Methapyrilene (MP) exposure of animals can result in an array of adverse pathological responses including hepatotoxicity. This study investigates gene expression and histopathological alterations in response to MP treatment in order to 1) utilize computational approaches to classify samples derived from livers of MP treated rats based on severity of toxicity incurred in the corresponding tissue, 2) to phenotypically anchor gene expression patterns, and 3) to gain insight into mechanism(s) of methapyrilene hepatotoxicity. Large-scale differential gene expression levels associated with the exposure of male Sprague-Dawley rats to the rodent hepatic carcinogen MP for 1, 3, or 7 days after daily dosage with 10 or 100 mg/kg/day were monitored. Hierarchical clustering and principal component analysis were successful in classifying samples in agreement with microscopic observations and revealed low-dose effects that were not observed histopathologically. Data from cDNA microarray analysis corroborated observed histopathological alterations such as hepatocellular necrosis, bile duct hyperplasia, microvesicular vacuolization, and portal inflammation observed in the livers of MP exposed rats and provided insight into the role of specific genes in the studied toxicological processes.Keywords. Toxicogenomics; gene expression; methapyrilene; toxicity classification; rat liver; histopathology; phenotypic anchorage; hepatotoxicity.INTRODUCTION Methapyrilene (MP) is an antihistaminic compound once used as a popular over-the-counter sleep-aid component and also used in cold and allergy medications. It was found to induce hepatocellular carcinomas and cholangiocarcinomas in rats (20, 31, 33) and was subsequently withdrawn from the market. However, its carcinogenicity appears to be species-specific because no evidence has been found of MPassociated carcinogenesis in mice (3), guinea pigs, hamsters (32), or humans (36).MP was negative in the DNA adduct formation assay (8, 9, 34) and has not been found to be mutagenic with the Ames assay or other mutation assays (7, 38). Furthermore, MP did not induce unscheduled DNA synthesis (4) and did not cause sister-chromatid exchange (24). These data are consistent with the hypothesis that MP is carcinogenic in rats via nonmutagenic mechanisms (36,54). MP is extensively metabolized by the liver (29, 53), and phase I metabolism plays a major role in its toxicity because cytochrome P450 inhibitors afford protection from the toxicity of MP (43). The oxidative potential of methapyrilene and/or metabolites and increased cellular proliferation have been proposed to play a central role in the observed toxicity (9,45,49). Bile duct cannulation of MP treated rats affords protection from MP hepatic toxicity suggesting that enterohepatic recirculation of glucuronidated metabolites plays a role in MP toxicity (45). In humans, methapyrilene has a very short half-life, a relatively high apparent volume of distribution, and total