Dimensionality of Motion and Binding Valency Govern Receptor-Ligand Kinetics As Revealed by Agent-Based Modeling

Spatiotemporal modeling quantifies cellular contributions to uptake of Aspergillus fumigatus in the human lung

The human lung is confronted daily with thousands of microbial invaders reaching the lower respiratory tract. An efficient response by the resident type 1 and type 2 alveolar epithelial cells (AECs) and alveolar macrophages (AMs) cells during the early hours of innate immunity is a prerequisite to maintain a non-inflammatory state, but foremost to rapidly remove harmful substances. One such human-pathogenic invader is the opportunistic fungus Aspergillus fumigatus. If the spherical conidia are not cleared in time, they swell reaching approximately twice of their initial size and germinate to develop hyphae around six hours post-infection. This process of morphological change is crucial as it enables the pathogen to invade the alveolar epithelium and to reach the bloodstream, but also makes it conspicuous for the immune system. During this process, conidia are first in contact with AECs then with migrating AMs, both attempting to internalize and clear the fungus. However, the relative contribution of AMs and AECs to uptake of A. fumigatus remains an open question, especially the capabilities of the barely investigated type 1 AECs. In this study, we present a bottom-up modeling approach to incorporate experimental data on the dynamic increase of the conidial diameter and A. fumigatus uptake by AECs and AMs in a hybrid agent-based model (hABM) for the to-scale simulation of virtual infection scenarios in the human alveolus. By screening a wide range of parameters, we found that type 1 AECs, which cover approximately 95% of the alveolar surface, are likely to have a greater impact on uptake than type 2 AECs. Moreover, the majority of infection scenarios across the regime of tested parameters were cleared through uptake by AMs, whereas the contribution to conidial uptake by AECs was observed to be limited, indicating that their crucial support might mostly consist in mediating chemokine secretion for AM recruitment. Regardless, as the first host cell being confronted with A. fumigatus conidia, our results evidence the large potential impact of type 1 AECs antimicrobial activities, underlining the requirement of increasing experimental efforts on this alveolar constituent.

Antibody-dependent enhancement and neutralization against CVB4 investigated in vitro and in silico through an agent-based model

The infection with coxsackievirus B4 (CVB4) can be enhanced in vitro by antibodies directed against the viral capsid protein VP4. In peripheral blood mononuclear cells, antibody-dependent enhancement (ADE) of CVB4 infection leads to the production of interferon alpha (IFN-α). To investigate ADE of CVB4-induced production of IFN-α, an agent-based model was constructed with enhancing and neutralizing antibodies. The model recapitulates viral neutralization and ADE in silico. The enhancing and neutralizing activities of serum samples were evaluated in vitro to confront the model predictions with experimental results. Increasing the incubation time of CVB4 with serum samples improves virus neutralization in silico as well as in vitro. It also results in ADE at lower antibody numbers in silico, which is confirmed in vitro with IFN-α production at lower serum concentrations. Furthermore, incubation of CVB4 with serum at a low temperature does not induce IFN-α production in vitro. Thus, taken together our results suggest that enhancing antibodies bind cryptic epitopes, more accessible with longer incubation time and at higher temperature due to changes in capsid conformation, consistent with previous results indicating that enhancing antibodies are anti-VP4 antibodies.

Surrogate infection model predicts optimal alveolar macrophage number for clearance of Aspergillus fumigatus infections

The immune system has to fight off hundreds of microbial invaders every day, such as the human-pathogenic fungus Aspergillus fumigatus. The fungal conidia can reach the lower respiratory tract, swell and form hyphae within six hours causing life-threatening invasive aspergillosis. Invading pathogens are continuously recognized and eliminated by alveolar macrophages (AM). Their number plays an essential role, but remains controversial with measurements varying by a factor greater than ten for the human lung. We here investigate the impact of the AM number on the clearance of A. fumigatus conidia in humans and mice using analytical and numerical modeling approaches. A three-dimensional to-scale hybrid agent-based model (hABM) of the human and murine alveolus allowed us to simulate millions of virtual infection scenarios, and to gain quantitative insights into the infection dynamics for varying AM numbers and infection doses. Since hABM simulations are computationally expensive, we derived and trained an analytical surrogate infection model on the large dataset of numerical simulations. This enables reducing the number of hABM simulations while still providing (i) accurate and immediate predictions on infection progression, (ii) quantitative hypotheses on the infection dynamics under healthy and immunocompromised conditions, and (iii) optimal AM numbers for combating A. fumigatus infections in humans and mice.

Agent-based modelling of iron cycling bacteria provides a framework for testing alternative environmental conditions and modes of action

Iron-reducing and iron-oxidizing bacteria are of interest in a variety of environmental and industrial applications. Such bacteria often co-occur at oxic-anoxic gradients in aquatic and terrestrial habitats. In this paper, we present the first computational agent-based model of microbial iron cycling, between the anaerobic ferric iron (Fe³⁺)-reducing bacteria Shewanella spp. and the microaerophilic ferrous iron (Fe²⁺)-oxidizing bacteria Sideroxydans spp. By including the key processes of reduction/oxidation, movement, adhesion, Fe²⁺-equilibration and nanoparticle formation, we derive a core model which enables hypothesis testing and prediction for different environmental conditions including temporal cycles of oxic and anoxic conditions. We compared (i) combinations of different Fe³⁺-reducing/Fe²⁺-oxidizing modes of action of the bacteria and (ii) system behaviour for different pH values. We predicted that the beneficial effect of a high number of iron-nanoparticles on the total Fe³⁺ reduction rate of the system is not only due to the faster reduction of these iron-nanoparticles, but also to the nanoparticles' additional capacity to bind Fe²⁺ on their surfaces. Efficient iron-nanoparticle reduction is confined to pH around 6, being twice as high than at pH 7, whereas at pH 5 negligible reduction takes place. Furthermore, in accordance with experimental evidence our model showed that shorter oxic/anoxic periods exhibit a faster increase of total Fe³⁺ reduction rate than longer periods.

Agent-Based Modeling of T Cell Receptor Cooperativity

Immunological synapse (IS) formation is a key event during antigen recognition by T cells. Recent experimental evidence suggests that the affinity between T cell receptors (TCRs) and antigen is actively modulated during the early steps of TCR signaling. In this work, we used an agent-based model to study possible mechanisms for affinity modulation during IS formation. We show that, without any specific active mechanism, the observed affinity between receptors and ligands evolves over time and depends on the density of ligands of the antigen peptide presented by major histocompatibility complexes (pMHC) and TCR molecules. A comparison between the presence or absence of TCR–pMHC centrally directed flow due to F-actin coupling suggests that centripetal transport is a potential mechanism for affinity modulation. The model further suggests that the time point of affinity measurement during immune synapse formation is critical. Finally, a mathematical model of F-actin foci formation incorporated in the agent-based model shows that TCR affinity can potentially be actively modulated by positive/negative feedback of the F-actin foci on the TCR-pMHC association rate k_on.