Diverse cell stimulation kinetics identify predictive signal transduction models

Abstract

The drive to understand cell signaling responses to environmental, chemical and genetic perturbations has produced outstanding fits of computational models to increasingly intricate experiments, yet predicting quantitative responses for new biological conditions remains challenging. Overcoming this challenge depends not only on good models and detailed experimental data but perhaps more so on how well the two are integrated. Our quantitative, live single-cell fluorescence imaging datasets and computational framework to model generic signaling networks show how different changing environments (hereafter 'kinetic stimulations') probe and result in distinct pathway activation dynamics. Utilizing multiple diverse kinetic stimulations better constrains model parameters and enables predictions of signaling dynamics that would be impossible using traditional step-change stimulations. To demonstrate our approach's generality, we use identified models to predict signaling dynamics in normal, mutated, and drug-treated conditions upon multitudes of kinetic stimulations and quantify which proteins and reaction rates are most sensitive to which extracellular stimulations.

Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments

“…The high osmolarity glycerol (HOG) MAPK pathway in the budding yeast Saccharomyces cerevisiae (Figure 3A) is an ideal model system (Brewster et al, 1993;Saito and Posas, 2012;Brewster and Gustin, 2014) for addressing the question how do rate sensitivity and rate thresholds impact cell signaling and phenotype (Thiemicke et al, 2019;Jashnsaz et al, 2020;Johnson et al, 2021). At the molecular level, pioneering studies found that one signaling branch is activated through the Synthetic Lethal of N-end rule (Sln1) osmosensing histidine protein kinase leading to activation of the MAPKKK's Suppressor of Sensor Kinase (Ssk2) and its paralog Ssk22 and converging on the MAPKK Polymyxin B Sensitivity (Pbs2) kinase through several intermediate proteins.…”

“…Activated Hog1 controls the regulation of cellular osmoadaptation and survival (Saito and Posas, 2012;Mitchell et al, 2015;Johnson et al, 2021). Because of this behavior of Hog1 nuclear enrichment, single-cell time-lapse microscopy and analysis have proven an excellent and sensitive way to monitor signaling responses to dynamic stimulation patterns in real-time (Figure 3) (Hersen et al, 2008;Mettetal et al, 2008;Muzzey et al, 2009;Patterson et al, 2010;Munsky et al, 2012;Mitchell et al, 2015;Granados et al, 2017;Thiemicke et al, 2019;Jashnsaz et al, 2021;Johnson et al, 2021). This single-cell analysis of Hog1 nuclear localization response to instant osmotic stress resulted in the discovery of perfect adaptation in this pathway (Figures 3C-E) (Hersen et al, 2008;Mettetal et al, 2008;Muzzey et al, 2009).…”

“…These signaling features might also be conserved or modulated throughout evolution because many of the signaling proteins are evolutionarily conserved. Quantitative data generated in these experiments will build the foundation for developing approaches for model inference, quantitative predictions, and computational screening of combinatorial protein regulation (Rahi et al, 2017;Jashnsaz et al, 2020;2021). The proposed approaches of non-acute cell perturbations are also amenable for dissecting many other signaling processes, such as signaling cross talk, cell cycle regulation, protein translation, phase separation, and gene regulation, which are all dependent on specific signaling dynamics.…”