Early breast cancer progression involves advancement through specific morphological stages including atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS) and invasive mammary carcinoma (IMC), although not necessarily always in a linear fashion. Observational studies have examined genetic, epigenetic and gene expression differences in breast tissues representing these stages of progression, but model systems which would allow for experimental testing of specific factors influencing transition through these stages are scarce. The 21T series cell lines, all originally derived from the same patient with metastatic breast cancer, have been proposed to represent a mammary tumor progression series. We report here that three of the 21T cell lines indeed mimic specific stages of human breast cancer progression (21PT-derived cells, ADH; 21NT-derived cells, DCIS; 21MT-1 cells, IMC) when grown in the mammary fat pad of nude mice, albeit after a year. To develop a more rapid, readily manipulatable in vitro assay for examining the biological differences between these cell lines, we have used a 3D Matrigel system. When the three cell lines were grown in 3D Matrigel, they showed characteristic morphologies, in which quantifiable aspects of stage-specific in vivo behaviors (ie, differences in acinar structure formation, cell polarization, colony morphology, cell proliferation, cell invasion) were recapitulated in a reproducible fashion. Gene expression profiling revealed a characteristic pattern for each of the three cell lines. Interestingly, Wnt pathway alterations are particularly predominant in the early transition from 21PTci (ADH) to 21NTci (DCIS), whereas alterations in expression of genes associated with control of cell motility and invasion phenomena are more prominent in the later transition of 21NTci (DCIS) to 21MT-1 (IMC). This system thus reveals potential therapeutic targets and will provide a means of testing the influences of identified genes on transitions between these stages of pre-malignant to malignant growth. KEYWORDS: breast cancer; tumor progression; expression microarray; atypical ductal hyperplasia; ductal carcinoma in situ; invasive mammary carcinoma Pathological and epidemiological evidence has led to a histological model of breast cancer evolution, in which stem cells from the terminal duct lobular unit give rise to atypical ductal hyperplasia (ADH) or atypical lobular hyperplasia, which can then progress to ductal carcinoma in situ (DCIS) or lobular carcinoma in situ, respectively, and eventually to invasive mammary carcinomas (IMC).1-6 These histological patterns are, however, most likely only rough phenotypic indications of underlying cellular and molecular events determining progression, 7 and may not necessarily occur in a linear fashion. There is currently much interest in identifying the nature of the cellular and molecular events involved, not only for use in determining at which point a lesion is most likely to progress to malignancy, but also in hopes of finding a way to halt ...