Application of genomics in preclinical drug safety evaluation

Basic and Clinical Pharmacology and Toxicology

Volumn 98, Issue 6, 2006, Pages 537-546

  Lord, Peter G ^a   Nie, Alex ^a   McMillian, Michael ^a  

^a JOHNSON AND JOHNSON PHARMACEUTICAL RESEARCH AND DEVELOPMENT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL MARKER; NEW DRUG; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR AGONIST; XENOBIOTIC AGENT;

BIOCHEMISTRY; DECISION MAKING; DNA MICROARRAY; DRUG INDUSTRY; DRUG RESEARCH; DRUG SAFETY; GENE EXPRESSION PROFILING; GENE FUNCTION; GENOMICS; HUMAN; IN VIVO STUDY; MOLECULAR BIOLOGY; NONHUMAN; PATHOLOGY; PREDICTION; PRIORITY JOURNAL; SHORT SURVEY; TECHNOLOGY; TOXICOGENETICS; TOXICOLOGY;

DRUG EVALUATION, PRECLINICAL; DRUG TOXICITY; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MICROARRAY ANALYSIS; RISK ASSESSMENT;

EID: 33646739979     PISSN: 17427835     EISSN: 17427843     Source Type: Journal    
DOI: 10.1111/j.1742-7843.2006.pto_444.x     Document Type: Short Survey

References (73)

1. Aardema M. J. MacGregor : Toxicology and genetic toxicology in the new era of "toxicogenomics": impact of "-omics" technologies. Mut. Res. 2002, 499, 13 25.
2. Adams M. D. J. M. Kelley J. D. Gocayne M. Dubnick M. H. Polymeropoulos H. Xiao C. R. Merril A. Wu B. Olde R. F. Moreno, et al. : Complementary DNA sequencing: expressed sequence tags and human genome project. Science 1991, 252, 1651 1656.
3. Barrass N. C. R. J. Price B. G. Lake T. C. Orton : Comparison of the acute and chronic mitogenic effects of the peroxisome proliferators methylclofenapate and lofibric acid in rat liver. Carcinogenesis 1993, 14, 1451 1456.
4. Bisgaard H. C. P. Nagy E. Santoni-Rugiu S. S. Thorgeirsson : Proliferation, apoptosis, and induction of hepatic transcription factors are characteristics of the early response of biliary epithelial (oval) cells to chemical carcinogens. Hepatology 1996, 23, 62 70.
5. Burczynski M. E. M. McMillian J. Ciervo J. B. Parker R. T. Dunn S. Hicken S. Farr M. D Johnson : Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol. Sci. 2000, 58, 399 415.
6. Carakostas M. C. A. K. Banerjee : Interpreting rodent clinical laboratory data in safety assessment studies: Biological and analytical components of variation. Fund. Appl. Toxicol. 1990, 15, 744 753.
7. Columbano A. T. Endoh A. Denda O. Noguchi D. Nakae K. Hasegawa G. M. Ledda-Columbano A. I. Zedda Y. Konishi : Effects of cell proliferation and cell death (apoptosis and necrosis) on the early stages of rat hepatocarcinogenesis. Carcinogenesis 1996, 17, 395 400.
8. Cosulich S. R. Roberts : Suppression of apoptosis by nongenotoxic carcinogens. In : Apoptosis in toxicology. Ed.: R. Roberts. Taylor & Francis, London, UK, 2000, pp. 169 186.
9. Crosby L. M. K. S. Hyder A. B. DeAngelo T. B. Kepler B. Gaskill G. R. Benavides L. Yoon K. T. Morgan : Morphologic analysis correlates with gene expression changes in cultured F344 rat mesothelial cells. Toxicol. Appl. Pharmacol. 2000, 169, 205 221.
10. Crunkhorn S. E. K. E. Plant G. G. Gibson K. Kramer J. Lyon P. G. Lord N. J. Plant : Gene expression changes in rat liver following exposure to liver growth agents: role of Kupffer cells in xenobiotic-mediated liver growth. Biochem. Pharmacol. 2004, 67, 107 118.
11. Farr S. R. T. Dunn : Gene expression applied to toxicology. Toxicol. Sci. 1999, 50, 1 9.
12. Garcia-Allan C. P. G. Lord J. M. Loughlin T. C. Orton J. E. Sidaway : Identification of phenobarbitone-modulated genes in mouse liver by differential display. J. Biochem. Mol. Toxicol. 2000, 14, 65 72.
13. Gerhold D. M. Lu J. Xu C. Austin C. T. Caskey T. Rushmore : Monitoring expression of genes involved in drug metabolism and toxicology using DNA microarrays. Physiol. Genomics 2001, 5, 161 170.
14. Greene N. : Computer software for risk assessment. J. Chem. Inform. Comput. Sci. 1997, 37, 148 150.
15. Greene N. P. N. Judson J. J. Langowski C. A. Marchant : Knowledge-based expert systems for toxicity prediction: DEREK, StAR and METEOR, SAR QSAR. Environ. Res. 1998, 10, 299 314.
16. Guengenrich F. P. : Pharmacogenomics of cytochrome P450 and other enzymes involved in biotransformation of xenobiotics. Drug Dev. Res. 2000, 49, 4 16.
17. Hamadeh H. K. P. R. Bushel S. Jayadev K. Martin O. DiSorbo S. Sieber L. Bennett R. Tennant R. Stoll J. C. Barrett K. Blanchard R. S. Paules C. A. Afshari : Gene expression analysis reveals chemical-specific profiles. Toxicol. Sci. 2002, 67, 219 231.
18. Harries H. M. S. T. Fletcher C. M. Duggan V. A. Baker : The use of genomics technology to investigate gene expression changes in cultured human liver cells. Toxicol. in Vitro 2001, 15, 399 405.
19. Hayes K. R. C. A. Bradfield : Advances in toxicogenomics. Chem. Res. Toxicol. 2005, 18, 403 414.
20. Issemann I. S. Green : Activation of a member of the steroid hormone receptor superfamily by peroxisome proliferators. Nature 1990, 347, 645 650.
21. Johnson D. E. H. I. Wolfgang : Predicting human safety: screening and computational approaches. Drug Discov. Today 2000, 5, 445 454.
22. Kasper P. G. Oliver B. Silva Lima T. Singer D. Tweats : Joint EFPIA/CHMP SWP workshop: the emerging use of omic technologies for regulatory non-clinical safety testing. Pharmacogenomics 2005, 6, 181 184.
23. Kier L. D. R. Neft L. Tang R. Suizu T. Cook K. Onsurez K. Tiegler Y. Sakai M. Ortiz T. Nolan U. Sankar A. P. Li : Applications of microarrays with toxicologically relevant genes (tox genes) for the evaluation of chemical toxicants in Sprague Dawley rats in vivo and human hepatocytes in vitro. Mutat. Res. 2004, 549, 101 113.
24. Lambert I. B. T. M. Singer S. E. Boucher G. R. Douglas : Detailed review of transgenic rodent mutation assays. Mutat. Res. - Rev. in Mutat. Res. 2005, 590, 1 280.
25. Lash L. H. R. N. Hines F. J. Gonzalez T. R. Zacharewski M. A. Rothstein : Genetics and susceptibility to toxic chemicals: do you (or should you) know your genetic profile? J. Pharmacol. Exp. Therap. 2003, 305, 403 409.
26. Lawrence J. W. Y. Li S. Chen J. G. DeLuca J. P. Berger D. R. Umbenhauer D. E. Moller G. Zhou : Differential gene regulation in human versus rodent hepatocytes by peroxisome proliferator-activated receptor (PPAR) alpha. PPAR alpha fails to induce peroxisome proliferation-associated genes in human cells independently of the level of receptor expresson. J. Biol. Chem. 2001, 276, 31521 31527.
27. Lesko L. J. R. A. Salerno B. B. Spear D. C. Anderson T. Anderson C. Brazell J. Collins A. Dorner D. Essayan B. Gomez-Mancilla J. Hackett S. M. Huang S. Ide J. Killinger J. Leighton E. Mansfield R. Meyer S. G. Ryan V. Schmith P. Shaw F. Sistare M. Watson A. Worobec : Pharmacogenetics and pharmacogenomics in drug development and regulatory decision making: report of the first FDAPWG-PhRMA-DruSafe Workshop. J. Clin. Pharmacol. 2003, 43, 342 358.
28. Liang P. A. Pardee : Differential display of eukaryotic messenger RNA by means of the polymerase chain reaction. Science 1992, 257, 967 971.
29. Lord P. G. K. A. Barne K. Kramer E. J. Bacon J. Mooney S. O'Brien P. J. Bugelski : cDNA microarrays in investigative toxicology: a study of differential gene expression in compound induced cardiac hypertrophy. Comments Toxicol. 2001, 7, 381 392.
30. Lord P. G. : Progress in applying genomics in drug development. Toxicol. Lett. 2004, 149, 371 375.
31. MacGregor J. T. : The future of regulatory toxicology: impact of the biotechnology revolution. Mutat. Res. 2003, 75, 236 248.
32. MacGregor J. T. S. Farr J. D. Tucker J. A. Heddle R. R. Tice K. W. Turteltaub : New molecular endpoints and methods for routine toxicity testing. Fundam. Appl. Toxicol. 1995, 26, 156 173.
33. Mattes W. B. S. D. Pettit, S-A. Sansone P. R. Bushel M. D. Waters : Database development in toxicogenomics: issues and efforts. Environ. Health Perspect. 2004, 112, 495 505.
34. McMillian M. A. Y. Nie J. B. Parker A. Leone M. Kemmerer S. Bryant J. Herlich L. Yieh A. Bittner X. Liu J. Wan M. D. Johnson : Inverse gene expression patterns for macrophage activating hepatotoxicants and peroxisome proliferators in rat liver. Biochem. Pharmacol. 2004, 67, 2141 2165.
35. Milano J. J. McKay C. Dagenais L. Foster-Brown F. Pognan R. Gadient R. T. Jacobs A. Zacco B. Greenberg P. J. Ciacio : Modulation of Notch processing by γ-secretase inhibitors causes intestinal goblet cell metaplasia and induction of genes known to specify gut secretory lineage differentiation. Toxicol. Sci. 2004, 82, 341 358.
36. Nadadur S. S. M. C. J. Schladweiler U. P. Kodavanti : A pulmonary rat gene array for screening altered expression profiles in air pollutant-induced lung injury. Inhal. Toxicol. 2000, 12, 1239 1254.
37. Nuwaysir E. F. M. Bittner J. Trent J. C. Barrett C. A. Afshari : Microarrays and toxicology: the advent of toxicogenomics. Mol. Carcinogenesis 1999, 24, 153 159.
38. Oberemm A. L. Onyon U. Gundert-Remy : How can toxicogenomics inform risk assessment? Toxicol. Appl. Pharmacol. 2005, 207, 592 598.
39. Pennie W. D. N. J. Woodyatt T. C. Aldridge G. Orphanides : Application of genomics to the definition of the molecular basis for toxicity. Toxicol. Lett. 2001, 120, 353 358.
40. Pennie W. S. D. Pettit P. G. Lord : Toxicogenomics in risk assessment: An overview of an HESI collaborative research program. Environm. Health Perspect. 2004, 112, 417 419.
41. Peters J. M. R. C. Cattley F. J. Gonzalez : Role of PPARα in the mechanism of action of the nongenotoxic carcinogen and peroxisome proliferators Wy-14,643. Carcinogenesis 1997, 18, 2209 2033.
42. Peters J. M. T. Aoyama R. C. Cattley U. Nobumitsu T. Hashimoto F. J. Gonzalez : Role of peroxisome proliferators-activated receptor alpha in altered cell cycle regulation in mouse liver. Carcinogenesis 1998, 19, 1989 1994.
43. Peterson R. L. L. Casciotti L. Block M. E. Goad Z. Tong J. T. Meehan R. A. Jordan M. P. Vinlove V. R. Markiewicz C. A. Weed A. J. Dorner : Mechanistic toxicogenomic analysis of WAY-144122 administration in Sprague-Dawley rats. Toxicol. Appl. Pharmacol. 2004, 196, 80 94.
44. Petricoin E. F. J. L. Hackett L. J. Lesko R. K. Puri S. I. Gutman K. Chumakov J. Woodcock D. W. Feigal K. C. Zoon F. D. Sistare : Medical applications of microarray technologies: a regulatory science perspective. Nat. Genet. 2002, 32 suppl. 474 479.
45. Quackenbush J. : Computational analysis of microarray data. Nat. Rev. Genet. 2001, 2, 418 427.
46. Quackenbush J. : Data standards for 'omic' science. Nat. Biotechnol. 2004, 22, 613 614.
47. Rockett J. C. K. E. Swales D. J. Esdaile G. G. Gibson : Use of suppression-PCR subtractive hybridization to identify genes that demonstrate altered expression in male rat and guinea pig livers following exposure to Wy-14,643, a peroxisome proliferator and non-genotoxic hepatocarcinogen. Toxicology 2000, 144, 13 29.
48. Rodi C. P. R. T. Bunch S. W. Curtiss L. D. Kier M. A. Cabonce J. C. Davila M. D. Mitchell C. L. Alden D. L. Morris : Revolution through genomics in investigative and discovery toxicology. Toxicol. Pathol. 1999, 27, 107 110.
49. Salter A. H. K. C. Nilsson : Informatics and multivariate analysis of toxicogenomics data. Curr. Opin. Drug Discov. Devel. 2003, 6, 117 122.
50. Sansone S.-A. N. Morrison P. Rocca-Serra J. Fostel : Standardization initiatives in the (eco)toxicogenomics domain: a review. Comp. Funct. Genomics 2004, 5, 633 641.
51. Sawada H. K. Takami S. Asahi : A toxicogenomic approach to drug-induced phospholipidosis: analysis of its induction mechanism and establishment of a novel in vitro screening system. Toxicol. Sci. 2004, 83, 282 292.
52. Schena M. R. A. Heller T. P Theriault K. Konrad E. Lachenmeier R. W. Davis : Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 1998, 16, 301 306.
53. Schulte-Hermann R. W. Bursch B. Marian B. Grasl-Kraupp : Active cell death (apoptosis) and cellular proliferation as indicators of exposure to carcinogens. IARC Scientific Publications 1999, 146, 273 285.
54. Searfoss G. H. W. J. Jordan D. O. Calligaro E. J. Galbreath L. M. Schirtzinger B. R. Berridge H. Gao M. A. Higgins P. C. May T. P. Ryan : Adipsin, a biomarker of gastrointestinal toxicity mediated by a functional γ-secretase inhibitor. J. Biol. Chem. 2003, 278, 46107 46116.
55. Stribinskis V. K. S. Ramos : Decoding the riddle: the dawn of RNAi for the study of gene-gene and gene-environment interactions. Environ. Health Perspect. 2004, 112, A210 A211.
56. Suter L. L. E. Babiss E. B. Wheeldon : Toxicogenomics in predictive toxicology in drug development. Chem. Biol. 2004, 11, 161 171.
57. Thai S-F. J. W. Allen A. B. DeAngelo M. H. George J. C. Fuscoe : Detection of early gene expression changes by differential display in the livers of mice exposed to dichloroacetic acid. Carcinogenesis 2001, 22, 1317 1322.
58. Thompson M. B. : Clinical pathology in the National Toxicology Program. Toxicol. Pathol. 1992, 20, 484 488.
59. Tong W. X. Cao S. Harris H. Sun H. Fang J. Fuscoe A. Harris H. Hong Q. Xie R. Perkins L. Shi D. Casciano : ArrayTrack-Supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. Environ. Health Perspect. 2003, 111, 1819 1826.
60. Tugwood J. D. P. R. Holden N. H. James R. A. Prince R. A. Roberts : APPAR-alpha cDNA cloned from guinea pig liver encodes a protein with similar properties to the mouse PPARa: implications for species differences in response to peroxisome proliferators. Archiv. Toxicol. 1998, 72, 169 177.
61. Ulrich R. G. : The toxicogenomics of nuclear receptor agonists. Curr. Opin. Chem. Biol. 2003, 7, 505 510.
62. Ulrich R. S. H. Friend : "Toxicogenomics and drug discovery: will new technologies help us produce better drugs?" Nat. Rev. Drug Discov. 2002, 1, 84 88.
63. Velculescu V. E. L. Zhang B. Vogelstein K. W. Kinzler : Serial analysis of gene expression. Science 1995, 270, 484 487.
64. Ward J. J. Peters C. Perella F. Gonzalez : Receptor and nonreceptor-mediated organ specific toxicity of DEHP in PPAR-alpha null mice. Toxicol. Pathol. 1998, 26, 240 246.
65. Waring J. F. R. Ciurlionis R. A. Jolly M. Heindel R. G. Ulrich : Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol. Lett. 2001a, 120, 359 368.
66. Waring J. F. R. A. Jolly R. Ciurlionis P. Y. Lum J. T. Praestgaard D. C. Morfitt B. Buratto C. Roberts E. Schadt R. G. Ulrich : Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol. Appl. Pharmacol. 2001b, 175, 28 42.
67. Waring J. F. R. Gum D. Morfitt R. A. Jolly R. Ciurlionis M. Heindel L. Gallenberg B. Buratto R. G. Ulrich : Identifying toxic mechanisms using DNA microarrays: evidence that an experimental inhibitor of cell adhesion molecule expression signals through the aryl hydrocarbon nuclear receptor. Toxicology 2002, 181-182, 537 550.
68. Waters M. G. Boorman P. Bushel M. Cunningham R. Irwin A. Merrick K. Olden R. Paules J. Selkirk S. Stasiewicz B. Weis B. Van Houten N. Walker R. Tennant : Systems toxicology and the Chemical effects in Biological Systems (CEBS) knowledge base. Environ. Health Perspect. 2003, 111, 15 28.
69. Weingand K. G. Brown R. Hall D. Davies K. Gossett D. Neptun T. Waner T. Matsuzawa P. Salemink W. Froelke J. P. Provost G. Dal Negro J. Batchelor M. Nomura H. Groetsch A. Boink J. Kimball D. Woodman M. York E. Fabianson-Johnson M. Lupart E. Melloni : Harmonization of animal clinical pathology testing in toxicity and safety studies. The Joint Scientific Committee for International Harmonization of Clinical Pathology Testing. Fundam. Appl. Toxicol. 1996, 29, 198 201.
70. Woodyatt N. K. Lambe K. Myers J. Tugwood R. Roberts : The peroxisome proliferators (PP) response element (PPRE) upstream of the human acyl CoA oxidase gene is inactive in a sample human population: significance for species differences in response to PPs. Carcinogenesis 1999, 20, 369 375.
71. Wu W. S. E. Wildsmith A. J. Winkley R. Yallop F. J. Elcock P. J. Bugelski : Chemometric strategies for normalization of gene expression data obtained from cDNA microarrays. Anal. Chim. Acta 2001, 446, 451 466.
72. Yamazaki K. J. Kuromitsu I. Tanaka : Microarray analysis of gene expression changes in mouse liver induced by peroxisome proliferators-activated receptor α agonists. Biochem. Biophys. Res. Commun. 2002, 290, 1114 1122.
73. Yang Y. E. A. G. Blomme J. F. Waring : Toxicogenomics in drug discovery: from preclinical studies to clinical trials. Chem. Biol. Interact. 2004, 150, 71 85.