Advertisement

The role of toxicoproteomics in assessing organ specific toxicity

  • B. Alex Merrick
  • Frank A. Witzmann
Part of the Experientia Supplementum book series (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.

Keywords

Select Reaction Monitoring Shotgun Proteomics Preclinical Species Major Urinary Protein Preclinical Assessment 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 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: 413–422PubMedGoogle Scholar
  2. 2.
    Leighton JK (2005) Application of emerging technologies in toxicology and safety assessment: Regulatory perspectives. Int J Toxicol 24: 153–155PubMedGoogle Scholar
  3. 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: S29–41PubMedGoogle Scholar
  4. 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: 1–22PubMedGoogle Scholar
  5. 5.
    Bandara LR, Kennedy S (2002) Toxicoproteomics-A new preclinical tool. Drug Discov Today 7: 411–418PubMedGoogle Scholar
  6. 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: 122–130Google Scholar
  7. 7.
    Wetmore BA, Merrick BA (2004) Toxicoproteomics: Proteomics applied to toxicology and pathology. Toxicol Pathol 32: 619–642PubMedGoogle Scholar
  8. 8.
    Waters MD, Fostel JM (2004) Toxicogenomics and systems toxicology: Aims and prospects. Nat Rev Genet 5: 936–948PubMedGoogle Scholar
  9. 9.
    Turner SM (2006) Stable isotopes, mass spectrometry, and molecular fluxes: Applications to toxicology. J Pharmacol Toxicol Methods 53: 75–85PubMedGoogle Scholar
  10. 10.
    Merrick BA, Bruno ME (2004) Genomic and proteomic profiling for biomarkers and signature profiles of toxicity. Curr Opin Mol Ther 6: 600–607PubMedGoogle Scholar
  11. 11.
    Silbergeld EK, Davis DL (1994) Role of biomarkers in identifying and understanding environmentally induced disease. Clin Chem 40: 1363–1367PubMedGoogle Scholar
  12. 12.
    Hood L, Heath JR, Phelps ME, Lin B (2004) Systems biology and new technologies enable predictive and preventative medicine. Science 306: 640–643PubMedGoogle Scholar
  13. 13.
    Lin J, Qian J (2007) Systems biology approach to integrative comparative genomics. Expert Rev Proteomics 4: 107–119PubMedGoogle Scholar
  14. 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: 181–184PubMedGoogle Scholar
  15. 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: 277–295PubMedGoogle Scholar
  16. 16.
    MacGregor JT (2003) The future of regulatory toxicology: Impact of the biotechnology revolution. Toxicol Sci 75: 236–248PubMedGoogle Scholar
  17. 17.
    Hackett JL, Gutman SI (2005) Introduction to the Food and Drug Administration (FDA) regulatory process. J Proteome Res 4: 1110–1113PubMedGoogle Scholar
  18. 18.
    Yeh ET (2005) High-sensitivity C-reactive protein as a risk assessment tool for cardiovascular disease. Clin Cardiol 28: 408–412PubMedGoogle Scholar
  19. 19.
    Amacher DE (2002) A toxicologist’s guide to biomarkers of hepatic response. Hum Exp Toxicol 21: 253–262PubMedGoogle Scholar
  20. 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: 307–325PubMedGoogle Scholar
  21. 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: 149–171PubMedGoogle Scholar
  22. 22.
    Bilello JA (2005) The agony and ecstasy of “OMIC” technologies in drug development. Curr Mol Med 5: 39–52PubMedGoogle Scholar
  23. 23.
    Koop R (2005) Combinatorial biomarkers: From early toxicology assays to patient population profiling. Drug Discov Today 10: 781–788PubMedGoogle Scholar
  24. 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, 263–281Google Scholar
  25. 25.
    Merrick BA, Madenspacher JH (2005) Complementary gene and protein expression studies and integrative approaches in toxicogenomics. Toxicol Appl Pharmacol 207: 189–194PubMedGoogle Scholar
  26. 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: 3–17PubMedGoogle Scholar
  27. 27.
    Freeman WM, Hemby SE (2004) Proteomics for protein expression profiling in neuroscience. Neurochem Res 29: 1065–1081PubMedGoogle Scholar
  28. 28.
    Yates JR (2004) Mass spectral analysis in proteomics. Annu Rev Biophys Biomol Struct 33: 297–316PubMedGoogle Scholar
  29. 29.
    Bhat VB, Choi MH, Wishnok JS, Tannenbaum SR (2005) Comparative plasma proteome analysis of lymphoma-bearing SJL mice. J Proteome Res 4: 1814–1825PubMedGoogle Scholar
  30. 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: 1132–1139PubMedGoogle Scholar
  31. 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: 415–424PubMedGoogle Scholar
  32. 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: 994–999PubMedGoogle Scholar
  33. 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: 1442–1450PubMedGoogle Scholar
  34. 34.
    Colinge J, Chiappe D, Lagache S, Moniatte M, Bougueleret L (2005) Differential proteomics via probabilistic peptide identification scores. Anal Chem 77: 596–606PubMedGoogle Scholar
  35. 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: 4193–4201PubMedGoogle Scholar
  36. 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: 18928–18933PubMedGoogle Scholar
  37. 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: 2339–2347PubMedGoogle Scholar
  38. 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: 6940–6945PubMedGoogle Scholar
  39. 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: 265–273PubMedGoogle Scholar
  40. 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: 1487–1502PubMedGoogle Scholar
  41. 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: 246–263Google Scholar
  42. 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–A477Google Scholar
  43. 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: 102Google Scholar
  44. 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: 303–311PubMedGoogle Scholar
  45. 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: 1454–1459PubMedGoogle Scholar
  46. 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: 2176–2185PubMedGoogle Scholar
  47. 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: 18–26PubMedGoogle Scholar
  48. 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: 986–990PubMedGoogle Scholar
  49. 49.
    Petricoin E,Wulfkuhle J, Espina V, Liotta LA (2004) Clinical proteomics: Revolutionizing disease detection and patient tailoring therapy. J Proteome Res 3: 209–217PubMedGoogle Scholar
  50. 50.
    Issaq HJ, Conrads TP, Prieto DA, Tirumalai R, Veenstra TD (2003) SELDI-ToF MS for diagnostic proteomics. Anal Chem 75: 148A–155APubMedGoogle Scholar
  51. 51.
    Diamandis EP (2004) Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: Opportunities and potential limitations. Mol Cell Proteomics 3: 367–378PubMedGoogle Scholar
  52. 52.
    Cutler P (2003) Protein arrays: The current state-of-the-art. Proteomics 3: 3–18PubMedGoogle Scholar
  53. 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: 177–202PubMedGoogle Scholar
  54. 54.
    Kaplowitz N (2004) Drug-induced liver injury. Clin Infect Dis 38 Suppl 2: S44–48Google Scholar
  55. 55.
    Maddrey WC (2005) Drug-induced hepatotoxicity: 2005. J Clin Gastroenterol 39: S83–89PubMedGoogle Scholar
  56. 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: 161–225PubMedGoogle Scholar
  57. 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: 1236–1248PubMedGoogle Scholar
  58. 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: 1170–1179PubMedGoogle Scholar
  59. 59.
    Amacher DE (2005) Drug-associated mitochondrial toxicity and its detection. Curr Med Chem 12: 1829–1839PubMedGoogle Scholar
  60. 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: 1760–1774PubMedGoogle Scholar
  61. 61.
    Laskin DL, Laskin JD (2001) Role of macrophages and inflammatory mediators in chemically induced toxicity. Toxicology 160: 111–118PubMedGoogle Scholar
  62. 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: 1165–1171PubMedGoogle Scholar
  63. 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: 59–67PubMedGoogle Scholar
  64. 64.
    Ito Y, Bethea NW, Abril ER, McCuskey RS (2003) Early hepatic microvascular injury in response to acetaminophen toxicity. Microcirculation 10: 391–400PubMedGoogle Scholar
  65. 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: 2148–2161PubMedGoogle Scholar
  66. 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: 377–396PubMedGoogle Scholar
  67. 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: 135–150PubMedGoogle Scholar
  68. 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: 1835–1862PubMedGoogle Scholar
  69. 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: 61–72PubMedGoogle Scholar
  70. 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: 213–227PubMedGoogle Scholar
  71. 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: 924–933PubMedGoogle Scholar
  72. 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: 101–110PubMedGoogle Scholar
  73. 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: 105–136PubMedGoogle Scholar
  74. 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: 563–566PubMedGoogle Scholar
  75. 75.
    Nelson SD (1995) Mechanisms of the formation and disposition of reactive metabolites that can cause acute liver injury. Drug Metab Rev 27: 147–177PubMedGoogle Scholar
  76. 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: 857–875PubMedGoogle Scholar
  77. 77.
    Staels B, Fruchart JC (2005) Therapeutic roles of peroxisome proliferator-activated receptor agonists. Diabetes 54: 2460–2470PubMedGoogle Scholar
  78. 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: 757–770PubMedGoogle Scholar
  79. 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: 468–478PubMedGoogle Scholar
  80. 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: 318–332PubMedGoogle Scholar
  81. 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: 116–138PubMedGoogle Scholar
  82. 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: 868–880PubMedGoogle Scholar
  83. 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: 1877–1885PubMedGoogle Scholar
  84. 84.
    Low TY, Leow CK, Salto-Tellez M, Chung MC (2004) A proteomic analysis of thioacetamideinduced hepatotoxicity and cirrhosis in rat livers. Proteomics 4: 3960–3974PubMedGoogle Scholar
  85. 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: 3235–3245PubMedGoogle Scholar
  86. 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: 25318–25323PubMedGoogle Scholar
  87. 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: 3226–3245PubMedGoogle Scholar
  88. 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: 3506–3519PubMedGoogle Scholar
  89. 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: 3055–3065PubMedGoogle Scholar
  90. 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: 107–130PubMedGoogle Scholar
  91. 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: 3991–4000PubMedGoogle Scholar
  92. 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: 4245–4253PubMedGoogle Scholar
  93. 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: 1796–1803PubMedGoogle Scholar
  94. 94.
    Witzmann FA, Li J (2004) Proteomics and nephrotoxicity. Contrib Nephrol 141: 104–123PubMedGoogle Scholar
  95. 95.
    Davis JW, Kramer JA (2006) Genomic-based biomarkers of drug-induced nephrotoxicity. Expert Opin Drug Metab Toxicol 2: 95–101PubMedGoogle Scholar
  96. 96.
    Janech MG, Raymond JR, Arthur JM (2007) Proteomics in renal research. Am J Physiol Renal Physiol 292: F501–512PubMedGoogle Scholar
  97. 97.
    Mihatsch MJ, Thiel G, Ryffel B (1989) Cyclosporin A: Action and side-effects. Toxicol Lett 46: 125–139PubMedGoogle Scholar
  98. 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: 1273–1283PubMedGoogle Scholar
  99. 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: 253–258PubMedGoogle Scholar
  100. 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: 2055–2061PubMedGoogle Scholar
  101. 101.
    Serkova N, Christians U (2003) Transplantation: Toxicokinetics and mechanisms of toxicity of cyclosporine and macrolides. Curr Opin Investig Drugs 4: 1287–1296PubMedGoogle Scholar
  102. 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: 340–348PubMedGoogle Scholar
  103. 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: 10556–10563PubMedGoogle Scholar
  104. 104.
    Guan N, Ding J, Deng J, Zhang J, Yang J (2004) Key molecular events in puromycin aminonucleoside nephrosis rats. Pathol Int 54: 703–711PubMedGoogle Scholar
  105. 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: C1309–1318PubMedGoogle Scholar
  106. 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: 2491–2497PubMedGoogle Scholar
  107. 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: 2819–2838PubMedGoogle Scholar
  108. 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: 73–82PubMedGoogle Scholar
  109. 109.
    Thongboonkerd V, Klein JB, Arthur JM (2003) Proteomic identification of a large complement of rat urinary proteins. Nephron Exp Nephrol 95: e69–78PubMedGoogle Scholar
  110. 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: 3647–3658PubMedGoogle Scholar
  111. 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: 235–243PubMedGoogle Scholar
  112. 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: 225–234PubMedGoogle Scholar
  113. 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: 536–540PubMedGoogle Scholar
  114. 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: 195–206PubMedGoogle Scholar
  115. 115.
    Bandara LR, Kelly MD, Lock EA, Kennedy S (2003) A potential biomarker of kidney damage identified by proteomics: Preliminary findings. Biomarkers 8: 272–286PubMedGoogle Scholar
  116. 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: 463–473PubMedGoogle Scholar
  117. 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: 155–164PubMedGoogle Scholar
  118. 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: 29885–29898PubMedGoogle Scholar
  119. 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: 89–100PubMedGoogle Scholar
  120. 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–F1006PubMedGoogle Scholar
  121. 121.
    Vercauteren FG, Bergeron JJ, Vandesande F, Arckens L, Quirion R (2004) Proteomic approaches in brain research and neuropharmacology. Eur J Pharmacol 500: 385–398PubMedGoogle Scholar
  122. 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: 45–62PubMedGoogle Scholar
  123. 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: 1314–1319PubMedGoogle Scholar
  124. 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: 953–959PubMedGoogle Scholar
  125. 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: 111–126PubMedGoogle Scholar
  126. 126.
    Yang YH, Xi ZG, Chao FH, Yang DF (2005) Effects of formaldehyde inhalation on lung of rats. Biomed Environ Sci 18: 164–168PubMedGoogle Scholar
  127. 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: 130–137Google Scholar
  128. 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: L399–410PubMedGoogle Scholar
  129. 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: pl6Google Scholar
  130. 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: 867–877PubMedGoogle Scholar
  131. 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: 2092–2108PubMedGoogle Scholar
  132. 132.
    Gagna CE, Winokur D, Clark Lambert W (2004) Cell biology, chemogenomics and chemoproteomics. Cell Biol Int 28: 755–764PubMedGoogle Scholar
  133. 133.
    Beillard E, Witte ON (2005) Unraveling kinase signaling pathways with chemical genetic and chemical proteomic approaches. Cell Cycle 4: 434–437PubMedGoogle Scholar
  134. 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: 291–302PubMedGoogle Scholar
  135. 135.
    Merrick BA, Tomer KB (2003) Toxicoproteomics: A parallel approach to identifying biomarkers. Environ Health Perspect 111: A578–579PubMedGoogle Scholar
  136. 136.
    Quackenbush J (2005) Extracting meaning from functional genomics experiments. Toxicol Appl Pharmacol 207: 195–199PubMedGoogle Scholar
  137. 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: 585–601PubMedGoogle Scholar
  138. 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: 268–277PubMedGoogle Scholar
  139. 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: 59–65PubMedGoogle Scholar
  140. 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: 943–951PubMedGoogle Scholar

Copyright information

© Birkhäuser Verlag/Switzerland 2009

Authors and Affiliations

  • B. Alex Merrick
    • 1
  • Frank A. Witzmann
    • 2
  1. 1.National Institute of Environmental Health Sciences (NIEHS)Research Triangle ParkUSA
  2. 2.Indiana University School of MedicineIndianapolisUSA

Personalised recommendations