We aimed to study the effects of the TGF-beta pathway in breast cancer stem cell (BCSC) regulation. To define a role of the TGF-beta pathway in the regulation of human BCSCs, we have analyzed a panel of breast cancer cell lines that represent the molecular heterogeneity present in primary tumors. In vitro and in vivo assays showed that TGF-beta differentially regulates BCSCs populations of cell lines from different transcriptional profile clusters (Neve et al. 2006). A transcriptomic approach was performed to identify a TGF-beta self-renewal promoting gene signature. An integrated bioinformatic analysis found this signature to be a prognostic pathway signature in ER-/basal human breast cancer. We are now focusing on trying to unravel the underlying molecular mechanisms of the dual effects of TGF-beta in BCSCs.