146
Views
22
CrossRef citations to date
0
Altmetric
Review

Use of proteomics for the discovery of early markers of drug toxicity

, BSc MSc, , BSc PhD, , BSc PhD, , BSc PhD CBiol MlBiol & , BSc ARCS PhD
Pages 689-704 | Published online: 19 Oct 2007

Bibliography

  • KOLA I, LANDIS J: Can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discov. (2004) 3(8):711-715.
  • DIMASI JA, HANSEN RW, GRABOWSKI HG: The price of innovation: new estimates of drug development costs. J. Health Econ. (2003) 22(2):151-185.
  • WETMORE BA, MERRICK BA: Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol. Pathol. (2004) 32(6):619-642.
  • BANDARA LR, KENNEDY S: Toxicoproteomics – a new preclinical tool. Drug Discov. Today (2002) 7(7):411-418.
  • SINHA A, SINGH C, PARMAR D, SINGH MP: Proteomics in clinical interventions: achievements and limitations in biomarker development. Life Sci. (2007) 80(15):1345-1354.
  • KENNEDY S: The role of proteomics in toxicology: identification of biomarkers of toxicity by protein expression analysis. Biomarkers (2002) 7(4):269-290.
  • PARK BK, KITTERINGHAM NR, POWELL H, PIRMOHAMED M: Advances in molecular toxicology–towards understanding idiosyncratic drug toxicity. Toxicology (2000) 153(1-3):39-60.
  • PARK BK, KITTERINGHAM NR, MAGGS JL, PIRMOHAMED M, WILLIAMS DP: The role of metabolic activation in drug-induced hepatotoxicity. Annu. Rev. Pharmacol. Toxicol. (2005) 45:177-202.
  • AMACHER DE: Reactive intermediates and the pathogenesis of adverse drug reactions: the toxicology perspective. Curr. Drug Metab. (2006) 7(3):219-229.
  • GAO J, ANN GARULACAN L, STORM SM et al.: Identification of in vitro protein biomarkers of idiosyncratic liver toxicity. Toxicol. In Vitro (2004) 18(4):533-541.
  • TANG W: Drug metabolite profiling and elucidation of drug-induced hepatotoxicity. Expert Opin. Drug Metab. Toxicol. (2007) 3(3):407-420.
  • KROEGER M: How omics technologies can contribute to the ‘3R’ principles by introducing new strategies in animal testing. Trends Biotechnol. (2006) 24(8):343-346.
  • ELLINGER-ZIEGELBAUER H, STUART B, WAHLE B, BOMANN W, AHR HJ: Comparison of the expression profiles induced by genotoxic and nongenotoxic carcinogens in rat liver. Mutat. Res. (2005) 575(1-2):61-84.
  • HANASH S: Disease proteomics. Nature (2003) 422(6928):226-232.
  • THOME-KROMER B, BONK I, KLATT M et al.: Toward the identification of liver toxicity markers: a proteome study in human cell culture and rats. Proteomics (2003) 3(10):1835-1862.
  • MAN WJ, WHITE IR, BRYANT D et al.: Protein expression analysis of drug-mediated hepatotoxicity in the Sprague–Dawley rat. Proteomics (2002) 2(11):1577-1585.
  • MERRICK BA, MADENSPACHER JH: Complementary gene and protein expression studies and integrative approaches in toxicogenomics. Toxicol. Appl. Pharmacol. (2005) 207(2 Suppl.):189-194.
  • ANDERSON NL, COPPLE DC, BENDELE RA, PROBST GS, RICHARDSON FC: Covalent protein modifications and gene expression changes in rodent liver following administration of methapyrilene: a study using two-dimensional electrophoresis. Fundam. Appl. Toxicol. (1992) 18(4):570-580.
  • STEINER S, WITZMANN FA: Proteomics: applications and opportunities in preclinical drug development. Electrophoresis (2000) 21(11):2099-2104.
  • WU WW, WANG G, BAEK SJ, SHEN RF: Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res. (2006) 5(3):651-658.
  • ISHIHAMA Y: Proteomic LC-MS systems using nanoscale liquid chromatography with tandem mass spectrometry. J. Chromatogr. A. (2005) 1067(1-2):73-83.
  • AEBERSOLD R, MANN M: Mass spectrometry-based proteomics. Nature (2003) 422(6928):198-207.
  • LIN D, TABB DL, YATES Jr, III: Large-scale protein identification using mass spectrometry. Biochim. Biophys. Acta (2003) 1646(1-2):1-10.
  • KARAS M, HILLENKAMP F: Laser desorption ionization of proteins with molecular masses exceeding 10,000 daltons. Anal. Chem. (1988) 60(20):2299-2301.
  • FENN JB, MANN M, MENG CK, WONG SF, WHITEHOUSE CM: Electrospray ionization for mass spectrometry of large biomolecules. Science (1989) 246(4926):64-71.
  • SMITH RD: Trends in mass spectrometry instrumentation for proteomics. Trends Biotechnol. (2002) 20(12 Suppl.):S3-S7.
  • MENESES-LORENTE G, GUEST PC, LAWRENCE J et al.: A proteomic investigation of drug-induced steatosis in rat liver. Chem. Res. Toxicol. (2004) 17(5):605-612.
  • MENESES-LORENTE G, WATT A, SALIM K et al.: Identification of early proteomic markers for hepatic steatosis. Chem. Res. Toxicol. (2006) 19(8):986-998.
  • WIECKOWSKA A, ZEIN NN, YERIAN LM et al.: In vivo assessment of liver cell apoptosis as a novel biomarker of disease severity in nonalcoholic fatty liver disease. Hepatology (2006) 44(1):27-33.
  • KAPLOWITZ N: Drug-induced liver injury. Clin. Infect. Dis. (2004) 38(Suppl. 2):S44-S48.
  • RIFAI N, GILLETTE MA, CARR SA: Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. (2006) 24(8):971-983.
  • GORG A, WEISS W, DUNN MJ: Current two-dimensional electrophoresis technology for proteomics. Proteomics (2004) 4(12):3665-3685.
  • DUNN MJ: Quantitative two-dimensional gel electrophoresis: from proteins to proteomes. Biochem. Soc. Trans. (1997) 25(1):248-254.
  • YAMAMOTO T, KIKKAWA R, YAMADA H, HORII I: Identification of oxidative stress-related proteins for predictive screening of hepatotoxicity using a proteomic approach. J. Toxicol. Sci. (2005) 30(3):213-227.
  • KIKKAWA R, YAMAMOTO T, FUKUSHIMA T, YAMADA H, HORII I: 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. (2005) 30(1):61-72.
  • KIKKAWA R, FUJIKAWA M, YAMAMOTO T et al.: In vivo hepatotoxicity study of rats in comparison with in vitro hepatotoxicity screening system. J. Toxicol. Sci. (2006) 31(1):23-34.
  • AMACHER DE, ADLER R, HERATH A, TOWNSEND RR: Use of proteomic methods to identify serum biomarkers associated with rat liver toxicity or hypertrophy. Clin. Chem. (2005) 51(10):1796-1803.
  • KLENO TG, LEONARDSEN LR, KJELDAL HO et al.: Mechanisms of hydrazine toxicity in rat liver investigated by proteomics and multivariate data analysis. Proteomics (2004) 4(3):868-880.
  • KLENO TG, KIEHR B, BAUNSGAARD D, SIDELMANN UG: Combination of ‘omics’ data to investigate the mechanism(s) of hydrazine-induced hepatotoxicity in rats and to identify potential biomarkers. Biomarkers (2004) 9(2):116-138.
  • RUEPP SU, TONGE RP, SHAW J, WALLIS N, POGNAN F: Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol. Sci. (2002) 65(1):135-150.
  • TONGE R, SHAW J, MIDDLETON B et al.: Validation and development of fluorescence two-dimensional differential gel electrophoresis proteomics technology. Proteomics (2001) 1(3):377-396.
  • LOPEZ MF, MELOV S: Applied proteomics: mitochondrial proteins and effect on function. Circ. Res. (2002) 90(4):380-389.
  • ONG SE, MANN M: Mass spectrometry-based proteomics turns quantitative. Nat. Chem. Biol. (2005) 1(5):252-262.
  • GUPTA N, WOLLSCHEID B, WATTS JD et al.: Quantitative proteomic analysis of B cell lipid rafts reveals that ezrin regulates antigen receptor-mediated lipid raft dynamics. Nat. Immunol. (2006) 7(6):625-633.
  • WELCH KD, WEN B, GOODLETT DR et al.: Proteomic identification of potential susceptibility factors in drug-induced liver disease. Chem. Res. Toxicol. (2005) 18(6):924-933.
  • PROKAI L, ZHARIKOVA AD, STEVENS SM Jr: Effect of chronic morphine exposure on the synaptic plasma-membrane subproteome of rats: a quantitative protein profiling study based on isotope-coded affinity tags and liquid chromatography/mass spectrometry. J. Mass Spectrom. (2005) 40(2):169-175.
  • SARIOGLU H, BRANDNER S, JACOBSEN C et al.: Quantitative analysis of 2,3,7,8-tetrachlorodibenzop-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels. Proteomics (2006) 6(8):2407-2421.
  • ONG SE, KRATCHMAROVA I, MANN M: Properties of 13C-substituted arginine in stable isotope labeling by amino acids in cell culture (SILAC). J. Proteome Res. (2003) 2(2):173-181.
  • UNWIN RD, PIERCE A, WATSON RB, STERNBERG DW, WHETTON AD: Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol. Cell Proteomics (2005) 4(7):924-935.
  • ZIESKE LR: A perspective on the use of iTRAQ reagent technology for protein complex and profiling studies. J. Exp. Bot. (2006) 57(7):1501-1508.
  • MOTOYAMA A, VENABLE JD, RUSE CI, YATES Jr III: Automated ultra-high-pressure multidimensional protein identification technology (UHP-MudPIT) for improved peptide identification of proteomic samples. Anal. Chem. (2006 78(14):5109-5118.
  • KIRKPATRICK DS, GERBER SA, GYGI SP: The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods (2005) 35(3):265-273.
  • ANDERSON L, HUNTER CL: Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins. Mol. Cell Proteomics (2006) 5(4):573-588.
  • BEYNON RJ, DOHERTY MK, PRATT JM, GASKELL SJ: Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides. Nat. Methods (2005) 2(8):587-589.
  • PRATT JM, SIMPSON DM, DOHERTY MK et al.: Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes. Nat. Protoc. (2006) 1(2):1029-1043.
  • JENKINS RE, KITTERINGHAM NR, HUNTER CL et al.: Relative and absolute quantitative expression profiling of cytochromes P450 using isotope-coded affinity tags. Proteomics (2006) 6(6):1934-1947.
  • DE GROOT MJ: Designing better drugs: predicting cytochrome P450 metabolism. Drug Discov. Today (2006) 11(13-14):601-606.
  • SEIBERT V, WIESNER A, BUSCHMANN T, MEUER J: Surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI TOF-MS) and ProteinChip technology in proteomics research. Pathol. Res. Pract. (2004) 200(2):83-94.
  • DIAMANDIS EP: Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol. Cell Proteomics (2004) 3(4):367-378.
  • CHU R, ZHANG W, LIM H et al.: Profiling of acyl-CoA oxidase-deficient and peroxisome proliferator Wy14,643-treated mouse liver protein by surface-enhanced laser desorption/ionization ProteinChip biology system. Gene Expr. (2002) 10(4):165-177.
  • DARE TO, DAVIES HA, TURTON JA et al.: Application of surface-enhanced laser desorption/ionization technology to the detection and identification of urinary parvalbumin-α: a biomarker of compound-induced skeletal muscle toxicity in the rat. Electrophoresis (2002) 23(18):3241-3251.
  • CHAURAND P, CORNETT DS, CAPRIOLI RM: Molecular imaging of thin mammalian tissue sections by mass spectrometry. Curr. Opin. Biotechnol. (2006) 17(4):431-436.
  • MEISTERMANN H, NORRIS JL, AERNI HR et al.: Biomarker discovery by imaging mass spectrometry: transthyretin is a biomarker for gentamicin-induced nephrotoxicity in rat. Mol. Cell Proteomics (2006) 5(10):1876-1886.
  • CRAIG A, SIDAWAY J, HOLMES E et al.: Systems toxicology: integrated genomic, proteomic and metabonomic analysis of methapyrilene induced hepatotoxicity in the rat. J. Proteome Res. (2006) 5(7):1586-1601.
  • JOYCE AR, PALSSON BO: The model organism as a system: integrating ‘omics’ data sets. Nat. Rev. Mol. Cell Biol. (2006) 7(3):198-210.
  • WATERS MD, FOSTEL JM: Toxicogenomics and systems toxicology: aims and prospects. Nat. Rev. Genet. (2004) 5(12):936-948.
  • HEIJNE WH, KIENHUIS AS, VAN OMMEN B, STIERUM RH, GROTEN JP: Systems toxicology: applications of toxicogenomics, transcriptomics, proteomics and metabolomics in toxicology. Expert Rev. Proteomics (2005) 2(5):767-780.
  • FELLA K, GLUCKMANN M, HELLMANN J et al.: Use of two-dimensional gel electrophoresis in predictive toxicology: identification of potential early protein biomarkers in chemically induced hepatocarcinogenesis. Proteomics (2005) 5(7):1914-1927.
  • STEINER S, GATLIN CL, LENNON JJ et al.: Cholesterol biosynthesis regulation and protein changes in rat liver following treatment with fluvastatin. Toxicol. Lett. (2001) 120(1-3):369-377.
  • FOUNTOULAKIS M, BERNDT P, BOELSTERLI UA et al.: Two-dimensional database of mouse liver proteins: changes in hepatic protein levels following treatment with acetaminophen or its nontoxic regioisomer 3-acetamidophenol. Electrophoresis (2000) 21(11):2148-2161.
  • NEWSHOLME SJ, MALEEFF BF, STEINER S, ANDERSON NL, SCHWARTZ LW: Two-dimensional electrophoresis of liver proteins: characterization of a drug-induced hepatomegaly in rats. Electrophoresis (2000) 21(11):2122-2128.
  • STEINER S, GATLIN CL, LENNON JJ et al.: Proteomics to display lovastatin-induced protein and pathway regulation in rat liver. Electrophoresis (2000) 21(11):2129-2137.
  • LOW TY, LEOW CK, SALTO-TELLEZ M, CHUNG MC: A proteomic analysis of thioacetamide-induced hepatotoxicity and cirrhosis in rat livers. Proteomics (2004) 4(12):3960-3974.
  • IIDA M, ANNA CH, HARTIS J et al.: Changes in global gene and protein expression during early mouse liver carcinogenesis induced by non-genotoxic model carcinogens oxazepam and Wyeth-14,643. Carcinogenesis (2003) 24(4):757-770.
  • HEIJNE WH, STIERUM RH, SLIJPER M, VAN BLADEREN PJ, VAN OMMEN B: Toxicogenomics of bromobenzene hepatotoxicity: a combined transcriptomics and proteomics approach. Biochem. Pharmacol. (2003) 65(5):857-875.
  • WHITE IR, MAN WJ, BRYANT D et al.: Protein expression changes in the Sprague Dawley rat liver proteome following administration of peroxisome proliferator activated receptor α and Γ ligands. Proteomics (2003) 3(4):505-512.
  • BANDARA LR, KELLY MD, LOCK EA, KENNEDY S: A potential biomarker of kidney damage identified by proteomics: preliminary findings. Biomarkers (2003) 8(3-4):272-286.
  • BANDARA LR, KELLY MD, LOCK EA, KENNEDY S: A correlation between a proteomic evaluation and conventional measurements in the assessment of renal proximal tubular toxicity. Toxicol. Sci. (2003) 73(1):195-206.
  • CHARLWOOD J, SKEHEL JM, KING N et al.: Proteomic analysis of rat kidney cortex following treatment with gentamicin. J. Proteome Res. (2002) 1(1):73-82.
  • CUTLER P, BELL DJ, BIRRELL HC et al.: An integrated proteomic approach to studying glomerular nephrotoxicity. Electrophoresis (1999) 20(18):3647-3658.
  • LIAO PC, KUO YM, HSU HC, CHERNG CG, YU L: Local proteins associated with methamphetamine-induced nigrostriatal dopaminergic neurotoxicity. J. Neurochem. (2005) 95(1):160-168.
  • YAMAMOTO T, FUKUSHIMA T, KIKKAWA R, YAMADA H, HORII I: Protein expression analysis of rat testes induced testicular toxicity with several reproductive toxicants. J. Toxicol. Sci. (2005) 30(2):111-126.
  • MERRICK BA, BRUNO ME, MADENSPACHER JH et al.: Alterations in the rat serum proteome during liver injury from acetaminophen exposure. J. Pharmacol. Exp. Ther. (2006) 318(2):792-802.
  • VENKATRAMAN A, LANDAR A, DAVIS AJ et al.: Modification of the mitochondrial proteome in response to the stress of ethanol-dependent hepatotoxicity. J. Biol. Chem. (2004) 279(21):22092-22101.
  • LANTZ RC, LYNCH BJ, BOITANO S et al.: Pulmonary biomarkers based on alterations in protein expression after exposure to arsenic. Environ. Health Perspect. (2007) 115(4):586-591.
  • PAWELETZ CP, WIENER MC, SACHS JR et al.: Surface enhanced laser desorption ionization spectrometry reveals biomarkers for drug treatment but not dose. Proteomics (2006) 6(7):2101-2107.
  • BEYER S, WALTER Y, HELLMANN J et al.: Comparison of software tools to improve the detection of carcinogen induced changes in the rat liver proteome by analyzing SELDI-TOF-MS spectra. J. Proteome Res. (2006) 5(2):254-261.
  • IZZOTTI A, BAGNASCO M, CARTIGLIA C, LONGOBARDI M, DE FLORA S: Proteomic analysis as related to transcriptome data in the lung of chromium(VI)-treated rats. Int. J. Oncol. (2004) 24(6):1513-1522.
  • KIM BJ, HOOD BL, ARAGON RA et al.: Increased oxidation and degradation of cytosolic proteins in alcohol-exposed mouse liver and hepatoma cells. Proteomics (2006) 6(4):1250-1260.
  • PRAT O, BERENGUER F, MALARD V et al.: Transcriptomic and proteomic responses of human renal HEK293 cells to uranium toxicity. Proteomics (2005) 5(1):297-306.
  • MELONI BP, VAN DYK D, COLE R, KNUCKEY NW: Proteome analysis of cortical neuronal cultures following cycloheximide, heat stress and MK801 preconditioning. Proteomics (2005) 5(18):4743-4753.
  • MANIRATANACHOTE R, MINAMI K, KATOH M, NAKAJIMA M, YOKOI T: Dephosphorylation of ribosomal protein P0 in response to troglitazone-induced cytotoxicity. Toxicol. Lett. (2006) 166(3):189-199.
  • SARIOGLU H, BRANDNER S, JACOBSEN C et al.: Quantitative analysis of 2,3,7,8-tetrachlorodibenzop-dioxin-induced proteome alterations in 5L rat hepatoma cells using isotope-coded protein labels. Proteomics (2006) 6(8):2407-2421.

Websites

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.