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Witmond M, Keizer E, Kiffen B, Huck WTS, van Buggenum JAGL. Dynamic hydrogen peroxide levels reveal a rate-dependent sensitivity in B-cell lymphoma signaling. Sci Rep 2024; 14:4265. [PMID: 38383739 PMCID: PMC10882005 DOI: 10.1038/s41598-024-54871-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/17/2024] [Indexed: 02/23/2024] Open
Abstract
Although in vivo extracellular microenvironments are dynamic, most in vitro studies are conducted under static conditions. Here, we exposed diffuse large B-cell lymphoma (DLBCL) cells to gradient increases in the concentration of hydrogen peroxide (H2O2), thereby capturing some of the dynamics of the tumour microenvironment. Subsequently, we measured the phosphorylation response of B-cell receptor (BCR) signalling proteins CD79a, SYK and PLCγ2 at a high temporal resolution via single-cell phospho-specific flow cytometry. We demonstrated that the cells respond bimodally to static extracellular H2O2, where the percentage of cells that respond is mainly determined by the concentration. Computational analysis revealed that the bimodality results from a combination of a steep dose-response relationship and cell-to-cell variability in the response threshold. Dynamic gradient inputs of varying durations indicated that the H2O2 concentration is not the only determinant of the signalling response, as cells exposed to more shallow gradients respond at lower H2O2 levels. A minimal model of the proximal BCR network qualitatively reproduced the experimental findings and uncovered a rate-dependent sensitivity to H2O2, where a lower rate of increase correlates to a higher sensitivity. These findings will bring us closer to understanding how cells process information from their complex and dynamic in vivo environments.
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Affiliation(s)
- Melde Witmond
- Institute for Molecules and Materials (IMM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Emma Keizer
- Institute for Molecules and Materials (IMM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Bas Kiffen
- Institute for Molecules and Materials (IMM), Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials (IMM), Radboud University Nijmegen, Nijmegen, The Netherlands.
| | - Jessie A G L van Buggenum
- Institute for Molecules and Materials (IMM), Radboud University Nijmegen, Nijmegen, The Netherlands.
- Single Cell Discoveries (SCD), Utrecht, The Netherlands.
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2
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Samad SS, Schwartz JM, Francavilla C. Functional selectivity of Receptor Tyrosine Kinases regulates distinct cellular outputs. Front Cell Dev Biol 2024; 11:1348056. [PMID: 38259512 PMCID: PMC10800419 DOI: 10.3389/fcell.2023.1348056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Functional selectivity refers to the activation of differential signalling and cellular outputs downstream of the same membrane-bound receptor when activated by two or more different ligands. Functional selectivity has been described and extensively studied for G-protein Coupled Receptors (GPCRs), leading to specific therapeutic options for dysregulated GPCRs functions. However, studies regarding the functional selectivity of Receptor Tyrosine Kinases (RTKs) remain sparse. Here, we will summarize recent data about RTK functional selectivity focusing on how the nature and the amount of RTK ligands and the crosstalk of RTKs with other membrane proteins regulate the specificity of RTK signalling. In addition, we will discuss how structural changes in RTKs upon ligand binding affects selective signalling pathways. Much remains to be known about the integration of different signals affecting RTK signalling specificity to orchestrate long-term cellular outcomes. Recent advancements in omics, specifically quantitative phosphoproteomics, and in systems biology methods to study, model and integrate different types of large-scale omics data have increased our ability to compare several signals affecting RTK functional selectivity in a global, system-wide fashion. We will discuss how such methods facilitate the exploration of important signalling hubs and enable data-driven predictions aiming at improving the efficacy of therapeutics for diseases like cancer, where redundant RTK signalling pathways often compromise treatment efficacy.
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Affiliation(s)
- Sakim S. Samad
- Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Division of Evolution, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Jean-Marc Schwartz
- Division of Evolution, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Chiara Francavilla
- Division of Molecular and Cellular Functions, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
- Section of Protein Science and Biotherapeutics, Department of Bioengineering and Biomedicine, Danish Technical University, Lyngby, Denmark
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3
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Jashnsaz H, Neuert G. Phenotypic consequences of logarithmic signaling in MAPK stress response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.05.570188. [PMID: 38106069 PMCID: PMC10723343 DOI: 10.1101/2023.12.05.570188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
How cells respond to dynamic environmental changes is crucial for understanding fundamental biological processes and cell physiology. In this study, we developed an experimental and quantitative analytical framework to explore how dynamic stress gradients that change over time regulate cellular volume, signaling activation, and growth phenotypes. Our findings reveal that gradual stress conditions substantially enhance cell growth compared to conventional acute stress. This growth advantage correlates with a minimal reduction in cell volume dependent on the dynamic of stress. We explain the growth phenotype with our finding of a logarithmic signal transduction mechanism in the yeast Mitogen-Activated Protein Kinase (MAPK) osmotic stress response pathway. These insights into the interplay between gradual environments, cell volume change, dynamic cell signaling, and growth, advance our understanding of fundamental cellular processes in gradual stress environments.
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
- Lead Contact
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4
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Son M, Wang AG, Keisham B, Tay S. Processing stimulus dynamics by the NF-κB network in single cells. Exp Mol Med 2023; 55:2531-2540. [PMID: 38040923 PMCID: PMC10766959 DOI: 10.1038/s12276-023-01133-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/27/2023] [Accepted: 09/18/2023] [Indexed: 12/03/2023] Open
Abstract
Cells at the site of an infection experience numerous biochemical signals that vary in amplitude, space, and time. Despite the diversity of dynamic signals produced by pathogens and sentinel cells, information-processing pathways converge on a limited number of central signaling nodes to ultimately control cellular responses. In particular, the NF-κB pathway responds to dozens of signals from pathogens and self, and plays a vital role in processing proinflammatory inputs. Studies addressing the influence of stimulus dynamics on NF-κB signaling are rare due to technical limitations with live-cell measurements. However, recent advances in microfluidics, automation, and image analysis have enabled investigations that yield high temporal resolution at the single-cell level. Here, we summarize the recent research which measures and models the NF-κB response to pulsatile and fluctuating stimulus concentrations, as well as different combinations and sequences of signaling molecules. Collectively, these studies show that the NF-κB network integrates external inflammatory signals and translates these into downstream transcriptional responses.
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Affiliation(s)
- Minjun Son
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
| | - Andrew G Wang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
- Medical Scientist Training Program, University of Chicago, Chicago, IL, 60637, USA
| | - Bijentimala Keisham
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA.
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA.
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5
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Li K, Ma Y, Xia X, Huang H, Li J, Wang X, Gao Y, Zhang S, Fu T, Tong Y. Possible correlated signaling pathways with chronic urate nephropathy: A review. Medicine (Baltimore) 2023; 102:e34540. [PMID: 37565908 PMCID: PMC10419604 DOI: 10.1097/md.0000000000034540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Hyperuricemia nephropathy, also known as gouty nephropathy, refers to renal damage induced by hyperuricemia caused by excessive production of serum uric acid or low excretion of uric acid. the persistence of symptoms will lead to changes in renal tubular phenotype and accelerate the progress of renal fibrosis. The existence and progressive aggravation of symptoms will bring a heavy burden to patients, their families and society, affect their quality of life and reduce their well-being. With the increase of reports on hyperuricemia nephropathy, the importance of related signal pathways in the pathogenesis of hyperuricemia nephropathy is becoming more and more obvious, but most studies are limited to the upper and lower mediating relationship between 1 or 2 signal pathways. The research on the comprehensiveness of signal pathways and the breadth of crosstalk between signal pathways is limited. By synthesizing the research results of signal pathways related to hyperuricemia nephropathy in recent years, this paper will explore the specific mechanism of hyperuricemia nephropathy, and provide new ideas and methods for the treatment of hyperuricemia nephropathy based on a variety of signal pathway crosstalk and personal prospects.
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Affiliation(s)
- Kaiqing Li
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Yanchun Ma
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Xue Xia
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Huili Huang
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Jianing Li
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Xiaoxin Wang
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Yang Gao
- Heilongjiang University of Traditional Chinese Medicine, Harbin, China
| | - Shuxiang Zhang
- Institute of Traditional Chinese Medicine, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Tong Fu
- Brandeis University, Waltham, MA
| | - Ying Tong
- First Affiliated Hospital, Heilongjiang University of Chinese Medicine, Harbin, China
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6
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Thiemicke A, Neuert G. Rate thresholds in cell signaling have functional and phenotypic consequences in non-linear time-dependent environments. Front Cell Dev Biol 2023; 11:1124874. [PMID: 37025183 PMCID: PMC10072286 DOI: 10.3389/fcell.2023.1124874] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/08/2023] [Indexed: 04/08/2023] Open
Abstract
All cells employ signal transduction pathways to respond to physiologically relevant extracellular cytokines, stressors, nutrient levels, hormones, morphogens, and other stimuli that vary in concentration and rate in healthy and diseased states. A central unsolved fundamental question in cell signaling is whether and how cells sense and integrate information conveyed by changes in the rate of extracellular stimuli concentrations, in addition to the absolute difference in concentration. We propose that different environmental changes over time influence cell behavior in addition to different signaling molecules or different genetic backgrounds. However, most current biomedical research focuses on acute environmental changes and does not consider how cells respond to environments that change slowly over time. As an example of such environmental change, we review cell sensitivity to environmental rate changes, including the novel mechanism of rate threshold. A rate threshold is defined as a threshold in the rate of change in the environment in which a rate value below the threshold does not activate signaling and a rate value above the threshold leads to signal activation. We reviewed p38/Hog1 osmotic stress signaling in yeast, chemotaxis and stress response in bacteria, cyclic adenosine monophosphate signaling in Amoebae, growth factors signaling in mammalian cells, morphogen dynamics during development, temporal dynamics of glucose and insulin signaling, and spatio-temproral stressors in the kidney. These reviewed examples from the literature indicate that rate thresholds are widespread and an underappreciated fundamental property of cell signaling. Finally, by studying cells in non-linear environments, we outline future directions to understand cell physiology better in normal and pathophysiological conditions.
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Affiliation(s)
- Alexander Thiemicke
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN, United States
- Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, United States
- Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN, United States
- *Correspondence: Gregor Neuert,
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7
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Abstract
The ability of bacteria to respond to changes in their environment is critical to their survival, allowing them to withstand stress, form complex communities, and induce virulence responses during host infection. A remarkable feature of many of these bacterial responses is that they are often variable across individual cells, despite occurring in an isogenic population exposed to a homogeneous environmental change, a phenomenon known as phenotypic heterogeneity. Phenotypic heterogeneity can enable bet-hedging or division of labor strategies that allow bacteria to survive fluctuating conditions. Investigating the significance of phenotypic heterogeneity in environmental transitions requires dynamic, single-cell data. Technical advances in quantitative single-cell measurements, imaging, and microfluidics have led to a surge of publications on this topic. Here, we review recent discoveries on single-cell bacterial responses to environmental transitions of various origins and complexities, from simple diauxic shifts to community behaviors in biofilm formation to virulence regulation during infection. We describe how these studies firmly establish that this form of heterogeneity is prevalent and a conserved mechanism by which bacteria cope with fluctuating conditions. We end with an outline of current challenges and future directions for the field. While it remains challenging to predict how an individual bacterium will respond to a given environmental input, we anticipate that capturing the dynamics of the process will begin to resolve this and facilitate rational perturbation of environmental responses for therapeutic and bioengineering purposes.
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8
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Hernández-Elvira M, Sunnerhagen P. Post-transcriptional regulation during stress. FEMS Yeast Res 2022; 22:6585650. [PMID: 35561747 PMCID: PMC9246287 DOI: 10.1093/femsyr/foac025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/25/2022] [Accepted: 05/10/2022] [Indexed: 11/12/2022] Open
Abstract
To remain competitive, cells exposed to stress of varying duration, rapidity of onset, and intensity, have to balance their expenditure on growth and proliferation versus stress protection. To a large degree dependent on the time scale of stress exposure, the different levels of gene expression control: transcriptional, post-transcriptional and post-translational, will be engaged in stress responses. The post-transcriptional level is appropriate for minute-scale responses to transient stress, and for recovery upon return to normal conditions. The turnover rate, translational activity, covalent modifications, and subcellular localisation of RNA species are regulated under stress by multiple cellular pathways. The interplay between these pathways is required to achieve the appropriate signalling intensity and prevent undue triggering of stress-activated pathways at low stress levels, avoid overshoot, and down-regulate the response in a timely fashion. As much of our understanding of post-transcriptional regulation has been gained in yeast, this review is written with a yeast bias, but attempts to generalise to other eukaryotes. It summarises aspects of how post-transcriptional events in eukaryotes mitigate short-term environmental stresses, and how different pathways interact to optimise the stress response under shifting external conditions.
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Affiliation(s)
- Mariana Hernández-Elvira
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, Lundberg Laboratory, University of Gothenburg, P.O. Box 462, S-405 30 Göteborg, Sweden
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9
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de Nadal E, Posas F. OUP accepted manuscript. FEMS Yeast Res 2022; 22:6543702. [PMID: 35254447 PMCID: PMC8953452 DOI: 10.1093/femsyr/foac013] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/15/2022] Open
Affiliation(s)
- Eulàlia de Nadal
- Corresponding author: Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona c/ Baldiri Reixac, 10. 08028 Barcelona - Spain. E-mail:
| | - Francesc Posas
- Corresponding author: Institute for Research in Biomedicine (IRB Barcelona) Parc Científic de Barcelona c/ Baldiri Reixac, 10. 08028 Barcelona - Spain. E-mail:
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10
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Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
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11
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Krause HB, Bondarowicz H, Karls AL, McClean MN, Kreeger PK. Design and implementation of a microfluidic device capable of temporal growth factor delivery reveal filtering capabilities of the EGFR/ERK pathway. APL Bioeng 2021; 5:046101. [PMID: 34765858 PMCID: PMC8566012 DOI: 10.1063/5.0059011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/15/2021] [Indexed: 12/30/2022] Open
Abstract
Utilizing microfluidics to mimic the dynamic temporal changes of growth factor and cytokine concentrations in vivo has greatly increased our understanding of how signal transduction pathways are structured to encode extracellular stimuli. To date, these devices have focused on delivering pulses of varying frequency, and there are limited cell culture models for delivering slowly increasing concentrations of stimuli that cells may experience in vivo. To examine this setting, we developed and validated a microfluidic device that can deliver increasing concentrations of growth factor over periods ranging from 6 to 24 h. Using this device and a fluorescent biosensor of extracellular-regulated kinase (ERK) activity, we delivered a slowly increasing concentration of epidermal growth factor (EGF) to human mammary epithelial cells and surprisingly observed minimal ERK activation, even at concentrations that stimulate robust activity in bolus delivery. The cells remained unresponsive to subsequent challenges with EGF, and immunocytochemistry suggested that the loss of an epidermal growth factor receptor was responsible. Cells were then challenged with faster rates of change of EGF, revealing an increased ERK activity as a function of rate of change. Specifically, both the fraction of cells that responded and the length of ERK activation time increased with the rate of change. This microfluidic device fills a gap in the current repertoire of in vitro microfluidic devices and demonstrates that slower, more physiological changes in growth factor presentation can reveal new regulatory mechanisms for how signal transduction pathways encode changes in the extracellular growth factor milieu.
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Affiliation(s)
- Harris B Krause
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Hanna Bondarowicz
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Alexis L Karls
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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12
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Jashnsaz H, Fox ZR, Munsky B, Neuert G. Building predictive signaling models by perturbing yeast cells with time-varying stimulations resulting in distinct signaling responses. STAR Protoc 2021; 2:100660. [PMID: 34286292 PMCID: PMC8273411 DOI: 10.1016/j.xpro.2021.100660] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This protocol provides a step-by-step approach to perturb single cells with time-varying stimulation profiles, collect distinct signaling responses, and use these to infer a system of ordinary differential equations to capture and predict dynamics of protein-protein regulation in signal transduction pathways. The models are validated by predicting the signaling activation upon new cell stimulation conditions. In comparison to using standard step-like stimulations, application of diverse time-varying cell stimulations results in better inference of model parameters and substantially improves model predictions. For complete details on the use and results of this protocol, please refer to Jashnsaz et al. (2020). Diverse time-varying cell stimulations result in distinct signaling activation dynamics Signaling models fit step stimuli responses well but result in poor predictions Distinct responses upon diverse time-varying stimulations improve model predictions Temporal stimulation of pathways result in novel signaling dynamics and mechanisms
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Affiliation(s)
- Hossein Jashnsaz
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
| | - Zachary R Fox
- Inria Paris, Paris 75012, France.,Institut Pasteur, USR 3756 IP CNRS, Paris 75015, France.,Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523 USA
| | - Brian Munsky
- Keck Scholars, School of Biomedical Engineering, Colorado State University, Fort Collins, CO 80523 USA.,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523 USA
| | - Gregor Neuert
- Department of Molecular Physiology and Biophysics, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA.,Department of Biomedical Engineering, School of Engineering, Vanderbilt University, Nashville, TN 37232 USA.,Department of Pharmacology, School of Medicine, Vanderbilt University, Nashville, TN 37232 USA
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