A multi-tiered map of EMT defines major transition points and identifies vulnerabilities

Summary TGFβ mediated epithelial to mesenchymal transition (EMT) proceeds through hybrid ‘E/M’ states. A deeper understanding of these states and events which regulate entry to and exit from the E/M states is needed for therapeutic exploitation. We quantified >60,000 molecules across ten time points and twelve omic layers in mammary epithelial cells. Proteomes of whole cells, phosphoproteins, nucleus, extracellular vesicles, secretome and membrane resolved major shifts, E→E/M and E/M→M during EMT, and defined state-specific signatures. Metabolomics identified early activation of arachidonic acid pathway and an enzyme-mediated switch from Cytochrome P450 to Cyclooxygenase / Lipoxygenase branches during E→E/M. Single-cell transcriptomics identified GLIS2 as an early modulator of EMT. Integrative modeling-predicted combinatorial inhibition of AURKB, PP2A and SRC exposed vulnerabilities at E→E/M juncture. Covariance analysis revealed remarkable discordance between proteins and transcripts, and between proteomic layers, implying insufficiency of current approaches. Overall, this dataset provides an unprecedented resource on TGFβ signaling, EMT and cancer.