Current status and future prospects of toxicogenomics in drug discovery

Drug Discovery Today

Volumn 19, Issue 5, 2014, Pages 562-578

  Khan, Saifur R ^a   Baghdasarian, Argishti ^a   Fahlman, Richard P ^a   Michail, Karim ^a,b   Siraki, Arno G ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

^b Alexandria University Faculty of Pharmacy   (Egypt)

Author keywords

[No Author keywords available]

Indexed keywords

MICRORNA; NEW DRUG;

BIOINFORMATICS; DRUG APPROVAL; DRUG RESEARCH; EPIGENETICS; GENE EXPRESSION; GENOMICS; ORGANISMS; PATIENT SAFETY; PROTEOMICS; REVIEW; TOXICOGENETICS; ANIMAL; CLINICAL TRIAL (TOPIC); DRUG DEVELOPMENT; FORECASTING; HUMAN; PROCEDURES; TRENDS;

ANIMALS; CLINICAL TRIALS AS TOPIC; DRUG DISCOVERY; FORECASTING; HUMANS; TOXICOGENETICS;

EID: 84901486398     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2013.11.001     Document Type: Review

References (128)

1. K.E. Lasser et al. Timing of new black box warnings and withdrawals for prescription medications J. Am. Med. Assoc. 287 2002 2215 2220
2. S.M. Paul et al. How to improve R&D productivity: the pharmaceutical industry's grand challenge Nat. Rev. Drug Discov. 2010
3. M.D. Waters, and J.M. Fostel Toxicogenomics and systems toxicology: aims and prospects Nat. Rev. Genet. 5 2004 936 948
4. W.W. Weber Toxicogenomics: history and current applications, linking genetic makeup to drug responsiveness could lead to better, safer therapies while enhancing drug discovery and development ASM News 2004 70
5. E.F. Nuwaysir et al. Microarrays and toxicology: the advent of toxicogenomics Mol. Carcinog. 24 1999 153 159
6. K.A. Baken et al. Toxicogenomics in the assessment of immunotoxicity Methods 41 2007 132 141
7. E. Pennisi Human genome. A low number wins the GeneSweep Pool Science 300 2003 1484
8. H. Guo et al. Mammalian microRNAs predominantly act to decrease target mRNA levels Nature 466 2010 835 840
9. P. Landgraf et al. A mammalian microRNA expression atlas based on small RNA library sequencing Cell 129 2007 1401 1414
10. S.R. Khan et al. Gene delivery system: a developing arena of study for the new era of medicine Recent Pat. DNA Gene Seq. 6 2012 2 9
11. S.R. Khan et al. Targeting strategies and nanocarriers in vaccines and therapeutics Res. Biotechnol. 2 2011 8 20
12. S. Lin et al. Zebrafish: an in vivo model for nano EHS studies Small 2012 1608 1618
13. S. Das et al. Nanoparticles influence on expression of cell cycle related genes in Drosophila: a microarray-based toxicogenomics study Toxicol. Environ. Chem. 94 2012 952 957
14. Y. Omidi et al. Microarray analysis of the toxicogenomics and the genotoxic potential of a cationic lipid-based gene delivery nanosystem in human alveolar epithelial a549 cells Toxicol. Mech. Methods 18 2008 369 378
15. R.G. Ramos, and K. Olden Gene-environment interactions in the development of complex disease phenotypes Int. J. Environ. Res. Public Health 5 2008 4 11
16. L. Yang et al. Genomewide characterization of non-polyadenylated RNAs Genome Biol. 12 2011 R16
17. J.E. Wilusz et al. A triple helix stabilizes the 3′ ends of long noncoding RNAs that lack poly(A) tails Genes Dev. 26 2012 2392 2407
18. A. Schroeder et al. BMC Mol. Biol. 7 2006 3
19. R.D. Irwin et al. Application of toxicogenomics to toxicology: basic concepts in the analysis of microarray data Toxicol. Pathol. 32 Suppl. 1 2004 72 83
20. S. Streit et al. Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues Nat. Protoc. 4 2009 37 43
21. G.A. Churchill Fundamentals of experimental design for cDNA microarrays Nat. Genet. 32 Suppl. 2002 490 495
22. J. Ezendam et al. Toxicogenomics of subchronic hexachlorobenzene exposure in Brown Norway rats Environ. Health Perspect. 112 2004 782 791
23. M. Bilban et al. Normalizing DNA microarray data Curr. Issues Mol. Biol. 4 2002 57 64
24. T.B. Kepler et al. Normalization and analysis of DNA microarray data by self-consistency and local regression Genome Biol. 3 2002 RESEARCH0037
25. T. Park et al. Evaluation of normalization methods for microarray data BMC Bioinform. 4 2003 33
26. R.A. Irizarry et al. Exploration, normalization, and summaries of high density oligonucleotide array probe level data Biostatistics 4 2003 249 264
27. S. Baginsky et al. Gene expression analysis, proteomics, and network discovery Plant Physiol. 152 2010 402 410
28. F. Ozsolak et al. Direct RNA sequencing Nature 461 2009 814 818
29. M. Consortium et al. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements Nat. Biotechnol. 24 2006 1151 1161
30. W. Slikker Jr. Of genomics and bioinformatics Pharmacogen. J. 10 2010 245 246
31. L. Shi et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models Nat. Biotechnol. 28 2010 827 838
32. S. Marguerat et al. Next-generation sequencing: applications beyond genomes Biochem. Soc. Trans. 36 Pt 5 2008 1091 1096
33. A. Mortazavi et al. Mapping and quantifying mammalian transcriptomes by RNA-Seq Nat. Methods 5 2008 621 628
34. K.D. Hansen et al. Removing technical variability in RNA-seq data using conditional quantile normalization Biostatistics 13 2012 204 216
35. F. Ozsolak et al. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation Cell 143 2010 1018 1029
36. J.F. Thompson, and P.M. Milos The properties and applications of single-molecule DNA sequencing Genome Biol. 12 2011 217
37. Z. Su et al. Comparing next-generation sequencing and microarray technologies in a toxicological study of the effects of aristolochic acid on rat kidneys Chem. Res. Toxicol. 24 2011 1486 1493
38. C. Lema, and M.J. Cunningham MicroRNAs and their implications in toxicological research Toxicol. Lett. 198 2010 100 105
39. A. Molnar et al. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii Nature 447 2007 1126 1129
40. X. Yang et al. Identification of urinary microRNA profiles in rats that may diagnose hepatotoxicity Toxicol. Sci. 125 2012 335 344
41. J. Ward et al. Plasma microRNA profiles distinguish lethal injury in acetaminophen toxicity: a research study World J. Gastroenterol. 18 2012 2798 2804
42. P.J. Starkey Lewis et al. Circulating microRNAs as potential markers of human drug-induced liver injury Hepatology 54 2011 1767 1776
43. K. Wang et al. Circulating microRNAs, potential biomarkers for drug-induced liver injury Proc. Natl. Acad. Sci. U. S. A. 106 2009 4402 4407
44. M.J. Jetten et al. Omics analysis of low dose acetaminophen intake demonstrates novel response pathways in humans Toxicol. Appl. Pharmacol. 259 2012 320 328
45. M. Fabbri et al. Whole genome analysis and microRNAs regulation in HepG2 cells exposed to cadmium ALTEX 29 2012 173 182
46. E. van Rooij The art of microRNA research Circ. Res. 108 2011 219 234
47. Y. Zheng et al. Glucocorticoids inhibit lipopolysaccharide-mediated inflammatory response by downregulating microRNA-155: a novel anti-inflammation mechanism Free Radic. Biol. Med. 52 2012 1307 1317
48. S.S. Ajay et al. Accurate and comprehensive sequencing of personal genomes Genome Res. 21 2011 1498 1505
49. M. Nielsen et al. MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing Anim. Genet. 41 2010 159 168
50. S.P. Gygi et al. Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology Proc. Natl. Acad. Sci. U. S. A. 97 2000 9390 9395
51. P. Wu, and D.W. Grainger Toward immobilized antibody microarray optimization: print buffer and storage condition comparisons on performance Biomed. Sci. Instrum. 40 2004 243 248
52. P.H. O'Farrell High resolution two-dimensional electrophoresis of proteins J. Biol. Chem. 250 1975 4007 4021
53. H. Issaq, and T. Veenstra Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives Biotechniques 44 2008 700
54. W.J. Henzel et al. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases Proc. Natl. Acad. Sci. U. S. A. 90 1993 5011 5015
55. P.L. Ferguson, and R.D. Smith Proteome analysis by mass spectrometry Annu. Rev. Biophys. Biomol. Struct. 32 2003 399 424
56. M. Fountoulakis 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 21 2000 2148 2161
57. M.A. Isbell et al. Identification of proteins adducted by reactive naphthalene metabolites in vitro Proteomics 5 2005 4197 4204
58. M. Unlu et al. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts Electrophoresis 18 1997 2071 2077
59. Y. Hu et al. Recent advances in gel-based proteome profiling techniques Mol. Biotechnol. 28 2004 63 76
60. S. Viswanathan et al. Two-dimensional difference gel electrophoresis Nat. Protoc. 1 2006 1351 1358
61. O. Greengauz-Roberts et al. Saturation labeling with cysteine-reactive cyanine fluorescent dyes provides increased sensitivity for protein expression profiling of laser-microdissected clinical specimens Proteomics 5 2005 1746 1757
62. E. Boitier et al. A comparative integrated transcript analysis and functional characterization of differential mechanisms for induction of liver hypertrophy in the rat Toxicol. Appl. Pharmacol. 252 2011 85 96
63. D.S. Krause, and R.A. Van Etten Tyrosine kinases as targets for cancer therapy N. Engl. J. Med. 353 2005 172 187
64. F.M. Ndikum-Moffor et al. Immunochemical detection of hepatic cocaine-protein adducts in mice Chem. Res. Toxicol. 11 1998 185 192
65. W.A. Korfmacher Principles and applications of LC-MS in new drug discovery Drug Discov. Today 10 2005 1357 1367
66. S.E. Ong et al. Stable isotope labeling by amino acids in cell culture. SILAC, as a simple and accurate approach to expression proteomics Mol. Cell. Proteomics 1 2002 376 386
67. E. Emmott et al. Quantitative proteomics using SILAC coupled to LC-MS/MS reveals changes in the nucleolar proteome in influenza A virus-infected cells J. Proteome Res. 9 2010 5335 5345
68. F. Lamoureux et al. Quantitative proteomic analysis of cyclosporine-induced toxicity in a human kidney cell line and comparison with tacrolimus J. Proteomics 75 2011 677 694
69. T. Geiger et al. Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics Nat. Protoc. 6 2011 147 157
70. L. Flintoft Animal models: proteomics goes live in the mouse Nat. Rev. Genet. 9 2008 655
71. M. Kruger et al. SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function Cell 134 2008 353 364
72. R.S. Obach Pharmacologically active drug metabolites: impact on drug discovery and pharmacotherapy Pharmacol. Rev. 65 2013 578 640
73. K. Begriche et al. Drug-induced toxicity on mitochondria and lipid metabolism: mechanistic diversity and deleterious consequences for the liver J. Hepatol. 54 2011 773 794
74. H.J. Issaq et al. Analytical and statistical approaches to metabolomics research J. Sep. Sci. 32 2009 2183 2199
75. F. Li et al. Profiling the reactive metabolites of xenobiotics using metabolomic technologies Chem. Res. Toxicol. 24 2011 744 751
76. J.M. Prot et al. Predictive toxicology using systemic biology and liver microfluidic 'on chip' approaches: application to acetaminophen injury Toxicol. Appl. Pharmacol. 259 2012 270 280
77. Z.Z. Fang et al. Metabolic map and bioactivation of the anti-tumour drug noscapine Br. J. Pharmacol. 167 2012 1271 1286
78. K. Hollywood et al. Metabolomics: current technologies and future trends Proteomics 6 2006 4716 4723
79. X. Liu et al. 1H NMR-based metabolomic analysis of triptolide-induced toxicity in liver-specific cytochrome P450 reductase knockout mice Metabolomics 8 2012 907 918
80. R. Banerjee et al. Metabolomics of brain and reproductive organs: characterizing the impact of gestational exposure to butylbenzyl phthalate on dams and resultant offspring Metabolomics 8 2012 1012 1025
81. M. Pirmohamed Pharmacogenetics of idiosyncratic adverse drug reactions Handb. Exp. Pharmacol. 196 2010 477 491
82. M. Umer, and Z. Herceg Deciphering the epigenetic code: an overview of DNA methylation analysis methods Antioxid. Redox Signal. 18 2013 1972 1986
83. T. Kouzarides Chromatin modifications and their function Cell 128 2007 693 705
84. R.E. Watson et al. The value of DNA methylation analysis in basic, initial toxicity assessments Toxicol. Sci. 79 2004 178 188
85. P.S. Yan et al. Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray Methods Mol. Biol. 507 2009 89 106
86. T.H. Huang et al. Methylation profiling of CpG islands in human breast cancer cells Hum. Mol. Genet. 8 1999 459 470
87. P.W. Laird Principles and challenges of genome-wide DNA methylation analysis Nat. Rev. Genet. 11 2010 191
88. R. Mukhopadhyay et al. The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide Genome Res. 14 2004 1594 1602
89. I. Keshet et al. Evidence for an instructive mechanism of de novo methylation in cancer cells Nat. Genet. 38 2006 149 153
90. H. Hayatsu Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis: a personal account Proc. Jpn. Acad. Ser. B 84 2008 321 330
91. J. Moggs et al. Investigative safety science as a competitive advantage for Pharma Expert Opin. Drug Metab. Toxicol. 8 2012 1071 1082
92. J. Schmidt et al. Phenobarbital mediates an epigenetic switch at the constitutive androstane receptor (CAR) target gene Cyp2b10 in the liver of B6C3F1 mice PLoS ONE 6 2011 e18216
93. Committee on Applications of Toxicogenomic Technologies to Predictive Toxicology Applications of Toxicogenomic Technologies to Predictive Toxicology and Risk Assessment 2007 National Academies Press
94. I. Muhlberger et al. Computational analysis workflows for Omics data interpretation Methods Mol. Biol. 719 2011 379 397
95. P. Hogeweg, and B. Hesper Interactive instruction on population interactions Comput. Biol. Med. 8 1978 319 327
96. C.A. Afshari et al. The evolution of bioinformatics in toxicology: advancing toxicogenomics Toxicol. Sci. 120 Suppl. 1 2011 S225 S237
97. D. Szklarczyk et al. The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored Nucleic Acids Res. 39 Database issue 2011 D561 D568
98. A. Zhang et al. Proteomic identification network analysis of haptoglobin as a key regulator associated with liver fibrosis Appl. Biochem. Biotechnol. 169 2013 832 846
99. Z. Hu et al. VisANT: an integrative framework for networks in systems biology Brief. Bioinform. 9 2008 317 325
100. L. Stanberry et al. Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile Metabolites 3 2013 741 760
101. B. Palsson, and K. Zengler The challenges of integrating multi-omic data sets Nat. Chem. Biol. 6 2010 787 789
102. R. Shen et al. Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis Bioinformatics 25 2009 2906 2912
103. R. Shen et al. Reconstructing tumor-wise protein expression in tissue microarray studies using a Bayesian cell mixture model Bioinformatics 24 2008 2880 2886
104. I. Pedruzzi et al. HAMAP in 2013, new developments in the protein family classification and annotation system Nucleic Acids Res. 41 2012 D584 D589
105. T.I. Oprea et al. Chemical information management in drug discovery: optimizing the computational and combinatorial chemistry interfaces J. Mol. Graph. Model. 18 2000 541
106. W.L. Haisler et al. Three-dimensional cell culturing by magnetic levitation Nat. Protoc. 8 2013 1940 1949
107. F.K. Brown Chemoinformatics: what is it and how does it impact drug discovery Annu. Rep. Med. Chem. 33 1998 37 384
108. C.R. Williams-Devane et al. Toward a public toxicogenomics capability for supporting predictive toxicology: survey of current resources and chemical indexing of experiments in GEO and ArrayExpress Toxicol. Sci. 109 2009 358 371
109. C.R. Williams-DeVane et al. DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages Bioinformatics 25 2009 692 694
110. Q. Zhu et al. WENDI: A tool for finding non-obvious relationships between compounds and biological properties, genes, diseases and scholarly publications J. Cheminform. 2 2010 6
111. H.J. Federsel Handing over the baton: connecting medicinal chemistry with process R&D Drug News Perspect. 21 2008 193 199
112. K. Briggs et al. Inroads to predict in vivo toxicology: an introduction to the eTOX project Int. J. Mol. Sci. 13 2012 3820 3846
113. I. Kola, and J. Landis Can the pharmaceutical industry reduce attrition rates? Nat. Rev. Drug Discov. 3 2004 711 715
114. Anon An Approach to Using Toxicogenomic Data in U.S. EPA Human Health Risk Assessments: A Dibutyl Phthalate Case Study 2009 US Environmental Protection Agency
115. J. Barretina et al. The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity Nature 483 2012 603 607
116. L. Suter et al. Toxicogenomics in predictive toxicology in drug development Chem. Biol. 11 2004 161 171
117. H. Sone et al. Profiles of Chemical Effects on Cells (pCEC): a toxicogenomics database with a toxicoinformatics system for risk evaluation and toxicity prediction of environmental chemicals J. Toxicol. Sci. 35 2010 115 123
118. Y. Yang et al. Toxicogenomics in drug discovery: from preclinical studies to clinical trials Chem. Biol. Interact. 150 2004 71 85
119. W.B. Mattes et al. Database development in toxicogenomics: issues and efforts Environ. Health Perspect. 112 2004 495 505
120. R.P. Hanzlik et al. The reactive metabolite target protein database (TPDB): a web-accessible resource BMC Bioinform. 8 2007 95
121. C.J. Mattingly et al. The comparative toxicogenomics database (CTD): a resource for comparative toxicological studies J. Exp. Zool. 305A 2006 689 692
122. T.C. Wiegers et al. Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD) BMC Bioinform. 2009 10
123. M.J. Liguori et al. Microarray analysis in human hepatocytes suggests a mechanism for hepatotoxicity induced by trovafloxacin Hepatology 41 2005 177 186
124. J.F. Waring et al. Microarray analysis of lipopolysaccharide potentiation of trovafloxacin-induced liver injury in rats suggests a role for proinflammatory chemokines and neutrophils J. Pharmacol. Exp. Ther. 316 2006 1080 1087
125. P.J. Shaw et al. Coexposure of mice to trovafloxacin and lipopolysaccharide, a model of idiosyncratic hepatotoxicity, results in a unique gene expression profile and interferon gamma-dependent liver injury Toxicol. Sci. 107 2009 270 280
126. J. Woodcock, and R. Woosley The FDA Critical Path Initiative and its influence on new drug development Annu. Rev. Med. 59 2008 1 12
127. F. Goodsaid, and F.W. Frueh Implementing the U.S. FDA guidance on pharmacogenomic data submissions Environ. Mol. Mutagen. 48 2007 354 358
128. W. Slikker Of genomics and bioinformatics Pharmacogenom. J. 10 2010 245 246