NF-κB Dynamics Discriminate between TNF Doses in Single Cells.

Although cytokine-dependent dynamics of nuclear factor κB (NF-κB) are known to encode information that regulates cell fate decisions, it is unclear whether single-cell responses are switch-like or encode more information about cytokine dose. Here, we measure the dynamic subcellular localization of NF-κB in response to a range of tumor necrosis factor (TNF) stimulation conditions to determine the prevailing mechanism of single-cell dose discrimination. Using an information theory formalism that accounts for signaling dynamics and non-responsive cell subpopulations, we find that the information transmission capacity of single cells exceeds that predicted from a switch-like response. Instead, we observe that NF-κB dynamics within single cells contain sufficient information to encode multiple, TNF-dependent cellular states, and have an activation threshold that varies across the population. By comparing single-cell responses to an internal, experimentally observed reference, we demonstrate that cells can grade responses to TNF across several orders of magnitude in concentration. This suggests that cells contain additional control points to fine-tune their cytokine responses beyond the decision to activate.

[1]  G. Lahav,et al.  Encoding and Decoding Cellular Information through Signaling Dynamics , 2013, Cell.

[2]  Alexander Hoffmann,et al.  Stimulus Specificity of Gene Expression Programs Determined by Temporal Control of IKK Activity , 2005, Science.

[3]  Peter Scheurich,et al.  TNFR1‐induced activation of the classical NF‐κB pathway , 2011, The FEBS journal.

[4]  Mohammad A. Qasaimeh,et al.  NF-κB signalling and cell fate decisions in response to a short pulse of tumour necrosis factor , 2016, Scientific Reports.

[5]  T. Elston,et al.  Stochasticity in gene expression: from theories to phenotypes , 2005, Nature Reviews Genetics.

[6]  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.

[7]  J. Ferrell,et al.  Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity. , 2014, Trends in biochemical sciences.

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

[9]  Bo Sun,et al.  Dynamic Sampling and Information Encoding in Biochemical Networks. , 2016, Biophysical journal.

[10]  H. Habelhah,et al.  TNFR1 signaling kinetics: spatiotemporal control of three phases of IKK activation by posttranslational modification. , 2013, Cellular signalling.

[11]  Uri Alon,et al.  Dynamics and variability of ERK2 response to EGF in individual living cells. , 2009, Molecular cell.

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

[13]  I. Nemenman,et al.  Information Transduction Capacity of Noisy Biochemical Signaling Networks , 2011, Science.

[14]  Lea Goentoro,et al.  Evidence that fold-change, and not absolute level, of beta-catenin dictates Wnt signaling. , 2009, Molecular cell.

[15]  L. Tsimring,et al.  Accurate information transmission through dynamic biochemical signaling networks , 2014, Science.

[16]  A. Oudenaarden,et al.  Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences , 2008, Cell.

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

[18]  Jean Marx,et al.  Inflammation and Cancer: The Link Grows Stronger , 2004, Science.

[19]  J. Tinevez,et al.  TNF and IL-1 exhibit distinct ubiquitin requirements for inducing NEMO–IKK supramolecular structures , 2014, The Journal of cell biology.

[20]  I. Nemenman,et al.  Cellular noise and information transmission. , 2014, Current opinion in biotechnology.

[21]  Allan R. Brasier,et al.  Identification of Direct Genomic Targets Downstream of the Nuclear Factor-κB Transcription Factor Mediating Tumor Necrosis Factor Signaling* , 2005, Journal of Biological Chemistry.

[22]  Anne E Carpenter,et al.  CellProfiler: image analysis software for identifying and quantifying cell phenotypes , 2006, Genome Biology.

[23]  J. Pollard,et al.  Distinct role of macrophages in different tumor microenvironments. , 2006, Cancer research.

[24]  B. Aggarwal Signalling pathways of the TNF superfamily: a double-edged sword , 2003, Nature Reviews Immunology.

[25]  Jeremy E. Purvis,et al.  p53 Dynamics Control Cell Fate , 2012, Science.

[26]  M. Bianchi,et al.  NF-κB oscillations translate into functionally related patterns of gene expression , 2016, eLife.

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

[28]  Sankar Ghosh,et al.  Signaling to NF-kappaB. , 2004, Genes & development.

[29]  Paul H. C. Eilers,et al.  Enhancing scatterplots with smoothed densities , 2004, Bioinform..

[30]  Alexander Hoffmann,et al.  The Dynamics of Signaling as a Pharmacological Target , 2013, Cell.

[31]  Gal Chechik,et al.  Timing of Gene Expression Responses to Environmental Changes , 2009, J. Comput. Biol..

[32]  Eric J. Deeds,et al.  Fundamental trade-offs between information flow in single cells and cellular populations , 2017, Proceedings of the National Academy of Sciences.

[33]  Allan R Brasier,et al.  A TNF-induced gene expression program under oscillatory NF-κB control , 2005, BMC Genomics.

[34]  J. Beebe-Dimmer,et al.  Chronic Inflammation: A Common and Important Factor in the Pathogenesis of Neoplasia , 2006, CA: a cancer journal for clinicians.

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

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

[37]  D. Green,et al.  DNA damaging agents induce expression of Fas ligand and subsequent apoptosis in T lymphocytes via the activation of NF-kappa B and AP-1. , 1998, Molecular cell.

[38]  P. Tak,et al.  NF-κB: a key role in inflammatory diseases , 2001 .

[39]  T. Lawrence The nuclear factor NF-kappaB pathway in inflammation. , 2009, Cold Spring Harbor perspectives in biology.

[40]  Shizuo Akira,et al.  Signaling to NF-?B by Toll-like receptors , 2007 .

[41]  Ryan A. Kellogg,et al.  Digital signaling decouples activation probability and population heterogeneity , 2015, eLife.