Abstract
Phosphosignaling networks control cellular processes. We built kinase-mediated regulatory networks elicited by thrombin stimulation of brain endothelial cells using two computational strategies: Temporal Pathway Synthesizer (TPS), which uses phosphoproteomics data as input, and Temporally REsolved KInase Network Generation (TREKING), which uses kinase inhibitor screens. TPS and TREKING predicted overlapping barrier-regulatory kinases connected with unique network topology. Each strategy effectively describes regulatory signaling networks and is broadly applicable across biological systems.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
For the revised manuscript, we have developed strategies to evaluate the model predictions using orthogonal measurements not used for building the networks. Specifically, we compared predictions made by the TPS network on the impact of kinase inhibitors on barrier permeability with the kinase inhibitor screen data. We also compared predictions made by the TREKING network on barrier-regulatory kinases with the western blot data on their changes of activity upon thrombin stimulation. We have demonstrated that both approaches are able to inform the underlying kinase-mediated phosphosignaling important for barrier regulation. Moreover, we compared the phosphorylation interactions inferred by the models with the canonical thrombin signaling pathway from Reactome knowledgebase and noted their minimal overlap in terms of kinase phosphorylation. This highlights the power of systems-level network reconstruction methodologies in revealing novel signaling events important for modulating cellular phenotypes.
