Ulcerative colitis (UC) and Crohn’s disease (CD) are the two common forms of inflammatory bowel disease (IBD). They share similar clinical and demographic features as well as harbor key differences in tissue damage and prognosis. Previous studies indicated that they contributed to the increased rick to Colorectal cancer (CRC). However, whether UC and CD share inflammatory signatures still remains controversial. In addition, no inflammatory signatures have been reported on CRC. To answer these questions, a comprehensive study has been conducted on collected microarray datasets. Our analysis suggests that although CD and UC share common inflammatory pathways, they also present difference. Especially, CD patients are likely to have type I response, while UC patients are inclined to undergo type II response. Pathway enrichment analysis on CRC uncovered two potential CRC-specific inflammatory pathways.

The ATP sensitive potassium channel (KATP) in mouse colonic smooth muscle cell is a complex containing a pore forming subunit (Kir6.1) and a sulfonyl urea receptor subunit (SUR2B). These channels are responsible for maintaining the cellular excitability of the smooth muscle cell which in turn regulates the motility patterns in the colon. We used whole-cell voltage-clamp techniques to study the alterations in these channels in smooth muscle cells in experimental model of colitis (colonic inflammation). Colitis was induced in BALB/C mice following an intracolonic administration of trinitrobenzene sulfonic acid (TNBS). KATP currents were measured at Vh -60 mV in high K+ external solution. The dose-response to levcromakalim (LEVC), a KATP channel opener, was significantly shifted to the left in the inflamed smooth muscle cells. Both the affinity and maximal currents induced by LEV were enhanced in inflammation. The EC50 in control was 6259 nM (n=10) and 422 nM (n=8) in inflamed colon while the maximal currents were 9.9 ± 0.71 pA/pF (60 μM) in control and 39.7 ± 8.8 pA/pF (3 μM) following inflammation. Similar to LEVC, KATP currents activated by sodium hydrogen sulfide (NaHS) (10-1000 μM) were significantly greater in inflamed compared to controls. In control cells, pretreatment with 100 µM NaHS shifted the EC50 for LEV-induced currents from 2838 nM (n=6) to 154 nM (n=8). These data suggest that NaHS can act as an allosteric modulator for LEV-induced KATP currents. Decreased colonic motility may result from enhanced KATP activation by increased release of H2S in colitis.

Substantial evidence in the literature shows that tobacco smoking has complex and divergent effects on inflammatory bowel diseases (IBD). It ameliorates ulcerative colitis (UC); whereas it aggravates the risk of Crohn’s disease (CD) and affects the disease course and severity. Studies have shown that nicotine has a positive influence on symptoms of UC. Also, it is demonstrated that nicotinic acetylcholine receptor, especially α7 subunit plays an essential component in the vagus nerve-based cholinergic anti-inflammatory effects. In the present study, we explored the effect of nicotine and α7 nicotinic agonists treatment in the DSS colitis mouse model. We also investigated the effects of cotinine, a major metabolite of nicotine, in the model. Methods: Different groups of C57BL6 mice, as well as α7, α5, and β2 nicotinic receptor knock out mice, and their littermates wild-type nicotinic receptor male adult mice were given DSS solution freely in the drinking water for 7 consecutive days after which tap water was given on the 8th day. We measured a Disease Activity Index (DAI) that includes body weight loss, blood presence in stools, stool consistency, local rectal irritation and length of the colon. The mice were then sacrificed on day 8 to allow examination of the entire colon. Disease severity and colon tissue histology and inflammatory markers including colonic myeloperoxidase (MPO) and colonic tumor necrosis factor-α (TNF-α) were evaluated. Levels of MPO and TNF-α were determined by enzyme-linked immunosorbent assay analysis of the homogenized colon samples. The effect of oral, subcutaneous, mini pump nicotine, and oral cotinine treatments were examined on experimental colitis induced by 2.5% DSS in mice. In addition, we measured the plasma levels of the nicotine and cotinine in our treatment protocols. Results: The DSS 2.5% model of colitis is easily induced in mice. Administration of low doses of oral nicotine (12.5 and 25 μg/ml), but not high doses in DSS-treated mice displayed a significant decrease in disease activity index value, total histological damage scores, as well as colonic level of TNF-α compared to the control group. However, the anti-inflammatory effect of nicotine was not seen with chronic s.c., mini pump nicotine or oral cotinine administration. Differences in plasma levels of nicotine and cotinine do not seem to account for this lack of effect. Moreover, neither nicotine nor cotinine reversed colon length shortening in DSS-treated mice, except with the 0.5 mg/kg s.c. dose of nicotine. There was no change in MPO activity among the groups treated with oral or s.c. nicotine. Cotinine oral administration on its own failed to show a significant effect in the DSS model of colitis. α7 KO mice displayed a significantly increased in DAI value starting from day 4 till day 8, histological damage scores and TNF-α levels of were increased significantly compared to their littermate WT mice. Moreover, pretreatments with PHA-543613 (8 mg/kg), a selective α7 agonist, and choline chloride (40 ug/ml), an α7 nAChR natural agonist, significantly reduced clinical parameters in DSS-treated mice; however, they slightly inhibited the increase in the colonic TNF-α levels compare with vehicle DSS-treated mice. Moreover, PNU-120596 (3 mg/kg), a positive allosteric modulator for α7 nAChRs, significantly reduced DAI value and total histological damage score in DSS-treated mice. Conclusion: Results obtained from this study highlight that dose and route of administration play a critical role in the protective effect of nicotine in the DSS mouse colitis model. Also, these data suggest that α7 nAChR has a protective role in colitis with narrower therapeutic index. Data obtained from this study further understanding of the effect of nicotine in UC and may contribute in the development of new pharmaceutical designs for targeting nAChRs for the treatment of ulcerative colitis.

In diploma thesis we deal with inflammatory bowel diseases. The theoretical part describes etiology, pathogenesis, clinical symptoms, out-of-body manifestation and drug therapy. Current knowledge about the relationship between nutrition and disease is described. Since inflammatory bowel diseases are incurable, therapy pays attention to keep the patient in remission and preventing relapse. Nutrition therapy plays an important role in achieving these goals. In the practical part, we deal with the level of nutrition awareness of patients, in the form of a questionnaire and a non- standardized interview. We also study the influence of education on vitamin levels in patients. We determine whether they know the importance of eating and eating nutrients in their illnesses. From the background, it can be appreciated that information resources are insufficient for patients. Patients would also welcome more detailed education, and therefore part of the practical part of the educational material for patients with Crohn's disease. Key words: Crohn's disease, ulcerative colitis, nutrition, education, diet

For over two decades, the study of genetics has been making significant progress towards understanding the causes of common disease. Across a wide range of complex disorders there have been hundreds of associated loci identified, largely driven by common genetic variation. Now, with the advent of next-generation sequencing technology, we are able to interrogate rare and low frequency variation in a high throughput manner for the first time. This provides an exciting opportunity to investigate the role of rarer variation in complex disease risk on a genome-wide scale, potentially o↵ering novel insights into the biological mechanisms underlying disease pathogenesis. In this thesis I will assess the potential of this technology to further our understanding of the genetics of complex disease, using inflammatory bowel disease (IBD) as an example. After first reviewing the history of genetic studies into IBD, I will describe the analytical challenges that can occur when using sequencing to perform case-control association testing at scale, and the methods that can be used to overcome these. I then test for novel IBD associations in a low coverage whole genome sequencing dataset, and uncover a significant burden of rare, damaging missense variation in the gene NOD2, as well as a more general burden of such variation amongst known inflammatory bowel disease risk genes. Through imputation into both new and existing genotyped cohorts, I also describe the discovery of 26 novel IBD-associated loci, including a low frequency missense variant in ADCY7 that approximately doubles the risk of ulcerative colitis. I resolve biological associations underlying several of these novel associations, including a number of signals associated with monocyte-specific changes in integrin gene expression following immune stimulation. These results reveal important insights into the genetic architecture of inflammatory bowel disease, and suggest that a combination of continued array-based genome- wide association studies, imputed using substantial new reference panels, and large scale deep sequencing projects will be required in order to fully understand the genetic basis of complex diseases like IBD.

There is increasing evidence that psychological stress and associated mood disorders are linked with, and can adversely affect the course of inflammatory bowel disease (IBD). Stress is perceived to be relieved by smokers, and this, like a lack of knowledge about its adverse effects, and nicotine dependence, could contribute to continued smoking by patients with Crohn’s disease (CD). Stress has previously been shown to influence disease course in patients with inactive ulcerative colitis (UC) but its influence in acute severe UC is not known. Emerging trial evidence supports the suggestion that psychologically-orientated therapy may ameliorate IBD-associated mood disorders, but there is no strong data yet to indicate that stress management has a beneficial effect on the activity or course of IBD. In addition gut-focussed hypnotherapy has been successfully used in the setting of functional bowel disorders. The 4 main hypotheses tested in thesis are: 1. In patients with IBD: (1) poor knowledge of the effects of smoking on their disease and/or (2) high nicotine dependence explain the higher prevalence of smoking in CD than UC 2. Anxiety, depression and stress are more common and worsen outcome in patients with acute severe UC. 3. Stress management in the form of psychotherapy given by a counsellor has a beneficial effect on the activity and course of IBD. 4. Gut-focussed hypnotherapy reduces the relapse rate in patients with UC. The major findings are as follows: 1. Despite more patients with CD being smokers, they were better informed about the effects of smoking on their own disease than UC patients. Nicotine dependence was no higher in patients with CD than UC. In IBD patients as a whole, nicotine dependence was lower than in smokers’ clinic clients and comparable to that of the general population, suggesting that most IBD patients could be weaned off smoking successfully in the IBD clinic.

Detection of evolutionarily conserved pathogen motifs by pattern recognition receptors (PRRs), particularly on dendritic cells (DCs), is crucial for adequate immune responses. Defects in DC function are known to be associated with inflammatory bowel disease (IBD). The endocannabinoid system (ECS) is the system through which exocannabinoids such as Δ⁹-tetrahydrocannabinol and cannabidiol signal. Regarding inflammation, cannabinoids generally exert anti-inflammatory effects, including on experimental colitis. However, most work has been performed in animal models and less is known about the function of this system in human immune cells, particularly DCs. Monoacylglycerol lipase (MGLL) is the key enzyme for hydrolysis of the endocannabinoid 2-arachidonoylglycerol, and a member of the serine hydrolase enzyme superfamily. This thesis defines the activity of serine hydrolase enzymes for the first time in human DCs upon stimulation by NOD2/TLR2 ligands using activity-based protein profiling (ABPP). MGLL is shown to be ubiquitously upregulated upon stimulation of DCs and in monocyte-derived macrophages. Through pharmacological inhibition studies, MGLL is demonstrated to regulate cellular and secreted lipids, not limited to endocannabinoids. However, overall DC function is independent of this enzyme suggesting that the effects of lipid modulation may be on bystander cells. Challenging the current literature, MGLL inhibition with a novel inhibitor worsens murine Citrobacter rodentium colitis. Finally, ABPP demonstrates a rich serine hydrolome in colonic tissue from human IBD with many enzymes previously undefined in this disease. Gene expression of ECS components suggests the enzymes ABHD12 and DAGLα/β may be potential markers of field change in IBD.

There is an unmet need for novel biomarker discovery in Inflammatory Bowel Diseases (IBD) to aid clinical management in several clinical settings including diagnosis and prognosis. With an ever-advancing repertoire of biological therapies on the horizon, it is important to personalise treatments at an early stage. The aim of this thesis is to explore the clinical utility of novel blood-based biomarkers in diagnosis, disease classification and prognosis in 2 cohorts: newly diagnosed IBD and acute severe colitis. Investigating the circulating methylome, 290 probes exhibited Holm significant IBD-associated methylation differences, including VMP1/MIR21 (p=7.5×10-14) and RPS6KA2 (1.1×10-19) and were consistent within the European cohort. 11 Differentially methylated positions (DMPs) predicted treatment escalation after Holm adjustment (top probe p=0.003). A panel of 6 probes identified 2 patient subgroups that have significantly different disease courses (Hazard Ratio (HR) 10.5, 95%CI: 4.3-25.6; logrank p=1.5×10-24). The 6 probe marker outperformed conventional biomarkers in predicting treatment escalation (hsCRP > 4mg/L, HR 3.2(1.7-5.8), logrank p=0.0004 and Alb < 36g/L, HR 2.9(1.5-5.6), p=0.0001). Within the same cohort, a novel proximity extension assay (PEA) was then utilised to identify novel diagnostic and prognostic protein markers. 61 proteins were significantly associated with IBD including MMP12 (Holm-adjusted p=4.1×10-26). A total of 9 proteins predicted disease course in this cohort. Using a panel of 7 randomly selected top prognostic probes, 2 patient groups were identified that had significantly different disease courses: logrank p=2.2×10-10, HR 5.6(2.0-15.6), outperforming conventional biomarkers in predicting treatment escalation (hsCRP > 4mg/L, HR 3.2(1.7- 5.8), logrank p=0.0003 and Alb < 36g/L, HR 2.7(1.4-5.2), p=0.0004). In a subcohort, serum calprotectin (SC) and conventional blood markers were investigated for their utility in diagnosis and prognosis in IBD. SC performed at par with CRP at differentiating IBD from controls with an area under the curve (AUC) of 0.87 (CI 0.81-0.92). For prognostication, both albumin and SC remained significant predictors of treatment escalation in IBD (logrank test p=5.1×10-5). MicroRNAs (miRNA) are small non-coding nucleic acids that have the capacity to modulate gene expression. Using small RNA sequencing in acute severe colitis (ASUC) and healthy controls (HC), 10 serum-based miRNA markers were significantly associated with acute severe colitis, including miR-30a-5p. Validating the findings using qPCR, miR-30a-5p was downregulated in ASUC (p=0.003). Furthermore, miR30a-5p remained a significant predictor of eventual colectomy in acute colitis (logrank test p=0.0014). These data highlight the translational potential for methylation, miRNA and proteomic biomarkers in diagnosing and prognosticating in IBD.

Epigenetic alterations including DNA methylation and microRNAs may provide important insights into gene-environment interaction in complex immune diseases such as inflammatory bowel disease (IBD). An integrative genome-wide approach was used to analyse whole blood genetic, DNA methylation and gene expression data in 240 newly diagnosed IBD patients and 190 controls. Using the Illumina 450k array, differences in whole blood DNA methylation were observed in IBD cases versus controls including 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs). The top DMP (RPS6KA2, discovery Holm adjusted p=1.22×10-16, replication p=1×10-9) and DMRs (VMP1, ITGB2, TXK) were replicated in an independent cohort using pyrosequencing. Paired genetic and epigenetic data allowed the identification of methylation quantitative trait loci (meQTL); two of the five DMRs (VMP1, ITGB2) demonstrated significant association with genetic polymorphisms. Methylation in the VMP1/microRNA-21 region was significantly associated with two single nucleotide polymorphisms (cg18942579 -rs10853015 [meQTL FDR adjusted p=9.4 × 10-5], cg16936953 - rs8078424 [meQTL FDR adjusted p=8.8 × 10-5]), both of which are in linkage disequilibrium with a known IBD susceptibility variant (rs1292053). Separated leukocyte methylation data highlight the cell type of origin of epigenetic signals seen in whole blood. IBD-associated hypermethylation within the TXK gene transcription start-site negatively correlated with gene expression in whole blood and CD8+ T-cells, but not other cell types, highlighting that cell-specificity and gene location-specificity of DNA methylation change is critical when associating methylation and gene expression. These data offer significant translational potential as diagnostic biomarkers. Least absolute shrinkage and selection operator (lasso) modelling identified 30 methylation probes can be used to accurately discriminate IBD cases from controls (Area under receiver operating characteristic curve = 0.898, sensitivity = 90.6%, specificity = 84.7%). MicroRNAs (miRNA) are small non-coding nucleic acids that have the capacity to modulate gene expression. MiRNAs have been increasingly implicated in many of the important IBD pathogenic pathways including autophagy, intestinal epithelial barrier integrity and the Th17 pathway. In common with all epigenetic mechanisms, miRNA expression is dynamic and cell-specific. Small RNA sequencing (RNA-seq) was performed on RNA extracted from CD14+, CD4+ and CD8+ cells isolated from 8 newly diagnosed cases of ileal or ileocolonic CD and 8 age and sex matched controls. There was a median of 2.4 million reads per sample (range 132,800-12.8 million reads per sample). One microRNA was differentially expressed in CD compared with controls (hsa-miR-503-5p log fold change = 0.7, FDR adjusted p = 9.1 × 10-5) in CD4+ lymphocytes, however this finding did not remain significant when alternative normalisation methods were used. The small number of cases used in microRNA analyses raises the possibility of both type I and II error, and limits the ability to draw firm conclusion from this series of experiments. Site-specific differences in DNA methylation in IBD relate to underlying genotype and associate with cell-specific alteration in gene expression. This is the most detailed characterisation of the epigenome carried out in IBD to date. The findings strongly validate this approach in complex disease, are replicable, and provide clear translational opportunities.

Submitted by Jorge Silva (jorgelmsilva@ufrrj.br) on 2017-04-11T22:00:26Z No. of bitstreams: 1 2016 - Gabriela de Carvalho Cid.pdf: 11957327 bytes, checksum: 96764b1f2d588fc114d23dde6f1806e1 (MD5) / Made available in DSpace on 2017-04-11T22:00:26Z (GMT). No. of bitstreams: 1 2016 - Gabriela de Carvalho Cid.pdf: 11957327 bytes, checksum: 96764b1f2d588fc114d23dde6f1806e1 (MD5) Previous issue date: 2016-02-29 / CAPES / Mechanic natural skin lesions in horses caused by thorns of Mimosa spp. are described. Between the three plant species identified as responsible for the lesions, Mimosa setosa was present in greater quantity (80%) in the pasture, whilst M. debilis and M. pudica existed in lower proportion. Three ulcerative dermatitis outbreaks were observed during rainy periods of April to May 2013, December 2013 to February 2014 and April to May of the same year. Twenty-five horses from the Sector of Animal Reproduction, Federal Rural University of Rio de Janeiro, showed ulcerative skin lesions with irregular borders, hemorrhagic exudate, sometimes covered with scabs, located mainly in the regions of the pastern, fetlock, scapular-humeral joints, upper and lower lips, nose, nostrils, cheeks and chamfer. Seven horses were biopsied and histopathological examination revealed ulceration of the skin with inflammatory infiltrate by macrophages and neutrophils, delimited by granulation tissue. In some cases, microspicules of these plants (hirsute trichomes) were found throughout the inflammatory reaction. The diagnosis of skin dermatitis, caused by traumatic action of the plants, was based on the presence of Mimosa spp. in the pasture, on the characteristic clinic-pathological features and on recovery of the horses after their removal from the pasture. This appears to be the first report of the occurrence of ulcerative dermatitis caused by Mimosa setosa, as dermatitis caused by the others has been described before. / Descrevem-se les?es de natureza mec?nico-traum?tica na pele de equ?deos causadas por espinhos de Mimosa spp. Dentre as tr?s esp?cies da planta identificadas como respons?veis pelas les?es, M. setosa estava presente em maior quantidade e M. debilis e M. pudica encontravam-se em menor propor??o na pastagem. Ocorreram tr?s surtos de dermatite ulcerativa em per?odos chuvosos de abril a maio de 2013, dezembro de 2013 a fevereiro de 2014 e abril a maio deste mesmo ano. Vinte e cinco equinos do Setor de Reprodu??o Animal da Universidade Federal Rural do Rio de Janeiro apresentaram les?es ulcerativas na pele com contornos irregulares, exsudato serosanguinolento, por vezes recobertas com crostas. Localizadas principalmente nas regi?es da quartela, boleto, articula??es escapulo-umeral, l?bios superiores e inferiores, focinho, narinas, bochechas e chanfro. Sete animais foram biopsiados e o exame histopatol?gico revelou ulcera??o da epiderme e infiltrado inflamat?rio constitu?do por macr?fagos e neutr?filos, delimitado por tecido de granula??o subjacente. Em alguns casos, foram observados microesp?culos das referidas plantas (tricomas hirsutos) em meio ? rea??o inflamat?ria. O diagn?stico de dermatite cut?nea causada pela a??o traum?tica da planta baseou-se na presen?a de Mimosa spp. na pastagem, nos achados cl?nico-patol?gicos caracter?sticos e na recupera??o dos animais ap?s a retirada destes do pasto. Trata-se da primeira observa??o sobre a ocorr?ncia de dermatite ulcerativa causada por Mimosa setosa.