Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling
MetadataShow full item record
CitationEstrada, Javier, Natalie Andrew, Daniel Gibson, Frederick Chang, Florian Gnad, and Jeremy Gunawardena. 2016. “Cellular Interrogation: Exploiting Cell-to-Cell Variability to Discriminate Regulatory Mechanisms in Oscillatory Signalling.” PLoS Computational Biology 12 (7): e1004995. doi:10.1371/journal.pcbi.1004995. http://dx.doi.org/10.1371/journal.pcbi.1004995.
AbstractThe molecular complexity within a cell may be seen as an evolutionary response to the external complexity of the cell’s environment. This suggests that the external environment may be harnessed to interrogate the cell’s internal molecular architecture. Cells, however, are not only nonlinear and non-stationary, but also exhibit heterogeneous responses within a clonal, isogenic population. In effect, each cell undertakes its own experiment. Here, we develop a method of cellular interrogation using programmable microfluidic devices which exploits the additional information present in cell-to-cell variation, without requiring model parameters to be fitted to data. We focussed on Ca2+ signalling in response to hormone stimulation, which exhibits oscillatory spiking in many cell types and chose eight models of Ca2+ signalling networks which exhibit similar behaviour in simulation. We developed a nonlinear frequency analysis for non-stationary responses, which could classify models into groups under parameter variation, but found that this question alone was unable to distinguish critical feedback loops. We further developed a nonlinear amplitude analysis and found that the combination of both questions ruled out six of the models as inconsistent with the experimentally-observed dynamics and heterogeneity. The two models that survived the double interrogation were mathematically different but schematically identical and yielded the same unexpected predictions that we confirmed experimentally. Further analysis showed that subtle mathematical details can markedly influence non-stationary responses under parameter variation, emphasising the difficulty of finding a “correct” model. By developing questions for the pathway being studied, and designing more versatile microfluidics, cellular interrogation holds promise as a systematic strategy that can complement direct intervention by genetics or pharmacology.
Citable link to this pagehttp://nrs.harvard.edu/urn-3:HUL.InstRepos:27822281
Showing items related by title, author, creator and subject.
ErbB2, EphrinB1, Src Kinase and PTPN13 Signaling Complex Regulates MAP Kinase Signaling in Human Cancers Vermeer, Paola D.; Bell, Megan; Lee, Kimberly; Vermeer, Daniel W.; Wieking, Byrant G.; Bilal, Erhan; Bhanot, Gyan; Ganesan, Shridar; Klingelhutz, Aloysius J.; Hendriks, Wiljan J.; Drapkin, Ronny I.; Lee, John H. (Public Library of Science, 2012)In non-cancerous cells, phosphorylated proteins exist transiently, becoming de-phosphorylated by specific phosphatases that terminate propagation of signaling pathways. In cancers, compromised phosphatase activity and/or ...
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction Saez-Rodriguez, Julio; Alexopoulos, Leonidas G; Epperlein, Jonathan; Samaga, Regina; Lauffenburger, Douglas A; Klamt, Steffen; Sorger, Peter Karl (Nature Publishing Group, 2009)Large-scale protein signalling networks are useful for exploring complex biochemical pathways but do not reveal how pathways respond to specific stimuli. Such specificity is critical for understanding disease and designing ...
Locasale, Jason Wei (BioMed Central, 2008)Background: Signal duration (e.g. the time over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage ...