NIHRDataInsights/HRCSData huggingface dataset:
Title: R Phillips, KNUST Ghana. Pathogenesis and management of M. ulcerans disease, Buruli ulcer
Funder: Medical Research Council

Abstract: Buruli ulcer is a neglected tropical disease caused by infection with Mycobacterium ulcerans (Mu) which is common in remote rural parts of West African countries including Ghana. The disease results initially in a subcutaneous painless nodule tethered to the skin or an intradermal plaque both of which ulcerate centrally. Oedematous disease is the most severe form of disease and it occurs in about 15% of cases. It may extend to a whole limb. Antibiotic treatment with rifampicin and streptomycin for 8 weeks is now standard. The main aim of the proposed studies is to investigate markers for patients with early infection in whom the bacterial load is low and production of the M. ulcerans toxin mycolactone is limited. It is proposed that such patients will respond rapidly to antibiotic treatment and that a shortened course of antibiotics will be adequate. A prospective observational study will be undertaken in patients diagnosed accurately to have Mu infection. Biomarkers will be investigated in serum using multianalyte profiling by Luminex. The immune response to Mu antigens will be studied and lymphocyte populations will be analysed by flow cytometry. Tissue mycolactone concentration will be measured by a cytotoxicity assay and by mass spectrometry. Paradoxical reactions are seen in 10% of cases during or after antibiotic treatment. The pathogenesis of these reactions and of oedematous disease will be investigated using the same techniques to measure the immune response to Mu antigens, serum biomarkers and tissue mycolactone concentration.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES;6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Replication of influenza virus at the molecular level
Funder: Medical Research Council

Abstract: The proposed research programme aims to uncover fundamental aspects of structure and function of influenza virus as well as virus-host interactions and host responses to viral infection. The main focus is the viral transcriptional machinery, a multi-subunit enzyme complex, which transcribes and replicates the viral RNA genome in a host cell-dependent manner. This enzyme, which consists of the viral RNA polymerase and nucleoprotein, is essential for the virus to replicate and is an important determinant of host range and virulence. The research objectives are to determine the molecular mechanisms of transcription and replication of the viral RNA genome by this transcriptional machinery, to identify and characterise the molecular interactions it makes with the host cell, and to determine the implications of these interactions for cell tropism, host range and virulence. The proposal builds on the achievements of my research over a 20 year period, in the last 10 years supported by a Senior Research Fellowship and 5-year Research Grant from the MRC. We will use the latest state-of-the-art technologies in single-molecule imaging (FRET), super-resolution microscopy (PALM and STORM), structural biology and proteomics in combination with methods from biochemistry, cell biology and virology. Recombinant proteins for structural analysis will be expressed using recombinant baculovirus technology (Multi-Bac) allowing the expression of multiple proteins from a single baculovirus in insect cells. Influenza virus mutants for cell biology and animal studies will be generated by reverse genetics. Virulence studies will use established animal models for influenza. Impacts of this research will include understanding the emergence of influenza strains with pandemic potential, discovery of novel viral and cellular drug targets, and the development of novel vaccines by reverse genetics. Promising avenues will be exploited in collaboration with industrial partners.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The interactions between Clostridium difficile, intestinal microbiota and the host response in hospitalised patients
Funder: Medical Research Council

Abstract: Reduction in C. difficile infection (CDI) related morbidity and mortality is a current healthcare imperative. To develop appropriate sustained interventions, a holistic integrated view of the pathogen, the host response and the intestinal microbiota during infection is required. Our central hypothesis is that variation in C. difficile genetics, the composition of the resident intestinal microbiota and the repertoire of host factors, including the humoral immune response, shape the clinical outcome of CDI. To this end we will evaluate in unprecendented detail the pathogen genome sequence, intestinal microbial composition and the host response in a case-control study of CDI hospitalised patients. Rigorous statistical comparisons of data from the organism, intestinal microbiota and host response in relation to a patient disease severity index will enable selected genes/proteins to be chosen for functional analysis. To determine their role, defined/complemented mutants and wild type strains will be compared in several relevant in vivo-relevant assays. Potential biomarkers of disease severity will be assessed based on the combined clinical and molecular profile. Additionally, we will identify key bacterial groups important in re-establishing healthy microbiota during infection. Such analysis will investigate the role of the microbiota in providing colonisation resistance against CDI and will give new information on the bacterial species important in the re-establishment of healthy microbiota after infection, with applications in the rational design of microbial replacement therapy. This integrated clinical case control study will provide for the first time a comprehensive comparison of the pathogen, host response and the role of the intestinal microbiota in CDI that will afford new clues to pathogenesis with practical implications in terms of diagnosis and therapeutic interventions.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Metabolic regulation of tissue destruction in tuberculosis.
Funder: Medical Research Council

Abstract: This project will investigate the hypothesis that metabolic pathways regulate gene expression and secretion of matrix metalloproteinases (MMPs) in tuberculosis (TB) by a HIF-dependent mechanism. Specific aims are, first, to investigate the interaction between metabolic pathways and proinflammatory cytokine/MMP gene expression and secretion in TB-infected human macrophages and in a multicellular model of infection. Second, involvement of HIF-1a and AMPK in metabolic control of key MMPs in TB will be examined. Finally, indicators of glycolysis and upregulation of key signalling pathways will be investigated in TB patients. In a cellular model of TB, the effect of glucose, glucose restriction, 2-deoxyglucose and galactose on TNF, IL-1 and MMP gene expression (qPCR) and secretion (ELISA, luminex & zymography) by human monocyte-derived macrophages and primary respiratory epithelial cells will be examined. The effect of succinate will be assessed in dose-response and kinetic experiments and the effect of 2-DG on succinate dehydrogenase activity will be measured using a colorimetric assay based on formation of nitroblue diformazan. Using specific chemical inhibitors, siRNA technology and a dual-luciferase gene reporter system, the potentially key role of the transcription factor NF-kB will be investigated. Next, in the purpose-built hypoxia chamber in our Category 3 TB laboratory, the role of HIF-1 in this process will be determined.The expression of pyruvate kinase M2 (which interacts with HIF-1) and the upstream proline hydroxylases 2/3 will be analysed. On the basis of preliminary data, the linking regulatory role of a peak AMPK will be investigated. In TB patients, lactate concentrations in lymph nodes will be measured as a marker of glycolysis. Lung biopsies will be stained for the active form of AMPK with dual staining for pyruvate kinase M2 and HIF-1 as appropriate. These studies will be the first to define the interaction between metabolism and tissue damage in TB.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Structure and function of the Pseudomonas aeruginosa type VI secretion system: On the bacteriophage trail
Funder: Medical Research Council

Abstract: The type VI secretion system (T6SS) is conserved in bacteria and is used to subvert host cell response or to kill competing bacteria. Pseudomonas aeruginosa has 3 T6SS gene clusters. H1-T6SS is induced in mutants lacking the regulatory gene retS and could be studied in vitro. The T6SS is made of 13 core components, of which some display homologies with bacteriophage tail components. The bacteriophage injects DNA in target cells and it is proposed that the T6SS functions by making localized puncture in the bacterial envelope to allow secretion/injection of toxins. It is noteworthy that the few similarities between T6SS and bacteriophage, namely VgrG and Hcp, could only be predicted by 3D structural comparisons. Amino acid sequence comparisons fail to show that these components have greatly diverged in the course of evolution. We predict that other T6SS components will have similarity with bacteriophage tail components. In order to document the correlation between T6SS and bacteriophage we will solve the structure of 7 T6SS components, HsiABCEFGH. The structures of these components will inform site directed mutagenesis studies which will be conducted to assess the assembly and function of the T6SS machine. Standard protein secretion assay and a newly developed bacterial competition assay will also be used. The structures of T6SS components will be solved using primarily X-ray crystallography and NMR (where appropriate) and the individual structures are unlikely to fully elucidate the T6SS mechanism. Advances in EM instrumentation and image reconstruction methods now allow the architecture of large macromolecular assemblies to be elucidated. We will therefore use cryo-EM methods to characterize T6SS sub-complexes based on data from our HsiABCEFGH interaction network and combine these EM envelopes with high-resolution models of individual or sub-components to obtain pseudo-atomic models for the T6SS complex.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Developing and evaluating a framework for the rational design of antibiotic prescribing policies in resource-constrained hospital settings
Funder: Medical Research Council

Abstract: Empirical antibiotic therapy for hospitalized patients should be chosen based on consideration of the likely pathogens, local antibiotic susceptibility patterns, patient-specific factors relating to severity of illness and risk of infection with a resistant organism, cost-effectiveness, and the impact of the antibiotic on the selection for resistant bacteria within the patient and the hospital. Designing antibiotic polices to satisfy these complex and competing requirements is difficult. Wide variation in resistance patterns and different local incidence rates with different organisms prevent simple generalization of findings from clinical trials. Currently setting-specific choices of empirical therapy are made using clinical judgement alone, without the support of quantitative analysis or a coherent framework for balancing the competing requirements. We hypothesize that patient outcomes could be improved in a cost-effective (and potentially cost-saving) manner and antibiotic resistance reduced by implementing an evidence-based approach to the design of antibiotic policies. This proposal aims to develop and evaluate such a framework for the rational design of antibiotic policies and to quantify the value of improving prescribing through investment in enhanced diagnostic capability. This will involve developing, extending and synthesizing a suite of phenomenological and mechanistic modelling approaches for quantifying the impact of prescribing decisions on patient and population-level outcomes. We propose to evaluate this approach using both in silico experiments using real hospital data and in a cluster-randomized trial. While this proposal has global significance, we will focus exclusively on the choice of empirical therapy in low and middle income countries in Asia, where the potential health benefits are greatest and where the prevalence, local impact and international significance of antibiotic resistance make it a global health priority.


Research activity codes: 7.3 MANAGEMENT AND DECISION MAKING;8.3 POLICY, ETHICS AND RESEARCH GOVERNANCE
Health categories: INFECTION
Title: Community randomised evaluation of socioeconomic intervention to prevent TB
Funder: Medical Research Council

Abstract: BACKGROUND: TB kills more people than any other single infection. New interventions are needed to strengthen TB control. Poverty hampers access to care, increases vulnerability and is the main determinant of global TB rates. Socioeconomic interventions for TB control have been proposed but there is little evidence to guide how they should be used. PRELIMINARY DATA: Socioeconomic intervention increased equitable access to TB care in our published 4-year pilot study. HYPOTHESIS: Socioeconomic intervention prevents TB by synergistically improving access to TB care and reducing TB vulnerability. POPULATION: impoverished shantytown households in which one resident has recently been diagnosed as having TB disease, putting the other residents at high risk of TB disease. PROPOSAL: A community randomised-controlled study will include 12,552 members of 1,874 households in periurban Lima shantytowns with a registered population of 307,623. The impact of a complex socioeconomic intervention will be assessed by comparing 12 intervention versus 12 control shantytowns. The integrated community-based intervention was developed in our pilot study and includes a social dimension (community mobilisation for health promotion to inform care) and an economic dimension (conditional cash transfers to incentivise and enable care and reduce poverty-related TB vulnerability). OUTCOMES: The primary outcome will be the impact of the social and economic interventions preventing TB disease assessed by combining incident TB post-intervention with a final prevalence survey of all participants. Secondary outcomes will be the impact of the interventions increasing equitable access to TB care, reducing poverty and associated TB vulnerability and reduction in community TB rates. CONCLUSION: This study will provide the first evidence assessing the potential of socioeconomic intervention to prevent TB and its potential to expand TB care into community TB control.


Research activity codes: 3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING
Health categories: INFECTION
Title: MRC Centre for Outbreak Analysis and Modelling Renewal
Funder: Medical Research Council

Abstract: The threat to human populations from new and re-emerging pathogens has been highlighted in recent years by the 2003 SARS epidemic, the pandemic potential of the highly pathogenic H5N1 avian influenza strain and the 2009 H1N1 pandemic. Preparedness is therefore a key policy priority for public health agencies and governments worldwide. In addition, as novel vaccines, antimicrobials and other interventions are developed for endemic diseases, there is a need to extrapolate from clinical trial results to determine which combination of interventions gives the optimal (or most cost-effective) control strategy for a specific disease in a particular setting. In this context, modern epidemiological modelling and analysis methods have proven themselves increasingly powerful tools for giving insight into the patterns of emergence of novel outbreaks, the transmission dynamics of endemic diseases and the options available for the control of both. In the last 4 years, the Centre for Outbreak Analysis and Modelling has facilitated the exploitation of cutting-edge quantitative epidemiological research by public health agencies and policy makers tasked with delivering response strategies to infectious disease threats. Before the founding of the Centre, much of the interaction between the (world leading) researchers at the Centre and public health agencies (such as HPA, CDC or WHO) was sporadic and unsystematic, being difficult to fund from traditional project grants. Centre funding allows dedicated investment into the development and maintenance of close collaborative partnerships with HPA, CDC, WHO and BMGF. Centre funding supports a core technical capacity available to all projects, and pays for dedicated 'liaison' staff - postdocs who spend substantial time at WHO and CDC. Internally, Centre funding supports capacity-building, enhanced collaboration and an enhanced focus on career development - as well as vocational training of staff in public/global health agencies.


Research activity codes: 2.4 SURVEILLANCE AND DISTRIBUTION;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: Immunity in the face of diversity and the development of novel potent HCV vaccines
Funder: Medical Research Council

Abstract: The long term goal is to develop effective T cell vaccines to tackle hepatitis C virus (HCV) diversity. HCV exists globally as seven major genotypes, multiple subtypes and swarms of variants within each host. Within the UK genotype-1 and subtype-3a are equally prevalent - a unique feature of the epidemic. To date I have, in collaboration, developed a highly immunogenic HCV T cell vaccine in healthy volunteers. This consists of simian and human adenoviral (Ad) vectors derived from rare serotypes, in addition to Modified Vaccinia Ankara (MVA) vectors, used in heterologous prime/boost regimens. Both vectors encode the entire non-structural (NS) genotype-1b HCV proteins (1995 amino-acids) Significant immunogenicity is also induced in HCV infected patients, though the mean magnitude of the response is lower. My aims are to identify the determinants of the relative immune non-responsiveness in HCV infected patients. This will be achieved through the detailed characterisation of innate RNA signatures and adaptive T cell immunity, at baseline and in response to vaccination, in association with viral sequence analysis. This will give insight into the mechanism of T cell non-responsiveness that is the hallmark of many persistent viral infections. I will assess the immune correlates of viral clearance in HCV subtype-3a infection through the assessment of T and B cell immunity in natural infection. This will aid the rational design of effective UK HCV vaccines. Finally I will design a prophylactic vaccine for "broad" HCV coverage based on conserved peptide fragments. This will be delivered through the generation of a global relative prevalence HCV subtype dataset, and the "virtual" design of novel immunogens through computer algorithms that interrogate the dataset. Vaccines encoding the novel immunogens will be assessed in pre-clinical models. Delivering these aims will facilitate the rational development of novel HCV vaccines within the UK and globally.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Design of HIV vaccines that stimulate T cell and NK cell immunity
Funder: Medical Research Council

Abstract: This goal of this programme of research is to contribute to the development of an effective vaccine to combat infection with human immunodeficiency virus type 1 (HIV-1). We will focus on cellular immune responses, aiming to design strategies that: 1) Induce CD4 follicular helper T cell (TFH) responses that enhance the generation of HIV-1 broadly-neutralising antibodies 2) Elicit optimally-protective HIV-specific CD8 T cell responses 3) Enhance natural killer (NK) cell-mediated HIV control We will employ a combination of i. in vitro immunovirological studies; ii. advances in understanding of virus-immune system interactions during HIV infection gained by analysis of unique sample series from subjects acutely-infected with HIV and chronic patients with different clinical outcomes; and iii. insights from detailed analysis of specific aspects of the immune responses elicited in human vaccine trials, to inform the rational design of optimally-effective HIV vaccine immunogens. Techniques used in the proposed work will include a breadth of cellular and molecular methods for evaluating the phenotype and functions of innate and T cell subsets, including novel assays for analysis of HIV-specific TFH activity, recently-developed methods for evaluation of naïve and pre-immunisation memory T cell repertoires and Nanostring-based gene expression analyses; together with multiple virological, proteomics-based and bioinformatics techniques with which we have expertise in-house strengthened by input from local and international collaborators. A key element to this proposal is that it will synergise with the new NIH-funded Center for HIV/AIDS Vaccine Immunogen Design, of which the applicants are part, and with other vaccine research ongoing in Oxford. This will facilitate achievement of the objectives above both by providing access to reagents/samples and by supporting complementary studies that add value to the work in this programme.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Macrophage provenance, proliferation and plasticity in nematode infection
Funder: Medical Research Council

Abstract: Proliferation of resident macrophages in response to the Th2 cytokine, IL-4, is a newly discovered form of inflammation that can occur without the need for recruitment of monocytes from the blood. However, when a pro-inflammatory stimulus leads to blood monocyte recruitment, IL-4 will also induce proliferation of the recruited population. In both settings, IL-4 induces an alternative macrophage activation programme characterised by anti-inflammatory and tissue reparative genes. Both IL-4 and macrophages are required for the control of nematode infection but the specific factors required are not known. Our primary aim is to understand the functional consequences of alternative macrophage activation and proliferation in the context of nematode infection and to investigate functional differences between recruited and resident macrophages. We have developed an elegant tool box to look at global vs. cell intrinsic aspects of macrophage activation/proliferation that include bone marrow chimeras to track cell origins and restrict mutations to specific cell compartments as well as macrophage transfer procedures. We will use serous cavity models (both reductionist IL-4 injection and nematode infection) for the ease with which cells can be enumerated, manipulated and assessed. The tractability of these models means that we can address key questions about the basic requirements for proliferation and alternative activation that can be applied more broadly in different tissues. For readouts, we will use our well- developed and quantitative assessments of alternative activation but additionally assess macrophage genes that are IL-4-dependent in both and human and mouse and determine whether elements that regulate cell cycle do so independently of these genes or not. By unravelling pathways that the mammalian host has evolved to resist or tolerate nematode infection, this programme will expand our basic understanding of inflammatory processes.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION