Introduction : La maladie de Crohn (MC), maladie inflammatoire chronique intestinale, est une maladie multifactorielle, d’origine inconnue. La dysbiose bactérienne a été largement évoquée dans la pathogénèse de la MC. Notre objectif était de caractériser la flore fongique, conjointement à la flore bactérienne au cours de formes familiales de MC.Méthodes: Nous avons utilisé une plateforme de séquençage à haut débit pour caractériser la flore fongique et bactérienne fécale, échantillonnée dans 9 familles multiplexes atteints de MC (20 patients, et 28 sujets sains apparentés), et 4 familles contrôles (21 individus sains non apparentés). Une analyse bioinformatique a été réalisée pour analyser l’abondance, la biodiversité, et les interactions microbiennes.Résultats : Le microbiote fécal des membres issus des familles multiplexes était statistiquement différent de celui des membres issus des familles contrôles. L’analyse en composantes principales a montré qu’au sein des familles multiplexes, les membres malades et sains partageaient un répertoire fongique commun. Les patients MC avaient en revanche un microbiote enrichi en Candida tropicalis, Escherichia coli et en Serratia marcescens, et appauvri en bactéries dites bénéfiques (Faecalibacterium prausnitzii). De plus les taux d’ASCA (Anticorps anti- S. cerevisiae), marqueur sérologique de MC étaient corrélées à la présence de C. tropicalis (P = .01). Enfin nous avons mis en évidence une synergie entre C. tropicalis, E. coli, et S. marcescens, suggérant une interaction microbienne in vivo participant à l’initiation de l’inflammation intestinale. Ces données ont été validées par la suite avec un modèle de biofilm.Conclusion : Dans ces formes familiales de MC, les interactions microbiennes entre bactéries et champignons sont déterminantes dans l’initiation de la réponse inflammatoire. / Introduction: Crohn's disease (CD) results from a complex interplay between host genetic factors and endogenous microbial communities.Methods: In the current study, we used Ion Torrent sequencing to characterize the gut bacterial microbiota (bacteriome) and fungal community (mycobiome) in patients with CD and their non-diseased first degree relatives (NCDR) in 9 familial clusters living in Northern France/Belgium, and in healthy individuals from 4 families living in the same area (non-CD unrelated, NCDU). Principal components analysis, diversity, and abundance analyses were conducted and CD-associated inter- and intra-kingdom microbial correlations determined. Significant microbial interactions were identified and validated using single- and mixed-species biofilms.Results: CD and NCDR groups clustered together in the mycobiome, but not in bacteriome. Microbiota of familial (CD, NCDR) samples were distinct from that of non-familial (NCDU) samples. Abundance of Serratia marcescens (SM), Escherichia coli (EC) was elevated in CD patients, while that of beneficial bacteria was decreased. Abundance of the fungus Candida tropicalis (CT) was significantly higher in CD compared to NCDR (P = .003), and positively correlated with levels of anti–Saccharomyces cerevisiae antibody (ASCA). Abundance of CT was positively correlated with SM and EC, suggesting these organisms interact in the gut. The mass and thickness of Triple species (CT+SM+EC) biofilm were significantly higher than single and double species biofilm. CT biofilms comprised of blastospores, while double and triple species biofilms were enriched in hyphae. SM used fimbriae to co-aggregate or attach with CT/EC, while EC closely apposed with CT. Conclusion: Specific inter-kingdom microbial interactions may be key determinants in CD.

<p>The aim of this thesis was to investigate health-related quality of life (HRQoL) and coping strategies for individuals with ulcerative colitis (UC) or Crohn’s disease (CD), and to study the effect of a group-based patient information on anxiety/depression and HRQoL. HRQoL and anxiety/depression were investigated (n=492) (Study I). In Study II, anxiety/depression, HRQoL, satisfaction with information and evaluation of the patient information were studied (n=49). Coping with disease activity was investigated in 166 patients reporting current exacerbation (Study III). Fifteen patients were interviewed about disease-related stress, how this is managed and the need of support from the health care (Study IV). Patients with UC reported better HRQoL and less anxiety/depression than did patients with CD during both remission and exacerbation. Satisfaction with information had increased at follow-up 6 months after patient information. The information and the possibility to discuss with lecturers and group members were valued as most important. No change was found in anxiety/depression or HRQoL at follow-up. Both problem-focused and emotion-focused strategies were employed to cope with disease activity, with no difference between patients with UC or CD. The urgent need of toilet availability and stress associated to social situations were the major disease-related stressors. This stress was managed by finding out the location of toilets, bringing toilet paper and extra underwear and emptying bowel before an activity. The patients wanted information and possibilities to talk to experienced staff and to other patients about how to live with the disease. This thesis shows that HRQoL for some patients with UC, and primarily for patients with CD, is impaired. Thus medical staff should be observant of the psychosocial well-being of patients with CD and also of patients with relapse. Methods to identify and support patients with anxiety/depression and poor HRQoL need to be developed. Interventions should target the patient’s specific problems and at appropriate times.</p>

The aim of this thesis was to investigate health-related quality of life (HRQoL) and coping strategies for individuals with ulcerative colitis (UC) or Crohn’s disease (CD), and to study the effect of a group-based patient information on anxiety/depression and HRQoL. HRQoL and anxiety/depression were investigated (n=492) (Study I). In Study II, anxiety/depression, HRQoL, satisfaction with information and evaluation of the patient information were studied (n=49). Coping with disease activity was investigated in 166 patients reporting current exacerbation (Study III). Fifteen patients were interviewed about disease-related stress, how this is managed and the need of support from the health care (Study IV). Patients with UC reported better HRQoL and less anxiety/depression than did patients with CD during both remission and exacerbation. Satisfaction with information had increased at follow-up 6 months after patient information. The information and the possibility to discuss with lecturers and group members were valued as most important. No change was found in anxiety/depression or HRQoL at follow-up. Both problem-focused and emotion-focused strategies were employed to cope with disease activity, with no difference between patients with UC or CD. The urgent need of toilet availability and stress associated to social situations were the major disease-related stressors. This stress was managed by finding out the location of toilets, bringing toilet paper and extra underwear and emptying bowel before an activity. The patients wanted information and possibilities to talk to experienced staff and to other patients about how to live with the disease. This thesis shows that HRQoL for some patients with UC, and primarily for patients with CD, is impaired. Thus medical staff should be observant of the psychosocial well-being of patients with CD and also of patients with relapse. Methods to identify and support patients with anxiety/depression and poor HRQoL need to be developed. Interventions should target the patient’s specific problems and at appropriate times.

Malignant tumours of the small intestine are rare. Age-standardised incidence in Europe is between 0.5-1.5 per 100 000. As the small intestine represents more than 90 % of the gastrointestinal mucosal surface, it is surprising that it gives rise to less than 2 % of gastrointestinal malignancies. The dominating histological subtypes are carcinoids and adenocarcinomas. We used three population-based registries in Sweden to study survival, second malignant tumours, causes of death, and Crohn’s disease as a risk factor for small intestinal adenocarcinoma and carcinoid. We evaluated tumour site, sex, age, and year of diagnosis as prognostic factors. For adenocarcinomas there was no difference in survival between duodenal and jejunal/ileal tumours. Women with jejunal/ileal adenocarcinomas showed higher probabilities of survival than men, while no such relation was found for duodenal tumours. Old age correlated with poor survival for duodenal tumours, and prognosis has improved in later years. For carcinoids, duodenal tumours had a more favourable prognosis than jejunal/ileal tumours. There was no difference in survival between sexes. Old age correlated with poor survival, and survival has improved in recent years. Female patients with adenocarcinoma had increased risk of acquiring cancer in the genital organs and breasts, and both sexes had increased risks of second tumours in the gastrointestinal tract and skin. Men with carcinoid tumours had increased risk of prostate cancer. Both sexes had increased risk of malignant melanoma and malignancies of endocrine organs. Patients with adenocarcinoma had increased risk of dying from malignant diseases other than the primary small intestinal cancer and from gastrointestinal disease. The cohort with carcinoid had higher than expected risk of dying from malignant disease, gastrointestinal disease, and cardiovascular disease. Patients with Crohn’s disease had increased risk of small intestinal adenocarcinoma and carcinoid, and the risk has increased for patients diagnosed in recent years.

Genome-wide association studies have implicated autophagy in Crohn’s Disease (CD) pathogenesis. The functional relevance of autophagy in CD remains unknown. I hypothesized that autophagy is involved in microRNA silencing, another process implicated in CD pathogenesis. MicroRNAs are short non-coding RNAs that are loaded onto RNA-induced silencing complex (RISC) and promote degradation and/or repress translation of target mRNAs. RISC formation and turnover occurs on endosomal membranes. Since autophagosomes and endosomes are closely related and RISC components are downstream effectors of microRNA silencing, I hypothesized that autophagy affects RISC, hence modulates microRNA expression. Using immunoblotting and immunofluorescence, I showed that Ago2, a critical component of RISC, is increased in cells with defective autophagy. Using microarray technology, I discovered 5 microRNAs that are differentially expressed in these cells. Taken together, my results propose a compelling mechanism by which autophagy regulates Ago2, thereby affects miRNA expression, which is implicated in the development of CD.

Genome-wide association studies have implicated autophagy in Crohn’s Disease (CD) pathogenesis. The functional relevance of autophagy in CD remains unknown. I hypothesized that autophagy is involved in microRNA silencing, another process implicated in CD pathogenesis. MicroRNAs are short non-coding RNAs that are loaded onto RNA-induced silencing complex (RISC) and promote degradation and/or repress translation of target mRNAs. RISC formation and turnover occurs on endosomal membranes. Since autophagosomes and endosomes are closely related and RISC components are downstream effectors of microRNA silencing, I hypothesized that autophagy affects RISC, hence modulates microRNA expression. Using immunoblotting and immunofluorescence, I showed that Ago2, a critical component of RISC, is increased in cells with defective autophagy. Using microarray technology, I discovered 5 microRNAs that are differentially expressed in these cells. Taken together, my results propose a compelling mechanism by which autophagy regulates Ago2, thereby affects miRNA expression, which is implicated in the development of CD.

The overall aims of this thesis were to investigate the incidence of inflammatory bowel disease in the Uppsala Region of Sweden, to study the clinical course and the impact of the disease with regards to complications. Patients in Uppsala County were included in the study from the 1st of January 2005 and patients in Falun, Eskilstuna and Åland counties from the 1st of January 2007. The study was closed for all centres on the 31st of December 2009. Mean population in the study region was 305,381 in 2005–2006 and 642,117 in 2007–2009. The mean incidence for ulcerative colitis (UC) during the time period 2005-2009 was 20.0 /100,000/year (95% CI: 16.1-23.9) and for Crohn’s disease (CD) it was 9.9/100,000/year (95% CI: 7.1-12.6). The combined incidence for UC or CD in the area was thus 29.9/100,000/year (95% CI: 25.1-34.7). Half of the UC patients relapsed during the first year. Risk factors for relapse were female gender and young age. Colectomy during the first year was uncommon (2.5%). CD patients with complicated disease had longer symptom duration before diagnosis and less often diarrhoea and blood in stools compared to patients with non-complicated disease. The risk for surgery during the first year was 12%. The prevalence of anaemia at the time of diagnosis was 30% and after one year 18%. Anaemia was more common among newly diagnosed patients with CD compared with UC. 13% of the UC patients developed an acute severe episode. During the first 90 days 22% of these patients were subjected to colectomy. There was a significant difference between University and County hospitals in colectomy frequency (7.5% vs. 41%). The cumulative prevalence of treatment complications was 12% at the hospital with low colectomy rate versus 41% at the hospitals with high colectomy rate. In conclusion, the incidence of UC and CD in Sweden was high compared to international studies. Colectomy frequency for UC during the first year was low. Patients with complicated CD at the time of diagnosis had longer symptom duration and less alarming symptoms compared to uncomplicated disease. Anaemia was a common trait among patients with newly diagnosed IBD and more effort is needed to treat anaemia in these patients. Severe UC can be treated safely with prolonged medical therapy instead of colectomy.

This thesis investigated the number and function of natural killer T-cells (NK T-cells) as a function of age, in coeliac disease, Crohn’s disease and ulcerative colitis. NK T-cells are a newly appreciated class of immune cells that are able to regulate the activity of the broader T-cell population. NK T-cells have been implicated in animal models of autoimmune disease and in human autoimmune disease. A subset of NK cells express the T-cell receptor (TCR) and are termed NK T-cells. In humans a further small subset of NK T-cells express an invariant TCR α chain (Vα24Jα18) and contain the immunoregulatory cell population that is distinguished from classical T-cells by promptly producing interleukin-4 (IL-4). Invariant NK T-cells (iNK T-cells) have the surface phenotype of Vα24+ Vβ11+ T-cells and express CD161+ NK markers. They are CD4+ (single positive; SP) or CD4- (double negative; DN), CD1d restricted and are α-galactosylceramide (α-GalCer) reactive. NKT cells have been implicated in numerous autoimmune disorders. Early work showed a major deficiency of NKT cell numbers in nonobese diabetic (NOD) mice, a well-established model of spontaneous, autoimmune T-cell mediated insulin-dependent diabetes. Both the number of NKT cells and function, as assessed by IL-4 release following TCR ligation, are dramatically reduced in NOD mice. NK T-cells have been implicated in other models of autoimmunity such as, experimental allergic encephalomyelitis (EAE). They have since been investigated and shown to be deficient in a number of human autoimmune diseases including, systemic sclerosis (SSc), and systemic lupus erythematosus (SLE), multiple sclerosis, atopic asthma, atopic dermatitis, rheumatoid arthritis, type 1 diabetes mellitus and scleroderma. The basis of the work presented within this thesis originated from the deficiency of NK T-cells in models of autoimmune diseases and human autoimmune diseases. The initial aim of this thesis was to investigate the phenotype and function of Vα24+ NK T-cells in normal healthy control subjects and with respect to age. The original aim was to investigate whether NK cells, T-cells, NK T-like cells and invariant NK T-cells (iNK T-cells) are deficient in coeliac disease, Crohn’s disease and/or ulcerative colitis. Blood was collected for flow cytometry from normal control subjects, subjects with coeliac disease, Crohn’s disease and ulcerative colitis. The number of circulating NK cells, T-cells, NK T-like cells and iNK T-cells was assessed by three-colour flow cytometry. Intracellular cytokine production was measured after in vitro anti-CD3/ anti-CD28 antibodies, gluten fraction 3 and PMA:ionomycin stimulation. Vα24+ T-cells were quantified in ileocolonic biopsies by immunofluorescence and as mRNA by relative and real-time PCR (RT-PCR). The number of circulating Vα24+ T-cells and iNK T-cells decrease with age in normal healthy control subjects. Cytokine production was also affected by age. The work of this thesis has identified a subpopulation of otherwise normal healthy individuals whom have normal numbers of circulating Vα24+ T-cells, reduced numbers of circulating Vα24+ Vβ11+ T-cells and consequently iNK Tcells. Circulating CD161+ NK cells, Vα24+ T-cells and the SP subset of Vα24+ Tcells were reduced in coeliac disease. The low numbers of circulating Vα24+ T-cells was independent of diet. The number of circulating Vα24+ Vβ11+ Tcells were reduced in coeliac disease, and as a consequence, the number of circulating Vα24+ Vβ11+ α-GalCer/CD1d tetramer+ and Vα24+ 6B11+ iNK T-cells were reduced. The deficiency of Vα24+ T-cells was not confined to the blood, but observed within the intestinal mucosa. Intestinal Vα24 mRNA expression from subjects with coeliac disease was reduced compared to levels in normal subjects as assessed by relative and RT-PCR. Thus, Vα24+ T-cells were deficient in coeliac disease both systemically and mucosally. Cytokine production by Vα24+ T-cells, 6B11+ and Vα24+ α-GalCer/CD1d tetramer+ iNK T-cells after 4 h in vitro anti-CD3 stimulation was also impaired in subjects with coeliac disease. Circulating CD56+, CD57+, CD94+, CD161+ NK cells were reduced in Crohn’s disease and ulcerative colitis. Vα24+ T-cells and the SP subset of Vα24+ T-cells were reduced in Crohn’s disease but not in ulcerative colitis. Circulating Vα24+ Vβ11+ T-cells, Vα24+ Vβ11+ α-GalCer/CD1d tetramer+ and Vα24+ 6B11+ iNK T-cells were deficient in both Cohn’s disease and ulcerative colitis. The deficiency of Vα24+ T-cells was also observed within the intestinal mucosa. Intestinal Vα24 mRNA expression from Crohn’s disease and ulcerative colitis was reduced compared to levels in normal subjects as assessed by relative and RT-PCR. Cytokine production by Vα24+ T-cells, 6B11+ and Vα24+ α-GalCer/CD1d tetramer+ iNK T-cells after 4 h in vitro anti-CD3 stimulation was impaired for subjects with Crohn’s disease and ulcerative colitis. In summary, Vα24+ T-cell number and function were affected by age. Further investigations are warranted to see if deficiency of this immunoregulatory population is associated with disease. The decrease and dysfunction in immunoregulatory cells, Vα24 T-cells and iNK T-cells could contribute to the pathogenesis of coeliac disease, Crohn’s disease and ulcerative colitis. Coeliac disease, Crohn’s disease and ulcerative colitis are polygenetic diseases in which environmental factors play a significant role in disease development and state. The reduced numbers of iNK T-cell along with their impaired function may only be two factors. Presumably, other factors are involved. Nevertheless, iNK T-cells offer a potential target for the therapeutic intervention of coeliac disease, ulcerative colitis and Crohn’s disease. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1345088 / Thesis (Ph.D.) - University of Adelaide, School of Medicine, 2008

This thesis investigated the number and function of natural killer T-cells (NK T-cells) as a function of age, in coeliac disease, Crohn’s disease and ulcerative colitis. NK T-cells are a newly appreciated class of immune cells that are able to regulate the activity of the broader T-cell population. NK T-cells have been implicated in animal models of autoimmune disease and in human autoimmune disease. A subset of NK cells express the T-cell receptor (TCR) and are termed NK T-cells. In humans a further small subset of NK T-cells express an invariant TCR α chain (Vα24Jα18) and contain the immunoregulatory cell population that is distinguished from classical T-cells by promptly producing interleukin-4 (IL-4). Invariant NK T-cells (iNK T-cells) have the surface phenotype of Vα24+ Vβ11+ T-cells and express CD161+ NK markers. They are CD4+ (single positive; SP) or CD4- (double negative; DN), CD1d restricted and are α-galactosylceramide (α-GalCer) reactive. NKT cells have been implicated in numerous autoimmune disorders. Early work showed a major deficiency of NKT cell numbers in nonobese diabetic (NOD) mice, a well-established model of spontaneous, autoimmune T-cell mediated insulin-dependent diabetes. Both the number of NKT cells and function, as assessed by IL-4 release following TCR ligation, are dramatically reduced in NOD mice. NK T-cells have been implicated in other models of autoimmunity such as, experimental allergic encephalomyelitis (EAE). They have since been investigated and shown to be deficient in a number of human autoimmune diseases including, systemic sclerosis (SSc), and systemic lupus erythematosus (SLE), multiple sclerosis, atopic asthma, atopic dermatitis, rheumatoid arthritis, type 1 diabetes mellitus and scleroderma. The basis of the work presented within this thesis originated from the deficiency of NK T-cells in models of autoimmune diseases and human autoimmune diseases. The initial aim of this thesis was to investigate the phenotype and function of Vα24+ NK T-cells in normal healthy control subjects and with respect to age. The original aim was to investigate whether NK cells, T-cells, NK T-like cells and invariant NK T-cells (iNK T-cells) are deficient in coeliac disease, Crohn’s disease and/or ulcerative colitis. Blood was collected for flow cytometry from normal control subjects, subjects with coeliac disease, Crohn’s disease and ulcerative colitis. The number of circulating NK cells, T-cells, NK T-like cells and iNK T-cells was assessed by three-colour flow cytometry. Intracellular cytokine production was measured after in vitro anti-CD3/ anti-CD28 antibodies, gluten fraction 3 and PMA:ionomycin stimulation. Vα24+ T-cells were quantified in ileocolonic biopsies by immunofluorescence and as mRNA by relative and real-time PCR (RT-PCR). The number of circulating Vα24+ T-cells and iNK T-cells decrease with age in normal healthy control subjects. Cytokine production was also affected by age. The work of this thesis has identified a subpopulation of otherwise normal healthy individuals whom have normal numbers of circulating Vα24+ T-cells, reduced numbers of circulating Vα24+ Vβ11+ T-cells and consequently iNK Tcells. Circulating CD161+ NK cells, Vα24+ T-cells and the SP subset of Vα24+ Tcells were reduced in coeliac disease. The low numbers of circulating Vα24+ T-cells was independent of diet. The number of circulating Vα24+ Vβ11+ Tcells were reduced in coeliac disease, and as a consequence, the number of circulating Vα24+ Vβ11+ α-GalCer/CD1d tetramer+ and Vα24+ 6B11+ iNK T-cells were reduced. The deficiency of Vα24+ T-cells was not confined to the blood, but observed within the intestinal mucosa. Intestinal Vα24 mRNA expression from subjects with coeliac disease was reduced compared to levels in normal subjects as assessed by relative and RT-PCR. Thus, Vα24+ T-cells were deficient in coeliac disease both systemically and mucosally. Cytokine production by Vα24+ T-cells, 6B11+ and Vα24+ α-GalCer/CD1d tetramer+ iNK T-cells after 4 h in vitro anti-CD3 stimulation was also impaired in subjects with coeliac disease. Circulating CD56+, CD57+, CD94+, CD161+ NK cells were reduced in Crohn’s disease and ulcerative colitis. Vα24+ T-cells and the SP subset of Vα24+ T-cells were reduced in Crohn’s disease but not in ulcerative colitis. Circulating Vα24+ Vβ11+ T-cells, Vα24+ Vβ11+ α-GalCer/CD1d tetramer+ and Vα24+ 6B11+ iNK T-cells were deficient in both Cohn’s disease and ulcerative colitis. The deficiency of Vα24+ T-cells was also observed within the intestinal mucosa. Intestinal Vα24 mRNA expression from Crohn’s disease and ulcerative colitis was reduced compared to levels in normal subjects as assessed by relative and RT-PCR. Cytokine production by Vα24+ T-cells, 6B11+ and Vα24+ α-GalCer/CD1d tetramer+ iNK T-cells after 4 h in vitro anti-CD3 stimulation was impaired for subjects with Crohn’s disease and ulcerative colitis. In summary, Vα24+ T-cell number and function were affected by age. Further investigations are warranted to see if deficiency of this immunoregulatory population is associated with disease. The decrease and dysfunction in immunoregulatory cells, Vα24 T-cells and iNK T-cells could contribute to the pathogenesis of coeliac disease, Crohn’s disease and ulcerative colitis. Coeliac disease, Crohn’s disease and ulcerative colitis are polygenetic diseases in which environmental factors play a significant role in disease development and state. The reduced numbers of iNK T-cell along with their impaired function may only be two factors. Presumably, other factors are involved. Nevertheless, iNK T-cells offer a potential target for the therapeutic intervention of coeliac disease, ulcerative colitis and Crohn’s disease. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1345088 / Thesis (Ph.D.) - University of Adelaide, School of Medicine, 2008

Thesis (Ph.D.) - University of Glasgow, 2009. / Ph.D. thesis submitted to the Division of Developmental Medicine, Faculty of Medicine, University of Glasgow, 2009. Includes bibliographical references. Print version also available.