Quantitative characterization and analysis of the dynamic NF- (cid:1) B response in microglia

Background: Activation of the NF- (cid:1) B transcription factor and its associated gene expression in microglia is a key component in the response to brain injury. Its activation is dynamic and is part of a network of biochemical species with multiple feedback regulatory mechanisms. Mathematical modeling, which has been instrumental for understanding the NF- (cid:1) B response in other cell types, offers a valuable tool to investigate the regulation of NF- (cid:1) B activation in microglia at a systems level. Results: We quantify the dynamic response of NF- (cid:1) B activation and activation of the upstream kinase IKK using ELISA measurements of a microglial cell line following treatment with the pro-inflammatory cytokine TNF a . A new mathematical model is developed based on these data sets using a modular procedure that exploits the feedback structure of the network. We show that the new model requires previously unmodeled dynamics involved in the stimulus-induced degradation of the inhibitor I (cid:1) B a in order to properly describe microglial NF- (cid:1) B activation in a statistically consistent manner. This suggests a more prominent role for the ubiquitin-proteasome system in regulating the activation of NF- (cid:1) B to inflammatory stimuli. We also find that the introduction of nonlinearities in the kinetics of IKK activation and inactivation is essential for proper characterization of transient IKK activity and corresponds to known biological mechanisms. Numerical analyses of the model highlight key regulators of the microglial NF- (cid:1) B response, as well as those governing IKK activation. Results illustrate the dynamic regulatory mechanisms and the robust yet fragile nature of the negative feedback regulated network. Conclusions: We have developed a new mathematical model that incorporates previously unmodeled dynamics to characterize the dynamic response of the NF- (cid:1) B signaling network in microglia. This model is the first of its kind for microglia and provides a tool for the quantitative, systems level study the dynamic cellular response to

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

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

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

[4]  Mustafa Khammash,et al.  Parameter Estimation and Model Selection in Computational Biology , 2010, PLoS Comput. Biol..

[5]  R. Deshaies,et al.  Detection of Sequential Polyubiquitylation on a Millisecond Time-Scale , 2009, Nature.

[6]  Timothy K Lee,et al.  A Noisy Paracrine Signal Determines the Cellular NF-κB Response to Lipopolysaccharide , 2009, Science Signaling.

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

[8]  A. Hoffmann,et al.  Understanding NF-κB signaling via mathematical modeling , 2008, Molecular systems biology.

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

[10]  Marek Kimmel,et al.  Single TNFα trimers mediating NF-κB activation: stochastic robustness of NF-κB signaling , 2007, BMC Bioinformatics.

[11]  David G. Spiller,et al.  Single-cell time-lapse imaging of the dynamic control of NF-κB signalling , 2007 .

[12]  Hana Kim,et al.  A Fourth IκB Protein within the NF-κB Signaling Module , 2007, Cell.

[13]  L. Hood,et al.  Reverse Engineering of Biological Complexity , 2007 .

[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]  K. Sneppen,et al.  Minimal model of spiky oscillations in NF-κB signaling , 2006 .

[16]  Antonio Leonardi,et al.  ABIN-1 Binds to NEMO/IKKγ and Co-operates with A20 in Inhibiting NF-κB* , 2006, Journal of Biological Chemistry.

[17]  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.

[18]  Kwang-Hyun Cho,et al.  The influence of the signal dynamics of activated form of IKK on NF‐κB and anti‐apoptotic gene expressions: A systems biology approach , 2006, FEBS letters.

[19]  Andre Levchenko,et al.  Transient IκB Kinase Activity Mediates Temporal NF-κB Dynamics in Response to a Wide Range of Tumor Necrosis Factor-α Doses* , 2006, Journal of Biological Chemistry.

[20]  D. Baltimore,et al.  Achieving Stability of Lipopolysaccharide-Induced NF-κB Activation , 2005, Science.

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

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

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

[24]  S. Fuchs,et al.  The many faces of β-TrCP E3 ubiquitin ligases: reflections in the magic mirror of cancer , 2004, Oncogene.

[25]  K. Nakayama,et al.  Impaired degradation of inhibitory subunit of NF-κB (IκB) and β-catenin as a result of targeted disruption of the β-TrCP1 gene , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[26]  C. Brosnan,et al.  Cytokines: Powerful Regulators of Glial Cell Activation , 2003, The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry.

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

[28]  H. Suzuki,et al.  NEDD8 recruits E2‐ubiquitin to SCF E3 ligase , 2001, The EMBO journal.

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

[30]  G Cantarella,et al.  Recruitment of the IKK signalosome to the p55 TNF receptor: RIP and A20 bind to NEMO (IKKgamma) upon receptor stimulation. , 2000, Immunity.

[31]  D. S. Broomhead,et al.  Synergistic control of oscillations in the NFk B signalling pathway , 2000 .

[32]  Michael Karin,et al.  The Beginning of the End: IκB Kinase (IKK) and NF-κB Activation* , 1999, The Journal of Biological Chemistry.

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

[34]  Hiroshi Suzuki,et al.  IκBα Ubiquitination Is Catalyzed by an SCF-like Complex Containing Skp1, Cullin-1, and Two F-Box/WD40-Repeat Proteins, βTrCP1 and βTrCP2 , 1999 .

[35]  H. Pahl,et al.  Activators and target genes of Rel/NF-kappaB transcription factors. , 1999, Oncogene.

[36]  M. Mann,et al.  Identification of the receptor component of the IκBα–ubiquitin ligase , 1998, Nature.

[37]  C. Kaltschmidt,et al.  NF-kB: a crucial transcription factor for glial and neuronal cell function , 1997, Trends in Neurosciences.

[38]  A. Ciechanover,et al.  Stimulation-dependent I kappa B alpha phosphorylation marks the NF-kappa B inhibitor for degradation via the ubiquitin-proteasome pathway. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[39]  T. Maniatis,et al.  Signal-induced site-specific phosphorylation targets I kappa B alpha to the ubiquitin-proteasome pathway. , 1995, Genes & development.

[40]  M. Kendall.  Statistical Methods for Research Workers , 1937, Nature.