Abstract
Traditional models of toxicity have relied on dissecting chemical action into pharmacokinetic and pharmacodynamic processes. However, the integration of genomic information with toxicology will enhance our basic understanding of these processes and significantly change the way we apply toxicological information to risk assessment and regulatory problems. In this article, we summarize the application of gene expression information and polymorphism discovery to four areas in toxicology: toxicity testing, cross-species extrapolation, understanding mechanism of action, and susceptibility.
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- Alevizos I., Mahadevappa M., Zhang X., Ohyama H., Kohno Y., Posner M., Gallagher G. T., Varvares M., Cohen D., Kim D. Oral cancer in vivo gene expression profiling assisted by laser capture microdissection and microarray analysis. Oncogene. 2001 Sep 27;20(43):6196–6204. doi: 10.1038/sj.onc.1204685. [DOI] [PubMed] [Google Scholar]
- Aronow B. J., Toyokawa T., Canning A., Haghighi K., Delling U., Kranias E., Molkentin J. D., Dorn G. W., 2nd Divergent transcriptional responses to independent genetic causes of cardiac hypertrophy. Physiol Genomics. 2001 Jun 6;6(1):19–28. doi: 10.1152/physiolgenomics.2001.6.1.19. [DOI] [PubMed] [Google Scholar]
- Brown M. P., Grundy W. N., Lin D., Cristianini N., Sugnet C. W., Furey T. S., Ares M., Jr, Haussler D. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):262–267. doi: 10.1073/pnas.97.1.262. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bucher J. R., Portier C. J., Goodman J. I., Faustman E. M., Lucier G. W. Workshop overview. National Toxicology Program Studies: principles of dose selection and applications to mechanistic based risk assessment. Fundam Appl Toxicol. 1996 May;31(1):1–8. doi: 10.1006/faat.1996.0070. [DOI] [PubMed] [Google Scholar]
- Eisen M. B., Spellman P. T., Brown P. O., Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863–14868. doi: 10.1073/pnas.95.25.14863. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Elbashir Sayda M., Harborth Jens, Weber Klaus, Tuschl Thomas. Analysis of gene function in somatic mammalian cells using small interfering RNAs. Methods. 2002 Feb;26(2):199–213. doi: 10.1016/S1046-2023(02)00023-3. [DOI] [PubMed] [Google Scholar]
- Guengerich F. P. The Environmental Genome Project: functional analysis of polymorphisms. Environ Health Perspect. 1998 Jul;106(7):365–368. doi: 10.1289/ehp.98106365. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hamadeh Hisham K., Bushel Pierre R., Jayadev Supriya, DiSorbo Olimpia, Bennett Lee, Li Leping, Tennant Raymond, Stoll Raymond, Barrett J. Carl, Paules Richard S. Prediction of compound signature using high density gene expression profiling. Toxicol Sci. 2002 Jun;67(2):232–240. doi: 10.1093/toxsci/67.2.232. [DOI] [PubMed] [Google Scholar]
- Hughes T. R., Marton M. J., Jones A. R., Roberts C. J., Stoughton R., Armour C. D., Bennett H. A., Coffey E., Dai H., He Y. D. Functional discovery via a compendium of expression profiles. Cell. 2000 Jul 7;102(1):109–126. doi: 10.1016/s0092-8674(00)00015-5. [DOI] [PubMed] [Google Scholar]
- Koop B. F. Human and rodent DNA sequence comparisons: a mosaic model of genomic evolution. Trends Genet. 1995 Sep;11(9):367–371. doi: 10.1016/s0168-9525(00)89108-8. [DOI] [PubMed] [Google Scholar]
- Lachenbruch P. A. An almost unbiased method of obtaining confidence intervals for the probability of misclassification in discriminant analysis. Biometrics. 1967 Dec;23(4):639–645. [PubMed] [Google Scholar]
- Lucier G. W., Schecter A. Human exposure assessment and the National Toxicology Program. Environ Health Perspect. 1998 Oct;106(10):623–627. doi: 10.1289/ehp.106-1533173. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Meyer U. A., Skoda R. C., Zanger U. M. The genetic polymorphism of debrisoquine/sparteine metabolism-molecular mechanisms. Pharmacol Ther. 1990;46(2):297–308. doi: 10.1016/0163-7258(90)90096-k. [DOI] [PubMed] [Google Scholar]
- Poland A., Knutson J. C. 2,3,7,8-tetrachlorodibenzo-p-dioxin and related halogenated aromatic hydrocarbons: examination of the mechanism of toxicity. Annu Rev Pharmacol Toxicol. 1982;22:517–554. doi: 10.1146/annurev.pa.22.040182.002505. [DOI] [PubMed] [Google Scholar]
- Puga A., Maier A., Medvedovic M. The transcriptional signature of dioxin in human hepatoma HepG2 cells. Biochem Pharmacol. 2000 Oct 15;60(8):1129–1142. doi: 10.1016/s0006-2952(00)00403-2. [DOI] [PubMed] [Google Scholar]
- Rieder M. J., Taylor S. L., Clark A. G., Nickerson D. A. Sequence variation in the human angiotensin converting enzyme. Nat Genet. 1999 May;22(1):59–62. doi: 10.1038/8760. [DOI] [PubMed] [Google Scholar]
- Sachidanandam R., Weissman D., Schmidt S. C., Kakol J. M., Stein L. D., Marth G., Sherry S., Mullikin J. C., Mortimore B. J., Willey D. L. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature. 2001 Feb 15;409(6822):928–933. doi: 10.1038/35057149. [DOI] [PubMed] [Google Scholar]
- Schmidt-Nielsen K. Scaling in biology: the consequences of size. J Exp Zool. 1975 Oct;194(1):287–307. doi: 10.1002/jez.1401940120. [DOI] [PubMed] [Google Scholar]
- Tamayo P., Slonim D., Mesirov J., Zhu Q., Kitareewan S., Dmitrovsky E., Lander E. S., Golub T. R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A. 1999 Mar 16;96(6):2907–2912. doi: 10.1073/pnas.96.6.2907. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Thomas R. S., Rank D. R., Penn S. G., Zastrow G. M., Hayes K. R., Pande K., Glover E., Silander T., Craven M. W., Reddy J. K. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol. 2001 Dec;60(6):1189–1194. doi: 10.1124/mol.60.6.1189. [DOI] [PubMed] [Google Scholar]
- Ueshima Y., Tsutsumi M., Takase S., Matsuda Y., Kawahara H. Acetaminophen metabolism in patients with different cytochrome P-4502E1 genotypes. Alcohol Clin Exp Res. 1996 Feb;20(1 Suppl):25A–28A. doi: 10.1111/j.1530-0277.1996.tb01722.x. [DOI] [PubMed] [Google Scholar]
- Vanden Heuvel J. P. Peroxisome proliferator-activated receptors (PPARS) and carcinogenesis. Toxicol Sci. 1999 Jan;47(1):1–8. doi: 10.1093/toxsci/47.1.1. [DOI] [PubMed] [Google Scholar]
- Venter J. C., Adams M. D., Myers E. W., Li P. W., Mural R. J., Sutton G. G., Smith H. O., Yandell M., Evans C. A., Holt R. A. The sequence of the human genome. Science. 2001 Feb 16;291(5507):1304–1351. doi: 10.1126/science.1058040. [DOI] [PubMed] [Google Scholar]
- Waring J. F., Jolly R. A., Ciurlionis R., Lum P. Y., Praestgaard J. T., Morfitt D. C., Buratto B., Roberts C., Schadt E., Ulrich R. G. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol Appl Pharmacol. 2001 Aug 15;175(1):28–42. doi: 10.1006/taap.2001.9243. [DOI] [PubMed] [Google Scholar]
- Wood A. J., Stein C. M., Woosley R. Making medicines safer--the need for an independent drug safety board. N Engl J Med. 1998 Dec 17;339(25):1851–1854. doi: 10.1056/NEJM199812173392512. [DOI] [PubMed] [Google Scholar]
- Ziegler J. Health risk assessment research: the OTA report. Environ Health Perspect. 1993 Oct;101(5):402–406. doi: 10.1289/ehp.101-1519854. [DOI] [PMC free article] [PubMed] [Google Scholar]