Cell fate decisions are specified by the dynamic ERK interactome

Signalling and Proteomics Laboratory, The Beatson Institute for Cancer Research, Glasgow G61 1BD, UK.
Nature Cell Biology (Impact Factor: 19.68). 12/2009; 11(12):1458-64. DOI: 10.1038/ncb1994
Source: PubMed


Extracellular signal-regulated kinase (ERK) controls fundamental cellular functions, including cell fate decisions. In PC12, cells shifting ERK activation from transient to sustained induces neuronal differentiation. As ERK associates with both regulators and effectors, we hypothesized that the mechanisms underlying the switch could be revealed by assessing the dynamic changes in ERK-interacting proteins that specifically occur under differentiation conditions. Using quantitative proteomics, we identified 284 ERK-interacting proteins. Upon induction of differentiation, 60 proteins changed their binding to ERK, including many proteins that were not known to participate in differentiation. We functionally characterized a subset, showing that they regulate the pathway at several levels and by different mechanisms, including signal duration, ERK localization, feedback, crosstalk with the Akt pathway and differential interaction and phosphorylation of transcription factors. Integrating these data with a mathematical model confirmed that ERK dynamics and differentiation are regulated by distributed control mechanisms rather than by a single master switch.

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    • "Both amplitude (dose) and duration of input signals provide information that regulates cellular decisions. The duration of Epidermal Growth Factor (EGF) stimulation modulates ERK dynamics and controls differentiation (Santos et al., 2007; von Kriegsheim et al., 2009; Ahmed et al., 2014). Glucose sensing in plants showed that cells have gene regulatory network mechanisms to allow similar responses to a short, intense or sustained, moderate stimulus (Fu et al., 2014). "
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    ABSTRACT: Digital signaling enhances robustness of cellular decisions in noisy environments, but it is unclear how digital systems transmit temporal information about a stimulus. To understand how temporal input information is encoded and decoded by the NF-κB system, we studied transcription factor dynamics and gene regulation under dose- and duration-modulated inflammatory inputs. Mathematical modeling predicted and microfluidic single-cell experiments confirmed that integral of the stimulus (or area, concentration × duration) controls the fraction of cells that activate NF-κB in the population. However, stimulus temporal profile determined NF-κB dynamics, cell-to-cell variability, and gene expression phenotype. A sustained, weak stimulation lead to heterogeneous activation and delayed timing that is transmitted to gene expression. In contrast, a transient, strong stimulus with the same area caused rapid and uniform dynamics. These results show that digital NF-κB signaling enables multidimensional control of cellular phenotype via input profile, allowing parallel and independent control of single-cell activation probability and population heterogeneity.
    eLife Sciences 10/2015; 4. DOI:10.7554/eLife.08931 · 9.32 Impact Factor
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    • "With this compromise, proteomic measurements of time-dependent changes in signaling pathways can be obtained using targeted, multiplexed and quantitative approaches, such as MRM-MS coupled with stable isotope dilution (SID) [53-55], in vitro kinase assays [56], quantitative immunoblotting and enzyme-linked immunosorbent assays (ELISAs) [57] or protein arrays [58-60]. By monitoring dynamic changes in these PPIs, temporal data have been used to reconstruct signaling pathways involved in cell differentiation and apoptosis [61-63]. In addition, immuno-enrichment of phosphotyrosine residues and quantitative MS methods have previously explored time-dependent changes in signaling downstream of epidermal growth factor receptor (EGFR) [64,65]; the combination of MS, phosphorylation motif–directed antibodies, and phosphorylated serine-threonine–binding modules (e.g., 14-3-3 proteins or the Polo-box domain of Polo-like kinases) identified signaling networks involved in cell migration, metabolism, mitosis, and DNA damage [66-68]; and the use of analog-specific protein kinase mutants and MS identified comprehensive lists of substrates, e.g., those previously unknown to cyclin-dependent kinase 1-cyclin B, with the potential of expanding our understanding of kinase-substrate connections in signaling networks [69,70]. "
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    Clinical Proteomics 06/2014; 11(1):22. DOI:10.1186/1559-0275-11-22
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    • "Neurite outgrowth is an important aspect of neuronal plasticity and regeneration in neuropathological conditions and neural injury [27]. Consistent with previous reports [28,29], in this study, more than 20% of NGF-stimulated PC12 cells had neurites that were twice the cell body length after exposure to RA4. Although the effects of IH on neuronal cell differentiation remain poorly understood, a previous study reported that 10 cycles of IH (1% O2 for 24 h, following a 24-h recovery period under RA) suppressed retinoic acid-induced differentiation of neuroblastoma cells [9]. "
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    Journal of Biomedical Science 05/2014; 21(1):46. DOI:10.1186/1423-0127-21-46 · 2.76 Impact Factor
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