Hydroquinone (HQ) is a rodent carcinogen and a potential human carcinogen. Glutathione conjugation of HQ enhances its biological reactivity, and 2,3,5-tris-(glutathion-S-yl)hydroquinone (TGHQ) is a potent nephrotoxicant and nephrocarcinogen in the Eker rat. Moreover, a single exposure of primary epithelial cells derived from Eker rat kidneys to TGHQ transforms these cells into an immortalized phenotype (quinol-thioether transformed rat renal epithelial (QT-RRE) cells). The Eker rat bears a mutation in one allele of the tuberous sclerosis-2 (Tsc-2) tumor suppressor gene, which predisposes the animals to the development of spontaneous and chemical-induced renal cell carcinoma. Thus, the Eker rat provides a unique model for elucidating the mechanisms of renal tubular epithelial carcinogeneisis. cDNA microarray analysis of QT-RRE3 cells and of tumor tissue derived from the kidneys of Eker rats treated with TGHQ revealed alterations (by threefold or greater) in the expression of a total of 80 genes. Fifteen percent of these genes exhibited similar expression patterns in both QT-RRE cells and tumor tissue. The differentially expressed genes primarily participate in three major areas: (1) signal transduction or in the regulation of signal transduction (extracellular signal regulated kinase 2 (ERK2); protein kinase CK2; protein kinase B; c-jun; NF-kappaB; ras-related GTPases; annexins), (2) stress response, tissue remodeling, and DNA repair (glutathione-S-transferases; procollagen c proteinase enhancer; plasminogen activator; tissue inhibitor of metalloprotease 3; apurinic/apyrimidic endonuclease), and (3) electron transport and energy homeostasis (cytochrome c oxidase subunits). The changes in the expression of many of these genes was confirmed by reverse transcription (RT)-polymerase chain reactions (PCR) using primers specific for the differentially expressed genes. As an example, the annexin I and II genes, implicated in signal transduction, were highly induced in tumor tissue and also in dysplastic lesions isolated from the kidneys of rats treated chronically with TGHQ. The annexin I and II proteins were also upregulated in tumor tissue, which probably play an important role in TGHQ-induced nephrocarcinogenesis. Moreover, in the present study, a tumorigenicity assay using athymic nude mice revealed that QT-RRE cell lines formed tumors when injected in the subcutis of nude mice, providing evidence that the cells are malignantly transformed. Histopathological analysis further indicated that the tumors were composed of neoplastic cells, resembling renal carcinoma cells with varying degrees of atypia, with the presence of apoptotic and mitotic figures.