NIHRDataInsights/HRCSData huggingface dataset:
Title: Defining the cytoplasmic architecture that control bacterial type three secretion
Funder: Medical Research Council

Abstract: Many pathogenic bacteria use nano-machines to inject proteins into their hosts' cells to promote infection and colonisation by the bacterium. One such machine is called the Type Three Secretion System or T3SS. This application seeks to investigate the way in which bacteria select and secrete proteins by using a combination of different structural and functional methods. In particular we will study two protein complexes known as the Export Apparatus (EA) and the C-ring that are assembled within the bacterium which genetic evidence suggests are important for the process of selecting which proteins should be injected into the host and are also implicated in the actual process of driving injection. By using structural and biochemical methods to define how these parts of the machine are constructed and complementing this with in vivo studies of structurally-informed mutations within the components from which the machines are constructed we hope to deduce the molecular mechanisms of control of secretion. Since this machinery is only found in bacteria there is the potential that a good understanding of the T3SS will eventually lead to new antibiotics which are designed to specifically interfere with this key pathogenic activity.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Geographic genetic profiling of human Plasmodium malaria
Funder: Medical Research Council

Abstract: We propose to develop: 1. A library of apicoplast and mitochondrial genomic sequence variants across multiple human Plasmodium species P. falciparum, P. vivax, P. ovale curtisi, P. ovale wallikeri, P. malariae, and P. knowlesi using existing raw genomic sequence data generated by collaborating investigators with external funding. 2. A statistical algorithm to infer informative SNP haplotypes within and between species from complex mixed infections. The perfect linkage disequilibrium or "perfect phylogeny" across the co-inherited organelle SNPs leads to an opportunity to construct phylogenetic trees that represent the relationship between haplotypes. Crucially this allows modelling approaches to disaggregate complex mixed infections. 3. Prototype barcodes based on newly generated mt/apico sequences for Pv, Po, Pm, and Pk, in partnership with collaborators; 4. A proof of principle. In collaboration with overseas research colleagues who have raw genomic sequence data suspected to contain mixed species co-infection (e.g. P. falciparum + P. malariae in Kenya, P. falciparum+P. vivax in Thailand). Colleagues at the National Institute of Parasitic Diseases at the Chinese Center for Disease Control and Prevention in Shanghai, China are genotyping local and putative imported infections from archived bloodspot samples and we will reanalyse these using the published Pf barcoding methodology of 23 SNPs developed using a classification and regression tree (CART) algorithm (Preston et al Nature Communications in press). 5. An online resource, which summarises the library of mt/api genomic variants and barcode haplotypes, and facilitates the input of sequence data for the rapid identification of species and the potential geographic source of (imported) infections.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: Tuberculosis in recent migrants to the UK: Examining new-entrant health screening and delays to diagnosis from the patient's perspective.
Funder: Medical Research Council

Abstract: In 2012, there were 8.6 million new cases of tuberculosis (TB) worldwide and 1.3 million deaths with over 9000 cases of active TB in the UK, of which 75% were in patients born abroad. The Home Office, NICE and Public Health England all recommend targeted TB screening processes either pre-entry, at the border or in the community. Reports from patients suggests that these are not systematically implemented and are, at best, ad-hoc. Alongside this, new migrants who do develop active TB often struggle to access the UK healthcare system. This leads to delays in diagnosis and consequently higher risk of disease transmission, higher costs and avoidable morbidity and mortality. This study will explore the experiences of TB patients who have recently migrated to the UK of TB screening and access to healthcare. Methods: This is a mixed methods study. 100 sequentially recruited patients who have recently been diagnosed with TB and who have migrated to the UK within the last 3 years will be invited to complete a survey. From this group a maximum variety sample of up to 40 patients will be selected. Qualitative data will be collected from this group using audio-taped interviews. Similar interview techniques will also be used to collect data from up to 20 key professionals and community members. Anticipated outcomes: This project will provide detailed insight into the limitations of the current systems for TB screening and healthcare provision for migrants. The results will highlight key strategic areas which should be targeted with a view to reducing the disease burden of TB in the UK. It is likely some of the findings will be applicable to migrant groups within other settings (and with other infectious diseases) and to TB screening in other major urban centres within countries of low TB prevalence.


Research activity codes: 8.1 ORGANISATION AND DELIVERY OF SERVICES;8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES)
Health categories: INFECTION
Title: A Spatial Framework for Optimising Control at the Local Level: Coordinated strategies for Neglected Tropical Diseases and Malaria (FOCAL-NTD)
Funder: Medical Research Council

Abstract: This project aims to develop a spatial framework for optimising the coordinated control of spatially heterogeneous neglected tropical diseases i.e. Human African Trypanosomiasis (HAT), schistosomiasis and lymphatic filariasis (LF), together with malaria coinfection at the local level. This will involve: identifying factors associated with local level spatial variability in disease risk; developing spatial sampling strategies for monitoring changes in the disease distribution over time; and developing intervention targeting strategies. Further, community-based surveillance tools will be developed as a low-cost method of obtaining local level disease information. Georeferenced data on disease prevalence, plus high resolution environmental, demographic, socio-economic and intervention data for Malawi and Uganda will be obtained from project collaborators, publicly available data sources and commercial satellite imagery. Using a binomial geostatistical modelling approach, these data will be analysed to quantify the relationship between potential risk factors and disease risk, culminating in the production of risk maps. These maps will be used to targeted disease intervention strategies. Further, a series of 'in silico' experiments will be undertaken to determine the influence of spatial sampling strategies on the resulting estimated risk map. More traditional sampling techniques will be compared with novel 'flexible' sampling strategies in which sampling locations are selected according to their potential to reduce the uncertainty in the estimated risk surface. Lastly, mobile phone-based surveillance tools will be developed and tested by community members in Malawi and Uganda to determine their potential for obtaining local information on intervention activities. The outcomes of this project have the potential to guide policy makers and disease control programmes to adopt more effective strategies, and thus simultaneously accelerate towards control/elimination.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.3 PSYCHOLOGICAL, SOCIAL AND ECONOMIC FACTORS;3.1 PRIMARY PREVENTION INTERVENTIONS TO MODIFY BEHAVIOURS OR PROMOTE WELL-BEING
Health categories: INFECTION
Title: MICA: Ad4HIV, A Phase I Trial Investigating Ad4, MVA and Protein Immunisation Strategies to Maximise Protective Antibody Responses to HIV-1 Envelope
Funder: Medical Research Council

Abstract: A safe and effective preventive HIV vaccine remains a key priority for global public health. The RV144 Phase IIb efficacy trial showed an estimated efficacy of 31% suggesting that a vaccine to prevent HIV-1 infection may be closer than previously thought. Although the mechanistic correlates of protection remain obscure, reduced risk of HIV acquisition correlated with a range of functional antibody characteristics. This modest and short-lived immune protection, based on a non-replicating canarypox vector prime and recombinant envelope protein boost regime, suggests the need for much more potent vaccine-induced protective antibody responses at the mucosal portals of viral entry. A mucosal replicating vector system generating local Env antigen persistence could potentially lead to higher levels of protective mucosal and systemic neutralizing antibodies. We propose a phase I clinical trial based on a replication-competent Adenovirus 4 (Ad4) vectored prime, combined with recombinant trimeric envelope protein boosts administered with or without an attenuated poxvirus (MVA) to identify the most immunogenic strategy for the induction of durable mucosal and systemic protective antibody responses. Priming will be done with oral replication competent Ad4 encoding membrane expressed HIV-1 envelope gp150 (Ad4-EnvCN54) followed by parentally administered rgp140 protein adjuvanted with synthetic Monophosphoryl Lipid A (MPLA) in an aqueous formulation with or without boost with a modified pox virus (MVA) encoding rgp120. All vaccines are based on the CN54 Clade C HIV. The primary immunogenicity end-points will be systemic Env antibody titre with a secondary end-point of mucosal (vaginal/rectal) antibody titre. Exploratory endpoints will include a wider panel of immunological assessments including antibody neutralization and cellular immunity. This will facilitate up-selection of the most promising regime to accelerate development towards a phase IIb study in Africa.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Epidermal growth factor receptor antagonists: Effect on regulatory T cells, and use as an adjuvant treatment for infectious disease
Funder: Medical Research Council

Abstract: Infectious diseases are a major burden to mankind and new approaches to treat infections as well as enhance vaccination efficiency are urgently required. The immunosuppressive effect of FoxP3 expressing regulatory T-cells (Tregs) is a substantial hurdle in the induction of protective immune responses, and diminishing Treg activity would be an exciting potential novel immunotherapy. It has recently been shown that Tregs are dependent on Epidermal Growth Factor Receptor (EGFR) signalling for optimal function, and that Tregs show diminished suppressive capacity during the therapeutic application of EGFR-inhibitors. This project aims to establish whether reduced Treg activity (by EGFR-blockade) enhances pathogen-specific immune responses during infection and vaccination. Infected mice will be treated with the EGFR-specific tyrosine kinase inhibitor Gefitinib, a drug already in wide clinical application. To test whether EGFR inhibition can induce pathogen clearance, a Litomosoides sigmodontis infection model will be used. For this chronic helminth infection it is established that Treg-function prevents pathogen clearance. In parallel, to test whether EGFR inhibition can enhance the efficacy of immunization, We will examine the effect on vaccination response using the Modified Vaccinia Ankara-Ovalbumin model. MVA contains an EGFR ligand, which we will attempt to delete to increase vaccine efficacy.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The role of Jam-C trafficking in endothelial vascular function
Funder: Medical Research Council

Abstract: The endothelium plays a crucial role in responding to an infection or tissue injury: In the recruitment of leukocytes to the site, and in tissue repair and angiogenesis. Adhesion receptors have a fundamental role in endothelial function governing many of these processes. Recent research suggests that rather than being present at fixed levels on the plasma membrane, some adhesion receptors exist in dynamically trafficked pools that can redistribute reflecting endothelial status. Of particular interest is the junctional adhesion molecule-C (Jam-C), a type-1 integral membrane protein of the Ig superfamily that has been shown to mediate numerous endothelial cell functions. Most notably Jam-C mediates aspects of leukocyte transendothelial cell migration, angiogenesis and vascular permeability. Importantly Jam-C expression and function has been associated with multiple inflammatory disease states such as arthritis, peritonitis, acute pancreatitis, ischemia reperfusion injury, pulmonary inflammation and atherosclerosis. Its receptor function is mediated by homophilic interactions as well as interactions with Jam-B on endothelial cells and Mac-1 on leukocytes. Jam-C is present at the cell surface and enriched at cellular junctions but there is also good evidence that it is present in intracellular pools and that the amount present in vesicles varies with the inflammatory status as well as the presence of permeability or pro-angiogenic factors. In particular, Ischemia reperfusion injury causes marked intracellular redistribution of Jam-C, the function and mechanism of this redistribution is as yet unclear. We aim to develop biochemical, live cell imaging and EM assays to investigate intracellular Jam-C traffic. Using these assays we will determine the motifs in Jam-C and molecular machinery required. We will then use this information to determine the functional significance of Jam-C trafficking on models of leukocyte transmigration, permeability and angiogenesis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: An integrative approach to deciphering the entry process in Herpesviruses
Funder: Medical Research Council

Abstract: A detailed description of the structures of macromolecular complexes can be very valuable for understanding cellular processes, including those that are targeted and modified by pathogens. However, due to current limitations of experimental techniques, the only way to achieve a comprehensive characterisation of these structures is to adopt an integrative approach that combines information from multiple sources. At present there are very few methods attempting to do so systematically. Here we aim to integrate multiple experimental and computational approaches to characterise complexes formed between herpesviruses and their host during the entry stage of infection. The field of 3D EM is increasingly important in molecular and cellular biology, owing to advances in hardware and software that improve image quality and experimental efficiency. One advantage is that the resulting maps often correspond to large and heterogeneous complexes that are difficult to study by other techniques. In tomography in particular, new biological insights arise from structure determination of macromolecular machinery in the native cellular context (here membranes). Here, we propose to build on Topf group's previous work on data integration and develop a method that efficiently and accurately combines the structures of individual components with low-resolution maps of the complexes they form. These maps will result from cryo electron tomography combined with sub-tomogram averaging and classification performed in the Grünewald lab. The method will allow the inclusion of additional spatial information from chemical cross-linking coupled with mass spectrometry and protein-protein interaction (PPI) networks. The resulting models of sub-complexes mediating herpesvirus entry could potentially lead to the discovery of novel functional details about the infection process. Additionally the Grünewald group will continue to refine image data acquisition and image processing tools and pipelines.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Epigenetic regulation of DNA repeats and genome stability in Candida albicans
Funder: Medical Research Council

Abstract: C. albicans is the most prevalent human fungal pathogen. It normally lives as commensal in humans but, in certain environmental conditions, such as those found in immunocompromised patients, it can become virulent causing systemic life-threating diseases. Emergence of drug-resistant C. albicans strains poses an additional public health problem. C. albicans is a highly successful pathogen partly due to its remarkable genome plasticity. The C. albicans genome is relatively stable in normal laboratory growth conditions but it becomes unstable under stress conditions, such as an anti-fungal treatment. Even though very little is known about mechanisms inducing C. albicans genome plasticity, it is clear that DNA repeats play an important role in this process. Our major goal is to understand the role of DNA repeats in modulating C. albicans genome plasticity. In many organisms, genome stability at DNA repeats is ensured by the assembly of a heterochromatin structures inhibitory to recombination. The chromatin status associated with C. albicans DNA repeats is uncharacterised and it is unknown whether it contributes to genome stability. In this project, we will employ a combination of low-throughput and high-throughput approaches to determine the chromatin state associated with C. albicans DNA repeats and assess the role of chromatin in C. albicans genome plasticity upon environmental changes.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Regulation of CD4 T cell and HIV-1 gene expression by Sam68
Funder: Medical Research Council

Abstract: Sam68 is a cellular RNA binding protein that controls multiple steps of cellular gene expression and also regulates HIV-1 gene expression. To determine how Sam68 controls gene expression in primary human CD4 T cells, we will use RNA-seq to determine which RNAs change their abundance, alternative splicing, poly(A) site selection and translation efficiency upon T cell activation in a Sam68-dependent manner. We will then identify in vivo Sam68 RNA binding sites and use Bayesian networks to develop a predictive Sam68 target network. We will also determine if Sam68 controls the expression of functionally related proteins or pathways. Overall, these experiments will identify 1) the specific human CD4 T cell mRNAs that Sam68 regulates on a genome-wide level, 2) whether these mRNAs encode proteins that control related immunological functions, 3) the specific step(s) of gene expression that Sam68 regulates and 4) how the location of Sam68 RNA binding sites controls alternative splicing. This information can be used to understand how Sam68-regulated cellular RNAs control activated CD4 T cell function. We will also characterise how HIV-1 infection of primary human CD4 T cells affects Sam68-regulated cellular RNAs and how Sam68 regulates HIV-1 gene expression. This will allow two important analyses. First, we will determine if HIV-1 infection regulates cellular gene expression by altering Sam68 activity or availability, which could alter the expression of immunologically active proteins. Second, we will compare how Sam68 regulates cellular and HIV-1 RNAs. It will be interesting to determine if HIV-1 RNAs interact with Sam68 in an identical manner to cellular mRNAs, if a subset of cellular mRNAs are regulated more similarly to HIV-1 RNAs than other cellular mRNAs, or if HIV-1 RNAs interact with Sam68 differently than cellular mRNAs to control viral gene expression, which may indicate that Sam68 is a potential antiretroviral target.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Investigating naturally occurring regulation of human IgE-mediated hypersensitivity using hookworm-schistosome co-infection
Funder: Medical Research Council

Abstract: From our previous immunological observations among schistosome and hookworm co-infected populations in Uganda, we hypothesis that human hookworm infection modulates the IgE effector mechanisms triggered by exposure to schistosome adult worm antigen. We propose to conduct population based parasitological screens for selection of an adult case-control cohort of S. mansoni mono-infected controls and S. mansoni and hookworm co-infected cases for immunological analysis of IgE effector and regulatory immune mechanisms. The project aims to inform research into type-2 associated diseases by identifying potential targets of modulation, and the mechanism by which these responses are regulated. To determine IgE effector mechanisms regulated in those with hookworm infection, a dual approach of ex vivo and in vivo responsiveness to worm derived antigens will be taken. Ex vivo we will examine control of basophil reactivity at the cellular and serological levels. We will use treatment with praziquantel, which disrupts the adults worm integrity, to examine in vivo responses, through read outs of the type-2 cytokine responses and eosinophil migration known to occur in the 24-hours following treatment. These assays will be combined with flow-cytometry analysis of the activation state of basophils, and eosinophils, both key effector cells in the type-2 immune response. B cell modulation of IgE production through cell surface and circulating soluble levels of its low affinity receptor CD23 will also be addressed. Flow cytometry will also be used to address the second objective of identifying increases in regulatory cells and molecules that may confer type-2 response modulation in those infected with hookworm. Treg, Tr1 and Breg cell numbers will be being analysed, along with co-inhibitory signals, CTLA-4 and PD-1. These results will be analysed along side plasma measurements of the regulatory cytokine IL-10 and humoral IgG4 blocking responses.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION