Systems modelling of TGF-β/Hippo signalling crosstalk uncovers molecular switches that coordinate YAP transcriptional complexes

Abstract

The Hippo pathway is an evolutionarily conserved signaling network that integrates diverse cues to regulate cell fate and organ homeostasis. The central downstream pathway protein is the transcriptional co-activator Yes-associated protein (YAP). Although capable of inducing gene transcription, YAP cannot bind DNA directly. Instead, it mediates transcriptional activity through interaction with distinct DNA-binding transcriptional factors (TFs), including TEAD, SMAD, and p73, to form active and functionally opposing transcriptional complexes. Growing evidence in mammals demonstrates that YAP has a dual role and can either promote cell proliferation or apoptosis, which underpin its ability to function as both an oncogene or a tumour suppressor depending on the specific context. However, the mechanisms by which YAP coordinates its distinct transcriptional complexes and mediates context-dependent function remain poorly defined. This is in part due to the lack of systems-level studies that can decrypt the complexities of upstream signalling pathways and their crosstalk, which together dictate the transcriptional regulation at the YAP level. Here, we undertake an integrative systems-based approach combining computational network modelling and experimental studies to interrogate the dynamic formation of and transition between the YAP-SMAD and YAP-p73 transcriptional complexes, which control proliferative and apoptotic gene expression, respectively. We developed a new experimentally-validated mathematical model of the TGF-{beta}/Hippo signalling crosstalk and used this model to elucidate dynamic network behaviour. Our integrative studies uncovered previously unknown molecular switches that control the YAP-SMAD/p73 complexes in an on/off, switch-like manner. RASSF1A and ITCH were identified as major regulators of the switches, whereby a graded increase in ITCH expression can trigger YAP to abruptly switch from binding p73 to SMAD, swiftly promoting proliferative gene expression. Further, adjusting the model to reflect cell type-specific protein expression profiles using both in-house and publicly available experimental data enabled us to study the YAP switches under diverse and varied cellular contexts. Overall, our studies provide a new quantitative and systems-level understanding of the dynamic regulation of functionally opposing YAP transcriptional complexes in mammalian cells.