Sampling the environment: Antigen presentation and T cell regulation by intestinal epithelial cells

The human intestine hosts a huge number of friendly bacteria that live in a mutually beneficial arrangement with us - we provide a nutrient-rich habitat for them and they produce some vitamins and help prevent infection with harmful bacteria. The basis of this peaceful co-existence is that our immune system learns to tolerate these beneficial bacteria, while remaining poised to respond to any harmful bacteria that infect our intestine. However, in some individuals, this tolerance breaks down and the immune system attacks the beneficial bacteria, leading to the development of inflammatory bowel diseases (IBD), which are chronic, debilitating disorders of the intestine. The causes of IBD are not known and there is no current cure. Instead, treatment involves long-term administration of immune suppressive drugs, which have side effects that include an increased risk of infection and cancer. A better understanding on how the immune system malfunctions in the intestine during IBD is necessary in order to develop new and improved therapies.

The cells that line the human gut are called intestinal epithelial cells, which form a key barrier that limits exposure of our immune system to the bacteria that live in our gut. However, how these epithelial cells interact with our immune system and contribute to the maintenance of tolerance in our intestine is not well understood. In this project we will investigate the response pattern of the intestinal epithelial cell in the healthy gut and during inflammation and specifically focus on the crosstalk between epithelial cells and the immune system and look at how this is altered during harmful inflammatory responses, like IBD.

T helper cells, a type of white blood cells, represent one of the key cell types of the immune system. In IBD patients, the harmful inflammation is caused by T helper cells that respond to beneficial intestinal bacteria. However, T helper cells do not recognise the bacteria directly, but are activated by other types of white blood cells that take up and digest the bacteria and then present fragments of the bacterial proteins, termed antigens, on their surface. However, it has been found that intestinal epithelial cells are also capable of presenting antigens, but whether this leads to activation of T helper cells is unclear and it has been proposed that instead this may be an important way of inducing tolerance to beneficial bacteria in the intestine. The key aim of this project is to study how antigen presentation by intestinal epithelial cells influences T helper cells. To achieve this, we will use genetically modified mice in which the intestinal epithelial cells lack the ability to present antigens. We will analyze the T helper cell responses in the gut of those animals and examine if these change during different models of intestinal infection and inflammation. Any alterations will reveal how antigen presentation by intestinal epithelial cells impacts on the reactivity of the immune system towards intestinal bacteria.

To identify key molecules involved in the crosstalk between intestinal epithelial cells and T helper cells, we will use a new technique that allows us to grow and culture the intestinal epithelial cells. The great advantage of this 'in vitro' system is that the factors and cells involved can be selectively manipulated and key pathways can be clearly identified. Furthermore, intestinal epithelial cells will be grown from healthy people or patients with IBD and tested for their ability to present antigen. A better understanding of how intestinal epithelial cells contribute towards the control of T helper cell responses in the gut may lead to the development of novel therapies for IBD.

The aim of the project is to define the response of intestinal epithelial cells (IEC) during intestinal inflammation and to assess how this impacts on intestinal immune regulation. This is of special interest in the context of inflammatory bowel disease (IBD), were regulatory pathways fail and the immune system drives a pathogenic T cell response towards commensal bacteria.
Our preliminary data indicate that the antigen processing and presentation pathway is the most highly enriched pathway in IEC during colitic conditions. Therefore, we aim to assess the functional consequences of MHCII antigen presentation by IEC on the immune cell compartment during homeostasis and during conditions of intestinal infection and inflammation. This will be achieved by generating transgenic mice in which MHCII expression is selectively ablated in IEC through the lineage-specific expression of the Cre recombinase. The CD4+ T cell compartments of these mice will be analyzed during homeostasis and in models of bacterially-triggered intestinal inflammation that reproduce many aspects of the inflammatory pathology associated with human IBD.
These analyses will be complemented by using primary IEC organoids as APC in a co-culture system with ova-specific CD4+ T cells (OTII cells). We will use this ex vivo system to address the antigen processing and presentation capabilities of IEC as well as the impact it has on the activation, proliferation and differentiation of CD4+ T cells.
Furthermore, to confirm the validity of our results in a human system, primary IEC organoids will be generated from healthy or IBD patients and analysed for their antigen processing and presentation capabilities, as well as their responses to inflammatory stimuli.
A better understanding of the crosstalk between IEC and T cells in the intestinal mucosa may lead to the development of novel therapies for IBD.

Direct academic beneficiaries of the knowledge gained through this project will include other researchers in the UK and abroad who are working on the pathogenesis of inflammatory bowel disease (IBD). In addition, we envisage that our findings may have a significant impact not only in the field of mucosal immunology, but also on additional disciplines in areas of immunology and chronic inflammation. The mechanisms of T cell regulation by local tissue cells are relevant not only in the intestine, but may also apply to inflammatory or infectious diseases at other barrier surfaces, such as the lung or skin. Therefore, the results of our project may stimulate other researchers to undertake a wider assessment of the role of epithelial cells as antigen presenters in other contexts.

As well as offering new avenues for the regulation of harmful inflammatory pathology, our results may reveal strategies to circumvent normal regulatory pathways that operate in the intestine and in other tissues. Many major pathogens responsible for extensive mortality and morbidity, such as influenza virus, HIV, enteropathogenic bacteria and parasites, invade the body through mucosal surfaces. Therefore, a better understanding of the role of tissue cells like epithelial cells in shaping local T cell responses could help uncover new strategies to optimise immune defense pathways at mucosal surfaces, which is relevant for designing vaccines against mucosal diseases.

The results of this research may also have potential benefits for the pharmaceutical industry. The identification of novel IEC-T cell crosstalk pathways and detailed characterization of their effects in the healthy and diseased gut should identify new targets for drug design and may stimulate the development of new approaches needed to direct drugs to specific host cell types.

Indirectly, in the longer term, the results of this basic research may impact clinical practice in IBD. Identification of novel pathways that contribute to tolerance or regulation at the intestinal mucosa could lead gastroenterologists to investigate new avenues for therapy and to better patient outcomes as new therapies are selectively applied to appropriate patient sub-groups. In turn, these improvements in clinical practice should provide significant financial benefits to local health authorities through a more economical employment of resources. For example, the improved knowledge could help avoid unnecessary use of expensive drugs as well as decreased hospitalization of patients.

The ultimate potential beneficiaries of this basic research are IBD patients. The chronic, debilitating nature of this disease, as well as the side effects associated with most of the long-term conventional immune suppressive therapies, emphasizes the need for new and better treatments that can significantly improve patient health and quality of life. The identification of new targets for biological therapies and effective translation into clinical practice is illustrated by the recent success of TNF blockers, which are now widely employed in IBD patients. However, the high proportion of patients who do not respond, or who become refractory to TNF blockers, illustrates the heterogeneity of these disorders and the need for targeting novel therapies to the patient groups who are likely to derive most benefit. Genetic associations in humans, as well as studies in mouse disease models, implicate epithelial barrier defects as a strong predisposing factor for the development of IBD. Therefore, a better understanding of the responses of IEC in the inflamed environment, and their effects on the regulation of pathogenic T cell responses in the gut, may facilitate the development of novel therapeutic targets for a selected subsets of IBD patients.