NIHRDataInsights/HRCSData huggingface dataset:
Title: The parameters of tissue-resident macrophage autonomy
Funder: Medical Research Council

Abstract: A new paradigm is emerging in macrophage biology; the autonomous tissue resident population that exists without replenishment by the hematopoietic system. The limits of this concept are not yet understood, nor have the mechanisms been properly studied that allow the persistence of these cells in the steady state and in the face of inflammation. In this project, revolutionary tools developed to identify tissue stem cells by permitting spatial and temporal analysis of cell proliferation history and detection of clonal restriction within populations will be applied to the field of murine macrophage biology together with methods that distinguish hematopoietic and tissue-derived macrophages to establish: (1) the contribution of proliferation to steady-state maintenance of tissue macrophages, (2) whether stem-like precursors of resident cells exist and to determine their identity and regenerative capacity, (3) if stable conversion of recruited hematopoietic cells into resident macrophages occurs under physiological conditions, and whether converted cells differ functionally or faithfully reproduce the resident phenotype, and (4) whether conversion of hematopoietic cells is a consequence of exhausting the regenerative capacity of the resident population or their precursors. These questions will be addressed in several tissues at different stages of neonatal and adult development, during chronic tissue injury, and following treatment with cytokines (IL-4 or CSF-1) that drive elevated self-renewal of resident populations in different inflammatory environments, in order to model changes that may occur with age or under conditions of chronic or recurring inflammation. In addition to fundamentally advancing our basic knowledge of macrophage biology, this work will influence the design of therapeutics that target macrophages during disease and an appraisal of whether stem cells or monocytes can be exploited to manipulate resident cells for our own benefit.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Understanding lipid antigen presentation in intestinal homeostasis and inflammation
Funder: Medical Research Council

Abstract: The mammalian intestine contains a complex mixture of microorganisms that perform many metabolic functions and are critical for the establishment of tissue homeostasis. Consequently, the immune system has developed strategies to maintain the mutualistic relation with the microbiota while preventing bacterial spread. However, while the mucosal immune system is central for host protection, its aberrant activation and/or failure of regulation can lead to inflammatory and autoimmune diseases, as is the case of inflammatory bowel disease (IBD). It is increasingly appreciated that the initiation and quality of tissue-associated immune responses are regulated by tissue-resident T cells of which NKT cells are clear examples. NKT cells are activated by lipid antigens presented by the surface molecule CD1. Upon activation, NKT cells secrete large amounts of cytokines and induce downstream activation of different cell types. Numerous studies support the role of NKT cells/CD1 in the maintenance of mucosal homeostasis and in the induction of IBD, although the mechanisms underlying these processes remain unclear. This proposal aims to understand the mechanisms regulating NKT cell function and CD1-lipid presentation in the intestine. We aim to build a comprehensive picture of NKT cell distribution and phenotype within gastro-intestinal compartments in homeostatic conditions. With this established, we will focus on the response of these cells to challenge and in the interactions with antigen presenting cells that will determine their activation during IBD induction. Additionally, we will explore the role of NKT cells in the generation of IgA, which is one of the main tools for the maintenance of intestinal homeostasis. These studies will provide a better understanding of the factors that modulate intestinal immunity, with the potential to improve therapies for patients suffering from intestinal inflammatory diseases and possibly a broader range of disorders.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: The role of miR-132 in the immune response to pathogens
Funder: Medical Research Council

Abstract: An appropriate immune response requires coordination of a multitude of initiating, amplifying and resolving signals and processes. Understanding the mechanisms that ensure an optimal equilibrium between activating and regulatory immune processes is of utmost importance for the treatment of infectious diseases. In this project, we propose that microRNAs act as molecular integrators of the immune response through their ability to concurrently regulate expression of several genes in a tissue- and cellular state-specific manner. In particular, we will investigate the function of miR-132, a critical component of the regulatory arm of the innate immune response. We have recently found that genetic deletion of miR-132 provides protection against infection and infection-associated tissue remodeling. Our studies suggest that miR-132 negatively regulates inflammation by simultaneously limiting the interferon response and promoting angiogenesis. These findings will be used as a solid platform in the proposed project, which will investigate in-depth the effects of miR-132 on the inflammatory response to infection. Using unique gene knockout models and a tractable in vivo infection model, we will dissect the mechanisms employed by miR-132 at the cellular and molecular level, focusing on the role of miR-132 in macrophages and endothelial cells and its interactions with p300, a master transcriptional co-activator, and Rasa1, a fundamental signaling effector. In addition to gaining crucial insight into immunological mechanisms, the proposed studies will reveal how miR-132 interacts with its targets in a context-dependent manner to perform its function in different cell types. Therefore this project will result in significant conceptual advancements in the fields of immunology and microRNA biology, and also set the foundation towards the development of novel therapeutic approaches in infectious diseases.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Role of Mef2D in inflammation
Funder: Medical Research Council

Abstract: The aim of this work is to determine the roles that Mef2D plays in regulating the immune system. Mef2D is a transcription factor and our preliminary data indicate that it represses TLR induced IL-10 production in macrophages. Knockout of Mef2D increases IL-10 production by TLR4 stimulated bone marrow derived macrophages and as a result represses TNF, IL-6 and IL-12 production. In vivo IL-10 is a key anti-inflammatory cytokine and is implicated in several pathologies including endotoxic shock, infection, psoriasis, inflammatory bowel disease and arthritis. We will therefore examine the mechanism by which Mef2D acts in macrophages, determine if its role is restricted to macrophages and examine the consequence of loss of Mef2D function in disease models. For the first aim we will make use of primary bone marrow derived macrophages to study the regulation of Mef2D by cell signaling using established biochemical and cell biological techniques. In addition we will use RNAseq approaches to get a genome wide picture of the role of Mef2D in TLR induced transcription in macrophages. We will combine this with ChIP experiments to demonstrate Mef2D localization to its target promoters. To determine if Mef2D functions in a similar manner in other immune cells we will isolate dendritic cells, T cells and B cells from wild type and Mef2d knockout mice to determine the contribution of Mef2D to the induction of IL-10 in these cells downstream of appropriate stimuli. In parallel we will also examine the role of Mef2D in these cells for the transcription of other target genes that we identify in our BMDM studies. Finally we will determine the role of Mef2D in selected immune disease models using our knockout mice. Initially we will look at models of endotoxic shock and toxic contact eczema, as these models are known to be influenced by macrophage derived IL-10. Depending on what roles we find for Mef2D in other cells types this list may be expanded or modified as appropriate.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: INFLUENCE OF IRON METABOLISM ON THE REGULATION OF INTRA-HEPATIC INFLAMMATORY RESPONSES
Funder: Medical Research Council

Abstract: A sizeable proportion of liver transplant recipients spontaneously develop a state of immune tolerance that allows them to discontinue all immunosuppression and yet sustain normal graft function. In an attempt to characterize this group of patients we recently completed a large multi-centre drug withdrawal trial. Tolerance was found to be associated with iron metabolism parameters (i.e recipients requiring lifelong immunosuppression displayed lower hepcidin and serum iron levels than tolerant patients). To investigate the potential causal link between iron metabolism, intra-hepatic alloimmune responses, and tolerance, we have performed preliminary experiments in rodent models of immune-mediated liver damage that indicate that decreased iron and/or hepcidin levels markedly interfere with baseline intra-hepatic gene expression, inhibit intra-hepatic T cell function, and could interfere with regulatory T cell generation and/or function. These preliminary results suggest that iron homeostasis plays a previously unrecognised role in regulating the balance between liver inflammation and immune tolerance. The aims of the current proposal are to elucidate the exact cellular and molecular pathways through which iron and/or hepcidin modulate inflammatory liver injury, interfere with lymphocyte function and/or migration, and regulate tolerance. Experiments will be performed in murine models of inflammatory liver damage and in a rat model of orthotopic liver transplantation. The project will contribute to elucidate the mechanisms responsible for the development of transplantation tolerance following liver transplantation and will provide insight into the pathogenesis of liver inflammatory disorders.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Biology of patrolling monocytes in inflammation
Funder: Medical Research Council

Abstract: The objectives of the proposed integrated programme of work are: Aim 1 will investigate the mechanisms responsible for endothelial cell killing by Ly6Clow monocytes. We will analyse in vivo using intravital microscopy and electron microscopy the role of membrane dependent necroptosis, reactive oxygen species, NETs formation, IFNAR, and platelets, in Ly6Clow monocyte retention inside capillaries and TLR7 dependent necrosis of endothelial cells. Aim 2 will test the hypothesis that NR4A1 controls the differentiation and homeostasis of murine and human Ly6Clow/CD14 dim monocytes. We will examine the role of NR4A1 in a conditional hematopoietic Nr4a1 deficient model, and perform RNA-seq and ChIP-seq analysis to analyse and compare the target genes of Nr4a1 in mice and human monocytes. Aim 3 will test the hypothesis that Ly6Clow monocytes control endothelial damage in glomerulonephritis due to immune complex deposition and in a TLR7/8 sensitive tumor model. We will examine the role of Ly6Clow monocytes and TLR signalling in glomerulonephritis following injection of an antibody against the glomerular basement membrane (GBM) which generates a glomerular inflammatory response via immune complex formation in the glomerulus and in the vascularisation of B16F10 tumors. Aim 1 and 2 will be started in parallel at the start of the project. They address at the cellular and molecular levels the mechanisms that control the differentiation and functions of ly6C-low monocytes and their human CD14dim counterparts. The experimental systems, technological approaches and mouse lines we will be using are in place in the laboratory, and we have assembled a team of outstanding collaborators with whom we have established collaborations. Aim 3 will be started in year 3, to best incorporate results from the previous aims This aim will investigate the roles of ly6C-low monocytes in pathological conditions such as glomerulonephritis and tumor growth, and the mechanisms involved


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Checkpoint governing B cell fate decisions in human gut-associated lymphoid tissue.
Funder: Medical Research Council

Abstract: We have shown that the T2 subset of transitional B cells enters the gut associated lymphoid tissue where some become activated. We hypothesise that the response of T2 cells to the microbiota in GALT determines their fate, thus constituting a checkpoint in B cell development. We have evidence that this system fails in SLE and could thus protect against autoimmunity. We now wish to ask: 1. Do activated transitional B cells in GALT have the properties of cells that will live or die? We know that cells enter and become activated in GALT, but the tissue does not accumulate them, so we wish to decipher their fate by flow cytometry and cell culture. 2. How do the specificities of the activated versus the non-activated cells differ? Whatever the fate of transitional B cells, it is likely to be dependent on the specificity of the B cell receptor. We propose to determine the specificity of T2 cells in GALT that are activated or not, and compare their specificities. 3. Is there any evidence that activated transitional B cell can enter the IgA response? The intestinal IgA response is the largest and most extensive B cell response in the body. Some of this IgA is known to be polyspecific or autoimmune which are also features of transitional B cells that are removed from the B cell repertoire as it matures. We will therefore ask if GALT transitional B cells can be co-otped into the IgA response. 4. Is there evidence that transitional B cells activated in GALT acquire functional properties? Some transitional cells can be immunomodulatory, a property that would be highly relevant to the mucosal microenvironment. Extravasation of T2 cells into GALT and activation of a subset of them would alter the repertoire of the T2 cell population that remained naive and unactivated. Understanding the consequences of this for intestinal and systemic immunity is therefore a high priority.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: The role of CCR8 in cutaneous vaccination
Funder: Medical Research Council

Abstract: The methodology for the proposed mouse work is up and running in the laboratories of the principal investigator (Moser) and the co-applicant (Gallimore). The second co-applicant (McCully) has substantial experience in mouse models of peritoneal inflammation, which complements well with the expertise of processing skin and other mouse tissues in the Moser laboratroy. Mouse model-specific expertise is provided by our collaborators. In addition, our human studies have prepared us (Moser/McCully) well for carrying out the proposed in vitro studies with T cells recovered from mouse blood/spleen and tissues. Aim 1 focuses on in vitro studies with mouse T cells that include the measurement of cell surface proteins, including CCR8, on T cells generated under diverse stimulatory conditions. The findings of aim 1 feed directly into aim 2. Aim 2 studies the kinetics of CCR8 expression in OVA-specific T cells during cutaneous vaccination with OVA/CFA. Core studies will include T cell isolation form various mouse tissues followed by their phenotypic analysis (flow cytometry). These studies will benefit from the CCR8 staining methods defined in aim 1. Aim 3 addresses the question of the importance of CCR8 (and its chemokine ligands CCL1 and CCL8) in the generation of a OVA-specific memory T cell compartment in mouse skin tissue. The necessary mouse models have been made available to us by our collaborators and the examinations require the same techniques as applied in aim 2. Aim 4 includes "control" experiments for assessing the degree of skin-specificity of the CCR8 migration system. Again, the relevant mouse models and expertise are provided to us by our collaborators.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: The roles and control of CD4+ effector and regulatory T-cells in biliary autoimmunity.
Funder: Medical Research Council

Abstract: This project aims to characterise the immunopathology of the autoimmune biliary diseases (AIBD) primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC). It also aims to explore potential therapeutic options for AIBD by using the T-regulatory (Treg) deficient FoxP3KO mouse as a model. We will survey archived explant liver tissue from AIBD patients. Using multiparameter confocal microscopy, we will characterise subtypes and spatial relations of the inflammatory infiltrate with particular attention to TH1, TH2, Treg and TH-17 cell populations. We will then assess peripheral blood lymphocyte populations using flow cytometry for similar patterns. We will evaluate FoxP3KO mice that develop peri-biliary inflammation and specific autoantibodies. We will then continue to assess how the disease of mice co-deficient in the tumour necrosis factor receptors OX40 and/or CD30 is ameliorated: we have previously shown that this ameliorates general phenotype but not explored hepatic manifestations. We will then explore the effects of OX40 and CD30 blockade via antibodies to their respective cognate ligands. In this instance, FoxP3KO T-cell transfer into lymphocyte deficient mice will be used as the model to ensure the recipients are large enough to allow antibody injection. Hepatobiliary disease will be assessed by liver histology, serum liver biochemistry, autoantibody indirect immunofluorescence and ELISA, and flow cytometric analysis of hepatic lymphocytes. We will then assess whether Treg transfer ameliorates liver disease in FoxP3KO mice by transfer of whole T-cell populations and using the methods described above. We will explore whether prior exposure to otherwise tissue-restricted antigen is important for Treg function by comparing AIRE-KO against wildtype donors. Finally we will compare Tregs from OX40 and/or CD30 deficient donors.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Human and Mouse Artificial Lymph Nodes: Novel technology to Reduce and Replace the use of animal models in clinical and developmental immunology
Funder: National Centre for the Replacement, Refinement and Reduction of Animals in Research

Abstract: Lymph nodes have an essential role in the initiation of protective immune responses. In this proposal we will utilise human and mouse adipose derived stem cells (ADSCs) and peripheral blood lymphocytes and dendritic cells to generate artificial lymph node (ALN) structures in vitro. This represents a novel approach to the analysis of human immune function and mouse lymph node development, organisation and function. This technology will have key applications in toxicology and mechanistic studies of new therapeutics and as a tool to determine the role of specific signalling pathways and physical forces in LNs, thus replacing and reducing animals in research. The development and application of human monoclonal antibody (mAb) to treat disease requires determination of toxicology and efficacy and understanding the mechanism of action. The current approach utilises large numbers of mice and non-human primate models and surrogate antibodies that are not the best predictor of human immune system. Through the development of ALNs we will generate a technology to address key questions on mAb safety and efficacy in vitro replacing and reducing mouse and non-human primates in therapeutic development. We have developed a methodology to differentiate ADSCs into T and B cell lymphoid stroma. ProBioGen has developed bioreactor technology that can maintain the survival and function of human lymphocytes over 4 weeks in culture. In this research program we will bring the two technologies together to construct a human ALN that contain all the key cell types and organisation found in vivo in highly structured 3D culture system. With the joint expertise in stromal cell culture, human immunology, 3D culture systems, bioreactors and measurements of immune responses in vitro we believe we can not only develop the technology to assay and visualise human immune responses in vitro but can commercialise the culture system, directly reducing the use of animals in drug development


Research activity codes: 5.9 RESOURCES AND INFRASTRUCTURE (TREATMENT DEVELOPMENT);1.5 RESOURCES AND INFRASTRUCTURE (UNDERPINNING)
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Signalling pathways of leukocyte migration in silico
Funder: National Centre for the Replacement, Refinement and Reduction of Animals in Research

Abstract: The aim of this project is to develop zebrafish as an in silico system to study the dynamical processes of the innate immune response. The transparent skin of zebrafish embryos made it an ideal model organism to investigate cell migration processes using fluorescent time-lapse microscopy. The innate immune system of zebrafish embryos closely assembles that of humans and is at early stages clearly separable from the adaptive response. Many different data types, such as cell migration imaging data or transcriptomics data, have been collected over the past years. However, the full potential of such data has not been explored so far. I will perform a detailed network analysis of immune cell signalling pathways in zebrafish. The constructed network will be used to generate an improved model of macrophage and neutrophil migration during acute injury. In particular, the cell dynamics will be described by an agent-based hybrid model, which will capture the internal cellular signalling process of each individual cell, as well as the migration process inside the extracellular matrix. Most cell migration data have been analysed using simple statistics, e.g. the velocity of a cell or the straightness index of a cell. Such statistics fail to describe the detailed migration process. I will further develop random walk models and analysis tools to identify migration patterns in 2D, but even more important in 3D. The developed algorithms will provide powerful tools to study migration processes. The analysis of leukocyte migration in 3D will be the basis to develop a 3 dimensional in silico model of the innate immune response in zebrafish. This model will be extended to the whole organism level.


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