Table 1.
List of regulatory components.
Figure 1.
Left: (simplified) TCR signalling pathway. The node denoted NFAT represents the joint activity of NFAT and AP1. Middle: generic cytokine module. IL_e represents the cytokine present in the environment; IL represents the autocrine production of the same cytokine; ILR1 and ILR2 represent two different receptor sub-chains; ILR represents the activated receptor, which in turn activates STAT. Right: IL2R regulation and its effect on cell proliferation. The bottom row gives the logical functions used for one of the components of each module. “” and “
” stand for AND and OR logical operators, respectively.
Table 2.
List of cytokines.
Figure 2.
Th differentiation regulatory graph, encompassing 65 components.
The 13 input components are colored in black. Ellipses denote Boolean components while rectangles denote ternary components. Green arrows denote activations, whereas red blunt ones denote inhibitions. A peculiar blue arrow denotes the unique dual interaction. The greyed-out components have been reduced to generate the regulatory graph displayed in Figure 3.
Figure 3.
Reduced Th regulatory graph, encompassing 34 components.
This graph has been obtained by applying the reduction method described in Section “Model reduction” to the full model shown in Figure 2. Indirect interactions resulting from the reduction are displayed using dotted lines. Greyed-out components can be further reduced to generate a more compact model, which still keeps the most relevant Th differentiation markers.
Figure 4.
Definition of alternative Th subtypes based on the expression of the master regulators.
Each of the four master genes considered (TBET, GATA3, RORGT and FOXP3) is positively auto-regulated. The first five rows correspond to the canonical Th cell subtypes expressing no (Th0) or a single master regulator (Th1, Th17, Th2, Treg). The remaining rows correspond to hybrid Th cell subtypes that express more than one of the master regulators, i.e. that show hybrid patterns. Additional positive circuits (proliferation and STAT3-related) generate further subtypes. The circuit analysis predicts 48 stable patterns (4 for each of the 12 groups; each pattern corresponds to one cell of the table under the heading “Other circuits”). Only 28 of these patterns (greyed cells) are compatible with at least one of the input combinations considered here (cf. Figure 5). The values in the cells indicate how many input combinations are compatible with this stable state. Five patterns are not compatible with any input combination (cells with dashes).
Figure 5.
Environmental conditions used for the simulations.
Each row corresponds to one prototypic environment, defined in terms of combinations of APC and of seven different cytokine inputs. Presence/absence of the different inputs is denoted by grey/white cells. The coloured tile code defined in the first column is used in Figure 7 to denote environmental conditions.
Figure 6.
Context-dependent stable states and their component expression patterns.
A grey cell denotes the activation of the corresponding component (column entries) for the corresponding stable state (row entries). Black cells denote higher activity levels (in the case of multi-level components). Note that the values of the input nodes are omitted here. A state stable for a given input combination may become unstable for other input values. Relationships between these stable states and selected environmental conditions (described in Figure 5) are given in Figure 7. Activated cells (i.e. expressing NFAT and producing lineage-specific cytokines) and anergic cells (i.e. expressing NFAT but no lineage-specific cytokine) are indicated, when this classification clearly applies. Note that different stable states sharing a common pattern in terms of expression of master regulators but differing in the expression of other components are identified as the same Th cell subtype (as in the case of Th2 Foxp3+ RORt+ subtype at the end of the table).
Figure 7.
Stability of Th cell subtypes and environment-dependent transitions.
This figure summarises several simulation rounds, displaying the context-dependent stable states (column entries) reached depending on eliciting initial states (row entries) and environmental conditions (coloured tiles). The coloured tile code for environmental conditions is defined in Figure 5.
Figure 8.
Graphical representation of the plasticity of cell subtypes depending on the environment.
The Th cell subtypes observed in silico are grouped into three main constellations (Th0, Th1 and Th2, delimited by different backgrounds). The different panels correspond to different environmental conditions listed in Figure 5: (a) no stimulation, (b) APC only, (c) pro-Th1, (d) pro-Th2, (e) pro-Treg, and (f) pro-Th17. Arrows between cell lineages denote switches elicited by the corresponding environment. Cell colouring denotes the activity of the master regulators: GATA3 (blue), T-bet (red), Foxp3 (green) and RORt (orange).