Context-dependent regulatory mechanisms control site-specific information processing within the MEK/ERK module

The impact of the cellular context and receptor type on the dynamics of phosphorylation cycles in signaling pathways are unclear. We employ an unbiased approach to identify network alterations that explain phosphorylation dynamics of the MEK/ERK module in response to hepatocyte growth factor or interleukin-6, comparing primary hepatocytes with the immortalized cell line HaCaT. By combining quantitative mass spectrometry with dynamic modeling, we elucidate the network structure in primary hepatocytes. For HaCaT, our model predicts additional dual feedback regulation, which we experimentally identify as DUSP6 and paxillin. Model analyses reveal switch-like ERK phospho-form distribution profiles in primary hepatocytes that are severely altered in HaCaT, explaining threshold, sensitivity and saturation behavior. We apply our approach to human hepatocellular carcinoma samples and identify, as predicted, elevated threonine-phosphorylated ERK levels in the tumor. This suggests that the prevalence of the mono-phosphorylated ERK rather than the doubly phosphorylated ERK is indicative for dysregulated proliferation.