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No description available.

Le CD154 est une glycoprotéine transmembranaire de type II, appartenant à la famille des facteurs de nécrose tumorale (TNF) et s’exprime d’une façon transitoire à la surface des lymphocytes T activés et des plaquettes. Notre laboratoire a démontré que la forme membranaire devient soluble suite à un clivage enzymatique par les métalloprotéinases (ADAM-10 et ADAM-17). De plus, il a été montré que le CD154 soluble (sCD154) peut aussi être relâché du milieu intracellulaire sans qu’il soit exprimé à la surface cellulaire suite à un clivage enzymatique intracellulaire entre les résidus acide Glutamique 112 (E112) et Méthionine 113 (M113). Les deux formes du CD154, soluble et membranaire, possèdent une structure trimérique nécessaire pour son activité biologique. Son récepteur principal, le CD40, est une glycoprotéine de type I appartenant à la famille des récepteurs des TNFs. Il est exprimé constitutivement à la surface des cellules B, des cellules dendritiques, des macrophages, des basophiles, des plaquettes, ainsi qu’à la surface de certaines cellules non hématopoïétiques telles que les cellules endothéliales, les fibroblastes et les cellules du muscle lisse vasculaire. Outre le CD40, quatre autres récepteurs appartenant à la famille des intégrines, ont été identifiés: l’αIIbβ3, l’α5β1, l’αMβ2, l’αvβ3 et l’α4β1. Les études de notre laboratoire ont démontré que l’interaction du CD154 avec ses récepteurs induit une activation bidirectionnelle, cependant, on a observé que le clivage du CD154 de la membrane cellulaire reste une propriété privilège au CD40. Le travail illustré dans cette thèse consiste à étudier l’inhibition du clivage enzymatique du CD154 et son effet dans la régulation de la réponse immune. Les résultats générés ci-dessous montrent que le CD154 résistant au clivage est un stimulant plus important que sa forme clivable. En effet, la double mutation des résidus E112 et M113 du CD154 abolit sa libération spontanée du milieu intracellulaire ainsi que son clivage de la membrane médié par le CD40 sans affecter sa liaison à ce dernier. Ce mutant s'est avéré capable d'induire une réponse apoptotique plus importante des cellules B, des réponses prolifératives plus prononcées et déclenche la différenciation des cellules B humaines d’une manière plus significative que le CD154-WT. De plus, notre étude met en évidence le développement et la caractérisation d'un anticorps monoclonal (mAb), le Clone 8, capable d'inhiber la libération/le clivage du CD154 à partir des cellules et ainsi de le maintenir à la surface cellulaire et d'augmenter sa puissance en tant qu'activateur des réponses induites par le CD40. Le Clone 8 est capable de lier le CD154 murin et d’inhiber son clivage de la surface cellulaire de la même façon que celle étudiée dans les cellules humaines. Ces travaux vont permettre le passage de cet anticorps bloquant le clivage du CD154 au stade des essais cliniques afin de mettre en place un nouveau traitement efficace pour les maladies auto-immunes et le cancer. / CD154 is a type II transmembrane glycoprotein belonging to the tumor necrosis factor superfamily (TNF), that is transiently expressed on the surface of activated T cells and platelets. We have demonstrated that this membrane form becomes soluble following an enzymatic cleavage by metalloproteinases (ADAM-10 and ADAM-17). CD154 also exists in a soluble form originating from a direct release of an intracellular processing without being expressed on the cell surface. This fragment is the result of an intracellular enzymatic cleavage between the residues Glutamic acid at position 112 (E112) and Methionine at position 113 (M113). Both soluble and membrane-bound forms of CD154 occur as non-covalently-linked homotrimers a property conveying to CD154 its biological activity. Its main receptor, CD40, is a type I glycoprotein belonging to the TNF receptor family. It is constitutively expressed on the surface of immune and non-immune cells including B cells, dendritic cells, macrophages, basophils, endothelial cells, fibroblasts, and vascular smooth muscle cells. CD154 was also shown to bind other receptors: αIIbβ3, α5β1, αMβ2, αvβ3 and α4β1 integrin. We have shown that the interaction of CD154 with its receptors induces bidirectional activation, however, only CD40 was capable of inducing the cleavage of CD154 from T cell surface. Our results here consist in studying the inhibition of the enzymatic cleavage of CD154 and its effect in the regulation of the immune response. Our data show that the cleavage resistant CD154 is a more potent stimulant than its cleavable form. Indeed, the double mutation of residues E112 and M113 of CD154 abolishes its spontaneous release from the intracellular milieu as well as its cleavage from the membrane. This mutant was found to be able to induce a stronger apoptotic response from B cells, induce more pronounced proliferative responses and trigger human B cell differentiation in a more significant way than CD154-WT. In addition, our study highlights the development and characterization of a monoclonal antibody (mAb), Clone 8, capable of inhibiting the release/cleavage of CD154 from cells and thus maintain it on the cell surface and increase its potency as an activator of CD40-induced responses. Clone 8 binds murine CD154 and inhibit its cell surface cleavage in the same way that in human cells. This study will allow the passage of this antibody blocking the cleavage of CD154 to the stage of clinical trials to develop a novel tool to treat diseases in which CD154 is implicated.

Les vecteurs viraux dérivés du virus adéno-associé (AAV) apparaissent depuis deux décennies, comme des outils efficaces pour le transfert de gène in vivo. Cependant, malgré une faible immunogénicité et une absence de toxicité in vivo, leur optimisation requiert encore un effort important vers une meilleure compréhension de leur biologie et, en particulier, de leur interaction avec le système immunitaire. Au cours de ce travail de thèse, nous avons utilisé une méthode de sélection dirigée in vitro dans le but d’obtenir un variant de capside capable de transduire efficacement un type cellulaire non-permissif aux vecteurs AAV : les cellules dendritiques (DC). En effet, ces cellules jouent un rôle primordial dans l’établissement de la réponse immunitaire et, par conséquent, dans la persistance de l’expression du transgène in vivo. Cette technologie, très répandue dans la communauté AAV, a permis de sélectionner un variant de capside aux propriétés très intéressantes. La mutation sélectionnée, caractérisée in vitro comme induisant une instabilité de la capside, a permis d’identifier et de surmonter un point de blocage majeur dans le processus de transduction des DC par les vecteurs AAV consistant dans l’étape de décapsidation du génome du vecteur dans le noyau cellulaire. De manière intéressante, le variant obtenu exhibe un avantage en terme de transduction non seulement dans les DC mais aussi dans différents modèles de cellules primaires humaines (e.g. HUVEC) ou animales (OBC), peu ou pas permissive à l’AAV. De plus, des expériences de transfert de gène in vivo réalisées dans un modèle murin, indiquent que le variant sélectionné conduit à une meilleure expression du transgène, possiblement due à la mise en place d’un processus de tolérisation. Les propriétés remarquables de ce variant de capside, font de lui un candidat intéressant pour des applications médicales. / Vectors derived from the Adeno-associated virus (AAV) have emerged as an efficient system for in vivo gene transfer. However, despite their low immunogenicity and good tolerance in vivo, a better characterization of the host-AAV interaction is required to be able to fully exploit AAV’s potential fora gene therapy or gene vaccination. In this PhD project, we have used an in vitro directed evolution strategy to select an AAV capsid variant able to transduce human dendritic cell (DC), a non-permissive cell type which plays a critical role in the initiation of immune responses and, consequently, on the persistence of the expression of transgene in vivo. This procedure allowed us to identify an AAV variant characterized by a decreased stability of the capsid in vitro. The use of this mutant as a vector to transduce human DC resulted in an improved uncoating of the vector genome in the cell nucleus, thus identifying this step as major barrier toward DC transduction. Interestingly, the selected variant also displayed an increased transduction efficiency not only in DC but also in different primary human and animal cell types, poorly or non-permissive to AAV. Finally, when injected in mice, this AAV variant resulted in a higher expression of the transgene, associated to a low level of immune responses, suggesting the induction of tolerant state. The remarkable features suggest that our selected variant capsid is a promising candidate for medical applications.

Dans l'imagerie moléculaire par ultrasons, des microbulles sont fonctionnalisées avec des ligands. Après injection intraveineuse, ces microbulles ciblées s'accrochent aux marqueurs présents sur l'endothélium tumoral et permettent une détection non-invasive. Dans cette thèse, l'imagerie moléculaire par ultrasons a été développée pour la détection de la nétrine-1, qui est surexprimée dans 70% des cancers du sein et promeut la survie cellulaire. Une nouvelle thérapie moléculaire interférant avec la nétrine-1 a été développée et nécessite l'identification des patientes qui pourront bénéficier de ce traitement. Avec l'imagerie moléculaire de la nétrine-1, il a été possible de discriminer les tumeurs positives pour la nétrine-1 des tumeurs négatives. Par sa capacité à détecter de manière spécifique la nétrine-1 présentée sur l'endothélium des tumeurs, cette technique d'imagerie pourrait donc devenir un test d'accompagnement pour la thérapie d'interférence de la nétrine-1 chez les patientes atteintes de cancer du sein.La destruction ciblée des microbulles par ultrasons induit la cavitation et la sonoporation qui perméabilisent le tissu et facilite la délivrance locale de médicaments. De plus, cette destruction ciblée peut induire l'infiltration de cellules immunitaires et la libération d'antigènes tumoraux, déclenchant une réponse immunitaire anti-tumorale. Dans cette thèse, nous avons quantifié l'activation de la réponse immunitaire dans le carcinome hépatocellulaire, suivant la délivrance de nanoparticules chargés en microARN-122 et anti-microARN-21. Dans les nœuds lymphocytaires tumoraux, une baisse d'expression des cytokines pro-tumorales et une augmentation d'expression des cytokines anti-tumorales ont été observées, suggérant une réponse thérapeutique positive. L'approche thérapeutique de destruction ciblée des microbulles par ultrasons pour la délivrance de micro-ARN s'avère donc être un outil immuno-modulatoire puissant / Ultrasound molecular imaging uses microbubbles as ultrasound contrast agents which are functionalized with targeting ligands. Upon intravenous injection, targeted microbubbles bind to molecular markers presented on the tumor endothelium and enable the non-invasive assessment cancer-related biomarkers. In the present thesis, ultrasound molecular imaging was developed for detection of netrin-1, which is upregulated in 70% of metastatic breast cancer and promotes cell survival. A newly developed netrin-1 interference therapy requires the identification of patients who overexpress the target protein and, could benefit from anti-netrin-1 therapy. In vivo imaging of netrin-1 showed a significantly increased imaging signal in netrin-1-positive breast tumors compared to netrin-1-negative breast tumors and normal mammary glands. The results suggest that ultrasound molecular imaging allows accurate detection of netrin-1 on the endothelium of netrin-1-positive tumors and has the potential to become a companion diagnostic for netrin-1 interference therapy in breast cancer patients.Ultrasound-targeted microbubble destruction triggers cavitation and sonoporation thereby permeabilizing the tissue and facilitating local drug delivery. Further, immune cell infiltration and tumor antigen release are induced and trigger anti-tumor immune responses. In the present thesis, ultrasound-targeted microbubble destruction-mediated delivery of anti-cancer microRNA-122 and anti-microRNA-21 is studied for immune response activation in hepatocellular carcinoma, in which the immune microenvironment is deregulated. Tumor lymph nodes showed pro-tumor cytokine downregulation and anti-tumor cytokine upregulation, suggesting an overall positive therapy response with regard to the tumor immunology. The results identified ultrasound-targeted microbubble destruction-mediated miRNA delivery as a potent immuno-modulatory therapeutic approach

Ο S. epidermidis αποτελεί κύριο μέλος της χλωρίδας του δέρματος και των βλεννογόνων του ανθρώπου, ενώ συνιστά ένα από τα συχνότερα παθογόνα που προκαλούν νοσοκομειακές λοιμώξεις, ιδιαίτερα σε ανοσοκατασταλμένους ή ασθενείς φέροντες προσθετικά υλικά. Κύριος λοιμογόνος παράγοντας του S. epidermidis είναι ο σχηματισμός βιομεμβράνης. Διάφοροι πολυσακχαρίτες έχουν απομονωθεί από την εξωκυττάρια ουσία του S. epidermidis και έχουν συσχετισθεί με το σχηματισμό βιομεμβράνης καθώς και με την παθογόνο δράση τους. Ο πλέον μελετημένος και εδραιωμένος είναι ο ΡΙΑ, ενώ οι άλλοι πολυσακχαρίτες (PS/A ή PNSG ή PNAG και το SSA) απεδείχθησαν τελικώς ότι είναι ταυτόσημοι ή χημικώς ανάλογοι του ΡΙΑ. Ο ΡΙΑ είναι μία ομογλυκάνη αποτελούμενη από μονάδες Ν-ακετυλογλυκοζαμίνης συνδεδεμένες με β-1,6-γλυκοζιτικό δεσμό και η σύνθεσή του ελέγχεται από ένζυμα που κωδικοποιούνται από τον icaADBC γενετικό τόπο. Η εξωκυττάρια ουσία του S. epidermidis περιέχει επίσης έναν πολυσακχαρίτη, τον 20-kDaPS, ο οποίος απομονώθηκε από ερευνητές του Πανεπιστημίου Πατρών και αποτελείται κυρίως από γλυκόζη, Ν-ακετυλογλυκοζαμίνη, και είναι μερικώς θειωμένος. Ο 20-kDaPS αντιορός αναστέλλει την προσκόλληση του S. epidermidis στα ενδοθηλιακά κύτταρα και την εμφάνιση βακτηριακής κερατίτιδας σε κουνέλια. Με βάση αναλύσεις κλινικών στελεχών, ο 20-kDaPS εκφράζεται σε μεγάλο ποσοστό στελεχών S. epidermidis, ενώ δεν ανευρέθηκε σε στελέχη άλλων πηκτάση αρνητικών σταφυλοκόκκων. Η παρεμβολή αλληλουχιών εισδοχής σε διάφορα σημεία του icaADBC οπερονίου, το οποίο ελέγχει τη σύνθεση του ΡΙΑ, δεν παρεμβάλλεται στην έκφραση του 20-kDaPS. Η κατεργασία βακτηριακών κυττάρων S. epidermidis με το ένζυμο dispersin B, το οποίο διασπά ειδικά τον β-1,6-γλυκοζιτικό δεσμό που συνθέτει το πολυμερές του ΡΙΑ, και με μετα-περιοδικό νάτριο που διασπά το δεσμό μεταξύ των ατόμων άνθρακα C-3 και C-4 των μονομερών Ν-ακετυλογλυκοζαμίνης, οδηγεί σε διάσπαση της βιομεμβράνης, χωρίς όμως να διαφοροποιείται αντιγονικά ο 20-kDaPS. Τα κλάσματα, μετά την έκλουση της εξωκυττάριας ουσίας του S. epidermidis από στήλη Q-Sepharose, που εμφανίζουν τη μεγαλύτερη ανοσοδραστικότητα για τον ΡΙΑ, στερούνται πλήρως 20-kDaPS. Η προεπώαση κλινικού στελέχους που δεν εκφράζει τον 20-kDaPS με τον πολυσακχαρίτη αναστέλλει την ενδοκυττάρωση, ενώ η προεπώαση του πρότυπου στελέχους ATCC35983 που συνθέτει τον 20-kDaPS με ειδικό αντιορό ενισχύει την ενδοκυττάρωση από τα ανθρώπινα μακροφάγα. Κατά συνέπεια, ο icaADBC γενετικός τόπος δεν εμπλέκεται στη σύνθεση του 20-kDaPS. Οι ανοσοχημικές και χρωματογραφικές ιδιότητες του PIA και του 20-kDaPS είναι διακριτές. Ο 20-kDaPS πιθανό να επιδεικνύει αντιφαγοκυτταρική δράση, ενώ τα ειδικά αντισώματα έχουν δράση οψωνίνης. Η οργάνωση των βακτηρίων εντός βιομεμβράνης προστατεύει από τις αντιμικροβιακές ουσίες και το σύστημα ανοσίας. Τα βακτήρια εντός βιομεμβράνης περιέχουν στην εξωκυττάρια ουσία τους μεγαλύτερα ποσά ΡΙΑ από τα ελεύθερα αναπτυσσόμενα, πλαγκτονικά κύτταρα. Τα βακτήρια εντός βιομεμβράνης επιδεικνύουν μεγαλύτερη ικανότητα για προσκόλληση και επιβίωση εντός των ανθρώπινων μακροφάγων από τα πλαγκτονικά κύτταρα. Τα βακτήρια εντός βιομεμβράνης επάγουν την παραγωγή μικρότερων ποσών φλεγμονωδών κυτταροκινών, όπως ο TNFα, καθώς και Th1 κυτταροκινών, όπως οι IL-12p40, IL-12p70 and IFN-γ, ενώ ενισχύουν τις IL-8, GM-CSF και IL-13. Οι συγκεκριμένες παρατηρήσεις αφορούν ζωντανά βακτηριακά κύτταρα καθώς και βακτηριακά κύτταρα μονιμοποιημένα με φορμαλδεΰδη. Τα ανωτέρω δεδομένα συνάδουν με την ήπια συμπτωματολογία των σχετιζόμενων με βιομεμβράνη λοιμώξεων S. epidermidis και τη διαφυγή της επιτήρησης του ανοσολογικού συστήματος. Συμπερασματικά, ο 20-kDaPS αποτελεί κύριο συστατικό της εξωκυττάριας ουσίας του S. epidermidis με αντιφαγοκυτταρικές και ανοσορρυθμιστικές ιδιότητες. Οι ανοσοχημικές και χρωματογραφικές ιδιότητες του 20-kDaPS είναι πλήρως διακριτές του ΡΙΑ, του κύριου πολυσακχαρίτη που σχετίζεται με το σχηματισμό βιομεμβράνης, ενώ ο γενετικός τόπος icaADBC δε ρυθμίζει τη σύνθεση του 20-kDaPS. Η οργάνωση των βακτηρίων εντός βιομεβράνη εξασφαλίζει αντίσταση στην ενδοκυττάρια θανάτωσή τους από τα μακροφάγα και καταστολή της ανοσιακής απόκρισης. / The skin commensal and opportunistic pathogen Staphylococcus epidermidis is a leading cause of hospital-acquired and biomaterial-associated infections. The polysaccharide intercellular adhesin (PIA), a homoglycan composed of β-1,6-linked N-acetylglucosamine residues, synthesized by enzymes encoded by the icaADBC operon is a major functional factor in biofilm accumulation, promoting virulence in experimental biomaterial-associated S. epidermidis infections. Extracellular mucous layer extracts of S. epidermidis contain another major polysaccharide, referred to as 20-kDa polysaccharide (20-kDaPS), composed mainly out of glucose, N-acetylglucosamine, and being partially sulfated. 20-kDaPS antiserum prevents adhesion of S. epidermidis on endothelial cells and development of experimental keratitis in rabbits. Here we provide experimental evidence that 20-kDaPS and PIA represent distinct molecules and that 20-kDaPS is implicated in endocytosis of S. epidermidis bacterial cells by human monocyte-derived macrophages. Analysis of 75 clinical coagulase-negative staphylococci from blood-cultures and central venous catheter tips indicated that 20-kDaPS is expressed exclusively in S. epidermidis but not in other coagulase-negative staphylococcal species. Tn917-insertion in various locations in icaADBC in mutants M10, M22, M23, and M24 of S. epidermidis 1457 are abolished for PIA synthesis, while 20-kDaPS expression appears unaltered as compared to wild-type strains using specific anti-PIA and anti-20-kDaPS antisera. While periodate oxidation and dispersin B treatments abolish immuno-reactivity and intercellular adhesive properties of PIA, no abrogative activity is exerted towards 20-kDaPS immunochemical reactivity following these treatments. PIA polysaccharide I-containing fractions eluted from Q-Sepharose were devoid of detectable 20-kDaPS using specific ELISA. Preincubation of non-20-kDaPS-producing clinical strains with increasing amounts of 20-kDaPS inhibits endocytosis by human macrophages, whereas, preincubation of 20-kDaPS-producing strain ATCC35983 with 20-kDaPS antiserum enhances bacterial endocytosis by human macrophages. In conclusion, icaADBC is not involved in 20-kDaPS synthesis, while the chemical and chromatographic properties of PIA and 20-kDaPS are distinct. 20-kDaPS exhibits anti-phagocytic properties, whereas, 20-kDaPS antiserum may have a beneficial effect on combating infection by 20-kDaPS-producing S. epidermidis. As stated above, biofilm formation is a major virulence factor of S. epidermidis. Biofilm protects bacterial cells from antimicrobial agents and components of the immune system. Interactions of peripheral blood mononuclear cells and monocyte derived macrophages with planktonic or biofilm phase S. epidermidis cells were also studied. Biofilm phase bacteria exhibited higher attachment, as well as, a ten fold higher intracellular survival in monocyte-derived macrophages than their planktonic counterparts. Stimulation of peripheral blood mononuclear cells and monocyte derived macrophages was performed with live or formalin-fixed bacterial cells. Supernatant concentration of selected cytokines was measured by Luminex® xMAP™ technology at different time points. As compared to planktonic phase, biofilm phase bacteria elicited lower amounts of proinflammatory cytokines and Th1 response cytokines, such as TNFα, IL-12p40, IL-12p70 and IFN-γ, whereas, they enhanced production of IL-8, GM-CSF and IL-13. This phenomenon was independent of formalin pretreatment. Taken together, these results may contribute to interpretation of observed silent course of biofilm associated infections. In conclusion, 20-kDaPS represents a major component of S. epidermidis extracellular matrix and data show that 20-kDaPS posseses antiphagocytic and immunomodulatory properties. 20-kDaPS and PIA are immunochemically and chromatographically discrete molecules, whereas icaADBC locus is not involved in 20-kDaPS synthesis. Biofilm mode of growth ensures higher resistance rates to intracellular killing and down regulation of immune responses.

Les mycotoxines sont des métabolites secondaires des moisissures qui peuvent naturellement contaminer de nombreux supports (céréales, fruits, papiers peints, compost). Dans ces travaux de thèse, nous avons focalisé notre intérêt sur deux mycotoxines produites principalement par les champignons du genre Fusarium, appartenant toutes deux au même groupe des trichothécènes, le déoxynivalénol (DON) et la toxine T-2 (T-2). Les objectifs de cette thèse ont été de déterminer les effets de ces deux toxines sur la mise en place des réponses immunitaires au sein de la muqueuse respiratoire et intestinale. L’ensemble de ces études a été réalisé chez le porc, espèce cible de ces contaminants et animal modèle pour l’Homme. Les résultats de ces travaux ont montré que ces deux toxines affectent la réponse immunitaire. Au niveau du tractus respiratoire, une faible dose de toxine T-2 altère l’activation des macrophages alvéolaires lorsqu’ils sont stimulés par les agonistes des TLRs -4, -2/6 (lipopolysaccharides et acides lipoteichoïques, respectivement) en diminuant la synthèse du composé antimicrobien NO et des cytokines pro-inflammatoires IL-1β et TNF-α. Cette immunosuppression pourrait alors conduire à une susceptibilité plus accrue des porcs à des infections opportunistes. Au niveau du tractus intestinal, à l’état basal, nous avons mis en évidence que le DON comme la toxine T-2 induit une forte réponse inflammatoire innée associée à la stimulation de la voie IL-17 en inhibant le développement des cellules T régulatrices. Des études mécanistiques ont permis de déterminer que les cytokines associées à la voie IL-17 suite à une exposition aux trichothécènes, sont produites par une des sous-populations de cellules T innées, les cellules Tγδ productrices d’IL-17. La troisième partie de ce travail a porté sur l’utilisation de la souche Lactobacillus sobrius DSM 16698T dans le but de lutter contre les effets immunomodulateurs générés lors d’une exposition aux trichothécènes. Les résultats de ce travail ont montré que cette souche bactérienne est capable de réduire les effets inflammatoires IL-17 et de rétablir les paramètres impliqués dans les fonctions de la barrière intestinale, suite à une exposition ex vivo et in vivo au DON. En revanche, cette souche a peu d’effet contre la toxine T-2. L’ensemble de ce travail de thèse suggère donc qu’une exposition à de faibles doses de trichothécènes pourrait accroître la susceptibilité des animaux aux perturbations de nature infectieuse ou inflammatoire. / Mycotoxins are fungi secondary metabolites that can contaminate a lot of environments worldwild such as cereals, fruits, wallpapers, and compost heaps. Throughout this phD work, we focused on two mycotoxins mainly produced by Fusarium species, both belonging to the trichothecenes group: the deoxynivalenol (DON) and the T-2 toxin (T-2). The aims of this study were to determine the effects of these two toxins on the immune response implementation in respiratory and intestinal mucosa. Studies were performed on swine being a target species of these contaminants and a model species for Humans. The results of these works proved that these two mycotoxins can affect the immune response. In the respiratory tract, a low dose of T-2 toxin alters the activation of the alveolar macrophages when they are stimulated by the agonists of TLRs -4 and -2/6 (lipopolysaccharides and lipoteichoic acids, respectively). This alteration is due to the decrease of the synthesis of the anti-microbial compound NO and the pro-inflammatory cytokines such as IL-1β and TNF-α. This immunosuppression can induce the emergence of opportunist infections in pig. In the intestinal tract, in background level, we demonstrated that DON as well as T-2 toxin induces a strong inflammatory immune response associated with stimulation of IL-17 pathway by inhibiting of the development of regulatory T cells. Mechanistic studies were used to determine the production origin of the cytokin associated to the IL-17 pathway. This cytokine is produced by one of the subpopulations of Tregs, the Tγδ cells IL-17 producing when exposed to trichothecenes. The third part of this work was about the use of Lactobacillus sobrius DSM 16698T strain to counteract the immunomodulatory effects induced after trichothecen exposure. The results of this study showed that this bacterial strain is able to reduce IL-17 inflammatory effect and is also able to re-etablish the parameters involved in the intestinal barrier functions in ex vivo and in vivo response to DON. Nevertheless, this strain is less effective against the T-2 toxin. Taken together, results of this phD suggest that an exposure to low doses of trichothecens could be intensify the susceptibility of animal to infectious or inflammatory disease.

Le virus Lassa entraine une fièvre hémorragique endémique en Afrique de l’Ouest et représente un problème de santé publique. Les connaissances sur la pathogénèse et les réponses immunitaires associées à la maladie sont partielles. Nous avons suivi les paramètres pathologiques, virologiques et immunologiques associés aux infections létales et non létales du LASV chez le singe cynomolgus. Le tableau clinique a été caractérisé par une dépression, une anorexie, une perte de poids et une asthénie chez les animaux survivants, tandis que ces mêmes symptômes ont été accompagnés de fièvre, de difficultés respiratoires et d’épistaxis chez les animaux infectés par une dose létale. Seuls ces derniers ont montré une perturbation des paramètres de coagulation, une rhabdomyolyse et une hausse des marqueurs de lésions rénales. Nous avons observé un tropisme radicalement différent en fonction de la sévérité de la maladie, avec une dissémination virale dans les organes plus importante et plus rapide chez les animaux décédés, la présence de particules infectieuses plus nombreuses et des modifications anatomopathologiques plus sévères. Une réponse immunitaire innée et adaptative précoce et puissante a été associée avec le contrôle de l’infection et la survie tandis que les infections fatales ont été caractérisées par une réponse inflammatoire ressemblant au choc septique, une défaillance de la réponse immunitaire ainsi qu’une réplication virale incontrôlée. Cette étude permet d’améliorer nos connaissances de la pathogénèse de la fièvre de Lassa et d’apporter des marqueurs d’infection prédictifs de la maladie / Lassa virus causes a hemorrhagic fever endemic in West Africa and represents a threat for civilians. The pathogenesis and the immune responses associated with the disease are poorly understood. We followed pathological, virological and immunological parameters associated with fatal and non-fatal Lassa virus infection in the cynomolgus monkey. The clinical picture was characterized by depression, anorexia, weight loss and asthenia in survivors whereas the same symptoms were supported by fever, respiratory difficulties and epistaxis in animals infected with the lethal dose. Only fatalities have shown coagulation parameters dysfunction, rhabdomyolysis and an increase of renal function markers. We observed a different viral tropism in a function of the disease severity, with viral dissemination in organs that was more important and faster in fatalities, the appearance of numerous infectious particles number and more severe pathologic changes. Early and robust innate and adaptive immune response has been associated with the control of infection and recovery whereas fatal infections were characterized by a sepsis like inflammatory response, defective immune response as well as uncontrolled viral replication. This study sheds light on the pathogenesis of Lassa fever and reveals infection markers predictive of the disease outcome

Cytotoxic T-lymphocytes (CTLs) are important components of the adaptive immune system and function by scanning the intracellular environment so as to detect and de-stroy infected cells. CTL responses play a major role in controlling virus-infected cells such as in HIV or influenza and cells infected with intracellular bacteria such as in tuberculosis. To do so they require the antigens to be presented to them, which is fulfilled by the major histocompatibility complex (MHC), commonly known as human leukocyte antigen or HLA molecules in humans. Recognition of antigenic peptides to Class-1 HLA molecules is a prerequisite for triggering CTL immune responses. Individuals differ significantly in their ability to respond to an infection. Among the factors that govern the outcome of an infection, HLA polymorphism in the host is one of the most important. Despite a large body of work on HLA molecules, much remains to be understood about the relationship between HLA diversity and disease susceptibility. High complexity arises due to HLA allele polymorphism, extensive antigen cross-presentability, and host-pathogen heterogeneity. A given allele can recognize a number of different peptides from various pathogens and a given peptide can also bind to a number of different individuals. Thus, given the plurality in peptide-allele pairs and the large number of alleles, understanding the differences in recognition profiles and the implications that follow for disease susceptibilities require mathematical modelling and computational analysis. The main objectives of the thesis were to understand heterogeneity in antigen presentation by HLA molecules at different scales and how that heterogeneity translates to variations in disease susceptibilities and finally the disease dynamics in different populations. Towards this goal, first the variations in HLA alleles need to be characterized systematically and their recognition properties understood. A structure-based classification of all known HLA class-1 alleles was therefore attempted. In the process, it was also of interest to see if understanding of sub-structures at the binding grooves of HLA molecules could help in high confidence prediction of epitopes for different alleles. Next, the goal was to understand how HLA heterogeneity affect disease susceptibilities and disease spread in populations. This was studied at two different levels. Firstly, modelling the HLA genotypes and CTL responses in different populations and assessing how they recognized epitopes from a given virus. The second approach involved modelling the disease dynamics given the predicted susceptibilities in different populations. Influenza H1N1 infection was used as a case study. The specific objectives addressed are: (a) To develop a classification scheme for all known HLA class-1 alleles that can explain epitope recognition profiles and further to dissect the physic-chemical features responsible for differences in peptide specificities, (b) A statistical model has been derived from a large dataset of HLA-peptide complexes. The derived model was used to identify the interdependencies of residues at different peptide and thereby, rationalize the HLA class-I allele binding specificity at a greater detail, (c) To understand the effect of HLA heterogeneity on CTL mediated disease response. A model of HLA genotypes for different populations was required for this, which was constructed and used for estimating disease response to H1N1 via the prediction of epi-topes and (d) To model disease dynamics in different populations with the knowledge of the CTL response-grouping and to evaluate the effect of heterogeneity on different vaccination strategies. Each of the four objectives listed above are described subsequently in chapters 2 to 5, followed by Chapter 6 which summarises the findings from the thesis and presents future directions. Chapter 1 presents an introduction to the importance of the function of HLA molecules, describes structural bioinformatics as a discipline and the methods that are available for it. The chapter also describes different mathematical modelling strategies available to study host immune responses. Chapter 2 describes a novel method for structure-based hierarchical classification of HLA alleles. Presently, more than 2000 HLA class-I alleles are reported, and they vary only across peptide-binding grooves. The polymorphism they exhibit, enables them to bind to a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern due to multiplicity in their associations. Thus, a powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. The study reports a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification with 7 supergroups was derived, each further categorized to yield a total of 72 groups. An independent clustering scheme based only on the similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explains the basis for the observed clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues that contribute to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants. The results are presented in an interactive web- server http://proline.iisc.ernet.in/hlaclassify. In Chapter 3, the knowledge of structural features responsible for generating peptide recognition specificities are first analysed and then utilized for predicting T-cell epi-topes for any class-1 HLA allele. Since identification of epitopes is critical and central to many of the questions in immunology, a study of several HLA-peptide complexes is carried out at the structural level and factors are identified that discriminate good binder peptides from those that do not. T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics, critically dependent on experimentally obtained training data. Analysis of the training set from IEDB for several alleles indicate that sampling of the peptide space is extremely sparse covering only a tiny fraction of all possible nonamer space, and also heavily skewed, thus restricting the range of epitope prediction. A new epitope prediction method is therefore developed. The method has four distinct modules, (a) structural modelling, estimating statistical pair-potentials and constraint derivation, (b) implicit modelling and interaction profiling, (c) binding affinity prediction through feature representation and (d) use of graphical models to extract peptide sequence signatures to predict epitopes for HLA class I alleles . HLaffy is a novel and efficient epitope prediction method that predicts epitopes for any HLA Class-1 allele, by estimating binding strengths of peptide-HLA complexes which is achieved through learning pair-potentials important for peptide binding. It stands on the strength of mechanistic understanding of HLA-peptide recognition and provides an estimate of the total ligand space for each allele. The method is made accessible through a webserver http://proline.biochem.iisc.ernet.in/HLaffy. In chapter 4, the effect of genetic heterogeneity on disease susceptibilities are investigated. Individuals differ significantly in their ability to respond to an infection. Among the factors that govern the outcome of an infection, HLA polymorphism in the host is one of the most important. Despite a large body of work on HLA molecules, much remains to be understood about how host HLA diversity affects disease susceptibilities. High complexity due to polymorphism, extensive cross-presentability among HLA alleles, host and pathogen heterogeneity, demands for an investigation through computational approaches. Host heterogeneity in a population is modelled through a molecular systems approach starting with mining ‘big data’ from literature. The in-sights derived through this is used to investigate the effect of heterogeneity in a population in terms of the impact it makes on recognizing a pathogen. A case study of influenza virus H1N1 infection is presented. For this, a comprehensive CTL immunome is defined by taking a consensus prediction by three distinct methods. Next, HLA genotypes are constructed for different populations using a probabilistic method. Epidemic incidences in general are observed to correlate with poor CTL response in populations. From this study, it is seen that large populations can be classified into a small number of groups called response-types, specific to a given viral strain. Individuals of a response type are expected to exhibit similar CTL responses. Extent of CTL responses varies significantly across different populations and increases with increase in genetic heterogeneity. Overall, the study presents a conceptual advance towards understanding how genetic heterogeneity influences disease susceptibility in individuals and in populations. Lists of top-ranking epitopes and proteins are also derived, ranked on the basis of conservation, antigenic cross-reactivity and population coverage, which pro- vide ready short-lists for rational vaccine design (flutope). Next, in Chapter 5, the effect of genetic heterogeneity on disease dynamics has been investigated. A mathematical framework has been developed to incorporate the heterogeneity information in the form of response-types described in the previous chap-ter. The spread of a disease in a population is a complex process, controlled by various factors, ranging from molecular level recognition events to socio-economic causes. The ‘response-typing’ described in the previous chapter allows identification of distinct groups of individuals, each with a different extent of susceptibility to a given strain of the virus. 3 different approaches are used for modelling: (i) an SIR model where different response types are considered as partitions of each S, I and R compartment. Initially SIR models are developed, such that the S compartment is sub-divided into further groups based on the ‘response-types’ obtained in the previous chapter. This analysis shows an effect in infection sweep time, i.e., how long the infection stays in the population. A stochastic model incorporates the environmental noise due to random variation in population influx, due to birth, death or migration. The system is observed to show higher stability in the presence of genetic heterogeneity. As the contagion spreads only through direct host to host contact. The topology of the contact network, plays major role in deciding the extent of disease dynamics. An agent based computational framework has been developed for modelling disease spread by considering spatial distribution of the agents, their movement patterns and resulting contact probabilities. The agent-based model (ABM) incorporates the temporal patterns of contacts. The ABM is based on a city block model and captures movement of individuals parametrically. A new concept of system ‘characteristic time’ has been introduced in context of a time-evolving network. ‘Characteristic time’ is the minimum time required to ensure, every individual is connected to all other individuals, in the time aggregated contact network. For any given temporal system, disease time must exceed ‘characteristic time’ in order to spread throughout the population. Shorter ‘characteristic time’ of the system is suggestive of faster spread of the disease. A disease spread network is constructed which shows how the disease spreads from one infected individual to others in the city, given the contact rules and their relative susceptibilities to that viral strain. A high degree of population heterogeneity is seen to results in longer disease residence time. Susceptible individuals preferentially get infected first thereby exposing more susceptible individuals to the disease. Vaccination strategies are derived from the model, which indicates that vaccinating only 20% of the agents, who are hub nodes or highly central nodes and who also have a high degree to susceptible agents, lead to high levels of herd immunity and can confer protection to the rest of the population. Overall, the thesis has provided biologically meaningful classification of all known HLA class-1 alleles and has unravelled the physico-chemical basis for their peptide recognition specificities. The thesis also presents a new algorithm for estimating pep-tide binding affinities and consequently predicting epitopes for all alleles. Finally the thesis presents a conceptual advance in relating HLA diversity to disease susceptibilities and explains how different populations can respond differently to a given infection. A case study with the influenza H1N1 virus identified populations who are most susceptible and those who are least susceptible, in the process identifying important epitopes and responder alleles, providing important pointers for vaccine design. The influence of heterogeneity and response-typing on disease dynamics is also presented for influenza H1N1 infection, which has led to the rational identification of effective vaccination strategies. The methods and concepts developed here are fairly generic and can be adapted easily for studying other infectious diseases as well. Three new web-resources, a) HLAclassify, b) HLaffy and c) Flutope have been developed, which host pre-computed results as well as allow interactive querying to an user to perform analysis with a specific allele, peptide or a pathogenic genome sequence.