Time-resolved dissection of early phosphoproteome and ensuing proteome changes in response to TGF-β

Transforming growth factor-beta (TGF-beta) signaling promotes cell motility by inducing epithelial-to-mesenchymal transitions (EMTs) in normal physiology and development, as well as in pathological conditions, such as cancer. We performed a time-resolved analysis of the proteomic and phosphoproteomic changes of cultured human keratinocytes undergoing EMT and cell cycle arrest in response to stimulation with TGF-beta. We quantified significant changes in 2079 proteins and 2892 phosphorylation sites regulated by TGF-beta. We identified several proteins known to be involved in TGF-beta-induced cellular processes, such as the cytostatic response, extracellular matrix remodeling, and epithelial dedifferentiation. In addition, we identified proteins involved in other cellular functions, such as vesicle trafficking, that were not previously associated with TGF-beta signaling. Although many TGF-beta responses are mediated by phosphorylation of the transcriptional regulators of the SMAD family by the TGF-beta receptor complex, we observed rapid kinetics of changes in protein phosphorylation, indicating that many responses were mediated through SMAD-independent TGF-beta signaling. Combined analysis of changes in protein abundance and phosphorylation and knowledge of protein interactions and transcriptional regulation provided a comprehensive representation of the dynamic signaling events underlying TGF-beta-induced changes in cell behavior. Our data suggest that in epithelial cells stimulated with TGF-beta, early signaling is a mixture of both pro- and antiproliferative signals, whereas later signaling primarily inhibits proliferation.