Genistein, the primary isoflavone component of soy, consumed in the diet during the prepubertal period only, and the combined prepubertal and adult periods, suppresses chemically induced mammary cancer in rats. Gestational or adult-only exposures do not provide protection. An inverse relation exists between cancer susceptibility and mammary gland differentiation. The current study used proteomic technology to investigate genistein mechanisms of action as related to programming against chemically induced mammary cancer. Rats were injected subcutaneously with 500 microg genistein/g body weight on d 16, 18, and 20 postpartum. At d 21, mammary glands were subjected to 2-dimensional polyacrylamide gel electrophoresis. After gel scanning, image analysis, and MS, 6 proteins were determined to be differentially regulated and identified. One protein, GTP-cyclohydrolase 1 (GTP-CH1), was confirmed as being significantly upregulated at d 21 by immunoblot analysis. Investigation of downstream signaling from GTP-CH1 showed that tyrosine hydroxylase was upregulated and vascular endothelial growth factor receptor 2 (VEGFR2) was downregulated in the mammary glands of 50-d-old rats treated with genistein in the prepubertal period. This and previous work suggest that early prepubertal exposure to genistein enhances cell proliferation by upregulating GTP-CH1 and the epidermal growth factor (EGF)-signaling pathway, and hence cell differentiation and gland maturation. This unique developmental maturation leads to a new biochemical blueprint, whereby the cells have reduced EGF signaling and VEGFR2, which renders the mature mammary gland less proliferative and less susceptible to cancer. This study demonstrated the usefulness of proteomics for the discovery of novel pathways that may be involved in cancer prevention.