NIHRDataInsights/HRCSData huggingface dataset:
Title: Chemokine-mediated innate immune responses to arthropod bites and their viruses
Funder: Medical Research Council

Abstract: The threat to health posed by arthropod-borne viruses, arboviruses, has increased substantially. Globalisation facilitates their spread, whilst global warming increases their range. This has been most dramatically demonstrated by the re-emergence of Chikungunya Virus, which has infected millions since 2005. Europe, once confident in its isolation from arbovirus infections is now at risk from several arboviruses, in particular those spread by mosquitoes such as Chikungunya virus and by ticks such as Tick-borne Encephalitis Virus. There are no effective treatments and it is hard to predict the timing or nature of their outbreaks. Chemokines are a critical aspect of the immune response that controls the migration of leukocytes. This project will focus on chemokine-mediated innate immune responses to arthropod bites and their viruses. It will use an experimentally tractable mouse model system combining the tools and expertise from two major centres of research. The combination of their facilities, reagents, resources and expertise will generate a novel project that merges related but disparate areas of research. The project will study two key stages of infection that are little understood; (1) innate immunity at the site of the mosquito bite and (2) spread of the virus from the bite site to systemic circulation. (1) When arboviruses are inoculated from either a mosquito or a tick, compared to inoculation by needle, disease is considerably worse with higher mortality. Given the speed of both viraemia and potentiation by bites following arthropod-delivered arbovirus infection, modulation of infection by bites is most likely to be mediated by effects on innate immune responses. Gene expression of chemokines and other important innate immune genes will be assayed following bites and their relative importance to viral dissemination determined using transgenic mice. The ability of bites to modulate adaptive immune responses through these chemokine-drive processes will be tested using a powerful reductionist in vivo model. (2) The ability of virus to spread from bite site to initiate a viraemia determines the outcome of disease severity. Virus that expresses marker genes will be tracked from the bite site and its route determined. Skin, lymph nodes, blood and lymph fluid obtained by cannulation will be examined and mechanisms of virus spread determined. These studies will provide new insights that will define fundamental processes and functions of innate immunity, chemokines, leukocyte migration and arthropod vector biology in the initiating stages of arboviral infections; an important class of emerging infections that constitute an increasing threat to human health. A fuller understanding will aid our responses during current and future epidemics. By studying the fundamental mechanisms underpinning these processes we can better understand the complex interplay between mammals, viruses and their arthropod vectors.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Influenza A virus NS1 and PI3 Kinase: A structural investigation of their biological interaction
Funder: Medical Research Council

Abstract: The non-structural (NS1) protein of influenza A viruses is a multifunctional protein with roles that include inhibiting innate intracellular anti-viral responses, including the interferon (IFN) response, and in modulating virus replication and host-cell physiology (reviewed in Hale et al. JGV, 89, 2359). Whilst much has been learnt about the molecular mechanisms by which NS1 performs many of its multiple functions, there is still much to be learnt, especially with regards relating function to its structure, and in using the information gained for the improvement of human and animal health through the development of novel anti-viral drugs and the design of improved vaccines. The influenza NS1 protein is comprised of a RNA-binding domain and an effector domain that are joined by a flexible linker. It is unclear how a protein of such relatively small size can interact with so many distinct binding partners to elicit such a diverse range of responses. In this proposal we will use reverse and forward genetics, molecular, biochemical and cellular approaches, and structural studies to further address important questions concerning the function and structure of this essential viral virulence factor. More specifically, we will better define how and why influenza A viruses activates PI3 kinase.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The Legionella pneumophila type IV secretion system effector proteins LtpD and LtpJ
Funder: Medical Research Council

Abstract: Legionella pneumophila is an intracellular, water-borne pathogen and the major causative agent of Legionnaires? disease, a severe form of acute pneumonia. Following inhalation, the bacteria are internalised by alveolar macrophages and epithelial cells where they replicate within a vacuole, known as the LCV. The LCV, which exhibits many characteristics of the endoplasmic reticulum (ER), avoids phagolysosome fusion. Avoidance of lysosomal degradation and recruitment of ER markers require translocation of type IV secretion system effectors, which target specific host cell proteins. A conservative estimation suggests that L. pneumophila encodes over 200 effectors; the function of most remains unknown. Our initial step in establishing a Legionella project at Imperial College involved sequencing the prototype L. pneumophila serogroup 1 strain 130b. We found that L. pneumophila 130b encodes 146 effectors, 10 of which were not reported before and were named LtpA-J (Schroeder et al., 2010, J. Bacteriol. In press). We have shown that these novel effectors are present, at various frequencies, in clinical and environmental L. pneumophila isolates. The focus of this project is on the novel effectors LtpD and LtpJ. Preliminary studies performed in our laboratory over the last two years revealed that translocated LtpD is phosphorylated and localised to the LCV, while ectopic expression of LtpD altered vesicular trafficking. Unexpectedly, we found that LtpJ appeared to be involved in biogenesis of novel tubular structures, which emanated from and often connected distant LCVs. Based on the resemblance between the LptJ-induced tubular structures and the Salmonella induced filaments (Sifs), which are needed for Salmonella intracellular survival and replication, we named them Legionella induced filaments (Lifs). The aim of this project is to use a combination of advanced imaging, biochemical and cellular techniques in conjunction with a range of infection models, to investigate the role of LtpD and LtpJ in Legionella pathogenesis. This work will provide new insights into L. pneumophila infection and subversion of host cell processes by intracellular bacterial pathogens of humans.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Design, synthesis, and assessment of specific iNKT cell agonists for clinical applications
Funder: Medical Research Council

Abstract: Invariant natural killer T cells (iNKT cells) are one of the key sentinel cells of the innate immune system. Their activation by foreign lipid antigens, dictates and directs a subsequent adaptive immune response to this stimulus, and in this way, microbial activation of iNKT cells can result in dendritic and B cell maturation, promoting specific cellular and antibody responses against invading pathogens. iNKT cells are also important mediators of cancer immunosurveillance, acting via direct recognition and lysis of malignant cells or through subsequent Th1 cytokine release, which promotes NK cell anti-tumour activity. These properties indicate their potential clinical application in developing both anti-microbial and anti-tumour vaccination/treatment strategies. In contrast to these immune-system-activating properties, iNKT cells also play a major role in suppressing autoimmune responses via induction of inhibitory Th2 cytokines and/or promotion of regulatory T cells to self-lipid antigens. In this mode of operation, they have the potential to suppress autoimmune diseases, such as NOD, EAE, and SLE. Whilst iNKT cells exhibit wide-ranging responses to activation, the key challenge remains how to activate and manipulate the different potential functions of iNKT cells selectively, through the use of specific agonists, which can then be translated into clinical applications. We believe this is now possible through a greater understanding of the structure-activity relationships (SARs) that govern iNKT-TCR-CD1d interactions, which can direct the design of new agonists towards predictable biological outcomes. By studying the SARs of previously identified glycolipid agonists, we have already identified a number of parameters including: i) binding affinity, ii) direct presentation or requirement for internalisation and processing, and iii) co-stimulatory molecule recruitment and activation, that dictate the type of immune response that results upon iNKT cell activation. We now propose to generate new iNKT cell agonists with simplified architectures and tailored immunological responses, which can be applied for therapeutic use. Assessment of their clinical potential will also be enhanced by the incorporation of various novel human in vitro assays into our bioactivity screening programme.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: TGF-beta activation by gut dendritic cells: identifying a critical pathway in regulation of chronic parasitic infection
Funder: Medical Research Council

Abstract: A massive world health problem is chronic infection with helminth parasites, which affect ~ 2.5 billion people in the developing world. Helminth infections result in severe economic and health burdens in affected countries, but at treatments at present are extremely limited. To develop chronicity, helminths must somehow evade host Th2-type immune responses aimed at expelling the parasite. However, the mechanisms underlying how helminths avoid host immunity during chronic infection are poorly understood. Determining the cellular and molecular pathways utilised by helminths during development of chronicity will be critical in identifying potential novel therapeutic targets to alleviate chronic helminth infection. A vital immune regulatory cytokine is transforming growth factor-beta (TGFbeta), which is produced by many cells but always as a latent complex that must be activated in order to function. TGFbeta has important immunosuppressive properties, with mice lacking TGFbeta1 (the major isoform expressed in the immune system) dying from multi-organ inflammatory disease. An attractive hypothesis therefore is that helminths can manipulate the TGFbeta activation/signalling axis to dampen host immune responses directed against the parasite, thus facilitating development of chronic infection. Our exciting preliminary data indicate that this is indeed the case. Thus, we show that mice lacking expression of the TGFbeta-activating integrin alphavbeta8 specifically on dendritic cells are completely protected from chronic infection with the intestinal helminth Trichuris muris (an established model for the human parasite Trichuris trichura, which affects over 1 billion people world-wide). However, how reduced TGFbeta activation by dendritic cells results in protection from chronic parasitic infection, and how helminths modulate this important pathway to facilitate chronicity is completely unknown. Our proposal therefore aims to determine fundamental cellular and molecular mechanisms that are critical for the development of chronic intestinal helminth infection, highlighting a central role for integrin-mediated TGFbeta activation by dendritic cells. Additionally, we will determine how gut helminths modulate this critical pathway, and whether important mechanisms identified can be extended to other helminth and non-helminth infections. Our cutting edge approaches and expertise, coupled with key collaborations in place, will therefore identify a potential novel therapeutic target for preventing and treating chronic helminth infection.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: A universal T cell vaccine for HIV-1
Funder: Medical Research Council

Abstract: The best solution to the HIV/AIDS epidemic is development of an effective prophylactic vaccine. T cell stimulating vaccines offer a realistic alternative, or supplement to, antibody inducing vaccines. The latter are proving extremely difficult to generate and T cell stimulating vaccines, while not preventing infection, do ameliorate disease in monkey/SIV models. However, virus variability is a major problem resulting in poor recognition of infecting virus and easy escape of virus from early T cell control. These issues could be avoided by focusing vaccine-induced T cell responses on conserved regions of HIV-1. While most patients with chronic HIV-1 infection do make some T cell responses to conserved regions, these responses are usually weak (subdominant) and, like broadly neutralizing antibody responses, develop too late in the infection to provide real benefit. We have constructed immunogen HIVconsv, which is derived from the 14 least variable HIV-1 segments and contains over 200 epitopes, and have shown that it stimulates strong T cell responses in mice and in rhesus macaques. Phase I clinical trials in Oxford evaluating safety and immunogenicity of three HIVconsv vaccines delivered as plasmid DNA, recombinant MVA and recombinant chimpanzee adenovirus have started. Here, we shall further refine the vaccine design to improve the prototype immunogen, vaccine vectors and their formulation. We shall test different vaccination regimens to maximize T cell induction and assess surrogate efficacy in inbred and outbred mice. We shall make a second ?mosaic? immunogen complementing HIVconsv, which will improve perfect matching of amino acids to HIV-1 variants from clades A,B,C and D from 72% to 90%. We shall study in depth vaccine-induced responses in humans, looking at how well the known conserved (but often subdominant in HIV-1 infection) epitopes are presented by antigen-presenting cells exposed to these constructs. We shall examine how efficiently the HIVconsv-specific T cells recognize and kill HIV-1-infected cells. We shall employ state-of-the-art proteomics (tandem MS/nanoflow RPLC) to obtain a comprehensive picture of conserved region peptide processing and presentation on the cell surface, and comparing epitope presentation from the HIVconsv vaccines and HIV-1. This will indicate whether the HIVconsv needs further optimization. Results generated from this programme together with our complementing, separately funded components (non-human primate and human trials) will be key in assessing the suitability of conserved region T cell vaccines for efficacy trials in high-risk human cohort(s), either alone or with an antibody-based vaccine.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Cryptococcal meningitis: addressing an urgent global health problem using a translational pharmacological approach
Funder: Medical Research Council

Abstract: BACKGROUND: Cryptococcal meningitis is an urgent global health problem. The goal of induction antifungal therapy is to achieve rapid fungal killing because this is associated with improved clinical outcomes. In the UK this is usually achieved with 2-weeks of i.v. amphotericin B deoxycholate?flucytosine. In much of the developing world there are inadequate resources to enable prolonged administration of i.v. drugs or the detection and management of drug-related toxicity. The inability to give i.v. induction therapy is a significant therapeutic obstacle. Importantly, however, the use of shorter induction regimens that still achieve rapid fungicidal activity would facilitate the administration of optimal antifungal therapy in resource poor settings. This research will use well-validated experimental models of cryptococcal meningitis and state-of-the-art mathematical modelling techniques to identify candidate antifungal regimens for resource-poor settings. These regimens can then be immediately expedited for study in clinical trials. AIMS: Aim #1. Identify novel induction regimens of amphotericin B deoxycholate that result in the same or better fungicidal activity as 0.7 mg/kg/day administered to humans for 14 days Aim #II. Define the optimal dosage, schedule of administration and shortest duration of therapy of lipid preparations of amphotericin B that results in near maximal fungicidal activity Aim #III. Define optimal combination regimens and the shortest duration of therapy that results in the same or better fungicidal activity as standard antifungal combinations administered for 14 days METHODS: A well-validated murine model of cryptococcal meningitis will be used. The biomarker will be the fungal density in the brain. Pharmacokinetic and pharmacodynamic relationships will be elucidated by studying a range of clinically relevant regimens. Mathematical models that describe the time-course of drug concentrations (in serum and brain) and the associated antifungal effect will be fitted to each dataset. These mathematical models will be used to humanise the mouse in silico (i.e. in a simulator, drug will be given to a virtual mouse to generate a human-like concentration-time profile). The predicted antifungal effect resulting from these innovative regimens will be determined. Key findings will be further validated in a rabbit model of cryptococcal meningitis. SCIENTIFIC AND MEDICAL OPPORTUNITIES: This research will deliver: (1) new induction regimens for amphotericin B deoxycholate; (2) new induction regimens for lipid preparations of amphotericin B; and (3) new induction antifungal combination regimens. This proposal offers the real possibility to deliver a step change in the management of cryptococcal meningitis for the developing world.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Strategies of viral multi-functional regulator proteins
Funder: Medical Research Council

Abstract: In order to productively replicate viruses have evolved a panoply of mechanisms to overcome and, in many cases utilize components of complex host pathways. In order to successfully orchestrate the cellular environment for the support of viral replication and based on their inherently limited genome sizes many viruses have adopted approaches that incorporate multiple functions into single proteins. This application aims to dissect the molecular bases for the coordination of the multiple functions that the Rep protein from the human adeno-associated virus (AAV) utilizes in order to support its complex lifestyle. Furthermore, this application is a component of a collaboration with a US laboratory that has recently been funded to determine the structures and biophysical characteristics of AAV Rep complexes. Our UK component outlined here aims at dissecting the functional relevance of these complexes within the context of the viral life cycle.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: The role of the stress-induced transcription factor, CHOP, in the induction of IL-23 by intracellular bacteria.
Funder: Medical Research Council

Abstract: We have recently made the seminal observation that ER stress profoundly and qualitatively alters APC cytokine secretion, boosting the production of a specific group of mediators including interleukin (IL-23). We have identified that the ER stress induced transcription factor CHOP is activated by intracellular bacterial infection, and is involved in the regulation of IL-23 gene expression. We hypothesize that the ability of intracellular bacteria to induce the expression of stress proteins can profoundly affect the nature of innate and adaptive immune responses they elicit. Here, we propose to identify the host cell stress pathways that induce CHOP transcription in response to infection of myeloid APCs with intracellular bacteria. We will also determine if other intracellular bacterial pathogens induce CHOP activation, and identify specific bacterial components that are able to initiate host cell stress. Thus, we will elucidate how cell stress induced by important human pathogens influences the quality of innate immune responses. Moreover, we will characterise stress responses as novel mechanisms linking intracellular bacterial infection to diseases where IL-23 is known to play an important role in pathology.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Developmental Clinical Study - UK HVC 003 DMP Phase I Prime-Boost-ReBoost HIV vaccine trial
Funder: Medical Research Council

Abstract: A safe and effective preventive HIV vaccine remains one of the highest priorities for international public health. Despite slow progress, a recent phase III trial (RV144) demonstrated significant protection against HIV infection through a prime-boost strategy with a canary-pox viral vector (ALVAC), followed by an ENV (GP120) protein boost. The immune correlates of protection remain obscure, but consensus is that both antibodies to HIV and a strong cellular immune response are required. The UK HIV Vaccine Consortium (UK HVC) has developed a series of HIV immunogens with freedom to undertake clinical research, so that diverse combinations of viral vectors, DNA, protein and adjuvant can be directly compared to define the most immunogenic vaccine immunisation strategy. By building on our previous vaccine studies, we believe that the HVC 003 DMP immunisation strategies will be more immunogenic than the partially successful RV144. The UK HVC 003 DMP trial proposes to study two prime-boost strategies using GMP products. The priming will be done with DNA followed by modified pox (MVA) and boost with rGP140 protein adjuvanted with GLA. The study will compare 3X DNA followed by 2X MVA and 2X rGP140/GLA, versus 3X DNA, followed by concurrent MVA/rGP140/GLA, with a primary end-point of ENV antibody titre and secondary end-points of neutralisation and cellular immunity. If safe and highly immunogenic, we would wish to optimise the immunisation schedule through another comparative study and proceed with a phase II/III study in East and Southern Africa, as a university-based and led public-private partnership, based on the Microbicides Development Programme model.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION