A gene regulatory network to control EMT programs in development and disease

Epithelial to Mesenchymal Transition (EMT) plays pivotal roles during development and diseases like cancer and fibrosis, through the activation of several EMT transcription factor (EMT-TF) families, including Snail, Zeb, Twist and Prrx. Prior data from the laboratory showed that the patterns of PRRX1 and SNAIL1 expression were complementary in chicken embryos and cancer cells, and that their functions in EMT subprograms, such as the regulation of stemness, also seemed to be distinct. Here, after examining zebrafish, chicken and mouse embryos, we find that this complementary expression of Snail1 and Prrx1 is conserved during vertebrate development. Moreover, analyzing public single-cell RNA sequencing databases of breast, head-and-neck cancer or melanoma patients and from mouse pulmonary fibrosis, we confirmed that this complementary expression is also present in pathological EMTs. By studying the transcriptome of cancer cells, gain and loss of function experiments for the two EMT-TFs, and the use of animal models, we describe a novel gene regulatory network (GRN) where Snail1 and Prrx1 form a double-negative feedback loop, involving miR-15 family. We have found that this GRN triggers an expression switch from Snail1 to Prrx1, with Snail1 being an early-response gene to EMT-inducing signals, which is followed by the activation of Prrx1 that in turn attenuates Snail1 expression through miR-15 family. We have also validated this GRN in vitro and in vivo highlighting its relevance in development and disease