Solving Immunology?

Emergent responses of the immune system result from the integration of molecular and cellular networks over time and across multiple organs. High-content and high-throughput analysis technologies, concomitantly with data-driven and mechanistic modeling, hold promise for the systematic interrogation of these complex pathways. However, connecting genetic variation and molecular mechanisms to individual phenotypes and health outcomes has proven elusive. Gaps remain in data, and disagreements persist about the value of mechanistic modeling for immunology. Here, we present the perspectives that emerged from the National Institute of Allergy and Infectious Disease (NIAID) workshop 'Complex Systems Science, Modeling and Immunity' and subsequent discussions regarding the potential synergy of high-throughput data acquisition, data-driven modeling, and mechanistic modeling to define new mechanisms of immunological disease and to accelerate the translation of these insights into therapies.

Self-harm to preferentially harm the pathogens within: non-specific stressors in innate immunity.

Therapies with increasing specificity against pathogens follow the immune system's evolutionary course in maximizing host defence while minimizing self-harm. Nevertheless, even completely non-specific stressors, such as reactive molecular species, heat, nutrient and oxygen deprivation, and acidity can be used to preferentially harm pathogens. Strategic use of non-specific stressors requires exploiting differences in stress vulnerability between pathogens and hosts. Two basic vulnerabilities of pathogens are: (i) the inherent vulnerability to stress of growth and replication (more immediately crucial for pathogens than for host cells) and (ii) the degree of pathogen localization, permitting the host's use of locally and regionally intense stress. Each of the various types of non-specific stressors is present during severe infections at all levels of localization: (i) ultra-locally within phagolysosomes, (ii) locally at the infected site, (iii) regionally around the infected site and (iv) systemically as part of the acute-phase response. We propose that hosts strategically use a coordinated system of non-specific stressors at local, regional and systemic levels to preferentially harm the pathogens within. With the rising concern over emergence of resistance to specific therapies, we suggest more scrutiny of strategies using less specific therapies in pathogen control. Hosts' active use of multiple non-specific stressors is likely an evolutionarily basic defence whose retention underlies and supplements the well-recognized immune defences that directly target pathogens.

Divergent COVID-19 Disease Trajectories Predicted by a DAMP-Centered Immune Network Model.

COVID-19 presentations range from mild to moderate through severe disease but also manifest with persistent illness or viral recrudescence. We hypothesized that the spectrum of COVID-19 disease manifestations was a consequence of SARS-CoV-2-mediated delay in the pathogen-associated molecular pattern (PAMP) response, including dampened type I interferon signaling, thereby shifting the balance of the immune response to be dominated by damage-associated molecular pattern (DAMP) signaling. To test the hypothesis, we constructed a parsimonious mechanistic mathematical model. After calibration of the model for initial viral load and then by varying a few key parameters, we show that the core model generates four distinct viral load, immune response and associated disease trajectories termed "patient archetypes", whose temporal dynamics are reflected in clinical data from hospitalized COVID-19 patients. The model also accounts for responses to corticosteroid therapy and predicts that vaccine-induced neutralizing antibodies and cellular memory will be protective, including from severe COVID-19 disease. This generalizable modeling framework could be used to analyze protective and pathogenic immune responses to diverse viral infections.

Inflammation and Disease: Modelling and Modulation of the Inflammatory Response to Alleviate Critical Illness.

Critical illness, a constellation of interrelated inflammatory and physiological derangements occurring subsequent to severe infection or injury, affects a large number of individuals in both developed and developing countries. The prototypical complex system embodied in critical illness has largely defied therapy beyond supportive care. We have focused on the utility of data-driven and mechanistic computational modelling to help address the complexity of critical illness and provide pathways towards discovering potential therapeutic options and combinations. Herein, we review recent progress in this field, with a focus on both animal and computational models of critical illness. We suggest that therapy for critical illness can be posed as a model-based dynamic control problem, and discuss novel theoretical and experimental approaches involving biohybrid devices aimed at reprogramming inflammation dynamically. Together, these advances offer the potential for Model-based Precision Medicine for critical illness.

Pathogen transfer through environment-host contact: an agent-based queueing theoretic framework.

Queueing theory studies the properties of waiting queues and has been applied to investigate direct host-to-host transmitted disease dynamics, but its potential in modelling environmentally transmitted pathogens has not been fully explored. In this study, we provide a flexible and customizable queueing theory modelling framework with three major subroutines to study the in-hospital contact processes between environments and hosts and potential nosocomial pathogen transfer, where environments are servers and hosts are customers. Two types of servers with different parameters but the same utilization are investigated. We consider various forms of transfer functions that map contact duration to the amount of pathogen transfer based on existing literature. We propose a case study of simulated in-hospital contact processes and apply stochastic queues to analyse the amount of pathogen transfer under different transfer functions, and assume that pathogen amount decreases during the inter-arrival time. Different host behaviour (feedback and non-feedback) as well as initial pathogen distribution (whether in environment and/or in hosts) are also considered and simulated. We assess pathogen transfer and circulation under these various conditions and highlight the importance of the nonlinear interactions among contact processes, transfer functions and pathogen demography during the contact process. Our modelling framework can be readily extended to more complicated queueing networks to simulate more realistic situations by adjusting parameters such as the number and type of servers and customers, and adding extra subroutines.

Combining robust state estimation with nonlinear model predictive control to regulate the acute inflammatory response to pathogen.

The inflammatory response aims to restore homeostasis by means of removing a biological stress, such as an invading bacterial pathogen. In cases of acute systemic inflammation, the possibility of collateral tissue damage arises, which leads to a necessary down-regulation of the response. A reduced ordinary differential equations (ODE) model of acute inflammation was presented and investigated in [10]. That system contains multiple positive and negative feedback loops and is a highly coupled and nonlinear ODE. The implementation of nonlinear model predictive control (NMPC) as a methodology for determining proper therapeutic intervention for in silico patients displaying complex inflammatory states was initially explored in [5]. Since direct measurements of the bacterial population and the magnitude of tissue damage/dysfunction are not readily available or biologically feasible, the need for robust state estimation was evident. In this present work, we present results on the nonlinear reachability of the underlying model, and then focus our attention on improving the predictability of the underlying model by coupling the NMPC with a particle filter. The results, though comparable to the initial exploratory study, show that robust state estimation of this highly nonlinear model can provide an alternative to prior updating strategies used when only partial access to the unmeasurable states of the system are available.

Mathematical Modeling of Early Cellular Innate and Adaptive Immune Responses to Ischemia/Reperfusion Injury and Solid Organ Allotransplantation.

A mathematical model of the early inflammatory response in transplantation is formulated with ordinary differential equations. We first consider the inflammatory events associated only with the initial surgical procedure and the subsequent ischemia/reperfusion (I/R) events that cause tissue damage to the host as well as the donor graft. These events release damage-associated molecular pattern molecules (DAMPs), thereby initiating an acute inflammatory response. In simulations of this model, resolution of inflammation depends on the severity of the tissue damage caused by these events and the patient's (co)-morbidities. We augment a portion of a previously published mathematical model of acute inflammation with the inflammatory effects of T cells in the absence of antigenic allograft mismatch (but with DAMP release proportional to the degree of graft damage prior to transplant). Finally, we include the antigenic mismatch of the graft, which leads to the stimulation of potent memory T cell responses, leading to further DAMP release from the graft and concomitant increase in allograft damage. Regulatory mechanisms are also included at the final stage. Our simulations suggest that surgical injury and I/R-induced graft damage can be well-tolerated by the recipient when each is present alone, but that their combination (along with antigenic mismatch) may lead to acute rejection, as seen clinically in a subset of patients. An emergent phenomenon from our simulations is that low-level DAMP release can tolerize the recipient to a mismatched allograft, whereas different restimulation regimens resulted in an exaggerated rejection response, in agreement with published studies. We suggest that mechanistic mathematical models might serve as an adjunct for patient- or sub-group-specific predictions, simulated clinical studies, and rational design of immunosuppression.