Vanderbilt University

2006 Highlights

  • Mechanisms Involved in DNA Damage and Genetic Stability
  • Clinical Aspects of Oxidative Stress
  • Mechanisms of Chemical Damage of Proteins

    • Mechanisms Involved in DNA Damage and Genetic Stability
    A long-standing interest in the Vanderbilt Core Center has been the mechanisms by which DNA is damaged and the biochemical responses. DNA damage occurs with both exogenous and endogenous chemicals. Responses include mutation, repair, and signaling of biological responses to cells. These events are important not only with regard to cancer but also aging, teratology, and cardiovascular diseases.

    The research in this area is supported by a number of NIH R01 grants and a program project (NIH P01 ES05355, PI: M. Stone). The research is heavily dependent on some of the facility cores in the Core Center, particularly Mass Spectrometry and Structural Biology (formerly termed NMR & Crystallography). Center Investigators involved in this research include Drs. Burk, Cortez, Egli, Guengerich, Harris, Marnett, Pietenpol, Rizzo, and Stone. Investigators in this area have regular meetings to discuss research, and the program is very collaborative (some collaborations are with other institutions).

    The research covers various facets of the research field ranging from chemistry to cell biology and utilizes sophisticated approaches including mass spectrometry, NMR spectrometry, X-ray crystallography, transient-state kinetics, and various biological methods. More than 20 X-ray crystal structures of DNA-DNA polymerase complexes have been solved.

    Selected Publications

    • Ball HL, Cortez D. ATRIP oligomerization is required for ATR-dependent checkpoint signaling. J Biol Chem. 2005 280: 31390-6.
    • Bren U, Zupan M, Guengerich FP, Mavri J. Chemical reactivity as a tool to study carcinogenicity: Reaction between chloroethylene oxide and guanine. J Org Chem. 2006 71: 4078-84.
    • Brown KL, Deng JZ, Iyer RS, Iyer LG, Voehler MW, Stone MP, Harris CM, Harris TM. Unraveling the aflatoxin-FAPY conundrum: structural basis for differential replicative processing of isomeric forms of the formamidopyrimidine-type DNA adduct of aflatoxin B1. J Am Chem Soc. 2006 128: 15188-99.
    • Cho YJ, Wang H, Kozekov ID, Kozekova A, Kurtz AJ, Jacob J, Voehler M, Smith J, Harris TM, Rizzo CJ, Lloyd RS, Stone MP. Orientation of the crotonaldehyde-derived N2-[3-oxo-1(S)-methyl-propyl]-dG DNA adduct hinders interstrand cross-link formation in the 5’-CpG-3’ sequence. Chem Res Toxicol. 2006 19: 1019-29.
    • Cho YJ, Wang H, Kozekov ID, Kurtz AJ, Jacob J, Voehler M, Smith J, Harris TM, Lloyd RS, Rizzo CJ, Stone MP. Stereospecific formation of interstrand carbinolamine DNA cross-links by crotonaldehyde- and acetaldehyde-derived alpha-CH3-gamma-OH-1,N2-propano-2’-deoxyguanosine adducts in the 5’-CpG-3’ sequence. Chem Res Toxicol. 2006 19: 195-208.
    • Choi JY, Angel KC, Guengerich FP. Translesion synthesis across bulky N2-alkyl guanine DNA adducts by human DNA polymerase kappa. J Biol Chem. 2006 281: 21062-72.
    • Choi JY, Chowdhury G, Zang H, Angel KC, Vu CC, Peterson LA, Guengerich FP. Translesion synthesis across O6-alkylguanine adducts of recombinant human DNA polymerases. J Biol Chem. 2006 281: 38244-56.
    • Choi JY, Guengerich FP. Kinetic evidence for inefficient and error-prone bypass across bulky N2-guanine DNA adducts by human DNA polymerase iota. J Biol Chem. 2006 281: 12315-24.
    • Choi JY, Stover JS, Angel KC, Chowdhury G, Rizzo CJ, Guengerich FP. Biochemical basis of genotoxicity of heterocyclic arylamine food mutagens: Human DNA polymerase eta selectively produces a two-base deletion in copying the N2-guanyl adduct of 2-amino-3-methylimidazo[4,5-f]quinoline but not the C8 adduct at the NarI G3 site. J Biol Chem. 2006 281: 25297-306.
    • Choi JY, Zang H, Angel KC, Kozekov ID, Goodenough AK, Rizzo CJ, Guengerich FP.  Translesion synthesis across 1,N2-ethenoguanine by human DNA polymerases. Chem Res Toxicol. 2006 9: 879-86.
    • Egli M, Lubini P, Pallan PS.  The long and winding road to the structure of homo-DNA. Chem Soc Rev. 2007 36: 31-45.
    • Egli M, Pallan PS, Pattanayek R, Wilds CJ, Lubini P, Minasov G, Dobler M, Leumann CJ, Eschenmoser A. Crystal structure of homo-DNA and nature’s choice of pentose over hexose in the genetic system. J Am Chem Soc. 2006 128: 10847-56.
    • Eoff RL, Irimia A, Egli M, Guengerich FP. Sulfolobus solftataricus DNA polymerase DPo4 is partially inhibited by “wobble” pairing between O6-methylguanine and cytosine but accurate bypass is preferred. J Biol Chem. 2007 282: 1456-67.
    • Feng Z, Hu W, Marnett LJ, Tang MS. Malondialdehyde, a major endogenous lipid peroxidation product, sensitizes human cells to UV- and BPDE-induced killing and mutagenesis through inhibition of nucleotide excision repair. Mutat Res. 2006 601: 125-36.
    • Gold B, Marky LM, Stone MP, Williams LD. A review of the role of the sequence-dependent electrostatic landscape in DNA alkylation patterns. Chem Res Toxicol. 2006 19: 1402-14.
    • Hinow P, Rogers CE, Barbieri CE, Pietenpol JA, Kenworthy AK, DiBenedetto E. The DNA binding activity of p53 displays reaction-diffusion kinetics. Biophys J. 2006 91: 330-42.
    • Irimia A, Zang H, Loukachevitch LV, Eoff RL, Guengerich FP, Egli M. Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by the Sulfolobus solfataricus DNA polymerase Dpo4. Biochemistry. 2006 45: 5949-56.
    • Liu L, Watanabe K, Fang Q, Williams KM, Guengerich FP, Pegg AE. Effect of alterations of key active site residues in O6-alkylguanine-DNA alkyltransferase on its ability to modulate the genotoxicity of dibromoethane. Chem Res Toxicol. 2007 20:155-63.
    • Lovejoy CA, Lock K, Yenamandra A, Cortez D. DDB1 maintains genome integrity through regulation of Cdt1. Mol Cell Biol. 2006 26: 7977-90.
    • Myers JS, Cortez D.  Rapid activation of ATR by ionizing radiation requires ATM and Mre11. J Biol Chem. 2006 281: 9346-50.
    • Otteneder MB, Knutson CG, Daniels JS, Hashim M, Crews BC, Remmel RP, Wang H, Rizzo C, Marnett LJ.  In vivo oxidative metabolism of a major peroxidation-derived DNA adduct, M1dG. Proc Natl Acad Sci U S A. 2006 103: 6665-9.
    • Shimada T, Guengerich FP. Inhibition of human cytochrome P450 1A1-, 1A2-, and 1B1-mediated activation of procarcinogens to genotoxic metabolites by polycyclic aromatic hydrocarbons. Chem Res Toxicol. 2006 19: 288-94.
    • Stover JS, Chowdhury G, Zang H, Guengerich FP, Rizzo CJ. Translesion synthesis past the C8- and N2-deoxyguanosine adducts of the dietary mutagen 2-Amino-3-methylimidazo[4,5-f]quinoline in the NarI recognition sequence by prokaryotic DNA polymerases. Chem Res Toxicol. 2006 19: 1506-17.
    • Wang F, DeMuro NE, Elmquist CE, Stover JS, Rizzo CJ, Stone MP. Base-displaced intercalated structure of the food mutagen 2-amino-3-methylimidazo[4,5-f]quinoline in the recognition sequence of the NarI restriction enzyme, a hotspot for -2 bp deletions. J Am Chem Soc. 2006 128: 10085-95.
    • Wang H, Kozekov ID, Kozekova A, Tamura PJ, Marnett LJ, Harris TM, Rizzo CJ. Site-specific synthesis of oligonucleotides containing malondialdehyde adducts of deoxyguanosine and deoxyadenosine via a postsynthetic modification strategy. Chem Res Toxicol. 2006 19: 1467-74.
    • West JD, Marnett LJ. Endogenous reactive intermediates as modulators of cell signaling and cell death. Chem Res Toxicol. 2006 19: 173-94. Review.
    • Yang Z, Roginskaya M, Colis LC, Basu AK, Shell SM, Liu Y, Musich PR, Harris CM, Harris TM, Zou Y. Specific and efficient binding of xeroderma pigmentosum complementation group A to double-strand/single-strand DNA junctions with 3’- and/or 5’-ssDNA branches. Biochemistry. 2006 45: 15921-15930.
    • Zang H, Chowdhury G, Angel KC, Harris TM, Guengerich FP. Translesion synthesis across polycyclic aromatic hydrocarbon diol epoxide adducts of deoxyadenosine by Sulfolobus solfataricus DNA polymerase Dpo4. Chem Res Toxicol. 2006 19: 859-67.
    • Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, Egli M, Guengerich FP. Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem. 2006 281: 2358-72.

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    Clinical Aspects of Oxidative Stress
    One area of concentrated interest in the Core Center is research on oxidative stress. Oxidative stress is implicated in many environmental health issues, and the translational research in this area is linked to important basic research in the Core Center. Some of the clinical research is supported by a program project grant (NIH P01 ES13125, PI: N. Porter), R01 grants from several NIH institutes, and the Core Center’s Integrative Health Sciences Facility Core. Center Investigators involved in the translational research include Drs. Aschner, Brown, Burk, Hartert, Ikizler, Marnett, Morrow, and Porter.

    These studies also involve scientists at other institutions, including several NIEHS core centers. These studies are directed toward roles of oxidative stress in a variety of disease states including neurotoxicity, renal, cardiovascular, pulmonary, cancer, and others.

    Selected Publications

    • Anning PB, Coles B, Morton J, Wang H, Uddin J, Morrow JD, Dey SK, Marnett LJ, O’Donnell VB. Nitric oxide deficiency promotes vascular side effects of cyclooxygenase inhibitors. Blood. 2006 108: 4059-62.
    • Babaev VR, Ding L, Reese J, Morrow JD, Breyer MD, Dey SK, Fazio S, Linton MF. Cyclooxygenase-1 deficiency in bone marrow cells increases early atherosclerosis in apolipoprotein E- and low-density lipoprotein receptor-null mice. Circulation. 2006 113: 108-17.
    • Bingle L, Lewis CE, Corke KP, Reed MW, Brown NJ. Macrophages promote angiogenesis in human breast tumour spheroids in vivo. Br J Cancer. 2006 94: 101-7.
    • Block G, Dietrich M, Norkus E, Jensen C, Benowitz NL, Morrow JD, Hudes M, Packer L. Intraindividual variability of plasma antioxidants, markers of oxidative stress, C-reactive protein, cotinine, and other biomarkers. Epidemiology. 2006 17: 404-12.
    • Breedlove HA, Smith AM, Burk RF, Hill KE, Shapiro CL. Serum selenium measurements in women with early-stage breast cancer with and without chemotherapy-induced ovarian failure. Breast Cancer Res Treat. 2006 97: 225-30.
    • Brown NJ, Muldowney JA 3rd, Vaughan DE. Endogenous NO regulates plasminogen activator inhibitor-1 during angiotensin-converting enzyme inhibition. Hypertension. 2006 47: 441-8.
    • Burk RF, Norsworthy BK, Hill KE, Motley AK, Byrne DW. Effects of chemical form of selenium on plasma biomarkers in a high-dose human supplementation trial. Cancer Epidemiol Biomarkers Prev. 2006 15: 804-10.
    • Cai Q, Gao YT, Chow WH, Shu XO, Yang G, Ji BT, Wen W, Rothman N, Li HL, Morrow JD, Zheng W. Prospective study of urinary prostaglandin E2 metabolite and colorectal cancer risk. J Clin Oncol. 2006 24: 5010-6.
    • Cho KC, Himmelfarb J, Paganini E, Ikizler TA, Soroko SH, Mehta RL, Chertow GM. Survival by dialysis modality in critically ill patients with acute kidney injury. J Am Soc Nephrol. 2006 17: 3132-8.
    • Cotton RB, Hazinski TA, Morrow JD, Roberts LJ, Zeldin DC, Lindstrom DP, Lappalainen U, Law AB, Steele S. Cimetidine does not prevent lung injury in newborn premature infants. Pediatr Res. 2006 59: 795-800.
    • Davis TA, Gao L, Yin H, Morrow JD, Porter NA. In vivo and in vitro lipid peroxidation of arachidonate esters: the effect of fish oil omega-3 lipids on product distribution. J Am Chem Soc. 2006 128: 14897-904.
    • Enriquez R, Wu P, Griffin MR, Gebretsadik T, Shintani A, Mitchel E, Carroll KN, Hartert TV. Cessation of asthma medication in early pregnancy. Am J Obstet Gynecol. 2006 195: 149-53.
    • Erikson KM, Dorman DC, Fitsanakis V, Lash LH, Aschner M. Alterations of oxidative stress biomarkers due to in utero and neonatal exposures of airborne manganese. Biol Trace Elem Res. 2006 111: 199-215.
    • Erikson KM, Thompson K, Aschner J, Aschner M. Manganese neurotoxicity: A focus on the neonate. Pharmacol Ther. 2007 in press.
    • Globe J, Smythe A, Kelty CJ, Reed MW, Brown NJ, Ackroyd R. The effect of photodynamic therapy (PDT) on oesophageal motility and acid clearance in patients with Barrett’s oesophagus. J Photochem Photobiol B. 2006 85: 17-22.
    • Gupta RC, Milatovic S, Dettbarn WD, Aschner M, Milatovic D. Neuronal oxidative injury and dendritic damage induced by carbofuran: Protection by memantine. Toxicol Appl Pharmacol. 2007 in press.
    • Hu Y, Block G, Norkus EP, Morrow JD, Dietrich M, Hudes M. Relations of glycemic index and glycemic load with plasma oxidative stress markers. Am J Clin Nutr. 2006 84: 70-6.
    • Hulgan T, Hughes M, Sun X, Smeaton LM, Terry E, Robbins GK, Shafer RW, Clifford DB, McComsey GA, Canter JA, Morrow JD, Haas DW. Oxidant stress and peripheral neuropathy during antiretroviral therapy: an AIDS clinical trials group study. J Acquir Immune Defic Syndr. 2006 42: 450-4.
    • Ikizler TA, Himmelfarb J. Trials and trade-offs in haemodialysis vascular access monitoring. Nephrol Dial Transplant. 2006 21: 3362-3.
    • Johnson JC, Schmidt CR, Shrubsole MJ, Billheimer DD, Joshi PR, Morrow JD, Heslin MJ, Washington MK, Ness RM, Zheng W, Schwartz DA, Coffey RJ, Beauchamp RD, Merchant NB. Urine PGE-M: A metabolite of prostaglandin E2 as a potential biomarker of advanced colorectal neoplasia. Clin Gastroenterol Hepatol. 2006 4: 1358-65.
    • Kozak KR, Milne GL, Morrow JD, Cuiffo BP. Hypertrophic osteoarthropathy athogenesis: a case highlighting the potential role for cyclo-oxygenase-2-derived prostaglandin E2. Nat Clin Pract Rheumatol. 2006 2: 452-6.
    • Landar A, Zmijewski JW, Dickinson DA, Le Goffe C, Johnson MS, Milne GL, Zanoni G, Vidari G, Morrow JD, Darley-Usmar VM. Interaction of electrophilic lipid oxidation products with mitochondria in endothelial cells and formation of reactive oxygen species. Am J Physiol Heart Circ Physiol. 2006 290: H1777-87.
    • Lin CL, Hsu YT, Lin TK, Morrow JD, Hsu JC, Hsu YH, Hsieh TC, Tsay PK, Yen HC. Increased levels of F2-isoprostanes following aneurysmal subarachnoid hemorrhage in humans. Free Radic Biol Med. 2006 40: 1466-73.
    • Milne GL, Morrow JD. Isoprostanes and related compounds: update 2006. Antioxid Redox Signal. 2006 8: 1379-84. Review.
    • Morrow JD. The isoprostanes - unique products of arachidonate peroxidation: their role as mediators of oxidant stress. Curr Pharm Des. 2006 12: 895-902. Review.
    • Muthian G, Raikwar HP, Johnson C, Rajasingh J, Kalgutkar A, Marnett LJ, Bright JJ. COX-2 inhibitors modulate IL-12 signaling through JAK-STAT pathway leading to Th1 response in experimental allergic encephalomyelitis. J Clin Immunol. 2006 26: 73-85.
    • Nieman DC, Henson DA, Dumke CL, Oley K, McAnulty SR, Davis JM, Murphy EA, Utter AC, Lind RH, McAnulty LS, Morrow JD. Ibuprofen use, endotoxemia, inflammation, and plasma cytokines during ultramarathon competition. Brain Behav Immun. 2006 20: 578-84.
    • Pupim LB, Flakoll PJ, Ikizler TA. Exercise improves albumin fractional synthetic rate in chronic hemodialysis patients. Eur J Clin Nutr. 2007 in press.
    • Pupim LB, Majchrzak KM, Flakoll PJ, Ikizler TA. Intradialytic oral nutrition improves protein homeostasis in chronic hemodialysis patients with deranged nutritional status. J Am Soc Nephrol. 2006 17: 3149-57.
    • Reckamp KL, Krysan K, Morrow JD, Milne GL, Newman RA, Tucker C, Elashoff RM, Dubinett SM, Figlin RA. A phase I trial to determine the optimal biological dose of celecoxib when combined with erlotinib in advanced non-small cell lung cancer. Clin Cancer Res. 2006 12: 3381-8.
    • Siew ED, Pupim LB, Majchrzak KM, Shintani A, Flakoll PJ, Ikizler TA. Insulin resistance is associated with skeletal muscle protein breakdown in non-diabetic chronic hemodialysis patients. Kidney Int. 2007 in press.
    • Singh AM, Moore PE, Gern JE, Lemanske Jr RF, Hartert TV. Bronchiolitis to asthma: A review and call for studies of gene-viral interactions in asthma causation. Am J Respir Crit Care Med. 2007 175: 108-19.
    • Venarske DL, Busse WW, Griffin MR, Gebretsadik T, Shintani AK, Minton PA, Peebles RS, Hamilton R, Weisshaar E, Vrtis R, Higgins SB, Hartert TV. The relationship of rhinovirus-associated asthma hospitalizations with inhaled corticosteroids and smoking. J Infect Dis. 2006 193: 1536-43.
    • Yilmaz MI, Korkmaz A, Kaya A, Sonmez A, Caglar K, Topal T, Eyileten T, Yenicesu M, Acikel C, Oter S, Yaman H, Aktug H, Oguz Y, Vural A, Ikizler TA. Hyperbaric oxygen treatment augments the efficacy of a losartan regime in an experimental nephrotic syndrome model. Nephron Exp Nephrol. 2006 104: e15-22.
    • Yin H, Gao L, Tai HH, Murphey LJ, Porter NA, Morrow JD. Urinary prostaglandin F2alpha is generated from the isoprostane pathway and not the cyclooxygenase in humans. J Biol Chem. 2007 282: 329-336.
    • Yin Z, Milatovic D, Aschner JL, Syversen T, Rocha JB, Souza DO, Sidoryk M, Albrecht J, Aschner M. Methylmercury induces oxidative injury, alterations in permeability and glutamine transport in cultured astrocytes. Brain Res. 2007 in press.

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    Mechanisms of Chemical Damage of Proteins
    Another area of interest in basic research is the mechanisms of how electrophilic chemicals interact with proteins. Many chemicals of interest in the area of environmental health are known to be converted in the body to such reactive species, including many endogenous compounds such as those generated in situations of oxidative stress. Recently methods have been developed to identify the proteins modified by these chemicals and the sites of modifications. Studies in this area are necessary in the overall plan to characterize the nature of the biological processes triggered by these events.

    Some of this research is relevant to the translational work done with oxidative stress and also the toxicity of drug candidates. The work involves chemistry and particularly proteomics. This research is supported in part by numerous NIH R01 grants to individual investigators, a program project grant (NIH P01 ES13125, PI: N. Porter), and the Proteomics Facility Core. Investigators involved include Drs. Caprioli, Guengerich, Liebler, and Marnett.

    Selected Publications

    • Boutte AM, Woltjer RL, Zimmerman LJ, Stamer SL, Montine KS, Manno MV, Cimino PJ, Liebler DC, Montine TJ. Selectively increased oxidative modifications mapped to detergent-insoluble forms of Abeta and beta-III tubulin in Alzheimer’s disease. FASEB J. 2006 20: 1473-83.
    • Chacon A, Masterson DS, Yin H, Liebler DC, Porter NA. N-Terminal amino acid side-chain cleavage of chemically modified peptides in the gas phase: a mass spectrometry technique for N-terminus identification. Bioorg Med Chem. 2006 14: 6213-22.
    • Chaurand P, Norris JL, Cornett DS, Mobley JA, Caprioli RM. New developments in profiling and imaging of proteins from tissue sections by MALDI mass spectrometry. J Proteome Res. 2006 5: 2889-900.
    • Codreanu SG, Adams DG, Dawson ES, Wadzinski BE, Liebler DC. Inhibition of protein phosphatase 2A activity by selective electrophile alkylation damage. Biochemistry. 2006 45: 10020-9.
    • Dennehy MK, Richards KA, Wernke GR, Shyr Y, Liebler DC. Cytosolic and nuclear protein targets of thiol-reactive electrophiles. Chem Res Toxicol. 2006 19: 20-9.
    • Druckova A, Marnett LJ. Characterization of the amino acid adducts of the enedial derivative of teucrin A. Chem Res Toxicol. 2006 19: 1330-40.
    • Greco TM, Hodara R, Parastatidis I, Heijnen HF, Dennehy MK, Liebler DC, Ischiropoulos H. Identification of S-nitrosylation motifs by site-specific mapping of the S-nitrosocysteine proteome in human vascular smooth muscle cells. Proc Natl Acad Sci U S A. 2006 103: 7420-5.
    • Liebler DC. The poisons within: application of toxicity mechanisms to fundamental disease processes. Chem Res Toxicol. 2006 19: 610-3.
    • Reyzer ML, Caprioli RM. MALDI-MS-based imaging of small molecules and proteins in tissues. Curr Opin Chem Biol. 2007 in press.
    • Suman SP, Faustman C, Stamer SL, Liebler DC. Redox instability induced by 4-hydroxy-2-nonenal in porcine and bovine myoglobins at pH 5.6 and 4 degrees C. J Agric Food Chem. 2006 54: 3402-8.
    • Szapacs ME, Riggins JN, Zimmerman LJ, Liebler DC. Covalent adduction of human serum albumin by 4-hydroxy-2-nonenal: kinetic analysis of competing alkylation reactions. Biochemistry. 2006 45: 10521-8.
    • Watanabe K, Guengerich FP. Limited reactivity of formyl chloride with glutathione and relevance to metabolism and toxicity of dichloromethane. Chem Res Toxicol. 2006 19: 1091-6.

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