The ability to sense and respond to external environmental signals is closely regulated by a plurality of cell signaling pathways, thereby maintaining homeostasis. In particular, the inflammatory signaling cascade contributes to cellular homeostasis and regulates responses prompted by external stimuli. Such responses are diverse and range from a variety of processes, including tissue repair, cell fate decisions, and even immune-cell signaling. As with any signaling cascade, strict regulation is required for proper functioning, as abnormalities within the pathway are often associated with pathologic outcomes. A hyperactive inflammatory response within the gastrointestinal tract, for example, contributes to inflammatory bowel disease (IBD), presenting as Crohn’s disease or ulcerative colitis. Furthermore, as a chronic condition, IBD is associated with an increased risk for the development of colitis-associated cancer. In order to resolve inflammation and thus restore homeostasis, negative regulation may be utilized to mediate the activity of inflammatory molecules. The mechanistic action of a specific negative regulator of interest, interleukin receptor associated kinase M (IRAK- M), is explored in detail within the present dissertation. Investigation of IRAK-M in mouse models of colitis, which mimics human IBD, and in mouse models of inflammation-driven tumorigenesis, which models colitis associated cancer, demonstrated that loss of this molecule contributes to host protection. Therefore, IRAK- M may be a suitable target for inhibition in order to advance therapeutic options for human patients afflicted with a GI-related inflammatory disease, such as IBD and colitis associated cancer. Furthermore, an ex vivo method that models the interaction of intestinal epithelial cells with microbes present in the GI tract was optimized and is described in the present dissertation. This method takes advantage of primary intestinal derived organoids, also termed “mini-guts”, which display similar features corresponding to intestinal tissue in vivo. For this reason, the use of “mini-guts” has several advantages, particularly for the enhancement of personalized medicine. The method discussed herein aims to normalize experimental conditions in order to enhance reproducibility, which can further be used to uncover microbial-epithelial interactions that contribute to a pathological state, such as IBD. Finally, this method of intestinal epithelial cell culture was utilized to evaluate the role of a protein, termed NF-κB inducing kinase (NIK), in intestinal epithelial cell growth and proliferation. Ultimately, ex vivo organoid culture can serve as an important model system to study the contribution of NIK in intestinal stem cell renewal, cancer progression, as well as in maintenance of the integrity of the gastrointestinal barrier. / Ph. D. / Inflammation is a tightly regulated physiologic process that is employed by body systems such as the gastrointestinal (GI) tract to handle pathogenic insult, aid in wound healing, and help prevent infections. When abnormal inflammatory responses occur, this can lead to the progression of severe diseases such as ulcerative colitis and Crohn's disease. When inflammation persists in the GI tract, such as in inflammatory bowel disease, this can predispose patients to the development of inflammation- associated colorectal cancer. In order to improve the treatment options for patients afflicted with these maladies, this dissertation is aimed at studying the signaling pathways of the innate immune system that regulate such inflammatory responses. Furthermore, this body of work encompasses a detailed method for isolating and culturing intestinal stem cells, which can be applied in personalized medicine for patients with intestinal diseases. This method was utilized in this dissertation to study genetically modified intestinal stem cells, and can further be used to investigate the interactions of intestinal epithelial cells with pyogenic bacteria that contribute to inflammatory maladies in the GI tract.

The interaction between epithelial cells and macrophages is integral to mucosal immune fate: determining the decision between tolerance and immune activation/inflammation. Endotoxin tolerisation (ET) is a circumstance where cells go through a hypo-responsive state, unable to respond to further endotoxin-LPS challenge. Mucosal macrophages (MΦs) have a dual functionality that determines tolerance to commensal organisms or immune response to entropathogens such as E. coli. In the case of mucosal inflammatory pathologies, such as Crohn’s disease, this state of tolerance is broken, resulting in destruction of gut mucosal tissue where the macrophage phenotype has been altered from a regulatory M2-like subset phenotype to an inflammatory M1-like subset phenotype, responding to both pathogenic and commensal bacteria. Chronic inflammation by bacterial pathogen related molecular patterns (PAMPs), such as LPS, is well established to induce tolerisation. The aims of this project were firstly, to characterise the control of macrophage differentiation in a mucosal setting by investigating the immunomodulatory effects of PAMPs, such as LPS in presence or absence of TNFα and to investigate ET mechanisms associated with MΦ subsets responding to the entropathogen E. coli K12-LPS. Secondly, to investigate the effect of epithelial cells on macrophage subsets behaviour upon inflammation and ET. M1- and M2-like MΦs were generated in vitro from the THP-1 monocyte cell line by differentiation with PMA and vitamin D3, respectively, whereas differentiated epithelial cells (Caco-2) were obtained by long term culturing for 21 days. A transwell co-culture system of Caco2 cells and MΦ subsets was developed to mimic the cell-to-cell cross-talk between epithelial cells and immune cells. Mono- and co-culture models were pre-treated with either LPS, TNFα or IL-1β prior to stimulation by PAMPs. TNFα, IL-1β, IL-18, IL-6 and IL-10 were qualified by ELISA. Cytokines, PRRs and endogenous negative regulatory molecules were detected by RT-PCR and WB and epithelial barrier function was measured by trans epithelial electrical resistance (TEER). ET induced by K12-LPS failed to demonstrate a differential subset-specific response in MΦ mono-culture system whereas, LPS differentially suppress LPS induced cytokine expression in MΦ co-culture system. Tolerised M1- and M2-like MΦs exhibited a significant reduction in expression and secretion of pro-inflammatory cytokines and comparable levels of anti-inflammatory cytokine, IL-10. The suppression of pro-inflammatory cytokine in these MΦs appeared to be linked to the differential TLR4 expression and up-regulation of negative regulators, such as IRAK-M and Tollip. In addition, MΦ subsets differentially responded to inflammation induced by pro-inflammatory cytokines, TNFα and IL-1β in mono- and co-culture models. In conclusion, tolerisation induced in MΦs is presented by the suppression of pro-inflammatory cytokine, which is associated with corresponding up-regulation of IL-10, TLR4 receptor and the negative regulators, in a subset-independent manner. In the case of cross-talk between epithelial cells and macrophages however, a differential sensitivities to ET was displayed. These findings allow more understanding of MΦ subsets functions and ET mechanisms, which may be beneficial for the development of in-vitro models of MΦ subsets and therapeutics targeting Crohn’s diseases.