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NOD2 is an intracellular innate immune receptor expressed in dendritic cells and gastrointestinal epithelial cells. Polymorphisms in the NOD2 gene convey a strong predisposition to Crohn’s disease (CD), a form of inflammatory bowel disease. Understanding the function of NOD2, and in what way it is aberrant in the presence of NOD2 polymorphisms, would confer a valuable paradigm for understanding Crohn’s pathogenesis. CD is thought to arise both from defects in the gut mucosal barrier and from a dysregulated Th17 immune response to commensal gut flora. Aberrant expression of IL-23 is present in both human CD and in murine models of colitis. Wild-type NOD2 contributes to NFκB activation and pro-inflammatory cytokine production on recognition of its cognate ligand, a function that is lost in CD-associated mutations. How the predominantly loss-of-function CD-NOD2 contributes to the pro-inflammatory response present in Crohn’s is not yet understood. In this thesis a set of experiments is described that aim to shed light on the function of NOD2, firstly through identification of negative regulators of immune activation that are dependent on NOD2 for their expression. This work identifies the microRNAs that are expressed following NOD2 triggering in human dendritic cells. Specifically, up-regulation of the miR-29 family was found to be dependent on wild-type NOD2 function. A number of novel miR-29 targets and their functional consequences are presented, including the cytokine subunits IL-12p40 and IL-23p19, directly linking NOD2 polymorphisms and aberrant IL-23 expression. Secondly, a project aiming to identify components of the NOD2 signalling complex (or signalosome) is described. To this end I employed a model system that involved tagging NOD2, and stable expression in a human cell line. These clones were validated for expression and function before an immunoprecipitation protocol was optimised. Mass spectrometry analysis of these samples identified the known NOD2-interacting protein Erbin.

Πρόσφατα δεδομένα υποδεικνύουν ότι η έκφραση του p75NTR και των Trk υποδοχέων των νευροτροφινών (TrkA, TrkB, TrkC) είναι ιδιαίτερα σημαντική όχι μόνο στη νευρωνική επιβίωση κατά τη διάρκεια της ανάπτυξης και την ενήλικο ζωή αλλά και σε ποικίλες κυτταρικές διαδικασίες όπως η ανοσολογική απάντηση του οργανισμού σε φλεγμονές. Ο σκοπός αυτής της μελέτης ήταν να ερευνήσει την κυτταρική εντόπιση και κατανομή του p75NTR και των Trk υποδοχέων των νευροτροφινών στην ελκώδη κολίτιδα σε σύγκριση με το φυσιολογικό έντερο του ενήλικα ανθρώπου χρησιμοποιώντας την ανοσοϊστοχημική μέθοδο. Στη μελέτη συμπεριελήφθησαν 45 περιπτώσεις ελκώδους κολίτιδας και 5 δείγματα φυσιολογικού εντέρου. Παρατηρήθηκε αύξηση της έκφρασης όσον αφορά τους TrkA υποδοχείς τόσο στο επιθήλιο όσο και στα κύτταρα του εντερικού νευρικού συστήματος στο φλεγμονώδες σε σχέση με το φυσιολογικό έντερο. Έντονη έκφραση των TrkB υποδοχέων ταυτοποιήθηκε στο μυϊκό τοίχωμα των αγγείων και στα εντεροενδοκρινή κύτταρα του επιθηλίου στο φλεγμονώδες και στο φυσιολογικό έντερο. Μειωμένη έκφραση, τόσο στο επιθήλιο όσο και στο εντερικό νευρικό σύστημα, όσον αφορά την έκφραση των TrkB και TrkC υποδοχέων παρατηρήθηκε στις περιπτώσεις ελκώδους κολίτιδας σε σχέση με το φυσιολογικό έντερο. Ο p75NTR παρουσίασε έκφραση αποκλειστικά στα πλέγματα του νευρικού συστήματος, τόσο στο φυσιολογικό όσο και στο φλεγμονώδες έντερο. Τα παραπάνω αποτελέσματα υποδεικνύουν ότι οι νευροτροφίνες μέσω της δέσμευσής τους με τους Trk υποδοχείς και τον p75NTR πιθανόν εμπλέκονται στην παθογένεια των φλεγμονών όπως η ελκώδης κολίτιδα κατά την ενήλικο ζωή. / -

Innate immune activation is thought to play a central role in IBD pathogenesis because genetic polymorphisms in NOD2 and NLRP3, cytosolic innate immune receptors belonging to the NLR family, have been associated with IBD susceptibility. However, the mechanisms through which NLR mutations predispose to IBD remain unclear. The aim of this project was to dissect the functional roles of different NLRs in intestinal inflammation. Using the well-established DSS-induced colitis model as well as experimental models of IBD based on infection with Helicobacter hepaticus, we found that Nod2 expression was significantly increased at the peak of intestinal inflammation, and remained elevated throughout the resolution process. This observation suggests a possible role for Nod2 in the resolution of inflammation. Conversely, upon infection with the acute intestinal pathogen Citrobacter rodentium, Nlrp3-/- mice suffered from increased bacterial colonization as early as 3 days post infection, resulting in exacerbated intestinal inflammation and severe weight loss. Analysis of irradiation bone marrow chimeras showed that the protection required Nlrp3 activation in the non-haematopoietic compartment. Furthermore, this protective mechanism was independent of the inflammasome-associated cytokines IL-1β or IL-18. Therefore, this study implicates Nlrp3 activation in intestinal tissue cells as having a crucial role in controlling pathogenic bacterial colonization, providing a potential mechanism by which NLRP3 polymorphisms could lead to increased susceptibility to IBD.

Crohn's Disease (CD) is a debilitating condition characterised by chronic intermittent intestinal inflammation. More than 90 genetic polymorphisms are associated with CD susceptibility, including several in genes of the innate immune system. Here I present a series of experiments designed to enhance our knowledge of the roles of CD-associated polymorphisms in pathogenesis. Many therapeutic regimens are employed in CD treatment, but patients' responses to treatment and disease progression vary widely. There is great interest in studying whether analysis of patients' genotype at CD-associated polymorphisms can be used to predict their disease course, and guide clinical decision-making. To answer these questions, it is essential to be able routinely and cost- effectively to genotype patients at the full range of known CD-associated polymorphisms. The first project presented here describes the design and initial successful testing of a CD-specific genotyping microarray for use in genotype-phenotype studies. The polymorphism most strongly associated with CD susceptibility is in the pattern recognition receptor NOD2; the remaining experiments presented here study the function of NOD2 in primary human monocyte-derived Dendritic Cells (DCs). First, a microarray study is presented which characterises global transcriptional responses to NOD2 stimulation in DCs. NOD2 stimulation is shown to enhance transcriptional changes induced by Toll-Like Receptor 2 stimulation, and NOD2-mediated transcriptional regulation is shown to be lost in DCs expressing CD-associated NOD2 variants. Second, experiments are presented which describe development of a new protocol for proteomic analysis of post-translational protein modifications, and which identify a number of novel candidate targets of NOD2 signalling in DCs. Finally, a project is presented which demonstrates for the first time that NOD2 stimulation induces autophagy in DCs, in an NF-kB and RIPK2-dependent pathway. CD-associated polymorphisms in NOD2 and ATG 16Ll abolish NOD2-mediated autophagy induction, resulting in impaired bacterial handling and antigen presentation.

La maladie de Crohn est présente principalement dans les pays industrialisés. En France, elle touche 1 personne sur 1000. L’incidence est de 5 pour 100000 habitants par an. A l’heure actuelle sa pathogénie reste mal expliquée et de nombreux facteurs interviennent (facteurs génétiques, immunologiques et environnementaux). Il semble donc essentiel de mieux comprendre la pathogénie de la maladie de Crohn afin d’identifier des cibles thérapeutiques permettant d’améliorer sa prise en charge et d’identifier des facteurs prédictifs de la récidive post-opératoire et des complications post-opératoires afin de personnaliser la prise en charge de chaque patient. Dans ce travail nous avons montré qu'un variant génétique de CARD8 (rs2043211) est un facteur de risque de récidive post-opératoire. Cette association n’est pas influencée par les autres facteurs de risque connus comme le tabagisme actif. L’identification de CARD8 comme un facteur de risque génétique de risque de récidive chirurgicale est d’un intérêt particulier puisqu’il pourrait devenir une nouvelle cible thérapeutique pour le traitement de la maladie de Crohn dans la période post-opératoire. Notre travail a également montré qu'un variant génétique de NOD2 (rs5743289) est un facteur de risque de complications intra-abdominales infectieuses post-opératoires (CIIP) après chirurgie dans la maladie de Crohn. L’identification de NOD2 comme un gène à risque pour la survenue de CIIP pourrait permettre d’établir une stratification précoce des patients à haut risque de CIIP chez qui la chirurgie devra être planifiée et prédire les patients à haut risque de CIIP. Des études sur larges effectifs avec cohorte de réplication restent encore nécessaires avant que les patients puissent bénéficier des retombées de ces outils en pratique courante / Crohn's disease occurs mainly in industrialized countries. In France it affects 1 person in 1000. The incidence is 5 per 100,000 persons per year. At present its pathogenesis remains poorly explained and many factors are involved (genetic, immunological and environmental). It seems essential to better understand Crohn's disease pathogenesis in order to identify therapeutic targets to improve its management and to identify predictors of postoperative recurrence and postoperative complications to customize the care of each patient. In this work we showed that a genetic variant of CARD8 (rs2043211) is a risk factor for postoperative recurrence. This combination is not influenced by the other known risk factors such as active smoking. Identifying CARD8 as a genetic risk factor for risk of surgical recurrence is of particular interest since it may become a novel therapeutic target for the treatment of Crohn's disease in the post-operative period. Our work has also shown that a genetic variant of NOD2 (rs5743289) is a risk factor for postoperative intraabdominal infectious complications (CIIP) after surgery in Crohn's disease. The identification of NOD2 gene as a risk factor for the occurrence of CIIP could establish an early stratification of patients at high risk for CIIP in whom surgery should be planned and predict patients at high risk for CIIP. Studies with large numbers replication cohort are still necessary before patients can enjoy the benefits of these tools in clinical practice

Leukocyte extravasation is mediated in part by tissue specific chemotactic cytokines (chemokines) and specific chemokine receptors expressed on the surface of circulating cells. C-C chemokine ligand CCL25 is expressed exclusively in the intestine and thymus and mediates chemotaxis by cells expressing receptor CCR9. This chemokine and receptor pair may be relevant in the pathogenesis of intestinal inflammation, in diseases such as Crohn’s disease (CD) and coeliac disease. In this thesis I investigated CCR9 expression in situ, in tissues affected by intestinal inflammation, and also examined the effects of CCR9 antagonist treatment in patients. In vitro I investigated CCR9 function using human peripheral blood T cells enriched for CCR9 by cell sorting or all-trans retinoic acid treatment. Using tissues collected as part of a clinical trial in CD testing CCR9 antagonist, CCX282-B, I investigated ways of measuring if treatment reduced the number of CCR9 expressing cells in the intestinal mucosa. However, in situ staining for CCR9 by immunohistochemistry was unsuccessful, and in this thesis, I explored reasons why this might be the case. Treatment with CCX282-B did however, show a tendency to reduce T cell density in the intestinal mucosa, although results were highly variable between individuals. In an examination of human CCR9 function in vitro I demonstrate for the first time that CCL25 stimulates CCR9 surface internalization. These data clarify the observation that CCR9 staining by IHC produces poor results in tissues where ligand is abundant, such as the intestine and thymus. I describe a novel technique for measuring calcium flux in two populations simultaneously by flow cytometry, which confirmed that in a heterogeneous population of cells, only CCR9 expressing cells respond to CCL25 by calcium flux. Variability in clinical trials is partly created by the use of concomitant medications, and in CD, corticosteroids are widely used. For the first time I show that glucocorticoids (GC) impair CCR9 mediated chemotaxis, calcium flux and intracellular signalling without changes to CCR9 mRNA and surface protein expression. Reduced CCR9 mediated signalling was accompanied by an enhanced expression and function of co-expressed CXCR4, demonstrating that the effects of GC were receptor-specific and not mediated by non-specific toxicity or inhibition of cell signalling. In a second study CCX282-B was tested in patients with coeliac disease, and in this trial, there was no reported concomitant use of GCs. It was confirmed that dietary gluten stimulates significant T cell recruitment to the intestinal mucosa with a pronounced accumulation of intraepithelial lymphocytes (IEL) and a rise in the frequency of FoxP3 expressing cells. Patients on CCX282-B had lower IEL counts, and an equivalent proportion of FoxP3 expressing T cells, suggesting that CCR9 blockade restricted the recruitment of effector T cell subsets. This thesis confirms that the accumulation of T cells is central to inflammation in the intestine and that modulating chemokine receptor function may affect this. Furthermore, this thesis demonstrates that the function of CCR9 is suppressed by GCs, which are widely used therapeutically and therefore could identify a novel mechanistic basis for their activity in CD.

Inflammatory bowel disease (IBD), which includes the subtypes Crohn's disease (CD) and ulcerative colitis (UC), is a common disease particularly in the Western world. IBD is characterised by inflammation of the small intestine and/or colon. The two subtypes affect different gut locations but both show an increased intestinal permeability or the 'leaky gut syndrome'. This led to the hypothesis that tight junction (TJ) proteins expressed in the epithelium may affect the intestinal permeability as a cause or effect of IBD.Initially, variants in the CARD15, IL23R and ATG16L1 genes, previously associated with an increased risk of IBD, were genotyped in a cohort of 500 IBD (295 CD and 205 UC) patients and 877 matched controls. These variants were significantly associated in our cohort. A random effects meta-analysis was undertaken on all previously reported CD associations with the variant rs2241880 from ATG16L1 (n=25, p=0.0017, OR: 1.36 95% CI 1.12-1.66) and with rs11209026 from IL23R (n=26, p=0.0006, OR: 0.37 95% CI 0.21-0.67), showing pooled odds ratios consistent with those reported in our cohort. Individuals carrying >1 CARD15 mutant variant were found to have a 2.5 fold increased risk of CD (p=0.0001). Candidate TJ proteins were chosen on the basis of previous reported associations and through the investigation of the claudin proteins which are abundant at TJs. Twenty one candidate genes were selected and 79 variants successfully genotyped in up to 1063 IBD (502 CD and 478 UC) and 870 control patients. Significant associations were detected with variants in the CLDN1, CLDN5 and CDH1 genes with CD; CLDN5, CLDN8 and CDH1 variants were associated to IBD; and the rs7791132 variant (between CLDN4 and ELN) and a CDH1 variant were associated to UC. The CLDN1 rs6809685 variant trended towards association in a Toronto ascertained IBD replication cohort (genotypic p=0.04, allelic p=0.06) suggesting this may be a novel IBD susceptibility variant. Small intestinal biopsies from CD patients with known rs6809685 genotypes showed a dose dependent reduced immunohistochemical staining of claudin 1 with carriage of the mutant G allele. Claudin 1 helps seal TJs and reduced levels may increase risk of CD.Peroxisome proliferator activator receptors (PPARs) can directly affect TJ proteins and could therefore affect intestinal permeability. Twelve PPARγ variants were genotyped in up to 1050 IBD (502 CD and 467 UC) and 725 control patients. Significant genotypic associations were found with the rs2067819 variant in CD (p=0.05) and IBD (p=0.02), and also the rs13099634 variant in UC (P=0.02). There was a strong gender difference particularly for rs2067819 and rs4135247, where allelic associations were highly significant and increased risk of IBD in men (p=0.01 and p=0.007 respectively). However no significant associations were found in the female cohort. Troglitazone a PPARα agonist increased Caco2 cell transepithelial electrical resistance (TEER), a marker of TJ integrity, and increased expression of claudins -3 and -4. In contrast, the PPARα antagonist GW6471 reduced the TEER without causing cell death and PPARγ ligands did not affect TEER measurements. In summary, using a robust cohort of cases and controls the data indicates that variants in genes encoding TJ proteins may affect susceptibility to IBD and that PPARs can regulate these proteins altering intestinal permeability.

Des études d'associations pangénomiques ont démontré une relation entre le taux plasmatique de la vitamine B12 et le polymorphisme du gène FUT2 (fucosyltransferase 2). Dans des modèles expérimentaux, le statut sécréteur pour FUT2 a été impliqué dans la susceptibilité à l'infection par Helicobacter pylori (H. pylori). Nous avons évalué l'influence du polymorphisme FUT2 461 G>A sur les marqueurs du métabolisme des monocarbones dans deux populations ambulatoires en Europe et en Afrique de l'Ouest ainsi que la possible association entre l'infection par H. pylori et le polymorphisme de FUT2. Nous avons mis en évidence une influence de FUT2 461 G>A sur le taux plasmatique de la vitamine B12 mais n'avons pas retrouvé d'influence du statut sérologique pour H. pylori sur cette association, du moins chez les sujets ambulatoires en Europe et en Afrique de l'Ouest. L'hyperhomocystéinémie est un marqueur de carence en donneurs de méthyle. Plusieurs travaux ont évalué le taux plasmatique de l'homocystéine au cours des maladies inflammatoires chroniques de l'intestin (MICI) et ont abouti à des résultats mitigés. Par ailleurs, l'ampleur de l'association entre le métabolisme de l'homocystéine et les MICI reste méconnue. Nous avons réalisé une méta-analyse afin : (i) d'évaluer l'association entre le métabolisme de l'homocystéine et les MICI et (ii) d'étudier le risque de thrombose lié à l'hyperhomocystéinémie au cours des MICI. Le risque d'hyperhomocystéinémie était significativement plus élevé chez les patients avec une MICI en comparaison aux sujets contrôles. L'évaluation du risque de thrombose associé à l'hyperhomocystéinémie au cours des MICI requiert des études complémentaires. Un statut carencé en folates était associé à un impact plus fort du polymorphisme MTHFR C677T sur le risque primaire de MICI. L'hyperhomocystéinémie et plusieurs polymorphismes sur les gènes du métabolisme des monocarbones sont associés au risque primaire et à la sévérité de la maladie de Crohn (MC). L'hyperhomocystéinémie augmente l'activité de la superoxyde dismutase (SOD), un marqueur fiable et validé du stress oxydatif. A l'aide d'un SNP array Illumina exhaustif du métabolisme des monocarbones, nous avons (i) étudié les déterminants génétiques (single nucleotide polymorphisms, SNPs) associés au taux plasmatique de l'homocystéine et de la SOD chez des patients suivis pour une MC et (ii) recherché les SNPs associés à l'âge du diagnostic de la MC. Deux SNPs étaient indépendamment associés au taux plasmatique de l'homocystéine (MTHFR, AHCY). Cinq SNPs étaient indépendamment associés au taux plasmatique de la SOD. Parmi ces cinq SNPs, trois sont liés à la vitamine B12 (FUT2, CUBN, et TCN2), un aux folates (GGH), et un dernier à la synthèse cellulaire de l'homocystéine (AHCY). Par ailleurs, nous avons mis en évidence deux SNPs associés à un âge précoce du diagnostic de la MC (CHDH, ABCB1). / Genome wide association studies demonstrated an association between plasma vitamin B12 and FUT2 (fucosyltransferase 2). It has been suggested that the association between FUT2 and low plasma vitamin B12 level may be the consequence of an increased susceptibility to Helicobacter pylori (H. pylori) infection. We evaluated the association between FUT2 461G>A polymorphism and vitamin B12 and investigated whether the influence of FUT2 on H. pylori serology is part of the mechanisms that underlie this association, in two populations from Europe and West Africa. In this study we confirmed the influence of FUT2 461 G>A polymorphism on plasma vitamin B12 level and found no influence of H. pylori serological status on this association, at least in ambulatory subjects from Europe and West Africa. The magnitude of the association between homocysteine metabolism and inflammatory bowel diseases (IBD) is unknown while the association between hyperhomocysteinemia and thrombosis remains controversial in IBD. We conducted a systematic review of the literature and performed a meta-analysis to examine these issues. The risk of hyperhomocysteinemia is significantly higher in IBD patients when compared to controls. The risk assessment of hyperhomocysteinemia-related thrombosis in IBD requires further investigation. Deficient folate status is associated with a higher impact of MTHFR C677T polymorphism on IBD risk. Hyperhomocysteinemia and several gene variants of one-carbon metabolism are associated with the occurrence and severity of Crohn's disease (CD). Hyperhomocysteinemia results in part from methyl donors deficiency - which is frequent in patients with CD - and increases the activity of superoxide dismutase (SOD), a validated and reliable marker of oxidative stress. We designed a 384-plex GoldenGate oligo pool assay for the comprehensive one-carbon metabolism genotyping using Illumina platform. The aims of this study were (i) to assess genetic determinants of plasma homocysteine and superoxide dismutase (SOD) levels in patients with IBD and (ii) to look for single nucleotide polymorphisms (SNPs) associated with age at CD onset. Two SNPs were associated with plasma homocysteine level (MTHFR, AHCY). Five SNPs were independently associated with plasma SOD level. Of these five SNPs, three are related to vitamin B12 (FUT2, CUBN, and TCN2), one is related to folate (GGH), and the last one to homocysteine (AHCY). In addition, we identified two SNPs associated with early CD onset (CHDH, ABCB1)