NIHRDataInsights/HRCSData huggingface dataset:
Title: MICA:Synthetic untranslated regions for direct delivery of therapeutic mRNAs
Funder: Medical Research Council

Abstract: Injection of proteins is a common approach for vaccination and other therapies, such as insulin for diabetes and monoclonal antibodies to treat various diseases, including cancer. An alternative way to provide proteins in patients is direct injection of an appropriately formulated mRNA. This approach has particular utility in situations where a rapid response to a new infectious agent is required, for example in a pandemic. This is because manufacturing a novel mRNA is rapid and more predictable than proteins. The efficacy of an mRNA in vivo is influenced by its stability and translatability. These factors are governed in part by untranslated regions (UTRs) flanking the open reading frame. A stable, highly translated mRNA will produce more protein for longer, which has the potential to reduce the frequency of injections and the dose of mRNA required, reducing side effects caused by an immune response to the injected mRNA. Furthermore, a smaller dose requirement reduces the manufacturing burden for scaling up a potential vaccine in a pandemic. Thus, there is a critical need to understand the contribution of UTR sequence determinants to mRNA half-life and translation efficiency, and to use this knowledge to identify optimal UTRs for use in therapeutic mRNAs. The stability and translatability of an mRNA are partly regulated by trans-acting factors (e.g. RNA binding proteins), which recognise motifs within the UTRs and bind to elicit their activities. We will combine motifs with desirable properties to create synthetic UTRs (SUTRs) selected for stability and translatability. We will also perform directed evolution on naturally occurring UTRs, selected for their intrinsic stability and translatability to generate UTRs with improved characteristics for in vivo administration. Using the knowledge gained from screening SUTRs we will develop an artificial intelligence approach for in silico design of UTRs with optimal properties tailored to specific target tissues.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Myeloid cells in type 2 immunity: unravelling susceptibility and resistance to tissue nematode infection
Funder: Medical Research Council

Abstract: Helminth infection is characterised by a type 2 immune response with polarisation of macrophages toward an M(IL-4) phenotype. It is increasingly recognised that macrophage functionality relies not only on direct cytokine signals but cellular origin and tissue environment. This programme is built around the pleural cavity, a tissue containing two predominant macrophage populations: monocyte-derived small cavity macrophages (SCMac) and large cavity macrophages (LCMac) which have a 'residency' gene expression module, conferred by the tissue niche. We will use the filarial nematode Litmosoides sigmodontis (Lito) as a model of pleural infection and as a tool to study M(IL-4) cells more generally. Mirroring divergent outcomes in human filariasis, susceptibility to Lito infection is dependent on host genotype, with striking differences in M(IL-4) cells between resistant and susceptible strains of mice. In resistant C57BL/6 mice LCMac expand greatly through proliferation and become M(IL-4) polarised. In susceptible BALB/c mice there are relatively more SCMac-like cells which appear incapable of acquiring a full LCMac-residency or M(IL-4) programme. Aim 1 seeks to explain if strain differences are a result of intrinsic differences in macrophage programming, alterations of the tissue niche or due to differences in Th2 cell activity. The next 2 aims focus on resistant C57BL/6 mice as a model of type 2 immunity culminating in worm killing. Aim 2 looks upstream of macrophages to identify the cell-cell interactions in the pleural cavity and essential co-factors that drive M(IL-4) polarisation and proliferation. Aim 3 will look downstream of M(IL-4) cells to assess their contribution to worm killing and tissue integrity in the pleural cavity using mice which lack specific residency, M(IL-4) or proliferation gene modules. This programme will advance our knowledge of the activation and function of M(IL-4) cells and provide novel information on the function of the pleural space.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Screening for, and characterisation of, novel immune cell extravasation genes in Drosophila, mice and man
Funder: Medical Research Council

Abstract: We have developed a new in vivo model to search for novel genes that might drive immune cell extravasation from vessels to wounds, which allows us to utilise the live-imaging opportunities of translucent Drosophila pupae, together with their genetic tractability. We have already identified one novel "extravasation" gene (Tre1) which is essential for this process in flies. We now have pilot data showing that murine neutrophils lacking the mammalian ortholog of Tre1, GPR84, exhibit a clear inability to breach vessel walls, indicating our screening approaches in the fly offer a powerful approach to reveal novel vertebrate extravasation genes. Here we propose a multi-disciplinary investigation of immune cell extravasation in fly and mouse models and extension towards human studies, through human cell co-culture and population health approaches. We will perform an in-depth characterisation of the role of Tre1/GPR84, with in vivo studies providing mechanistic detail and human assays to explore clinical relevance. We will exploit the unique genetic tractability of Drosophila to perform large-scale screens in pupae and subsequently adult flies (using tissue-specific RNAis) to identify novel genes required for extravasation in either immune or vessel cells. We will be guided by RNA-seq studies revealing those genes upregulated at the time of extravasation. Building on our Tre1/GPR84 findings, we aim to establish a pipeline to validate novel extravasation targets from our Drosophila screens in our established murine intravital imaging assays (using lineage-specific knockouts) as well as testing how these genes impact physiological responses such as peritonitis and wound-healing. To complement our in vivo studies, we will examine whether the human orthologs of these genes are required for extravasation in flow assays with human leukocytes and endothelial cells, and search for associations with human inflammation-related pathologies using genetic epidemiology techniques.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Interrogating NRK1 activity as a central regulator of CD4+ T cell metabolism, fate and function
Funder: Medical Research Council

Abstract: CD4+ T cells co-ordinate the immune response and are essential for adaptive immunity and protection from infectious disease. Consistently, CD4+ T cell dysfunction is associated with uncontrolled infection, whilst, conversely, their dysregulated activity is implicated in chronic inflammatory and immune-mediated disease. Despite recent therapeutic advances, these conditions continue to cause significant morbidity to many patients and place substantial financial burdens on the NHS. In the last decade, research has revealed that CD4+ T cell fate and function are fundamentally underpinned by dynamic changes in their metabolism. Furthermore, T cell metabolic dysfunction is reported in chronic viral infection and numerous autoinflammatory diseases, including systemic lupus erythematosus (SLE), type I diabetes and multiple sclerosis (MS). This has raised the exciting possibility of targeting CD4+ T cell metabolism as a novel therapeutic approach to correct their activity in these conditions, which has support from initial laboratory studies. Yet, the concerted activity of numerous diverse and flexible metabolic pathways supports T cell function, meaning that targeting one enzyme or pathway in isolation may have limited efficacy. Therefore, identification of central metabolic regulators in these cells would significantly advance this area of research and translation into new therapies. Our pilot data identify that activity of the NAD synthesis enzyme, nicotinamide riboside kinase 1 (NRK1) within CD4+ T cells has a profound effect on their overall metabolic capacity and immune function, and may therefore be one such central regulator. The proposed research will interrogate this in significant depth, employing cutting-edge metabolic analyses alongside established immunological approaches including experimental models of infectious and immune-mediated disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Pleural cavity as a driver of ventilator-induced systemic inflammation
Funder: Medical Research Council

Abstract: Although mechanical ventilation is an indispensible tool in modern intensive care, it also contributes to morbidity and mortality of patients, a phenomenon termed ventilator-induced lung injury (VILI). This is believed to occur due to an inappropriate inflammatory response within the lungs, followed by systemic propagation of inflammation leading to multi-organ failure. This has been explained in terms of VILI promoting movement of mediators across the alveolar-epithelial barrier into the blood. However there is little direct evidence to support this. Here we propose a novel hypothesis, that the pleural cavity is in fact the driver of ventilator-induced systemic inflammation. Our preliminary data provide strong evidence for this alternative mechanism, demonstrating that VILI upregulates cytokines in the pleural space and activates pleural macrophages and mesothelial cells. Moreover, translocation of proteins from the pleural space into the circulation is very rapidly enhanced. To explore this hypothesis we will firstly use our well-established mouse VILI model to determine the nature and kinetics of inflammation in the pleural cavity, and how the response compares to that in the alveoli and blood. We will then carry out in vitro cell culture experiments to elucidate how different cell types within the pleural cavity communicate with each other. We will explore the contribution of pleural cavity inflammation to systemic / non-pulmonary organ inflammation during VILI by blocking various (identified) inflammatory pathways within the pleural space. Finally we will clarify the translational potential of our findings by carrying out experiments in a more 'clinically-relevant' scenario incorporating underlying lung injury, and in a large animal (pig) model of ventilation. If successful, this study has the potential to change the focus of VILI research, and introduce new options for treatment of ventilated patients by targeting the inflamed pleural cavity.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Local oxidised phospholipids within the pleural cavity: fuelling macrophage response during inflammation?
Funder: Medical Research Council

Abstract: The pleural cavity is formed by a double layer of mesothelial membranes which encompass the lungs; mesothelial cells secrete pleural fluid which provides a niche for the accumulation of immune cells predominated by large cavity macrophages (LCM) & innate-like B cells (IBC). Pleural LCM provide a significant layer of protection against external pathogens, allergens & carcinogens that enter the body via the lungs. Energy & lipid usage in pleural LCM is not well understood. Oxidised phospholipids (OxPLs) are coming to the fore as regulators of metabolism, where in the context of classical inflammatory stimuli exposure results in induction of a macrophage hyper-metabolic state; the role of oxPL on LCM function during type-2 inflammation is unknown. Lipid peroxidation occurs due to the presence of intracellular oxidants during normal metabolic processes (fatty acid oxidation), or as a result of inflammation (via ROS). Oxidation specific epitopes such as those present within oxLDL, an oxPL mixture, can be recognised by IgM. Fat associated lymphoid clusters (FALCs) are key sites of local IgM secretion during pleural infection & inflammation. Murine models of global secretory IgM & macrophage CD36 deficiency will be used to determine the role of oxPL recognition in modulation of the phenotypic & metabolic profile of LCM & IBC responses during diverse models of type-1 & type-2 pleural inflammation. Sources & cellular uses of oxPL will be determined via investigations into lung, FALC, & pleural fluid in vitro, in vivo & within human pleural effusate. This project has potential to reveal novel metabolic targets for modulation of pleural immune cell phenotype & function enabling design of therapeutics to improve patient outcomes during lung disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Investigating the role of LAG3 in regulatory and effector T cells in systemic lupus erythematosus
Funder: Medical Research Council

Abstract: Systemic lupus erythematosus (SLE) is thought to develop due to the breakdown of tolerance mechanisms that control the immune response to self. There is a paucity of treatments available for patients with SLE. GSK have developed a depleting anti-LAG3 antibody based on the rationale that LAG3 is expressed on activated T cells and that LAG3 positive cells are associated with production of IFNgamma. The development of this anti-LAG3 antibody is being progressed in clinical trials in ulcerative colitis and psoriasis. Whilst there are a number of LAG3 blocking antibodies in development for oncology indications, as far as we are aware this anti-LAG3 antibody is the only depleting anti-LAG3 antibody in clinical development. There is no commercially available LAG3 depleting antibody. LAG3 expression has also been associated with regulatory T cell populations. There are abnormalities in LAG3 expressing T cells in the peripheral blood of SLE patients, with a recent publication suggesting increased CD4+CD25+LAG3+ T cells with defective regulatory function in patients with active SLE. Our pilot data for this proposal suggests a threefold increase in CD4+LAG3+ in lupus patient peripheral blood compared to healthy controls. With the increasing recognition that LAG3 is expressed on regulatory in addition to activated T cells, albeit some with defective function, this proposal seeks to identify the distribution and function of LAG3+ cells in the T cell populations within peripheral blood and urine (as an indicator of tissue infiltration relevant to lupus nephritis) in SLE. Progression to an experimental medicine approach integrated within a clinical trial using anti-LAG3 antibody would be dependent upon the data from this proposal indicating that the predominant expression of LAG3 was associated with pathogenic rather than regulatory T cells in SLE and that the in vitro effects of this antibody in SLE PBMC was to reduce inflammation.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MRC Transition Support Award CDA Edward Hutchinson
Funder: Medical Research Council

Abstract: This Transition Support award aims firstly to complete three well-established studies, and then to consolidate those with the other findings of my CDA to enable a new way of understanding how influenza virus infections propagate within the host. The three studies are: (1) A detailed, integrative model of the structure and composition of an influenza virion, combining proteomics, lipidomics, direct RNA sequencing and cryoelectron tomography to identify its fixed and flexible features. (2) A novel mechanism whereby, as an infection proceeds, the virions shed from an infected cell change their composition and become more infectious, allowing them to overcome the antiviral defences of surrounding cells. (3) Mapping the competing post-translational modifications of lysines in influenza virus proteins and identifying their regulatory effects. Along with the work already completed in the CDA, these provide tools to examine how viruses propagate within a host. It is important to note that the host has typically been treated as a black box: initiation of infection by a single virus particle is extremely well-studied, as is transmission of virus particles between hosts. What happens within the host has been much harder to assess. We know that influenza viruses produce discrete lesions in the respiratory epithelium and replicate in them to high titres. We can infer from genome reassortment that coinfection within these lesions is common. And we have recently become aware that, although only a minority of influenza virus particles are fully infectious, a large proportion of particles are 'semi-infectious' and can drive an infection through complementation. By combining the tools we developed for studying variation in influenza virions with advanced experimental models of differentiated airway epithelia and with tracheal explants, we will provide the first experimental model of the heterogeneous collective of virions underpinning every natural influenza virus infection.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Determining functional immunity after SARS-CoV-2 vaccination or natural infection in haemodialysis patients at high-risk of COVID-19
Funder: Medical Research Council

Abstract: Patients with comorbidities have a higher likelihood of death from SARS-CoV-2 infection. Amongst those worst affected are patients with end-stage kidney disease (ESKD), who are 45 times more likely to die than matched populations. Tragically, ESKD patients requiring haemodialysis (ESKDHD) cannot shield and face unavoidable risks of infection through the necessity to attend hospital for treatment. Despite their intrinsic susceptibility to COVID-19, ESKD patients can generate antiviral antibodies and thus may respond to vaccination. Nevertheless, it is unknown if after natural infection or vaccination: i) anti-viral serum and mucosal (salivary) antibodies are induced and maintained comparably to matched controls; ii) antibodies are functional and neutralise infection/promote opsonisation; iii) Whether host immune cells (neutrophils/macrophages) +/- antibody control virus infection. To answer these unknowns we will address the following hypothesis and objectives: Hypothesis "Antibodies and immune cells from vaccinated or naturally-infected ESKD-HD patients and matched controls are equally effective at neutralizing SARS-CoV-2 infection"Objectives: 1. To identify the nature, magnitude and longevity of the systemic and mucosal B cell response to SARS-CoV-2 in naturally-infected or vaccinated ESKD-HD patients 2. To determine the functionality and neutralising capacity of serum and salivary antibodies generated by ESKD-HD patients at different times post-vaccination/infection 3. To determine the capacity of different immune/non-immune cells from ESKD-HD patients to resist infection in the presence or absence of antibodies From these studies, we will understand if virus-specific antibodies are friends or foes in these clinically extremely vulnerable patients and inform our approach to treatment, shielding and the benefits of vaccination.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;3.4 VACCINES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: MICA: A randomised, double blind, controlled mechanistic study of obinutuzumab versus rituximab in ANCA-associated vasculitis (ObiVas)
Funder: Medical Research Council

Abstract: Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis (AAV) is rare, autoimmune disease with a UK prevalence of 250 per million. The immunopathogenesis includes neutrophil activation by B-cell-derived ANCAs, activation of the alternative complement pathway, and dysregulated T-cell responses that result in a necrotizing vasculitis of small blood vessels. The only licensed therapy, rituximab, depletes B-cells and induces remission in 60-80% of patients, but repeated doses are needed to prevent relapses. There is a dissociation between peripheral B cell depletion and the persistence of B-cells in the tissue after rituximab, with evidence of ongoing B and T-cell interaction and antigen presentation, which we have demonstrated using a safe and reliable nasal biopsy technique to provide sequential fresh tissue samples of a disease-relevant site in AAV. Incomplete tissue B cell depletion drives lower response rates and high relapse rates with rituximab therapy. Obinutuzumab, a Type II mAb also against CD20, is a more potent B-cell depletor than rituximab with superior tissue B-cell depletion in primates, and superior clinical efficacy in the treatment of haematological malignancy (phase III) and lupus nephritis (phase II). We hypothesise that obinutuzumab use in AAV will (1) result in more effective B-cell depletion in the tissue, (2) attenuate the aberrant T-cell response, (3) delay B-cell reconstitution. To investigate these hypotheses, we propose an experimental medicine study comparing the mechanistic effects of rituximab versus obinutuzumab in AAV. We will randomise up to 20 patients with active AAV to either rituximab or obinutuzumab. Patients will be followed up for 18 months. Baseline and 3-month nasal mucosal biopsies will enable evaluation of the extent of B-cell depletion in the tissue, which is the primary objective of this study. Differential effects on B-T-cell interaction, subsets and activation status in the tissue will also be examined.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM
Title: Mechanisms of host:parasite immune regulation during Schistosoma mansoni infection
Funder: Medical Research Council

Abstract: Schistosomiasis is one of the most highly-morbid and intractable parasitic diseases with no available vaccine. Its aetiological agents are platyhelmiths of the genus Schistosoma, that reside in their host vasculature. Despite persistent exposure to the host immune system, parasites can survive for many years, suggesting the existence of immune subversion mechanisms. Therapeutic intervention in humans and passive transfer of humoral immunity in animal models demonstrate however the existence of antibody-mediated protective host immunity. Because of their direct accessibility to the immune system, cell-surface and secreted parasite proteins are the most likely protagonists of immunosuppression and the primary targets of host protective immunity. Using a unique library of over 130 biochemically-active cell surface and secreted S. mansoni proteins produced in mammalian cells, I will perform serological and protein interaction studies to identify the parasite proteins involved in these mechanisms. Two unique serum collections from IFNgR knock-out mice and Brazilian patients with drug-induced resistance to re-infection will be used against the protein library to identify antigens associated with resistance to infection. Through protein interaction studies between the parasite library and an existing resource of human leukocyte receptors, I will identify new host:parasite pairs involved in immunomodulation. Finally, using a novel synthetic biology approach, I will investigate highly diverse Schistosoma gene families believed to play a role in immune escape - the micro-exon genes. I will test selected vaccine candidates in a murine model of S. mansoni infection and determine their function on host immune cells' activation and communication using a high-content imaging technique called pharmacoscopy. The study of host:parasite interactions during the host immune response to infection will uncover new vaccine candidates and improve our understanding of S. mansoni biology.


Research activity codes: 3.4 VACCINES;5.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM