Transforming growth factor-βs (TGF-βs) have complex roles in tumorigenesis, with context-dependent effects that can either suppress or promote tumor progression. The dogma is that tumor suppressive effects are active in the early stages of carcinogenesis, but that later pro-progression effects come to dominate. Since TGF-β antagonists of various types are in early phase clinical trials in cancer, it is important to know whether the tumor suppressive effects of TGF-β are still intact in any tumors at the time of diagnosis and treatment. Existing TGF-β-related gene expression signatures were not designed a priori to discriminate the tumor suppressive from the tumor promoting activities. To address this question, we applied integrated ChIP-chip and transcriptomic approaches in the MCF10A-based model of breast cancer progression. We have previously shown that TGF-β has tumor suppressor activity in the less malignant cell lines of the series (MCF10A, MCF10AT1k, MCF10Ca1h), but that this effect is lost in the most malignant cell line (MCF10Ca1a). The tumor suppressor activity is dependent on the downstream signaling component Smad3. Using promoter-wide ChIP-chip, we found that the genomic landscape of TGF-β induced Smad3 binding differed dramatically between the four cell lines, despite their close genetic relatedness. Interestingly, TGF-β induced Smad3 binding only at genetic loci that were already transcriptionally active, suggesting that TGF-βs may primarily play a modulator rather than an instigator role in regulating transcription. This feature probably contributes significantly to the known contextuality of TGF-β activity. By focusing on the two malignant cell lines (MCF10CA1h and MCF10CA1a), we identified a core signature of 26 TGF-β/Smad3 regulated genes that were specifically associated with the tumor suppressor activity of TGF-β. Unexpectedly, the direction of regulation of 25% of these genes by TGF-β differed in vitro and in vivo, highlighting a further novel contribution to TGF-β contextuality, and emphasizing the importance of including in vivo data in this type of analysis. The in vivo weighted form of the TGF-β/Smad3 tumor suppressor signature was associated with good outcome in estrogen-receptor positive breast cancer patients, suggesting that TGF-β tumor suppressive pathways are still active and influencing disease outcome in a subset of patients’ tumors at the time of surgery. TGF-β is a potent growth inhibitor for most epithelial cells, but anti-proliferative effects made only a minor contribution to the tumor suppressor activity in the breast cancer cohorts. Instead, novel tumor suppressor effects of TGF-β captured by this approach included the restoration of tumor suppressive EphrinA signaling, leading to increased tumor cell differentiation. The results have important implications for patient stratification in ongoing clinical trials with TGF-β antagonists.

Citation Format: Misako Sato, Mitsutaka Kadota, Binwu Tang, Yu-an Yang, Mengge Shan, Jia Weng, Michael Welsh, Aleksandra Michalowski, Howard Yang, Robert Clifford, Maxwell Lee, Lalage M. Wakefield. An integrated genomic approach specifically dissects out the tumor suppressor aspect of TGF-β in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4310. doi:10.1158/1538-7445.AM2013-4310