Movies, measurement, and modeling: the three Ms of mechanistic immunology

Image-based systems biology of infection

The successful treatment of infectious diseases requires interdisciplinary studies of all aspects of infection processes. The overarching combination of experimental research and theoretical analysis in a systems biology approach can unravel mechanisms of complex interactions between pathogens and the human immune system. Taking into account spatial information is especially important in the context of infection, since the migratory behavior and spatial interactions of cells are often decisive for the outcome of the immune response. Spatial information is provided by image and video data that are acquired in microscopy experiments and that are at the heart of an image-based systems biology approach. This review demonstrates how image-based systems biology improves our understanding of infection processes. We discuss the three main steps of this approach--imaging, quantitative characterization, and modeling--and consider the application of these steps in the context of studying infection processes. After summarizing the most relevant microscopy and image analysis approaches, we discuss ways to quantify infection processes, and address a number of modeling techniques that exploit image-derived data to simulate host-pathogen interactions in silico.

Cell-autonomous and environmental contributions to the interstitial migration of T cells

A key to understanding the functioning of the immune system is to define the mechanisms that facilitate directed lymphocyte migration to and within tissues. The recent development of improved imaging technologies, most prominently multi-photon microscopy, has enabled the dynamic visualization of immune cells in real-time directly within intact tissues. Intravital imaging approaches have revealed high spontaneous migratory activity of T cells in secondary lymphoid organs and inflamed tissues. Experimental evidence points towards both environmental and cell-intrinsic cues involved in the regulation of lymphocyte motility in the interstitial space. Based on these data, several conceptually distinct models have been proposed in order to explain the coordination of lymphocyte migration both at the single cell and population level. These range from “stochastic” models, where chance is the major driving force, to “deterministic” models, where the architecture of the microenvironment dictates the migratory trajectory of cells. In this review, we focus on recent advances in understanding naïve and effector T cell migration in vivo. In addition, we discuss some of the contradictory experimental findings in the context of theoretical models of migrating leukocytes.

Mathematical and computational approaches can complement experimental studies of host-pathogen interactions

In addition to traditional and novel experimental approaches to study host-pathogen interactions, mathematical and computer modelling have recently been applied to address open questions in this area. These modelling tools not only offer an additional avenue for exploring disease dynamics at multiple biological scales, but also complement and extend knowledge gained via experimental tools. In this review, we outline four examples where modelling has complemented current experimental techniques in a way that can or has already pushed our knowledge of host-pathogen dynamics forward. Two of the modelling approaches presented go hand in hand with articles in this issue exploring fluorescence resonance energy transfer and two-photon intravital microscopy. Two others explore virtual or 'in silico' deletion and depletion as well as a new method to understand and guide studies in genetic epidemiology. In each of these examples, the complementary nature of modelling and experiment is discussed. We further note that multi-scale modelling may allow us to integrate information across length (molecular, cellular, tissue, organism, population) and time (e.g. seconds to lifetimes). In sum, when combined, these compatible approaches offer new opportunities for understanding host-pathogen interactions.

T cell migration dynamics within lymph nodes during steady state: an overview of extracellular and intracellular factors influencing the basal intranodal T cell motility

Naive T lymphocytes continuously recirculate through secondary lymphoid organs such as lymph nodes until they are eventually activated by recognizing cognate peptide/MHC-complexes on the surface of antigen-protecting cells. The intranodal T cell migration behavior leading to these crucial--and potentially rare--encounters during the induction of an adaptive immune response could not be directly addressed until, in 2002, the use of two-photon microscopy also allowed the visualization of cellular dynamics deep within intact lymph nodes. Since then, numerous studies have confirmed that, by default, naive T cells are extremely motile, scanning the paracortical T cell zone for cognate antigen by means of an apparent random walk. This review attempts to summarize the current knowledge of factors influencing the basal migration behavior of naive T lymphocytes within lymph nodes during steady state. Extracellular cues, such as the motility-promoting influence of CCR7 ligands and the role of integrins during interstitial migration, as well as intracellular signaling pathways involved in T cell motility, will be discussed. Particular emphasis is placed on structural features of the lymph node environment orchestrating T cell migration, namely the framework of fibroblastic reticular cells serving as migration "highways." Finally, new approaches to simulate the cellular dynamics within lymph nodes in silico by means of mathematical modeling will be reviewed.

Video-rate two-photon imaging of mouse footpad - a promising model for studying leukocyte recruitment dynamics during inflammation

Leukocyte recruitment is a key host defense mechanism to infection and a salient feature of autoimmune diseases such as arthritis. The cell dynamics of these processes are difficult to study due to the challenge of tracking cells flowing in the circulation and migrating through light scattering tissues. Here, we describe a noninvasive two-photon (2P) microscopy approach to study leukocyte homing in the mouse footpad. In the absence of inflammation, cells moved > several hundred microm/s in vessels and only rarely adhered to endothelium or entered the tissue parenchyma. In response to bacterial infection, neutrophils moved in small capillaries at reduced speeds of (14-45 microm/min) and rolled in larger vessels at 5-60 microm/min. Within minutes of adoptive transfer, neutrophils entered the connective tissue and crawled with a median velocity of 7.3 microm/min. 2P imaging has excellent spatiotemporal resolution and is a promising in vivo approach to study the cellular basis of inflammation.

Migration, cell-cell interaction and adhesion in the immune system

Migration is an essential function of immune cells. It is necessary to lead immune cell precursors from their site of generation to the places of maturation or function. Cells of the adaptive immune system also need to interact physically with each other or with specialized antigen presenting cells in lymphatic tissues in order to become activated. Thereby a complex series of controlled migration events, adhesive interactions and signalling responses is induced. Finally cells must be able to leave the activating tissues and re-enter the bloodstream from which they extravasate into inflamed tissue sites. Cells of the innate immune system can function directly without the need for previous activation. However, these cells have to adapt their function to a panoply of pathogens and environmental niches which can be invaded. The current review highlights the central aspects of cellular dynamics underlying adaptive and innate cellular immunity. Thereby a focus will be put on recent results obtained by microscopic observation of live cells in vitro or by intravital 2-photon microscopy in live animals.

T cell development in the thymus: From periodic seeding to constant output

T cell development occurs in the thymus throughout life. Recent experimental findings show that the seeding of the thymus by multi-potent stem cells from the bone marrow is periodic rather than continuous, as previously assumed. However it is well known that the output rate of cells from the thymus is relatively constant. A quantitative model is used to verify the current hypotheses regarding T cell development in the steady state mouse thymus. The results show that the thymus could be at a periodic steady state with out-of-phase thymocyte populations. Experiments to examine possible periodic fluctuations in the thymus are proposed and methods for further analysis are outlined.

Lymph node topology dictates T cell migration behavior

Adaptive immunity is initiated by T cell recognition of foreign peptides presented on dendritic cells (DCs) by major histocompatibility molecules. These interactions take place in secondary lymphoid tissues, such as lymph nodes (LNs) and spleen, and hence the anatomical structure of these tissues plays a crucial role in the development of immune responses. Two-photon microscopy (2PM) imaging in LNs suggests that T cells walk in a consistent direction for several minutes, pause briefly with a regular period, and then take off in a new, random direction. Here, we construct a spatially explicit model of T cell and DC migration in LNs and show that all dynamical properties of T cells could be a consequence of the densely packed LN environment. By means of 2PM experiments, we confirm that the large velocity fluctuations of T cells are indeed environmentally determined rather than resulting from an intrinsic motility program. Our simulations further predict that T cells self-organize into microscopically small, highly dynamic streams. We present experimental evidence for the presence of such turbulent streams in LNs. Finally, the model allows us to estimate the scanning rates of DCs (2,000 different T cells per hour) and T cells (100 different DCs per hour).

Spatial modelling of brief and long interactions between T cells and dendritic cells

In the early phases of an immune response, T cells of appropriate antigen specificity become activated by antigen-presenting cells in secondary lymphoid organs. Two-photon microscopy imaging experiments have shown that this stimulation occurs in distinct stages during which T cells exhibit different motilities and interactions with dendritic cells (DCs). In this paper, we utilize the Cellular Potts Model, a model formalism that takes cell shapes and cellular interactions explicitly into account, to simulate the dynamics of, and interactions between, T cells and DCs in the lymph node paracortex. Our three-dimensional simulations suggest that the initial decrease in T-cell motility after antigen appearance is due to "stop signals" transmitted by activated DCs to T cells. The long-lived interactions that occur at a later stage can only be explained by the presence of both stop signals and a high adhesion between specific T cells and antigen-bearing DCs. Furthermore, our results indicate that long-lasting contacts with T cells are promoted when DCs retract dendrites that detect a specific contact at lower velocities than other dendrites. Finally, by performing long simulations (after prior fitting to short time scale data) we are able to provide an estimate of the average contact duration between T cells and DCs.

Rules for modeling signal-transduction systems

Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of how a system works in terms of the biomolecules in the system and their possible states and interactions. A set of rules can be as easy to read as a diagrammatic interaction map, but unlike most such maps, rules have precise interpretations. Rules can be processed to automatically generate a mathematical or computational model for a system, which enables explanatory and predictive insights into the system's behavior. Rules are independent units of a model specification that facilitate model revision. Instead of changing a large number of equations or lines of code, as may be required in the case of a conventional mathematical model, a protein interaction can be introduced or modified simply by adding or changing a single rule that represents the interaction of interest. Rules can be defined and visualized by using graphs, so no specialized training in mathematics or computer science is necessary to create models or to take advantage of the representational precision of rules. Rules can be encoded in a machine-readable format to enable electronic storage and exchange of models, as well as basic knowledge about protein-protein interactions. Here, we review the motivation for rule-based modeling; applications of the approach; and issues that arise in model specification, simulation, and testing. We also discuss rule visualization and exchange and the software available for rule-based modeling.

Modelling Directional Guidance and Motility Regulation in Cell Migration

Although cell migration is an essential process in development, how cells reach their final destination is not well understood. Secreted molecules are known to have a migratory effect, but it remains unclear whether such molecules act as directional guidance cues or as motility regulators. There is potential to use signalling molecules in new medical therapies, so it is important to identify the exact role these molecules play. This paper focuses on distinguishing between inhibitory and repulsive effects produced by signalling molecules, based on recent experiments examining the effect of Slit, a secreted protein, on the migration of neurons from the brain. The primary role of Slit, whether it is an inhibitor or repellent of neurons, is in dispute. We present population-level continuum models and recast these in terms of transition probabilities governing individual cells. Various cell-sensing strategies are considered within this framework. The models are applied to the neuronal migration experiments. To resolve the particular role of Slit, simulations of the models characterising different cell-sensing strategies are compared at the population and individual cell level, providing two complementary perspectives on the system. Difficulties and limitations in deducing cell migration rules from time-lapse imaging are discussed.

Tracking thymocyte migration in situ

The dynamic process of thymocyte migration can now be visualized in real-time and in the context of the native thymic environment. With improved computational resources, key information can be extracted from real-time imaging data and the migratory behaviors of developing thymocytes can be quantitated. The extraction and exploitation of three dimensional data through time is providing new insight into the nature and regulation of intrathymic migration. In this review we discuss this interdisciplinary approach and the promise it holds for the study of thymocyte migration in situ.

In situ characterization of CD4+ T cell behavior in mucosal and systemic lymphoid tissues during the induction of oral priming and tolerance

The behavior of antigen-specific CD4⁺ T lymphocytes during initial exposure to antigen probably influences their decision to become primed or tolerized, but this has not been examined directly in vivo. We have therefore tracked such cells in real time, in situ during the induction of oral priming versus oral tolerance. There were marked contrasts with respect to rate and type of movement and clustering between naive T cells and those exposed to antigen in immunogenic or tolerogenic forms. However, the major difference when comparing tolerized and primed T cells was that the latter formed larger and longer-lived clusters within mucosal and peripheral lymph nodes. This is the first comparison of the behavior of antigen-specific CD4⁺ T cells in situ in mucosal and systemic lymphoid tissues during the induction of priming versus tolerance in a physiologically relevant model in vivo.

On imaging, speed, and the future of lymphocyte signaling

During a recent roundtable discussion, we captured some personal perspectives on the new insight that advanced imaging techniques promise to bring to the study of lymphocyte signaling. The experts present their views on the power of imaging, the problems that need to be overcome, and the potential of the technology.