NIHRDataInsights/HRCSData huggingface dataset:
Title: Molecular determinants of immune tolerance in Graves' disease
Funder: Medical Research Council

Abstract: Autoimmune thyroid diseases are the most prevalent of the autoimmune diseases (AID), with Graves' disease (GD) affecting close to 2% of women over a lifetime. Standard antithyroid drug (ATD) therapy results in remission in 50% of cases, which provides a tractable model to investigate the molecular determinants of restoration of immune tolerance. TSH receptor stimulating antibodies (TRAbs) play a pivotal role in the immunopathogenesis of GD, but the humoral immune response that drives this autoimmune process is poorly understood. My fellowship aims to identify how the humoral immune system in GD patients who sustain a prolonged remission following ATD therapy differs from those who relapse. The phenotype of remission or relapse one year after treatment will be determined in 120 GD patients who are about to stop thionamide therapy and used to categorise for my analyses, aiming for 50 or more patient samples available per group. Concentrations of B cell growth factors (BAFF, APRIL, CXCL13) and TRAbs will be measured by ELISA along with KRECs (qPCR) to determine whether plasma cells, the activity of existing B cells, or the generation of new B cells is independently driving the remission/relapse process. RNAseq of CD19+ B cells will allow a high-fidelity survey of cell-specific gene expression and identify those transcripts that are most differentially fold-changed between relapsing and remitting patients. The genomic underpinning of this differential expression will be explored using SNPs known to tag eQTLs in the original RNAseq patient dataset, and confirmed in a wider sample of available GD patient DNAs. This in depth exploration of B lymphocyte biology in treated GD will allow a molecular understanding of factors determining relapse or remission, will provide important prognostic information to stratify patient therapy and could lead to critical insights into the mechanisms behind long-term restoration of immune tolerance relevant to other AIDs.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Predicting the diagnosis of inflammatory and autoimmune arthritis using a data driven approach.
Funder: Medical Research Council

Abstract: Inflammatory and autoimmune arthritis (e.g. Rheumatoid arthritis, Spondyloarthritis, Psoriatic arthritis, Lupus) affects 1 in 12 women and 1 in 20 men. Aggressive treatment for inflammatory arthritis in the first few months has been shown to reduce the rate of disease progression. There is increasing evidence that the first few months after symptom onset represent a pathologically distinct phase of disease. This very early phase may translate into a therapeutic window of opportunity during which it may be possible to permanently switch off the disease process. However, catching the disease in the very early stages is difficult and for many people it can take years to be given a diagnosis and then this window of opportunity is lost. This fellowship proposes to use a data driven approach to examine if early predictors (such as symptoms, laboratory tests, co-morbidities, co-medication history, administrative codes) can be used to identify those who are likely to be given a diagnosis of inflammatory arthritis. The work examines the frequency of predictive codes before and after the diagnosis in those with the disease compared to controls. However, the temporal relationship is very important and so this requires the development and testing of novel analytical approaches. For example, a severe infection 7 years before a diagnosis may be predictive but an infection at any time in the patients history may not predictive. A pilot aspect of this work examining ankylosing spondylitis and separately psoriatic spondyloarthritis has been funded by the pharmacological company UCB and so this has direct relevance to be commercialised by pharma and technology industries. This Fellowship will build on this parallel work to expand new models developed to other conditions such as Lupus, Rheumatoid arthritis and enteropathic spondyloarthropathy.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Universal cells to overcome HLA barriers in regenerative medicine
Funder: Medical Research Council

Abstract: Universal human pluripotent stem cells (HPSC) will be generated using CRISPR mediated genome modification and their stealth, or ability to evade immunological responses, investigated. The project will be delivered in four workpackages (WP) over a three year period at UCL and UoC, with additional contributions from existing UKRMP hubs. 1. Methodologies to eliminate HLA, addressing 'missing self' and safety risks. CRISPR sgRNAs will be identified and validated for efficient HLA class I and II disruption and delivered using our hybrid lentiviral-CRISPR vector system. Transgenes encoding a replacement non-polymorphic HLA-G and/or a dimerising suicide gene will be coupled to CRISPR delivery, with Cas9 mRNA delivered transiently by electroporation. Alternative deamination base-editors will also be investigated to mitigate against the risk of translocation events in cells undergoing multiplexed editing. 2: Human pluripotent stem cell modification and differentiation Established HPSC lines (embryonic or induced) will be evaluated for their ability to support differentiation to hepatocytes or macrophages. Lines with optimal capacity will be selected for generation of universal hepatocytes (devoid of HLA lass I) or macrophages (devoid of HLA class I & II). In vitro sensitivity to anti-HLA antibodies will be examined, as well cellular responses mediated by healthy donor mismatched T and NK cells. 3: Characterization of genotoxicity risk Next generation sequencing will be used to quantify of on and off target activity. Sites of possible off target activity will be informed by Digenome analysis. Predicted translocations will be quantified by targeted qPCR and karyotypes assessed, including by FISH where possible. 4: Function and stealth of modified cell lines Persistence and immune-evasion of universal HSPC derived teratomas, macrophages and hepatocytes will be examined in humanised immunodeficient mice using healthy donor T and NK cells.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;5.2 CELLULAR AND GENE THERAPIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Cross-presentation & antigen import into the cytosol. What is the mechanism?
Funder: Medical Research Foundation

Abstract: Antigen cross-presentation plays a key role in the initiation of immune responses. This process allows dendritic cells (DCs) to present antigens to naive CD8+ T cells, activating them. Cross-presentation is important in scenarios where the DC itself does not express the antigen. During this process, extracellular antigen is first taken up by DCs. Following uptake, the antigen is the imported into the cytosol, where it can be processed by the proteasome and then loaded onto MHC class I. The exact mechanism underlying antigen cytosolic import remain unclear. We will develop an assay to monitor antigen import into the cytosol. Once this assay has been developed we will perform CRISPR/Cas9 screens to identify genes that might regulate cytosolic import. Hits from these screens will then be characterised using a variety of molecular techniques.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Stapled by design: New peptide-based therapeutic leads targeting protein-protein interactions in rheumatoid arthritis
Funder: Medical Research Scotland

Abstract: The interactions between proteins in a cell control many biological processes and so present attractive targets for therapeutic intervention. However, in contrast to the normal “lock and key” analogy for the development of small molecule drugs targeting enzyme activity, the surfaces involved in protein-protein interactions (PPIs) tend to be much larger and have less well-defined binding pockets. Thus PPIs present more challenging targets for therapeutic intervention, and they have largely been ignored. One emerging approach to targeting PPIs is to examine the structural information available for the protein complex, and to look for a short helical section within one of the proteins at the interface. Generating this excised portion of the structure in the laboratory leads to a molecule which is able to displace its parent protein from the protein complex, thus disrupting the normal biological function. A small number of drugs are currently under development based on this strategy. Sadly, short sections of the protein backbone (called peptides) do not tend to adopt the same structure as they have in the parent protein - so a technique termed “stapling” has been developed to constrain the structure of the peptide sequence, ideally to give the desired helix. As well as enhancing the binding capability of the therapeutic peptide, this approach has recently been shown to have the added benefits of improving its stability under biological conditions (important for potential drug candidates) and improving cell penetration (widening the scope of the approach). As yet, stapled peptides cannot be designed using computational techniques. In this project we will develop new tools for the prediction of the structure of stapled peptide sequences (Michel) and apply them to the rational design of stapled peptides (Hulme) which interact with two key proteins which are important in the inflammatory signalling pathways in rheumatoid arthritis (UCB).


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Factors contributing to the impact of CALcinoSis In sysTemic sclErosis (CALSITE Study)
Funder: Health Education England

Abstract: Calcinosis is an extremely painful and debilitating feature of Systemic Sclerosis (SSc), but very little research exists and so the treatment options remain limited. The aim of this proposal is to understand the important features in determining who develops calcinosis, to provide a focus for appropriate treatments. We will undertake three studies. First a national questionnaire to patients with SSc will determine the prevalence of calcinosis. Second, we will explore the impact of calcinosis on pain, disability and function. Finally, we will undertake a detailed imaging and vascular assessment to understand why calcinosis develops in order to develop better treatments.

Lay abstract: Calcinosis is an extremely painful and debilitating feature of Systemic Sclerosis (SSc), but very little research exists and so the treatment options remain limited. The aim of this proposal is to understand the important features in determining who develops calcinosis, to provide a focus for appropriate treatments. We will undertake three studies. First a national questionnaire to patients with SSc will determine the prevalence of calcinosis. Second, we will explore the impact of calcinosis on pain, disability and function. Finally, we will undertake a detailed imaging and vascular assessment to understand why calcinosis develops in order to develop better treatments.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Preventing Disease and Disability in Immune Mediated Inflammatory Diseases
Funder: Department of Health and Social Care

Abstract: At Risk of Developing RA and localised autoimmunity Aim: To establish a sustainable national referral network of individuals with imminent RA, develop risk models and use stratified populations for interventions Short  Risk factors validated in cohorts and develop regional programme  Establish prospective cohort of first degree relatives for mucosal autoimmunity and microbiome Medium  Proof of Concept (PoC) studies to demonstrate reduced progression Long  Develop protocol and external funding for a multi-centre trial reducing disease progression Immunotherapies in RA Aim: Early and established RA: aim cure and remission respectively through precision immunotherapies; by phenotyping and response prediction. Short  Accurately phenotype heterogeneous treatment responses using imaging techniques Medium  Deliver effective mechanistic studies with identification of disease strata and patient phenotypes Long  Deliver proof of concept (PoC) and novel stratified intervention studies Interventions based on stratified prognosis Aim: Develop intervention studies based on stratified prognosis in SSc and PsA. Short  Establish a sustainable national referral network from primary care of inception PsA and individuals with higher risk of Scleroderma Medium  PoC studies to demonstrate reduced progression Drug Repurposing and treatment toxicity Aim: Improve the management IMID through molecular phenotyping applying knowledge of pathogenesis, drug mechanisms and treatment toxicities Short  molecular diagnostics informing selection of biologics and/or opportunities for drug repurposing Medium to Long  methodology to interrogate large datasets, to evaluate clinical, biochemical and molecular predictors  health economic models that demonstrate commercial space for new technologies/therapies


Research activity codes: 3.5 RESOURCES AND INFRASTRUCTURE (PREVENTION)
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Structural biology of innate and adaptive immune signalling
Funder: The Francis Crick Institute

Abstract: The modification of proteins with ubiquitin is a key regulatory mechanism of almost all eukaryotic cellular processes and is crucial for maintaining protein homeostasis and normal cellular function. Attachment of ubiquitin to substrate proteins changes their behavior and function, and dysregulation of the ubiquitin system is linked to the development of many diseases. Ubiquitination of proteins is catalyzed by an enzymatic cascade involving E1 activating enzymes, E2 conjugating enzymes and E3 ubiquitin ligases that select the protein substrate and hence determine the specificity of the process. We aim to understand the molecular mechanisms underlying ubiquitination, which ensure that the correct substrate is selected and modified in the appropriate manner to elicit the required cellular response. In the long term we hope to use the molecular insights gained from our studies to develop novel strategies to treat diseases that are caused by malfunctioning of the ubiquitin system. We are particularly interested in the role of ubiqutination in immune and inflammatory signalling pathways and are focusing our studies on two families of E3 ligases that are key regulators of immune signalling networks: the TRIM (tripartite motif) family and the RBR (RING-between-RING) family of E3s. LUBAC is a prominent member of the RBR family and the only E3 ligase capable of synthesizing linear (M1 linked) ubiquitin chains that are key regulators of NF-kB signalling and apoptosis, and have recently been linked to cancer. LUBAC consists of multiple subunits that form a large macromolecular complex. We aim to understand how individual subunits contribute to subcellular localization of LUBAC, substrate selection and regulation of enzymatic activity. TRIM ligases are recognized as important regulators of innate immune signalling processes and their function is targeted by pathogens to suppress the host immune response. We aim to elucidate the molecular basis of TRIM ligase activity and the mechanisms employed by pathogens to interfere with TRIM activity. We are using a multi-disciplinary and integrated approach in our studies and employ biochemical and structural methods, complemented by chemistry, cell biology, computational biology and mass spectrometry.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Maintenance and regulation of peripheral immune responses
Funder: The Francis Crick Institute

Abstract: The MRC/Crick funded program in my lab focuses on the development, regulation and function of effector T cell responses with particular emphasis on Th17 cells. We have generated cytokine fate reporter mice to allow us to not only identify the cell types producing such cytokines, but also their fate in the course of immune responses. CD4 effector T cells are so far identified by intracellular staining for their hallmark cytokine, which requires a supraoptimal activation burst via PMA/ionomycin. Furthermore, it has become clear in the last years that some effector T cells, most notably Th17 cells can be highly plastic so that they lose their hallmark cytokine IL-17 and instead switch on other cytokines, a phenomenon that would make them invisible in standard detection methods based on intracellular cytokine staining. Generation of cytokine fate reporters clarified the issue of plasticity, which had become a critical factor in the development not only of effector T cells, but also of innate lymphoid cells (ILC). Our IL-17Cre fate reporter mouse made it possible to follow the development of Th17 cells beyond the induction of IL-17 to delineate their plasticity into a more pro-inflammatory state with the acquisition of additional cytokines and the loss of IL-17 production. This plasticity depended on exposure to the cytokine IL-23 and suggests that dysregulated inflammation with prolonged production of IL-23 underlies the propensity of Th17 cell mediated pathology in various autoimmune/inflammatory disorders. In contrast, intestinal Th17 cells, which are present under homeostatic conditions in the small intestinal lamina propria, undergo plasticity which extends their beneficial functions. With the IL-17Cre fate reporter we showed that a proportion of Th17 cells in Peyer’s patches undergoes plasticity to a follicular helper T cell profile (Tfh) and that these cells are instrumental in promoting T cell dependent IgA responses of PP B cells (Publication No.5). Another fate reporter mouse reporting the induction of IL-22 established that the major source of IL-22 under steady state conditions in the intestine are ILC3, whereas production switches to Th17 cells upon intestinal infection with the pathogen Citrobacter rodentium. Our data suggest that Th17 cells, rather than an additional subset of T cells are the source of IL-22 in infection. We also generated a fate reporter for IL-9 to detect IL-9 producing cell types. The IL-9 fate reporter clearly established that the major producers of IL-9 in vivo are ILC2 rather than T cells and that IL-9 has important functions in lung inflammation and helminth responses. All our fate reporter mice- especially the IL-17Cre reporter- have been in quite high demand and are deposited at the Jackson Labs (Il17atm1.1(icre)Stck/J Stock 016879; C57BL/6-Il22tm1.1(icre)Stck/J Stock 027524; B6.Cg-Tg(Il9-cre)#Stck/J Stock 024474).


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Activation of immune receptors
Funder: The Francis Crick Institute

Abstract: Our research is focused on B cell activation in antibody responses and in B cell pathology. Our main aims are to determine the molecular and physical mechanisms, by which B cells detect and capture foreign antigens. We have specifically focused on the biomechanics of B cell immune synapses with antigen presenting cells and developed biophysical, nano-mechanical, imaging, and genetic tools to investigate the role of cytoskeleton-generated forces in B cell responses. Our major findings were that B cell antigen extraction from immune synapses requires actin and myosin-generated pulling forces. These mechanical forces promote affinity discrimination of the B cells, i. e. the ability to respond to high affinity antigens better than to low affinity antigens. This mechanical affinity discrimination is enhanced in germinal centres, suggesting that B cell mechanics is important for selection of high affinity antibodies and for protection. Cumulatively, our results identified B cell mechanics as a novel mechanism regulating antigen recognition and B cell activation. These findings have implications for the design of vaccines aiming to promote selection of B cell clones with high affinity or broad specificity and for understanding of altered signalling in BCR-driven, GC-derived B cell malignancies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Dissecting a role for Hypoxia-Inducible Factor (HIF) and hypoxia-induced osteoclastic bone resorption in Rheumatoid Arthritis
Funder: Versus Arthritis

Abstract: Osteoclasts instigate juxta-articular bone destruction in Rheumatoid Arthritis (RA). The RA synovium is hypoxic and hypoxia increases osteoclastic bone resorption in a manner dependent on the Hypoxia-Inducible Factor (HIF) transcription factor. We will investigate this HIF-dependency using HIF inhibitors, non-hypoxic inducers of HIF and isoform-specific siRNA and compare effects on osteoclasts differentiated from RA monocytes and controls. HIF expression will be analysed in RA synovium, osteoarticular bone lesions and controls. Genes highlighted in a microarray of hypoxic versus normoxic osteoclasts will be investigated for their ability to promote bone resorption. Positive factors will be investigated immunohistochemically and effects on the activity of osteoclasts differentiated from RA monocytes will be compared with controls. This project will potentially identify molecular targets for the development of novel therapies to ameliorate pathological bone destruction in RA.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Randomised controlled trial of the clinical effectiveness, safety and cost effectiveness of adalimumab for the treatment of juvenile idiopathic arthritis associated uveitis (SYCAMORE) (09/51/01)
Funder: Versus Arthritis

Abstract: Primary objective: To compare the clinical effectiveness of adalimumab in combination with subcutaneous (s/c) methotrexate (MTX) versus s/c MTX alone, with regard to controlling disease activity in refractory uveitis associated with juvenile idiopathic arthritis (JIA) Secondary objectives: To evaluate short term safety and tolerability of adalimumab in combination with s/c MTX versus s/c MTX alone, with regards ocular complications of treatment, adverse events and laboratory assessments To determine quality of life and cost effectiveness of adalimumab in combination with MTX versus MTX alone in severe uveitis associated with JIA To determine the clinical effectiveness of adalimumab in combination with s/c MTX versus s/c MTX alone, with regard underlying JIA disease activity To determine the durability and magnitude of adalimumab efficacy response in sustaining inactive disease and achieving complete clinical remission To determine the long term safety of adalimumab in combination with s/c MTX versus s/c MTX alone To assess the efficacy of treatment with adalimumab to permit concomitant medication reduction, in particular regional and parental steroids To assess clinical implications of anti-adalimumab antibody (HAHA) development in relation to efficacy / hypersensitivity To develop a fully consented, trial-related biobank (e.g. serum, DNA, RNA) for subsequent investigation


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM