Carcinogenesis Advance Access originally published online on August 20, 2009
Carcinogenesis 2009 30(10):1805-1812; doi:10.1093/carcin/bgp190
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Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models
MicroArray Department and Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
1 Laboratory for Health Protection Research, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
2 Department of Toxicogenetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
* To whom correspondence should be addressed. Tel: +31 30 274 2102; Fax: +31 30 274 4446; Email: harry.van.steeg{at}rivm.nl
The carcinogenic potential of chemicals and pharmaceuticals is traditionally tested in the chronic, 2 year rodent bioassay. This assay is not only time consuming, expensive and often with a limited sensitivity and specificity but it also causes major distress to the experimental animals. A major improvement in carcinogenicity testing, especially regarding reduction and refinement of animal experimentation, could be the application of toxicogenomics. The ultimate aim of this study is to demonstrate a proof-of-principle for transcriptomics biomarkers in various tissues for identification of (subclasses of) carcinogenic compounds after short-term in vivo exposure studies. Both wild-type and DNA repair-deficient Xpa–/–/p53+/– (Xpa/p53) mice were exposed up to 14 days to compounds of three distinct classes: genotoxic carcinogens (GTXC), non-genotoxic carcinogens (NGTXC) and non-carcinogens. Subsequently, extensive transcriptomics analyses were performed on several tissues, and transcriptomics data were screened for potential biomarkers using advanced statistical learning techniques. For all tissues analyzed, we identified multigene gene-expression signatures that are, with a high confidence, predictive for GTXC and NGTXC exposures in both mouse genotypes. Xpa/p53 mice did not perform better in the short-term bioassay. We were able to achieve a proof-of-principle for the identification and use of transcriptomics biomarkers for GTXC or NGTXC. This supports the view that toxicogenomics with short-term in vivo exposure provides a viable tool for classifying (geno)toxic compounds.
Abbreviations: 2-AAF, 2-acetylaminofluorene; B[a]P, benzo[a]pyrene; CsA, cyclosporine A; DLDA-BW, diagonal linear discriminant analysis with a between-group to within-group sums of squares-based gene selection; GTXC, genotoxic carcinogens; MLN, mesenteric lymph node; NC, non-carcinogens; NCC-SC, nearest centroid classification with shrunken centroid gene selection; NGTXC, non-GTXC; SVM-RFE, support vector machines with recursive feature elimination; TBTO, tributyltin oxide; WT, wild-type; WY, Wyeth-14,643; Xpa/p53, Xpa–/–/p53+/–
Received April 22, 2009; revised July 27, 2009; accepted July 27, 2009.