Research ArticleImmunology

Cooperation between T cell receptor and Toll-like receptor 5 signaling for CD4+ T cell activation

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Science Signaling  16 Apr 2019:
Vol. 12, Issue 577, eaar3641
DOI: 10.1126/scisignal.aar3641
  • Fig. 1 The TCR signaling model.

    The model encompasses 110 nodes, including 2 externally controlled inputs (TCR and CD28), which are depicted in green, 6 activated transcription factors, which are in yellow, and 6 phenotypical outputs, which are in gray. Green arrows represent activation events, whereas red blunt-end arcs denote inhibition events. PICytokines, proinflammatory cytokines; AICytokines, anti-inflammatory cytokines.

  • Fig. 2 Computation of the stable states of the TCR model.

    The rows list the stable states identified with GINsim software for three distinct scenarios [wild type (WT), PKCθ KO, and PI3K KO] and three environmental conditions (Unstimulated, TCR stimulation, or TCR + CD28 stimulation). Note that only the relevant nodes are displayed. White cells (zero value) denote negligible activation of the corresponding components (columns), whereas blue cells (value of 1) denote substantial activation. Inputs are highlighted in green, phenotypical nodes are in gray, and the transcription factors induced during T cell activation are in yellow. CellCycleProg, cell cycle progression; ActinRem, actin remodeling.

  • Fig. 3 The TLR5 signaling model.

    The model encompasses 42 nodes, among which 1 corresponds to the TLR5 input (green), 3 correspond to three key transcription factors (yellow), and 3 correspond to phenotypical output nodes (gray). Green arrows represent activation events, whereas red blunt-end arcs denote inhibition events.

  • Fig. 4 Computation of the stable states of the TLR5 model.

    The rows list the stable states identified for three distinct scenarios [wild type (WT), TAK1 KO, and PI3K KO] and two environmental conditions (Unstimulated and TLR5 stimulation). White cells (value 0) denote negligible activation of the corresponding components (columns), whereas blue cells (value 1) denote substantial activation. Inputs are highlighted in green, phenotypical nodes are in gray, and the transcription factors induced during T cell activation are in yellow.

  • Fig. 5 The TCR + TLR5 merged model.

    The merged model encompasses 128 nodes, including 3 externally controlled inputs (TLR5, TCR, and CD28) and 6 phenotypic nodes (bottom). The pink nodes belong to the original TCR model, the blue nodes belong exclusively to the original TLR5 model, and the yellow nodes are shared between the two models. Green arrows represent activation events, whereas red blunt-end arcs denote inhibition events.

  • Fig. 6 Computation of the stable states for the TCR + TLR5 merged model.

    The rows list the stable states identified for three distinct scenarios [wild type (WT), PKCθ KO, and PI3K KO] and three environmental conditions (Unstimulated, TCR + CD28 stimulation, and TCR + TLR5 stimulation). White cells (value 0) denote negligible activation of the corresponding components (columns), whereas blue cells (value 1) denote substantial activation. Inputs are highlighted in green, phenotypical nodes are in gray, and the transcription factors induced during T cell activation are in yellow.

  • Fig. 7 Experimental assessment of AP-1, NF-κB, and CREB activities.

    We used flow cytometry to evaluate the phosphorylation of c-Jun, p65, and CREB1 as a measure of the activation of AP-1, NF-κB, and CREB, respectively. Naïve CD4+ T cells were left unstimulated or were stimulated under the indicated conditions for 1 hour (to measure p65 and CREB1 activation) or 3 hours (to measure c-Jun activation). The mean fluorescence intensity (MFI) values for the indicated phosphoproteins were determined by flow cytometry. The P values obtained by the Kruskal-Wallis test are indicated above the error bars, which correspond to the SEM. Each experiment was repeated at least three times with independent biological samples.

Supplementary Materials

  • stke.sciencemag.org/cgi/content/full/12/577/eaar3641/DC1

    Text S1. Modeling descriptions.

    Fig. S1. TCR molecular map built with the software CellDesigner 4.4.

    Fig. S2. TLR5 molecular map built with the software CellDesigner 4.4.

    Fig. S3. Chromatin states and RNA-seq data validating TLR5 expression.

    Fig. S4. Reduced TCR + TLR5 merged model.

    Fig. S5. Cellular characterization and TLR5 expression in naïve CD4+ T cells.

    Fig. S6. Comparison of our TCR model with the JSR model.

    Table S1. BLUEPRINT data used in this study.

    Table S2. Logical rules for the TCR model.

    Table S3. Logical rules for the TLR5 model.

    Table S4. Logical rules for the TCR + TLR5 merged model.

    Table S5. Global comparison between the JSR model and our model for the TCR signaling network.

    Table S6. Kruskal-Wallis test results for pp65.

    Table S7. Kruskal-Wallis test results for pc-Jun.

    Table S8. Kruskal-Wallis test results for pCREB.

    Data file S1. TCR molecular map (CellDesigner v4.4).

    Data file S2. TCR signaling model (GINsim v3.0b).

    Data file S3. TLR5 molecular map (CellDesigner v4.4).

    Data file S4. TLR5 signaling model (GINsim v3.0b).

    Data file S5. TCR + TLR5 merged model (GINsim v3.0b).

  • The PDF file includes:

    • Text S1. Modeling descriptions.
    • Legends for figures S1 and S2
    • Fig. S3. Chromatin states and RNA-seq data validating TLR5 expression.
    • Fig. S4. Reduced TCR + TLR5 merged model.
    • Fig. S5. Cellular characterization and TLR5 expression in naïve CD4+ T cells.
    • Fig. S6. Comparison of our TCR model with the JSR model.
    • Table S1. BLUEPRINT data used in this study.
    • Table S2. Logical rules for the TCR model.
    • Table S3. Logical rules for the TLR5 model.
    • Table S4. Logical rules for the TCR + TLR5 merged model.
    • Table S5. Global comparison between the JSR model and our model for the TCR signaling network.
    • Table S6. Kruskal-Wallis test results for pp65.
    • Table S7. Kruskal-Wallis test results for pc-Jun.
    • Table S8. Kruskal-Wallis test results for pCREB.
    • Legends for data files S1 to S5

    [Download PDF]

    Other Supplementary Material for this manuscript includes the following:

    • Fig. S1 (.pdf format). TCR molecular map built with the software CellDesigner 4.4.
    • Fig. S2 (.pdf format). TLR5 molecular map built with the software CellDesigner 4.4.
    • Data file S1 (.xml format). TCR molecular map (CellDesigner v4.4).
    • Data file S2 (.zginml format). TCR signaling model (GINsim v3.0b).
    • Data file S3 (.xml format). TLR5 molecular map (CellDesigner v4.4).
    • Data file S4 (.zginml format). TLR5 signaling model (GINsim v3.0b).
    • Data file S5 (.zginml format). TCR + TLR5 merged model (GINsim v3.0b).

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