Figure 1.
Schematic diagram of TNF-α and IL-10 mechanisms included in GranSim.
Regulatory T cells, activated macrophages, infected macrophages, and chronically infected macrophages are able to produce IL-10. IL-10 inhibits the production of TNF-α in all cell types. IL-10 indirectly prevents the recruitment of immune cells to the site of infection by inhibiting chemokine production. IL-10 limits the secondary regulatory mechanism (cell-cell contact, TGF-β, and other regulatory mechanisms) down regulation of activated macrophages by regulatory T cells. Activated macrophages, infected macrophages, chronically infected macrophages, resting macrophages (STAT1 or NFκB activated), cytotoxic T cells, and pro-inflammatory T cells are able to produce TNF-α. TNF-α directly induces recruitment of immune cells to the site of infection (lung). TNF-α induces production of IL-10 in activated macrophages, which represents the pro/anti inflammatory plasticity of activated macrophages. TNF-α, along with interferon-γ derived from pro-inflammatory T cells, induces activation of resting macrophages or it can induce the caspase-mediated apoptosis pathway found in all cell types.
Figure 2.
Schematic representation of the hybrid multi-scale ABM of the immune response to Mtb.
A. An overview of GranSim with a sub-section of model rules shown that represents known immune cell behaviors and interactions (Adapted from [13]). A full list of rules is available in Appendix S1 B. Schematic representation of single cell-level TNF-α and IL-10 binding and trafficking reactions. Model equations are shown in Table S1 in Appendix S2 and Table S2 in Appendix S2.
Figure 3.
Model validation of simulated granulomas at 200 days post-infection.
A. Simulation using baseline containment parameter set. B. Simulation using TNF-α knockout parameter set (baseline containment parameter set but with kRNA_Mac = 0 and kRNA_Tcell = 0). C. Interferon-γ knockout parameter set (baseline containment parameter set PSTAT1 = 0). Cell types are as follows: resting macrophages (resting Mφ), infected macrophages (infected Mφ), chronically infected macrophage (chronic Mφ), activated macrophage (activated Mφ), pro-inflammatory T cell (Tγ), cytotoxic T cell (Tc), regulatory T cell (Tr), and extracellular bacteria (Bext). Agent and bacteria colors are shown in the included legend. These same colors are used for subsequent images. Model parameters are given in Table S3 in Appendix S3, Table S4 in Appendix S3, and Table S5 in Appendix S3. For full length time-lapse simulations please see http://malthus.med.micro.umich.edu/lab/movies/TNF-IL10.
Figure 4.
Time course simulation results for baseline and IL-10 knockout scenarios.
Simulation using baseline containment parameter set at 200 days post-infection. B. Simulation using the IL-10 knockout parameter set at 200 days post-infection. Agents and bacteria colors are as in Figure 3. C–F. Simulation results at 50, 100, 150 and 200 days post-infection using the baseline containment parameter set (black bars) and the IL-10 knockout parameter set (white bars). The few simulations that lead to clearance of Mtb in a granuloma are not shown here (see Table S10 in Appendix S4). C. Total bacterial load. D. Number of activated Mφ. E. Number of apoptotic resting Mφ. F. Average tissue concentration of TNF-α (pM). For full length time-lapse simulations please see http://malthus.med.micro.umich.edu/lab/movies/TNF-IL10.
Figure 5.
Three main processes influence the concentrations of TNF-α and IL-10 and control infection outcome.
Model parameters that are relevant to TNF-α or IL-10 synthesis (synthesis influence), that control the spatial distribution of TNF-α or IL-10 (spatial influence), and that control the binding and signaling of TNF-α or IL-10 (signaling influence). These three parameter groups control the concentrations of TNF-α and IL-10 in the granuloma environment and thus in turn directly control infection outcome. Parameter groups are described in Table S4 in Appendix S3 and Table S5 in Appendix S3.
Table 1.
Molecular Scale TNF-α and IL-10 Model Parameters Significantly Correlated With Selected Model Outputs At 200 Days Post-Infection.
Figure 6.
Simulation results showing the effects of varying each influence in a granuloma environment.
Simulation results from 30 replications showing the effects of varying each of the three influences: the synthesis influence, signaling influence, and spatial influence (Figure 5; Table S4 and Table S5 in Appendix S3). Results using the baseline containment parameter set, labeled ‘base’, are included for comparison (parameter values in Table S4 in Appendix S3 and Table S5 in Appendix S3). A. Effects of mRNA synthesis rate of TNF-α by Mφ (‘Low’ kRNA_Mac = 0.5 #/cell*s, ‘High’ kRNA_Mac = 3.0 #/cell*s) and synthesis rate of IL-10 by activated Mφ (‘Low’ ksynthMacAct = 0.1 #/cell*s, ‘High’ ksynthMacAct = 1.0 #/cell*s). B. Effect of TNFR1 receptor density on Mφ (‘Low’ TNFR1mac = 500, ‘High’ TNFR1mac = 5000) and IL-10R receptor density on Mφ (‘Low’ IL10Rmac = 500, ‘High’ IL10Rmac = 5000). C. Effect of bound TNFR1 internalization rate constant (‘Low’ kint1 = 10−4 s−1, ‘High’ kint1 = 10−3 s−1) and bound IL-10R internalization rate constant (‘Low’ kint = 10−4 s−1, ‘High’ kint = 10−3 s−1). D. Effect of spatial range of TNF-α (‘Low’ DTNF = 1×10−8 cm2/s kdeg = 2.3×10−2 s−1, ‘High’ DTNF = 9×10−8 cm2/s kdeg = 5×10−5 s−1) and spatial range of IL-10 (‘Low’ DIL10 = 1×10−8 cm2/s kdeg = 1.6×10−2 s−1, ‘High’ DIL10 = 8×10−8 cm2/s kdeg = 1.8×10−6 s−1). Low indicates a lower value than baseline while high indicates a higher value than baseline.
Figure 7.
Altering the ratio of [TNF-α]/[IL-10] in a granuloma environment.
Simulation results at 200 days post-infection showing the effects of altering the ratio of average tissue concentrations of TNF-α to IL-10 in the granuloma environment ([TNF-α]/[IL-10]). A total of 296 simulations (4 replications) were performed yielding various values of [TNF-α]/[IL-10]. Comparison of the ratio of concentrations of TNF-α to IL-10 with: A. B. C. Total bacterial load, number of activated Mφ, and number of apoptotic resting Mφ as a function of [TNF-α]/[IL-10]. D. Host-Pathogen Index (H.P.I), a metric that combines the three previous measures as a function of [TNF-α]/[IL-10]. The green star is the average simulation result for the baseline containment parameter set. E–G. Representative granuloma snapshots at 200 days post-infection for each of the regions (1, 2, and 3) defined in Figure 7D. For full length time-lapse simulations please see http://malthus.med.micro.umich.edu/lab/movies/TNF-IL10.