Immunity and metabolism have been viewed as separate fields, however recent evidence show that these two systems are intimately integrated, share resources and cross-regulate each other. Activated immune cells have to alter their metabolism in order to support effector functions. On the other hand, viruses are obligatory parasites that counter and exploit host pathways, including metabolism, to effectively propagate. Like immune cells, viruses have to alter the metabolic profile of infected cells in order to propagate. The regulation of metabolism in immune cells or virally infected cells has been well studied. However, the precise metabolic regulation that ensues when both immune system and viral infection in immune cells interact and compete for the limited resources and metabolic pathways available is not clear. In this thesis, I have sought to investigate the integrative process by studying the metabolic programming of macrophages infected with murine cytomegalovirus (MCMV) The central hypothesis of this thesis is that productive infection of macrophages by MCMV takes advantage of the early inflammatory metabolomic reprogramming of activated macrophages to establish infection, and modulates metabolism at late stages of infection towards fatty acid (FA) production to promote viral progeny. To study this interaction, I have analysed the temporal profile of the transcriptome and metabolome of bone marrow derived macrophages (BMDM) infected with productive (WT) and non-productive (attenuated) (MCMV) strains. This aimed to unravel the host-directed versus virus-driven metabolic alterations. I show evidence indicating that during early times of productive and non-productive MCMV infection glycolysis is, in infected BMDM, markedly increased. Furthermore, pharmacological and siRNA mediated inhibition of glycolysis resulted in attenuation of viral growth demonstrating the dependency of MCMV on this pathway. Additionally, using interferon receptor A (IFNAR) and interferon receptor A (IFNB) deficient BMDM showed that type-I interferon (IFN) signalling is essential for the early upregulation of glycolysis that was observed. In addition to the changes in glycolysis, MCMV infection alters the tricarboxylic acid (TCA) cycle in infected BMDM. Metabolomic and transcriptomic data revealed a shift from catabolic to anabolic function for the TCA to promote production of TCA intermediates. Finally, the urea cycle is also altered both on transcriptional and metabolomic level, consistent with the support of Nitric oxide (NO) production which is a hallmark metabolite in classically activated macrophages. These changes observed in the TCA cycle and glycolysis are consistent with supporting the FA elongation pathway during late time points of productive infection. Only productive MCMV infection upregulates this pathway. At the same time, pharmacological and siRNA mediated inhibition of FA elongation pathway greatly attenuates viral growth. This indicates that MCMV growth is dependenton FA elongation. The effect was very specific for the elongation and not the de novo synthesis pathway indicating that MCMV remodels FA that already in the cells. It is argued, that in agreement to known literature, MCMV uses these FA for the formation of its lipid membrane. To further investigate the dependency of MCMV on FA elongation pathways I studied additional lipids pathway associated with the former. I found that MCMV infection also upregulates the triacylglycerol formation and membrane remodelling pathways, which are dependent on FA biosynthesis and elongation. The inhibition of triacylglycerol formation and membrane remodelling pathway also attenuated MCMV growth. This indicates that apart from the formation of its lipid membrane MCMV requires FA to remodel the cellular environment. I have also explored the effects of infection on regulating lipid mediators, in particular eicosanoids. Eicosanoids are lipid signalling molecules that can act as potent inflammation modulators. Here I demonstrated that productive MCMV infection specifically increases PGE2 production in infected BMDM. Moreover, addition of PGE2 increased viral replication in infected fibroblasts in comparison to non-treated cells, while pharmacological blocking of EP4 (PGE2 receptor) rescued the phenotype. These studies reveal how MCMV advantageously use inflammatory lipid pathways to promote growth In conclusion, the data presented in this thesis support my hypothesis and provide an insight in the role of metabolism during viral infection. Evidence is provided to show that MCMV co-ops the early alterations that metabolic pathways undergo in activated macrophage, including but not limited to glycolysis, TCA cycle and urea cycle. These early changes in metabolism appear to be coupled with upregulation of FA elongation pathways and remodeling of lipids in infected cells. Finally, MCMV co-ops the function of regulatory lipids, in particular PGE2, to promote viral growth. It is further argued that MCMV productive infection dictates these fatty acid metabolism alterations in order to remodel the host cell's environment, regulate the immune system response and provide resources for its lipid membrane.

The intestinal tissue is charged with a delicate immunological task. The intestinal immune system needs to be tolerant towards nutrients and microbiota present in the intestinal lumen, while simultaneously detecting and responding to dangers such as pathogens. A single-cell layer of intestinal epithelial cells (IECs) acts as a first line of defence. There is a T cell population located between the IECs that have been named intraepithelial lymphocytes (IELs). As the main lymphoid population within the intestinal barrier, IELs are thought to have an important role in intestinal homeostasis maintenance, as well as a role in intestinal inflammatory and autoimmune diseases such as inflammatory bowel disease and celiac disease. Despite extensive research on IEL biology, there are still questions remaining in terms of the development, maintenance and activation of IELs. Furthermore, IELs survive poorly in vitro, which hinders mechanistic insights. In this thesis, a co-culture system between IELs and intestinal organoids, "mini-guts", provides an in vitro model for IELs. With this IEL-organoid co-culture system, IELs associated with the organoids survive for at least 4 days. Additional findings suggest that IELs are kept in a poised state of activation due to differences in their mitochondria compared to other T cells found in spleen, lung and skin. Upon activation or intestinal inflammation, the mitochondrial mass in IELs increases. This increase correlates with effector functions such as cytokine production and proliferation. In addition, the composition of the mitochondria-specific lipid, cardiolipins, alters drastically in IELs after activation. These data support a model of mitochondria-dependent activation of IELs. The mitochondria-dependent activation in IELs appears to have at least two pathways: one T cell receptor-dependent and one microbiota-dependent. The latter pathway suggests a model in which IELs can become activated regardless of the cause of intestinal epithelial barrier damage.

Lors de l’obésité, les défauts d’expansion du tissu adipeux blanc sont à l’origine des désordres métaboliques. Lorsque les adipocytes atteignent leurs capacités maximales de stockage de triglycérides, des dépôts ectopiques de lipides apparaissent dans le foie et le muscle conduisant à la résistance à l’insuline. De plus, les adipocytes dysfonctionnels sécrètent des facteurs d’alertes établissant une inflammation dans le tissu adipeux. Cette inflammation est médiée par les communications entre les adipocytes et les cellules immunitaires qui sont contrôlées par l’endocytose et le trafic intracellulaire. L’endocytose et les protéines Rab gouvernant ce processus pourraient être des éléments clés de l’expansion du tissu adipeux. L’équipe a démontré que l’expression de Rab4b était diminuée dans le tissu adipeux de patients obèses diabétiques et de souris obèses. Nos travaux montrent que l’expression de Rab4b est diminuée dans les lymphocytes T du tissu adipeux de souris et de patients obèses. L’invalidation de Rab4b dans les lymphocytes T in vivo induit une résistance à l’insuline et une accumulation d’acides gras dans le foie et dans le muscle sous régime normal. Ces défauts sont dus à une inhibition de l’adipogenèse par l’IL-6 et l’IL-17, limitant l’expansion du tissu adipeux. L’augmentation de ces cytokines pro-inflammatoires est une conséquence de l’augmentation du nombre de lymphocytes Th17 et une diminution des lymphocytes T régulateurs. Nous décrivons un nouveau mécanisme par lequel l’expression de Rab4b dans les lymphocytes T régule les complications métaboliques de l’obésité en changeant les sous-populations de cellules immunitaires dans le tissu adipeux. / Expendability defect of adipose tissue during obesity is at the basis of obesity-related metabolic complications. Indeed, when adipocytes reach their maximal triglyceride storage capacity, ectopic lipid depots are appearing in liver and muscles, leading to insulin resistance. Moreover, dysfunctional adipocytes secrete alarming factors leading to adipose tissue inflammation. This inflammation is sustained by adipocytes and immune cells communications that are controlled by endocytosis and intracellular trafficking. Endocytosis and its governing proteins, the Rab GTPases, could be pivotal in the regulation of adipose tissue expandability. Our team has demonstrated that Rab4b expression is reduced in obese diabetic patients and mice adipose tissues. The present work demonstrates that Rab4b is decreased in adipose tissue T cells in both obese patient and mice. The depletion of Rab4b in T cells in vivo leads to insulin resistance and lipid accumulation in liver and muscles under normal diet. These defects are due to adipogenesis inhibition by IL-6 and IL-17, which limits adipose tissue expansion. These pro-inflammatory cytokines are increased in adipose tissue of the mice depleted for Rab4b in T cells because the number of Th17 is increased at the expense of the number of regulatory T cells. We describe here a new mechanism in which Rab4b expression in T cells control obesity-related metabolic complications by tuning T cells subpopulations in adipose tissue.

Suppression of anti-tumour immunity by the tumour microenvironment remains a major barrier to the development of broadly effective immunotherapies to treat solid tumours. Cytotoxic natural killer (NK) cells are vital to anti-cancer immunity and have shown clinical efficacy for treating hematologic malignancies. However, NK cell therapies have failed to be effective against solid tumours as cytotoxic NK cells become dysfunctional in the tumour microenvironment. While tumours hinder cytotoxic NK cells, they stimulate the tumour-promoting functions of regulatory NK cells. The mechanisms that dictate NK cell polarization and their fate in the tumour microenvironment remain poorly defined but harbour key therapeutic potential. Glucose-driven cellular metabolism has emerged as a central regulator of NK cell anti-tumour activity. Notably, tumour cells have deregulated metabolism, causing a metabolically hostile environment that is low in glucose and oxygen and high in metabolic waste. In the work presented, we demonstrate that NK cells expanded from cancer patients or healthy donors exert strong anti-tumour activity and dismantle the immunosuppressive tumour microenvironments of advanced ovarian and lung cancer. As a result, expanded NK cells were capable of sensitising initially non-responsive patient tumours to PD1 checkpoint-blockade therapy. Further, we uncover that the activity of cellular metabolic pathways plays a key role in NK cell functional fate in tumour microenvironment. We show that the tumour microenvironment induces paralysis of cytotoxic NK cell glucose metabolism to cause their dysfunction. However, reprogramming of NK cell metabolism through expansion arms expanded NK cells with enhanced metabolic flexibility which enabled their anti- tumour activity to be paradoxically strengthened by the tumour microenvironment. We further identify that regulatory NK cells have a distinct metabolic program compared to cytotoxic NK cells, including lower glucose-driven metabolism, that is amenable with the tumour microenvironment. Our work provides new mechanistic insight into how NK cell fate is regulated and how the pathological environment of a tumour capitalizes on this. This knowledge provides new therapeutic targets to intervene with the suppression of cytotoxic immunity in tumours. Further, this work identifies that expanded NK cells are a promising therapeutic candidate that exploit the metabolic hostility of the tumour microenvironment and synergize with other immunotherapies. / Thesis / Candidate in Philosophy / Harnessing the body’s natural immune defenses against cancer in the form of immunotherapy has emerged as a powerful treatment modality. Over the past decade, immune cell therapies have revolutionized the treatment of blood cancers like leukemia and lymphoma. Yet despite the potential, immune cell therapies have failed to be broadly effective against solid tumours because the anti-cancer activity of immune cells, such as Natural Killer (NK) cells, becomes severely impaired by the tumour environment. In this work, we identify that NK cells expanded from cancer patients and healthy donors overcome suppression by tumours and eliminate detectable tumour in pre-clinical models of advanced ovarian and lung cancer. These expanded NK cells also enhanced the functions of other immunotherapies. Further, we shed new light on how NK cells become dysfunctional in tumours. We uncover that NK cells undergo a metabolic energy crisis in tumours that causes their dysfunction, but that expanded NK cells have increased metabolic fitness which allows them to overcome this energy crisis and remain highly functional. Finally, we also characterize the metabolism of a subset of NK cells that are tumour-promoting and find that they harbour metabolic advantages to thrive in tumours. Overall, our work provides new insight as to how to overcome immunosuppression by tumours. This work identifies that expanded NK cells are a promising therapeutic candidate that exploit the hostility of tumours and synergize with other immunotherapies.

<p>Proper balancing of the activities of metabolic pathways to meet the challenge of providing necessary products for biosynthetic and energy demands of the cell is a key requirement for maintaining cell viability and allowing for cell proliferation. Cell metabolism has been found to play a crucial role in numerous cell settings, including in the cells of the immune system, where a successful immune response requires rapid proliferation and successful clearance of dangerous pathogens followed by resolution of the immune response. Additionally, it is now well known that cell metabolism is markedly altered from normal cells in the setting of cancer, where tumor cells rapidly and persistently proliferate. In both settings, alterations to the metabolic profile of the cells play important roles in promoting cell proliferation and survival.</p><p>It has long been known that many types of tumor cells and actively proliferating immune cells adopt a metabolic phenotype of aerobic glycolysis, whereby the cell, even under normoxic conditions, imports large amounts of glucose and fluxes it through the glycolytic pathway and produces lactate. However, the metabolic programs utilized by various immune cell subsets have only recently begun to be explored in detail, and the metabolic features and pathways influencing cell metabolism in tumor cells in vivo have not been studied in detail. The work presented here examines the role of metabolism in regulating the function of an important subset of the immune system, the regulatory T cell (Treg) and the role and regulation of metabolism in the context of malignant T cell acute lymphoblastic leukemia (T-ALL). We show that Treg cells, in order to properly function to suppress auto-inflammatory disease, adopt a metabolic program that is characterized by oxidative metabolism and active suppression of anabolic signaling and metabolic pathways. We found that the transcription factor FoxP3, which is highly expressed in Treg cells, drives this phenotype. Perturbing the metabolic phenotype of Treg cells by enforcing increased glycolysis or driving proliferation and anabolic signaling through inflammatory signaling pathways results in a reduction in suppressive function of Tregs. </p><p>In our studies focused on the metabolism of T-ALL, we observed that while T-ALL cells use and require aerobic glycolysis, the glycolytic metabolism of T-ALL is restrained compared to that of an antigen activated T cell. The metabolism of T-ALL is instead balanced, with mitochondrial metabolism also being increased. We observed that the pro-anabolic growth mTORC1 signaling pathway was limited in primary T-ALL cells as a result of AMPK pathway activity. AMPK pathway signaling was elevated as a result of oncogene induced metabolic stress. AMPK played a key role in the regulation of T-ALL cell metabolism, as genetic deletion of AMPK in an in vivo murine model of T-ALL resulted in increased glycolysis and anabolic metabolism, yet paradoxically increased cell death and increased mouse survival time. AMPK acts to promote mitochondrial oxidative metabolism in T-ALL through the regulation of Complex I activity, and loss of AMPK reduced mitochondrial oxidative metabolism and resulted in increased metabolic stress. Confirming a role for mitochondrial metabolism in T-ALL, we observed that the direct pharmacological inhibition of Complex I also resulted in a rapid loss of T-ALL cell viability in vitro and in vivo. Taken together, this work establishes an important role for AMPK to both balance the metabolic pathways utilized by T-ALL to allow for cell proliferation and to also promote tumor cell viability by controlling metabolic stress.</p><p>Overall, this work demonstrates the importance of the proper coupling of metabolic pathway activity with the function needs of particular types of immune cells. We show that Treg cells, which mainly act to keep immune responses well regulated, adopt a metabolic program where glycolytic metabolism is actively repressed, while oxidative metabolism is promoted. In the setting of malignant T-ALL cells, metabolic activity is surprisingly balanced, with both glycolysis and mitochondrial oxidative metabolism being utilized. In both cases, altering the metabolic balance towards glycolytic metabolism results in negative outcomes for the cell, with decreased Treg functionality and increased metabolic stress in T-ALL. In both cases, this work has generated a new understanding of how metabolism couples to immune cell function, and may allow for selective targeting of immune cell subsets by the specific targeting of metabolic pathways.</p> / Dissertation

Trichuris trichiura is a gastrointestinal dwelling nematode that infects almost 500 million people worldwide. T. muris occurs naturally in mice and is very closely related the human whipworm, making it a suitable model to dissect the immune response against the parasite. Studies using the Trichuris muris system have identified CD4+ T cells as dictators of the outcome of infection. In wild type mice, infection with a high dose of T. muris eggs leads to resistance and worm expulsion, which are dependent on a Th2 response and the secretion of type 2 cytokines especially interleukin (IL) 13. Chronicity is dependent on a Th1 response and occurs when mice are infected with a low dose of T. muris eggs. It is well established that metabolic changes are essential to promoting T cell activation and effector function. Moreover, during chronic infection the host immune system is continuously exposed to parasite antigen, which represents a metabolic challenge. This thesis has investigated the importance of T cell metabolism during response against T. muris. Data presented here show that low and high dose T. muris infections promote upregulation of the glycolytic pathway in CD4+ T cells. During later stages of chronic infection, CD4+ T cells displayed supressed glycolysis and mitochondrial respiration, and may be due to metabolic modulation imposed by the parasite. Leucine uptake via the amino acid transporter Slc7a5 was previously shown to be required for mTORC1 activation and for T cell effector function. Data presented here show that in early stages following a high dose T. muris infection, mice that lack Slc7a5 in T cells have delayed worm expulsion, impaired production of antibodies, and lower levels of IL-13. Their CD4+ T cells present reduced glycolytic rates when compared to cells from cohoused infected wild type mice. However, at later stages of infection, antibody, IL-13 and glycolytic levels were restored together with worm expulsion. CD4+ T cells from the early stage of infection showed reduced phosphorylation of mTOR, which suggested that impairment of function was mTOR dependent. Indeed, mice lacking mTOR in T cells fail to expel a high dose of parasites. They showed abrogation of IL-13 production, impairment in antibody class switching and their CD4+ T cells failed to upregulate glycolysis. Thus, this thesis shows that mTOR is essential for the proper functioning of T cells during T. muris infection and efficient amino acid transport plays a significant role. Taken together, these data show that metabolic orchestration of T cell function influences the capacity to effectively control helminth infection and that even subtle changes in T cell metabolic control can have a major effect on response phenotype.

No description available.

Obesity is characterized by hyperinsulinemia and chronic inflammation, contributing to insulin resistance and type 2 diabetes (T2D) risk. Pattern recognition receptors (PRRs) of the innate immune system, including Toll-like Receptors (TLRs) and Nod-like Receptors (NLRs), have been identified as propagators of metabolic inflammation. Circulating bacterial components exert distinct effects on inflammation and insulin sensitivity via TLRs and NLRs. Specific types of bacterial peptidoglycan engage NOD1 and NOD2. Activators of NOD1 increase inflammation and insulin resistance, while activators of NOD2 promote immune tolerance and insulin sensitivity. NOD1 and NOD2 use the common downstream adaptor RIPK2 to drive immune responses, but the role of RIPK2 in glucose homeostasis was unknown. RIPK2 is positioned to mediate effects of xenobiotics and microbial components on blood glucose. For example, tyrosine kinase inhibitors (TKIs) are being investigated for diabetes treatment. Improvements in blood glucose control have been observed in diabetic cancer patients receiving TKI therapy but the mechanism underlying these changes remains unclear. Several TKIs inhibit RIPK2. We sought to understand if TKIs that inhibit RIPK2 block inflammatory and metabolic consequences of NOD signalling. We hypothesized inhibition of inflammation via NOD1-RIPK2 by certain TKIs contributes to lowered blood glucose/improved insulin sensitivity in pre-clinical models of obesity. We showed that RIPK2 was required for acute glycemic consequences of NOD1 and NOD2 activation, and RIPK2-specific TKIs attenuated these glycemic effects. We found TKI-mediated improvements in blood glucose are independent of NOD-RIPK2 signalling during diet-induced obesity. However, RIPK2 mediated the effects of certain TKIs on blood insulin. Finally, we tested if RIPK2 mediated the effects of bacterial components derived from commensal microbiota. We found injection of upper intestinal microbe components lowered blood glucose via NOD2-RIPK2 signalling. These findings demonstrate that modulation of RIPK2 signalling by xenobiotic or microbial factors is an important contributor to blood glucose and insulin homeostasis. / Thesis / Doctor of Philosophy (PhD) / Obesity increases the risk of chronic diseases, including Type 2 Diabetes (T2D). Obesity stops insulin from working properly, leading to the inability to lower blood glucose. Obesity and T2D are linked to chronic, low-grade activation of the immune system. The immune system normally defends the body against microbes by inducing a pro-inflammatory response. Inflammation can also be activated or inhibited by drugs (xenobiotics), and different aspects of inflammation can increase or decrease blood glucose and insulin. A major unanswered question was how certain cancer drugs and bacterial components interact with the immune system to change blood glucose or insulin. This work tested how an innate immune pathway that detects bacterial cell wall components is influenced by cancer drugs and alters blood glucose and insulin in pre-clinical models. This work is targeted at understanding how new prebiotics or existing drugs can be tasked as therapeutic strategies for prediabetes and T2D.

Over the past 20 years, our collaborative research team at the Ottawa Hospital and the University of Ottawa have extensively investigated molecular and metabolic differences between individuals with obesity in the highest (DS) and lowest (DR) quintiles for rate of weight loss following 6 weeks of caloric restriction. Research on these cohorts of individuals with extreme phenotypes in diet-response has revealed that DS individuals have several skeletal muscle metabolic advantages, including increased proportions of type I oxidative fibres, increased mitochondrial proton leak, enhanced fatty acid metabolism, and a greater antioxidant capacity. Regular physical exercise provides a vast array of beneficial effects to metabolic health, including increases in skeletal muscle mitochondrial bioenergetic capacity and muscle cross-sectional area, leading to the hypothesis that exercise may be particularly beneficial to women with diet-resistant obesity. The overall aim of this thesis was to determine whether six weeks of exercise training improves skeletal muscle mitochondrial function and attenuates chronic low-grade inflammation in women with obesity previously identified as diet-sensitive (DS) and diet-resistant (DR). Here, we demonstrate that exercise training improves body composition, enhances cellular maximal respiration, and increases mitochondrial length preferentially in DR women. Contrary to our hypothesis, exercise training increased skeletal muscle IKK-NFκB inflammatory signaling to a greater extent in DR individuals, despite improvements in systemic cytokine concentrations. In response to an inflammatory challenge, LPS-treated primary myotubes derived from DR and DS skeletal muscle responded similarly and respiratory capacity was preserved. Taken together, these findings suggest that exercise can be especially beneficial as part of a treatment plan for DR individuals, and that DS and DR skeletal muscle have systemic and mechanistic differences in inflammatory responses.

Since their discovery, natural killer cells (NK) cells have been implicated as important players in cancer immunosurveillance. In recent years, researchers have taken advantage of this role by developing NK cell-based immunotherapies in the fight against cancer. While these treatments have been moderately successful against hematological malignancy, they are less effective against solid cancers. This lack of success partially results from the immunosuppressive effects of the tumor microenvironment (TME). While tumors use myriad processes to evade the immune system, the avid consumption of nutrients common to NK and cancer cell metabolism and the production of toxic waste products can have significant deleterious effects on NK cell anti-tumor function. However, it may be possible to avoid some of this tumor-induced inhibition of NK cell anti-tumor function by manipulating NK cell metabolism and/or environmental conditions. Recent studies have revealed that different activation regimens can affect the metabolic dependencies of different NK cell subsets. Furthermore, studies have identified potential targets in the TME that can make the environment less hostile for infiltrating NK cells. By considering the interrelationship of NK cell metabolism and function—especially in the TME—this thesis illuminates potential strategies to modulate immunometabolic suppression. Despite the promising work already done, many gaps in the knowledge of NK cell metabolism remain. Future work will need to investigate the specific molecular mechanisms linking metabolism and function, the role of tissue-resident NK cells in cancer immunosurveillance, and the influences of chronic disease and altered systemic metabolism on NK cell anti-tumor activity.