NIHRDataInsights/HRCSData huggingface dataset:
Title: Defining the role of peritoneal dendritic cells in tissue specific immunity and the clinical application of peritoneal dialysis
Funder: Medical Research Council

Abstract: Worldwide, >200,000 individuals rely on peritoneal dialysis (PD) for treatment of renal failure. In countries with developing economies this figure grows by 30% each year. However, only a third of PD patients manage to continue therapy beyond 3 years. This is partly due to unacceptably high mortality rate for end-stage renal failure patients, and compounding technique failures which prevent the long-term use of PD. Development of peritoneal fibrosis is linked to treatment duration, and repeated incidence of bacterial peritonitis. In PD patients, we have found that loss of membrane function is associated with the presence of IFN-gamma (correlated with IL-6) in dialysate while in an experimental model of multiple inflammatory episode-induced fibrosis, tissue pathology was dependent on IL-6, IFN-gamma and STAT1. We have identified a relative accumulation of novel dendritic cells (DC) in PD patient dialysate and have characterised cells with similar phenotype and responses to infection in experimental models. These novel DC are the major local producers of IL-12, represent the front line in response to microbial infection and may be key mediators of the tissue damaging IFN-gamma responses. This proposal will use powerful approaches (e.g. global transcriptional analysis and innovative in vivo modelling with adoptive transfers and in vivo lentiviral modification) to define: i) the role of peritoneal DC in inflammation-induced specific immunity; ii) the mechanisms that underpin the homeostatic and inflammatory trafficking/retention of DC in the peritoneum; iii) the activity of DC during the resolution of inflammation (e.g. their role in clearance of apoptotic cells); and iv) the prognostic value of monitoring peritoneal DC in dialysis patients. This will define novel aspects of clinically relevant tissue specific immunity, the initiation of the chronic disease process and it will also assess the potential of targeted immune-modulation therapies to ameliorate disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Mechanisms of Th2 cell-intrinsic hypo-responsiveness, and its impact on protective immunity and memory to parasitic helminths
Funder: Medical Research Council

Abstract: Helminth parasites infect over 2 billion people, representing a huge global disease burden. A key challenge to inducing protective immune memory lies in countering the dominant down-regulatory responses invoked during infection. We have demonstrated that CD4+ Th2 cells become intrinsically dysfunctional (hypo-responsive) during chronic helminth infection. This Th2 cell intrinsic hypo-responsiveness represents a novel form of anergy or exhaustion, is partially regulated by the PD-1/PD-L2 co-inhibitory pathway, and is a key element defining susceptibility to infection. This aims of this proposal are to elucidate, (1) the mechanisms of Th2 cell hypo-responsiveness and in particular the roles of PD-1 and PD-L2, (2) whether it occurs during human helminth infection, (3) its impact on Th2 cell memory and vaccine efficacy, (4) how it may be countered therapeutically to restore protective immunity. To address these aims I have developed the Litomosoides sigmodontis infection model of filariasis into a unique system for studying lymphocyte regulation during tissue nematode infection, and in particular for tracking and assessing the intrinsic functional quality of Th2 cells using IL-4gfp reporter mice. Novel mechanisms of hypo-responsiveness will be identified by gene array, and the PD-1/PD-L2 pathway elucidated using knock-out mice and chimaeras to restrict deficiencies to specific cell populations. We will relate Th2 cell hypo-responsiveness to human infection using gene expression data sets from filariasis patients, and stored PBMC samples from schistosomiasis patients. In addition to the direct implications for the design of vaccines or treatments to promote protective memory to helminths, this study will have relevance well beyond helminth immunology. It will fundamentally enhance our knowledge of Th2 biology, and provide novel approaches for tolerising pathogenic Th2 cells for the treatment of Th2-mediated allergies and fibrosis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Developing Computational Methods to Aid Infectious Disease Therapeutics Through Analysis of Protein Function Evolution
Funder: Medical Research Council

Abstract: The revolution in high-throughput genome sequencing has resulted in a large amount of data, particularly relating to organisms associated with infectious disease. The outstanding challenge is to relate this information to what occurs functionally at the molecular level. I will develop a unique resource specifically to handle genomes associated with infectious diseases bringing together protein structure, sequence, phylogeny, chemistry, and other interactions with macromolecules, to understand what evolutionary changes are required to alter a function. This will include the development of new methods for comparing polymer interactions such as with lipids, carbohydrates and DNA/RNA as well as integrating pathway and protein-protein interaction information. Cataloguing changes in function will be used to define rules to construct function prediction algorithms to further annotate pathogen genomes. Combining application of the methods developed with validation of function predictions, starting with proteins implicated in Kinetoplastid drug development will be tested in collaboration with experimental groups. One focus will be the enzyme(s) involved in activating the nitroheterocyclic pro-drugs that are the front-line treatment for Chagas disease, the most important parasitic infection in the Americas. Understanding what the cognate ligands and reactions are, as well as possible alternative enzymes with similar activities, is important for gaining insight into drug resistance. Function predictions will be expanded to other infectious disease genomes. Further, the framework will be applied to identify similarities between the metabolites catalogued and results of whole genome high-throughput screening of drug-like compound libraries on Schistosomes, a highly prevalent socio-economic debilitating disease. This could propose new potential drug targets or cross-targets and identify if the disrupted functions have similarities to other functions in vector or host organisms


Research activity codes: 1.4 METHODOLOGIES AND MEASUREMENTS;5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Picornavirus capsid protein VP4: Essential role in cell entry and conserved antiviral target
Funder: Medical Research Council

Abstract: The picornavirus capsid comprises sixty copies of each of VP1, VP2, VP3 (which form the icosahedral particle) and VP4 which is a small, myristoylated internal protein which stabilises the capsid structure. The capsid is dynamic and undergoes a process of 'breathing' whereby internal components the N-terminus of VP1 (VP1N) and the N-terminus of VP4 are transiently exposed at the surface. During cell entry, these components become irreversibly externalised and interact with membranes. The VP1N-membrane interaction tethers the particle to the membrane while VP4 is completely externalised from the particle and also associates with the membrane. There is biochemical evidence for the involvement of VP4 in the cell entry process and genetic evidence for its involvement in delivery of the viral RNA genome across the membrane into the cytoplasm. The applicants (and collaborators) have developed the use of model membranes and recombinant proteins as convenient systems for studying virus-membrane and VP4-membrane interactions. The results of our recent studies demonstrate for the first time that VP4 interacts with liposomes to make them permeable by the formation of multimeric membrane pores. The pores are size-selective, with a cut-off consistent with a pore that could transport single stranded RNA. We propose that during virus entry, VP4 forms a channel through which the viral RNA is delivered into the cytoplasm for infection to begin. Although VP4 is internal in the virion, capsid breathing exposes it at the surface, where it can interact with antibodies that neutralise infectivity. Importantly, VP4 is highly conserved and inhibitors therefore have good potential to be cross-protective. We therefore believe there is good justification for investigation of VP4 structure & function and proof-of-principle studies to understand and validate VP4 as an antiviral target.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Modelling disease emergence in heterogeneous populations
Funder: Medical Research Council

Abstract: Data on social interactions will be used to approximate contact structure, including interaction with animals. Disease transmission will be modelled stochastically; in particular, I will use multi-type branching processes to develop a framework in which heterogeneity in social contact - and hence transmission - can be incorporated along with pathogen adaptation. Analysis of the age distribution of disease cases during an outbreak will then be used to generate an inference method of distinguishing between different situations - for instance, stuttering transmission, whereby the disease fails to establish in the human population, or a full-scale epidemic. This will involve using approximate Bayesian computation (ABC), which bypass exact likelihood calculations by using summary statistics (such as the distribution of cases at the end of the outbreak). The potential for these techniques to be applied during an outbreak will be explored using data on the early progression of the 2009 H1N1 pandemic in the UK. Using simulated epidemic data generated from these models developed, I will also explore a statistical framework for inference of the effective reproductive ratio, with contact data used as a prior. Existing 'gold-standard' data augmentation approaches are computationally intensive for large populations, so I will look at alternative such as ABC and ABC based on sequential Monte Carlo (ABC-SMC), as well as branching process approximations. The performance of these frameworks will be tested against real disease case data from Southeast Asia, as well as simulated data.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: Quantifying pandemic risk caused by within-host evolution of influenza A/H5N1 viruses
Funder: Medical Research Council

Abstract: I want to assess the pandemic risk posed by the evolution of A/H5N1 influenza viruses within an infected host, through acquiring respiratory droplet transmissibility between humans. The description of the probability of a transmissible H5N1 virus emerging in nature is critical to estimate and mitigate the risk for H5N1 viruses to create a pandemic, and is important for international policy decisions on the strategies for surveillance, intervention and global eradication of the virus. I have built a mathematical model describing the within-host evolution of pathogens, which was published in Science earlier this year. I propose to assess the risk posed by H5N1 viruses by refining this model and through working closely with a wide network of expert collaborators, and designing experiments with them. I will design a framework for the analyses of the deep sequencing data, and use this to study infections with fully adapted viruses to increase our understanding of viral dynamics and within-host evolutionary processes. Through analysis of deep sequencing data from experimental samples and precious human H5N1 infection data, the evolutionary mechanisms will be complemented with information on the viral diversity at the start and during infection, fitness gains and losses for different mutants, the identification of functionally equivalent mutations, knowledge on the effects of glycan heterogeneity in the respiratory tract and studies on the mechanisms of respiratory droplet transmission. I will synthesise the gained fundamental insights into within-host pathogen evolution and the contributions to fundamental scientific knowledge arising from refined estimates for critical parameters, to design further experiments and, most importantly, to integrate this information and use it to continuously refine the risk assessment for a human pandemic through evolution of currently circulating H5N1 viruses.


Research activity codes: 7.4 RESOURCES AND INFRASTRUCTURE (DISEASE MANAGEMENT)
Health categories: INFECTION
Title: Connecting in-vivo optical imaging with dynamic modelling of host-pathogen interaction during bacterial infection
Funder: Medical Research Council

Abstract: The progression of a bacterial infection takes place over a range of spatial and temporal scales. Biomedical imaging is ideally suited to investigate disease progression in-vivo over time in small animals. To facilitate interpretation of in-vivo imaging results in terms of biological mechanisms, we propose to develop a modelling and statistical analysis framework that links these two. We will apply this to investigate host-pathogen interactions taking place when a mouse is infected with Citrobacter Rodentium, a model for Enterohaemorrhagic Escheria coli (EHEC). Mice infected with bioluminescent bacteria will be imaged using the IVIS system for bioluminescence/fluorescence tomography and X-ray CT. This will show the spatial and temporal distribution of the bacteria and fluorescently targeted immune cells. Our framework will consist of a spatio-temporal model that divides the mouse in several compartments in which biological processes take place that we will model using ordinary and stochastic differential equations. The model will be used to estimate key infection parameters for each compartment at a number of time points in light of the in-vivo measurements. We will base an initial model on available in-vivo imaging data and cellular and molecular data acquired post-mortem. The model will be further informed by performing experiments targeted at filling gaps in our mechanistic understanding, including in-vivo experiments of a wild-type mouse, histological analysis and FACS. We will use the (calibrated) model to simulate the outcome of knocking out parts of the immune system, based on which we will design and perform an experiment with a mutant mouse model. The experimental results will be used to validate and refine our model. This close integration of experimental and modelling efforts will provide immediate feedback between them. The resulting multi-compartment model can increase our understanding of disease mechanisms, and identify new targets for treatment.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: Protection from Mycobacterium tuberculosis infection: Learning from exposed but uninfected children
Funder: Medical Research Council

Abstract: Why do some children exposed to Mycobacterium tuberculosis (M.tb) show no signs of infection, whilst others in the same household become latently infected? We aim to define protective host immune mechanisms against infection by M.tb through characterizing differences between clinical phenotypes in an established household case-contact platform in The Gambia: 1. TB-exposed children without signs of M.tb infection ("protected"), 2. their latently infected siblings ("susceptible"), 3. age-matched but TB-unexposed community "controls." We hypothesize that "protected" siblings restrict mycobacterial growth more than their "susceptible" siblings and that this reflects cell death and linked eicosanoid pathways. Aim 1: To validate pilot data that "protected" children inhibit mycobacterial growth more than "susceptible siblings" Methods 1: Whole blood reporter-gene tagged M.tb infection with calculation of growth ratios. Aim 2: To measure cellular and inflammatory differences in responses of blood from "protected" and "susceptible" children to M.tb infection. Aim 2.1: To compare monocyte cell death modality. Methods 2.1: M.tb-infected monocytes will be evaluated for apoptosis by (a) Flow cytometry and (b) Cell-death detection ELISAPLUS immunoassay. Aim 2.2: To use an unbiased lipidomics approach to evaluate lipid mediator profiles. Methods 2.2: Ultra-performance liquid chromatography with tandem quadrupole mass spectrometry (UPLC-MS/MS) will quantify lipid inflammatory mediators. Aim 3: Manipulation of lipid mediators of interest in M.tb infection to provide mechanistic insight. Methods 3: Following analysis of Aim 2.2 data, selected drugs will be tested for impact upon mycobacterial growth, cell death modality and lipid mediators. OPPORTUNITIES The protective markers identified will aid vaccine evaluation, whilst the lipidomics opens avenues to investigate immunomodulation in TB.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Microbial translocation in HIV-infected children in Uganda
Funder: Medical Research Council

Abstract: It is widely accepted that HIV damages intestinal mucosal immunity, allowing microbial translocation. This causes increased circulating levels of immunostimulatory bacterial products. This immunostimulation in the presence of HIV infection causes immune activation, which is associated with poor therapeutic response, increased all-cause mortality and non-AIDS related morbidity. Trials are underway aiming to modify microbial translocation to improve outcome; but all are in adults, none are in children. A method used to support this hypothesis is identification of bacterial DNA in the bloodstream of HIV-infected people using broad-range molecular techniques, which are vulnerable to artefact. Little work has been done to identify bacterial species present, and minimal work has been done in HIV-infected children. What role microbial translocation plays in African settings is unclear, and the interactions of malnutrition, HIV and microbial translocation are yet to be elucidated. I propose to use broad-range and specific molecular techniques to identify the presence of translocated microbial DNA in Ugandan HIV-infected children. I will compare results before and after commencing ART and with Ugandan HIV-uninfected controls, along with longitudinal data on clinical, virological and immunological outcome, nutritional status and intestinal damage. The children will be recruited from an ongoing clinical trial based in Uganda and Zambia which has completed recruitment. Carers have already given consent for stored samples to be used in studies investigating HIV pathogenesis. This study should provide definitive answers about the presence and nature of circulating microbial products, and insights into their causes and potential control in HIV-infected children. There is potential for future development of therapeutic interventions aiming to modify microbial translocation in children and so improve outcome depending on the data generated by this project.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Dissecting mechanisms of granuloma formation in ANCA associated vasculitis
Funder: Medical Research Council

Abstract: This proposal will use a novel PR3-mediated in vitro granuloma model to investigate granulomata formation in AAV patients and attempt to translate this model to an in vivo setting. Our specific aims are to: 1. Define cellular requirements for PR3 induced granuloma formation. We will isolate PBMC and serum from AAV patients with PR3- or MPO-ANCA, with or without evidence of granuloma, healthy controls(HC), and patients with sarcoidosis. We will compare giant cell(GC) and granuoma formation in these groups using purified monocytes, monocytes with purified CD3 T cells, and whole PBMC, to understand the impact of B cells. The studies will be repeated using cells from HC or PR3-ANCA patients in the presence of PR3 or ATP with or without a P2X7 receptor antagonist to investigate whether this compound may represent a novel potential therapeutic target for granulomatous disease. 2. Defining the role of ANCA or the PR3-inhibitor alpha 1 anti-trypsin(A1AT) on granuloma formation. The granuloma model will be repeated using cells from GPA patients with or without ANCA and HC, in the presence or absence of purified LPS-free PR3-ANCA IgG, MPO-ANCA IgG, control IgG, diverse anti-PR3 mAb, or A1AT to test the effect on granuloma formation. 3. Examining if there are differences in gene expression between different multinucleate GC which mirror those found in tissue granuloma. Using different stimulation conditions with PR3, IL-4, ATP and concanavalin A, we will generate GC, isolate their RNA and microarray them to investigate differences resulting from the stimuli and compare them to GC isolated from patient tissue. 4. Can PR3-induced granuloma provoke disease in vivo? We will test the impact of persistent PR3 antigen expresion in C3HeB/FeJ mice known to be susceptible to development of necrotising granuloma and in vasculitis susceptible WKY rats. We will coat polystyrene beads with/without human PR3 or MPO, embed them in Matrigel and place them into different rodent tissues


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Whole Genome Sequencing as a unified platform for outbreak identification, resistance prediction and virulence profiling in Staphylococcus aureus
Funder: Medical Research Council

Abstract: The overall aim of the project is to develop whole genome sequencing (WGS) as a unified platform for outbreak identification, resistance prediction and virulence profiling of Staphylococcus aureus. The first objective is to evaluate WGS as a real-time method for the detection of S. aureus outbreaks. Outbreaks with strong epidemiological links will be used to establish cut-off values for the number of single nucleotide variants (SNVs) which can reliably identify outbreak isolates. For each outbreak, isolates will be collected from cases and controls and whole genome sequenced using the Illumina HiSeq platform. Phylogenetic trees will be constructed based on WGS and used to infer relatedness. These results will then be applied in real-time, using putative outbreaks and rapid sequencing (Illumina MiSeq platform) of case and control isolates in parallel with the routine investigation to compare the turnaround times. The second objective is to use WGS in the prediction and investigation of resistance phenotypes. All isolates plus 500 bacteraemias will be tested for susceptibility to anti-staphylococcal agents. Whole genome sequences will be screened using BLAST for the genes associated with resistance to these agents and the frequency of critical (false susceptibility by genetic testing), major (false resistance by genetic testing) and minor errors will be determined. The phenotypic effect of any novel variants which appear to confer resistance will be will be assessed by plasmid expression and allelic exchange in the susceptible S. aureus Newman strain. The final objective is to investigate the prevalence of virulence factors. Isolates will be screened using a BLAST search for a panel of virulence factors and compared with the clinical presentation. Isolates will also be screened for putative virulence factors, to compare prevalence in disease vs carriage to identify factors for future study.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION