Table 1:
A list of rules for all the agent types implemented in the hybrid model
| Name of agent | Agent type | Rules |
|---|---|---|
| Helicobacter pylori | H. pylori | Moves across the epithelial cell border if near damaged epithelial layer; proliferates in the lumen and LP; dies in LP and in the lumen due to the damage of epithelial cells by Th1 or Th17 cells |
| Macrophages | Monocyte | Proliferates in presence of effector DCs or damaged epithelial cells; proliferates in the LP; differentiates to regulatory macrophage based on the output from the macrophage ODE; differentiates to inflammatory macrophages in presence of IFN-γ; dies naturally |
| Resident | Proliferates in the presence of H. pylori; secretes IL-10; dies naturally; dies due to Th1 and Treg cells | |
| Regulatory | Proliferates and removes bacteria; dies; secretes IL-10 | |
| Inflammatory | Proliferates in the presence of damaged epithelial cells; dies naturally | |
| Dendritics | Immature | Moves from LP to epithelium compartment and from the epithelium to the LP; differentiates to tolerogenic DC in the presence of tolerogenic bacteria, both in epithelium and LP; differentiates to effector DC in the presence of H. pylori; proliferates in LP and GLN; dies naturally |
| Effector | Moves from LP to GLN; moves from epithelium to LP; secretes IL-6 and IL-12; dies naturally | |
| Tolerogenic | Moves from LP to GLN; moves from epithelium to LP; secretes TGF-β; dies naturally | |
| T cells | Naive | In the presence of effector DCs: differentiates to Th1 in the presence of IFN-γ or IL-12; differentiates to Th17 in the presences of IL-6 or TGF-β; in the presence of tolerogenic DCs: differentiates to iTreg in the presence of TGF-β; differentiates to Treg in the presences of IL-10; dies naturally |
| Th1 | Secretes IFN-γ; moves from GLN to LP; proliferates in LP and GLN; dies naturally | |
| Th17 | Secretes IL-17; in the presence of tolerogenic DC, transitions to iTreg cells; moves from GLN to LP; proliferates in LP and GLN;dies naturally | |
| iTreg | Secretes IL-10; in the presence of tolerogenic DC, transitions to iTreg cells;moves from GLN to LP; proliferates in LP and GLN; dies naturally | |
| Tr | Secretes IL-10;dies naturally;proliferates in the LP | |
| Epithelial | Healthy | Damaged by infectious bacteria;damaged by Th1 and Th17 cells; proliferates;secretes IL-6 and IL-12; dies naturally |
| Damaged | Transitions to healthy state in the presence of IL-10; dies naturally | |
| Bacteria | Infectious | Dies due to Th1 or Th17 or inflammatory macrophages or damaged epithelial cells;dies naturally;proliferates in the LP |
| Tolerogenic | Moves from lumen to the epithelium in the presence of damaged epithelial cells;becomes infectious if moves in the LP compartment; proliferates in lumen and LP; dies naturally |
Dies = is removed from the simulation; DC: dendritic cell; GLN: gastric lymph node; IFN-γ: interferon γ; IL: interleukin; iTreg: induced regulatory T cell; LP: lamina propria; TGF-β: transforming growth factor β; Th: T helper; Treg: regulatory T cell.