IntroductionBreast cancer researchers use cell lines to model myriad phenomena ranging from DNA repair to cancer stem cell phenotypes. Though appropriate, and even requisite, for many studies, the suitability of cell lines as tumour models has come into question owing to possibilities of tissue culture artefacts and clonal selection. These issues are compounded by the inability of cancer cells grown in isolation to fully model the in situ tumour environment, which also contains a plethora of non-tumour cell types. It is thus important to understand similarities and differences between cancer cell lines and the tumours that they represent so that the optimal tumour models can be chosen to answer specific research questions.MethodsIn the present study, we compared the RNA-sequencing transcriptomes of a collection of breast cancer cell lines to transcriptomes obtained from hundreds of tumours using The Cancer Genome Atlas. Tumour purity was accounted for by analysis of stromal and immune scores using the ESTIMATE algorithm so that differences likely resulting from non-tumour cells could be accounted for.ResultsWe found the transcriptional characteristics of breast cancer cell lines to mirror those of the tumours. We identified basal and luminal cell lines that are most transcriptionally similar to their respective breast tumours. Our comparison of expression profiles revealed pronounced differences between breast cancer cell lines and tumours, which could largely be attributed to the absence of stromal and immune components in cell culture. A focus on the Wnt pathway revealed the transcriptional downregulation or absence of several secreted Wnt antagonists in culture. Gene set enrichment analysis suggests that cancer cell lines have enhanced proliferation and glycolysis independent of stromal and immune contributions compared with breast cancer cells in situ.ConclusionsThis study demonstrates that many of the differences between breast cancer cell lines and tumours are due to the absence of stromal and immune components in vitro. Hence, extra precautions should be taken when modelling extracellular proteins in vitro. The specific differences discovered emphasize the importance of choosing an appropriate model for each research question.Electronic supplementary materialThe online version of this article (doi:10.1186/s13058-015-0613-0) contains supplementary material, which is available to authorized users.

Plasticity of neoplasia, whereby cancer cells attain stem-cell-like properties, is required for disease progression and represents a major therapeutic challenge. We report that in breast cancer cells NANOG, SNAIL and NODAL transcripts manifest multiple isoforms characterized by different 5' Untranslated Regions (5'UTRs), whereby translation of a subset of these isoforms is stimulated under hypoxia. The accumulation of the corresponding proteins induces plasticity and "fate-switching" toward stem cell-like phenotypes. Mechanistically, we observe that mTOR inhibitors and chemotherapeutics induce translational activation of a subset of NANOG, SNAIL and NODAL mRNA isoforms akin to hypoxia, engendering stem-celllike phenotypes. These effects are overcome with drugs that antagonize translational reprogramming caused by eIF2α phosphorylation (e.g. ISRIB), suggesting that the Integrated Stress Response drives breast cancer plasticity. Collectively, our findings reveal a mechanism of induction of plasticity of breast cancer cells and provide a molecular basis for therapeutic strategies aimed at overcoming drug resistance and abrogating metastasis.

The progression of cancer from localized to invasive disease is requisite for metastasis, and is often characterized by epithelial-to-mesenchymal transition (EMT) and alterations in cellular adhesion and migration. Studies have shown that this transition is associated with an up-regulation of embryonic stem cell-associated genes, resulting in a dedifferentiated phenotype and poor patient prognosis. Nodal is an embryonic factor that plays a critical role in promoting early invasive events during development. Nodal is silenced as stem cells differentiate; however, it re-emerges in adult life during placentation and mammary gland development, and is aberrantly expressed in many cancers. Here, we show that Nodal over-expression, in poorly-invasive breast cancer and choriocarcinoma cells, causes increased invasion and migration in vitro. Furthermore, we show that Nodal over-expression in these epithelial cancer types induces an EMT-like event concomitant with the internalization of E-Cadherin. This ability of Nodal to promote cellular invasion and EMT-like phenomena is dependent upon the phosphorylation of ERK1/2. Since Nodal normally signals through SMADs, these findings lend insight into an alternative pathway that is hijacked by this protein in cancer. To evaluate the clinical implications of our results, we show that Nodal inhibition reduces liver tumor burden in a model of spontaneous breast cancer metastasis in vivo, and that Nodal loss-of-function in aggressive breast cancer lines results in a decrease in invasive phenotypes. Our results demonstrate that Nodal is involved in promoting invasion in multiple cellular contexts, and that Nodal inhibition may be useful as a therapeutic target for patients with progressive disease.