genet 2007; 3: e207.
  • Chang L, Zhou B, Hu S et al. ATM-mediated serine 72 phosphorylation stabilizes ribonucleotide reductase small subunit p53R2 protein against MDM2 to DNA damage. Proc Natl Acad Sci USA 2008; 105: 18519–18524.
  • Kollberg G, Darin N, Benan K et al. A novel homozygous RRM2B missense mutation in association with severe mtDNA depletion. Neuromuscul Disord. 2009; 19: 147–150.
  • Liu X, Xue L, Yen Y Redox property of ribonucleotide reductase small subunit M2 and p53R2. Methods Mol Biol 2008; 477: 195–206.
  • Spinazzola A, Invemizzi F, Carrara F et al. Clinical and molecular features of mitochondrial DNA depletion syndromes. J Inherit Metab Dis 2009; 32: 143–158.
  • Tyynismaa H, Suomalainen A. Mouse models of mitochondrial DNA defects and their relevance for human disease. EMBO Rep 2009; 10: 137–143.
  • Ceryak S, Zingariello C, O'Brien T, Patierno SR. Induction of pro-apoptotic and cell cycle-inhibiting genes in chromium (VI)-treated human lung fibroblasts: lack of effect of ERK. Mol Cell Biochem 2004; 255: 139–149.
  • Fanzo JC, Reaves SK, Cui L et al. Zinc status affects p53, gadd45, and c-fos expression and caspase-3 activity in human bronchial epithelial cells. Am J Physiol 2001; 281: C751–C757.
  • Shih RS, Wong SH, Schoene NW, Lei KY. Suppression of Gadd45 alleviates the G2/M blockage and the enhanced phosphorylation of p53 and p38 in zinc supplemented normal human bronchial epithelial cells. Exp Biol Med ( Maywood) 2008; 233: 317–327.
  • Toyoshiba H, Sone H, Yamanaka T et al. Gene interaction network analysis suggests differences between high and low doses of acetaminophen. Toxicol AppL Pharmacol 2006; 215: 306–316.
  • Yamanaka T, Toyoshiba H, Sone H, Parham FM, Portier CJ. The TAO-Gen algorithm for identifying gene interaction networks with application to SOS repair in E. coll. Environ Health Perspect 2004; 112: 1614-1621.
  • Sone H, Imanishi S, Akanuma H et al. Gene expression signatures of environmental chemicals in cancer and in developmental disorders. In: Zhao BDM, Cadeans E. (eds) The roles of free radicals in biology and medicine. Beijing: Medimond, 2009; 45-52.
  • Chua PJ, Yip GW, Bay BH. Cell cycle arrest induced by hydrogen peroxide is associated with modulation of oxidative stress related genes in breast cancer cells. Exp Biol Med ( Maywood) 2009; 234: 1086–1094.
  • Feng XD, Huang SG, Shou JY et al. Analysis of pathway activity in primary tumors and NCI60 cell lines using gene expression profiling data. Genomics Proteomics Bioinformatics 2007; 5: 15–24.

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