Iron deficiency anemia (IDA) is the most common extraintestinal complication encountered in patients with Inflammatory Bowel Disease (IBD), and it is more prevalent in pediatric patients compared to adults (Rogler and Vavricka). The inflammation and blood loss from the disease impacts both the absorption and storage of iron in the body (Rogler and Vavricka). With the intent of establishing a standard of care for IDA treatment in patients with IBD, we conducted a prospective study of 104 consecutive pediatric patients to assess the safety and efficacy of intravenous (IV) iron therapy compared to oral therapy and no treatment, as well as the effects of iron therapy on patient quality of life. Efficacy was assessed by comparing the change in hemoglobin levels in the interval between admission to outpatient follow-up. The average time to the first ambulatory follow-up was 29.08 days. 69 patients received IV iron therapy, 17 patients received oral iron supplementation, and 18 patients had no treatment. Treatment with IV iron resulted in a statistically significant increase in hemoglobin levels (2.00 g/dL ± 1.57 g/dL, as mean ± standard deviation) from admission to the first follow-up ambulatory appointment (p < .0001). Patients receiving IV iron therapy also experienced a significantly greater mean increase in hemoglobin levels than those treated with oral iron (p = .0084) or no treatment (p = .0018). Further, patients treated with IV iron experienced a significant increase in their quality of life at follow-up compared to admission as measured by the Impact-III questionnaire (p = .0179). Our study illustrates the importance of screening pediatric patients with IBD for IDA and suggests that IV iron treatment is safe and more effective in raising hematologic and iron measures than orally- administered alternative options.

The role of histamine in chronic gastrointestinal diseases has been increasingly recognized in humans, but the role of histamine in the canine gastrointestinal tract has not been thoroughly investigated. The presence and distribution of all 4 histamine receptors (H1, H2, H3, and H4) in the stomach, duodenum, ileum, jejunum, and colon of healthy dogs were evaluated with a commonly employed immunohistochemistry technique using antibodies predicted to cross react with canine histamine receptors. All 4 histamine receptors were identified in the canine gastrointestinal tract, and differed in location and density within sections of the canine gastrointestinal tract. Antibody specificity was evaluated with Western blot. With the establishment of a method to study histamine receptors in the canine gastrointestinal tract, additional research to evaluate histamine receptors in dogs is warranted to further understand the pathophysiology and treatment of chronic canine enteropathies.

Diet is a key factor in the development and progression of Inflammatory Bowel Disease (IBD). A variety of diets have been studied with IBD patients. This cross-sectional survey identified current healthcare practitioner views on different diets and their efficacy with IBD patients. Diets were rated on awareness, compliance, and contributors to success by participants (n = 181). Frequencies were conducted, and ANOVA with Duncan pairwise comparison or chi-square analysis were used to determine significant differences. Most participants (96%) and 98% of registered dietitians (RD) considered using diet to help treat IBD patients. RDs perceived the low fiber or low residue diet easiest for patient compliance (4.2 ± 1.0, P < .05), and the specific carbohydrate diet hardest for patient compliance (2.4 ± 1.4). Initial and follow up consultations with a RD significantly contributed to patient success across all diets, and greater involvement from the RD may solve issues with compliance.

Background Reported outcomes for colorectal cancer associated with Inflammatory Bowel Disease are inconsistent. We compared survival outcomes in colorectal cancer patients with and without Inflammatory Bowel Disease using a population-based cohort and elicited prognostic factors associated with survival Methods Adult patients with a diagnosis of colorectal cancer in 2007-2015 were identified from the Ontario Cancer Registry. Those with Inflammatory Bowel Disease were detected via the validated Ontario Crohn’s and Colitis Cohort. Primary outcome measure was overall survival from time of colorectal cancer diagnosis until the date of death. Secondary outcome measures included treatments received and publicly-provided health care costs. Results Colorectal cancer was diagnosed in 67,137 with Inflammatory Bowel Disease present in 783 (1.2%). The Inflammatory Bowel Disease-associated colorectal cancer patients were younger at diagnosis (median range 55-59 vs 70-74, p<0.001). Five-year survival in Inflammatory Bowel Disease-associated patients was 56.4% (95% CI 52.6-59.9) and 57.0% (95% CI 56.6-57.4) in sporadic colorectal cancer (p=0.8). Inflammatory Bowel Disease was a significant predictor of death (Hazard Ratio=1.45, 95% CI 1.29-1.63, p<0.001) after adjusting for other variables. In patients under 50, 5-year survival was significantly (p<0.001) reduced in the Inflammatory Bowel Disease population (56.8%, 95% CI 49.4-63.5) compared with the sporadic colorectal cancer population (71.4%, 95% CI 70.0-72.7). Similar results were observed in those 50-64 years old. Conclusion Young patients (<65) with Inflammatory Bowel Disease-associated colorectal cancer have worse survival outcomes than young (<65) patients with sporadic colorectal cancer. These findings inform prognostication and may direct future research for this high-risk population. / Thesis / Master of Science (MSc) / Background Reported outcomes for colorectal cancer associated with Inflammatory Bowel Disease are inconsistent. We compared survival outcomes in colorectal cancer patients with and without Inflammatory Bowel Disease using a population-based cohort and elicited prognostic factors associated with survival Methods Adult patients with a diagnosis of colorectal cancer in 2007-2015 were identified from the Ontario Cancer Registry. Those with Inflammatory Bowel Disease were detected via the validated Ontario Crohn’s and Colitis Cohort. Primary outcome measure was overall survival from time of colorectal cancer diagnosis until the date of death. Secondary outcome measures included treatments received and publicly-provided health care costs. Results Colorectal cancer was diagnosed in 67,137 with Inflammatory Bowel Disease present in 783 (1.2%). The Inflammatory Bowel Disease-associated colorectal cancer patients were younger at diagnosis (median range 55-59 vs 70-74, p<0.001). Five-year survival in Inflammatory Bowel Disease-associated patients was 56.4% (95% CI 52.6-59.9) and 57.0% (95% CI 56.6-57.4) in sporadic colorectal cancer (p=0.8). Inflammatory Bowel Disease was a significant predictor of death (Hazard Ratio=1.45, 95% CI 1.29-1.63, p<0.001) after adjusting for other variables. In patients under 50, 5-year survival was significantly (p<0.001) reduced in the Inflammatory Bowel Disease population (56.8%, 95% CI 49.4-63.5) compared with the sporadic colorectal cancer population (71.4%, 95% CI 70.0-72.7). Similar results were observed in those 50-64 years old. Conclusion Young patients (<65) with Inflammatory Bowel Disease-associated colorectal cancer have worse survival outcomes than young (<65) patients with sporadic colorectal cancer. These findings inform prognostication and may direct future research for this high-risk population.

<p dir="ltr">Approximately 2.39 million Americans suffer from inflammatory bowel disease (IBD), an autoimmune disorder that is characterized by chronic inflammation of the gastrointestinal (GI) tract. Current treatment options for IBD, which are limited, include oral medications, surgery, and supportive care. These therapeutics often times are not effective and are associated with high toxicity. Thus, there is a pressing clinical need for a therapy that can be delivered both locally and precisely, while also having an improvement in efficacy and lower toxicity.</p><p dir="ltr">This study introduces three novel microrobot designs fabricated using stereolithography (SLA) 3D printing, which aims to address the challenges seen in IBD treatment. The microrobots utilize a reservoir design to encapsulate the drug for an on-demand release, allowing for improved control and precision. The SLA microrobots were evaluated for cytotoxicity as well as drug release capabilities. We were able to demonstrate a local release of a protein on-demand at a biologically relevant temperature. The integration of microrobots in IBD therapy has the capability to significantly improve patient outcomes and quality of life, offering a more efficient and less toxic treatment approach.</p>

The mucosal immune system encompasses a wide array of interactions that work in concert to protect an individual from harmful agents while retaining tolerance to molecules, microbes, and self-antigens that present no danger. The upheaval in the regulation-response balance is a critical aspect in both infectious and immune-mediated disease. To understand this balance and methods of its restoration, iterative and integrative modeling cycles on the pathogenesis of disease are necessary. In this thesis, I present three studies highlighting phases of a systems immunology cycle. Firstly, the thesis provides a description of the construction of a computational ordinary differential equation based model on the host-pathogen-microbiota interactions during Clostridium difficile infection and the use of this model for the development of the hypothesis that host-antimicrobial peptide production may correlate with increased disease severity and promote increased recurrence. Secondly, it provides insight into the necessity of trans-disciplinary analysis for the understanding of novel molecular targets in disease through the immunometabolic regulation of CD4+ T cell by NLRX1 in inflammatory bowel disease. Third, it provides the assessment of novel therapeutics in disease through the evaluation of LANCL2 activation in influenza virus infection. In total, the computational and experimental strategies used in this dissertation are critical foundational pieces in the framework of precision medicine initiatives that can assist in the diagnosis, understanding, and treatment of disease. / Ph. D.

Noncanonical NF-KB is an alternative NF-KB pathway that is critically involved in the development and maturation of the adaptive immune system. As such, it has typically been studied in B and T cell biology without application to complex organ systems such as the gut. The following work explores the contribution of noncanonical NF-KB to inflammatory and neoplastic disease in the gastrointestinal (GI) system, as well as the effects of its loss on GI health. Chapter 1 opens with an overview of gastrointestinal homeostasis and inflammation, with emphasis on the particular diseases studied in this body of work. Chapter 2 focuses on a review of noncanonical NF-KB function and components, as well as its applications in inflammatory bowel disease (IBD), a quintessential example of disruption of intestinal homeostasis. In Chapter 3 we determine the role of noncanonical NF-KB in allergic disease of the upper gastrointestinal tract, namely a novel model of the disease eosinophilic esophagitis. Our studies revealed that loss of NF-KB-inducing kinase (NIK), the bottleneck molecule in noncanonical NF-KB signaling, results in targeted esophageal inflammation, remodeling, and gene expression changes that are comparable to the human disease. In Chapter 4, we examine the role of noncanonical NF-KB in inflammatory bowel disease using biopsy samples from human IBD patients, and compare the expression of various components of the pathway to inflammation status and treatment response. Noncanonical NF-KB is upregulated in IBD patients, and also appears to be specifically upregulated in patients that have lost response to anti-TNF inhibitors, which are potent drugs that are widely used to treat IBD. In Chapter 5 we focus on NIK and its effects on stem cell function, growth, and inflammation-induced cancer in the gut. Loss of NIK in mice results in alterations in colonic stem cell function and changes in colonic microbiome, which predisposes them to the development of inflammation-induced carcinogenesis. Indeed, in human patients with colorectal cancer, noncanonical NF-KB is also suppressed. Overall, we have discovered multiple novel roles of noncanonical NF-KB signaling at multiple levels in the gut and in the context of a variety of diseases, and have greatly expanded the current body of knowledge as to the functions and effects of this pathway. / Ph. D. / The gastrointestinal system has a complex set of checks and balances to maintain overall health. If factors involved in the promotion or suppression of inflammation, the regulation of growth, or the prevention of tumor formation become dysregulated, there can be catastrophic consequences for the human body. The aim of this work is to investigate a pathway called noncanonical NF-κB in the development of various diseases in the GI tract. Noncanonical NF-κB is not a well understood pathway and to date has mostly been studied in the context of white blood cell development. However, we discovered that noncanonical NF-κB has several very important functions in the GI tract that have implications in conditions such as inflammatory bowel disease and colorectal cancer. First we explored the role of noncanonical NF-κB in the upper GI tract, namely the esophagus, and found that this signaling pathway is critically involved in the movement of white blood cells called eosinophils to the esophagus, resulting in throat inflammation in both mouse models and human patients. Secondly, we determined that this same pathway also has effects in the lower GI tract. Human patients with inflammatory bowel disease, especially those who develop resistance to popular medications, see an upregulation of this pathway in their colon tissue. Loss of this pathway in the colons of mice also causes changes in growth of the colonic epithelium, and predisposes them to the formation of colon cancer. Interestingly, in human colon cancer patients, we also see similar changes in expression of genes associated with this pathway. Overall, we have found many new and exciting roles for this underappreciated pathway in the gut.

Machine learning can provide insight and support for a variety of decisions. In some areas of medicine, decision-support models are capable of assisting healthcare practitioners in making accurate diagnoses. In this work we explored the application of these techniques to distinguish between two diseases in veterinary medicine; inflammatory bowel disease (IBD) and alimentary lymphoma (ALA). Both disorders are common gastrointestinal (GI) diseases in humans and animals that share very similar clinical and pathological outcomes. Because of these similarities, distinguishing between these two diseases can sometimes be challenging. In order to identify patterns that may help with this differentiation, we retrospectively mined medical records from dogs and cats with histopathologically diagnosed GI diseases. Since the pathology report is the key conveyer of this information in the medical records, our first study focused on its information structure. Other groups have had a similar interest. In 2008, to help insure consistent reporting, the World Small Animal Veterinary Association (WSAVA) GI International Standardization Group proposed standards for recording histopathological findings (HF) from GI biopsy samples. In our work, we extend WSAVA efforts and propose an information model (composed of information structure and terminology mapped to the Systematized Nomenclature of Medicine - Clinical Terms) to be used when recording histopathological diagnoses (HDX, one or more HF from one or more tissues). Next, our aim was to identify free-text HF not currently expressed in the WSAVA format that may provide evidence for distinguishing between IBD and ALA in cats. As part of this work, we hypothesized that WSAVA-based structured reports would have higher classification accuracy of GI disorders in comparison to use of unstructured free-text format. We trained machine learning models in 60 structured, and independently, 60 unstructured reports. Results show that unstructured information-based models using two machine learning algorithms achieved higher accuracy in predicting the diagnosis when compared to the structured information-based models, and some novel free-text features were identified for possible inclusion in the WSAVA-reports. In our third study, we tested the use of machine learning algorithms to differentiate between IBD and ALA using complete blood count and serum chemistry data. Three models (using naïve Bayes, neural networks, and C4.5 decision trees) were trained and tested on laboratory results for 40 Normal, 40 IBD, and 40 ALA cats. Diagnostic models achieved classification sensitivity ranging between 63% and 71% with naïve Bayes and neural networks being superior. These models can provide another non-invasive diagnostic tool to assist with differentiating between IBD and ALA, and between diseased and non-diseased cats. We believe that relying on our information model for histopathological reporting can lead to a more complete, consistent, and computable knowledgebase in which machine learning algorithms can more efficiently identify these and other disease patterns. / Ph. D.

Intestinal homeostasis is a delicate balance between suppression of immune responses against innocuous antigens and stimulation of immune responses against pathogens. Type I interferon (IFN-1) cytokines have both immunostimulatory and immunomodulatory effects. Colon mononuclear phagocytes (MP) constitutively produced IFN-1 in a TRIFdependent manner. We explored the function of endogenous IFN-1 in the colon using the T cell adoptive transfer model of colitis. Transfer of CD4⁺CD45RB^hi naïve T cells from wild type (WT) or IFNAR subunit 1 knockout (IFNAR1^-/-) mice into RAG^-/- hosts resulted in similar onset and severity of colitis. In contrast, RAG^-/- x IFNAR1^-/- double knockout (DKO) mice developed accelerated severe colitis compared to RAG^-/- hosts when transferred WT CD4⁺CD45RB^hi T cells. Although WT or IFNAR1^-/- regulatory T (Treg) cells equally prevented disease caused by CD45RB^hi naïve T cells, WT Treg cells co-transferred with naïve CD4⁺ T cells into DKO recipients failed to expand or maintain Foxp3 expression and gained effector functions in the colon. IFNAR signaling on host hematopoietic cells inhibited T cell-mediated colitis, but not innate colitis. MPs isolated from the colon lamina propria (cLP) required IFNAR signaling for the production of the anti-inflammatory cytokines, IL-10, IL-27, and IL-1RA, but not for the production of classic pro-inflammatory cytokines. IFN-1-dependent secretion of IL-1RA was particularly important in inhibiting the migration of inflammatory DCs with potent T cell proliferative capacity from the cLP to the mesenteric lymph nodes. Finally, preliminary results suggested that IFN-1 may shape the commensal microbiota, but is not essential for controlling specific colitis-inducing bacteria.

Introduction: Early growth response 1 (EGR1) is a zinc-finger transcription factor involved in the regulation of cell growth. It can act as either a tumour suppressor or a tumour promoter with a role in the induction of apoptosis in cancer cells by various pathways and is likely to play a role in colorectal cancer (CRC). EGR1 also appears to play a significant role in inflammatory pathways, therefore a possible role in Inflammatory Bowel Disease (IBD) is hypothesised. Patients with IBD have a greater risk of developing CRC, which is increased with duration of symptoms and severity of inflammation and dysplasia. The aim of this study is to determine whether EGR1 is differentially expressed in diseased colon tissue and to investigate novel EGR1-protein interactions in CRC cell lines. Methods: The relative EGR1 expression in CRC cell lines and in normal mucosa and tumours of colorectal cancer patients was determined by qRT-PCR. IBD patient samples were also examined for differential EGR1 expression levels by qRT-PCR, before and after stimulation with inflammatory mediators. Statistical analysis of the data was performed using ‘R’ statistical package, with the mixed-model ANOVA. Statistical significance was set at < 0.05. The genotype of three EGR1 variants was determined in the samples using PCR and sequencing, and the methylation status of regions of the EGR1 promoter was determined using bisulfite sequencing. A yeasttwo hybrid screen was conducted with EGR1 as bait, and screened against a SW480 CRC cell line library. Interesting novel interactions were investigated using immunocytochemistry and immunoprecipitation, as was the novel interaction between EGR1 and NOD2 and between EGR1 and components of the cytoskeleton. Results: Investigation into the relative EGR1 mRNA expression in CRC has shown that there is differential expression of EGR1 between matched normal mucosa and tumour. EGR1 expression is decreased in IBD patients compared with healthy controls. Induction of EGR1 by inflammatory stimuli also appears to be aberrant in these patients. The differential expression of EGR1 was not associated with aberrant methylation of a large region of the EGR1 promoter in either the CRC or IBD patients or with the genotype of EGR1 variants. EGR1 localises to both the cytoplasm and the nucleus in CRC cell lines and this study demonstrate interactions with the IBD susceptibility protein NOD2 and with components of the cyotskeleton. A yeast-two hybrid screen conducted with EGR1 as bait using a CRC cell line library has identified several other novel protein interactions of EGR1 in CRC cell lines. Conclusion: EGR1 is differentially expressed in both CRC and IBD, and in the case of IBD shows aberrant activity, suggesting that EGR1 may play a role in both colorectal diseases. EGR1 interacts with the IBD protein NOD2, and components of the cytoskeleton in CRC cells. Several novel protein interactions with EGR1 have been identified and warrant further study.