A Systematic Analysis of Signaling Reactivation and Drug Resistance

Abstract

Increasing evidence suggests that reactivation of initially inhibited signaling pathways causes drug resistance. Here, we reveal network topology features and molecular mechanisms that are necessary and sufficient for complete reactivation or overshoot of steady state signaling after drug treatment. Network-dependent drug resistance is commonly attributed to negative and positive feedback loops mediated by posttranslational modification or transcription and translation. We show that feedback loops, by themselves, cannot completely reactivate steady state signaling. De novo synthesized negative feedback regulators can lead to a transient overshoot but still cannot fully restore output signaling. At least two, activating and inhibitory, connection routes from an inhibited upstream protein to a downstream output must exist for complete reactivation of signaling. Irrespective of the network topology, drug-induced overexpression of a primary target or increase in its dimerization can restore or even paradoxically increase the pathway activity. Inhibitor-induced kinase dimerization cooperates with inhibitor-mediated alleviation of negative feedback. These findings will inform the development of new drugs that consider network context and guide the design of optimal combinations of existing drugs. As an example, we demonstrate that in RAS-mutant cancers the optimal combination to counterbalance ERK pathway reactivation and concomitant drug resistance is a combination of Type I½ and Type II RAF inhibitors.