Modelling microdomain-mediated protein sorting in immunological signalling

Compartmentalisation is a fundamental feature of biological systems. The organism as a whole can be seen as a single compartment of the wider ecosystem. At lower scales, we observe biological processes compartmentalised into organs, cells, cell subtypes and organelles. In the highly complex discipline of immunology, compartmentalisation is key in order to respond e ciently to foreign antigens and to maintain the balance between immunity and tolerance. Recent studies have raised questions about the role of compartmentalisation in lipid membranes, from the relatively well described immunological synapse, to the smaller, more transient lipid raft or microdomain. This thesis asks whether, and how, microdomains could in uence the formation of small receptor complexes. Speci cally, we approach what appears to be a simple surface reaction-di usion problem from multiple viewpoints: explicitly simulating particle di usion using a probabilistic pixel-based model, and deriving a deterministic relation between spatial parameters and the timecourse of chemical concentrations throughout the model space. We also show the equivalence between the predictions of these two models, further supporting the validity of our approach. We also embed the results of our model output in an existing model of the immunological response in order to determine the downstream consequences of enhanced receptor organisation. The study gives a broader understanding of the mechanisms involved in microdomain-mediated protein sorting, highlights the degree of interdependence on multiple spatial and chemical parameters and suggests numerous avenues for future research

Modélisation des Réarrangements Vα-Jα du TRA/TRD chez la souris et chez l'homme

V(D)J recombination constitutes a somatic site specific DNA recombination, which originates lymphocyte antigen receptor diversity in jawed vertebrates. Concerning the T cell receptor α chains, V and J genes are used from inside the TRA locus toward distal genes during the successive rearrangements, with no allelic exclusion at the genomic level. Experimental quantifications of particular V-J associations were performed in mouse, giving the tendencies of thymic and peripheral combinatorial repertoires. A stochastic numerical model, based on successive opening windows progressing over the V and J regions during the rearrangement rounds, revealed new insights in the understanding of the dynamical rules governing V-J rearrangements and provided a simulated combinatorial repertoire with the entire V-J association frequencies. In the transition to human, thymic quantifications of certain V-J associations were performed, providing a first experimental wide-ranging sampling of the human TRA combinatorial repertoire. The modeling modeling step offered a clear understanding of the dynamical building of the human α repertoire and proposed predictions on repertoire combinatorial diversity richness. Finally, the precise progression of gene accessibility to rearrangements, according to non-constant opening speeds, together with a synchronized opening of the J regions between both alleles, were sufficient to fully explain both the experimental V-J frequencies currently available for the two species as well as the interallelic J usage.La recombinaison V(D)J constitue une recombinaison somatique et site-spécifique de l'ADN à l'origine de la diversité des récepteurs antigéniques des lymphocytes T chez les vertébrés mandibulés. Concernant la chaîne α des récepteurs T, les gènes V et J sont utilisés depuis l'intérieur du locus TRA vers les gènes distaux durant des réarrangements successifs et ce sans exclusion allélique. La quantification expérimentale de certaines associations V-J chez la souris a permis de définir les tendances des répertoires combinatoires thymiques et périphériques. Un modèle numérique stochastique, basé sur des fenêtrages d'ouverture successives progressant sur les régions V et J durant les cycles de réarrangements, a permis une meilleure compréhension des règles dynamiques gouvernant les réarrangements V-J et a apporté la connaissance d'un répertoire combinatoire simulé renseignant les fréquences de toutes les associations V-J. Lors de la transition à l'homme, la quantification des associations V-J a été réalisée au niveau du thymus, constituant un premier échantillonnage à large échelle du répertoire combinatoire TRA humain. L'étape de modélisation a offert une compréhension claire de la construction dynamique du répertoire α humain et a permis de proposer des prédictions sur la diversité du répertoire combinatoire. Finalement, la progression de l'accessibilité des gènes aux réarrangements selon des vitesses d'ouverture non-constantes associée à une ouverture synchronisée des régions J entre les deux allèles se sont révélées suffisantes pour expliquer les fréquences V-J expérimentales présentement disponibles pour les deux espèces ainsi que l'utilisation interallélique des gènes J

An Agent-Based Model of the IL-1 Stimulated Nuclear Factor-kappa B Signalling Pathway

The transcription factor NF-κB is a biological component that is central to the regulation of genes involved in the innate immune system. Dysregulation of the pathway is known to be involved in a large number of inflammatory diseases. Although considerable research has been performed since its discovery in 1986, we are still not in a position to control the signalling pathway, and thus limit the effects of NF-κB within promotion of inflammatory diseases. We believe that computational modelling and simulation of the NF-κB signalling pathway will complement wet-lab experimental approaches, and will facilitate a more comprehensive understanding of this example of a complex biological system. In this study, we have developed an agent-based model of the IL-1 stimulated NF-κB signalling pathway, which has been calibrated to wet- lab data at the single-cell level. Through rigorous software engineering, which followed a principled approach to design and development by adherence to the CoSMoS process, we believe our model provides an abstracted view of the underlying real-world system, and can be used in a predictive capacity through in silico experimentation. A novel approach to domain modelling has been presented, which uses linear and multivariate statistical techniques to complement the Unified Modelling Language. Furthermore, in silico experimentation with the newly developed agent-based model, has confirmed the robust yet fragile nature of the signalling pathway. We have discovered that the pathway is robust to perturbations of cell membrane receptor component number, intermediate component number, and the temporal lag between cell membrane receptor activation and subsequent activation of IKK. Conversely however, in silico experimentation predicts that the pathway is sensitive to changes in the ratio of free IκBα to NF-κB, and fragile to basal dissociation of NF-κB-IκBα outside of a narrow range of probabilities