Receptor-Based Mechanism of Cell Memory and Relative Sensing in Mammalian Signaling Networks

Abstract

Mammalian cells operate in fluctuating environments by perceiving and reacting to a diverse set of extracellular stimuli 1 . Detecting relative rather than absolute changes in their environments may enable cells to make decisions in diverse biological contexts 2,3 .However, precise molecular mechanisms underlying such relative sensing by mammalian signaling networks are not well understood. Here we use a combined computational and experimental analysis to investigate the growth factor activated immediate-early phosphorylation response of protein kinase B (Akt). We demonstrate that activity-dependent receptor degradation allows cells to robustly detect fold changes in extracellular Epidermal Growth Factor (EGF) levels across orders of magnitude of EGF background concentrations. Interestingly, we show that the memory of the background stimulation is effectively encoded in the number of EGF receptors on the cell surface. We further demonstrate that the ability to sense relative changes by the Akt pathway extends to hepatocyte growth factor (HGF) signaling. We develop an analytical model that reveals key aggregate network parameters controlling the relative sensing capabilities of the system. The mechanism described in our study could play a role in multiple other sensory cascades where stimulation leads to a proportional reduction in the abundance of cell surface receptors. Beyond simple receptor and signal downregulation, this mechanism may allow cells to continuously monitor their environments and store the memory of past ligand exposures.peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission. To understand how the immediate-early dynamics of the EGFR/Akt pathway depends on the background level of EGF we used immunofluorescence to quantify the pAkt signal in human non-transformed mammary epithelial MCF10A cells (SI section II).In agreement with previous studies 9 , upon continuous stimulation with EGF, pAkt Prior exposure with EGF desensitized cells to subsequent EGF stimulations in a quantitative manner, i.e. maximal pAkt response to the same EGF stimulation (2 ng/ml) was monotonically attenuated with increasing pre-exposure EGF levels ( Figure 1d).These results suggest that the strength of the pAkt responses to EGF stimulation is modulated by background EGF levels and that this effect is mediated by the removal of activated EGFRs from cell surface 10 .peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/158774 doi: bioRxiv preprint first posted online Jul. 2, 2017; Table 1), and fitted the model using pAkt time courses and steady state sEGFR levels at different doses of EGF stimulations. Parameter optimization was performed using simulated annealing (SA) 15 (SI section III). Parameters of ODE models describing complex signaling networks are usually underdetermined with multiple distinct parameter sets producing similar fits to the data 16 . Th...

Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks

“…Based on the ability of MERIDIAN to predict single-cell abundance distributions across several in silico parameterizations of the EGFR/Akt pathway, we next investigated the performance of MERIDIAN with experimental data describing single-cell heterogeneity in mammalian cells. Toward that end, we used previously measured cell-to-cell variability in pAkt levels at early times after EGF stimulation in MCF10A cells (Lyashenko et al, 2018). In addition, we also measured data describing sEGFR abundance variability across MCF10A cells (STAR Methods).…”

“…In this work, we used distributions of cell-to-cell variability in phosphorylated Akt levels as well as cell surface EGFR levels. We used the experimental data on pAkt levels previously measured in Lyashenko et al (Lyashenko et al, 2018). sEGFR data was measured for this work.…”

“…Because of its central role in mammalian signaling, aberrations in the Akt pathway are implicated in multiple disorders (Manning and Toker, 2017). We apply MERIDIAN to infer the distribution over signaling parameters using previously collected experimental data on phosphorylated Akt (pAkt) (Lyashenko et al, 2018) and data on cell surface EGF receptor (sEGFR) abundance measured in MCF10A cells. We demonstrate that the parameter distribution inferred using MERIDIAN allows us to accurately predict the cell-to-cell heterogeneity of pAkt levels at late time points after stimulation as well as the heterogeneity of sEGFRs in response to EGF signal.…”