NIHRDataInsights/HRCSData huggingface dataset:
Title: Identifying and Characterizing Antiretroviral Interferon Stimulated Genes (ISGs)
Funder: Medical Research Council

Abstract: The hypothesis underlying this proposal is that more antiviral factors are yet to be identified. Over the last ten years, the work of many research groups has led to the characterization of several factors with antiviral activity, including APOBEC3, TRIM5, tetherin and SAMHD1, all of which target HIV-1. Despite arising independently, these factors share several traits, including that they are all interferon stimulated genes (ISGs). In many cases, human retroviruses, like HIV-1, have adapted to overcome the human ISG, but not the macaque orthologue. Using arrayed ISG-expression libraries of human and macaque origin, I will examine the ability of ~800 individual ISGs for their ability to inhibit the generation of a divergent array of retroviruses. I was previously part of a collaboration that reported the first use of large-scale ISG-expression screening. This approach dissected the ability of the interferon response to protect cells from different viruses (Schoggins et al., Nature 2011). Here I will utilize a different approach to examine the ability of ISGs to inhibit the generation of new infectious particles (rather than protect cells from incoming virions). This powerful method utilizes a 96-well plate format to coexpress individual ISGs along with plasmids encoding a particular retrovirus. Subsequent measurement of infectious particle production then rapidly reveals the presence of any antiviral activity amongst hundreds of ISGs. Additionally, I have already conducted extensive pilot screening to identify ISGs that might underlie the requirement for Nef to generate maximally infectious HIV-1 virions. This work has already identified a candidate factor whose action could be responsible for this phenotype. This ISG will be vigorously pursued using a variety of virology and cell biology methodologies that will focus on the relationships between this factor and Nef, viral envelope, and particle-infectivity.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFECTION
Title: Effectors of the Salmonella SPI-2 Type III secretion system
Funder: Medical Research Council

Abstract: Serovars of Salmonella enterica are important intracellular bacterial pathogens that cause a variety of human diseases, including gastroenteritis and typhoid fever. After internalisation by host cells into a vacuole, S. enterica produces a surface exposed type III secretion system (T3SS) encoded by the SPI-2 pathogenicity island; this needle-like structure and its translocon transfer approximately 30 different effectors across the vacuolar membrane into host cells. A major function of the SPI-2 T3SS is to enable intracellular bacterial replication and we have made significant progress on understanding the biochemical activities of some of the associated effectors. Other effectors seem to be involved in processes other than intracellular bacterial replication. The purpose of this proposal is to gain an understanding of their functions, through four specific objectives. First, we will characterize the mechanism of action of SpvD, an effector that appears to inhibit the host cell NF-kB pathway in a novel way. Second, we will identify effector(s) that interfere with presentation of MHC class II molecules and then study their mode(s) of action. Third, we will conduct host cell RNA-seq screens in macrophages infected with mutant strains to identify changes in mRNA levels, to provide information on effector function. Fourth, we will use state of the art proteomics techniques to identify host proteins that interact with effectors following their delivery into cells via the physiological route, in the context of infection. Further analysis of effector function will involve microbiology, molecular cell biology, biochemistry, and in vivo imaging. We will be aided by collaborations with experts in RNA-seq and mass spectrometry. Through this research we will gain a deeper understanding of the virulence mechanisms of an important intracellular pathogen. It could also help in the design of improved vaccines against Salmonella infections and possibly other diseases.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Structure of the Tat protein translocase
Funder: Medical Research Council

Abstract: The Tat protein transport system is essential for the virulence of most bacterial pathogens. Tat has the unusual and challenging task of exporting folded proteins across the cytoplasmic membrane. How Tat solves this problem is unknown. The Tat system comprises the three integral proteins TatA, TatB, and TatC. TatC acts as the central organising element onto which the other two components assemble. Substrate proteins are recognized by specific signal peptides which bind to sites in TatC and TatB. Determining the structure of the Tat transporter is essential if we are to elucidate the molecular mechanism of Tat transport. Indeed, structure determination alone should allow us to deduce the broad operating principles of the Tat apparatus. Building on our recent success in determining the crystal structure of the core TatC component [Nature (2012) 492: 210-214] we now aim to use X-crystallography to determine the structure of the full translocation site. Our approach will be to solve higher order Tat complexes built around the TatC core. Specifically we aim to obtain structures of: - TatB in complex with TatC - Substrate signal peptide in complex with TatC or TatBC - TatA in complex with TatBC, or TatBC plus signal peptide The availability of these structures will transform our understanding of Tat transport.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING;1.3 CHEMICAL AND PHYSICAL SCIENCES
Health categories: INFECTION
Title: Combination interventions for controlling malaria transmitted by pyrethroid resistant mosquitoes: A novel bed net with synergist and IRS formulation.
Funder: Medical Research Council

Abstract: The epidemic prone district of Muleba in NW Tanzania has been subject to campaigns of indoor residual spraying IRS for the last 5 years. A high frequency of pyrethoid resistance has evolved in Anopheles gambiae based on metabolic and site insensitivity mechanisms. In 2012 the prevalence of malaria parasitaemia in children under 14 years of age stood at 20%. A community randomised trial will address the questions: 'Can two innovative vector control tools - a long lasting insecticidal net which incorporates a synergist, and a long lasting indoor residual spray formulation - overcome insecticide resistance and prove more effective at controlling malaria than current practice? Will the combination prove more effective at controlling malaria and delaying further selection of resistance than either product individually? Will the new LLIN provide better individual protection to users than the standard LLIN? 48 clusters shall be subject to restricted randomisation into 4 arms: a) Standard pyrethroid LLIN b) Mixture LLIN (pyrethroid and synergist) c) Standard LLIN plus IRS with long-lasting organophosphate d) Mixture LLIN plus IRS with long-lasting organophosphate The objective is to determine whether malaria transmitted by pyrethroid resistant mosquitoes can be controlled using these innovative LLIN and IRS products either alone or in combination and to define future strategy for the region. Intervention impact shall be determined by: the prevalence of malaria parasitaemia, entomological inoculation rate, prevalence of anaemia, force of infection (serological conversion rate), selection of insecticide resistance genes. The trial shall generate the evidence to enable funding agencies and national programmes to decide whether the new generation of tools will control malaria in places showing increasing levels of insecticide resistance, and continue the reduction of malaria burden to a point where it is no longer a major public health problem.


Research activity codes: 3.2 INTERVENTIONS TO ALTER PHYSICAL AND BIOLOGICAL ENVIRONMENTAL RISKS
Health categories: INFECTION
Title: MICA: randomized trial of therapy shortening for minimal TB with new WHO-recommended doses and FDC drugs in African/Indian HIV+/HIV- children
Funder: Medical Research Council

Abstract: There is wide acknowledgement that TB in children has been neglected; due to lack of research, recommendations are frequently extrapolated from evidence in adults. TB in children differs from adults in important ways: although due to more immature immune systems, young children more often have disseminated disease, 60% childen have non-severe forms of primary TB disease including hilar/cervical lymphadenopathy with/out minimal parenchymal disease which, unlike adults, is paucibacillary and sputum smear negative. Key research questions relevant to these children include: (1) can treatment be shortened from the standard 6-month period used in sputum smear+ adults?; (2) what are the optimal doses of anti-TB drugs and their ratios in fixed-dose-combination 'baby pills' (FDCs) (3) how should treatment doses be adjusted when treating TB and HIV together in order to overcome known drug-drug interactions. The SHINE trial is designed as a 3-year randomised phase III clinical endpoint non-inferiority trial of 4- versus 6-months first-line daily treatment with anti-TB drugs in new WHO-recommended doses/ratios, in 1200 African and Indian children, with/without HIV infection and with limited pulmonary and/or extrapulmonary TB disease. Through nested pharmacokinetic substudies, we will determine if the WHO-proposed new drug doses and drug ratios for newly designed FDCs for children are appropriate when dosed according to WHO-proposed weightband tables. We will also assess interactions between rifampicin and relevant ARVs in HIV-TB co-infected children. Qualitative and economic sub studies will address implementation/ acceptiblity issues for families and healthcare workers of new drug dosing recommendations and the cost implications of treatment shortening. We will work closely with WHO and other bodies concerned with the implementation of evidence-based guidance for treatment for children with TB and TB/HIV co-infection worldwide.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: . Osier, KEMRI-CGMRC, Defining the merozoite targets of protective immunity against Plasmodium falciparum malaria through multi-centre cohort studies
Funder: Medical Research Council

Abstract: The development of an effective malaria vaccine remains an important research priority as the global malaria control agenda moves from reductions in morbidity and mortality, to elimination. Whilst our understanding of the molecular complexity of Plasmodium falciparum has grown tremendously in the last decade, this has not as yet been paralleled with equivalent strides in deciphering the targets of, and mechanisms underlying naturally acquired immunity. I hypothesize that this stems from i) failure to examine more than a handful of potential immune targets ii) failure to conduct sufficiently large studies with statistical power to investigate hundreds of associations iii) failure to take into account the wide variation in malaria transmission intensity observed in sub-Saharan Africa (SSA) and iv) failure to marry protective association studies with demonstration of immune effector mechanisms. I believe we are now in a position to tackle these shortcomings and propose to do the following: i) systematically analyze antibody responses to at least 120 distinct surface-exposed or associated merozoite proteins, and invasion ligands, ii) conduct a cohort study statistically powered to analyze multiple responses and combinations of responses - this will be achieved cost-effectively by re-using previously collected serum samples and epidemiological data from established cohorts in Africa, iii) standardizing the antigens tested, laboratory assays and analytical approaches iv) concurrently assessing antigen-specific antibody-dependent mechanisms of action. This will be the most definitive cohort study to date and provide strong evidence for or against malaria vaccine candidates. Demonstration of function will further strengthen the evidence, allowing for rational prioritization of the best candidates.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: I Okeke, University of Ibadan - Pathogenic lineages of enteric bacteria in Nigeria
Funder: Medical Research Council

Abstract: Enteric pathogens such as diarrhoeagenic Escherichia coli and Salmonella enterica are important causes of childhood illness and death in African countries. Very little is known about the epidemiology of these bacteria in Nigeria, including which lineages account for the burden of disease. In this proposal, we plan to determine the contributions of two enteric pathotypes, enteroaggregative E. coli (EAEC) and Salmonella, using a case-control study design. We will use sequence-based methods to identify predominant diarrheagenic lineages of both pathotypes in Nigeria and elucidate their recent evolutionary history. We will additionally use sequence-based methods to subtype invasive isolates recovered during the period of the case-control study and determine whether Salmonella lineages recovered from invasive infections are associated with diarrhoea and/or carried asymptomatically by healthy individuals. The study will yield information on the evolution and phylogeography typhoidal and non-typhoidal Salmonella and their role in invasive infections, which is relatively sparse for West Africa. It will additionally identify and characterize hypervirulent EAEC lineages, about which there is little information worldwide. Following characterization of key virulent lineages, we will devise DNA-based tests to facilitate their detection for epidemiological research and surveillance. Identification of such lineages will also inform vaccine development and public health policy. The research will be performed in the laboratory of an African Research Leader Candidate based at the University of Ibadan, the Co-I on this proposal, in collaboration with PI based at the Wellcome Trust Sanger Institute in Cambridge. The study will bring molecular bacteriology expertise to an important research centre in West Africa, facilitate training and capacity building and provide an important collaborative link for the Wellcome Trust Sanger Institute in West Africa.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: MICA: RIVER - Recent HIV Infection Viral Eradication Research
Funder: Medical Research Council

Abstract: Antiretroviral therapy (ART) has revolutionised survival in HIV infection; however, alone, ART is unable to eradicate the virus because of an inaccessible pool of infected cells in which the virus is transcriptionally silent (the proviral reservoir).Eradication of HIV from reservoirs is likely to require at least two interventions: 1) Transcriptional activation of HIV from latently infected cells, 2) elimination of these re-activated cells. We believe that Primary HIV Infection (PHI) represents the optimal timing for reservoir perturbation - the proviral reservoir is less established than in chronic disease, likely to be more susceptible to intervention and relatively homogeneous with limited time to incorporate viral escape mutations from the comparatively well preserved immune responses. In vitro studies showed that Histone Deacetylase Inhibitor (HDACi) agents such as Vorinostat, Panobinostat and Romidepsin target specific histones associated with HIV repression leading to activation of viral transcription. Data from a single dose and 14-day dosing of vorinostat in HIV+ individuals with chronic infection on ART showed that HDACi led to a 5-fold and 2.5-fold increase in viral transcription, respectively. However, critically, neither study reported elimination of reactivated cells. Therefore, as an adjunct to HDACi administration, we propose an immunisation strategy to stimulate HIV-specific responses that will recognise and kill re-activated "reservoir cells". We will use a prime-boost immunisation with recombinant replication-defective chimpanzee adenovirus and modified vaccinia Ankara vaccines carrying conserved HIV sequences, previously demonstrated to induce high levels of HIV-specific, cytotoxic CD8+ T-cells. This proof-of-concept study will test the hypothesis that a combination of HDACi-induced transcriptional activation, and potent HIV-specific T-cell immunisation at PHI, under ART suppression, will significantly reduce the proviral reservoir.


Research activity codes: 6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: IDENTIFYING HOST-PATHOGEN INTERACTIONS WHICH CAUSE SEVERE MALARIA
Funder: Medical Research Council

Abstract: Aim: To explain how host and pathogen interact to cause different severe malaria syndromes. Objectives: 1. a) To use RNA sequencing to identify differences in human and parasite gene expression which characterize cerebral malaria and hyperlactataemia. b) To identify key host and parasite pathways in cerebral malaria and hyperlactataemia. c) To determine interactions between host and parasite gene expression and features of severe malaria. 2. To assess how well experimental malaria infections in mice represent severe malaria in humans by comparative gene expression analysis. 3. To test the relevance of novel candidate pathways and host-pathogen interactions by manipulation in vitro and in vivo. Methodology: Dual RNA-Sequencing will be performed on archived whole blood RNA from Gambian children with different malaria syndromes. Differential expression of genes, pathway analysis and interaction analysis will be performed to identify mechanisms associated with severe malaria. Based on existing literature, and selective experiments, we will assess to what extent different combinations of mouse and Plasmodium species exhibit similar profiles of gene and pathway activity to human severe malaria. To validate the findings from the global gene expression analysis we will test selected pathways in culture systems involving parasites, endothelial cells and leukocytes, and in vivo where homologous pathways exist. Scientific Opportunities: This project should identify novel pathways which determine the phenotype of severe malaria, has the possibility to identify the importance of reciprocal interactions between host and pathogen in causing disease, and will generate a useful, publicly available, dataset of global host and parasite gene expression. Medical Opportunities: The identification of novel mechanisms involved in different severe malaria syndromes may allow tailored treatment of each syndrome, and development of much needed adjunctive therapies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: MICA: ERADICATE HIV-1: TARGETING THE HIV-1 RESERVOIR WITH NEW IMMUNOTHERAPEUTIC STRATEGIES
Funder: Medical Research Council

Abstract: There is no cure for HIV infection. The strategy of combining agents to activate the HIV viral reservoir in conjunction with immunotherapy is enticing as the most scalable approach to curing HIV. My aims are to prove the basic scientific justification for this strategy, through 3 key objectives: 1) 'To prove the antigenicity of latently infected cells'. I will expand our data showing that HIV-1 viral protein can be detected in latently-infected resting CD4 T cells, and that the proportion of cells producing protein can be increased using activators of transcription. Using unique immunological reagents - such as affinity-enhanced T cell receptors - I will demonstrate that viral proteins can be presented as antigens, leading to recognition and killing by T cells. 2) 'To develop and apply new assays for accurate measurement of the HIV-1 viral reservoir'. I will approach the problem that there is no gold standard assay that can be broadly applied to the measurement of the reservoir. I will utilise viral sequence data obtained using deep sequencing to infer the 'replication competent' reservoir. I will develop and apply Qualitative Quantitative PCR ('q2PCR' ) using cell lines, primary cell models and ex vivo patient samples. 3) 'To explore the enhanced potential for viral clearance in patients with Primary HIV-1 Infection (PHI)'. PHI is likely to be a critical time when the reservoir is most susceptible to intervention. Using newly established clinical PHI cohorts, I will explore how antiretroviral therapy (ART) when given in PHI - potentially in combination with other agents - might impact viral control and induce a state of remission, or 'post-treatment control'. Understanding PHI - and the impact of ART - would have a major bearing on strategies for eradicating HIV, and for guidelines on improved screening for patients. The work will be undertaken at a centre with a world-class record in HIV immunology and in collaboration with industry partners.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Salmonella subversion of GTPase signalling at the host cell membrane, a key aspect of pathogen infection
Funder: Medical Research Council

Abstract: Salmonella imposes a huge global burden of morbidity and mortality. A key early step in establishing this invasive infection is breaching the intestinal epithelium, and Salmonella achieves this by delivering virulence effector proteins directly into target cells, often to the plasma membrane. Here they manipulate host cell signalling pathways, to drive actin-dependent membrane ruffling and force pathogen internalisation, and to induce inflammation. To better understand these crucial events underlying infection, I developed a powerful in vitro reconstitution system to faithfully replicate signalling platforms in their native membrane environment. Using this, my laboratory has already revealed activation of the WAVE regulatory complex (WRC), one of the cell's key regulators of actin assembly and cell shape, is directed by a novel cooperation between Arf and Rac GTPases. We demonstrated the first instance of pathogen subversion of this newly uncovered aspect of cytoskeletal control, revealing a remarkable interplay between pathogen and host as two guanine nucleotide exchange factors (GEFs), Salmonella SopE and host ARNO, cooperate to exploit the Arf-Rac1-WAVE pathway for Salmonella cell invasion. We will build on these findings to fully define the Arf GTPase network subverted by Salmonella to activate WRC at the membrane. We will extend our studies to each of the distinct parallel GTPase-dependent mechanisms used by Salmonella to force entry into target cells, continuing to combine a range of biochemical, biophysical and cell biology approaches to provide a coherent molecular description of the Salmonella cell invasion platform. Finally we will disect how Salmonella and related pathogens hijack the host's innate immune response via manipulation of GTPase signalling. Defining how these multiple GTPase platforms are assembled, integrated and subverted will be crucial to understanding, and potentially intervening in, this pivotal early step in Salmonella infection.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION