NOD1 and NOD2 (nucleotide-binding oligomerization domain-containing proteins 1 and 2) are related innate immune receptors responsible for initiating a response to bacterial infection. They belong to a class of receptors known as Pattern Recognition Receptors (PRRs), which are germline encoded immune receptors that mediate various innate immune responses. These receptors recognize conserved microbial motifs known as Pathogen-Associated Molecular Patterns (PAMPs). The PRR-PAMP paradigm forms the bedrock of how innate immunity is understood today. As two of the first intracellular PRRs discovered, NOD1 and NOD2 came to define an entire subclass of PRRs, the NOD-like receptors (NLRs). PRRs relay their signals through protein:protein interaction motifs that typically adopt a characteristic Death Domain (DD) fold. NOD1 and NOD2 signal through their respective CAspase Recruitment Domains (CARDs), which are part of a DD subfamily. The CARDs of NOD1 and NOD2 interact with multiple downstream effectors and are thus situated at a key point for regulation and coordination of NOD1 and NOD2 signaling. To better understand this regulation, I structurally and functionally characterized interactions made by the CARDs of NOD1 and NOD2. Receptor Interacting Protein kinase 2 (RIP2) is an effector of both NOD1 and NOD2 that activates the NF-ΚB pathway to elicit an inflammatory response. I discovered a new binding interaction between the CARDs of NOD1 and NOD2 and ubiquitin. Furthermore, I elucidated a role for this interaction by showing that ubiquitin binds NOD1 and NOD2 CARDs competitively with the CARD of RIP2. Through biophysical and biochemical investigation, I identified mutants of NOD1 CARD that did not bind ubiquitin and were thus insensitive to its competitive effect on RIP2 binding. Utilizing this mutant in functional studies defined ubiquitin as a negative regulator of NOD1 signaling. Characterizing NOD1 allowed rational design of mutations that uncovered a similar role for ubiquitin in the NOD2 pathway. This introduces the potential for broader application of these findings in other DD-mediated pathways. NOD1 and NOD2 also bind the autophagy protein ATG16L. I investigated the molecular mechanisms of this interaction and found that NOD1 and NOD2 bind ATG16L through their CARDs. I also found that the domain on ATG16L responsible for binding NOD1 and NOD2 is the C-terminal WD40 Β-propeller. Furthermore, the CARD:Β-propeller interaction is sufficient to mediate interaction between NOD1 or NOD2 and ATG16L. The finding that the ATG16L Β-propeller also binds ubiquitin leaves open the possibility that ubiquitin regulates pathway selection by NOD1 and NOD2. Together, these studies advance our understanding of NOD1 and NOD2 signaling and lay the groundwork for further mechanistic investigations into coordination of inflammatory and autophagic signaling pathways by the immune system in general.

Through a binding partner the CARD15 gene activates NF-kB, a molecule with a role in the initiation of the inflammatory immune response. The gene is highly conserved in both structure and function in human and mouse and has recently been implicated as a disease resistance gene in Crohn's disease and Blau Syndrome in human. The gene's relationship to disease and its conservation between species suggests that it may also have a conserved role in bovine disease resistance. To elucidate the potential role of bovine CARD15 in disease resistance, the gene was characterized in cattle. Bovine CARD15 is located 4.2 cR5000 telomeric to ADCY7 on chromosome 18. It spans ~30 kb and is comprised of 12 exons, 11 of which are coding. Bovine CARD15 is expressed in many tissues, but is most abundant in peripheral blood leukocytes. An extensive comparative analysis between the bovine, mouse and human CARD15 genes revealed high levels of inter-species conservation in sequence, genomic structure and protein domains. Conserved putative regulatory motifs were identified in the three species comparison of the 5'UTR, 3'UTR and the intronic sequences flanking exons. Additionally, diverse regulatory motifs were identified in each of the species indicating an evolutionary divergence in the mechanisms of regulation of gene expression. To assess the extent of genetic diversity within bovine CARD15, 41 individuals from nine breeds representing two subspecies were sequenced and screened for polymorphisms. Thirty-six single nucleotide polymorphisms (SNPs) were identified including 26 within the gene transcript. Haplotypes were estimated for each individual and parsimonious SNP sets were identified with which the multi-locus Bos taurus and Bos indicus haplotypes may be reconstructed. There was a significantly higher rate of substitutions within Bos indicus than in Bos taurus. A significantly higher rate of nonsynonymous to synonymous substitutions was found in Bos taurus indicating that positive Darwinian selection is acting on the gene within this subspecies. Association analyses were performed between these SNP loci and haplotypes with Johne's disease. No overwhelming evidence for a simple causal relationship was detected. Assays are provided to screen populations of cattle for variation in the CARD15 gene.

Through a binding partner the CARD15 gene activates NF-kB, a molecule with a role in the initiation of the inflammatory immune response. The gene is highly conserved in both structure and function in human and mouse and has recently been implicated as a disease resistance gene in Crohn's disease and Blau Syndrome in human. The gene's relationship to disease and its conservation between species suggests that it may also have a conserved role in bovine disease resistance. To elucidate the potential role of bovine CARD15 in disease resistance, the gene was characterized in cattle. Bovine CARD15 is located 4.2 cR5000 telomeric to ADCY7 on chromosome 18. It spans ~30 kb and is comprised of 12 exons, 11 of which are coding. Bovine CARD15 is expressed in many tissues, but is most abundant in peripheral blood leukocytes. An extensive comparative analysis between the bovine, mouse and human CARD15 genes revealed high levels of inter-species conservation in sequence, genomic structure and protein domains. Conserved putative regulatory motifs were identified in the three species comparison of the 5'UTR, 3'UTR and the intronic sequences flanking exons. Additionally, diverse regulatory motifs were identified in each of the species indicating an evolutionary divergence in the mechanisms of regulation of gene expression. To assess the extent of genetic diversity within bovine CARD15, 41 individuals from nine breeds representing two subspecies were sequenced and screened for polymorphisms. Thirty-six single nucleotide polymorphisms (SNPs) were identified including 26 within the gene transcript. Haplotypes were estimated for each individual and parsimonious SNP sets were identified with which the multi-locus Bos taurus and Bos indicus haplotypes may be reconstructed. There was a significantly higher rate of substitutions within Bos indicus than in Bos taurus. A significantly higher rate of nonsynonymous to synonymous substitutions was found in Bos taurus indicating that positive Darwinian selection is acting on the gene within this subspecies. Association analyses were performed between these SNP loci and haplotypes with Johne's disease. No overwhelming evidence for a simple causal relationship was detected. Assays are provided to screen populations of cattle for variation in the CARD15 gene.

Submitted by KEREN BASTOS VALEZI null (keren.valezi@hotmail.com) on 2017-12-18T18:47:58Z No. of bitstreams: 1 Dissertação de Mestrado Keren Valezi.pdf: 1447594 bytes, checksum: 988c2b1fc1fbd371daf1230457df1fa9 (MD5) / Approved for entry into archive by Luciana Pizzani null (luciana@btu.unesp.br) on 2017-12-19T14:03:37Z (GMT) No. of bitstreams: 1 valezi_kb_me-int.pdf: 1447594 bytes, checksum: 988c2b1fc1fbd371daf1230457df1fa9 (MD5) / Made available in DSpace on 2017-12-19T14:03:37Z (GMT). No. of bitstreams: 1 valezi_kb_me-int.pdf: 1447594 bytes, checksum: 988c2b1fc1fbd371daf1230457df1fa9 (MD5) Previous issue date: 2017-11-01 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / A leishmaniose é uma doença antropozoonótica causada pelo protozoário do gênero Leishmania. Ele apresenta três formas clínicas, conhecidas como leishmaniose visceral, leishmaniose cutânea e leishmaniose mucocutânea. A leishmaniose visceral afeta dois milhões de indivíduos anualmente no mundo. Os fato res genéticos envolvidos na interação hospedeiro - parasita foram associados ao desfecho clínico da doença. Este estudo investigou pela primeira vez a associação de polimorfismos nos genes candidatos IL10, NOD2 e TLR1 com leishmaniose visceral na população b rasileira. Para isso, escolhemos três marcadores anteriormente associados a infecções causadas por parasitas intracelulares na população brasileira. Nós genotipificamos 135 pacientes e 380 controles saudáveis. A presença do alelo G do rs4833095 no gene TLR 1 foi fortemente associada à susceptibilidade a esta doença: análise do alelo G (OR 2.04; IC 1.22 - 3.39; p - value 0.0061); Análise do genótipo GG (OR 3,87; 95 %IC 1,85 - 8,08, p - valor 0,0003); Análise de portadores de G (OR 2,5; 95 %IC 1,33 - 5,00; valor p 0,0047) . Para o gene NOD2, também encontramos uma associação para o genótipo AA (OR 2.07 95 %IC 1.05 - 4.05, p - value 0.0335) do polimorfismo rs8057341. Finalmente, poderíamos confirmar a associação do marcador rs1800871 na região promotora do gene IL10 com susceptib ilidade à leishmaniose visceral, para o genótipo TT (OR 2,34; CI 95 %IC 1,11 - 4,94 p - value 0,0245). Conclusão. Nossos dados demonstram pela primeira vez a associação desses genes candidatos com leishmaniose visceral na população brasileira, colocando esses ma rcadores como candidatos fortes na composição de futuros painéis genéticos para prever o risco de infecções na população brasileira e para estudos de meta - análise em visceral leishmaniose / 193614-1

Staphylococcus aureus (S. aureus) is a gram-positive bacterium that causes mastitis in bovines and leads to financial losses to the dairy industry. Although antibody response plays a role in immune defense against S. aureus, cellular responses are of interest for vaccine development. A vaccine that stimulates both antibody and cellular responses could promote memory cell formation and provide effective protection against S. aureus. The superantigens and virulence factors secreted by live S. aureus (LSA) can interfere with immune responses and memory cell formation. Because irradiation reduces the metabolic activity and secretion of proteins, including S. aureus superantigens and hemolysins, we hypothesized the irradiated S. aureus (ISA) could drive immune cell responses. Dendritic cells (DC) were co-cultured with lymphocytes to study the cellular responses to ISA and LSA. Dendritic cells present antigens and polarize lymphocytes into different helper T (Th) cell types that drive cellular immune responses. The DC loaded with either ISA or LSA induced increased mRNA transcription of Th17-related cytokines and cytotoxic effector memory cell formation during antigen recall experiments. Lymphocytes co-cultured with LSA-loaded DC exhibited a higher fold-change in interferon (IFN) γ mRNA compared to ISA-loaded DC, suggesting the secreted antigens and the metabolic activity of S. aureus play a role in Th1 polarization. Th1 polarization can drive excessive inflammation and suppress beneficial Th17 responses. Bovine DC were stimulated with a mutant α-toxin deletion S. aureus strain to evaluate if α-toxin-mediated NOD2 receptor signaling activates Th1 polarization in response to S. aureus, which revealed that NOD2 mRNA transcription in DC was independent of α-toxin and that the deletion of α-toxin had no effect on the transcription of the cytokine IL-12 or the production of IFNγ by lymphocytes, events that drive Th1 polarization, in co-cultures. The deletion of accessory gene regulator (agr), which controls α-toxin production, reduced IFNγ production in lymphocytes co-cultured with the S. aureus-loaded DC, indicating that agr controlled the ability of S. aureus antigens to drive the Th1 polarization of lymphocytes. Overall, this thesis demonstrates that ISA is a promising source of antigens that stimulate memory cells formation and Th17 polarization in bovine immune cells. The reduced Th1 cytokine response to S. aureus was not dependent on α-toxin, but other virulence factors controlled by agr should be screened to determine the source of Th1 stimulation. / Ph. D. / Dairy cows’ health and productivity is negatively impacted by mastitis, infection starting at the mucosal surfaces of the udder. <i>Staphylococcus aureus</i> is a bacterium that can cause mastitis and there is no efficacious vaccine available. I explored the use of weakened <i>S. aureus</i> as a source of vaccine components and the α-toxins role in stimulating the immune cells like dendritic cells (DC) and lymphocytes. <i>S. aureus</i> was weakened using gamma irradiation to conserve the structural components of the bacterium and render it unable to secrete α-toxin. The DC were collected from dairy cows and stimulated with irradiated <i>S. aureus</i> and live <i>S. aureus</i> before lymphocytes were added to the cultures. The DC signaling, lymphocytes’ pro-inflammatory interferon gamma and mucosal immunity related interleukin responses were measured from RNA production. Memory cell formation and production of interferon gamma were measured from whole cells. The role of α-toxin in lymphocyte stimulation was further studied using a strain of bacterium that does not produce the toxin. Irradiated <i>S. aureus</i> induced low production of inflammatory interferon gamma compared to the live <i>S. aureus</i>. The α-toxin played no role in this, even if other components produced under the same regulatory element likely did, as shown by reduced interferon production in response to bacteria without the regulatory element. Irradiation of the bacterium did not reduce mucosal immunity related cytokine production or formation of memory cells. The irradiated <i>S. aureus</i> is a source for vaccine components that stimulate immune cells like DC and immunity to <i>S. aureus</i> on mucosal surfaces of the udder.

Células produtoras de IFN-? e IL-17A são envolvidas na proteção contra infecção por Leishmania infantum (L. infantum). Ainda não está claro como o sistema imune coordena, ou o parasito manipula, o balanço entre Th1 e Th17 durante a leishmaniose visceral (LV). Utilizando RNAseq, PCR array e citometria de fluxo, nós demonstramos que, enquanto o padrão Th1 é altamente induzido, o perfil Th17 é inibido durante a infecção por L. infantum, e que as células B compõem uma fonte importante de IL-17A nesse modelo. Usando animais Nod2-/- e Rip2-/- nós caracterizamos essa via como um regulador negativo de células Th17 na LV. Por outro lado, a potente indução de Th1 foi dependente da sinalização via NOD2-RIP2 em células dendríticas CD8??+XCR1+, o que foi crucial para produção de IL-12 através da fosforilação de p38 e JNK. Como consequência, camundongos Nod2-/- e Rip2-/- tiveram defeito na resposta Th1, aumento de Th17, e maiores cargas parasitárias comparado com camundongos WT. Juntos, os dados mostram que a via de NOD2-RIP2 desempenha um papel importante na modulação da resposta imune adaptativa e promove proteção contra LV causada por L. infantum / IFN-? and IL-17A-producing cells are described to be related to protection against Leishmania infantum (L. infantum) infection. How the immune system coordinates, or the parasite manipulates, the balance between Th1 and Th17 during visceral leishmaniasis (VL) is still unknown. We showed here that Th17 is suppressed during L. infantum infection and B cells are an important source of IL-17A in this model. By using Nod2-/- and Rip2-/- mice we characterized this pathway as a negative regulator for Th17 cells in VL. On the other hand, the high level of Th1 induction was dependent on the NOD2-RIP2 signaling in CD8?+XCR1+ dendritic cells (DCs), which was crucial for IL-12 production through the phosphorylation of p38 and JNK. As a consequence, Nod2-/- and Rip2-/- mice showed a Th1 defective response, more Th17, and higher parasite loads compared to WT mice. Together, the data demonstrate that NOD2-RIP2 signaling pathway plays a role in shaping adaptive immunity and promotes protection against VL caused by L. infantum

Células produtoras de IFN-? e IL-17A são envolvidas na proteção contra infecção por Leishmania infantum (L. infantum). Ainda não está claro como o sistema imune coordena, ou o parasito manipula, o balanço entre Th1 e Th17 durante a leishmaniose visceral (LV). Utilizando RNAseq, PCR array e citometria de fluxo, nós demonstramos que, enquanto o padrão Th1 é altamente induzido, o perfil Th17 é inibido durante a infecção por L. infantum, e que as células B compõem uma fonte importante de IL-17A nesse modelo. Usando animais Nod2-/- e Rip2-/- nós caracterizamos essa via como um regulador negativo de células Th17 na LV. Por outro lado, a potente indução de Th1 foi dependente da sinalização via NOD2-RIP2 em células dendríticas CD8??+XCR1+, o que foi crucial para produção de IL-12 através da fosforilação de p38 e JNK. Como consequência, camundongos Nod2-/- e Rip2-/- tiveram defeito na resposta Th1, aumento de Th17, e maiores cargas parasitárias comparado com camundongos WT. Juntos, os dados mostram que a via de NOD2-RIP2 desempenha um papel importante na modulação da resposta imune adaptativa e promove proteção contra LV causada por L. infantum / IFN-? and IL-17A-producing cells are described to be related to protection against Leishmania infantum (L. infantum) infection. How the immune system coordinates, or the parasite manipulates, the balance between Th1 and Th17 during visceral leishmaniasis (VL) is still unknown. We showed here that Th17 is suppressed during L. infantum infection and B cells are an important source of IL-17A in this model. By using Nod2-/- and Rip2-/- mice we characterized this pathway as a negative regulator for Th17 cells in VL. On the other hand, the high level of Th1 induction was dependent on the NOD2-RIP2 signaling in CD8?+XCR1+ dendritic cells (DCs), which was crucial for IL-12 production through the phosphorylation of p38 and JNK. As a consequence, Nod2-/- and Rip2-/- mice showed a Th1 defective response, more Th17, and higher parasite loads compared to WT mice. Together, the data demonstrate that NOD2-RIP2 signaling pathway plays a role in shaping adaptive immunity and promotes protection against VL caused by L. infantum

Le gène NOD2, impliqué dans les réponses immunitaires innées contre le peptidoglycane bactérien, est étroitement associé à la maladie de Crohn (MC) avec des Odd Ratio(OR) allant de 3 à 36 selon le génotype et a été initialement identifié par des analyses de liaisons génétiques. Les données des familles multiplexes (familles définies par la présence de trois ou plus de trois apparentés au premier degré atteints de MC) issues du registre EPIMAD ont été analysées. Il a été précédemment rapporté que dans les 22 familles multiplexes EPIMAD génotypées pour les 3 mutations majeures du gène NOD2une fréquence élevée de ces mutations du gène NOD2 : R702W, G908R et L1007fs, pouvait expliquer la fréquence élevée de MC dans ces familles. Cependant, quelques familles multiplexes EPIMAD ne présentaient aucune de ces mutations R702W, G908R et L1007fs.Afin d’identifier de nouvelles variations génétiques ayant un effet majeur dans la MC, un protocole de Whole Exome Séquencing (WES) a été effectué sur l’une de ces familles multiplexes EPIMAD (F49M) présentant quatre sujets atteints de MC sur deux générations.Une variation rare du gène NOD2, N1010K, s’est avérée présente chez tous les patients atteints et absente chez tous les sujets contrôles intrafamiliaux . L’évaluation in silico et la modélisation 3D ont mis en évidence un effet délétère hautement probable de la mutation de N1010K suggérant donc fortement qu’elle pourrait être un nouveau facteur de risque majeur impliqué dans la susceptibilité génétique à la maladie de Crohn. Elle pourrait expliquer l’agrégation familiale de la MC dans la famille analysée. La présence d’une maladie plus sévère chez les patients hétérozygotes composites N1010K/L1007fs plaide en faveur de l’effet délétère de la mutation N1010K.En plus de la caractérisation d’une nouvelle mutation rare du gène NOD2, 2 autres variants potentiels ont été identifiés : les mutations D359H et G33V respectivement des gènes BPIFB2 et DEFB132. Les protéines codées par ces gènes sont impliquées dans les mêmes voies de signalisation : la voie de signalisation des défensines ainsi que dans celle du système immunitaire inné. L’évaluation in silico des effet de ces mutations a mis en évidence un effet délétère hautement probable pour D359H et G33V des gènes BPIFB2et DEFB132. Ainsi, on peut supposer que bien que les deux mutations D359H du gèneBPIFB2 et G33V du gène DEFB132, soient localisés sur deux gènes différents impliquées dans les mêmes voies de signalisation, elles pourraient agir ensemble et conduire à un effet dysfonctionnel cumulatif impliqué également dans l’agrégation familiale de la MC dans la famille F49M.Ainsi, Pour la famille F49M, l’agrégation familiale pourrait reposer sur l’accumulation de plusieurs mutations à effet délétère (N1010K, D359H et G33V). / The NOD2 gene, involved in innate immune responses, has been found to be highlyassociated with Crohn’s Disease (CD). EPIMAD multiplex families with three or more CDaffectedmembers were previously reported to be related to a high frequency of NOD2gene mutations : R702W, G908R, and L1007fs. However, some rare EPIMAD CD multiplexfamilies were described without any of the common NOD2 linked-to-disease mutations.In order to identify new genetic variation(s) with amajor effect in CD, whole exomesequencing was performed on available subjects in a multiplex family (F49M), withoutknown common NOD2 mutations and comprising four patients affected with Crohn’s diseaseand three unaffected related subjects on two generations . A rare and, not yet, reportedmissense mutation of the NOD2 gene, N1010K, was detected and co-segregated acrossaffected patients (present in allmembers affectedwith CD and absent in all unaffected familialcontrol subjects). In silico evaluation of the deleterious effect of the mutation and3D modelling highlighted evidences for an adverse effect of the N1010K mutation withregard to the function of the NOD2 protein and the genetic risk of CD.Moreover, N1010Kand L1007fs as a compound heterozygous state in two, more severe CD family membersstrongly suggests that N1010K could be a new risk factor involved in Crohn’s disease geneticsusceptibility.In addition to the characterization of a new rare mutation of the NOD2 gene, 2 otherpotential variants have been identified : the D359H and G33V mutations, respectively, inthe BPIFB2 and DEFB132 genes. The proteins encoded by these genes are involved in thesame pathways : the pathway of defensins and the pathway of the innate immune system.In silico evaluation of the deleterious effect of mutations revealed a potential deleteriouseffect of D359H and G33V mutations. Thus, we could hypothesize that although the two mutations D359H and G33V are located on two different genes but involved in the same signaling pathways, they could act together and determine a cumulative dysfunctional effect also involved as determinants of the familial aggregation of Crohn’s disease in family F49M.Thus, for the F49M family, familial aggregation could be based on the accumulation of several deleterious mutations (N1010K, D359H and G33V).

The inflammatory bowel diseases (IBD) are chronic, relapsing and remitting diseases of the gastrointestinal tract. There are two main types of IBD: Crohn’s disease (CD) and ulcerative colitis (UC). The prevalence of IBD is highest in the western world, approximately 100-200 people per 100,000 are affected. In recent years there has been a marked increase in the incidence of CD and UC, in both adults and children (Henderson et al., 2012; Molodecky et al., 2012). This is particularly relevant in Scotland where recent research shows that there has been a 79% increase in the number of cases of paediatric IBD since the 1990’s (Henderson et al., 2012). A yeast 2 hybrid screen identified TLE1as an interacting partner of the known CD susceptibility gene; Nucleotide- binding oligomerisation protein 2 (Nod2). An initial genome wide association study (GWAS) also found an association between the rs6559629 SNP, located in Tle1 and ileal CD (p =3.1 x 10-5) and showed that carriage of the Tle1 risk allele increases the effects of Nod2 mutations in CD. TLE1 functions as a transcriptional co repressor in a variety of different cellular and developmental pathways The work presented in this thesis investigates the potential role of TLE1 in CD. This has been approached using four different strategies: sequencing TLE1 in CD patients and controls, analysing the effects of knocking down TLE1 on genome wide expression, investigating whether the known IBD susceptibility protein XBP1 binds to a predicted binding site in TLE1 and investigating TLE1 levels and localisation in human intestinal samples from CD patients and controls Sequencing TLE1 exons and introns 15/16 and 16/17 in a Scottish cohort of 24 CD patients and healthy controls identified a number of potentially pathogenic exonic and intronic SNPs. Two exonic SNPs and thirteen intronic SNPs were identified and these were further investigated in larger Scottish (203 CD cases, 190 HC) and European cohorts (6,333 CD cases and 15,056 HC) but were not present at statistically significantly different frequencies. Secondly, the effects of TLE1 knock down on genome wide expression were analysed using an Illumina HT12 expression chip. The results showed that TLE1 knock down significantly altered expression of 19 loci (Bonferroni) and 526 loci (FDR). Four of the 19 Bonferroni significant loci are potentially involved in CD: RIOK1 (p=4.3×10-3), SGPL1 (p=4.3×10-3), TUSC3 (p=1.8×10-2) and CCND1 (p=2.7×10-3). Furthermore, expression of SGPL1 and RIOK1 were shown to be differentially expressed at the mRNA level between inflamed patients and controls. The third approach investigates a predicted binding site for the known IBD susceptibility gene, XBP1 in TLE1 which was identified using the Haploreg program. This work shows, using chromatin immunoprecipitation, that exogenous XBP1 does not appear to bind to this predicted binding site. Finally, TLE1 expression was analysed in human intestinal resection samples from patients of known NOD2 status. This work shows that TLE1 and NOD2 are expressed in Paneth cells, however TLE1 expression is not altered in patients carrying CD associated NOD2 variants. In this work TLE1 sequence, expression and potential interacting proteins have been analysed. The results presented suggests multiple mechanisms by which TLE1 may be influencing susceptibility to CD including: the unfolded protein response (TUSC3), S1P signalling and ribosome biogenesis. They also implicate TLE1 in Paneth cell function alongside NOD2. The exact means by which TLE1 may play a role in IBD pathogenesis has yet to be fully elucidated.

Trichuris trichiura (T. Trichiura) is a large-intestinal dwelling nematode that affects over 1 billion people world-wide and thus has large global significance. Much of our understanding of T. trichiura infection comes from the study of the mouse model Trichuris muris (T. muris). However, how the immune system is initiated in response to helminth threat and how inflammation and pathology are resolved in T. muris infection still remain to be addressed. Here, I have attempted to provide insight into these questions. Previous work has shown resistance to T. muris infection is associated with the rapid recruitment of dendritic cells (DCs) to the colonic epithelium via epithelial production of CCL5 and CCL20. However, the epithelial-parasite interaction that drives chemokine production is not known. Pattern recognition receptor (PRRS) are critical mediators of pathogen recognition but there is no known (PRR) specific for T. muris. Here, we address the role of the cytosolic pattern recognition receptor Nod2, the location of which within the crypts correlates with the T. muris niche. In WT mice, in response to infection, there was a rapid influx of CD103+CD11c+ DCs into the colonic epithelium, whereas, this recruitment was impaired in Nod2 /- animals. In vitro and in vivo experiments confirmed the impairment in DC recruitment in Nod2-/- mice was attributable to the epithelial compartment. Subsequent work revealed decreased production of epithelial chemokines in the absence of functional Nod2. Thus, we have shown a novel role for Nod2 in the initiation the immune response to T. muris. We next addressed how pathology is regulated during T. muris infection. Firstly we investigated the role of arginase and Arg1-expressing macrophages in regulating pathology. My data showed that, unlike other gastrointestinal helminths, arginase and Arg1-expressing macrophages are not essential for resistance to T. muris or effective resolution of helminth-induced inflammation. I also addressed the role of DCs in the resolution of infection. DCs can regulate immune responses via the anti-inflammatory cytokine IL-10 and induction of regulatory T cells (Treg). I used an IL 10flox/floxCD11cCre transgenic model in which mice have DCs that cannot make IL-10. I found no role for CD11c+ cell mediated IL-10 production in the regulation of pathogen induced pathology in chronic T. muris infection. In summary I have been able to identify factors in the initiation of immunity to T. muris namely epithelial expression of Nod2. However, as arginase, Arg1-expressing macrophages and DC derived IL-10 appeared to play a redundant role in T. muris infection, the question as to how infection induced inflammation is resolved remains elusive.