Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states

[1]  Michael W. Davidson,et al.  The fluorescent protein palette: tools for cellular imaging. , 2009, Chemical Society reviews.

[2]  Yutaka Tagaya,et al.  Faculty Opinions recommendation of Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. , 2010 .

[3]  H. Kitano,et al.  A comprehensive map of the mTOR signaling network , 2010, Molecular systems biology.

[4]  S. Biswas,et al.  Endotoxin tolerance: new mechanisms, molecules and clinical significance. , 2009, Trends in immunology.

[5]  M. Bianchi,et al.  High-Throughput Analysis of NF-κB Dynamics in Single Cells Reveals Basal Nuclear Localization of NF-κB and Spontaneous Activation of Oscillations , 2014, PloS one.

[6]  Noula Shembade,et al.  Inhibition of NF-κB Signaling by A20 Through Disruption of Ubiquitin Enzyme Complexes , 2010, Science.

[7]  D. Kabelitz,et al.  Compartmentalization of TNF receptor 1 signaling: internalized TNF receptosomes as death signaling vesicles. , 2004, Immunity.

[8]  Roger J. Davis,et al.  TNF and MAP kinase signalling pathways. , 2014, Seminars in immunology.

[9]  A. Hoffmann,et al.  The I (cid:1) B –NF-(cid:1) B Signaling Module: Temporal Control and Selective Gene Activation , 2022 .

[10]  Norman W. Paton,et al.  Automated tracking of gene expression in individual cells and cell compartments , 2006, Journal of The Royal Society Interface.

[11]  D. Kirschner,et al.  A methodology for performing global uncertainty and sensitivity analysis in systems biology. , 2008, Journal of theoretical biology.

[12]  T. Kirchhausen,et al.  Use of dynasore, the small molecule inhibitor of dynamin, in the regulation of endocytosis. , 2008, Methods in enzymology.

[13]  Nancy A. Jenkins,et al.  Simple and highly efficient BAC recombineering using galK selection , 2005, Nucleic acids research.

[14]  Hong Wang,et al.  Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway. , 2006, Molecular bioSystems.

[15]  Nathan C Shaner,et al.  A guide to choosing fluorescent proteins , 2005, Nature Methods.

[16]  Ryan A. Kellogg,et al.  Noise Facilitates Transcriptional Control under Dynamic Inputs , 2015, Cell.

[17]  宁北芳,et al.  疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A , 2005 .

[18]  Jeff Hasty,et al.  Dual Delayed Feedback Provides Sensitivity and Robustness to the NF-κB Signaling Module , 2013, PLoS Comput. Biol..

[19]  Noula Shembade,et al.  The kinase IKKα inhibits activation of the transcription factor NF-κB by phosphorylating the regulatory molecule TAX1BP1 , 2011, Nature Immunology.

[20]  Claire V. Harper,et al.  Population robustness arising from cellular heterogeneity , 2010, Proceedings of the National Academy of Sciences.

[21]  Sankar Ghosh,et al.  NF-κB, the first quarter-century: remarkable progress and outstanding questions. , 2012, Genes & development.

[22]  A. Hoffmann,et al.  The IkappaB-NF-kappaB signaling module: temporal control and selective gene activation. , 2002, Science.

[23]  O. Ohara,et al.  Single-cell imaging of caspase-1 dynamics reveals an all-or-none inflammasome signaling response. , 2014, Cell reports.

[24]  H. Kitano,et al.  A comprehensive map of the toll-like receptor signaling network , 2006, Molecular systems biology.

[25]  C. Hill,et al.  Controlling Long-Term Signaling: Receptor Dynamics Determine Attenuation and Refractory Behavior of the TGF-β Pathway , 2013, Science Signaling.

[26]  Marek Kimmel,et al.  Stochastic regulation in early immune response. , 2006, Biophysical journal.

[27]  Oliver Medvedik,et al.  Stimulus Specificity of Gene Expression Programs Determined by Temporal Control of IKK Activity , 2013 .

[28]  S. Ghosh,et al.  Shared Principles in NF-κB Signaling , 2008, Cell.

[29]  D B Kell,et al.  Oscillations in NF-kappaB signaling control the dynamics of gene expression. , 2004, Science.

[30]  Lin-Feng Chen,et al.  Posttranslational modifications of NF-kappaB: another layer of regulation for NF-kappaB signaling pathway. , 2010, Cellular signalling.

[31]  M. Belich,et al.  Coordinate Regulation of TPL-2 and NF-κB Signaling in Macrophages by NF-κB1 p105 , 2012, Molecular and Cellular Biology.

[32]  H. Kitano,et al.  G-Protein Coupled Receptor Signaling Architecture of Mammalian Immune Cells , 2009, PloS one.

[33]  J. Rawlings,et al.  Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics , 2002 .

[34]  Boris N. Kholodenko,et al.  Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise , 2012, BMC Systems Biology.

[35]  David A. Rand,et al.  Physiological levels of TNFα stimulation induce stochastic dynamics of NF-κB responses in single living cells , 2010, Journal of Cell Science.

[36]  P. Evans,et al.  NF-kappaB suppression by the deubiquitinating enzyme Cezanne: a novel negative feedback loop in pro-inflammatory signaling. , 2008, The Journal of biological chemistry.

[37]  V. Dötsch,et al.  Ubiquitin binding mediates the NF-κB inhibitory potential of ABIN proteins , 2008, Oncogene.

[38]  Paul C. Boutros,et al.  NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data , 2012, Bioinform..

[39]  F. Maxfield,et al.  Endocytic recycling , 2004, Nature Reviews Molecular Cell Biology.

[40]  Christopher C. Goodnow,et al.  Differential activation of transcription factors induced by Ca2+ response amplitude and duration , 1997, Nature.

[41]  D. Baltimore,et al.  The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules , 2009, Nature Immunology.

[42]  Jennifer L. Osborn,et al.  Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.

[43]  R. Milo,et al.  Variability and memory of protein levels in human cells , 2006, Nature.

[44]  Pernille Yde,et al.  Modeling the NF-κB mediated inflammatory response predicts cytokine waves in tissue , 2011, BMC Systems Biology.

[45]  A. Hoffmann,et al.  Tunable signal processing through a kinase control cycle: the IKK signaling node. , 2013, Biophysical journal.

[46]  S. Ghosh,et al.  NF-κB, inflammation, and metabolic disease. , 2011, Cell metabolism.

[47]  W. Schneider-Brachert,et al.  Regulation of TNFR1 and CD95 signalling by receptor compartmentalization , 2008, Nature Reviews Molecular Cell Biology.

[48]  Somasekar Seshagiri,et al.  De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-κB signalling , 2004, Nature.

[49]  C. Mackay,et al.  Overlapping gene expression profiles in rheumatoid fibroblast-like synoviocytes induced by the proinflammatory cytokines interleukin-1 β and tumor necrosis factor , 2004, Inflammation Research.

[50]  Robin E C Lee,et al.  Fold change of nuclear NF-κB determines TNF-induced transcription in single cells. , 2014, Molecular cell.

[51]  Alexander Hoffmann,et al.  IκBɛ provides negative feedback to control NF-κB oscillations, signaling dynamics, and inflammatory gene expression , 2006, The Journal of cell biology.

[52]  Jacob J. Hughey,et al.  Single-cell variation leads to population invariance in NF-κB signaling dynamics , 2015, Molecular biology of the cell.

[53]  M. Sung,et al.  Sustained Oscillations of NF-κB Produce Distinct Genome Scanning and Gene Expression Profiles , 2009, PloS one.

[54]  Marek Kimmel,et al.  Mathematical model of NF- κB regulatory module , 2004 .

[55]  A. Oudenaarden,et al.  Cellular Decision Making and Biological Noise: From Microbes to Mammals , 2011, Cell.

[56]  Jeffrey W. Smith,et al.  Stochastic Gene Expression in a Single Cell , 2022 .

[57]  Rona S. Gertner,et al.  Single cell RNA Seq reveals dynamic paracrine control of cellular variation , 2014, Nature.

[58]  Eva E. Qwarnstrom,et al.  Dynamic Shuttling of Nuclear Factor κB between the Nucleus and Cytoplasm as a Consequence of Inhibitor Dissociation* , 2000, The Journal of Biological Chemistry.

[59]  Timothy K Lee,et al.  Single-cell NF-κB dynamics reveal digital activation and analogue information processing , 2010, Nature.

[60]  Marco Marcello,et al.  Interactive segmentation of clustered cells via geodesic commute distance and constrained density weighted Nyström method , 2010, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[61]  F. Alt,et al.  TRAF1 is a negative regulator of TNF signaling. enhanced TNF signaling in TRAF1-deficient mice. , 2001, Immunity.

[62]  David Baltimore,et al.  Encoding NF-kappaB temporal control in response to TNF: distinct roles for the negative regulators IkappaBalpha and A20. , 2008, Genes & development.

[63]  Douglas A. Lauffenburger,et al.  Polyfunctional responses by human T cells result from sequential release of cytokines , 2011, Proceedings of the National Academy of Sciences.

[64]  H. Kitano,et al.  A comprehensive pathway map of epidermal growth factor receptor signaling , 2005, Molecular systems biology.

[65]  Michael Karin,et al.  Positive and Negative Regulation of IκB Kinase Activity Through IKKβ Subunit Phosphorylation , 1999 .

[66]  D. S. Broomhead,et al.  Pulsatile Stimulation Determines Timing and Specificity of NF-κB-Dependent Transcription , 2009, Science.

[67]  Michael B. Elowitz,et al.  Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells , 2014, Molecular cell.

[68]  S. Paul,et al.  Cutting Edge: TCR Ligation Triggers Digital Activation of NF-κB , 2010, The Journal of Immunology.

[69]  Jonathan Timmis,et al.  Computational Models of the NF-KB Signalling Pathway , 2014, Comput..

[70]  M. Elowitz,et al.  Functional Roles of Pulsing in Genetic Circuits , 2013, Science.

[71]  A. Ma,et al.  Failure to regulate TNF-induced NF-kappaB and cell death responses in A20-deficient mice. , 2000, Science.

[72]  Gordon K Smyth,et al.  Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2004, Statistical applications in genetics and molecular biology.

[73]  R. Beyaert,et al.  The cytokine‐inducible zinc finger protein A20 inhibits IL‐1‐induced NF‐κB activation at the level of TRAF6 , 1999, FEBS letters.

[74]  P. Bousso,et al.  CD4+ T cells rely on a cytokine gradient to control intracellular pathogens beyond sites of antigen presentation. , 2012, Immunity.

[75]  D. Spiller,et al.  Quantitative dynamic imaging of immune cell signalling using lentiviral gene transfer. , 2015, Integrative biology : quantitative biosciences from nano to macro.

[76]  J. Ellenberg,et al.  Automatic real‐time three‐dimensional cell tracking by fluorescence microscopy , 2004, Journal of microscopy.

[77]  N. Copeland,et al.  A highly efficient recombineering-based method for generating conditional knockout mutations. , 2003, Genome research.

[78]  Paolo Tieri,et al.  Network, degeneracy and bow tie. Integrating paradigms and architectures to grasp the complexity of the immune system , 2010, Theoretical Biology and Medical Modelling.

[79]  Ming Yan,et al.  Alpha Interferon Induces Long-Lasting Refractoriness of JAK-STAT Signaling in the Mouse Liver through Induction of USP18/UBP43 , 2009, Molecular and Cellular Biology.

[80]  M. Lamy,et al.  Tumor necrosis factor and interleukin-1 serum levels during severe sepsis in humans. , 1989, Critical care medicine.

[81]  James R. Johnson,et al.  Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression , 2004, Science.

[82]  P. Sorger,et al.  Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis , 2009, Nature.

[83]  A. Hoffmann,et al.  Circuitry of nuclear factor kappaB signaling. , 2006, Immunological reviews.