NF-κB responds to absolute differences in cytokine concentrations

Son, Minjun; Wang, Andrew G.; Tu, Hsiung‐Lin; Metzig, Marie Oliver; Patel, Parthiv; Husain, Kabir; Lin, Jing; Murugan, Arvind; Hoffmann, Alexander; Tay, Savaş

doi:10.1126/scisignal.aaz4382

Cited by 38 publications

(49 citation statements)

References 74 publications

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“…This stimulation was specific to TNFɑ; addition of PBS + .1% BSA vehicle to RelA-mScarlet cells yielded no such response (Figure 2B, black trace, top panel). Previous studies have shown that TNFɑ induction leads to a coordinated first wave of translocation into the nucleus, followed by additional damped pulses (8,(30)(31)(32). Individual cell traces showed a similar finding, with some cells undergoing a short, single pulse within the first hour after induction, while other cells displayed two or more pulses of RelA translocation after induction (Figure 2B, inset, top panel).…”

Section: Rela-clasp Is Insensitive To Environmental Inputssupporting

confidence: 70%

Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression

Osimiri

Bonny

Takagishi

et al. 2022

Preprint

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Many transcription factors (TFs) translocate to the nucleus with varied dynamic patterns in response to different inputs. A notable example of such behavior is RelA, a subunit of NF-κB, which translocates to the nucleus with either pulsed or sustained dynamics, depending on the stimulus. Our understanding of how these dynamics are interpreted by downstream genes has remained incomplete, partly because ubiquitously used environmental inputs activate other transcriptional regulators in addition to RelA. Here, we use an optogenetic tool, CLASP (controllable light-activated shuttling and plasma membrane sequestration), to control RelA spatiotemporal dynamics in mouse fibroblasts and quantify their effect on downstream genes using RNA-seq. Using RelA-CLASP, we show for the first time that nuclear translocation of RelA, without post-translational modifications or activation of other transcriptional regulators, is sufficient to activate downstream genes. Furthermore, we find that TNFα, a common endogenous input, regulates many genes independently of RelA, and that this gene regulation is different from that induced by RelA-CLASP. Genes responsive to RelA-CLASP show a wide range of dynamics in response to a constant RelA input. We use a simple promoter model to recapitulate these diverse dynamic responses, as well as data collected in response to a pulsed RelA-CLASP input, and extract features of many RelA-responsive promoters. We also pinpoint many genes for which more complex models, involving feedback or multi-step promoters, may be needed to explain their response to constant and pulsed TF inputs. This study introduces a new robust tool for studying mammalian transcriptional regulation and demonstrates the power of optogenetic tools in dissecting the quantitative features of important cellular pathways.

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Section: Rela-clasp Is Insensitive To Environmental Inputssupporting

confidence: 70%

Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression

Osimiri

Bonny

Takagishi

et al. 2022

Preprint

Self Cite

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“…These analyses demonstrate that through post-transcriptional PTP feedback, desensitisation of JAK-STAT signalling renders cells with signal memory by responding to relative fold changes in IFN concentration. In comparison, the NF-κB system can detect absolute increases in cytokine concentration during relatively short (<2h) time intervals (Son et al 2021). Other systems use receptor availability to detect temporal changes in stimulus, for example, relative (fold) changes in early growth response (EGR) protein concentration (Lyashenko et al 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Underlying mechanisms involve complex regulatory networks with feedback loops that generate outputs depending on the signal type, strength, or duration (Bhalla and Iyengar 1999; Novak and Tyson 2008). For example, the temporal responses of the nuclear factor -κB (NF-κB) transcription factor encode different pathogen-derived molecules and cytokines of the immune system (Adelaja et al 2021; Martin et al 2020; Kellogg et al 2017) and adapts to rapidly changing inflammatory cues (Adamson et al 2016; DeFelice et al 2019; Ashall et al 2009; Tay et al 2010; Son et al 2021). The emergent properties of the cellular signalling networks serve as a paradigm to understand how immune cells process inflammatory cues (Dorrington and Fraser 2019).…”

Section: Introductionmentioning

confidence: 99%

Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation

Kalliara

Kardyńska

Bagnall

et al. 2022

Preprint

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Immune cells fine tune their responses to infection and inflammatory cues. Here, using live-cell confocal microscopy and mathematical modelling, we investigate interferon induced JAK-STAT signalling in innate immune macrophages. We demonstrate that transient exposure to IFN-γ stimulation induces a long-term desensitisation of STAT1 signalling and gene expression responses, revealing a dose- and time-dependent regulatory feedback that controls JAK-STAT responses upon re-exposure to stimulus. We show that IFN-α/β1 elicit different level of desensitisation from IFN-γ, where cells refractory to IFN-α/β1 are sensitive to IFN-γ, but not vice versa. We experimentally demonstrate that the underlying feedback mechanism involves regulation of STAT1 phosphorylation but is independent of new mRNA synthesis and cognate receptor expression. A new feedback model of the protein tyrosine phosphatase activity recapitulates experimental data and demonstrates JAK-STAT network’s ability to decode relative changes of dose, timing, and type of temporal interferon stimulation. These findings reveal that STAT desensitisation renders cells with signalling memory of type I and II interferon stimulation, which in the future may improve administration of interferon therapy.

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“…Of note, a follow-up study ( 66 ) indeed showed that the refractoriness was lost if il-1β was used as a subsequent stimulus instead of TNF-α, demonstrating the stimulus-specificity of this dynamical feature. The importance of the interplay between feedbacks was also been highlighted by a number of studies: a very recent study performed on 3T3 cells on a microfluidics platform shows how IκBs and A20 are key to make NF-κB respond to differences in the concentrations of environmental cytokines and provide a sort of activation memory that, again, was reproduced by mathematical models including both feedbacks ( 67 ).…”

Section: Insights On the Regulation Of Nf-κb Activity: How The Interp...mentioning

confidence: 99%

Insights on the NF-κB System Using Live Cell Imaging: Recent Developments and Future Perspectives

2022

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The transcription factor family of nuclear factor kappa B (NF-κB) proteins is widely recognized as a key player in inflammation and the immune responses, where it plays a fundamental role in translating external inflammatory cues into precise transcriptional programs, including the timely expression of a wide variety of cytokines/chemokines. Live cell imaging in single cells showed approximately 15 years ago that the canonical activation of NF-κB upon stimulus is very dynamic, including oscillations of its nuclear localization with a period close to 1.5 hours. This observation has triggered a fruitful interdisciplinary research line that has provided novel insights on the NF-κB system: how its heterogeneous response differs between cell types but also within homogeneous populations; how NF-κB dynamics translate external cues into intracellular signals and how NF-κB dynamics affects gene expression. Here we review the main features of this live cell imaging approach to the study of NF-κB, highlighting the key findings, the existing gaps of knowledge and hinting towards some of the potential future steps of this thriving research field.

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NF-κB responds to absolute differences in cytokine concentrations

Abstract: The behavior of the NF-κB pathway as a differentiator circuit enables the pathway to track changes in cytokine dose.

Cited by 38 publications

References 74 publications

Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression

Optogenetic control of RelA reveals effect of transcription factor dynamics on downstream gene expression

Post-transcriptional regulatory feedback encodes JAK-STAT signal memory of interferon stimulation

Insights on the NF-κB System Using Live Cell Imaging: Recent Developments and Future Perspectives

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