Liver cancer is the fifth most common cancer worldwide, with 437,000 cases reported in 1990. Yet a mutational model has not yet been developed for liver cancer, as it has for certain other cancers, such as colon cancer. A thorough understanding of the molecular events leading to neoplastic transformation of the liver requires a detailed comparison of the gene expression pattern in normal liver cells with that in cancer cells. We have performed gene expression profiling of normal and neoplastic livers. Using oligonucleotide microarrays, we compared liver tumors (from diethylnitrosamine-treated C3H/HeJ mice) with three different states of the normal liver: quiescent adult, regenerating adult and newborn. Although each comparison revealed hundreds of differentially expressed genes, only 22 genes were found to be deregulated in the tumors in all three comparisons. We also employed representational difference analysis to clone fragments of messenger RNAs differentially expressed in liver tumors versus regenerating livers. Although many of the same mRNAs were identified as in the oligonucleotide microarray experiments, we also cloned several new mRNAs that are differentially regulated in liver tumors. We have cloned the mouse complementary DNA of novel 4 and are currently isolating the human homologue of this unknown gene. We are using representational difference analysis and oligonucleotide microarrays to identify genes whose expression is deregulated in the development of human hepatocellular carcinomas. Using these models and techniques, we hope to identify common genetic alterations in the progression of liver cancer in both humans and mice.