TGFβ1-Induced EMT in the MCF10A Mammary Epithelial Cell Line Model Is Executed Independently of SNAIL1 and ZEB1 but Relies on JUNB-Coordinated Transcriptional Regulation

SIMPLE SUMMARY: While invading tumor-adjacent tissue, cancer cells often undergo epithelial-mesenchymal transition (EMT). A mechanistic understanding of EMT may therefore improve diagnostic and therapeutic options. Traditionally, EMT is thought to be regulated by SNAIL, TWIST, and ZEB transcription factors. Since this view is increasingly challenged, we aimed to examine the importance of traditional EMT regulators while identifying alternative factors potentially orchestrating EMT. By combining computational analyses of epigenomic and transcriptomic data with loss-of-function experiments, we demonstrate that JUNB, a component of the AP-1 transcription factor complex, is crucial for EMT in the MCF10A mammary epithelial cell line model, but not SNAIL proteins and ZEB1. We exploited the JUNB-dependence of EMT to define a gene signature which is controlled by TGFβ in multiple cancer entities and which is predictive of patient survival. Our results provide a more refined picture of the dynamic regulation of EMT and suggest that traditional models for EMT regulation may need to be revised. ABSTRACT: Epithelial-mesenchymal transition (EMT) fosters cancer cell invasion and metastasis, the main cause of cancer-related mortality. Growing evidence that SNAIL and ZEB transcription factors, typically portrayed as master regulators of EMT, may be dispensable for this process, led us to re-investigate its mechanistic underpinnings. For this, we used an unbiased computational approach that integrated time-resolved analyses of chromatin structure and differential gene expression, to predict transcriptional regulators of TGFβ1-inducible EMT in the MCF10A mammary epithelial cell line model. Bioinformatic analyses indicated comparatively minor contributions of SNAIL proteins and ZEB1 to TGFβ1-induced EMT, whereas the AP-1 subunit JUNB was anticipated to have a much larger impact. CRISPR/Cas9-mediated loss-of-function studies confirmed that TGFβ1-induced EMT proceeded independently of SNAIL proteins and ZEB1. In contrast, JUNB was necessary and sufficient for EMT in MCF10A cells, but not in A549 lung cancer cells, indicating cell-type-specificity of JUNB EMT-regulatory capacity. Nonetheless, the JUNB-dependence of EMT-associated transcriptional reprogramming in MCF10A cells allowed to define a gene expression signature which was regulated by TGFβ1 in diverse cellular backgrounds, showed positively correlated expression with TGFβ signaling in multiple cancer transcriptomes, and was predictive of patient survival in several cancer types. Altogether, our findings provide novel mechanistic insights into the context-dependent control of TGFβ1-driven EMT and thereby may lead to improved diagnostic and therapeutic options.