NIHRDataInsights/HRCSData huggingface dataset:
Title: African critical care registry network for pandemic surveillance, clinical management and research.
Funder: Medical Research Council

Abstract: Our group of LMIC based co-investigators and project partners from established critical care and pandemic networks aims to address the knowledge gaps that exist regarding the natural history and clinical course of COVID-19 related critical illness in seven African countries. In achieving this aim, we will address operational gaps in pandemic responsiveness by establishing a network with the infrastructure to identify optimal strategies for supportive care and interventions for the same patients. The aim will be achieved by 3 activities. 1. Implementing a setting-adapted (International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) Clinical Characterisation Protocol (CCP) compliant critical care registry. The near-real time registry with integrated ISARIC tier 0-2 CCP and capacity for clinical research will be implemented in 35 critical care sites in seven countries building on the methods used in the Wellcome-supported nine country Critical Care Asia (CCA) network. Registry data output will include epidemiology, quality of care processes, risk stratification and outcomes. A comprehensive national service evaluation of critical care services and an EARL evaluation will also be conducted. 2. Identifying stakeholder research priorities to optimise critical care processes and outcomes leveraging activity 1 data. We will facilitate Audit & Feedback workshops and research prioritisation exercises for site stakeholders (inc. public) using Activity 1 output to determine priorities for optimising COVID-19 clinical management and pandemic responsiveness, especially for the critically ill, obstetric and surgical populations. 3. Recruiting sites to registry enabled clinical trials. We will facilitate sites to participate in registry-enabled clinical trials mentored by our group and project partners. The registry infrastructure and specific data will optimise sampling strategies, patient recruitment and study monitoring.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION
Health categories: INFECTION
Title: Regulatory crosstalk between human Caspases & Guanylate Binding Proteins in antimicrobial host-defence
Funder: Medical Research Council

Abstract: Interferon-inducible Guanylate Binding Proteins (GBPs) are GTPases that mediate cell-intrinsic defence against intracellular bacteria, parasites, and viruses. GBPs promote inflammasome/caspase-mediated cell death and remove replicative niches of intracellular pathogens. Salmonella Typhimurium and Toxoplasma gondii infection of macrophages results in human GBP1-dependent restriction of pathogen replication and programmed cell death through caspase-4 and -8, respectively. Mechanistically, GBP1 required GTPase activity and C-terminal lipidation to traffic to microbial compartments and promote access of cytosolic sensors to Salmonella LPS and Toxoplasma DNA. Moreover, caspase-1 inactivates GBP1 over time by proteolyzing it at a conserved Asp residue and suppresses the GBP1-caspase-4 cell death pathway. We hypothesise that GBP2-5 are also regulated through temporal proteolysis in a feedback loop that balances cell death, cytokine maturation, and antimicrobial defence. Endogenous GBP1/2/5 can be farnesylated or geranylgeranylated as revealed by our sensitive chemical biology probes. We will deploy these new tools to test our hypothesis that differential lipidation controls GBP trafficking to pathogen-specific compartments. With our high-throughput Host Response to Microbe Analysis (HRMAn) workflow, we have discovered new genes that promote GBP-dependent cell-intrinsic immunity independently of cell death, which we will investigate in-depth to dissect new mechanisms of defence orchestrated by these major protein families. Taken together, we will delineate context-specific, family-wide regulatory crosstalk between human GBPs and caspases during infection. Hereditary mutations or deregulation of IFNs/inflammasomes/caspases exacerbates inflammation and are detrimental to host defence. Our elucidation of new regulatory mechanisms will be invaluable in the design of effective therapies directed at boosting innate immunity and preventing unwanted inflammation during infection.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Deciphering the molecular mechanisms and physiological consequences of macrophage polarisation during Salmonella infection
Funder: Medical Research Council

Abstract: As a key cell of the immune system, macrophages are equipped for pathogen destruction, yet they serve as a niche for the human disease-causing pathogen Salmonella enterica. By delivering virulence factors (effectors) across host cell membranes, Salmonella interferes with immune signalling, promoting its replication, persistence and systemic dissemination within the host. We recently showed that Salmonella effector SteE alters the amino acid and substrate specificity of the host serine/threonine kinase GSK3, enabling it to tyrosine-phosphorylate the anti-inflammatory and M2-polarising transcription factor, STAT3. We will now use transcriptomics in genetically modified macrophages to define SteE-regulated genes that are STAT3 dependent and independent. Then, ChIP-seq will be used to distinguish SteE-induced genes directly regulated by STAT3. Finally, after identifying novel targets for the kinase activity of the SteE/GSK3 complex we will investigate the role of these in mediating M2-like polarisation and Salmonella persistence. M2-polarised macrophages exhibit a distinct metabolic state compared to inflammatory M1 cells and Salmonella shifts the host metabolome; however, whether this represents an effector-mediated virulence mechanism is unknown. We will therefore study key metabolites in primary macrophages upon infection and determine whether they are regulated by SteE. Finally, we will use structural biology and biochemistry to understand the profound conformational changes occurring in SteE and GSK3 that enable the switch in GSK3 kinase specificity and elucidate the atomic mechanism of STAT3 phosphorylation by GSK3. This will provide valuable insight into key immune signalling processes and immunometabolism as well as pathogenesis mechanisms for this global pathogen. This may promote the development of novel anti-bacterial or immunoregulatory therapeutics, which are urgently needed with the rise of antibiotic-resistant bacterial strains.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Mechanistic basis of the antifungal potency of the airway epithelium
Funder: Medical Research Council

Abstract: I have demonstrated that phagocytic activities of the respiratory epithelium play a crucial role in host defence by killing ingested A. fumigatus spores, and that this defence is radically altered in human airway epithelial cells (AECs) from COPD patients. I thus hypothesise that AECs provide a critical antimicrobial defence against everyday spore exposure, and that aberrant spore uptake and killing promote Aspergillus-related lung disease. By exploiting my single-cell platforms to perform molecular and cellular studies of A. fumigatus-AEC interactions in vitro, in vivo and in primary AECs, this work aims to define, for the first time, the mechanistic basis of effective and dysfunctional A. fumigatus clearance by AECs. In particular, it aims to: 1)Identify the fungal cell wall components driving effective A. fumigatus clearance by AECs. This will be achieved measuring A. fumigatus uptake and intracellular killing during morphotype-specific in vitro challenges of AECs in the presence of selective fungal cell wall inhibitors and during in vitro and in vivo challenges with an extant panel of A. fumigatus cell wall mutants. 2)Define the epithelial components directing effective A. fumigatus clearance by AECs. This will be achieved analysing A. fumigatus uptake and intracellular killing in AECs, subjected to targeted and global CRISPR/Cas9 genome editing of plasma membrane epithelial proteins. 3) Characterise the molecular basis of dysfunctional AEC activities in COPD patients. This will be achieved testing the role of the identified fungal and epithelial components in comparison of commercially-acquired primary human AECs from donors with and without COPD. Understanding how the lung coordinates mucosal homeostasis and maintenance of airway sterility is of major clinical importance and will aid the identification of immunomodulators to facilitate treatment and limit respiratory damage following exposure to this and other respiratory pathogens.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Investigating post Transcriptional Essential Gene Regulation In Leishmania (InTEGRL)
Funder: Medical Research Council

Abstract: My aim is to use Leishmania mexicana as a cultured, genetically manipulable model to characterise key posttranscriptional regulators we have identified that are essential to Leishmania spp. differentiation and virulence. Host immune cells provide the environmental cues, and signal the parasites to differentiate to virulent amastigote stage human infective forms. Factors that regulate and promote this differentiation enable the cells to adapt to the new host environment, survive and spread. Essential regulators may serve as potential drug targets as Leishmania proteomes are very divergent from human. I will initiate the investigation by endogenously epitope-tagging the 12 essential RBPs that have been shown to drive differentiation and virulence in human-infective Leishmania parasites. These transgenic cells will then be uv-crosslinked in vivo to immunoprecipitate associating proteins (IP), RNAs (RNA IP) of regulators. To determine the location and requirements of protein:transcript associations I will use uv-crosslinking RIP CLIP techniques. Quantitative RNASeq and LC mass spectroscopy will be used to identify isolated mRNP factors which will be validated by additional RIPs and qRTPCR (RNAs) and associating proteins will be endogenous tagged with complementary IPs confirming novel mRNP interactions. The effect of candidate regulators on target transcripts and differentiation will be genetically tested by ectopic overexpression and protein depletion methods. The regulation of associating transcripts will be examined for impact on the protein level using epitope tags, reporter:UTR constructs and antibodies to promising trans-regulators and transcript targets. The mRNP interactions will be mapped and fuctional contributions toward parasite survival and infectivity will be determined and compared. Whether these mRNPs function in the same, divergent or independent pathways in differentiation and virulence will be investigated.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Molecular-level mapping of the human antibody response to hantavirus infection
Funder: Medical Research Council

Abstract: The transmission of pathogenic hantaviruses from small animals to humans can cause severe disease with mortality rates of up to 40%. Critically, there are currently no approved vaccines or therapeutics for the prevention or treatment of hantavirus infection. Although production of neutralising antibodies (nAbs) that target the hantavirus surface glycoproteins is essential for disease clearance and protection, little is known about the epitopes targeted by nAbs, nor their mechanism of action. Building upon the technologies developed in our previous MRC-funded research, we will isolate nAbs and cross-neutralising Abs (crnAbs) from the acute and convalescent phases of hantavirus infection in humans. Combining functional and state-of-the-art structural approaches, including X-ray crystallography and cryo-electron tomography, we will; (i) Define the relative contribution of human nAbs against the two hantaviral glycoproteins, Gn and Gc. (ii) Identify singly and cross-reactive epitopes on the hantavirus surface that are targeted by nAbs and crnAbs, respectively. (iii) Provide structure-based insights into immune recognition by nAbs and crnAbs. (iv) Define the mechanism(s) of action utilised by potent hantaviral nAbs and crnAbs. The molecular-level information delivered by this research will augment ongoing efforts to detect hantaviruses in the field and rationally develop antibody-based immunotherapeutics and therapeutics capable of preventing hantavirus infection. Furthermore, this project will improve our preparedness for the emergence of both known and novel pathogenic hantavirus species.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Mechanisms of spore engulfment in C. difficile
Funder: Medical Research Council

Abstract: C. difficile infections (CDIs) are a major cause of morbidity and mortality in UK hospitals, with recent outbreaks of more virulent strains posing an increasing challenge to healthcare. There is an urgent need for new, effective methods for infection control and treatment. The current pandemic has led to intense use of antimicrobials worldwide, further enhancing the risks of antimicrobial resistance in the near future. Spores are the infective agents in CDI and are also involved in disease recurrence and persistence. After asymmetric cell division, the smaller cell - the forespore - is engulfed by the mother cell, followed by maturation and release of the spore. We have shown (MRC NIRG) that 2 protein machineries - DP and Q:AH - are essential for sporulation. We will build on this work to further our understanding of the complex network required for engulfment - the engulfasome - and its role in disease, transmission and recurrence. We aim to: 1. Define the components and organisation of the engulfasome We will characterise interactions of DP and Q:AH in C. difficile and other potential engulfasome proteins and their three-dimensional organisation throughout engulfment. We will determine the structure of these complexes and the individual proteins to elucidate the molecular details of their mode of action. 2. Reveal the driving forces of engulfment We will reveal the composition and architecture of PG at different stages of sporulation and study the enzymatic activities involved in the process. This will reveal how PG remodelling drives engulfment. 3. Elucidate the role of spore engulfment in disease We will investigate the role of the engulfasome machineries in CDI using in vitro models as well as their impact on pathogenicity in acute and persistent animal disease. This project will enhance our knowledge of a fundamental process in CDI and allow a better understanding of how sporulation impacts CDI.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Klebsiella pneumonaie anti-immunology: exploiting mTORC1 to control cell-intrinsic immunity.
Funder: Medical Research Council

Abstract: Pneumonias due to multiple-drug resistant pathogens are an important public health problem and are major causes of morbidity and mortality worldwide. Of particular concern are the infections caused by Klebsiella pneumoniae. The isolation of Klebsiella strains resistant to "last resort" antimicrobials has significantly narrowed, or in some settings completely removed, the therapeutic options for the treatment of Klebsiella infections. Not surprisingly, K. pneumoniae has been singled out by the World Health Organization as an "urgent threat to human health" due to multidrug resistant strains. Less obvious, but central to pathogenesis, are the adaptations to the human immune system. However, our knowledge of the interface between Klebsiella and these pathways is still elementary, as it is our understanding of which of such responses benefit the host versus the pathogen. In this project, we will expose a Klebsiella immune evasion strategy based on hijacking the immunomodulatory functions of the cell master regulator mTORC1. We will use a multidisciplinary approach leveraging the power of biochemistry, cellular microbiology, proteomics and in vivo models. We will detail the signalling pathway exploited by Klebsiella to activate mTORC1, uncover how Klebsiella manipulates the localization of mTORC1 to the Klebsiella containing vacuole, identify the Klebsiella factors involved in mTORC1 activation, and dissect the effect of mTORC1 on Klebsiella infection biology. Finally, we also set out to provide compelling experimental pre-clinical evidence for host-directed therapeutics targeting this "covert" Klebsiella strategy. Altogether, this project will uncover a new angle of Klebsiella adaptations to survive in what should be a hostile environment. The findings of this project shall be the foundation for novel therapeutics based on enhancing innate host resistance to infection, and ameliorating pathophysiological tissue destruction.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Deciphering the role of secreted proteins at the host-parasite interface during chronic Toxoplasma gondii infection
Funder: Medical Research Council

Abstract: Toxoplasma gondii infects ~1/3rd of the human population and establishes long-term chronic infection, forming intracellular cysts predominantly in the brain. Reactivation of chronic parasites causes fatal encephalitis in the immunocompromised and substantial ocular disease. Despite the chronic cyst being critical for both transmission and pathology of the disease, we understand little of how the cyst forms and subverts host clearance mechanisms. Importantly, chronic stage parasites upregulate and secrete >80 putative effectors, including several kinases and phosphatases, suggesting they are required for the unique biology of chronic infection. The goal of this proposal is to determine how these secreted effectors contribute to the formation and defence of the cyst. To reach my goal I will use a cutting edge CRISPR screening method to identify which effectors are required to establish the chronic cyst in vitro and in vivo in an unbiased way. As a complementary approach, I will investigate how selected kinases and phosphatases and their targets contribute to the formation and growth of a healthy cyst using high-content imaging and biochemical approaches. I will further assess defence at the cyst wall in disease-relevant cell types (ocular and neuronal cells). This will establish a pipeline for analysis of newly identified effectors in cyst formation, growth and defence. In doing so, I will identify the requirements and vulnerabilities of this currently undruggable parasite stage. Moreover, by studying the effectors of this expert pathogen, I will identify the host cell signalling events it subverts to promote long-term infection, furthering our understanding of chronic host-pathogen interactions.


Research activity codes: 5.2 CELLULAR AND GENE THERAPIES
Health categories: INFECTION
Title: Household Transmission and Immunity to SARS-CoV-2 among Paediatric Clients of a Primary Care Center in a Low-resource Community in Rio de Janeiro
Funder: Medical Research Council

Abstract: This project aims to characterise household transmission dynamics in Manguinhos, an urban slum (favela), which has one of the lowest Human Development Index (HDI) scores of Rio de Janeiro/Brazil. We will also estimate the immunity of the study population against SARS-CoV-2. This will be a prospective study of household contacts of laboratory-confirmed SARS-CoV-2 infected and non-infected children and their families, following the WHO Household Transmission Investigation Protocol for COVID-19. We will recruit children 0 to 13 years of age who are brought to the local health care centre to receive free vaccinations. The clinic provides primary care to 4,300 children in this age group per month. After obtaining written informed consent from the child's guardian, samples will be collected at the clinic (oral fluid, nasopharyngeal and rectal swabs, and serum). The child's home will then be visited to collect samples from contacts. All samples will be screened for SARS-CoV-2 by PCR following the Charité protocol, and serum for IgG antibodies by ELISA or CLIA and for neutralising antibodies by FRNT. At the household we will collect samples at Days 1 (first visit), 14 and 28, every three months during the first year and twice in the second year. Clinical follow up will be done through telephone calls and video conferences by nurses and paediatricians from Day 0 to Day 28.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: INFECTION
Title: CO-CONNECT: COVID - Curated and Open aNalysis aNd rEsearCh plaTform
Funder: Medical Research Council

Abstract: CO-CONNECT is a collaborative project and it has four CO-PIs: Jefferson (Dundee), Sheikh (Edinburgh), Hopkins (PHE) and Quinlan (Nottingham). The UK has rich, globally important COVID-19 datasets, including large serology cohort studies funded by UKRI, Wellcome, DHSC/NHS, NIHR and the devolved administrations. However, this breadth of data creates a risk of fragmentation, inconsistent structure and access processes, severely limiting utility, timeliness and impact. Our vision is to transform UK COVID-19 diagnostic datasets to be Findable, Accessible, Interoperable and Reusable (FAIR) and couple this with expert data engineering, enabled by Health Data Research (HDR) UK, to catalyse responsible and trustworthy use of the data for research and innovation. We propose to support PIs and data custodians to link COVID-19 cohort, serology and other health and non-health datasets. This longitudinal linkage is vital to derive new scientific insights and deliver informed decisions about how best to control the spread of SARS-CoV-2. At present there are >30 independent studies with no streamlined approach to linkage to other health and non-health related datasets, lack of data standardisation, and no strategic approach to synthesise analyses across studies. SAGE (9th June) requested HDR to work with partners to develop the UK-wide serology and testing data research asset that is linkable to other data sources. This proposal has been prepared in response to this request. We have bought together 41 leaders from 29 different organisations and 44 data sources to address a major data engineering challenge by building upon existing UKRI investments, including the HDR BREATHE Hub, to create a 'one-stop' service for trustworthy, multi-stakeholder utilisation of curated COVID-19 data for public, private and third sector benefit.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY);2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY)
Health categories: INFECTION