NIHRDataInsights/HRCSData huggingface dataset:
Title: Targeting GSK-3 in antigen-specific immunotherapy
Funder: Medical Research Council

Abstract: Current therapies for allergies and autoimmune diseases treat the symptoms rather than the cause of the disease. The exception to this is antigen-specific immunotherapy (SIT) that aims to reinstate tolerance to the protein causing the disease. This approach has been applied in the field of allergy for over 100 years; however, the SIT approach has not yet transferred successfully from allergy to autoimmunity. Furthermore, SIT using intact allergens still runs the risk of inducing anaphylactic shock. The ultimate aim of this DPFS project is to develop an approach that enhances the efficacy and hence permits commercial development of SIT. Our laboratory has made two significant advances: first, we demonstrated that intact antigens can be replaced with synthetic peptides for effective SIT and second, we recently identified an enzyme whose inhibition greatly enhances the SIT effect, in vitro. As yet, the enzyme inhibitors tested have been poorly soluble and have not been tested in vivo for SIT. We will investigate a new enzyme inhibitor that is highly soluble and effective against the enzyme in vivo. This will be tested first against the enzyme in mouse and human lymphocytes in vitro. If effective, we will test how inhibiting the enzyme enhances SIT using animal models of autoimmune disease. We propose that transient enzyme inhibition in lymphocytes will enhance SIT thereby avoiding potential adverse effects of long-term drug administration. We believe that the combined safety of peptides rather than intact protein for SIT, along with the enhanced efficacy achievable with our enzyme inhibitor, will promote SIT to the forefront of preferred treatments for allergic and autoimmune diseases. The immediate goal of this project is to demonstrate the enhancement of SIT by targeting this particular enzyme, and to provide sufficient in vitro and in vivo evidence to interest industry in further development of this approach through collaboration.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Cell-type specific functions of autophagy in intestinal physiology and pathology
Funder: Medical Research Council

Abstract: The aim of this project is to define the roles of autophagy proteins in the regulation of immune and inflammatory responses in the intestine. In particular, we aim to assess the functions of autophagy proteins in intestinal epithelial cells (IEC) and in leukocytes during homeostasis in the intestine and during conditions of acute or chronic inflammation. This will be achieved by generating transgenic mice in which the inflammatory bowel disease (IBD) associated autophagy gene Atg16l1 is ablated in specific cell types (IEC or myeloid cells) through tissue-specific expression of the Cre recombinase. These conditional Atg16l1 knock-out mice will be assessed in models of bacterially-triggered intestinal inflammation that reproduce many aspects of the inflammatory pathology associated with human IBD. The impact of ablation of autophagy proteins in distinct cell types on the induction and regulation of IBD pathology will be assessed, as well as their effects on bacterial handling and immune defense in the gut. Factors and pathways that are identified in the mouse IBD models to be regulated by Atg16l1 will be verified by analyses of cell and tissue samples from IBD patients. A better understanding of the roles of autophagy proteins in intestinal homeostasis may lead to the development of novel therapies for IBD, particularly in patients who harbour mutations in autophagy genes.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Lipid bodies organelles and the cross-presentation of cell-associated antigens by MHC class I in phagocytic dendritic cells
Funder: Medical Research Council

Abstract: This proposal intend to analyze the contribution of Atg7 and of the Rab32 small GTPase to the cross-presentation of cellular antigens by phagocytic MHC class I in CD8+/CD103+ dendritic cells (DCs). The following mouse models for DC-specific gene inactivation will be generated : - Atg7lox/lox mice (M. Komatsu, Tokyo) X CD11c-cre DC-specific deleter strain (Jackson lab). - Rab32lox/lox (KOMP consortium) X CD11c-cre DC-specific deleter. We will decipher the function of autophagy during the phagocytic uptake of dead cells by DCs using cutting-edge microscopic approaches on Flt3L-derived bone marrow-derived DCs. Auto-phagosomes (monitored by LC3/Atg8-GFP and PtdIns(3)P-specific FYVE domain-GFP reporters), synthesis of lipid bodies (LBs, labelled with specific probes) and phagosome maturation will be monitored in various genetic settings. Dead fibroblast carrying model antigen (OVA) will be used as a phagocytic substrate for cross-presentation. Over-expression experiments of Rab32 (and activity-deficient mutants) into WT or autophagy-deficient DCs (CD11c-crexAtg7lox/lox) or LBs-deficient DCs (Adrp/Plin2-/-) will be performed to test the coordination of various genes and its impact on cross-presentation DCs. Finally, we will develop an in vivo model to test the function of Atg7 and Rab32 on cross-presentation by DCs in a physiological settings : presentation incompetent mouse recipients expressing a transgenic model antigen in all tissues (Ubi-OVA x H-2Kbm1/bm1) will be irradiated and reconstituted with H-2Kb/b bone marrow from WT or CD11c-crexAtg7lox/lox or CD11c-crexRab32lox/lox. After full hematopoietic reconstitution, constitutive cross-presentation of tissue model antigen (OVA) by donor bone-marrow derived DCs (of various genotypes) will be assessed using adoptive transfer of CFSE-labelled OVA-specific OT-I transgenic CD8+ T cells. This experiment should definitively address the role of Atg7 and Rab32 autophagy-promoting genes in cross-presentation by DCs.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Translating the Resolution of Inflammation: MC3 in human arthritis synovia
Funder: Medical Research Council

Abstract: We have investigated mechanisms of the host response for over 20 years, with a focus on mediators and pathways that are activated in our body to keep under check the inflammatory response mounted against xenobiotics and other injurious agents. Examples are dissection of the biology of corticosterone (the rodent equivalent to cortisol), Annexin A1 and - relevant here - melanocortins. Thus, there is a need for a better understanding of key regulatory elements both in relation to tissue response to injury and its development versus chronicity instead of resolution. Here we focus on a new potential effector of the resolution of inflammation, the melanocortin receptor type 3 (MC3). Supported by recently published work (and a wealth of unpublished data) produced collectively by the Applicants, this project puts forward the hypothesis that MC3 is a novel, and possibly discriminatory, effector of resolution. Often 'shaded' by the ubiquitous MC1 receptor, MC3 can be upregulated in conditions of inflammatory stress to convey inhibitory signals, perhaps in a ligand-biased fashion. We postulate that peripheral generation of MC ligands could also occur in the RA synovia. This research projects represents a step-change in current views of melanocortin biology, moving to a fully human experimentation. Supported by consistent preliminary data generated with human RA synovia (and fibroblasts), and supported by a linear rationale, we will assess: Aim 1: The regulation of MC3 expression, and other elements of the melanocortin pathway, in human synovia, attempting to relate it to the disease status (early vs. late arthritis; resolving vs. persistent arthritis) and therapeutic application (tissue analysis before and after treatment). Aim 2: The pharmacology of MC3 agonists, using peptide-mimetics and small molecules, defining their effect on human tissue and cell activation, to unveil the potential for this research for the development of future therapeutic agents.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: 1MICA - Is PI3Kgamma signalling organised in distinct membrane nano-domains?
Funder: Medical Research Council

Abstract: PI3Kgamma is a member of a small family of signalling enzymes, structurally distinct to the larger family of protein kinases, which operate in many receptor-sensitive networks. It has a very tissue specific distribution and is abundant in neutrophil-like cells. PI3Kg KO mice are normal under animal-house conditions but PI3Kg is required for a range of inflammatory reactions in vivo. These factors have driven large investment in the development of PI3Kg inhibitors as novel anti-inflammatories. PI3Kg is a heterodimer of a p110g catalytic subunit and either a p101 or p84 adaptor subunit and is controlled by Ras and G-betagamma proteins. Ras controls p110g directly and work in mice has revealed the physiological importance of this interaction. In contrast, the roles of p84, p101 and of Gbg remain debated and largely undefined in vivo. A favoured hypothesis, based on in vitro and "in transfecto" data, is that p84/p110g is regulated by Ras and p101/p110g by Gbg. Our unpublished data from a p84-/- mouse line shows p84 has unique roles in neutrophils. As a result of a collaboration with Roger Williams we can now derive mice expressing a point-mutated, fully-active Gbg-insensitive p110g. These mice, in conjunction with p84-/- x p101-/- and other published lines, will allow us to define how PI3Kg is regulated by Gbg and Ras in vivo and to test the above hypothesis directly. In the detail of our unpublished data we find that loss of p84, but not p101, abolishes fMLP-stimulated ROS formation, despite very similar impacts on the lipid product of PI3Kg activity, PIP3. We hypothesize this discrepancy results from PI3Kg being found in spatially discrete compartments based on membrane nano-domains. The access of PI3Kg, and hence PIP3, to these nano-domains is determined by adaptor-specific regulation and restricts signalling to similarly targeted PIP3-effectors. We aim to test this idea by visualizing endogenous PI3Kg at high resolution with a range of techniques.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Interleukin-21 (IL-21) in rheumatoid arthritis (RA): exploring its therapeutic potential for the development of a novel targeted biologic therapy.
Funder: Medical Research Council

Abstract: Our developmental plan follows 4 steps Step 1 Identification of IL-21 producing/target cells in RA We will employ confocal microscopy on RA synovial tissues and FACS on isolated RA synovial cells to identify IL-21 and IL-21R+ cells in in association with specific markers for Th1 (IFNg,T-bet, CXCR3), Th2 (IL-4/GATA-3), Th17 (IL-17A/F, Rorgt, CCR6) and TFh (CXCR5, ICOS, PD-1) cells. Additionally, IL-21R expression will be investigated on synovial B cells subsets and CD8+ T cells. Step 2 Functional role of IL-21 in inflammation, autoimmunity and tissue damage We will define the functional role of IL-21: in vitro: i) on human IL-21R+ RA synovial fibroblasts assessing the capacity of IL-21 to induce cytokines and MMPs (mRNA and protein) and ii) on synovial B cell activation, including B cell differentiation (FACS), AID/circular transcripts (rt-PCR) and class-switched antibodies (ELISA). in vivo: in the RA/SCID chimera by analysing IL-21-induced activation of pro-inflammatory pathways such as ELS function, B cell autoreactivity, production of inflammatory cytokines and stromal cell activation. Step 3 Pre-clinical development of IL-21 blocking agents We will directly contribute to the development of pre-clinical IL-21 therapeutics by testing their efficacy in vivo in the HuRA-SCID chimera on i) synovial inflammation and ELS; ii) B/T cell function; iii) autoantibody production and iv) stromal cell activation. Step 4 IL-21 in disease outcome and response to treatment in RA: a roadmap to patient stratification We will assess IL-21 and related pathways as biomarkers of disease evolution and response to treatment in prospective clinical studies in the MRC Pathobiology of Early Arthritis Cohort and in RA patients treated with IL6-R and TNFa biologics. Emerging data will be applied to clinical trial design based on IL-21 target validation, role in synovial immunopathology, development of IL-21 blocking reagents and stratification of patients for treatment


Research activity codes: 5.1 PHARMACEUTICALS;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: How do Migratory Dendritic Cell Populations Control Immune Responses in the Intestine?
Funder: Medical Research Council

Abstract: The intestinal immune system must maintain a delicate balance, retaining the ability to make appropriate responses to invading pathogens while also preventing unwanted and damaging responses against harmless commensal organisms and food antigens. Dendritic cells (DCs) acquire antigen in the intestinal lamina propria and continually migrate, via lymph, from the intestine to the mesenteric lymph nodes (MLNs), where they prime T cells and direct their differentiation. They are required for the initiation of intestinal immune responses, and are thought to control the polarisation of the responding T cells. Understanding the control of these responses is central for the development of oral vaccines, and for therapies to prevent or control inflammatory bowel diseases. Study of the immunology of migrating DCs has been hampered by the fact that they consist of a number of functionally different subsets that are difficult to definitively identify in intestinal tissues or in the MLN. Because DCs are exquisitely sensitive to their local environment, there are also significant challenges in purifying the DC subsets from intestinal tissues without altering their functions. For these reasons, the properties of migrating DCs are best studied after purification from the lymph of rats and larger animals. However, investigations in these species are hampered by a lack of immunological reagents, inbred strains, and transgenic animals. To investigate how migrating DCs interact with T cells and control intestinal T cell responses, we have previously developed techniques for purifying migrating intestinal DCs from murine thoracic duct lymph in the mouse, and for intra-lymphatic injection of cells. We will use these techniques to examine the functions of specific subsets of migrating DCs in initiating and polarising responses from cytotoxic T cells, Th1/17, and Th2 cells, to enable development of methods for targeting specific DC subsets and thus controlling intestinal T cell responses.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: RORgamma+ Innate Lymphoid Cells in Skin Wound Healing
Funder: Medical Research Council

Abstract: We have recently discovered a uniqure role for Notch signalling in epithelial cells driving the recruitment and function of innate lymphoid cells during normal wound healing. Notch1 and Notch2 signalling regulate different steps in the wound healing process; Notch2/jagged1 signalling induces TNF alpha production leading to CCL20 and subsequent recruitment of innate lymphoid cell (ILC) to the wound site. Subsequent Notch1 signalling in epithelial cells induces IL-23 production at the wound site activating ILCs and driving IL-22 expression. One of the key roles of innate lymphoid cells appears to be preventing T cell mediated pathology in wound sites. Thus Innate Lymphoid Cells have an unexpected role as regulators of wound pathology at mucosal surfaces thus we will address the following questions: 1) How do ILCs regulate pathology from forming during normal healing, in particular is this process dependent on the amount and timing of cytokine production? 2) The cytokines IL22 and IL23 are produced at the wound sites, which cells produce these cytokines and what is their functional relevence to wound closure? 3) Infections are commonly associated with wounds, what role does infection have in the production of different cytokines at the wound site and in particular why is the cytokine IL17 not found in normal wound healing? 4) How is the dynamics of immune cell entry and clearance from the wound microenvironment occur? Through combining genetic mouse models with functional assays, gene expression analysis and multi-photon imaging we will determine molecular mechanism of immune mediate regulation of normal wound healing in both mouse models and human disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Identification and characterisation of causal molecules for Crohn's disease and ulcerative colitis
Funder: Medical Research Council

Abstract: The aetiology and pathophysiology of CD and UC are different. There is evidence of an innate immune deficiency in CD and a mucosal abnormality combined with accentuated acute inflammation in UC. To identify potential causal molecules we studied microarray data collected from macrophages and from mucosal biopsies from CD and UC patients. We identified a number of abnormally expressed genes in macrophages from CD patients, and went on to demonstrate that two of these molecules, ADAMDEC1 and Optineurin have novel roles in mucosal immunity. We plan to screen other under-expressed molecules in a zebrafish bowel inflammation model, and if they demonstrate a strong phenotype we will investigate their function in knockout (KO) mice. These molecules will be examined for an epistatic interaction with NOD2 in double KO mice. Expression studies on the mucosa of UC patients revealed that Claudin 8 and FAM5C are grossly under-expressed in significant proportions of patients. FAM5C has never previously been associated with UC. We will perform expression studies on bowel biopsies patients from Iceland where there is a very high incidence of UC and a relatively small gene pool. Claudin 8 and FAM5C and candidate molecules from Iceland will be screened in zebrafish and those with a strong phenotype will be investigated in KO mice. We will investigate the cell biology and biochemistry of ADAMDEC1, Optineurin, Claudin 8, FAM5C and other strong candidates to establish the mechanistic basis upon which deficiencies predispose to IBD. Patterns of under expression of genes like FAM5C in the bowel mucosa might provide the basis for molecular diagnostic tests for UC. We are collaborating with Epsilon-3 Bio Ltd, who are developing drugs to enhance the immune response, and Phil Crosier who has a library of drugs licenced for other purposes that protect zebrafish against bowel damage, and will test their drugs in our mouse models with a view to using them therapeutically.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: The role of DNA Methylation as an epigenetic modifier of hepatic fibrosis progression in Non Alcoholic Fatty Liver Disease.
Funder: Medical Research Council

Abstract: Non-alcoholic fatty liver disease (NAFLD) represents a spectrum encompassing steatosis, steatohepatitis (NASH), cirrhosis and hepatocellular carcinoma. It is the commonest cause of liver dysfunction worldwide; the fastest rising in the UK. Whilst the majority of patients with the metabolic syndrome develop steatosis, only a minority go on to develop cirrhosis. Therefore, advances in understanding the pathogenesis and risk factors of progressive disease are urgently needed. I recently reported data suggesting an association between epigenetic remodelling of Peroxisome Proliferator Activated Receptor Gamma (PPARg) by DNA Methylation and disease progression in human NAFLD. I now aim to determine the mechanism by which epigenetic remodelling may influence disease progression. Methods Pyrosequencing for quantitative DNA Methylation analysis:- Tissue from animals with dietary induced NAFLD, >100 serial liver biopsies of patients with steatosis or progressive NAFLD, and laser dissection microscopy to assess whether DNA Methylation of PPARg is pre-set before disease, whether it changes as a consequence of disease progression and in which other genes and liver cells it occurs. I will assess whether these changes are seen in blood. Scientific/Medical opportunities This project is clinically relevant because it will further our understanding of the molecular events that lead to disease progression in NAFLD. Greater understanding of the nature of epigenetic gene changes may in the future outwith this project help to identify novel markers of NAFLD disease progression risk that could be used as part of stratified medicine to individualise patient assessment for importance of lifestyle modification, need for follow up and future anti-fibrotic drug development and trial enrichment.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Functional Genomics in SLE: A Transancestral Approach
Funder: Medical Research Council

Abstract: SLE is a generalized autoimmune disease whose aetiology is incompletely understood. It exhibits complex genetics with approximately 50 known susceptibility loci. The disease appears to be most common in non-European populations. Data from GWAS suggest that the majority of loci are shared, but it is unlikely that this sharing extends to the allelic level. Like many others in the field, we have ben successful in mapping disease loci, but have not convincingly identified susceptibility alleles at the majority of these loci. This lack of resolution in mapping is a major impediment to functional analysis. We aim to use transancestral mapping to identify causal alleles at lupus susceptibility loci. This approach exploits the variable patterns of linkage disequilibrium (LD) that are present in different human populations. The experimental plan is as follows. Resequence, to a high density, a set of seven functionally related SLE loci in 200 cases and 200 controls from each of four ancestries: European, African, Southeast Asian and north Indian. The libraries for sequencing will be generated by long range PCR. These data will generate a comprehensive panel of genetic variation at the loci, including insertion-deletion polymorphisms Based on LD and functional annotation, a common set of markers across each locus will be assembled. This marker set will be genotyped in larger cohorts, each comprising 1800 cases and 1800 controls in the same four ancestries. Using sharing and regression-based approaches we will compare the association patterns across the populations with the aim of identifying causal common alleles. Rare coding variants will also be investigated, if identified and enriched in cases, they have a strong likelihood of causality in view of the known association of each locus with disease. We propose to commence experimental investigation of the functional effect of one or two of the causal alleles that we identify.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM