Celiac disease is an autoimmune enteropathy driven by the ingestion of gluten in genetically predisposed individuals carrying HLA-DQ2 and/or -DQ8 genes. Currently, the only available treatment is a strict, life-long, gluten-free diet (GFD), which is very restrictive and not always effective, highlighting the need for alternative therapies. Celiac disease requires activation of both the innate (intraepithelial lymphocytes or IELs) and adaptive (lamina propria CD4+ T cells) arms of the immune system. Activation of these two pathways leads to the destruction of IEC and villous atrophy. Thus, IEC damage is a hallmark of CeD. However, IECs are not only the target of tissue damage; they also actively participate in CeD pathogenesis by translocating gluten peptides, expressing stress-induced markers, and releasing TG2 into the gut lumen to generate TG2-gluten complexes. Although IECs are known to express MHC, their role in gluten-dependent T cell activation has never been proven, partly because of the lack of an appropriate in vitro epithelial model expressing human MHC class II. This thesis aims to address this gap by developing a humanized organoid monolayer expressing the CeD risk gene HLA-DQ2.5, to investigate the interaction between IEC-gluten-T cells. The expression of epithelial MHC class II was evaluated in active and treated CeD patients, as well as in gluten-immunized and control (non-immunized; NI) DR3-DQ2.5 transgenic mice that express only CeD-associated MHC class II (HLA-DQ2.5). Active CeD patients and gluten-immunized DR3-DQ2.5 mice demonstrated higher expression of epithelial MHC class II compared with their treated and NI counterparts. Organoid monolayers developed from these mice and were treated with or without IFN-. Organoid monolayers derived from gluten-immunized DR3-DQ2.5 mice showed higher expression of MHC class II compared with NI mice, and this expression was upregulated by IFN- treatment. The functional consequences of MHC class II expression were determined by co-culturing organoid monolayers with CD4+ T cells in the presence of gluten and zein (a non-gluten protein). In the co-culture, gluten, but not zein, enhanced CD4+ T cell proliferation, activation, and release of cytokines, including IL-2, IFN- and IL-15, in the co-culture supernatants. Bacteria have recently emerged as modulators of inflammation in patients with CeD. It has been shown that opportunistic pathogens, including Pseudomonas aeruginosa, partially metabolize gluten into more immunogenic peptides. As such, the role of bacterially modified gluten in modulating the T cell response was assessed using the in vitro co-culture system I described. For this, monolayers were treated with the gluten pre-digested, or not, by elastase-producing P. aeruginosa or its lasB mutant. Gluten metabolized by P. aeruginosa, but not by the lasB mutant, significantly increased CD4+ T cell responses. In conclusion, MHC class II-expressing organoid monolayers are a functional model that can promote T cell responses under certain conditions. The model described in this thesis reveals a new immunomodulatory role for IECs in activating CD4+ T cells through MHC class II. This mechanism may serve to localize and further increase injury to the epithelium caused by gluten-specific CD4+ T cells in CeD. Therefore, therapeutics directed at IECs may offer a novel approach for modulating both adaptive and innate immunity in CeD, providing an alternative or adjuvant therapy to the current GFD treatment. / Thesis / Doctor of Philosophy (PhD) / Celiac disease is one of the most common food sensitivities, affecting approximately 1 in 100 people worldwide, including Canada. It occurs in people with specific genes (DQ2 and/or DQ8) when they eat gluten-containing foods such as wheat, barley, and rye. In people with celiac disease the immune system overreacts to gluten, damaging the lining of the upper gut, which we call “epithelium. This lining of cells constitutes the first barrier between the external world and our body, allowing in healthy conditions for nutrients to be absorbed but blocking the passage of gut microbes, some of which can cause disease or worsen gut inflammation. In patients with celiac disease, gluten crosses the epithelium into the gut tissue, where it activates specific cells of the immune system called “T cells”. Recently, there has been growing interest in whether the gut lining itself plays a role in triggering this immune response in celiac disease, though this has not yet been proven. If proven, this would suggest that the gut lining is responsible for directing the harmful immune response to gluten and should be considered a target site when developing therapies to prevent or treat celiac disease. This concept has been difficult to prove because we do not have a model to investigate this question. Such a model would require a gut lining that carries the genes linked to celiac disease. My thesis describes the development of such a model, made of a gut lining from a mouse genetically modified to carry human celiac disease genes. Using this model, I found that when the gut lining was exposed to certain molecules present in celiac patients (cytokines), it switched on other molecules that ultimately activated T cells. Additionally, I demonstrated that certain microbes, such as Pseudomonas aeruginosa, which are present in higher numbers in the upper gut of patients with celiac disease, can break down gluten into fragments that further activate T cells. The results validated the use of this model to understand what other co-factors can tip the balance in a person with celiac genes to remain healthy or develop inflammation. In summary, I demonstrated that the gut lining expressing celiac genes actively participates in the activation of immune cells that drive intestinal damage in celiac disease. This new model is a novel tool to continue to identify additional co-factors that predispose patients to celiac disease, as well as to screen for novel therapies for celiac disease. This is important, as the only currently available treatment is a strict lifelong gluten-free diet, which has many limitations, including frequent contamination and celiac disease reactivation.