NIHRDataInsights/HRCSData huggingface dataset:
Title: Lung health after pulmonary TB: designing strategies to improve long-term patient outcomes
Funder: Medical Research Council

Abstract: The Fellowship will build on the networks, cohort, and data generated during during the ongoing follow up of a cohort of post-TB patients in Blantyre, Malawi. Specific tasks to be completed include: 1. Data generated from the existing cohort follow up will be used to (a) Design a screening tool to identify patients with extensive post-TB lung damage at TB treatment completion in resource poor settings, and (b) Construct a multilevel longitudinal model to identify factors predicting adverse patient outcomes in the 2-4 years following treatment completion. 2. A case control study will be nested within the ongoing cohort follow up in Malawi, to determine the microbiology of colonising/infecting organisms amongst adults with PTLD. Molecular tools will be used to identity differences in microbiology between adults completing PTB treatment with/without evidence of PTLD, and well, community based controls with no history of PTB, with a focus on organisms commonly seen in those with structural lung damage that may require targeted management (Eg. P.aeruginosa, S.aureus, non-tuberculous mycobacteria). 3. Formal training in Health Systems, and a consolidative placement in a Health Policy institution will be used to produce a health systems analysis describing the challenges facing integration of acute TB services and chronic respiratory services in resource poor settings. Strategies to facilitate change in health service delivery models will be outlined. This document will be focused on care delivery in Blantyre, Malawi & Kampala, Uganda, with a view to further research / interventions in these areas as part of an Intermediate Fellowship. 4. An international collaborative network for PTLD research and clinical service delivery will be established, in order to share data and information on ongoing PTLD studies, agree on terminology to be used when describing PTLD, determine priorities for research & clinical care, and generate opportunities for collaboration.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES;8.1 ORGANISATION AND DELIVERY OF SERVICES
Health categories: INFECTION
Title: Structure-based vaccine design: using structural information from HIV-2 to design better HIV-1 immunogens
Funder: Medical Research Council

Abstract: Despite a massive effort from researchers around the world, there is still no effective vaccine that can protect people from HIV infection, and each year well over one million people around the world become newly infected with the virus. One of the main barriers to HIV vaccine design is that HIV-1 only rarely generates immune responses in infected people that are associated with long-term control of the virus without the need to take anti-HIV drugs on a regular basis. We are proposing a novel strategy to develop an HIV vaccine based on studying HIV-2, a virus closely related to HIV-1 which has caused the worldwide HIV epidemic. Unlike HIV-1, HIV-2 has only spread to a very limited amount beyond the area where humans first became infected with what was originally a monkey virus (SIVsmm) in West Africa, and the total number of people infected with HIV-2 appears to be falling rather than relentlessly increasing, as is the case for HIV-1. Moreover, a large proportion of people with HIV-2 infection (37% in one previous study) don't ever get sick, even without treatment, and have very low levels of virus in the bloodstream. One study in West Africa showed that if HIV-2-infected people subsequently became infected with HIV-1, they lived longer and were less likely to progress to AIDS compared to people newly-infected with HIV-1 without previous HIV-2 infection. This could suggest that immune responses generated by exposure to HIV-2 give some protection against HIV-1 progression to disease and could therefore help in strategies for vaccines and immune-based therapy. Taking HIV-2 infection as our model, we plan to study the key features of some of the virus proteins that the immune system is able to recognise in people who are naturally controlling the virus. This project involves a collaboration between two research groups, one in the UK and one in Japan, who have been working with one another for several years. We now want to take the opportunity to build up these collaborations with the aim of trying to develop a new HIV vaccine. The UK group has studied immune responses and the characteristics of the virus in HIV-2-infected people in West Africa for many years. The Japan group studies the structure of viral proteins and how they interact with the host immune system at the level of individual molecules. Working together they hope to discover what HIV-2 proteins look like to the human immune system and why this helps people with HIV-2 to make much stronger and more potent immune responses to HIV-2 than HIV-1-infected people do against HIV-1. We plan to identify proteins that can be developed as vaccine candidates and see if they are "seen" by the immune systems of people naturally infected with HIV-2 and HIV-1. If these look promising, they can be developed further by vaccine teams in the UK and Japan.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY);4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Functional investigation of Epstein-Barr virus infection and latent gene function using natural variants found in normal infections and cancer cells
Funder: Medical Research Council

Abstract: Epstein-Barr virus (EBV) contributes to several types of cancer and causes infectious mononucleosis. There is increasing evidence that natural variation in the EBV genome is important for disease pathogenesis and impacts on normal EBV biology. We have accumulated over 250 EBV genome sequences and will now focus on the consequences of the viral sequence variation for EBV-associated disease, biology and therapy. We shall - Use our new resources to re-evaluate the biology of type 1 and type 2 EBV, following the discovery that type 2 EBV infects T cells (in addition to B cells) - Test the significance of variation in EBNA1, the protein that controls maintenance replication of the viral genome but also has many other activities potentially relevant to cancer Specifically, we shall 1. Use our newly generated recombinant type 2 EBV bacterial artificial chromosome (BAC) to produce virus and investigate the ability of type 2 EBV to infect T cells. We shall investigate the effects on the T cell, and distinguish the contributions of EBV glycoprotein variants and EBV nuclear proteins (EBNAs) linked to type 1 and type 2 on B and T cell infection. 2. Test our hypothesis that type 2 EBV may be better at achieving infection and outgrowth of activated lymphocytes than type 1 EBV, potentially consistent with its higher prevalence in populations with chronic immune activation caused by other infectious diseases (eg Malaria). 3. Functionally investigate the very close type-specific linkage of EBNA2 and EBNA3s. We propose there must be some novel functional compatibility that explains why strains almost always have type 1 EBNA2 with type 1 EBNA3 or type 2 EBNA2 with type 2 EBNA3s. 4. Determine the functional impact of variation in EBNA1 that we have identified. We will examine the co-operative DNA binding, oligomerisation and anti-EBNA1 drug susceptibility. We shall also test the impact of variation on known EBNA1 functions that might contribute to EBV associated cancers


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: THE EPIDEMIOLOGY OF SCRUB TYPHUS AND RICKETTISIAL INFECTIONS IN A HIGHLY ENDEMIC RURAL SETTING IN SOUTH INDIA: POPULATION-BASED COHORT STUDY
Funder: Medical Research Council

Abstract: Scrub typhus is febrile illness caused by Orientia tsutsugamushi, bacteria related to the genus Rickettsia. The infection is transmitted by the larvae (chiggers) of trombiculid mites which infect mammals as incidental hosts. Scrub typhus occurs over much of tropical and subtropical East Asia, South Asia and South-east Asia. Scrub typhus is one of the main causes of febrile illness in endemic areas and if untreated has a high mortality. Despite being a major cause of complicated undifferentiated fever in Asia, little is known about the incidence and immunogenicity of scrub typhus infection. Basic epidemiological parameters to inform control efforts and vaccine development are not available. This is a population based cohort study in a highly endemic rural setting in south India aiming at estimating the incidence of serological, symptomatic and severe scrub typhus infection. In addition we will study two rickettsial infections occuring in the study area: flea-borne murine typhus and tick-borne spotted fever. Enrolled will be 40,000 individuals who will be followed up for the development of fever using active and passive surveillance. Active surveillance will include household screening every two months. Fever cases occuring in the past two months will be tested for Scrub typhus, murine typhus and spotted fever IgM. 1200 individuals will be followed up by annual serological testing to identify asymptomatic infections. The research includes spatial and socio-economic risk factor analysis. In an entomological study rodents carrying mite larvae will be trapped to compare the intensity of mite infestation between areas of high and low risk for human scrub typhus. The results from this study will help clinicians to elucidate the natural course of scrub typhus infection, health policy makers to estimate the global burden of disease and the scope for community-based interventions and immunologists to better understand the immunogenicity of single and repeat infections.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Characterisation and therapeutic manipulation of Flaviviridae innate immune evasion
Funder: Medical Research Council

Abstract: We have developed three series of novel cyclophilin inhibitors (CypI) and demonstrated that specific compounds activate innate immunity against hepatitis C virus (HCV) and are potent inhibitors of dengue virus (DV) and Zika virus (ZV). We will now measure replication of defined HCV/DV/ZV subgenomic replicon systems encoding luciferase and full length viruses in Cyp manipulated cells (RNAi/CRISPR or CypI) to identify the Cyps involved and the active CypI, and to define the role of innate immunity in the inhibitory process (by manipulating sensors and adapters to rescue inhibited infection). We will explain CypI antiviral specificity by correlating Cyp specificity (measured in recombinant protein binding assays) with antiviral specificity. We will examine the effect of Cyps on the viral replication compartments (confocal/electron microscopy), testing whether sensors colocalise with viral RNA/proteins on Cyp manipulation, and how host and viral proteins are relocalised when sensing is activated. We will discover which viral proteins are targeted by Cyps using binding assays between candidate proteins as well as by immunoprecipitating viral proteins and examining copurifying cellular proteins using mass spectrometry. We will determine how Cyp recruitment changes viral proteins using X-ray crystallography of Cyp-viral protein complexes. We will select virus CypI resistant mutants and characterise their sensitivity to innate immunity. We will identify the sensors and innate immune pathways activated by wild type and mutant viruses in Cyp manipulated cells. Overall, this work will define the Cyps acting as cofactors for Flaviviridae, explain how they aid in evasion of innate immune sensing, and produce a series of specific and potent inhibitors that disturb innate evasion to unleash the innate immune system against the virus as a new paradigm for antiviral prophylaxis and therapy.


Research activity codes: 4.2 EVALUATION OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: Using iPSC variation to define HIV-1 regulatory networks
Funder: Medical Research Council

Abstract: The goal of our programme is to discover, validate and characterise new HIV-1 regulatory factors and pathways. To this end, we will: 1) Screen human induced pluripotent stem cells (iPSCs) from the HipSci library and iPSCs that we will generate from clinical samples (from the Multicentre AIDS Cohort Study, MACS) for HIV-1 infection and replication phenotypes. HIV-1 infectivity will be assessed using a lentiviral vector expressing GFP and detected by microscopy and flow cytometry. Replication will be assessed by viral p24Gag release and progeny infectivity. We will use established assays to map the affected step(s) in the HIV-1 life cycle in cell lines presenting extreme replication phenotypes. 2) Correlate extreme phenotypes with molecular signatures of the cell lines at the genomic, transcriptomic and proteomic level, using bioinformatic tools to identify candidate regulatory host factors and pathways. We will leverage from experience in multi-dimensional reduction of phenotypic datasets using Bayesian algorithms tools such as Probabilistic Estimation of Expression Residuals (PEER) to integrate cell behaviour with -omics datasets. 3) Validate HIV-1-regulatory factors and pathways in cultured cells, CD4+ T cells and macrophages, by down regulation (shRNA, siRNA and CRIPSR/cas9) or ectopic overexpression of candidate genes. We will characterise the mechanism(s) of action using technologies that align, initially, with predicted biological activities. We will also repurpose existing drugs that target the newly discovered factors/pathways to test their effect on HIV-1 replication. Lastly, we will investigate the association of regulatory factors with AIDS clinical outcomes and disease progression from existing and emerging patient cohort data, such as the MACS. This work seeks to inform new therapeutic strategies to treat HIV-1.


Research activity codes: 4.1 DISCOVERY AND PRECLINICAL TESTING OF MARKERS AND TECHNOLOGIES
Health categories: INFECTION
Title: MICA Investigating CD1c lipid-antigen presentation and its role in tuberculosis
Funder: Medical Research Council

Abstract: CD1c presents lipid antigens to the T-cell receptors (TCR) of T-cells. Although CD1c presents mycobacterial-lipids to T-cells, the majority of CD1c-restricted T-cells recognise CD1c in the absence of microbial antigens, suggesting dual recognition of self and non-self-antigens. I have shown that ligand binding induces major CD1c protein reorganisation forming new T-cell binding surfaces, whereby remodelled CD1c appears to promote T-cell recognition. My findings suggest that CD1c bound-lipids serve primarily to remodel TCR binding surfaces on CD1c, but this recognition mechanism is not well understood. My preliminary data shows that several host glycerophopholipids, which are lipids also highly expressed by Mycobacterium tuberculosis (Mtb), are CD1c ligands for T-cells. However, CD1c-restricted T-cell recognition of Mtb-derived glycerophospholipids is unknown. Importantly, neither the molecular basis of how lipidCD1c regulates TCR recognition nor the functional role of T-cells that exhibit dual recognition of self- non-self-antigen is understood in human human tuberculosis (TB). My overarching hypothesis is that T-cells which exhibit dual self- non-self-antigen recognition regulate the host-pathogen interaction in TB. The first aim of the study is to define the molecular mechanisms underpinning T-cell recognition of CD1c. I will achieve this via a cross-disciplinary approach combining molecular dynamics with structural, mutational, and functional T-cell response to understand basic recognition mechanisms. In the second aim, using my unique CD1c tetramers I will clone T-cells and their TCRs to better understand these innate T-cell subsets. CD1c-restricted T-cells are subsequently used to understand T-cell recognition of CD1c bound lipids that are shared by host and pathogen. In the final aim, I will investigate the functional impact of CD1c and its restricted T-cells in human TB using a novel bioengineered 3 dimensional TB infection model.


Research activity codes: 1.1 NORMAL BIOLOGICAL DEVELOPMENT AND FUNCTIONING
Health categories: INFECTION
Title: Using single-cell RNAseq to investigate human malaria parasite transmission dynamics
Funder: Medical Research Council

Abstract: Here we propose to explore natural parasite populations and within-host diversity by harnessing the power of single cell transcriptomics. We will create a Malaria Cell Atlas for three species of human malaria parasites, covering the asexual stages that cause disease and the sexual stages responsible for transmission by Anopheles vector mosquitoes. After we complete these atlases, we will dive deeply into transmission dynamics for P. falciparum, the most prevalent species in Africa and the species responsible for the majority of deaths. We will use single cell RNA-seq to interrogate parasites from both symptomatic and asymptomatic cases, exploring in more resolution than ever before possible the diversity of parasite populations: how many transcriptional states and how many genotypes exist in a single person; how does diversity compare between asexual and sexual parasites; do patterns change as the season progresses; do patterns differ between those silently carrying the parasite versus suffering disease. Finally, we will explore actual transmission dynamics of these deeply interrogated populations of parasites by investigating parasite genetic diversity in mosquitoes fed directly on these parasites. To do this, we have partnered with Malian scientists, and we will be bringing single cell RNAseq to West Africa for the first time. Our approach will derive deep and meaningful biological insights on within-host and within-vector diversity from samples that are directly sourced from a natural infection setting. In sum, will (i) generate high resolution transcriptional maps of the most prevalent human malaria species in the blood of infected patients, including pathogenic and transmission stages (ii) interrogate the inter-host variation in transcriptomic and genetic diversity in different reservoirs of the parasite contributing to further transmission (iii) understand the sexual reproduction and within-vector dynamics of the infectious reservoir of the disease.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Redox regulation of protein functions in the plastid of Toxoplasma gondii
Funder: Medical Research Council

Abstract: Compartmentalization is fundamental for eukaryotic cells, allowing proteins to function in optimal biochemical environments. Redox control of protein function plays a critical role in defining compartmental functions, and thioredoxins (Trxs) are key players in this regulatory mechanism. Apicomplexan parasites are global killers and their ability to sustain infection depends on the functions of their plastid, the apicoplast. The apicoplast contains four compartments and is predicted to have seven Trxs, two of which control essential apicoplast housekeeping functions. Through functional study of all apicoplast Trxs (ATrxs) and their substrates we will create a comprehensive understanding of the redox regulatory network controlling apicoplast functions. This work will improve our understanding of how apicomplexans sustain infection, and will seed drug discovery. Aims 1. Trx control of protein function occurs via disulfide exchange. We will use the biochemical nature of this interaction to trap ATrxs with their substrates through genetic modification and to isolate and identify the substrates via pull-downs and proteomics analyses. Substrate identity will unravel the apicoplast pathways regulated by ATrxs and will point out new essential players in this redox control network beyond the ATrxs. 2. We will perform a systematic functional analysis of all ATrxs and of selected substrates, using our inducible knock-down system to deplete each of them, and will use our array of functional assays to analyze the phenotypes resulting from their depletion. This will provide an alternative and complementary approach to aim 1 for identifying the cellular pathways controlled by the ATrx redox network. We will also analyze the biochemical and cellular properties of substrates after depletion of their respective ATrxs. This will clarify the molecular mechanism of how the disulfide exchange between ATrxs and substrates achieves functional control of essential apicoplast pathway


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Broad and effective protection against influenza achieved by viral vectored vaccines
Funder: Medical Research Council

Abstract: Currently licensed influenza vaccines offer very low levels of protection despite annual review and updating of the vaccine composition. In adults over 65 years there has been little to no detectable protection despite annual revaccination. However it is known that T cell responses to conserved influenza antigens acquired by infection with influenza virus offer protection against symptomatic disease upon re-infection. We have demonstrated that these immune responses can be boosted by intramuscular vaccination by viral vectors expressing influenza nucleoprotein (NP) and matrix protein 1 (M1) in humans, and that the responses are protective against influenza challenge in small animals. We now propose to extend this work in a preclinical study in which we will include a third antigen, the external glycoprotein neuraminidase (NA), as well as NP and M1. Recent research has underlined the role of anti-NA antibodies in protection against influenza disease in humans. Additionally we will determine how the route of vaccination affects vaccine efficacy in mice and in pigs, which are a better model of human disease. Natural exposure to influenza virus results in tissue resident memory T cells in the lung, and whereas intramuscular immunisation of humans has been shown to boost these responses in the blood, the effect on memory responses in the lungs is not known, and cannot be studied directly in humans. We will pre-expose pigs to influenza virus in the respiratory tract, and then study the effect of different vaccination routes on humoral and cellular immunity to influenza virus, and on protective efficacy of vaccination. The results (vaccine efficacy, correlates of protection, degree of correlation between immune responses in blood and lung, possible improvement in efficacy by including NA as well as NP+M1) will inform future vaccine design and future clinical trial design.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION