177
Views
19
CrossRef citations to date
0
Altmetric
Review

Genomic and proteomic approaches for predicting toxicity and adverse drug reactions

&
Pages 29-37 | Published online: 23 Dec 2008

Bibliography

  • Mullin R. Drug development costs about $1.7 Billion. Chem Eng News 2003;81:8
  • Cunningham MJ. Genomics and proteomics: the new millennium of drug discovery and development. J Pharmacol Toxicol Methods 2000;44:291-300
  • Kennedy T. Managing the drug discovery/development interface. Drug Discov Today 1997;2:436-44
  • Yap CW, Cai CZ, Xue Y, et al. Prediction of torsade causing potential of drugs by support vector machine approach. Toxicol Sci 2004;79:170-7
  • Schneeweiss S, Hasford J, Göttler M, et al. Admissions caused by adverse drug events to internal medicine and emergency departments in hospitals: a longitudinal population-based study. Eur J Clin Pharmacol 2002;58:285-91
  • Pirmohamed M, James S, Meakin S, et al. Adverse drug reactions as cause of admission to hospital: prospective analysis of 18,820. patients BMJ 2004;329:15-9
  • Mjörndal T, Boman MD, Hägg S, et al. Adverse drug reactions as a cause for admissions to a department of internal medicine. Pharmacoepidemiol Drug Saf 2002;11:65-72
  • Lazarou J, Pomeranz BH, Corey PN. Incidence of adverse drug reactions in hospitalized patients: a meta-analysis of prospective studies. JAMA 1998;279:1200-5
  • Ernst FR, Grizzle AJ. Drug-related morbidity and mortality: updating the cost-of-illness model. J Am Pharm Assoc 2001;41:192-9
  • Lee PS, Lee KH. Genomic analysis. Curr Opin Biotechnol 2000;11:171-5
  • Aardema MJ, MacGregor JT. Toxicology and genetic toxicology in the new era of ‘toxicogenomics’: impact of ‘omics’ technologies. Mutat Res 2002;499:13-25
  • Urich R, Friend SH. Toxicogenomics and drug discovery: will new technologies help us produce better drugs? Nat Rev Drug Discov 2002;1:84-88
  • Nuwaysir EF, Bittner M, Trent J, et al. Microarrays and toxicology: the advent of toxicogenomics. Mol Carcinog 1999;24:153-159
  • Delongueville F, Bertholet V, Remacle J. DNA microarrays as a tool in toxicogenomics. Comb Chem High Throughput Screen 2004;7:207-211
  • Cooper CS. Applications of microarray technology in breast cancer research. Br Cancer Res 20013:158175
  • Lord PG. Progress in applying genomics in drug development. Toxicol Lett 2004;149:371-5
  • Bulera SJ, Eddy SM, Ferguson E, et al. RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology 2001;33:1239-58
  • Gerhold D, Lu M, XU J, et al. Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol Genomics 2001;5:161-70
  • Waring JF, Jolly RA, Ciurlionis R, et al. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol Appl Pharmacol 2001;175:28-42
  • Waring JF, Ciurlionis R, Jolly RA, et al. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 2001;120:359-68
  • Hamadeh HK, Bushel PR, Jayadev S, et al. Gene expression analysis reveals chemical specific profiles. Toxicol Sci 2002;67:219-31
  • Hamadeh HK, Bushel PR, Jayadev S, et al. Prediction of compound signature using high density gene expression profiling. Toxicol Sci 2002;67:232-240
  • McMillian M, Nie A, Parker JB, et al. Drug-induced oxidative stress in rat liver from a toxicogenomic perspective. Toxicol Appl Pharmacol 2005;207:S171-8
  • Hughes TR, Marton MJ, Jones AR, et al. Functional discovery via a compendium of expression profiles. Cell 2000;102:109-126
  • Mattingly CJ, Rosentein MC, Davis AP, et al. The Comparative Toxicogenomics Database: A cross-species resource for building chemical-gene interaction networks. Toxicol Sci 2006;92:587-95
  • Hayes KR, Vollrath AL, Zastrow GM, et al. EDGE: a centralized resource for the comparison, analysis, and distribution of toxicogenomic information. Mol Pharmacol 2005;67:1360-1368
  • Waters M, Stasiewicz S, Merrick BA, et al. Cebs-Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. Nucleic Acids Res 2008;36:D892-900
  • Hultin-Rosenberg L, Jagannathan S, Nilsson KC, et al. Predictive models of hepatotoxicity using gene expression data from primary rat hepatocytes. Xenobiotica 2006;36:112239
  • Leone AM, Kao LM, McMillian MK, et al. Evaluation of felbamate and other antiepileptic drug toxicity potential based on hepatic protein covalent binding and gene expression. Chem Res Toxicol 2007;20:600-8
  • Martin R, Rose D, Yu K, et al. Toxicogenomics strategies for predicting drug toxicity. Pharmacogenomics 2006;7:1003-16
  • Coe KJ, Nelson SD, Ulrich RG, et al. Profiling the hepatic effects of flutamide in rats: a microarray comparison with classical AhR ligands and atypical CYP1A inducers. Drug Metab Dispos 2006;34:1266-75
  • Ekins S, Kirillov E, Rakhmatulin EA, et al. A novel method for visualizing nuclear hormone receptor networks relevant to drug metabolism. Drug Metab Dispos 2005;33:474-81
  • Yoon BI, Li GX, Kitada K, et al. Mechanisms of benzene-induced hematotoxicity and leukemogenicity: cDNA microarray analyses using mouse bone marrow tissue. Environ Health Perspect 2003;111:1411-20
  • Kramer JA, Curtiss SW, Kolaja KL, et al. Acute Molecular markers of rodent hepatic carcinogenesis identified by transcription profiling. Chem Res Toxicol 2004;17:463-70
  • Eun JW, Ryu SY, Noh JH, et al. Discriminating the molecular basis of hepatotoxicity using the large-scale characteristic molecular signatures of toxicants by expression profiling analysis. Toxicology 2008;249:176-83
  • Sawada H, Takami K, Asahi S. A toxicogenomic approach to drug-induced phospholipidosis: analysis of its induction mechanism and establishment of a novel in vitro screening system. Toxicol Sci 2005;83:282-292
  • Cunningham ML, Lehman-McKeeman L. Applying toxicogenomics in mechanistic and predictive toxicology. Toxicol Sci 2005;83:205-206
  • Oberemm A, Onyon L, Gundert-Remy U. How can toxicogenomics inform risk assessment? Toxicol Appl Pharmacol 2005;207:5928
  • Boverhof DR, Zacharewski TR. Toxicogenomics in risk assessment: application and needs. Toxicol Sci 2006;89:352-60
  • Wetmore BA, Merrick BA. Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol Pathol 2004;32:619-42
  • Kruse U, Bantscheff M, Drewes G, et al. Chemical and pathway proteomics: Powerful tools for oncology drug discovery and personalized health care. Mol Cell Proteomics 2008;7:1887-901 [Epub ahead of print]
  • Steen H, Mann M. The ABC's (and XYZ's) of peptide sequencing. Nat Rev Mol Cell Biol 2004;5:699-711
  • Rozanas CR, Loyland SM. Capabilities using 2-D DIGE in proteomics research: the new gold standard for 2-D gel electrophoresis. Methods Mol Biol 2008;441:1-18
  • Villanueva J, Philip J, Chaparro CA, et al. Correcting common errors in identifying cancer-specific serum peptide signatures. J Proteome Res 2005;4:1060-72
  • Chaurand P, Schwartz SA, Reyzer ML, et al. Imaging mass spectrometry: principles and potentials. Toxicol Pathol 2005;33:92-101
  • Washburn MP, Wolters D, Yates, JR. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 2001;19:242-7
  • Shiio Y, Aebersold R. Quantitative proteome analysis using isotope-coded affinity tags and mass spectrometry. Nat Protoc 2006;1:139-145
  • Han DK, Eng J, Zhou H, Aebersold R. Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry. Nat Biotechnol 2001;19:946-51
  • Bantscheff M, Schirle M, Sweetman G, et al. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem 2007;389:1017-31
  • Thompson A, Schäfer J, Kuhn K, et al. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem 2003;75:1895-904
  • Wiese S, Reidegeld KA, Meyer HE, et al. Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 2007;7:340-50
  • Choe L, D'ascenzo M, Relkin NR, et al. 8-plex quantitation of changes in cerebrospinal fluid protein expression in subjects undergoing intravenous immunoglobulin treatment for Alzheimer's disease. Proteomics 2007;7:3651-60
  • Dayon L, Hainard A, Licker V, et al. Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags. Anal Chem 2008;80:2921-31
  • Issaq HJ, Conrads TP, Prieto DA, et al. Seldi-Tof MS for diagnostic proteomics. Anal Chem 2003;75:148A-55A
  • Diamandis EP. Mass spectrometry as a diagnostic and a cancer biomarker discovery tool: opportunities and potential limitations. Mol Cell Proteomics 2004;3:367-78
  • Semmes OJ, Feng Z, Adam BL, et al. Evaluation of serum protein profiling by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry for the detection of prostate cancer: I. Assessment of platform reproducibility. Clin Chem 2005;51:102-112
  • Sydor JR, Nock S. Protein expression profiling arrays: tools for the multiplexed high-throughput analysis of proteins. Proteome Sci 2003;1:3
  • Figeys D. Adapting arrays and lab-on-a-chip technology for proteomics. Proteomics 2002;2:373-82
  • Phizicky E, Bastiaens PI, Zhu H, et al. Protein analysis on a proteomic scale. Nature 2003;422:20815
  • Wilson DS, Nock S. Recent developments in protein microarray technology. Angew Chem Int Ed Engl 2003;42:494500
  • Lee Y, Lee EK, Cho YW, et al. ProteoChip: a highly sensitive protein microarray prepared by a novel method of protein immobilization for application of protein–protein interaction studies. Proteomics 2003;3:2289-2304
  • Phelan ML, Nock S. Generation of bioreagents for protein chips. Proteomics 2003;3:2123-2134
  • Cutler P. Protein arrays: the current state-of-the-art. Proteomics 2003;3:3-18
  • Chevalier S, Macdonald N, Tonge R, et al. Proteomic analysis of differential protein expression in primary hepatocytes induced by EGF, tumor necrosis factor or the peroxisome proliferators nafenopin. Eur J Biochem 2000;267:4624-4634
  • Collins BC, Clarke A, Kitteringham NR, et al. Use of proteomics for the discovery of early markers of drug toxicity. Expert Opin Drug Metab Toxicol 2007;3:689-704
  • Petricoin EF, Rajapaske V, Herman EH, et al. Toxicoproteomics: serum proteomic pattern diagnostics for early detection of drug induced cardiac toxicities and cardioprotection. Toxicol. Pathol 2004;32:122-30
  • Merrick BA, Bruno ME. Genomic and proteomic profiling for biomarkers and signature profiles of toxicity. Curr Opin Mol Ther 2004;6:600-7
  • Kennedy S. The role of proteomics in toxicology: identification of biomarkers of toxicity by protein expression analysis. Biomarkers 2002;7:269-290
  • Merrick BA, Tomer KB. Toxicoproteomics: A parallel approach to identifying biomarkers. Environ Health Perspect 2003;111:578-579
  • Wang Y, Cheung YH, Yang Z, et al. Proteomic approach to study the cytotoxicity of dioscin (saponin). Proteomics 2006;6:2422-32
  • Wang Y, Chiu JF, He QY. Proteomics approach to illustrate drug action mechanisms. Curr Drug Discov Technol 2006;3:199-209
  • Lei T, He QY, Cai Z, et al. Proteomic analysis of chromium cytotoxicity in cultured rat lung epithelial cells. Proteomics 2008;8:2420-9
  • Meneses-Lorente G, Watt A, Salim K, et al. Identification of early proteomic markers for hepatic steatosis. Chem Res Toxicol 2006;19:986-98
  • Gao J, Garulacan LA, Storm SM, et al. Identification of in vitro protein biomarkers of idiosyncratic liver toxicity. Toxicol In Vitro 2004;18:533-541
  • 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;31:23-34
  • Mian S, Ball G, Hornbuckle J, et al. A prototype methodology combining surface-enhanced laser desorption/ionization protein chip technology and artificial neural network algorithms to predict the chemoresponsiveness of breast cancer cell lines exposed to Paclitaxel and Doxorubicin under in vitro conditions. Proteomics 2003;3:1725-37
  • Anderson NL, Taylor J, Hofmann JP, et al. Simultaneous measurement of hundreds of liver proteins: application in assessment of liver function. Toxicol Pathol 1996;24:72-6
  • Weinstein JN, Myers TG, O'Connor PM. An information-intensive approach to the molecular pharmacology of cancer. Science 1997;275:343-9
  • Fang X, Shao L, Zhang H, et al. Web-based tools for mining the NCI databases for anticancer drug discovery. J Chem Inf Comput Sci 2004;44:249-57
  • Wysowski DK, Swartz L. Adverse drug event surveillance and drug withdrawals in the United States, 1969-2002: the importance of reporting suspected reactions. Arch. Intern Med 2005;165:1363-9

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.