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The role of toxicoproteomics in assessing organ specific toxicity

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Molecular, Clinical and Environmental Toxicology

Part of the book series: Experientia Supplementum ((EXS,volume 99))

Abstract

Aims of this chapter on the role of toxicoproteomics in assessing organ-specific toxicity are to define the field of toxicoproteomics, describe its development among global technologies, and show potential uses in experimental toxicological research, preclinical testing and mechanistic biological research. Disciplines within proteomics deployed in preclinical research are described as Tier I analysis, involving global protein mapping and protein profiling for differential expression, and Tier II proteomic analysis, including global methods for description of function, structure, interactions and post-translational modification of proteins. Proteomic platforms used in toxicoproteomics research are briefly reviewed. Preclinical toxicoproteomic studies with model liver and kidney toxicants are critically assessed for their contributions toward understanding pathophysiology and in biomarker discovery. Toxicoproteomics research conducted in other organs and tissues are briefly discussed as well. The final section suggests several key developments involving new approaches and research focus areas for the field of toxicoproteomics as a new tool for toxicological pathology.

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References

  1. Chapal N, Molina L, Molina F, Laplanche M, Pau B, Petit B (2004) Pharmacoproteomic approach to the study of drug mode of action, toxicity, and resistance: Applications in diabetes and cancer. Fundam Clin Pharmacol 18: 413–422

    PubMed  CAS  Google Scholar 

  2. Leighton JK (2005) Application of emerging technologies in toxicology and safety assessment: Regulatory perspectives. Int J Toxicol 24: 153–155

    PubMed  Google Scholar 

  3. Ross JS, Symmans WF, Pusztai L, Hortobagyi GN (2005) Pharmacogenomics and clinical biomarkers in drug discovery and development. Am J Clin Pathol 124 Suppl: S29–41

    PubMed  Google Scholar 

  4. Siest G, Marteau JB, Maumus S, Berrahmoune H, Jeannesson E, Samara A, Batt AM, Visvikis-Siest S (2005) Pharmacogenomics and cardiovascular drugs: Need for integrated biological system with phenotypes and proteomic markers. Eur J Pharmacol 527: 1–22

    PubMed  CAS  Google Scholar 

  5. Bandara LR, Kennedy S (2002) Toxicoproteomics-A new preclinical tool. Drug Discov Today 7: 411–418

    PubMed  CAS  Google Scholar 

  6. Petricoin EF, Rajapaske V, Herman EH, Arekani AM, Ross S, Johann D, Knapton A, Zhang J, Hitt BA, Conrads TP et al (2004) Toxicoproteomics: Serum proteomic pattern diagnostics for early detection of drug induced cardiac toxicities and cardioprotection. Toxicol Pathol 32 Suppl 1: 122–130

    Google Scholar 

  7. Wetmore BA, Merrick BA (2004) Toxicoproteomics: Proteomics applied to toxicology and pathology. Toxicol Pathol 32: 619–642

    PubMed  CAS  Google Scholar 

  8. Waters MD, Fostel JM (2004) Toxicogenomics and systems toxicology: Aims and prospects. Nat Rev Genet 5: 936–948

    PubMed  CAS  Google Scholar 

  9. Turner SM (2006) Stable isotopes, mass spectrometry, and molecular fluxes: Applications to toxicology. J Pharmacol Toxicol Methods 53: 75–85

    PubMed  CAS  Google Scholar 

  10. Merrick BA, Bruno ME (2004) Genomic and proteomic profiling for biomarkers and signature profiles of toxicity. Curr Opin Mol Ther 6: 600–607

    PubMed  CAS  Google Scholar 

  11. Silbergeld EK, Davis DL (1994) Role of biomarkers in identifying and understanding environmentally induced disease. Clin Chem 40: 1363–1367

    PubMed  CAS  Google Scholar 

  12. Hood L, Heath JR, Phelps ME, Lin B (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306: 640–643

    PubMed  CAS  Google Scholar 

  13. Lin J, Qian J (2007) Systems biology approach to integrative comparative genomics. Expert Rev Proteomics 4: 107–119

    PubMed  CAS  Google Scholar 

  14. Kasper P, Oliver G, Lima BS, Singer T, Tweats D (2005) Joint EFPIA/CHMP SWP workshop: The emerging use of omic technologies for regulatory non-clinical safety testing. Pharmacogenomics 6: 181–184

    PubMed  Google Scholar 

  15. Gibbs A (2005) Comparison of the specificity and sensitivity of traditional methods for assessment of nephrotoxicity in the rat with metabonomic and proteomic methodologies. J Appl Toxicol 25: 277–295

    PubMed  CAS  Google Scholar 

  16. MacGregor JT (2003) The future of regulatory toxicology: Impact of the biotechnology revolution. Toxicol Sci 75: 236–248

    PubMed  CAS  Google Scholar 

  17. Hackett JL, Gutman SI (2005) Introduction to the Food and Drug Administration (FDA) regulatory process. J Proteome Res 4: 1110–1113

    PubMed  CAS  Google Scholar 

  18. Yeh ET (2005) High-sensitivity C-reactive protein as a risk assessment tool for cardiovascular disease. Clin Cardiol 28: 408–412

    PubMed  Google Scholar 

  19. Amacher DE (2002) A toxicologist’s guide to biomarkers of hepatic response. Hum Exp Toxicol 21: 253–262

    PubMed  CAS  Google Scholar 

  20. Ross JS, Fletcher JA, Linette GP, Stec J, Clark E, Ayers M, Symmans WF, Pusztai L, Bloom KJ (2003) The Her-2/neu gene and protein in breast cancer 2003: Biomarker and target of therapy. Oncologist 8: 307–325

    PubMed  CAS  Google Scholar 

  21. Thier R, Bruning T, Roos PH, Rihs HP, Golka K, Ko Y, Bolt HM (2003) Markers of genetic susceptibility in human environmental hygiene and toxicology: The role of selected CYP, NAT and GST genes. Int J Hyg Environ Health 206: 149–171

    PubMed  CAS  Google Scholar 

  22. Bilello JA (2005) The agony and ecstasy of “OMIC” technologies in drug development. Curr Mol Med 5: 39–52

    PubMed  CAS  Google Scholar 

  23. Koop R (2005) Combinatorial biomarkers: From early toxicology assays to patient population profiling. Drug Discov Today 10: 781–788

    PubMed  CAS  Google Scholar 

  24. Merrick BA (2004) Introduction to high-throughput protein expression. In: HK Hamadeh, CA Afshari (eds): Toxicogenomics: Principles and Applications.Wiley and Sons, New York, 263–281

    Google Scholar 

  25. Merrick BA, Madenspacher JH (2005) Complementary gene and protein expression studies and integrative approaches in toxicogenomics. Toxicol Appl Pharmacol 207: 189–194

    PubMed  Google Scholar 

  26. Righetti PG, Castagna A, Antonucci F, Piubelli C, Cecconi D, Campostrini N, Antonioli P, Astner H, Hamdan M (2004) Critical survey of quantitative proteomics in two-dimensional electrophoretic approaches. J Chromatogr A 1051: 3–17

    PubMed  CAS  Google Scholar 

  27. Freeman WM, Hemby SE (2004) Proteomics for protein expression profiling in neuroscience. Neurochem Res 29: 1065–1081

    PubMed  CAS  Google Scholar 

  28. Yates JR (2004) Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 33: 297–316

    PubMed  CAS  Google Scholar 

  29. Bhat VB, Choi MH, Wishnok JS, Tannenbaum SR (2005) Comparative plasma proteome analysis of lymphoma-bearing SJL mice. J Proteome Res 4: 1814–1825

    PubMed  CAS  Google Scholar 

  30. Farkas D, Bhat VB, Mandapati S, Wishnok JS, Tannenbaum SR (2005) Characterization of the secreted proteome of rat hepatocytes cultured in collagen sandwiches. Chem Res Toxicol 18: 1132–1139

    PubMed  CAS  Google Scholar 

  31. Macdonald N, Chevalier S, Tonge R, Davison M, Rowlinson R, Young J, Rayner S, Robert R (2001) Quantitative proteomic analysis of mouse liver response to the peroxisome proliferator diethylhexylphthalate (DEHP). Arch Toxicol 75: 415–424

    PubMed  CAS  Google Scholar 

  32. Asara JM, Christofk HR, Freimark LM, Cantley LC (2008) A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen. Proteomics 8: 994–999

    PubMed  CAS  Google Scholar 

  33. Higgs RE, Knierman MD, Gelfanova V, Butler JP, Hale JE (2005) Comprehensive label-free method for the relative quantification of proteins from biological samples. J Proteome Res 4: 1442–1450

    PubMed  CAS  Google Scholar 

  34. Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L (2005) Differential proteomics via probabilistic peptide identification scores. Anal Chem 77: 596–606

    PubMed  CAS  Google Scholar 

  35. Liu H, Sadygov RG, Yates JR 3rd (2004) A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal Chem 76: 4193–4201

    PubMed  CAS  Google Scholar 

  36. Paoletti AC, Parmely TJ, Tomomori-Sato C, Sato S, Zhu D, Conaway RC, Connaway JW, Florens L, Washburn MP (2006) Quantitative proteomic analysis of distinct mammalian mediator complexes using normalized spectral abundance factors. Proc Natl Acad Sci USA 103: 18928–18933

    PubMed  CAS  Google Scholar 

  37. Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP (2006) Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae. J Proteome Res 5: 2339–2347

    PubMed  CAS  Google Scholar 

  38. Gerber SA, Rush J, Stemman O, Kirschner MW, Gygi SP (2003) Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS. Proc Natl Acad Sci USA 100: 6940–6945

    PubMed  CAS  Google Scholar 

  39. Kirkpatrick DS, Gerber SA, Gygi SP (2005) The absolute quantification strategy: A general procedure for the quantification of proteins and post-translational modifications. Methods 35: 265–273

    PubMed  CAS  Google Scholar 

  40. Old WM, Meyer-Arendt K, Aveline-Wolf L, Pierce KG, Mendoza A, Sevinsky JR, Resing KA, Ahn NG (2005) Comparison of label-free methods for quantifying human proteins by shotgun proteomics. Mol Cell Proteomics 4: 1487–1502

    PubMed  CAS  Google Scholar 

  41. Fitzpatrick DPG, You JS, Bemis KG, Wery JP, Ludwig JR, Wang M (2007) Searching for potential biomarkers of cisplatin resistance in human ovarian cancer using a label-free LC/MS-based protein quantification method. Proteomics Clin Appl 1: 246–263

    CAS  Google Scholar 

  42. Witzmann FA, Hong D, Rodd ZA, Simon JR, Truitt WA, Wang M (2007) Synaptosomal protein expression in nucleus accumbens after EtOH self-administration in the posterior VTA. FASEB J 21: A477–A477

    Google Scholar 

  43. Witzmann FA, Lee K, Wang M, Yemane Y, Witten ML (2007) Pulmonary effects of JP-8 jet fuel exposure-Label-free quantitative analysis of protein expression in alveolar type II epithelial cells using LC/MS. Toxicol Sci 96: 102

    Google Scholar 

  44. Florens L, Carozza MJ, Swanson SK, Fournier M, Coleman MK, Workman JL, Washburn MP (2006) Analyzing chromatin remodeling complexes using shotgun proteomics and normalized spectral abundance factors. Methods 40: 303–311

    PubMed  CAS  Google Scholar 

  45. Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Florens L, Washburn MP (2008) Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics. Proc Natl Acad Sci USA 105: 1454–1459

    PubMed  CAS  Google Scholar 

  46. Ott LW, Resing KA, Sizemore AW, Heyen JW, Cocklin RR, Pedrick NM, Woods HC, Chen JY, Goebl MG, Witzmann FA, Harrington MA (2007) Tumor necrosis factor-a-and interleukin-1-induced cellular responses: Coupling proteomic and genomic information. J Proteome Res 6: 2176–2185

    PubMed  CAS  Google Scholar 

  47. Janecki DJ, Bemis KG, Tegeler TJ, Sanghani PC, Zhai L, Hurley TD, Bosron WF, Wang M (2007) A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme. Anal Biochem 369: 18–26

    PubMed  CAS  Google Scholar 

  48. Carmella SG, Chen M, Zhang Y, Zhang S, Hatsukami DK, Hecht SS (2007) Quantitation of acrolein-derived (3-hydroxypropyl)mercapturic acid in human urine by liquid chromatographyatmospheric pressure chemical ionization tandem mass spectrometry: Effects of cigarette smoking. Chem Res Toxicol 20: 986–990

    PubMed  CAS  Google Scholar 

  49. Petricoin E,Wulfkuhle J, Espina V, Liotta LA (2004) Clinical proteomics: Revolutionizing disease detection and patient tailoring therapy. J Proteome Res 3: 209–217

    PubMed  CAS  Google Scholar 

  50. Issaq HJ, Conrads TP, Prieto DA, Tirumalai R, Veenstra TD (2003) SELDI-ToF MS for diagnostic proteomics. Anal Chem 75: 148A–155A

    PubMed  CAS  Google Scholar 

  51. Diamandis EP (2004) Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: Opportunities and potential limitations. Mol Cell Proteomics 3: 367–378

    PubMed  CAS  Google Scholar 

  52. Cutler P (2003) Protein arrays: The current state-of-the-art. Proteomics 3: 3–18

    PubMed  CAS  Google Scholar 

  53. Park BK, Kitteringham NR, Maggs JL, Pirmohamed M, Williams DP (2005) The role of metabolic activation in drug-induced hepatotoxicity. Annu Rev Pharmacol Toxicol 45: 177–202

    PubMed  CAS  Google Scholar 

  54. Kaplowitz N (2004) Drug-induced liver injury. Clin Infect Dis 38 Suppl 2: S44–48

    Google Scholar 

  55. Maddrey WC (2005) Drug-induced hepatotoxicity: 2005. J Clin Gastroenterol 39: S83–89

    PubMed  Google Scholar 

  56. Kalgutkar AS, Gardner I, Obach RS, Shaffer CL, Callegari E, Henne KR, Mutlib AE, Dalvie DK, Lee JS, Nakai Y et al (2005) A comprehensive listing of bioactivation pathways of organic functional groups. Curr Drug Metab 6: 161–225

    PubMed  CAS  Google Scholar 

  57. Steiner G, Suter L, Boess F, Gasser R, de Vera MC, Albertini S, Ruepp S (2004) Discriminating different classes of toxicants by transcript profiling. Environ Health Perspect 112: 1236–1248

    PubMed  CAS  Google Scholar 

  58. Kon K, Kim JS, Jaeschke H, Lemasters JJ (2004) Mitochondrial permeability transition in acetaminophen-induced necrosis and apoptosis of cultured mouse hepatocytes. Hepatology 40: 1170–1179

    PubMed  CAS  Google Scholar 

  59. Amacher DE (2005) Drug-associated mitochondrial toxicity and its detection. Curr Med Chem 12: 1829–1839

    PubMed  CAS  Google Scholar 

  60. Liu ZX, Govindarajan S, Kaplowitz N (2004) Innate immune system plays a critical role in determining the progression and severity of acetaminophen hepatotoxicity. Gastroenterology 127: 1760–1774

    PubMed  CAS  Google Scholar 

  61. Laskin DL, Laskin JD (2001) Role of macrophages and inflammatory mediators in chemically induced toxicity. Toxicology 160: 111–118

    PubMed  CAS  Google Scholar 

  62. James LP, Simpson PM, Farrar HC, Kearns GL, Wasserman GS, Blumer JL, Reed MD, Sullivan JE, Hinson JA (2005) Cytokines and toxicity in acetaminophen overdose. J Clin Pharmacol 45: 1165–1171

    PubMed  CAS  Google Scholar 

  63. Ishida Y, Kondo T, Tsuneyama K, Lu P, Takayasu T, Mukaida N (2004) The pathogenic roles of tumor necrosis factor receptor p55 in acetaminophen-induced liver injury in mice. J Leukoc Biol 75: 59–67

    PubMed  CAS  Google Scholar 

  64. Ito Y, Bethea NW, Abril ER, McCuskey RS (2003) Early hepatic microvascular injury in response to acetaminophen toxicity. Microcirculation 10: 391–400

    PubMed  CAS  Google Scholar 

  65. Fountoulakis M, Berndt P, Boelsterli UA, Crameri F, Winter M, Albertini S, Suter L (2000) Twodimensional database of mouse liver proteins: Changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol. Electrophoresis 21: 2148–2161

    PubMed  CAS  Google Scholar 

  66. Tonge R, Shaw J, Middleton B, Rowlinson R, Rayner S, Young J, Pognan F, Hawkins E, Currie I, Davison M (2001) Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics 1: 377–396

    PubMed  CAS  Google Scholar 

  67. Ruepp SU, Tonge RP, Shaw J, Wallis N, Pognan F (2002) Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci 65: 135–150

    PubMed  CAS  Google Scholar 

  68. Thome-Kromer B, Bonk I, Klatt M, Nebrich G, Taufmann M, Bryant S, Wacker U, Köpke A (2003) Toward the identification of liver toxicity markers: A proteome study in human cell culture and rats. Proteomics 3: 1835–1862

    PubMed  CAS  Google Scholar 

  69. Kikkawa R, Yamamoto T, Fukushima T, Yamada H, Horii I (2005) Investigation of a hepatotoxicity screening system in primary cell cultures-“what biomarkers would need to be addressed to estimate toxicity in conventional and new approaches?” J Toxicol Sci 30: 61–72

    PubMed  CAS  Google Scholar 

  70. Yamamoto T, Kikkawa R, Yamada H, Horii I(2005) Identification of oxidative stress-related proteins for predictive screening of hepatotoxicity using a proteomic approach. J Toxicol Sci 30: 213–227

    PubMed  CAS  Google Scholar 

  71. Welch KD, Wen B, Goodlett DR, Yi EC, Lee H, Reilly TP, Nelson SD, Pohl LR (2005) Proteomic identification of potential susceptibility factors in drug-induced liver disease. Chem Res Toxicol 18: 924–933

    PubMed  CAS  Google Scholar 

  72. Lee H, Yi EC, Wen B, Reily TP, Pohl L, Nelson S, Aebersold R, Goodlett DR (2004) Optimization of reversed-phase microcapillary liquid chromatography for quantitative proteomics. J Chromatogr B Analyt Technol Biomed Life Sci 803: 101–110

    PubMed  CAS  Google Scholar 

  73. Weber LW, Boll M, Stampfl A (2003) Hepatotoxicity and mechanism of action of haloalkanes: Carbon tetrachloride as a toxicological model. Crit Rev Toxicol 33: 105–136

    PubMed  CAS  Google Scholar 

  74. Liu Y, Liu P, Liu CH, Hu YY, Xu LM, Mu YP, Du GL (2005) [Proteomic analysis of proliferation and apoptosis in carbon tetrachloride induced rat liver fibrosis]. Zhonghua Gan Zang Bing Za Zhi 13: 563–566

    PubMed  CAS  Google Scholar 

  75. Nelson SD (1995) Mechanisms of the formation and disposition of reactive metabolites that can cause acute liver injury. Drug Metab Rev 27: 147–177

    PubMed  CAS  Google Scholar 

  76. Heijne WH, Stierum RH, Slijper M, van Bladeren PJ, van Ommen B (2003) Toxicogenomics of bromobenzene hepatotoxicity: A combined transcriptomics and proteomics approach. Biochem Pharmacol 65: 857–875

    PubMed  CAS  Google Scholar 

  77. Staels B, Fruchart JC (2005) Therapeutic roles of peroxisome proliferator-activated receptor agonists. Diabetes 54: 2460–2470

    PubMed  CAS  Google Scholar 

  78. Iida M, Anna CH, Hartis J, Bruno M, Wetmore B, Dubin JR, Sieber S, Bennett L, Cunningham ML, Paules RS et al (2003) Changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens oxazepam and Wyeth-14,643. Carcinogenesis 24: 757–770

    PubMed  CAS  Google Scholar 

  79. Edvardsson U, von Lowenhielm HB, Panfilov O, Nystrom AC, Nilsson F, Dahllöf B (2003) Hepatic protein expression of lean mice and obese diabetic mice treated with peroxisome proliferator-activated receptor activators. Proteomics 3: 468–478

    PubMed  CAS  Google Scholar 

  80. Richards VE, Chau B, White MR, McQueen CA (2004) Hepatic gene expression and lipid homeostasis in C57BL/6 mice exposed to hydrazine or acetylhydrazine. Toxicol Sci 82: 318–332

    PubMed  CAS  Google Scholar 

  81. Kleno TG, Kiehr B, Baunsgaard D, Sidelmann UG (2004) Combination of ‘omics’ data to investigate the mechanism(s) of hydrazine-induced hepatotoxicity in rats and to identify potential biomarkers. Biomarkers 9: 116–138

    PubMed  CAS  Google Scholar 

  82. Kleno TG, Leonardsen LR, Kjeldal HO, Laursen SM, Jensen ON, Baunsgaard D (2004) Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis. Proteomics 4: 868–880

    PubMed  CAS  Google Scholar 

  83. Chilakapati J, Shankar K, Korrapati MC, Hill RA, Mehendale HM (2005) Saturation toxicokinetics of thioacetamide: Role in initiation of liver injury. Drug Metab Dispos 33: 1877–1885

    PubMed  CAS  Google Scholar 

  84. Low TY, Leow CK, Salto-Tellez M, Chung MC (2004) A proteomic analysis of thioacetamideinduced hepatotoxicity and cirrhosis in rat livers. Proteomics 4: 3960–3974

    PubMed  CAS  Google Scholar 

  85. Xu XQ, Leow CK, Lu X, Zhang X, Liu JS,Wong WH, Asperger A, Deininger S, Eastwood Leung HC (2004) Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics. Proteomics 4: 3235–3245

    PubMed  CAS  Google Scholar 

  86. Kawada N, Kristensen DB, Asahina K, Nakatani K, Minamiyama Y, Seki S, Yoshizato K (2001) Characterization of a stellate cell activation-associated protein (STAP) with peroxidase activity found in rat hepatic stellate cells. J Biol Chem 276: 25318–25323

    PubMed  CAS  Google Scholar 

  87. Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS et al (2005) Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5: 3226–3245

    PubMed  CAS  Google Scholar 

  88. Ping P, Vondriska TM, Creighton CJ, Gandhi TK, Yang Z, Menon R, Kwon MS, Cho SY, Drwal G, Kellmann M et al (2005) A functional annotation of subproteomes in human plasma. Proteomics 5: 3506–3519

    PubMed  CAS  Google Scholar 

  89. Duan X, Yarmush DM, Berthiaume F, Jayaraman A, Yarmush ML (2004) A mouse serum twodimensional gel map: Application to profiling burn injury and infection. Electrophoresis 25: 3055–3065

    PubMed  CAS  Google Scholar 

  90. Gianazza E, Eberini I, Villa P, Fratelli M, Pinna C, Wait R, Gemeiner M, Miller I (2002) Monitoring the effects of drug treatment in rat models of disease by serum protein analysis. J Chromatogr B Analyt Technol Biomed Life Sci 771: 107–130

    PubMed  CAS  Google Scholar 

  91. Duan X, Yarmush D, Berthiaume F, Jayaraman A, Yarmush ML (2005) Immunodepletion of albumin for two-dimensional gel detection of new mouse acute-phase protein and other plasma proteins. Proteomics 5: 3991–4000

    PubMed  CAS  Google Scholar 

  92. Wait R, Chiesa G, Parolini C, Miller I, Begum S, Brambilla D, Galluccio L, Ballerio R, Eberini I, Gianazza E (2005) Reference maps of mouse serum acute-phase proteins: Changes with LPSinduced inflammation and apolipoprotein A-I and A-II transgenes. Proteomics 5: 4245–4253

    PubMed  CAS  Google Scholar 

  93. Amacher DE, Adler R, Herath A, Townsend RR (2005) Use of proteomic methods to identify serum biomarkers associated with rat liver toxicity or hypertrophy. Clin Chem 51: 1796–1803

    PubMed  CAS  Google Scholar 

  94. Witzmann FA, Li J (2004) Proteomics and nephrotoxicity. Contrib Nephrol 141: 104–123

    PubMed  CAS  Google Scholar 

  95. Davis JW, Kramer JA (2006) Genomic-based biomarkers of drug-induced nephrotoxicity. Expert Opin Drug Metab Toxicol 2: 95–101

    PubMed  CAS  Google Scholar 

  96. Janech MG, Raymond JR, Arthur JM (2007) Proteomics in renal research. Am J Physiol Renal Physiol 292: F501–512

    PubMed  CAS  Google Scholar 

  97. Mihatsch MJ, Thiel G, Ryffel B (1989) Cyclosporin A: Action and side-effects. Toxicol Lett 46: 125–139

    PubMed  CAS  Google Scholar 

  98. Benito B, Wahl D, Steudel N, Cordier A, Steiner S (1995) Effects of cyclosporine A on the rat liver and kidney protein pattern, and the influence of vitamin E and C coadministration. Electrophoresis 16: 1273–1283

    PubMed  CAS  Google Scholar 

  99. Steiner S, Aicher L, Raymackers J, Meheus L, Esquer-Blasco R, Anderson NL, Cordier A (1996) Cyclosporine A decreases the protein level of the calcium-binding protein calbindin-D 28 kDa in rat kidney. Biochem Pharmacol 51: 253–258

    PubMed  CAS  Google Scholar 

  100. Lee CT, Huynh VM, Lai LW, Lien YH (2002) Cyclosporine A-induced hypercalciuria in calbindin-D28k knockout and wild-type mice. Kidney Int 62: 2055–2061

    PubMed  CAS  Google Scholar 

  101. Serkova N, Christians U (2003) Transplantation: Toxicokinetics and mechanisms of toxicity of cyclosporine and macrolides. Curr Opin Investig Drugs 4: 1287–1296

    PubMed  CAS  Google Scholar 

  102. Mascarell L, Frey JR, Michel F, Lefkovits I, Truffa-Bachi P (2000) Increased protein synthesis after T cell activation in presence of cyclosporin A. Transplantation 70: 340–348

    PubMed  CAS  Google Scholar 

  103. Mascarell L, Auger R, Alcover A, Ojcius DM, Jungas T, Cadet-Daniel V, Kanellopoulos JM, Truffa-Bachi P (2004) Characterization of a gene encoding two isoforms of a mitochondrial protein up-regulated by cyclosporin A in activated T cells. J Biol Chem 279: 10556–10563

    PubMed  CAS  Google Scholar 

  104. Guan N, Ding J, Deng J, Zhang J, Yang J (2004) Key molecular events in puromycin aminonucleoside nephrosis rats. Pathol Int 54: 703–711

    PubMed  CAS  Google Scholar 

  105. Sundin DP, Meyer C, Dahl R, Geerdes A, Sandoval R, Molitoris BA (1997) Cellular mechanism of aminoglycoside tolerance in long-term gentamicin treatment. Am J Physiol 272: C1309–1318

    PubMed  CAS  Google Scholar 

  106. Witzmann FA, Fultz CD, Grant RA, Wright LS, Kornguth SE, Siegel FL (1998) Differential expression of cytosolic proteins in the rat kidney cortex and medulla: Preliminary proteomics. Electrophoresis 19: 2491–2497

    PubMed  CAS  Google Scholar 

  107. Shakib K, Norman JT, Fine LG, Brown LR, Godovac-Zimmermann J (2005) Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus. Proteomics 5: 2819–2838

    PubMed  CAS  Google Scholar 

  108. Charlwood J, Skehel JM, King N, Camilleri P, Lord P, Bugelski P, Atif U (2002) Proteomic analysis of rat kidney cortex following treatment with gentamicin. J Proteome Res 1: 73–82

    PubMed  CAS  Google Scholar 

  109. Thongboonkerd V, Klein JB, Arthur JM (2003) Proteomic identification of a large complement of rat urinary proteins. Nephron Exp Nephrol 95: e69–78

    PubMed  CAS  Google Scholar 

  110. Cutler P, Bell DJ, Birrell HC, Connelly JC, Connor SC, Holmes E, Mitchell BC, Monte SY, Neville BA, Pickford R et al (1999) An integrated proteomic approach to studying glomerular nephrotoxicity. Electrophoresis 20: 3647–3658

    PubMed  CAS  Google Scholar 

  111. Crowe CA, Yong AC, Calder IC, Ham KN, Tange JD (1979) The nephrotoxicity of p-aminophenol. I. The effect on microsomal cytochromes, glutathione and covalent binding in kidney and liver. Chem Biol Interact 27: 235–243

    PubMed  CAS  Google Scholar 

  112. Kaltenbach JP, Carone FA, Ganote CE (1982) Compounds protective against renal tubular necrosis induced by D-serine and D-2,3-diaminopropionic acid in the rat. Exp Mol Pathol 37: 225–234

    PubMed  CAS  Google Scholar 

  113. Kuhlmann MK, Horsch E, Burkhardt G,Wagner M, Kohler H (1998) Reduction of cisplatin toxicity in cultured renal tubular cells by the bioflavonoid quercetin. Arch Toxicol 72: 536–540

    PubMed  CAS  Google Scholar 

  114. Bandara LR, Kelly MD, Lock EA, Kennedy S (2003) A correlation between a proteomic evaluation and conventional measurements in the assessment of renal proximal tubular toxicity. Toxicol Sci 73: 195–206

    PubMed  CAS  Google Scholar 

  115. Bandara LR, Kelly MD, Lock EA, Kennedy S (2003) A potential biomarker of kidney damage identified by proteomics: Preliminary findings. Biomarkers 8: 272–286

    PubMed  CAS  Google Scholar 

  116. Chen JC, Stevens JL, Trifillis AL, Jones TW (1990) Renal cysteine conjugate b-lyase-mediated toxicity studied with primary cultures of human proximal tubular cells. Toxicol Appl Pharmacol 103: 463–473

    PubMed  CAS  Google Scholar 

  117. Lash LH, Qian W, Putt DA, Hueni SE, Elfarra AA, Krause RJ, Parker JC (2001) Renal and hepatic toxicity of trichloroethylene and its glutathione-derived metabolites in rats and mice: Sex-, species-, and tissue-dependent differences. J Pharmacol Exp Ther 297: 155–164

    PubMed  CAS  Google Scholar 

  118. de Graauw M, Tijdens I, Cramer R, Corless S, Timms JF, van de Water B (2005) Heat shock protein 27 is the major differentially phosphorylated protein involved in renal epithelial cellular stress response and controls focal adhesion organization and apoptosis. J Biol Chem 280: 29885–29898

    PubMed  Google Scholar 

  119. de Graauw M, Le Devedec S, Tijdens I, Smeets MB, Deelder AM, van de Water B (2007) Proteomic analysis of alternative protein tyrosine phosphorylation in 1,2-dichlorovinyl-cysteineinduced cytotoxicity in primary cultured rat renal proximal tubular cells. J Pharmacol Exp Ther 322: 89–100

    PubMed  Google Scholar 

  120. Korrapati MC, Chilakapati J, Witzmann FA, Rao C, Lock EA, Mehendale HM (2007) Proteomics of S-(1,2-dichlorovinyl)-L-cysteine-induced acute renal failure and autoprotection in mice. Am J Physiol Renal Physiol 293: F994–F1006

    PubMed  CAS  Google Scholar 

  121. Vercauteren FG, Bergeron JJ, Vandesande F, Arckens L, Quirion R (2004) Proteomic approaches in brain research and neuropharmacology. Eur J Pharmacol 500: 385–398

    PubMed  CAS  Google Scholar 

  122. Sheta EA, Appel SH, Goldknopf IL (2006) 2D gel blood serum biomarkers reveal differential clinical proteomics of the neurodegenerative diseases. Expert Rev Proteomics 3: 45–62

    PubMed  CAS  Google Scholar 

  123. Merten KE, Feng W, Zhang L, Pierce W, Cai J, Klein JB, Kang YJ (2005) Modulation of cytochrome C oxidase-va is possibly involved in metallothionein protection from doxorubicin cardiotoxicity. J Pharmacol Exp Ther 315: 1314–1319

    PubMed  CAS  Google Scholar 

  124. Elased KM, Cool DR, Morris M (2005) Novel mass spectrometric methods for evaluation of plasma angiotensin converting enzyme 1 and renin activity. Hypertension 46: 953–959

    PubMed  CAS  Google Scholar 

  125. Yamamoto T, Fukushima T, Kikkawa R, Yamada H, Horii I (2005) Protein expression analysis of rat testes induced testicular toxicity with several reproductive toxicants. J Toxicol Sci 30: 111–126

    PubMed  CAS  Google Scholar 

  126. Yang YH, Xi ZG, Chao FH, Yang DF (2005) Effects of formaldehyde inhalation on lung of rats. Biomed Environ Sci 18: 164–168

    PubMed  CAS  Google Scholar 

  127. Wheelock AM, Boland BC, Isbell M, Morin D, Wegesser TC, Plopper CG, Buckpitt AR (2005) In vivo effects of ozone exposure on protein adduct formation by 1-nitronaphthalene in rat lung. Am J Respir Cell Mol Biol 33: 130–137

    Google Scholar 

  128. Wheelock AM, Zhang L, Tran MU, Morin D, Penn S, Buckpitt AR, Plopper CG (2004) Isolation of rodent airway epithelial cell proteins facilitates in vivo proteomics studies of lung toxicity. Am J Physiol Lung Cell Mol Physiol 286: L399–410

    PubMed  CAS  Google Scholar 

  129. Collins MO, Yu L, Husi H, Blackstock WP, Choudhary JS, Grant SG (2005) Robust enrichment of phosphorylated species in complex mixtures by sequential protein and peptide metal-affinity chromatography and analysis by tandem mass spectrometry. Sci STKE 2005: pl6

    Google Scholar 

  130. Kim SY, Chudapongse N, Lee SM, Levin MC, Oh JT, Park HJ, Ho IK (2004) Proteomic analysis of phosphotyrosyl proteins in the rat brain: Effect of butorphanol dependence. J Neurosci Res 77: 867–877

    PubMed  CAS  Google Scholar 

  131. Wang M, Xiao GG, Li N, Xie Y, Loo JA, Nel AE (2005) Use of a fluorescent phosphoprotein dye to characterize oxidative stress-induced signaling pathway components in macrophage and epithelial cultures exposed to diesel exhaust particle chemicals. Electrophoresis 26: 2092–2108

    PubMed  CAS  Google Scholar 

  132. Gagna CE, Winokur D, Clark Lambert W (2004) Cell biology, chemogenomics and chemoproteomics. Cell Biol Int 28: 755–764

    PubMed  CAS  Google Scholar 

  133. Beillard E, Witte ON (2005) Unraveling kinase signaling pathways with chemical genetic and chemical proteomic approaches. Cell Cycle 4: 434–437

    PubMed  CAS  Google Scholar 

  134. Gao J, Garulacan LA, Storm SM, Opiteck GJ, Dubaquie Y, Hefta SA, Dambach DM, Dongre AR (2005) Biomarker discovery in biological fluids. Methods 35: 291–302

    PubMed  CAS  Google Scholar 

  135. Merrick BA, Tomer KB (2003) Toxicoproteomics: A parallel approach to identifying biomarkers. Environ Health Perspect 111: A578–579

    PubMed  Google Scholar 

  136. Quackenbush J (2005) Extracting meaning from functional genomics experiments. Toxicol Appl Pharmacol 207: 195–199

    PubMed  Google Scholar 

  137. Fostel J, Choi D, Zwickl C, Morrison N, Rashid A, Hasan A, Bao W, Richard A, Tong W, Bushel PR et al (2005) Chemical effects in biological systems-data dictionary (CEBS-DD): A compendium of terms for the capture and integration of biological study design description, conventional phenotypes, and’ omics data. Toxicol Sci 88: 585–601

    PubMed  CAS  Google Scholar 

  138. Kristensen DB, Kawada N, Imamura K, Miyamoto Y, Tateno C, Seki S, Kuroki T, Yoshizato K (2000) Proteome analysis of rat hepatic stellate cells. Hepatology 32: 268–277

    PubMed  CAS  Google Scholar 

  139. Reinheckel T, Korn S, Mohring S, Augustin W, Halangk W, Schild L (2000) Adaptation of protein carbonyl detection to the requirements of proteome analysis demonstrated for hypoxia/reoxygenation in isolated rat liver mitochondria. Arch Biochem Biophys 376: 59–65

    PubMed  CAS  Google Scholar 

  140. Witzmann FA, Fultz CD, Grant RA, Wright LS, Kornguth SE, Siegel FL (1999) Regional protein alterations in rat kidneys induced by lead exposure. Electrophoresis 20: 943–951

    PubMed  CAS  Google Scholar 

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Merrick, B.A., Witzmann, F.A. (2009). The role of toxicoproteomics in assessing organ specific toxicity. In: Luch, A. (eds) Molecular, Clinical and Environmental Toxicology. Experientia Supplementum, vol 99. Birkhäuser Basel. https://doi.org/10.1007/978-3-7643-8336-7_13

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