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Cited by 6Cytokine Signaling Pathways and InteractionsGene Regulatory Network AnalysisGenomics and Chromatin Dynamics

A Model for How Signal Duration Can Determine Distinct Outcomes of Gene Transcription Programs

Open access
Fowler, Kevin D., Kuchroo, Vijay K., Chakraborty, Arup K.·2012·PLoS ONE
DOI 10.1371/journal.pone.0033018PMC PMC3302786
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Abstract

The reason why IL-6 induces a pro-inflammatory response, while IL-10 induces an anti-inflammatory response, despite both cytokines activating the same transcription factor, STAT3, is not well understood. It is known that IL-6 induces a transient STAT3 signal and that IL-10 induces a sustained STAT3 signal due to the STAT3-induced inhibitor SOCS3's ability to bind to the IL-6R and not the IL-10R. We sought to develop a general transcriptional network that is capable of translating sustained signals into one response, while translating transient signals into a second response. The general structure of such a network is that the transcription factor STAT3 can induce both an inflammatory response and an anti-inflammatory response by inducing two different genes. The anti-inflammatory gene can bind to and inhibit the inflammatory gene's production and the inflammatory gene can bind to its own promoter and induce its own transcription in the absence of the signal. One prediction that can be made from such a network is that in SOCS3-/- mice, where IL-6 induces a sustained STAT3 signal, that IL-6 would act as an anti-inflammatory cytokine, which has indeed been observed experimentally in the literature.

AI snapshot

Written from the paper’s full text.

TL;DR

The paper proposes a transcriptional network in which the same transcription factor, pSTAT3, can drive either an inflammatory gene program or an anti-inflammatory gene program depending on signal duration. Transient pSTAT3 signals favor inflammatory gene I through positive feedback, while sustained signals favor anti-inflammatory gene A through negative feedback, predicting that IL-6 becomes anti-inflammatory in SOCS3−/− macrophages.

Key findings

  • In the model, a sustained signal (`kdeg,T = 0 min−1`) leads to dominant production of anti-inflammatory molecule A, whereas a transient signal (`kdeg,T = 1.0 min−1` for Model 1) leads to dominant production of inflammatory molecule I.
  • Sensitivity analysis identified 1809 parameter sets that produced the desired qualitative switch from pro-inflammatory to anti-inflammatory response as signal degradation rate changed.
  • Threshold analysis showed sustained signals (`kdeg,T < 10−3`) clearly produced an anti-inflammatory response, transient signals (`0.02 < kdeg,T < 1`) clearly produced an inflammatory response, and a crossover occurred for mildly transient signals (`10−3 < kdeg,T < 0.02`).
  • Decreasing pSTAT3 amplitude from 100 to 10 molecules shifted the crossover from a degradation rate of `0.01 min−1` to `0.001 min−1`; at `kdeg,T = 0.2 min−1`, 100% of cells were inflammatory at 100 pSTAT3 molecules versus 50% at 10 molecules.
  • The model predicts IL-6 will act as an anti-inflammatory cytokine on SOCS3−/− macrophages, with a stronger anti-inflammatory effect as IL-6 dose increases, matching the experimental result of Yasukawa et al.

Methods

  • A transcriptional network model was built with two genes, inflammatory gene I and anti-inflammatory gene A, both activated by pSTAT3; I has positive autoregulation, and A inhibits I. Model 1 assumes transcription factors dissociate after each transcription event; Model 2 assumes they do not.
  • The chemical master equations were solved stochastically with the Gillespie algorithm, and mean-field ODE solutions were also used for comparison. Parameters were taken from Table 1, with signal duration varied through `kdeg,T` from 0 to 10 min−1 and trajectories followed to 2000 min.
  • Sensitivity analysis divided parameters into nine classes and tested low, medium, and high values; in silico knockouts removed positive or negative feedback loops, and signal amplitude was varied by setting initial pSTAT3 to 10, 20, 50, or 100 molecules.

Limitations

  • The paper states that no experimentally derived parameters were used, that downstream thresholds and the 2000-minute cutoff are arbitrary, and that at 3.5 days any signal with nonzero degradation eventually produces I, so the model is not entirely self-contained.
  • The paper states that the positive feedback loop has not been directly observed in this system, that other STATs and heterodimer formation are beyond scope, and that common gene expression is not easily accounted for.
  • Evident from the text: the model uses coarse-grained generic genes I and A rather than specific inflammatory or anti-inflammatory genes, and its IL-6/IL-10 predictions rely on assumed `kdeg,T` values and threshold choices rather than direct fitting to experimental data.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1371/journal.pone.0033018

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

2 of 24 cited sources checked · 2 supported · 0 flagged

  • Findingown data

    For sustained signals in the model, at long times (2000 min), I is at much lower levels than A.

    “For sustained signals, the distributions appear similar in shape; however, I is at much lower levels than A (Figure 2C and Figure 2D).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.
  • Findingown data

    A 10-fold decrease in signal amplitude shifts the crossover from occurring at a degradation rate of 0.01 min^-1 to 0.001 min^-1.

    “The effects of amplitude modification can be observed within the crossover region from the inflammatory to anti-inflammatory response in that a 10-fold decrease in signal amplitude would shift the crossover from occurring at a degradation rate of 0.01 min−1 to 0.001 min−1.”
    Quote in the paperSubstantial claim
  • Findingreasoning

    For transient signals in the model, A remains at or around zero in all trajectories.

    “For transient signals, the molecular levels of I increase gradually with time in some of the trajectories, while A remains at or around zero in all of the trajectories (Figure 3A and Figure 3B).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.
  • Findingown data

    Bistability in I develops at approximately kdeg,T = 0.4 min−1.

    “It appears that bistability develops at approximately kdeg,T = 0.4 min−1 (Figure 4).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.
  • Findingnone given

    Setting the same threshold for I and A leads to no response in the crossover region.

    “An alternative choice is to set the thresholds to be the same for both I and A, which leads to no response in the crossover region (Figure 4B).”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. 13
  • May combine two claims. 30

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Mangan and Alon described the characteristics and features of feed-forward loops.

    “Mangan and Alon described the characteristics and features of feed-forward loops [30].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [30] S Mangan, 2003, Structure and function of the feed-forward loop network motif., Proc Natl Acad Sci U S A source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    A number of studies have investigated the effects of positive feedback loops on decision making.

    “A number of studies have investigated the effects of positive feedback loops on decision making [24], [29].”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [24] J Das, 2009, Digital signaling and hysteresis characterize Ras activation in lymphoid cells., Cell source
    • cites [29] W Xiong, 2003, A positive-feedback-based bistable ‘memory module’ that governs a cell fate decision., Nature source

  • Classified as probably not a substantial claim.

    Findingown data

    Different downstream thresholds for I and A (I = 100 molecules, A = 20 molecules) allow both responses to be observed in the intermediate crossover region.

    “Different downstream thresholds were chosen for I and A such that both responses are observed in the intermediate crossover region. The I threshold was set to 100 molecules, while the A threshold was set to 20 molecules.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Downstream gene programs are only initiated when I or A cross a threshold value in molecular number at any point in the time trajectory.
    • The authors state this as an assumption: The percent of I or A trajectories crossing the threshold directly corresponds to the percent of cells that exhibit pro-inflammatory or anti-inflammatory responses in an equivalent biological experiment.

  • May combine two claims.

    Findingown data

    For the given parameters, I can attain a higher maximal value than A because its transcription rate is an order of magnitude higher and it has a positive feedback loop.

    “For the given set of parameters, it is clear that I has the capability of attaining a higher maximal value since its transcription rate is an order of magnitude higher than A and since I has a positive feedback loop (Figure 2B and Figure 3A).”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    In Th17 differentiation, IL-17 mRNA starts to be transcribed in appreciable quantities after 1 day.

    “An example of a cellular decision becoming evident after 1 day is in Th17 differentiation, where IL-17 mRNA starts to be transcribed in appreciable quantities at this time (unpublished observations).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    For kdeg,T=0.2 min^-1, at 100 pSTAT3 molecules 100% of cells exhibit an inflammatory response; at 10 molecules, 50% exhibit an inflammatory response and 50% no response.

    “As an example, consider a kdeg,T value of 0.2 min−1. For a signal amplitude of 100 pSTAT3 molecules, 100% of cells assayed would exhibit an inflammatory response. With a 10-fold decrease in amplitude, 50% of cells would exhibit an inflammatory response, while the other 50% of cells would exhibit no response.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    Moderately sustained (kdeg,T<0.001 min^-1) or moderately transient (0.1<kdeg,T<0.01) signals are unaffected by changes in amplitude.

    “Signals that are moderately sustained (kdeg,T<0.001 min−1) or moderately transient (0.1<kdeg,T<0.01), are unaffected by these changes in amplitude.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    At 3.5 days cutoff, I and A thresholds can still be chosen to allow a cellular decision based on signal duration changes, but the peak in I is broader and the crossover region occurs at smaller signal degradation rates.

    “Performing the threshold analysis at 3.5 days, I and A thresholds can still be chosen to allow for a cellular decision to be made based on signal duration changes, but the peak in I is broader and the crossover region occurs at smaller values of the signal degradation rate (Figure S6B).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingreasoning

    When the negative feedback loop is knocked out in the model, the results for transient signals remain unchanged, and for sustained signals both I and A are produced in significant quantities.

    “When the negative feedback loop is knocked out, the results for transient signals remain unchanged since the positive feedback loop dominates the behavior (Figure S4). For sustained signals, both I and A would be produced in significant quantities.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

  • May combine two claims.

    Findingreasoning

    Decreasing signal amplitude to five or less leads to both inflammatory and anti-inflammatory responses for sustained signals in some trajectories, unless the inflammatory threshold is increased.

    “Decreasing the signal amplitude to five or less leads to both inflammatory and anti-inflammatory responses for sustained signals in some of the trajectories, unless the threshold for an inflammatory response is increased from that used to generate Figure 5 (data not shown).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In the model, cells with sustained signals (kdeg,T<10^-3) exhibit an anti-inflammatory response, while cells with transient signals (0.02<kdeg,T<1) exhibit an inflammatory response.

    “Cells with sustained signals (kdeg,T<10−3) clearly exhibit an anti-inflammatory response while cells with transient signals (0.02<kdeg,T<1) clearly exhibit an inflammatory response (Figure 4A and Figure 4B).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingreasoning

    For sustained signals in the model, the number of I molecules peaks at early times and then degrades, while the number of A molecules increases steadily through time.

    “For sustained signals, the number of I molecules peaks at early times and then degrades, while the number of A molecules increases steadily through time (Figure 2A and Figure 2B).”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

  • May combine two claims.

    Findingreasoning

    When the positive feedback loop is removed in the model, the results for sustained signals are virtually unchanged, and for transient signals both I and A remain at approximately zero.

    “When the positive feedback loop is removed, the results for sustained signals are virtually unchanged since the negative feedback loop dominates (Figure S3). For the transient case, both I and A would remain at approximately zero since both would be entirely signal dependent.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

  • May combine two claims.

    Findingreasoning

    For transient signals, the model predicts a pro-inflammatory response, so the percentage of inflammatory cells remains 100% for all amplitudes when WT macrophages are exposed to IL-6.

    “For transient signals, the model predicts a pro-inflammatory response, which is why the percentage of inflammatory cells remains at 100% for all amplitudes when WT macrophages are exposed to IL-6.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: IL-6 induces a moderately transient pSTAT3 signal approximated by kdeg,T=0.1 min^-1 in WT macrophages.
    • The authors state this as an assumption: LPS induces an inflammatory response on its own, so 100% of cells would be pro-inflammatory in the absence of IL-6 and IL-10.

  • May combine two claims.

    Premisecitation

    IL-6 elicits a pro-inflammatory response, while IL-10 signaling leads to an anti-inflammatory response, despite both receptors activating STAT3.

    “The reason why IL-6 induces a pro-inflammatory response, while IL-10 induces an anti-inflammatory response, despite both cytokines activating the same transcription factor, STAT3, is not well understood.”
    • Also stated in: § Introduction · plain
      “IL-6 elicits a pro-inflammatory response, while IL-10 signaling leads to an anti-inflammatory response [10].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [10] A Yoshimura, 2007, SOCS proteins, cytokine signaling and immune regulation., Nat Rev Immunol source

  • May combine two claims.

    Premisecitation

    IL-6 induces a transient STAT3 signal, while IL-10 induces a sustained STAT3 signal.

    “This leads to IL-6 inducing a transient STAT3 signal, while IL-10 induces a sustained STAT3 signal [10].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [10] A Yoshimura, 2007, SOCS proteins, cytokine signaling and immune regulation., Nat Rev Immunol source

  • May combine two claims.

    Premisecitation

    SOCS3 induced by STAT3 can bind to the IL-6 receptor but cannot bind to the IL-10 receptor.

    “One key distinction between the two pathways is that the inhibitor, suppressor of cytokine signaling 3 (SOCS3) induced by STAT3, can bind to the IL-6 receptor, but cannot bind to the IL-10 receptor.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [10] A Yoshimura, 2007, SOCS proteins, cytokine signaling and immune regulation., Nat Rev Immunol source

  • May combine two claims.

    Interpretationreasoning

    At later times when appreciable A is produced, the I signal shuts down but had already crossed the inflammatory threshold, leading to an early inflammatory response and a later anti-inflammatory response.

    “At later times when appreciable amounts of A are produced, the I signal shuts down but had already crossed the inflammatory response threshold leading to an observed inflammatory response starting at early times and also an anti-inflammatory response at later times.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Th17 differentiation is on the order of 5 days.

    “Immediate early gene transcription is on the order of minutes [25], while Th17 differentiation is on the order of 5 days [26].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [26] E Bettelli, 2006, Reciprocal developmental pathways for the generation of pathogenic effector Th17 and regulatory T cells., Nature source

  • May combine two claims.

    Interpretationreasoning

    The model predicts that both programs would be initiated for sustained signals when the negative feedback loop is blocked, but this is likely not biologically relevant since anti-inflammatory ability is removed; therefore sustained signals would likely lead to pro-inflammatory cells.

    “The model predicts that both programs would be initiated for sustained signals, but this is likely not biologically relevant since the ability of anti-inflammatory genes to act “anti-inflammatory” has been removed by the deletion of the negative feedback loop. Therefore, sustained signals would likely lead to pro-inflammatory cells in this system.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.

  • May combine two claims.

    Interpretationreasoning

    Blocking both feedback loops would cause the cell to choose both I and A for sustained signals or neither for transient signals.

    “The end result of blocking both the positive and negative feedback loops is that the cell would choose both I and A for sustained signals or neither for transient signals.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationreasoning

    The model is not entirely self-contained.

    “In this sense, the model is not entirely self-contained.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    Blocking the positive feedback loop would cause the cell to activate the anti-inflammatory gene program for sustained signals or neither program for transient signals.

    “The end result of blocking the positive feedback loop is that the cell would activate the anti-inflammatory gene program for sustained signals or neither program for transient signals.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Inflammatory protein I binds to its own promoter and induces its own transcription in this system.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

  • May combine two claims.

    Interpretationreasoning

    The limitation is not believed relevant under most biological situations because it would require longer than 3.5 days of steady signaling without other changes within the cell.

    “We do not believe that this limitation would be relevant under most biological situations since it would take longer than 3.5 days of steady signaling without any other changes within the cell for it to be an issue.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationreasoning

    The A gene has no positive feedback loops so it is entirely dependent on the signal and thus will not be produced in appreciable quantities by transient signals.

    “The A gene has no positive feedback loops so it is entirely dependent on the signal and thus will not be produced in appreciable quantities by transient signals.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.
    • The authors state this as an assumption: Transcription reactions are first order.
    • The authors state this as an assumption: Associated transcription factors dissociate each time a transcription reaction is carried out.
    • The authors state this as an assumption: mRNA translation of I and A are first order processes.
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.
    • The authors state this as an assumption: All species except genes decay at first order rates.
    • The authors state this as an assumption: Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

  • May combine two claims.

    Interpretationreasoning

    If both feedback loops are removed, since negative feedback is deleted, cells would likely be pro-inflammatory for sustained signals or neither for transient signals.

    “Again, since the negative feedback has been deleted, it would likely be observed that the cells are pro-inflammatory for sustained signals or neither for transient signals.”
    Quote in the paperSubstantial claim
    • The authors state this as an assumption: Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.

  • May combine two claims.

    Interpretationreasoning

    For transient signals, amplitude affects the number of cells exhibiting a given response but does not affect the type of response.

    “Therefore, amplitude only affects the number of cells exhibiting a given response for transient signals, but does not affect the type of response.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Immediate early gene transcription is on the order of minutes.

    “Immediate early gene transcription is on the order of minutes [25], while Th17 differentiation is on the order of 5 days [26].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [25] H Sun, 1993, MKP-1 (3CH134), an immediate early gene product, is a dual specificity phosphatase that dephosphorylates MAP kinase in vivo., Cell source

  • May combine two claims.

    Premisecitation

    Yasukawa et al. exposed SOCS3−/− macrophages to IL-6 and LPS and measured TNF and IL-12(p40) in the supernatant, showing that IL-6 acted anti-inflammatory.

    “A revealing experiment performed by Yasukawa et. al. in which they exposed SOCS3−/−macrophages to IL-6 and LPS and measured the concentration of two pro-inflammatory cytokines (TNF and IL-12(p40)) in the supernatant showed just the opposite [12].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [12] H Yasukawa, 2003, IL-6 induces an anti-inflammatory response in the absence of SOCS3 in macrophages., Nat Immunol source

  • May combine two claims.

    Premisecitation

    IL-10R has two motifs for STAT3 activation while the gp130 subunit of IL-6R has four, leading to IL-6R inducing a higher amplitude STAT3 signal.

    “Another key difference between the IL-10R and the IL-6R, besides their differing interactions with SOCS3, is that the IL-10R has two motifs for STAT3 activation while the gp130 subunit of the IL-6R has four, leading to the IL-6R inducing a higher amplitude STAT3 signal [13], [27], [28].”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [13] KC El Kasmi, 2006, General nature of the STAT3-activated anti-inflammatory response., J Immunol source
    • cites [27] KW Moore, 2001, Interleukin-10 and the interleukin-10 receptor., Annu Rev Immunol source
    • cites [28] D Kamimura, 2003, IL-6 signal transduction and its physiological roles: the signal orchestration model., Rev Physiol Biochem Pharmacol source

  • May combine two claims.

    Premisecitation

    In Yasukawa et al., as IL-6 dosage increased, pro-inflammatory cytokine concentration dropped, meaning IL-6 acted as an anti-inflammatory cytokine on SOCS3−/− macrophages.

    “As the dosage of IL-6 was increased, the pro-inflammatory cytokine concentration dropped meaning that IL-6 was acting as an anti-inflammatory cytokine on the SOCS3−/− macrophages.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [12] H Yasukawa, 2003, IL-6 induces an anti-inflammatory response in the absence of SOCS3 in macrophages., Nat Immunol source

  • May combine two claims.

    Interpretationcitation

    The model predicts no distinction between IL-10 acting on SOCS3−/− vs WT macrophages, as observed.

    “Since there is no distinction between IL-10 acting on SOCS3−/− or WT macrophages, the model predicts that no distinction will be seen experimentally, as was observed [12].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [12] H Yasukawa, 2003, IL-6 induces an anti-inflammatory response in the absence of SOCS3 in macrophages., Nat Immunol source
    • The authors state this as an assumption: IL-10 induces a slowly decaying pSTAT3 signal approximated by kdeg,T=0.003 min^-1 in both SOCS3−/− and WT macrophages.
    • The authors state this as an assumption: In the model, measuring secreted inflammatory cytokine concentrations translates to counting the percentage of trajectories crossing the I threshold for a set kdeg,T characteristic of macrophage type and cytokine.

  • May combine two claims.

    Interpretationreasoning

    As the number of A molecules is reduced, I becomes less regulated and will eventually win out.

    “As the number of A molecules is reduced, I becomes less regulated and will eventually win out.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    There has been extensive work in systems biology to identify network motifs.

    “There has been extensive work in the field of systems biology to identify network motifs [16], [17].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [16] U Alon, 2007, Network motifs: theory and experimental approaches., Nat Rev Genet source
    • cites [17] R Milo, 2002, Network motifs: simple building blocks of complex networks., Science source

  • Classified as probably not a substantial claim.

    Interpretationnone given

    The focus of this work was to show that a simple genetic network could explain differences between IL-6 and IL-10 signaling without resorting to more complicated arguments such as receptor-specific STAT3 conformational changes or unknown species.

    “Our focus in this work was not to propose a new signaling motif, but instead to show that a very simple genetic network could be used to explain the differences between IL-6 and IL-10 signaling without having to resort to using other more complicated arguments such as receptor-specific STAT3 conformational changes or effects due to unknown species.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationnone given

    The model may be applicable to a range of biological networks sensitive to signal duration.

    “Even though the model was presented in the context of IL-6/IL-10 signaling, it may be applicable to a range of biological networks which are sensitive to signal duration.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationnone given

    The model serves as a tool for visualizing how signal duration can lead to two different responses from the same genetic network activated by the same transcription factor from two different pathways.

    “The model serves as a tool for visualizing how the duration of the signal can lead to two different responses from the same genetic network activated by the same transcription factor from two different pathways.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationnone given

    The essential feature of the model is that both genes of interest are activated by the same transcription factor and one gene has a positive feedback loop to sustain itself in the absence of the main signal, but is also negatively regulated by the opposing gene.

    “The essential feature of the model is that both genes of interest are activated by the same transcription factor and that one of the genes has a positive feedback loop to sustain itself in the absence of the main signal, but is also negatively regulated by the opposing gene.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Our network contains components of previously identified motifs such as an autoregulatory positive feedback loop and a negative feedback loop.

    “Our network contains components of previously identified motifs such as an autoregulatory positive feedback loop [16]–[19] and a negative feedback loop.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites 16]–[19

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationreasoning

    The model may be applicable to IL-6/IL-10 signaling because all essential steps have been observed except the positive feedback loop: STAT3 induces both inflammatory and anti-inflammatory genes and anti-inflammatory genes inhibit inflammatory genes.

    “We believe that the model may be applicable to IL-6/IL-10 signaling since all essential steps of the model have been observed except for the positive feedback loop, namely that STAT3 induces both inflammatory and anti-inflammatory genes and that the anti-inflammatory genes inhibit the inflammatory genes.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    Because LPS induces an inflammatory response on its own, the ramping up period is not observed in the figure.

    “However, since LPS induces an inflammatory response on its own, the ramping up period is not observed in the figure.”
    Quote in the paperNot a substantial claim
    • The authors state this as an assumption: LPS induces an inflammatory response on its own, so 100% of cells would be pro-inflammatory in the absence of IL-6 and IL-10.
41 of 41

  • The paper relies on this without support.

    The reason IL-6 and IL-10 produce different responses despite both activating STAT3 is not well understood.

    “The reason why IL-6 induces a pro-inflammatory response, while IL-10 induces an anti-inflammatory response, despite both cytokines activating the same transcription factor, STAT3, is not well understood.”

  • The authors state this as an assumption.

    All inflammatory and anti-inflammatory genes can be represented by generic genes I and A.

    “In reality, there are many inflammatory and anti-inflammatory genes, but we will adopt a coarse-grained view of the system where all of these genes will be characterized by generic representative genes I and A, respectively.”

  • The authors state this as an assumption.

    Transcription reactions are first order.

    “DNA-bound pSTAT3 can induce transcription of I mRNA (Im) and A mRNA (Am), via reactions assumed to be assumed first order”

  • The authors state this as an assumption.

    Associated transcription factors dissociate each time a transcription reaction is carried out.

    “It is assumed that the associated transcription factors dissociate each time a transcription reaction is carried out.”

  • The authors state this as an assumption.

    mRNA translation of I and A are first order processes.

    “After transcription, the mRNA of I and A can be translated to fully functional proteins in assumed first order processes”

  • The authors state this as an assumption.

    Inflammatory protein I binds to its own promoter and induces its own transcription in this system.

    “Though we do not have direct experimental evidence for the existence of a positive feedback loop in this system, the addition of an autoregulatory positive feedback loop to our models is feasible since it has been identified as a general network motif [16], [17] and has been observed experimentally in other systems [18], [19].”

  • The authors state this as an assumption.

    Anti-inflammatory protein A binds to the promoter of gene I and impedes its transcription.

    “The network also contains a negative feedback loop where anti-inflammatory protein A is able to bind to the promoter of gene I and impede its transcription according to”

  • The authors state this as an assumption.

    All species except genes decay at first order rates.

    “Another important aspect of the network is that all species, except genes, can decay at assumed first order rates”

  • The authors state this as an assumption.

    Deactivation of I or A is caused by ubiquitin ligases or phosphatases in the nucleus that are present in large enough concentrations so that the reactions are first order.

    “Biologically, the deactivation of I or A would be caused by ubiquitin ligases or phosphatases in the nucleus, which are assumed to be present in large enough concentrations so that the reactions are first order.”

  • The authors state this as an assumption.

    Downstream gene programs are only initiated when I or A cross a threshold value in molecular number at any point in the time trajectory.

    “It is assumed that the downstream gene programs (inflammatory or anti-inflammatory) activated by I or A are only initiated when the respective molecules cross a threshold value in molecular number at any point in the time trajectory.”

  • The authors state this as an assumption.

    The percent of I or A trajectories crossing the threshold directly corresponds to the percent of cells that exhibit pro-inflammatory or anti-inflammatory responses in an equivalent biological experiment.

    “The percent of I or A trajectories crossing the threshold directly corresponds to the percent of cells that exhibit pro-inflammatory or anti-inflammatory responses in an equivalent biological experiment since each trajectory corresponds to 1 cell.”

  • The authors state this as an assumption.

    IL-6 induces a moderately transient pSTAT3 signal approximated by kdeg,T=0.1 min^-1 in WT macrophages.

    “We assume that IL-6 induces a moderately transient pSTAT3 signal that can roughly be approximated by a kdeg,T value of 0.1 min−1 in WT macrophages.”

  • The authors state this as an assumption.

    IL-10 induces a slowly decaying pSTAT3 signal approximated by kdeg,T=0.003 min^-1 in both SOCS3−/− and WT macrophages.

    “The second assumption is that IL-10 induces a slowly decaying pSTAT3 signal that can be approximated by a kdeg,T value of 0.003 min−1 in both SOCS3−/− and WT macrophages.”

  • The authors state this as an assumption.

    IL-6 and IL-10 induce similarly decaying pSTAT3 signals in SOCS3−/− macrophages, so the same kdeg,T value can be used.

    “IL-6 and IL-10 would conceivably induce similarly decaying pSTAT3 signals in SOC3−/− macrophages, so we can use the same kdeg,T value.”

  • The authors state this as an assumption.

    In the model, measuring secreted inflammatory cytokine concentrations translates to counting the percentage of trajectories crossing the I threshold for a set kdeg,T characteristic of macrophage type and cytokine.

    “In their experiment, Yasukawa et. al. measure concentrations of secreted inflammatory cytokines. In our model this translates to counting the percentage of trajectories (cells) that cross the imposed threshold value of I at any point for a set value of kdeg,T, which is characteristic to the macrophage type and the type of cytokine added along with LPS.”

  • The authors state this as an assumption.

    LPS induces an inflammatory response on its own, so 100% of cells would be pro-inflammatory in the absence of IL-6 and IL-10.

    “Since LPS induces an inflammatory response on its own, it is assumed that 100% of the cells would be pro-inflammatory in the absence of IL-6 and IL-10.”

  • The paper relies on this without support.

    LPS induces an inflammatory response in macrophages, so a decrease in inflammatory cytokine production is considered anti-inflammatory.

    “LPS induces an inflammatory response in macrophages, so a decrease in inflammatory cytokine production would be considered anti-inflammatory.”
17 of 17

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Authors
Fowler, K. D., Kuchroo, V. K., & Chakraborty, A. K.
Affiliations
  • Massachusetts Institute of Technology (US)
  • Brigham and Women's Hospital (US)
  • Ragon Institute of MGH, MIT and Harvard (US)
Corresponding author
Chakraborty, Arup K.
ORCID
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2012-03-13
Volume
7
Issue
3
Pages
e33018
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0033018
PMC
PMC3302786
OpenAlex
W2151779918
Semantic Scholar
b0f37106da38fc687b0c99afd5785f24a5d5eb2f
Cited by
6
References
31
Citations by year
2023: 1 · 2021: 2 · 2015: 1 · 2014: 2
FWCI
0.43
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • PubMed Central (submittedVersion, cc-by)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
  • Figshare (submittedVersion, cc-by)
Funders
National Institutes of Health
Topics
  • Health Sciences › Medicine › Oncology › Cytokine Signaling Pathways and Interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
Keywords
signal duration, STAT3, interleukin-6, IL-10, SOCS3, transcriptional regulatory networks, inflammation, anti-inflammatory response, negative feedback loop, transcriptional regulation
MeSH terms
Suppressor of Cytokine Signaling 3 Protein, Animals, Computer Simulation, Inflammation, Models, Biological, Signal Transduction, Transcriptional Activation, Interleukin-6, Interleukin-10, Mice, Knockout, Feedback, Physiological, STAT3 Transcription Factor, Suppressor of Cytokine Signaling Proteins, Mice, Gene Regulatory Networks

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-23.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-23.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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