NIHRDataInsights/HRCSData huggingface dataset:
Title: Treating the host in Dengue: mediators and pathways of resolution as a new therapeutic paradigm
Funder: Medical Research Council

Abstract: Experimental work is unveiling a novel therapeutic opportunity for treating bacterial and viral infection: targeting the host in order to augment its ability to 'deal' with the infective agent. To achieve this, we propose to exploit the biology of the Resolution of Inflammation investigating the properties of pro-resolving mediators (Annexin A1, lipoxins and resolvins). These are known to augment myeloid cell phagocytosis and killing function to avoid excessive cell activation that would lead to self-harm. This approach works in models of sepsis, influenza and bacteremia. Here we will focus on Dengue fever in view of: 1)its epidemic nature in Brazil with massive number of patients and ensuing impact on society, both from a health and economic perspective; 2)the lack of any therapeutic treatment, except for fluid replenishment; 3)the current inability to identify patients who will develop severe dengue which may be lethal. We will address the hypothesis that inadequate engagement of pro-resolving mediators contributes to the excessive inflammatory response observed in patients with the most severe forms of dengue infection. The specific aims of our integrated and translational project are: Aim 1. Define expression levels of pro-resolving mediators in dengue patients Aim 2. Define expression relevance of anti-inflammatory/pro-resolution mediators in experimental models of dengue infection in mice. This project will generate new knowledge in the pathogenesis of dengue allowing the identification of novel biomarkers for patient stratification and informing of novel therapeutic targets for future development and commercialization. Proof-of-concept pharmacological experiments with molecules identified in the pro-resolving screening will also be performed, paving the way to future translational investigations. As such this partnership will deliver novel science as well as practical IP-protectable strategic approaches for the clinical management of dengue.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The emergence of Zika virus in Brazil: investigating viral features and host responses to design preventive strategies.
Funder: Medical Research Council

Abstract: The mosquito-borne flavivirus Zika has recently emerged in Brazil, where large potential vector populations (Aedes aegypti mosquitoes) exist. This virus had been detected in Africa and other tropical regions of the world, but was imported into Brazil in all likelihood in the recent past. Symptoms can be similar to dengue virus or the also recently emerged chikungunya virus, thus complicating diagnosis, treatment and intervention strategies. Indeed, very little is known about the biology and molecular biology of Zika virus, but diagnosis currently also requires specialist set ups. Thus, the potential impact of this pathogen needs to be assessed and public health preparedness improved. This project brings together experts from various fields to work on the following aims that impact on our understanding of Zika virus: (i) monitor Zika virus circulation in selected areas (including virus isolation and genetic characterisation) and develop improved diagnostic methods to identify Zika virus; (ii) use patient material for immunological studies on Zika virus infection (cytokines and antibody responses, gene expression) and set up a mouse model to assess intervention strategies and study pathogenesis further; (iii) develop an infectious clone of Zika virus for reverse genetics studies of the virus and vaccine design (including tools to produce virus-like particles); (iv) study viral antagonism of host responses at cellular level. As arbovirus infections are on the rise, there is an urgent need to share knowledge and improve the capacity response of research centers. Effective collaborative projects and networks can lead to effective ways to disease control, and this network on Zika virus can in the long term also help other countries affected by this virus.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Regulating the trans-regulators: Investigating the PRMT7 molecular pathway as an epigenetic regulator of Leishmania spp. virulence
Funder: Medical Research Council

Abstract: Our aim is to use Leishmania major parasites to isolate and characterise the PRMT7-driven molecular pathway which regulates Leishmania spp. virulence in vivo. Previously, we demonstrated that PRMT7 levels are inversely proportional to Leishmania parasite virulence (Ferreira et al., 2014). We will first dissect exactly how PRMT7 levels impact parasite virulence in mammalian cells. We will do this by genetically increasing and decreasing levels of PRMT7 enzyme and tracking parasite differentiation capacity to metacyclic (mammalian transmissive) versus amastigote (mammalian-infective) lifecycle stage parasites using stage-specific markers including RNA and protein expression, human serum sensitivity and proliferation. We will further examine whether levels of PRMT7 impact the disease-causing amastigotes' ability to infect and proliferate within human immune cells to discriminate differentiation capacity from virulence. We will verify candidate trans-regulatory RNA binding protein (RBP) targets of PRMT7 by in vitro biochemical methylation analyses and genetically manipulate target RBP levels to examine their potential role in parasite virulence. Preliminary in vitro data supports a direct interaction in which E.coli-derived PRMT7 modifies target RBPs in an arginine glycine (RGG-motif) dependent manner. If a candidate trans-regulator is confirmed to be both a target of PRMT7 and implicit in parasite differentiation and/or virulence, we will isolate associating transcripts and examine whether PRMT7 and RBP levels regulate these RNAs. Lastly, we will examine the structure/function relationship of target RBP trans-regulators in the presence/absence of PRMT7, methylation, protein binding partners, and associating RNAs using a variety of complementary biochemical, biophysical and structural techniques. We have already established protocols for production of recombinant RBPs which we can methylate in vitro using recombinant PRMT7.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Optimizing strategies to diagnose and control intestinal Schistosomiasis in low and moderate endemicity areas of Brazil
Funder: Medical Research Council

Abstract: Current diagnostic methods for intestinal schistosomiasis (detection of eggs in stool by Kato-Katz (KK)) are limited and may be particularly unreliable at low levels of infection, as would be expected after several rounds of treatment or in regions where transmission is low. In order to overcome some of the pitfalls of the KK method, there has been interest in developing new, more sensitive tests for the diagnosis of schistosomiasis. Antigen detection in urine (CCA) has been documented to be a sensitive and specific alternative to KK in several moderate and high endemnicity settings. Specific data comparing the performance of microscopy and antigen detection tests in low Schistosomiasis prevalence settings, however, is currently lacking. In this context, the primary aim of this project is to compare the performance of CCA with KK in the low endemic area of Minas Gerais State, and in a moderate endemic area of Sergipe State Brazil. An additional diagnostic, CAA, will also be used in order to increase the robustness of the assessment of CCA & KK. Furthermore, the present study aims to enhance knowledge of the spatial distribution of schistosomiasis in Minas Gerais province, Brazil that will assist planning of the preventive chemotherapy strategy for the national schistosomiasis control programme.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Characterization of Leishmania-Specific T cells in human skin and blood during cutaneous and mucocutaneous leishmaniasis
Funder: Medical Research Council

Abstract: Leishmania (Viannia) brasiliensis causes a wide spectrum of cutaneous disease ranging from self-healing cutaneous leishmaniasis (CL) to tissue destructive mucocutaneous leishmaniasis (MCL) in humans. During infection CD4+ and CD8+ naïve T cells are driven to expand into different subsets including memory compartments which are crucial to infection control and tissue damage observed during CL and MCL. Although Leishmania-reactive memory T cells have been characterised in blood from both CL and MCL patients, little is known about the differentiation/function of these cells in the skin/lesion site. Factors such as persistent antigen stimulation and inflammatory state have been found to play a key role in directing the development of CD4+ and CD8+ differentiation into effector memory (EM) T cells (CD28-CD27-CD45RA-) and also EM T cells that re-express CD45RA (CD28-CD27-CD45RA+; EMRA). These EMRA cell which exhibit terminal differentiation and senescence characteristics contribute to diminished immune responses due to their increased expression of surface inhibitory receptors, DNA damage and reduced replicative capacity.. Mechanisms of memory T cell terminal differentiation during Leishmania infection are still unknown, however may assist the understanding of immune response diversity observed between CL and MCL. In this context, the present study aims to investigate the frequency, differentiation and effector function of CD4+ and CD8+ memory T cell from blood and skin of CL and MCL patients caused by L. brasiliensis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Protein antibiotics for the treatment of Pseudomonas aeruginosa lung infection
Funder: Medical Research Council

Abstract: Chronic lung infection with Pseudomonas aeruginosa (PA) and the consequent progressive decline in lung function is the major cause of mortality in cystic fibrosis (CF) patients. The antibiotics that are currently available for the treatment of PA infection are inadequate and there is an urgent need to develop new therapeutic options to increase the current median age at death of CF patients, which is 29 years. The University of Glasgow team led by Dr Dan Walker have demonstrated that highly selective protein antibiotics, known as pyocins, show potent activity against PA in the planktonic and biofilm states and this potency translates directly to the treatment of PA in an in vivo model of lung infection. Therefore, pyocins have the potential to transform our ability to treat chronic PA lung infection and offer a therapeutic strategy that could extend the lifespan of CF patients. Dr Walker's team have identified a lead pyocin candidate, pyocin S5, which displays strong efficacy against diverse strains of PA in an in vivo model of lung infection. In this model, pyocin S5 displays a potency several orders of magnitude in excess of tobramycin, which is widely used for the treatment of PA lung infection in CF patients. The aim of the DPFS programme is to optimise methods for the formulation, delivery and manufacture of the lead pyocin and to generate preclinical toxicology and safety pharmacology data for the administration of pyocin S5 by nebulisation. The data generated during the course of this award will provide the basis for post-DPFS clinical trial authorisation (CTA) application to perform a first-in-man study in patients with cystic fibrosis.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: A novel P. vivax pre-erythrocytic malaria vaccine for broad coverage: Progression to GMP manufacture of a clinical vaccine lot
Funder: Medical Research Council

Abstract: Amongst the approximately 50 malaria vaccine candidates entering clinical trials, only two types have shown repeated clinical efficacy and remain under active development for P. falciparum malaria. These are a virus-like particle (VLP) targeting the malaria sporozoite and vectored vaccines targeting the liver-stage of the parasite's life-cycle. Both vaccine types have been shown to be safe and very immunogenic but a cost-effective deployment will require a wider coverage to prevent the two major malaria parasites: P. falciparum and P. vivax. We have recently developed a VLP presenting the P. vivax circumsporozoite on its surface. This new VLP, known as Rv21, is able to provide complete, sterile protection to 100% of the mice receiving only 5ug of Rv21 in Matrix M adjuvant, using a homologous prime boost vaccination regimen. This result contrasts with the 0% efficacy induced by heterologous prime boost regimens using recombinant chimpanzee adenovirus and MVA, which is a vaccination regimen develop at the Jenner Institute and used for other diseases. The Rv21 vaccine candidate has a series of repeats belonging to the VK210 and VK247 alleles. This design has the aim to provide protection against the two types of P. vivax parasites that circulate in the world. Using our novel P. berghei transgenic parasites expressing the VK210 and VK247 P. vivax CSP proteins, we have found that our vaccine provides high protective levels against parasites expressing either protein. The primary objectives of this proposal are to: -Produce Rv21 to GMP standards and we will deliver a product suitable for a future phase I clinical trial in quantity and quality. We will rely on the Jenner's clinical biomanufacturing facility (CBF) to produce the vaccine, which has recently succeeded in producing a similar VLP for falciparum: R21. -We will perform toxicology and stability testing. -We will apply for ethics and regulatory approvals for a future clinical trial.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Structure Elucidation and Characterization of the Venus Kinase Receptors of a Philippine Isolate of Schistosoma japonicum
Funder: Medical Research Council

Abstract: Aligned with UK's official development assistance programme, we propose and seek funding for a study aimed to develop novel anti-schistosome fecundity therapeutics through combined experimental and computational approaches. We will produce, characterise, and elucidate the structure of Venus Kinase Receptors (VKRs) from Philippine isolate of S. japonicum. Through computer-aided drug design, we will screen small molecule inhibitors of VKR proteins and test lead compounds on viable schistosome worms in vitro. We will solve the crystal structure of the VKRs. S. mansoni VKRs are activated by different ligands, L-arginine and calcium ions. We will be performing ligand binding assays using ITC and/or SPR spectroscopy to probe their binding affinities. We will perform Molecular Dynamics simulations of the whole VKR proteins with and without their respective ligands. Key interactions between the ligand binding site and the ligand will provide hints to the understanding of receptor activation and signalling in addition to the crystal structures. Through computer-aided drug design, we will screen small molecule inhibitors of VKR proteins and test lead compounds using kinase activity assay and mass spectrometry. To carry out this complex task, our team will be composed of expertise in different specializations: molecular parasitology (Dr. Leonardo), molecular biology (Dr. Bascos), biochemistry (Dr. Yu-Roberto), structural biology (Dr. Beis), synthetic organic chemistry (Dr. Sabido), molecular biophysics (Dr. Nellas), and computational chemistry (Mr. Gomez). This study is collaborative in nature, a partnership between UK and the Philippines, allowing capacity building in the Philippines. Thus, we seek funding for procurement of instrument and training of personnel in membrane protein production and X-ray crystallography.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: ENSURE: Enhanced surveillance for control and elimination of malaria in the Philippines
Funder: Medical Research Council

Abstract: Malaria surveillance in low transmission settings is hampered by poor diagnostics. Whilst the majority of infections missed are probably of little consequence clinically, being asymptomatic and low parasite density, they can infect mosquitoes and maintain transmission. This is of concern in areas of southeast Asia where there is the threat of artemisinin drug resistance; elimination of all parasites is widely considered the best way to stop the spread of resistance. Sensitive molecular methods can identify low density infections and, when combined with serological approaches, detect antibodies in those who have been exposed to infection. Together these two methods can more accurately identify areas where active transmission is ongoing and/or specific groups most at risk, such as migrant workers. Collection of samples through large scale community surveys is not practicable for most control programmes; sensible operational approaches are needed. One option is through health facilities which represent an ideal source of contact with local populations. We have previously demonstrated that facility-based surveys generate malariometric data that correlate well with data collected from the local community and schools. In this study we will use molecular and serological analysis of samples collected from regular surveys of facility attendees in three areas of the Philippines to generate data on infection and exposure in the community. We will combine these data with routinely collected epidemiological data, which we will embellish using enhanced tablet computer-based maps to create iteratively improved maps of areas where transmission is occurring. We will work closely with the malaria control programme on laboratory and facility aspects to ensure successful implementation, training and include improvements or changes identified as work progresses. The ultimate goal is to develop an approach that can be easily absorbed into the existing health system.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: INFECTION
Title: HIV G.E.T (Gaming, Engaging and Testing) Project
Funder: Medical Research Council

Abstract: According to PDOH (2015), 748 individuals were newly diagnosed, since last years report, to be HIV Ab seropositive, a 51% increase in cases compared to May 2014. Among the newly diagnosed cases, 96% were male with a median age of 28 years old (range: 16-69 yrs. old), 28% were youth (15-24 years old), and 37% came from National Capital Region (Metro Manila area). In addition, 86% of the sexually transmitted HIV cases were MSM, 7% were Overseas Filipino Workers, and 11% were engaging in transactional sex. HIV rapid tests are simple to perform with two or more tests providing confirmed results in 30 minutes or less in a serial or a parallel algorithm. A parallel algorithm will be used for the study. The WHO pre-qualifies rapid test kits with a diverse and standardized set of specimens collected globally, requiring test kits to have a minimum sensitivity >99% and specificity >98%. Quality-assured rapid testing has facilitated the movement from laboratory-based testing to other settings, and it has been highlighted that with good training, performance of non-laboratory workers is similar to laboratory staff. HIV testing strategies that rely on rapid testing are widely used in outreach settings with MSM in concentrated epidemic settings. They have been shown to improve the uptake of testing, increase dramatically the proportion of those receiving their results, and improve linkage rates to care and treatment programmes. The approach to game development and analysis will be conducted trough customised tried and tested frameworks for evaluating games for health. Development of the digital game will be completed in the Unity3d version 4.x engine, or an equally standard, industry-grade middleware package to allow for customisation by other software developers and alleviate concerns over the longevity of development partners.


Research activity codes: 4.4 POPULATION SCREENING
Health categories: INFECTION
Title: Triple-D Targets: The UK-Philippines Dengue Diagnostic and Drug Targets Research Consortium
Funder: Medical Research Council

Abstract: We will adopt an integrated 'omics approach, to correlate dengue disease severity with viral sequence variation and changes in the host transcriptome and proteome, using whole blood and serum samples from dengue patients with well-defined clinical outcomes. Existing serum samples (from the NIH-UPM biobank) from the following 5 patient groups will be selected for viral metagenomic and proteomic analysis a) classical DF, b) DHF, c) DSS, d) acute febrile illness (non-dengue) and e) healthy volunteers (5 of each). Metagenomics will generate viral sequence data for analysis by the UoG's bespoke bioinformatics pipeline. Serum proteins will be identified and quantified by tandem mass tagging of the peptides prepared from serum proteins by tryptic digest followed by high-throughput LC-MS/MS analysis. A second phase of 'omics analysis will utilise prospectively collected samples. The samples will correspond to the above disease conditions except that multiple patient samples will be collected a) upon enrolment, b) during significant clinical events and c) convalescence. Along with sample storage, clinical variables for patients will also be collected. Further serum samples will be analysed by metagenomics to design virus-specific capture probes for NGS target enrichment. 100 whole blood samples (10 of each dengue condition at 3 times and 10 controls) and corresponding serum samples will be used for RNAseq transcriptomic and proteomic studies respectively. The clinical and 'omics datasets will be integrated using a bespoke bioinformatics pipeline and software designed by the partners. This will identify candidate mRNA and protein biomarkers which will be validated by qRT-PCR and targeted proteomics using a larger prospective sample collection. Validated biomarkers will form the basis for novel diagnostic tests to predict severe dengue disease. Bioinformatics analysis will also identify host pathways that are potentially druggable, using an in silico modelling approach.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION