NIHRDataInsights/HRCSData huggingface dataset:
Title: Interferon and Human Pandemic Viruses
Funder: Wellcome Trust

Abstract: We wish to define the key interferon (IFN)-stimulated gene (ISG) effectors for three pathogenic human viruses – HIV-1, SARS-CoV-2 and influenza virus – and understand the molecular basis for antiviral function. Specific ISGs will be identified in unbiased gene silencing (siRNA/ CRISPRi) screens, some of which we have developed. For HIV-1, we will initially focus on the antiviral mechanisms and post-transcriptional regulation of post-entry inhibitors we have identified, human-TRIM5alpha and MX2, including the central roles played by ubiquitination and phosphorylation. Our discovery that NCOA7 suppresses endocytic virus infection (e.g., SARS-CoV-2) provides the opportunity to study how the endolysosomal system can be dysregulated, potentially through altering vacuolar-ATPase activity. New screens for ISGs targeting SARS-CoV-2 or influenza virus will be undertaken using wild-type viruses as well as engineered strains carrying disruptions in candidate IFN- or ISG-antagonists. We will explore the molecular mechanisms and regulatory pathways used by the most potent ISGs using multiple complementary experimental approaches, including proteomic and approved drug screens, and determine how these viruses escape or survive ISG action. By understanding the ISG effectors that can control these viruses, we will gain fresh insights into viral replication strategies, disease processes and host immunity, and inform future antiviral therapeutic development.

Lay abstract: HIV-1, SARS-CoV-2 and influenza virus are cumulatively responsible for over two million deaths in 2020. Like all viruses, their growth and onward transmission are heavily dependent on the exploitation of cellular processes and components provided by the host. Conversely, an array of host immune mechanisms inhibit virus replication and provide protection against future infections. Interferons (IFNs) are host proteins produced in response to virus infection that mobilise a protective antiviral state in cells by activating IFN-stimulated genes (ISGs). Our research will employ cutting-edge gene discovery technologies to identify the key ISGs that inhibit each of these three viruses. We will elucidate the mechanisms of antiviral action of relevant ISGs, and determine if these viruses have countermeasures enabling evasion from ISG-mediated suppression. By deepening the understanding of the delicate balance between these competing forces, we will add to the knowledge base from which antiviral therapeutics and vaccines can be rationally designed.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: How does the purine metabolic checkpoint FAMIN prevent immunopathology?
Funder: Wellcome Trust

Abstract: Children with Still's disease, the paradigm of autoinflammation-cum-autoimmunity, are predisposed to developing a cytokine storm with excessive activation of T lymphocytes upon viral infection. Loss-of-function of FAMIN is the sole known cause for monogenic Still's disease. We de-orphaned FAMIN as an unprecedented purine nucleoside enzyme that combines ADA-, PNP- and MTAP-like activities with adenosine phosphorolysis – challenging fundamental principles of purine metabolism. Dendritic cells with absent FAMIN activity prime for excess antigen-specific cytotoxicity, IFN&gamma; secretion, and T cell expansion, resulting in exaggerated virus-specific T cell responses and immunopathology. Enhanced priming is already manifest with hypomorphic FAMIN-I254V, for which ~6.3% of mankind is homozygous, and which predisposes for Crohn's disease and leprosy. Here we will address FAMIN biology from virtually atomic to organismal resolution: We will explore how FAMIN operates in a cell, and how it controls energy metabolism, ascertaining redox and pH homeostasis. We will investigate how FAMIN in dendritic cells potently restrains T cell priming, and whether the FAMIN-coordinated biochemical mechanisms are involved in often fatal virus-induced cytokine release syndromes. This work will reveal an ancient biochemical mechanism that potently controls adaptive immune activation at a very fundamental level, providing insight into immunity to pathogens, autoinflammation and autoimmunity.

Lay abstract: Still's disease is a severe disease in children that starts with daily recurring high fever, a rash and lymph node enlargement, and morphs over weeks into a debilitating arthritis. Worse, virus infection can lead to an often fatal cytokine storm. Loss-of-function of FAMIN is the sole known cause for familial Still's disease. We discovered that FAMIN is an unprecedented enzyme involved in the metabolism of adenine and guanine, hence the nucleobases of the genetic code and energy currency of the cell. FAMIN is very ancient, with predecessors already present in bacteria. Its discovery changes our understanding of a very fundamental process of life. A partially active genetic variant of FAMIN is carried by ~6% of the population, and predisposes for Crohn's disease, an inflammatory bowel disease, and leprosy, a chronic infection. Here we explore how FAMIN defects predispose for these conditions, and how that might be prevented and treated.

Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: Immune fingerprinting of bacterial infections in cirrhosis (PMF)
Funder: Welsh Government Office for Science

Abstract: Liver disease affects two million people in the UK and kills 800 people in Wales each year. Regardless of the underlying cause a common pathway of inflammation leads to development of fibrosis leading to cirrhosis over time. In cirrhosis the immune system becomes increasingly dysregulated with the release of pro- and then anti-inflammatory signalling molecules (cytokines). In advanced cirrhosis there is increased risk of infection, kidney failure and mortality. Diagnosis of infection is challenging as patients may not mount fevers or release typical markers of infection. Transfusion of human albumin is very beneficial in spontaneous bacterial peritonitis but its role in other infections is less clear. Previous work at Cardiff University has demonstrated that different infections can result in specific cytokine profiles or ‘immune fingerprints’ allowing earlier diagnosis. I hypothesise that different infections in cirrhosis will result in the release of specific immune fingerprints allowing diagnosis, prognostication and stratifying patients to personalised treatment regimens. I shall recruit healthy donors and patients with cirrhosis with and without infections and measure blood and ascitic fluid cytokines. This will result in a large complex dataset which I will interrogate with cutting edge machine learning techniques to predict the best markers to stratify patients.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: Developing 3D-printed ceramic monolithic adsorption technology for life-threatening inflammatory conditions
Funder: Royal Academy of Engineering

Abstract: This project will develop a technology to treat life-threatening inflammatory conditions which cause the normally protective immune system to attack the body, including sepsis and COVID-19. Cytokines control the immune system and play a key role in these conditions, and the project will fabricate an adsorption technique to remove harmful cytokines.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: MOSAIC - cohort of hospitalised H1N1 patients
Funder: Medical Research Council

Abstract: We have assembled a team of 42 investigators from England and Scotland, bringing their combined expertise to the intensive study of a group of hospitalised patients with influenza. The integration and coordination of all the studies is a logistic challenge, and case ascertainment, definition and sample collection underpins the collaborative network. On this base, some of the UKs best clinical and basic research groups will conduct an integrated|study of influenza virology, host RNA transcriptome and of cellular and humoral immune responses to influenza viral infection. The same patients will also be tested for levels of soluble mediators (cytokines and chemokines) in various body fluids, so allowing the crosscorrelation of the clinical features, virology and RNA transcription profiles on a population|basis. All of this will be linked to the study of the host genome and the bacterial and viral|microbiota present in the respiratory tract as disease evolves, using 16s RNA methods to characterise bacterial populations without the need for culture. The collaborative study of a single set of hospitalised individuals will lead to a wealth of information and the cross correlations between different research outputs will provide|unprecedented opportunities for understanding the pathogenesis of influenza.Research Framework, the Health Protection Agency, London School of Hygiene and Tropical Medicine and the Sanger Institute.|


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: Nematode surface properties and genetics, drug sensitivity and bacterial infection
Funder: Medical Research Council

Abstract: The external surface of an animal provides a protective barrier, allowing normal development, physiology and interactions with the environment, and also constitutes a major area for attack by pathogens. This proposal explores nematode surface coat development, biochemistry and interaction with pathogens, using the nematode C. elegans. Much of the proposal stems from discovery of two virulent and complementary bacterial pathogens for C. elegans called Verde1 and Verde2. These provide selective tools for exploring the genetics of surface coat and bacterial interaction. We propose investigations in six areas: 1. Surface mutant genetics, carrying out selections and RNAi screens for genes affecting bacterial infection and surface permeability. Suppressor screens for modifiers of existing mutants will be performed, to reveal gene interaction networks. 2. C. elegans drug sensitivity. Many of the surface mutants are increased in drug sensitivity, as a result of increased permeability and drug uptake. We will investigate drug permeation, aiming to improve C. elegans-based drug screens. 3. Nematode surface biochemistry. We will analyse the carbohydrate and protein composition of surface coat, use tagged transgenes and mass-spectrometry. 4. Pathogen genetics. We will determine genome sequences for Verde1 and Verde2, and investigate their virulence and adhesion properties. 5. Cellular swelling and developmental plasticity. Infection by Verde2, as with a previously studied pathogen Microbacterium nematophilum, induces a protective cellular swelling reaction in rectal epithelial cells. We will investigate the cell biology, mechanism and function of this morphological change. 6. Analysis of pathogen detection and innate immune changes. Both Verde1 and Verde2 induce specific defense responses in infected worms We will investigate the signal transduction pathways involved, and the nature of possible bacterial triggers for these immune reactions


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: Importance of the pro-inflammatory effects of the capsule during invasive Streptococcus pneumoniae infection
Funder: Medical Research Council

Abstract: Streptococcus pneumoniae pneumonia is one of the commonest causes of severe infection in adults and children both in developed and developing countries. Although inflammation is required to control bacterial replication, an excess inflammatory response contributes to the complications of severe S. pneumoniae infection including septic shock, acute lung injury, and brain damage during meningitis. Recently the inflammatory response has also been implicated in tight junction downregulation allowing bacterial invasion across epithelial layers, so promoting bacterial invasion. Hence the factors that influence the inflammatory response to are critical mediators of severe infection and potentially could be new therapeutic targets to improve the high mortality and morbidity of severe S. pneumoniae infections. Recent data from drs Brown and Noursadeghi's laboratories has shown that unexpectedly unencapsulated S. pneumoniae induce a weaker macrophage pro-inflammatory response than encapsulated bacteria. Although the capsule inhibited translocation of NFKB into the nucleus, encapsulated strains stimulated increased transcription of various cytokines and a greater release of TNFa, IL-6 and IL-1B. The purpose of this project is to (a) characterize whether these affects of the capsule on inflammation affect disease development using rodent models of septic shock and acute lung injury and cell culture models of tissue invasion, (b) to use bacterial mutants and inhibitors of inflammatory pathways to identify the mechanisms underpinning the increased inflammatory response to encapsulated bacteria; and (c) to further investigate the clinical relevance of capsule on inflammation by using capsular switched mutant strains and well characterised clinical isolates to assess whether variations in inflammatory responses between S. pneumoniae strains are related to capsular serotype, and hence could contribute towards serotype-dependent differences in disease phenotypes.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: The role of monocytes and macrophages in the outcome of acute liver failure
Funder: Medical Research Council

Abstract: Sepsis is of major cause of mortality in both acute liver failure (ALF) and severe alcoholic hepatitis (AH), termed ALF syndromes. Our work indicates that circulating monocytes (Mo) and hepatic macrophages (H-mac) are responsible for the observed immunoparesis and play a major role in the pathogenesis and outcome of ALF syndromes. Our objectives are to assess whether circulating Mo dysfunction accounts for the susceptibility to sepsis and poor outcome in ALF syndromes. We will investigate if changes in functional characteristics of H-Mac and their production of anti-inflammatory mediators are responsible for monocyte dysfunction in ALF syndromes. Mo/H-Mac will be isolated and phenotypically characterised using a FACS-based lineage gating strategy. Functional analyses will consist of a number of FACS and ELISA based techniques that detect the secretion of inflammatory mediators, TLR intracellular signalling pathways, the degree of apoptosis, phagocytosis/oxidative burst activity and antigen presentation capabilities to recall antigen. In addition, in vitro analyses will assess the effects of ALF/AH sera and anti-inflammatory mediators on monocyte function. Functional characterisation of H-macs will be performed at the different phases of experimental ALF and compared to that of explanted H-macs. Using co-culture of H-macs with parenchymal and non-parenchymal cells and knock-out in experimental ALF models, we will determine key mediators and mechanisms that induce a switch in function of h-macs to promote the resolution of inflammation, tissue repair/regenerative processes. Liver disease is the 5th commonest cause of death in the UK and rising sharply in prevalence. This work will increase our understanding of mechanisms of hepatic injury and infection in ALF syndromes, generate targeted therapies to attenuate liver injury and reduce infection, thus improving the prohibitively high mortality rate encountered in these conditions.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: The Adhesin Complex Protein (ACP) of Neisseria meningitidis: vaccine potential and biological properties
Funder: Medical Research Council

Abstract: Currently, there are no vaccines available for routine immunisation against serogroup B Neisseria meningitidis. The most promising vaccine currently with the European Medicines Agency is Bexsero(4CMenB), the product of a reverse vaccinology approach. However, this will not be a 'universal vaccine' as the vaccine antigen composition will provide coverage in the UK of only ~73%. Thus, antigens of greater conservation that can provide cross-protection are eagerly sought. We have selected from the outer membrane proteome a protein called the Adhesin Complex Protein (ACP) for study as a potential vaccine antigen. We have shown that ACP can induce serum antibodies that kill heterologous strains and that it functions as an adhesin especially for epithelial cells. Our proposal to MRC is to investigate further the vaccine potential and biological role of ACP. 1. Vaccine potential: this will involve determining sequence conservation and the number of different ACP types and expression levels amongst meningococcal strains. Anti-ACP sera and monoclonal antibodies will be generated for structural, biological and functional assays. Notably, we will examine the structure of ACP by NMR/crystallography. We will also test different ACP-vaccines for their ability to induce cross-protective bactericidal antibody responses. 2. Biological role of ACP. We will identify the cell surface receptor for ACP using a retagging approach and MALDI-TOF and siRNA gene silencing of putative receptors to confirm identity. The hypothesis that NadA and ACP act in concert to mediate bacterial adherence will also be tested. We will explore the role of ACP in meningococcal and gonococcal tropism for mucosal epithelia and the biological changes that ACP induces in human cells, including receptor-mediated upregulation of inflammatory responses. Our proposal will provide conclusive proof that ACP deserves consideration for inclusion in new MenB vaccines.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;3.4 VACCINES
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: mTOR control of effector CD4+ T cell activation during malaria infection
Funder: Medical Research Council

Abstract: The CD4+ T cell response to blood stage malaria infection has a biphasic nature; inflammatory effector CD4+ T cells that are primed during the early stages of infection are instructed to become less-inflammatory during the later stages of infection. This evolution of response is believed to be a self-protective mechanism to limit immune-mediated pathology. Importantly, the molecular events that orchestrate this transition are still unknown. In this proposal we hypothesize that the mammalian target of rapamycin complex (mTOR), which controls cellular glycolytic metabolism, as well as amino acid transport, lipid biosynthesis and mRNA translation, serves as a master intracellular signalling node within effector CD4+ T cells during malaria infection, integrating environmental and immunological signals, to adjust their inflammatory function. Indeed, our preliminary data shows that malaria-induced effector CD4+ T cells exhibit different metabolic profiles, controlled by mTORC1, during early and late stages of infection, concomitant with modification in effector function. In this proposal we will demonstrate the importance of mTOR in controlling effector CD4+ T cell priming, differentiation and function during malaria infection. We will perform detailed analyses of CD4+ T cell metabolism using pathway transcriptional profiling techniques and nutrient utilisation assays and we will integrate these analyses with immunological investigations of cellular activation, function and phenotype. Subsequently, we will identify the key immunological signals that function to modify CD4+ T cell metabolism during malaria, and how this ultimately impacts on the outcome of infection. The results from this proposal will represent a significant step forward in understanding how CD4+ T cell responses are controlled during malaria infection and will, generically, be the first detailed integrated study of CD4+ T cell metabolism and immunity in vivo during any infectio


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION
Title: Establishment of non-transformed, continuously growing, alternatively activated mouse macrophage cell lines
Funder: National Centre for the Replacement, Refinement and Reduction of Animals in Research

Abstract: Macrophages are crucial in defence against pathogens. They have two major types, the pro-inflammatory classically activated/M1 macrophages and alternatively activated/M2 macrophages. Interleukin(IL)-4 and IL-13 drive the formation of M2 macrophages that are considered to be anti-inflammatory and beneficial in tissue remodelling but harmful in certain bacterial infections and in allergic diseases. Recent studies indicate that, in contrast to most other macrophages, lung M2 macrophages proliferate in response to IL-4 in vivo. A significant part of research on M2 macrophages are done in the mouse system. M2 macrophages currently used in vitro have a limited life-span requiring the extensive and repeated use of animals. The aim of our proposed studies is to set up permanently growing, primary, alternatively activated macrophage cell lines to reduce the need for animals as a source of similar cells and to improve the existing macrophage research repertoire. Recently we established a novel method producing primary, GM-CSF dependent, continuously growing lung alveolar macrophage (AM)-like cells (MPI cells). Our most recent data show that IL-4 or IL-13 treatment induces an M2 like phenotype in the MPI cells. Here, we want to establish IL-4 treated MPI cells as a faithful model of alternatively activated Ams To prove their usefulness in infection research these MPI cells will be compared to existing primary M2 macrophage systems We will analyse global gene expression patterns in alternatively activated un-induced or stimulated MPI macrophages with RNA sequencing and measure the levels of relevant proteins important in M2 macrophages and innate signalling as well. We will also characterize alternatively activated MPI cell responses to a range of selected important pulmonary pathogens. Accomplishment of this project can drastically reduce the number of animals in this area and the proposed system would provide a powerful new tool in biomedical science.


Research activity codes: 2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY);2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFLAMMATORY AND IMMUNE SYSTEM;INFECTION