NIHRDataInsights/HRCSData huggingface dataset:
Title: Mechanism underlying the development of Crohn's disease: the role of optineurin in macrophages
Funder: Medical Research Council

Abstract: Background Crohn‘s disease (CD) is a chronic inflammatory condition of the gastrointestinal (GI) tract that affects approximately 85,000 individuals in the United Kingdom and causes significant morbidity and loss of earning. Genome-wide association studies have identified genes that suggest an aberrant interaction between bowel contents and the immune system resulting in CD. Recent work in our laboratory revealed a common phenotype for CD with impaired bacterial clearance due to decreased neutrophil accumulation. The latter is likely related to abnormal macrophage function because of decreased pro-inflammatory cytokine secretion required for neutrophil chemotaxis. This was not due to reduced gene transcription but to targeted intracellular destruction of cytokine precursors in lysosomal compartments. A clue to the underlying mechanism for this was provided by the differential transcription profiles for genes encoding vesicular trafficking proteins in macrophages. These findings echo recent genome-wide association studies in CD that have identified associations with vesicular trafficking proteins. A subsequent microarray study on CD patients analysed using outlier analysis software revealed a number of abnormally expressed molecules in macrophages. The most striking was optineurin (OPTN), which is involved in vesicular trafficking. OPTN was decreased in 8 CD patients (13%). OPTN interacts with vesicular trafficking proteins such as huntingtin, Rab8, and myosin VI, which are involved in post-Golgi trafficking to lysosomes and vesicle fusion events. Aims I hypothesise that OPTN plays a central role in the pathogenesis of CD via defects in vesicular trafficking and cytokine secretion in macrophages resulting in decreased neutrophil accumulation and bacterial clearance. I aim to: 1. Determine the DNA sequence, expression and distribution of OPTN in monocytes, macrophages and the GI tract of CD patients. 2. Define the mechanism by which OPTN is involved in the secretion of cytokines by macrophages when stimulated by bacteria. Methodology Ethical approval has been granted to study patients with CD at University College London and Royal Free Hospitals. The OPTN promoter and exons will be resequenced. OPTN expression in the GI tract will be determined using immunohistochemistry and laser capture microdissection of GI macrophages from bowel biopsies. To define the functional effects of wild-type and mutant OPTN in macrophage cytokine secretion, immunoprecipitation, confocal microscopy and molecular cloning techniques will be utilised. Scientific and medical opportunities I hope to identify mutations in OPTN and define the mechanisms causing defective vesicular trafficking and cytokine secretion in macrophages. This will enable potential therapeutic targets and drugs to be developed for CD.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: The role and mechanism of action of p110delta PI3K signalling in gastrointestinal immunity and inflammation.
Funder: Medical Research Council

Abstract: The central hypothesis of our proposal is that gut health is maintained by the interplay between the gut tissue (host genetics) and its luminal contents (microbiota and pathogens). A better understanding of these complex interactions holds the key for unravelling molecular and cellular events responsible for a variety of gastrointestinal inflammatory conditions. Phosphoinositide 3-kinases (PI3Ks) are a conserved family of lipid kinases which generate lipid second messengers. Mammals have 8 isoforms of PI3K, subdivided into three classes, most of which are expressed by innate immune cell populations, particularly phagocytes. Some PI3K isoforms have been implicated in host defence, inflammation and colitis but the underlying molecular mechanisms remain unexplored. Herein, we propose to investigate why mice targeted in the gene encoding class I p110delta isoform, highly expressed in leukocytes, develop spontaneous colitis mediated by microbiota. We have so far established that in myeloid, dendritic cell population, p110delta PI3K positively couples and controls signalling downstream of nucleotide oligomerisation domain (NOD)1/NOD2 receptors that regulate mucosal host defence and tolerance to commensal microorganisms. We now propose to explore this new mouse model of colitis through a molecular framework of studies involving biased and unbiased approaches involving cell biological, proteomic and microbiome sequencing studies along with in vivo infection models to unravel key biological phenomena driving gastrointestinal pathology.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: VacA mediated immunomodulation
Funder: Medical Research Council

Abstract: Helicobacter pylori colonises 50% of the world's population and is associated with a variety of gastric diseases including adenocarcinoma. Having co-evolved with the human race over 60,000 years, Hp has adapted to manipulate the immune system to prevent clearance. Over the last few decades, the prevalence of Hp has reduced, whilst the prevalence of chronic immune-mediated diseases such as asthma and multiple sclerosis (MS) have dramatically increased. We and others have shown that the virulence factor VacA (vacuolating cytotoxin A) is an important driver of the immune response to Hp. Recent research has shown that it influences dendritic cell maturation, inducing a toleragenic state. We have shown that the vacA gene is always present but highly polymorphic, with these polymorphisms directly influencing activity. We hypothesise that the most active form of VacA will have the most significant immunomodulatory properties. Objectives 1. To characterise the strength of tolerogenic activity of different VacA types on murine dendritic cells in vitro. 2. To characterise the effect of VacA on human monocyte-derived dendritic cells in vitro. 3. To investigate the role of VacA-mediated effects on murine immune responses in vivo and determine their impact in a mouse model of multiple sclerosis. Design/Methodology Murine bone marrow derived dendritic cells and human monocyte derived dendritic cells will be co-cultured with a panel of vacA mutants. Flow cytometry will be performed to evaluate maturation and activation. ELISA for specific cytokines will also be undertaken. Hp matured dendritic cells will then be cultured with naive T cells. Differentiation will be assessed by flow cytometry and cytokine ELISA. In vivo work will then be carried out in a mouse model of infection. Scientific/Medical opportunities This will provide a better understanding of the immune response to Hp and help explain why infection appears to be protective of certain immune mediated diseases.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: Premature death and organ hypofunction after severe acute pancreatitis results from cellular senescence - mechanisms and new opportunities for therapy
Funder: Medical Research Council

Abstract: Even after an apparently complete clinical recovery from an episode of critical illness - for which severe acute pancreatitis (AP) is a paradigm - life expectancy is reduced. In this fellowship, I will investigate the molecular mechanisms that underpin that deleterious legacy, with particular focus on increased flux through kynurenine monooxygenase (KMO) as a key contributor to sterile systemic inflammation and post-inflammatory senescence. I will define precisely the mechanistic contribution of the kynurenine pathway of tryptophan metabolism, and specifically KMO, on whole-organism and organ-specific accelerated senescence following sterile systemic inflammation using the paradigm model of acute pancreatitis (AP) in human patients and experimental animal models. This coherent portfolio of experiments will dissect the mechanisms by which increased kynurenine pathway flux initiates the DNA damage response (DDR), focusing on oxidative stress generated by the KMO product 3-hydroxykynurenine (3HK), and examining closely the role of the telomere deprotection response (TDR), using models in yeast, primary human lung fibroblasts in vitro, and experimental mouse and rat models of AP. With collaborators, I will develop and validate a novel PET tracer in order to define the organ-specific KMO activity profile during experimental AP and allow correlation with organ-specific post-inflammatory senescence at subsequent time points. Biological indices of the DDR, TDR, the senescence-associated secretory phenotype, cellular and whole-organism senescence will be examined in models and contextualized to chronic organ hypofunction in a clinical cohort as a legacy of human AP and AP-MODS.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: The crosstalks between immune cells, bacteria and epithelial cells in the intestine: elucidating their cellular and molecular mechanisms
Funder: Medical Research Council

Abstract: The maintenance of intestinal homeostasis depends on a delicate balance between the immune system, the intestinal epithelium and the gut microbiota. Abnormal changes in these compartments and on their interactions can have local and systemic consequences, leading to major health problems including Inflammatory Bowel Disease (IBD), cancer, diabetes and obesity. The overall aim of this research program is to identify novel pathways that regulate the communication between immune cells such as innate lymphoid cells (ILC), the intestinal epithelium, and both commensal and pathogenic microorganisms, to be able to pharmacological target these pathways in order to ameliorate intestinal inflammation. For that, we will be using our novel 3D system of co-culture of ILC with intestinal organoids. Our system allows to study the differentiation and functions of intestinal ILC and their interactions with the epithelial and microbial compartments under reductionist and controlled conditions that closely mimic the intestinal environment. In these co-cultures, the ILC surround the exterior of the organoids, which corresponds to the lamina propria while bacteria or bacterial products are microinjected into the lumen of the organoid. Candidate pathways for the regulation of these interactions, which were previously identified by us, will be validated using our novel system and in vivo approaches. Importantly, we aim to translate our findings by testing the importance of these pathways in the human setting using in co-cultures of human intestinal organoids with human lymphocytes. By understanding the cellular and molecular mechanisms that regulating the interactions between immune cells, the intestinal epithelium and specific bacteria this research programme will lead to the discover of new pathways that potentially can be therapeutically targeted in order to promote intestinal homeostasis and prevent/treat intestinal associated diseases such as IBD, diabetes and cancer.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: Establishing a collaboration to enable effective nutritional targeting of age-related immune decline and intestinal microbial dysbiosis
Funder: Medical Research Council

Abstract: The challenge we will address is the limited understanding of links between nutrition, microbial diversity and inflammation/immune senescence in older adults. Our project will provide a step-change in the UK's research capability in this field and through our multidisciplinary collaboration we will develop a virtual nutritional immunology research centre open to all who wish to participate. We will provide leadership through a) hosting a series of three workshops; b) the development and distribution of standard operating procedures; c) the publication of three papers (one per workshop) outlining best practice for research in the areas of human nutrition and human nutrition clinical trials, nutritional immunology and the intestinal microbiome. We will conduct a feasibility study to test our ability to successfully recruit and conduct interventions in older adults with high levels of completion and compliance, test our standard operating procedures, process and exchange samples, integrate and understand our data, and generate robust pilot data for more definitive multi-centre trials of nutritional approaches for targeting the intestinal microbiota and the immune system in older people. The feasibility study will involve an intervention in 80 people aged over 70 years with vitamin D and probiotics, given alone and together over 3 months. Older people often have low vitamin D status and intestinal dysbiosis both of which can affect low-grade inflammation and immune competence. Key outcomes of the feasibility study will relate to the impact of the interventions on inflammation, immune function and intestinal microbiota. We will use mathematical modelling to understand the interactions among these outcomes in the context of older people and of our interventions. We will plan future trials and develop a strategy to ensure sustainability of our collaboration. We will link with the wider academic community, the public, industry, NGOs, and existing relevant European projects.


Research activity codes: 1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING);3.3 NUTRITION AND CHEMOPREVENTION
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: Investigating the lymphatic system in intestinal inflammation
Funder: Medical Research Council

Abstract: Inflammatory bowel disease (IBD) is a chronic immune-mediated inflammatory disease affecting the gastrointestinal tract with loss of response to all therapies remaining a major challenge. Variable response to treatment suggests heterogeneity in the underlying disease processes and highlights the need for a deeper understanding of the cellular basis of IBD in order to develop alternative therapeutics. Multiple studies demonstrate increased lymphatic density in IBD, with a recent report showing impingement of lymphatic vessels in the mesentery of patients with Crohn's Disease. This confirms that IBD is associated with observable structural changes in the lymphatic vessels. Furthermore, stimulating lymphangiogenesis by augmenting vascular endothelial growth factor C (VEGFC) in mouse models has been shown to ameliorate inflammation in the colon, skin, joint and heart. Furthermore, inhibition of lymphangiogenesis by inhibiting VEGFC worsens murine colitis, arthritis, skin inflammation and resolution following myocardial infarction. These reports provide evidence that manipulation of the lymphatic system is a possible way to ameliorate inflammation and thus warrant further study in IBD. In particular we suspect that multiple cell types including stromal cells regulates lymphangiogenesis and this may form the grounds for a novel therapeutic target in IBD. There are clear opportunities arising from this work: if we better understand the mechanisms of the resolution of inflammation then we will be well-placed to contribute towards rational design of novel therapeutics for patients with IBD. Key objectives: 1. Create a cellular atlas of lymphatic endothelial subsets in the colon in health, inflammation and resolution of colitis 2. Elucidate the cellular and molecular basis by which colonic lymphangiogenesis is regulated 3. Functionally assess how manipulation of the colonic and colonic mesenteric lymphatic endothelium affects the resolution of inflammation


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: Keeping to the Rhythm: Circadian and Metabolic Entrainment of IgA Responses in Health and Disease
Funder: Wellcome Trust

Abstract: The mucosal immune system is critical for human health; mediating both immunity against pathogens and maintaining mutualism with the microbiota. In contrast, dysregulation of mucosal immune function and homeostatic host-commensal interactions results in chronic inflammatory and metabolic disease e.g. Inflammatory Bowel Disease, obesity and liver disease. Within the intestinal tract, Immunoglobulin A (IgA) is secreted in huge quantities by tissue-resident Plasma Cells to ensure a mutualistic balance of commensal microbial species, which metabolise dietary nutrients to the benefit of the host. We demonstrate the magnitude of intestinal IgA secretion is entrained by signals associated with feeding, which imprint circadian rhythms onto Plasma Cells that act to align metabolically demanding immune surveillance with times of waking activity. In turn, circadian IgA secretion imprint daily oscillations in commensal microbial species. Despite our findings, the mechanistic basis and physiological relevance of this complex dialogue remain poorly understood. Here we will comprehensively define the molecular pathways that dictate IgA rhythmicity, and determine the consequences of this cross-regulation for host-microbial interactions, immunity and disease. Together this study will provide a step change in our understanding of how the diet, microbiota and mucosal immune system engage in complex temporal crosstalk to ensure metabolic and immune health.

Lay abstract: The immune system maintains human health, both through protective responses against harmful pathogens, and also by preventing inflammation driven by otherwise beneficial microbes that live inside us. Our intestines are home to specialized immune cells known as Plasma Cells, which secrete large quantities of antibody (Immunoglobulin A; IgA), that maximize the benefits of the "commensal microbiota". We have discovered a previously unappreciated dialogue between IgA responses, our diet and the microbiota. Specifically, we found that Plasma Cells respond to metabolic signals associated with feeding to regulate the magnitude of antibody secretion over the course of a 24-hour day. These cues align the Circadian Clock within these immune cells, and cause both Plasma Cells and commensal microbes to take on rhythmic behavior. We will determine how rhythmic IgA secretion facilitates beneficial interactions with the microbiota and diet, and determine how loss of this circadian regulation leads to metabolic and inflammatory diseases.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: Decoding macrophage functional heterogeneity in the pathogenesis of Crohn's disease
Funder: Wellcome Trust

Abstract: The accumulation of intestinal macrophages (iM&phi;s) and presence of a distinct mononuclear phagocyte gene-expression profile, predict treatment failure and adverse clinical outcomes in Crohn's disease (CD). Preliminary scRNA-seq data demonstrates that a transcriptionally distinct iM&phi; subtype (CD-M&Phi;) accumulates in human and murine colitis, which I have prospectively validated. Unbiased CD-M&Phi;-epithelium, ligand-receptor interaction analyses reveals CD-M&Phi; derived activin signals to cognate receptors on colonic epithelium. CD-M&Phi;s are the exclusive iM&phi; source of activin in mouse and humans, a TGF-&beta; superfamily member with cell-specific cytokine, growth and hormone effects. Activin administration to human colonic epithelium inhibits proliferation with a dose-dependent effect on cytokine, chemokine and pattern recognition gene expression. Aims 1. Define iM&phi; heterogeneity and dynamics in CD 2. Interrogate the functional role of a novel pathogenic subset (CD-M&Phi;) in regulating intestinal inflammation 3. Investigate CD-M&Phi; driven activin signalling as a therapeutic target for intestinal inflammation Methods Using a novel, human, biopsy-based sampling approach, I will perform scRNA-seq of iM&phi;s in newly diagnosed, treatment naive CD patients, with longitudinal, flow cytometry-based intestinal characterisation to reveal iM&phi; dynamics over time. Lastly, I will manipulate cell-specific activin-signalling in transgenic animals and primary human epithelium co-culture models to probe the mechanisms of activin-mediated epithelium dysfunction in CD.

Lay abstract: Crohn's disease is a lifelong, incurable, debilitating condition of unknown cause, characterised by repeated episodes of bowel inflammation. Modern therapy incompletely treats inflammation such that <50% of patients have complete bowel healing despite treatment, with many more patients becoming resistant to treatment over time. Intestinal macrophages are increasingly thought to be key mediators of these inflammatory processes in CD, but paradoxically also have numerous beneficial roles in the healthy gastrointestinal tract. Thus, exploring how subtypes of macrophage drive inflammation in CD may lead to more specific and novel therapies. Once key pathways and subsets are identified, I will use animal models of intestinal inflammation to show the precise function of these cells. By completing this research, I will have characterised the intestinal macrophage composition in health and in CD, how this changes over time and how this can be targeted to promote prompt resolution of inflammation.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL
Title: Environmental influences on intestinal homeostasis and inflammation
Funder: Wellcome Trust

Abstract: The aryl hydrocarbon receptor is an environmental sensor that recognises either xenobiotic pollutants or endogenous physiological ligands and influences homeostatic as well as inflammatory immune and tissue responses particularly in skin, lung and gut. We propose to investigate the impact of AhR signalling in intestinal epithelial cells during homeostasis as well as in infection, inflammation and the formation of intestinal cancer. We will define genes and pathways in IEC that are influenced by AhR signalling both via the ligand dependent pathway as well as an evolutionary conserved ‘non-classical’ pathway. We are focusing on regulation of the AhR pathway, building on our recent discovery that interference with feedback regulation of AhR signaling via cytochrome P45 (Cyp1) metabolizing enzymes has deleterious consequences for the integrity of the intestinal barrier, protection against pathogens and susceptibility to cancerogenesis. However, administration of AhR ligands in vivo or In intestinal organoid cultures may correct such defects, opening therapeutic possibilities. We will explore the organoid culture system in patients with IBD or colon cancer to test whether patients with intestinal disorders show dysregulated AhR activity and whether this is amenable to therapeutic intervention with dietary ligands.

Lay abstract: The aryl hydrocarbon receptor is an environmental sensor that responds to either environmental pollutants such as dioxin or to endogenous, non-toxic ligands. Since it is clear that inflammatory diseases are highly influenced by environmental exposures this particular factor offers the opportunity to study the mechanisms of how environmental trigger influence infections, inflammation and the development of cancer particularly in the gut, where AhR is highly expressed. We want to find out what genes and pathways are affected by AhR in intestinal epithelium, where absence of AhR or inadequate activation have negative consequences leading to higher susceptibility to intestinal infection as well as inflammation-induce cancer development. Some of our data indicate that dietar AhR ligands (from vegetable sources) can improve such inflammatory disorders and we would like to study the underlying mechanism of this in mouse models as well as in cultured gut cells from humans.

Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;ORAL AND GASTROINTESTINAL