Discriminating different classes of toxicants by transcript profiling

Environmental Health Perspectives

Volumn 112, Issue 12, 2004, Pages 1236-1248

  Steiner, Guido ^a   Suter, Laura ^a   Boess, Franziska ^a   Gasser, Rodolfo ^a   de Vera, Maria Cristina ^a   Albertini, Silvio ^a   Ruepp, Stefan ^a  

^a F HOFFMANN LA ROCHE LTD   (Switzerland)

Author keywords

Liver; Microarray; Predictive toxicology; Rat; Support vector machines; Toxicogenomics

Indexed keywords

1,2 DICHLOROBENZENE; 4,4' METHYLENEDIANILINE; AFLATOXIN B1; AMINEPTINE; AMIODARONE; ANTIDIABETIC AGENT; BIOLOGICAL MARKER; BROMOBENZENE; CARBON TETRACHLORIDE; CHLORPROMAZINE; COUMARIN; CYCLOSPORIN A; GENTAMICIN; GLIBENCLAMIDE; HYDRAZINE; PARACETAMOL; PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR AGONIST; PHALLOIDIN; PIRINIXIC ACID; THIOACETAMIDE;

ANIMAL EXPERIMENT; ARTICLE; BLOOD CHEMISTRY; CONTROLLED STUDY; DNA FINGERPRINTING; DNA MICROARRAY; DRUG DISCRIMINATION; DRUG EFFECT; FEASIBILITY STUDY; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; LIVER HISTOLOGY; LIVER TOXICITY; MALE; MOUSE; NEPHROTOXICITY; NONHUMAN; PRIORITY JOURNAL; RAT STRAIN; VALIDATION PROCESS;

ANIMALIA;

EID: 4444360916     PISSN: 00916765     EISSN: None     Source Type: Journal    
DOI: 10.1289/ehp.7036     Document Type: Article

References (59)

1. Alizadeh AA, Ross DT, Perou CM, Van De Rijn M. 2001. Towards a novel classification of human malignancies based on gene expression patterns. J Pathol 195:41-52.
2. Alon U, Barkai N, Notterman DA, Gish K, Ybarra S, Mack D, et al. 1999. Broad patterns of gene expression revealed by clustering analysis of tumor and normal colon tissues probed by oligonucleotide arrays. Proc Natl Acad Sci USA 96:6745-6750.
3. 1-induced hepatic steatosis: role of carbonyl compounds and active diols on steatogenesis. Lancet 353:747-748.
4. Andrew AS, Warren AJ, Barchowsky A, Temple KA, Klei L, Soucy NV, et al. 2003. Genomic and proteomic profiling of responses to toxic metals in human lung cells. Environ Health Perspect 111:825-838.
5. Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, Baker BS, et al. 2002. Gene expression during the life cycle of Drosophila melanogaster. Science 297:2270-2275.
6. Asamoto M, Tsuda H, Kato T, Ito N, Masuko T, Hashimoto Y, et al. 1989. Strain differences in susceptibility to 2-acetylaminofluorene and phenobarbital promotion of hepatocarcinogenesis: immunohistochemical analysis of cytochrome P-450 isozyme induction by 2-acetyl-aminofluorene and phenobarbital. Jpn J Cancer Res 80:1041-1046.
7. Boess F, Kamber M, Romer S, Gasser R, Muller D, Albertini S, et al. 2003. Gene expression in two hepatic cell lines, cultured primary hepatocytes, and liver slices compared to the in vivo liver gene expression in rats: possible implications for toxicogenomics use of in vitro systems. Toxicol Sci 73:386-402.
8. Boser BE, Guyon IM, Vapnik VN. 1992. A training algorithm for optimal margin classifiers. In: Proceedings of the 5th Annual International Conference on Computational Learning Theory, 27-29 July 1992, Pittsburgh, Pennsylvania. Pittsburgh, PA:ACM Press, 144-152.
9. Brem RB, Yvert G, Clinton R, Kruglyak L. 2002. Genetic dissection of transcriptional regulation in budding yeast. Science 296:752-755.
10. Brown MPS, Grundy WN, Lin D, Cristianini N, Sugnet CW, Furey TS, et al. 2000. Knowledge-based analysis of microarray gene expression data by using support vector machines. Proc Natl Acad Sci USA 97:262-267.
11. Bulera SJ, Eddy SM, Ferguson E, Jatkoe TA, Reindel JF, Bleavins MR, et al. 2001. RNA expression in the early characterization of hepatotoxicants in Wistar rats by high-density DNA microarrays. Hepatology 33:1239-1258.
12. Burczynski ME, McMillian M, Ciervo J, Li L, Parker JB, Dunn RT II, et al. 2000. Toxicogenomics-based discrimination of toxic mechanism in HepG2 human hepatoma cells. Toxicol Sci 58:399-415.
13. Chang CC, Lin CJ. 2001. LIBSVM: a library for support vector machines. Available: http://www.csie.ntu.edu.tw/~cjlin/libsvm [1 January 2003].
14. Cristianini N, Shawe-Taylor J. 2000. An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods. Cambridge, UK:Cambridge University Press.
15. Donald S, Verschoyle RD, Edwards R, Judah DJ, Davies R, Riley J, et al. 2002. Hepatobiliary damage and changes in hepatic gene expression caused by the antitumor drug ecteinascidin-743 (ET-743) in the female rat. Cancer Res 62:4256-4262.
16. Eisen MB, Spellman PT, Brown PO, Botstein D. 1998. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci USA 95:14863-14868.
17. Enard W, Khaitovich P, Klose J, Zollner S, Heissig F, Giavalisco P, et al. 2002. Intra- and interspecific variation in primate gene expression patterns. Science 296:340-343.
18. Everitt B. 1974. Cluster Analysis. London:Heinemann.
19. Farrell GC. 1994. Drug-Induced Liver Disease. London:Churchill Livingstone.
20. Fracasso ME, Leone R, Cuzzolin L, Del Soldato P, Velo GP, Benoni G. 1990. Indomethacin induced hepatic alterations in mono-oxygenase system and faecal Clostridium perfringens enterotoxin in the rat. Agents Actions 31:313-316.
21. Furey TS, Cristianini N, Duffy N, Bednarski DW, Schummer M, Haussler D. 2000. Support vector machine classification and validation of cancer tissue samples using microarray expression data. Bioinformatics 16:906-914.
22. Guyon IM, Weston J, Barnhill S, Vapnik VN. 2002. Gene selection for cancer classification using support vector machines. Mach Learn 46:389-442.
23. Hamadeh HK, Bushel PR, Jayadev S, DiSorbo O, Bennett L, Li L, et al. 2002a. Prediction of compound signature using high density gene expression profiling. Toxicol Sci 67:232-240.
24. Hamadeh HK, Bushel PR, Jayadev S, Martin K, Di Sorbo O, Sieber S, et al. 2002b. Gene expression analysis reveals chemical-specific profiles. Toxicol Sci 67:219-231.
25. Hamadeh HK, Knight BL, Haugen AC, Sieber S, Amin RP, Bushel PR, et al. 2002c. Methapyrilene toxicity: anchorage of pathologic observations to gone expression alterations. Toxicol Pathol 30:470-482.
26. Hansmannel F, Clemencet MC, Le Jossic-Corcos C, Osumi T, Latruffe N, Nicolas-Frances V. 2003. Functional characterization of a peroxisome proliferator response-element located in the intron 3 of rat peroxisomal thiolase B gene. Biochem Biophys Res Commun 311:149-155.
27. Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, et al. 2000. 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome Biol 1:3-21.
28. Heijne WH, Slitt AL, van Bladeren PJ, Groten JP, Klaassen CD, Stierum RH, et al. 2004. Bromobenzene-induced hepatotoxicity at the transcriptome level. Toxicol Sci 79:411-422.
29. Joliffe IT. 1986. Principal Component Analysis. New York:Springer.
30. Kaiser R, Gottschalk G. 1972. Elementare Tests zur Beurteilung von Messdaten [in German]. Mannheim/Wien/Zuerich:Bibliographisches Institut 18-21.
31. Kita Y, Shiozawa N, Jin WH, Majewski RR, Besharse JC, Greene AS, et al. 2002. Implications of circadian gene expression in kidney, liver and the effects of fasting on pharmacogenomic studies. Pharmacogenetics 12:55-65.
32. Knodell RG. 1975. Effects of chlorpromazine on bilirubin metabolism and biliary secretion in the rat. Gastroenterology 69:965-972.
33. Kohonen T. 1995. Self Organizing Maps. Berlin:Springer.
34. Kulkarni SG, Duong H, Gomila R, Mehendale HM. 1996. Strain differences in tissue repair response to 1,2-dichlorobenzene. Arch Toxicol 70:714-723.
35. Lee CH, Olson P, Evans RM. 2003. Minireview: lipid metabolism, metabolic diseases, and peroxisome proliferator-activated receptors. Endocrinology 144:2201-2207.
36. Lindon JC, Nicholson JK, Holmes E, Antti H, Bollard ME, Keun H, et al. 2003. Contemporary issues in toxicology: the role of metabonomics in toxicology and its evaluation by the COMET project. Toxicol Appl Pharmacol 187:137-146.
37. 1-induced oxidative stress in cultured rat hepatocytes. Free Radic Res 31:559-568.
38. Masubuchi Y, Saito H, Horie T. 1998. Structural requirements for the hepatotoxicity of nonsteroidal anti-inflammatory drugs in isolated rat hepatocytes. J Pharmacol Exp Ther 287:208-213.
39. Matthews BW. 1975. Comparison of the predicted and observed secondary structure of t4 phage lysozyme. Biochim Biophys Acta 405:442-451.
40. Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, et al. 2002. Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109:307-320.
41. Ramaswamy S, Ross KN, Lander ES, Golub TR. 2003. A molecular signature of metastasis in primary solid tumors. Nat Genet 33:49-54.
42. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, et al. 2001. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci USA 98:15149-15154.
43. Ruepp S, Tonge RP, Shaw J, Wallis N, Pognan F. 2002. Genomics and proteomics analysis of acetaminophen toxicity in mouse liver. Toxicol Sci 65:135-150.
44. Schölkopf B, Guyon IM, Weston J. 2003. Statistical learning and kernel methods in bioinformatics. In: Artifical Intelligence and Heuristic Methods in Bioinformatics (Frasconi P, Shamir R, eds). Amsterdam:IOS Press, 1-21.
45. Schölkopf B, Smola A. 2002. Learning with Kernels. Cambridge, MA:MIT Press.
46. Smela ME, Currier SS, Bailey EA, Essigmann JM. 2001. The chemistry and biology of aflatoxin B(1): from mutational spectrometry to carcinogenesis. Carcinogenesis 22:535-545.
47. Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, Wong WH, et al. 2002. Extensive and divergent circadian gene expression in liver and heart. Nature 417:78-83.
48. Suter L, Haiker M, De Vera MC, Albertini S. 2003. Effect of two 5-ht(6) receptor antagonists on the rat liver: a molecular approach. Pharmacogenomics J 3:320-334.
49. Thomas RS, Rank DR, Penn SG, Zastrow GM, Hayes KR, Pande K, et al. 2001. Identification of toxicologically predictive gene sets using cDNA microarrays. Mol Pharmacol 60:1189-1194.
50. 1 in isolated perfused rat liver. Toxicol Appl Pharmacol 41:523-534.
51. Van de Vijver MJ, He YD, van't Veer LJ, Dai H, Hart AA, Voskuil DW, et al. 2002. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med 347:1999-2009.
52. Vapnik VN. 1998. Statistical Learning Theory. New York:Wiley.
53. Vomel T, Platt D. 1986. Age-dependent phagocytosis of erythrocytes by the isolated perfused rat liver after galactosamine hepatitis and alpha-naphthylisothiocyanate cholestasis. Arch Gerontol Geriatr 5:351-539.
54. Wang Y, Rea T, Bian J, Gray S, Sun Y. 1999. Identification of the genes responsive to etoposide-induced apoptosis: application of DNA microarray technology. FEBS Lett 445:269-273.
55. Waring JF, Ciurlionis R, Jolly RA, Heindel M, Ulrich RG. 2001a. Microarray analysis of hepatotoxins in vitro reveals a correlation between gene expression profiles and mechanisms of toxicity. Toxicol Lett 120:359-368.
56. Waring JF, Jolly RA, Ciurlionis R, Lum PY, Praestgaard JT, Morfitt DC, et al. 2001b. Clustering of hepatotoxins based on mechanism of toxicity using gene expression profiles. Toxicol Appl Pharmacol 175:28-42.
57. Yeang C, Ramaswamy S, Tamayo P, Mukherjee S, Rifkin RM, Angelo M, et al. 2001. Molecular classification of multiple tumor types. Bioinformatics 17:316-322.
58. Zhang W, Wang H, Song SW, Fuller GN. 2002. Insulin-like growth factor binding protein. 2: Gene expression microarrays and the hypothesis-generation paradigm. Brain Pathol 12:87-94.
59. Zimmermann N, King NE, Laporte J, Yang M, Mishra A, Pope SM, et al. 2003. Dissection of experimental asthma with DNA microarray analysis identifies arginase in asthma pathogenesis. J Clin Invest 111:1863-1874.