Prediction of carcinogenic potential by a toxicogenomic approach using rat hepatoma cells

The long‐term rodent bioassay is the standard method to predict the carcinogenic hazard of chemicals for humans. However, this assay is costly, and the results take at least two years to produce. In the present study, we conducted gene expression profiling of cultured cells exposed to carcinogenic chemicals with the aim of providing a basis for rapid and reliable prediction of carcinogenicity using microarray technology. We selected 39 chemicals, including 17 rat hepatocarcinogens and eight compounds demonstrating carcinogenicity in organs other than the liver. The remaining 14 were non‐carcinogens. When rat hepatoma cells (MH1C1) were treated with the chemicals for 3 days at a non‐toxic dose, analysis of gene expression changes with our in‐house microarray allowed a set of genes to be identified differentiating hepatocarcinogens from non‐carcinogens, and all carcinogens from non‐carcinogens, by statistical methods. Moreover, optimization of the two gene sets for classification with an SVM and LOO‐CV resulted in selection of 39 genes. The highest predictivity was achieved with 207 genes for differentiation between non‐hepatocarcinogens and non‐carcinogens. The overlap between the two selected gene sets encompassed 26 genes. This gene set contained significant genes for prediction of carcinogenicity, with a concordance of 84.6% by LOO‐CV SVM. Using nine external samples, correct prediction of carcinogenicity by SVM was 88.9%. These results indicate that short‐term bioassay systems for carcinogenicity using gene expression profiling in hepatoma cells have great promise. (Cancer Sci 2006; 97: 1002–1010)