Time-resolved mapping of genetic interactions to model rewiring of signaling pathways

Context-dependent
changes in genetic vulnerabilities are important to understand the wiring of
cellular pathways and variations in different environmental conditions. However,
methodological frameworks to investigate the plasticity of genetic networks
over time or in response to external stresses are lacking. To analyze the
plasticity of genetic interactions, we performed an arrayed combinatorial RNAi
screen in Drosophila cells at
multiple time points and after pharmacological inhibition of Ras signaling
activity. Using an image-based morphology assay to capture a broad range of phenotypes,
we assessed the effect of 12768 pairwise RNAi perturbations in six different
conditions. We found that genetic interactions form in different trajectories
and developed an algorithm, termed MODIFI, to analyze how genetic interactions rewire
over time. Using this framework, we
identified more statistically significant interactions compared to end-points
assays and further observed several examples of context-dependent crosstalk
between signaling pathways such as an interaction between Ras and Rel which is dependent
on MEK activity.