Fecal microbiota transplantation (FMT) is the process by which fecal suspension from a healthy individual is transferred into the gastrointestinal tract of another individual in an attempt to cure certain diseases. This transplantation process has been accredited as being a potential remedy for a growing number of diseases that have been associated with gut microbial imbalances. Interest in FMT has largely been driven by the science community’s increasing interest in the gut microbiome and its role in potentially regulating a multitude of different functions and processes within the human body. One disease that has been found to respond exceptionally well to FMT treatments is Clostridium difficile infection (CDI). However, while FMT has demonstrated high cure rates for CDI, this transplantation process is no panacea. In fact, the results from FMT treatments on other diseases, such as Inflammatory Bowel Disease (IBD), have not been as impressive as CDI’s. This review will examine the existing literature surrounding FMT usage on IBD and will propose a series of experiments and studies needed to truly test the safety and efficacy of FMT for IBD patients. This review will also reference current literature documenting FMT treatments for CDI as a comparative tool for investigating if this form of bacteriotherapy is indeed a viable therapeutic option for treating IBD.

Introduction: Inflammatory pouch complications, including pouchitis, chronic pouchitis (CP) and a Crohn’s disease-like phenotype (CDL) of the pouch following ileal pouch-anal anastomosis (IPAA), are relatively common, and arise via unknown mechanisms. The phenotypic similarities between pouch inflammation and inflammatory bowel disease (IBD) suggest there may be common pathways involved in both disorders. The aim of this thesis is to investigate the serological, genetic and microbial factors contributing to the development of pouch inflammation in a large, well characterized patient cohort. Methods: Subjects with IPAA were recruited, and clinical and demographic information was obtained through medical chart review and patient questionnaire, allowing patients to be grouped based on post-surgical phenotype. Blood and tissue was collected for genetic, serological and microbial analyses. Anti-microbial antibodies were detected using enzyme-linked immunosorbent assay (ELISA), genotyping was carried out using the Illumina Goldengate custom SNP assay and Sequenome iPLEX platform, and tissue-associated microbial communities were assessed using 454 pyrosequencing. Results: Among our cohort, smoking was associated with CDL (P=0.003) and Ashkenazi Jewish heritage with CP (P<0.008). NOD2insC (rs2066847) (P=7.4x10-5), anti-CBir1 (P<0.0001) and ASCA (IgG) (P=0.03) were significantly associated with inflammatory pouch outcomes. Additional SNPs in NOX3, DAGLB, and NCF4 were also marginally associated with pouch outcome. A multi-variable risk model combining clinical, serologic and genetic markers was constructed and could differentiate between chronic pouch inflammatory phenotypes and no pouchitis. Genus level microbial analysis demonstrated that several organisms (Bacteroides, Parabacteroides, Blautia and Moryella) were detected less frequently among the inflammatory outcome groups (P<0.05). These associations remained significant even following adjustment for antibiotic use, smoking, country of birth and gender. Conclusions: CD-associated anti-microbial antibodies and genetic markers are associated with chronic inflammatory pouch phenotypes. Additionally, changes in the composition of the pouch associated microbiome are associated with inflammation. These observations suggest that similar mechanisms may be involved in non-surgical IBD and pouchitis.

Background and objectives: Physical fitness and stress resilience may influence the risk of gastrointestinal (GI) disease. High physical fitness level may reduce levels of systemic inflammation while psychosocial stress exposure can increase inflammation levels and intestinal permeability. The main objectives are to evaluate if poorer physical fitness and stress resilience in adolescence are associated with a raised risk of inflammatory bowel disease (IBD), peptic ulcer disease (PUD) and GI infections in adulthood and to assess evidence of causality. Materials and methods: Swedish registers provided information on a cohort of approximately 250,000 men who underwent military conscription assessments in late adolescence (1969 –1976) with follow-up until December 2009 (up to age 57 years). Cox regression evaluated the associations of physical fitness and stress resilience in adolescence with subsequent GI disease risk in adulthood. Results and conclusions: IBD: Poor physical fitness was associated with an increased risk of IBD. The association may be explained (in part) by prodromal disease activity reducing exercise capacity and therefore fitness. Low stress resilience was associated with an increased risk of receiving an IBD diagnosis. Stress may not be an important cause of IBD but may increase the likelihood of conversion from subclinical to symptomatic disease. PUD: Low stress resilience was associated with an increased risk of PUD. This may be explained by a combination of physiological and behavioural mechanisms that increase susceptibility to H. pylori infections and other risk factors. GI infections: Low stress resilience was associated with a reduced risk of GI infections, including enteric infections rather than the hypothesised increased risk.

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.

INTRODUCTION: The techniques currently in practice to diagnose and assess interval disease activity in patients with inflammatory bowel disease (IBD) are costly and invasive. Physicians typically rely on information derived from a combination of endoscopic, radiologic, and histologic studies to diagnose and determine the extent and severity of the two most common forms of IBD, Crohn disease (CD) and ulcerative colitis (UC). The development of noninvasive methods of assessing response to therapy is of increasing importance to pediatric healthcare providers. Previous studies have demonstrated that serum and fecal biomarkers are reliable measures of inflammation in the gastrointestinal tract. However, existing biomarkers are non-specific and their levels can be elevated in the context of either acute and chronic inflammation (IBD) or infection. As such, further studies are required to develop newer and novel biomarkers that have greater specificity for use in the diagnosis and interval assessment in children and adults with IBD. OBJECTIVES: The goal of this study is to further assess the relationship between biomarkers in the stool and serum of patients with IBD that are being treated with the anti-TNF therapy, infliximab (Remicade). To accomplish this, we will assess the changes in serum and fecal biomarker levels over the course of treatment and correlate the changes in fecal and serum biomarker levels with clinical, biochemical, and endoscopic outcome variables. METHODS: We conducted a prospective longitudinal cohort study in pediatric patients with IBD receiving long-term immunosuppressive therapy with Remicade. Pediatric patients diagnosed with either CD or UC who receive Remicade at Boston Children’s Hospital were recruited. Patients were drawn from subsets of patients that were either naïve to Remicade, had received Remicade for less than 6 months, or had received Remicade for more than one year at the time of enrollment. We collected longitudinal data over the course of their first 6 consecutive infusions following enrollment, including blood and stool samples, disease activity indexes, as well as a patient-reported outcome measure (IMPACT-III Questionnaire) at each infusion session. RESULTS: A total of 33 patients with IBD who fit our eligibility criteria and provided informed consent were enrolled to date. Of these, 20 had a CD diagnosis and 13 had a UC diagnosis. We collected baseline serum, fecal, and IMPACT-III score data and followed enrolled patients over the course of subsequent infusions. Mean baseline fecal ASCA levels from 8 CD and 6 UC patients were 0.08±0.021 OD and 0.02±0.0015 OD, respectively. At baseline, serum lactoferrin (p<0.10), calprotectin (p<0.10), ESR (p<0.05), and CRP (p<0.10) were significantly higher among CD patients. CONCLUSION: Our data demonstrate the potential for serum and fecal biomarkers to evaluate therapeutic response to Remicade. Completion of study enrollment and data collection will be necessary to determine if individual or combinations of fecal and serum biomarkers yield the most robust measures for use in the diagnosis and interval assessment of children and adults with IBD.

Iron deficiency anemia (IDA) is a common extra-intestinal manifestation of inflammatory bowel disease (IBD). It is particularly common in the pediatric population, with 40-60% of pediatric patients with IBD meeting criteria for anemia (Aljomah et al, 2018). A number of studies have examined the use of both IV and oral iron treatments to treat anemia in IBD, but few have examined the safety and efficacy of these treatments in children and how they impact a patient’s health-related quality of life. We conducted a prospective cohort study of 79 pediatric patients admitted to Boston Children’s Hospital for management of their IBD. 48 of these patients received IV iron, 13 received oral iron, and 12 were not treated with either. Treatment with IV iron resulted in a statistically significant increase in hemoglobin of 1.75g/dL+/-1.4g/dL (mean +/- SD) from admission to the time of their first post-discharge visit (p=0.0001). Prescription of oral iron at the time of discharge did not result in a significant increase in hemoglobin over the same interval (p=0.481). Though there was a positive trend, IV iron treatment did not result in a significant change in health-related quality of life (HRQOL) measurements as measured by the IMPACT-III questionnaire (p=0.06). Our study suggests that IDA is common in patients admitted for management of their IBD, IV iron is more efficacious in raising hemoglobin, and that larger studies will be needed to more fully demonstrate the impact of effective iron repletion on overall quality of life in these patients.

INTRODUCTION: Physiologic and pathophysiologic inflammation is mediated, at least in part, by the generation and release of reactive oxygen species into the local tissue milieu. The chronic inflammation observed in patients with inflammatory bowel disease (IBD) is thought to begin in the lining of the intestine and may progress to involve the entire bowel wall.In an effort to assess disease activity, clinicians rely on costly and technically invasive procedures such as colonoscopies. As such, there is currently a need for the development of less invasive and more cost-effective methods for use in the diagnosis and interval assessment of children and adults with these chronic intestinal inflammatory disorders. OBJECTIVES: The objective of this study was to first determine if ambient redox status can be reliably measured in the stool of patients with IBD. A second aim of the study was to determine if ambient stool redox status was related to underlying diagnosis, clinical disease activity, or response to therapy in patients with IBD . METHODS: We first our ability to measure redox redox standards using three different commercially available devices. Once demonstrated, we then the process of performing sample analysis under various conditions (room tempererture, refrigerated, frozen, or spun/unspun) to determine the conditions under which we were able to achieve the most stable redox assessments. Finally, we conducted a small pilot cohort study in hospitalized pediatric patients with IBD to assess if stool redox status informed about disease activityWe collected stool samples from seven patients admitted to the inpatient gastrointestinal service at Boston Children’s Hospital during a period extending from November of 2018 to March of 2019. RESULTS: Preliminary studies confirmed our ability to accurately measure relative redox status (RRS) using three different apparatuses. Furthermore, we were able to generate dilution curves using juices known to include oxidants, with linear regression r2 values of 0.99. In our patient population, we confirmed our ability to generate a reliable readings and consistent RRS measurements over. Frozen samples displayed less stable and higher RRS than those either refrigerated or kept at room temperature for up to 8-hours. This suggests that freeze-thaw cycles may impact adversely on the stability of oxidants and antioxidants in our samples. The RRS measurements from stool samples collected from patients who were exhibiting active symptoms of their IBD measured about -400 mV, while samples collected from hospitalized patients without IBD manifest RRS readings of about 100 mV. CONCLUSION: This preliminary study demonstrates our ability to measure RRS in the stool of patients with and without IBD. The stability we observed in samples that were either stored at room temperature or refrigerated demonstrated that these represented optimal storage options. Additionally, measurements from homogenized stool samples appeared to be more variable when compared to the relatively smaller range from centrifuged samples. Initial studies indicated a strong difference in RRS measurements between patients with inflammatory and non-inflammatory GI disease or inactive IBD. This difference suggests that measurements of RRS could provide a quantitative real-time assessments of disease activity and response to therapy in patients with IBD.

As Doenças Inflamatórias Intestinais (DII), como a colite ulcerativa e a doença de Crohn, são resultados de uma resposta imune desregulada no intestino de indivíduos geneticamente suscetíveis apresentando disbiose intestinal. Essas doenças geralmente são tratadas com anticorpos monoclonais, como o anti-TNF, Infliximab (IFX). No entanto, pouco se sabe como o bloqueio do TNF afeta a resposta do hospedeiro quando ocorre uma nova quebra da homeostase intestinal, durante a recidiva da doença. Neste estudo, avaliamos os efeitos tardios do tratamento com IFX na colite experimental com um novo desafio de disbiose. Camundongos tratados com IFX tiveram remissão da colite. No entanto, o tratamento não protegeu contra a recidiva da doença, o que resultou no aumento de células mononucleares circulantes e diminuição de neutrófilos, em contraste com a redução da atividade de macrófagos e aumento da infiltrado de neutrófilos no cólon após o desafio. Esses animais também apresentaram diminuição da barreira linfocitária epitelial e aumento de linfócitos na lâmina própria do cólon, que também continha elevado número de células dendríticas inflamatórias CD11b+CD11c+CD103-. O tratamento da colite com IFX seguido de um desafio de microbiota levou à redução de linfócitos TCD4, TCD8 e ?? intraepiteliais, com acúmulo de células T ativadas, memória residentes e efetoras na lâmina própria, em comparação com o número reduzido desses linfócitos na ausência de tratamento com IFX. Além disso, o bloqueio do TNF reduziu a expressão de IL-1? e IL-6 e aumentou a expressão de CYP11B1, uma enzima esteroidogênica responsável pela produção de cortisol anti-inflamatório. Porém o desafio antigênico elevou significativamente a expressão de IL-13, mas reduziu a expressão das enzimas esteroidogênicas, CYP11A1 e CYP11B1O. O mais interessante é que a permeabilidade intestinal foi aumentada, assim como a atividade de proliferação das células nos linfonodos mesentéricos. Esses dados sugerem que, embora o IFX possa controlar a inflamação na colite aguda, seus efeitos tardios comprometem a capacidade do hospedeiro de lidar com um novo desafio, como uma disbiose intestinal que ocorre durante a recaída da doença / Inflammatory Bowel Diseases (IBD), such as ulcerative colitis and Crohn\'s disease, are the result of a dysregulated immune response in the intestine of genetically susceptible individuals presenting with intestinal dysbiosis. These diseases are usually treated with monoclonal antibodies, such as anti-TNF, Infliximab (IFX). However, little is known about how TNF blockade affects host response when a new break in intestinal homeostasis occurs during relapse of the disease. In this study, we evaluated the late effects of IFX treatment in experimental colitis with a new challenge of dysbiosis. Mice treated with IFX had remission of colitis. However, the treatment did not protect against disease recurrence, which resulted in increased circulating mononuclear cells and decreased neutrophils, in contrast to reduced macrophage activity and increased neutrophil infiltrate in the colon after challenge. These animals also had a decrease in the lymphocyte epithelial barrier and increased lymphocytes in the lamina propria of the colon, which also contained a high number of inflammatory dendritic cells CD11b+CD11c+CD103-. Treatment of IFX colitis followed by a microbiota challenge led to reduction of intraepithelial TCD4, TCD8 and ?? lymphocytes with accumulation of activated T cells, resident and effector memory in the lamina propria, compared to the reduced number of these lymphocytes in the absence of treatment with IFX. In addition, TNF blockade reduced IL-1? and IL-6 expression and increased expression of CYP11B1, a steroidogenic enzyme responsible for the production of anti-inflammatory cortisol. However, antigen challenge significantly elevated IL-13 expression, but reduced expression of steroidogenic enzymes, CYP11A1 and CYP11B1. Interestingly, the intestinal permeability was increased, as was the proliferation activity of the cells in the mesenteric lymph nodes. These data suggest that although IFX can control inflammation in acute colitis, its late effects compromise the host\'s ability to cope with a new challenge, such as intestinal dysbiosis that occurs during relapse of the disease

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.