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A series of investigations examining the importance of genetic factors in the development of the inflammatory bowel diseases (IBD) namely Crohn’s disease (CD), Ulcerative Colitis (UC) and Indeterminate Colitis (IC) has been undertaken in Scottish children. This has been performed by collection of clinical details and DNA from children with IBD, then analysing the contribution of various candidate genes to both disease susceptibility and disease phenotype. In order to carry out these studies the presenting features of a large cohort of children from across Scotland with IBD diagnosed at less than 16 years were collected, both by examination of hospital case records and by patient interview and questionnaire. For each patient a detailed analysis was made of disease phenotype at presentation including detailed examination of disease location, disease behaviour and growth parameters. A repository of clinical material (DNA, plasma and lymphocytes) was collected from children to accompany the detailed clinical parameters allowing genotype-phenotype analysis at a later stage. Additionally, DNA was also collected from parents where possible to facilitate family based association analysis of candidate genes by transmission disequilibrium testing. A previous DNA repository of healthy Scottish controls had been collected previously and the data generated was available for use in this study. The phenotypic data was collected using an established phenotypic classification (the Vienna classification) used in adult studies as well as a personally devised paediatric phenotypic classification designed for use in this thesis. Firstly, the contribution of the three common mutations within the NOD2/CARD15 gene (R702W, G908R and Leu1007finsC) was analysed in 247 children with IBD. The Leu1007finsC variant was associated with Crohn’s disease by case-control (p = 0.01) and TDT analysis (p = 0.006). Genotype phenotype analysis demonstrated NOD2/CARD15 variants were strongly associated with several markers of disease severity in CD most notably with an increased need for surgery on multifactorial analysis. Then to examine the further contribution of other mutations within the whole NOD2/CARD15 gene, the 12 exons of the gene were sequenced in 24 paediatric CD patients, to identify any additional SNPs that may have conferred an increased susceptibility to CD. Two mutations (V955I, M863V) identified in xii sequencing were genotyped in a large patient cohort, but were not found to confer increased disease susceptibility. Next, the contribution of IBD5 locus was analysed in 299 children with IBD studying 5 SNPs, including mutations in the proposed candidate genes OCTN 1 and 2. Allele frequencies of OCTN1/2 variants were significantly higher in IBD/CD cases (p<0.04). The homozygous mutant OCTN1/2 haplotype was increased in IBD and UC patients (p = 0.02 for both) compared to healthy controls. OCTN1/2 variants however were not independent of the background IBD5 risk haplotype in conferring disease susceptibility. Genotype- phenotype analysis demonstrated association of the risk haplotype with both lower weight and body mass index centiles at diagnosis as analysed by multifactorial analysis. The contribution of the 113 G/A mutation within the discs, large homolog 5 (DLG5) gene was examined in 296 children with IBD. TDT analysis demonstrated a significant association with IBD (p<0.05). Genotype-phenotype analysis demonstrated associations with higher social class, male sex and taller children. Finally, the Anti-Saccharomyces cerevisiae antibodies (ASCA) status of 301 IBD patients was determined. CD patients had a higher prevalence of ASCA antibodies compared to UC patients and healthy controls (p<0.001 for both). A positive ASCA antibody was more common in CD patients with markers of more severe disease and on multifactorial analysis in patients with CD involvement of the oral cavity (p = 0.001). In summary, the candidate genes examined thus far in children with IBD in Scotland have demonstrated a relatively minor contribution to disease susceptibility but have been demonstrated to be associated with specific disease phenotypes in patients with Crohn’s disease. The use of a novel paediatric phenotypic classification in this thesis has allowed description of these novel genotype-phenotype associations.

Inflammatory Bowel Diseases, Crohn's Disease and Ulcerative colitis, are idiopathic chronic conditions with multifactorial determinants. In general, terms, intestinal inflammation results from abnormal host-microbe interactions. Alterations in homeostasis involve host genetic factors, environmental cues and unique luminal microbial niches. We have examined the coordinated expressions of several molecular targets relevant to the mucosal immune system and identified signature biomarkers of IBD. Qualitative and quantitative changes in the composition of microbiota can be related to unique immuno-phenotypes. This in turn can have more systemic effects that involve energy metabolism. Adiponectin, an adipose tissue derived adipokine, can restore cellular ATP levels and fulfills innate immune functions. We have concluded that IBD might represent a state of adiponectin resistance relating to chronic inflammation and obesity status. Lastly we hypothesized that activation of xenobiotic pathway (AHR-aryl hydrocarbon receptor) can further modulate host immune and metabolic responses, and thus contribute to IBD phenotypes. We found that IBD is associated with robust mucosal, aryl hydrocarbon receptor pathway and related to proinflammatory cytokine secretion. We conclude that IBD heterogeneity is reflected through distinct immunophenotypes. Furthermore, environmental cues that involve the AhR receptor and adipose tissue derived adiponectin are important regulators of the inflammatory process in IBD.

Substituted tetrazines have been found to undergo facile inversed electron demand Diels-Alder reactions with “tunable” reaction rates. By varying the substituents on tetrazine, cycloaddition rate variations of over 200 fold have been achieved with the same dienophile. Coupled with the availability of different dienophiles, such as norbornene, the reaction rate difference can be over 14,000 folds. These substituted tetrazines can be very useful for selective labeling under different conditions. This finding paves the way to utilize tetrazine conjugation reactions for not only DNA but also stage labeling work. Carbon monoxide (CO) belongs to the gasotransmitter family of signalling molecules in the mammalian systems with importance on par with that of NO and H2S. Studies have shown that endogenous production of CO has anti-inflammatory, anti-proliferative, and anti-apoptotic effects in mammalian system. Besides of the conventional metal-based carbon monoxide releasing molecules (CORMs) to deliver CO for therapeutic purposes, organic CO prodrugs represent a new direction. Here we report the “click and release” approached to release CO. Unlike the metal-based CORMs, our system does not contain transition metal and liberates CO with controllable manner and possesses potential tunable releasing rate property under physiological conditions.

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.

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder that occurs as a consequence of a genetic mutation that results in an overly aggressive immune response to normal bacteria. Metabolomics is a new born cousin to genomics and proteomics and involves a high throughput identification, characterization and quantification of small molecule metabolites generated by the organism. This study will show that metabolomics can be an effective tool in studying the differences between wild type and IL 10 KO mice as they age in axenic and conventional environments, and the onset of disease in a conventional environment. I show specific changes upon colonizing axenic mice with fecal bacteria that are similar to changes occurring over 16 weeks of conventional growth. Several bacterial metabolites have been identified that may play a role in the pathogenesis or provide clues to the interactions of the gut microbiota with the intestinal immune system. / Experimental Medicine

Abstract Nutritional status affects every aspect of a child?s health. Thorough nutritional assessment is hampered by the lack of a single comprehensive tool, which can cover all aspects of nutritional assessment. In three distinct studies, this thesis investigated the nutritional status of hospitalised children, children with coeliac disease and children with inflammatory bowel disease. Study 1 The objectives of this study were to assess prevalence of malnutrition and nutritional risk, and define demographic and anthropometric factors associated with nutritional risk among hospitalized children. In this cross sectional study, 157 hospitalised children were assessed for nutritional status using nutritional risk score (NRS) and anthropometric measurements. We found that 4.5%, 8.9%, 15.1% and 10.4% children were wasted, stunted, overweight and obese respectively. However, with the NRS, 47.8% of the children were at high nutritional risk. These children at high risk had lower weight for age (p=0.02), lower BMI percentiles for age (p=0.001) and longer hospitalization (p=0.001) than children at no risk. Study 2 The objectives of this study were to determine nutritional parameters in children with coeliac disease. Twenty-five children with coeliac disease and an equal number of age and gender matched controls were enrolled and anthropometric measurements, BIA and leptin levels were analysed in all. No significant differences were found between the children with coeliac disease and controls in these parameters. BMI percentile correlated with leptin levels in children with coeliac disease. Study 3 The objectives of this study were to determine anthropometric parameters and leptin levels in children with IBD and ascertain if BMI correlates with leptin levels in these children. Thirty children with IBD and 60 age and gender matched controls were enrolled. Anthropometric measurements and leptin levels were analysed and compared with controls. IBD children had significantly low weight for age (p=0.002), BMI percentiles (p=0.001) and leptin levels (p=0.009) compared to controls. There was a correlation between BMI and leptin levels in IBD children. In conclusion, this thesis has shown that one quarter of hospitalized children were overweight or obese, and further, that half of the hospitalised children were at high risk of nutritional deterioration and these children had longer hospital stay than children at no risk. Children with coeliac disease had similar anthropometric measurements, body compartments and leptin levels to controls. However, children with IBD had lower anthropometric measurements and leptin levels, indicating under-nutrition. Nutritional assessment should be a mandatory part of clinical management with nutritional status assessed by various tools including NRS, anthropometry, BIA and leptin levels.

Abstract Nutritional status affects every aspect of a child?s health. Thorough nutritional assessment is hampered by the lack of a single comprehensive tool, which can cover all aspects of nutritional assessment. In three distinct studies, this thesis investigated the nutritional status of hospitalised children, children with coeliac disease and children with inflammatory bowel disease. Study 1 The objectives of this study were to assess prevalence of malnutrition and nutritional risk, and define demographic and anthropometric factors associated with nutritional risk among hospitalized children. In this cross sectional study, 157 hospitalised children were assessed for nutritional status using nutritional risk score (NRS) and anthropometric measurements. We found that 4.5%, 8.9%, 15.1% and 10.4% children were wasted, stunted, overweight and obese respectively. However, with the NRS, 47.8% of the children were at high nutritional risk. These children at high risk had lower weight for age (p=0.02), lower BMI percentiles for age (p=0.001) and longer hospitalization (p=0.001) than children at no risk. Study 2 The objectives of this study were to determine nutritional parameters in children with coeliac disease. Twenty-five children with coeliac disease and an equal number of age and gender matched controls were enrolled and anthropometric measurements, BIA and leptin levels were analysed in all. No significant differences were found between the children with coeliac disease and controls in these parameters. BMI percentile correlated with leptin levels in children with coeliac disease. Study 3 The objectives of this study were to determine anthropometric parameters and leptin levels in children with IBD and ascertain if BMI correlates with leptin levels in these children. Thirty children with IBD and 60 age and gender matched controls were enrolled. Anthropometric measurements and leptin levels were analysed and compared with controls. IBD children had significantly low weight for age (p=0.002), BMI percentiles (p=0.001) and leptin levels (p=0.009) compared to controls. There was a correlation between BMI and leptin levels in IBD children. In conclusion, this thesis has shown that one quarter of hospitalized children were overweight or obese, and further, that half of the hospitalised children were at high risk of nutritional deterioration and these children had longer hospital stay than children at no risk. Children with coeliac disease had similar anthropometric measurements, body compartments and leptin levels to controls. However, children with IBD had lower anthropometric measurements and leptin levels, indicating under-nutrition. Nutritional assessment should be a mandatory part of clinical management with nutritional status assessed by various tools including NRS, anthropometry, BIA and leptin levels.

Abstract Nutritional status affects every aspect of a child?s health. Thorough nutritional assessment is hampered by the lack of a single comprehensive tool, which can cover all aspects of nutritional assessment. In three distinct studies, this thesis investigated the nutritional status of hospitalised children, children with coeliac disease and children with inflammatory bowel disease. Study 1 The objectives of this study were to assess prevalence of malnutrition and nutritional risk, and define demographic and anthropometric factors associated with nutritional risk among hospitalized children. In this cross sectional study, 157 hospitalised children were assessed for nutritional status using nutritional risk score (NRS) and anthropometric measurements. We found that 4.5%, 8.9%, 15.1% and 10.4% children were wasted, stunted, overweight and obese respectively. However, with the NRS, 47.8% of the children were at high nutritional risk. These children at high risk had lower weight for age (p=0.02), lower BMI percentiles for age (p=0.001) and longer hospitalization (p=0.001) than children at no risk. Study 2 The objectives of this study were to determine nutritional parameters in children with coeliac disease. Twenty-five children with coeliac disease and an equal number of age and gender matched controls were enrolled and anthropometric measurements, BIA and leptin levels were analysed in all. No significant differences were found between the children with coeliac disease and controls in these parameters. BMI percentile correlated with leptin levels in children with coeliac disease. Study 3 The objectives of this study were to determine anthropometric parameters and leptin levels in children with IBD and ascertain if BMI correlates with leptin levels in these children. Thirty children with IBD and 60 age and gender matched controls were enrolled. Anthropometric measurements and leptin levels were analysed and compared with controls. IBD children had significantly low weight for age (p=0.002), BMI percentiles (p=0.001) and leptin levels (p=0.009) compared to controls. There was a correlation between BMI and leptin levels in IBD children. In conclusion, this thesis has shown that one quarter of hospitalized children were overweight or obese, and further, that half of the hospitalised children were at high risk of nutritional deterioration and these children had longer hospital stay than children at no risk. Children with coeliac disease had similar anthropometric measurements, body compartments and leptin levels to controls. However, children with IBD had lower anthropometric measurements and leptin levels, indicating under-nutrition. Nutritional assessment should be a mandatory part of clinical management with nutritional status assessed by various tools including NRS, anthropometry, BIA and leptin levels.

Chronic inflammatory conditions such as Crohn's disease (CD) and Ulcerative colitis (UC) are risk factors for colon cancer. TGFβ has been shown to be dysregulated in colon cancer. Bacteria-induced inflammation is necessary for the induction of colon cancer in TGFβ mouse models. However, the mechanism by which TGFβ regulates the inflammatory response in these models is not well elucidated. It was our thought that we needed to be able to distinguish what was TGFβ dependent and what was inflammation dependent. To do this we created 2 colonies of Smad3 mice. One colony was housed with normal colonic bacteria (Smad3-uninfected animals) and the other colony (Smad3-infected animals) had chronic H. hepaticus infection. As previously seen the Smad3⁻/⁻- infected animals developed colitis and carcinoma (~40%). In the absence of H. hepaticus infection SMAD3 was found to negatively regulate TLR4 expression. This was then exacerbated with the addition of H. hepaticus resulting extreme up-regulation of TLR4 and the downstream effectors IRAK4 and NF-κB in Smad3⁻/⁻-infected colonic tissues. Examination of adaptive immune regulation in this model demonstrated that SMAD3 was necessary for FOXP3 expression in H. hepaticus-infected splenocytes. Loss of SMAD3 resulted in up-regulation of IL17 and reduced iTreg populations. These data demonstrate the important role SMAD3 has in maintaining tolerance to microbial populations through both the innate and adaptive immune systems.