Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

Kinase and phosphatase overexpression drives tumorigenesis and drug resistance in many cancer types. Signaling networks reprogrammed by protein overexpression remain largely uncharacterized, hindering discovery of paths to therapeutic intervention. We previously developed a single cell proteomics approach based on mass cytometry that enables quantitative assessment of overexpression effects on the signaling network. Here we applied this approach in a human kinome- and phosphatome-wide study to assess how 649 individually overexpressed proteins modulate the cancer-related signaling network in HEK293T cells. Based on these data we expanded the functional classification of human kinases and phosphatases and detected 208 novel signaling relationships. In the signaling dynamics analysis, we showed that increased ERK-specific phosphatases sustained proliferative signaling, and using a novel combinatorial overexpression approach, we confirmed this phosphatase-driven mechanism of cancer progression. Finally, we identified 54 proteins that caused ligand-independent ERK activation with potential as biomarkers for drug resistance in cells carrying BRAF mutations.