NIHRDataInsights/HRCSData huggingface dataset:
Title: The Mycobacterium tuberculosis Cell Envelope: unravelling complex cell wall assembly and the identification of potential new drug targets
Funder: Medical Research Council

Abstract: Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), has a unique cell envelope, which accounts for its unusual low permeability and hence, contributes to resistance against common antibiotics. Our integrated programme of studies is aimed at coordinating a continued investigation into the basic biochemistry and physiology, and drug targeting potential of the mycolyl-arabinogalactan-peptidoglycan (mAGP) complex of M. tuberculosis, including key aspects related to the essential immunogens, lipoarabinomannan (LAM) and alpha-glucan. Firstly, we will build on our previous studies on mycolate biosynthesis and the mode of action of mycolate targeted inhibitors, such as isoxyl and SQ109, thus providing a focus on the biochemical and structural characterisation of key enzymatic components of the fatty acid/mycolic acid metabolism and catabolism pathways. Secondly, we will extend our characterisation of the assembly of the complex AG matrix, with an emphasis on the role of glycosyltransferases, as well as related enzymes leading to the synthesis of the key immunogenic cell envelope components, LAM and alpha-glucan. Finally, we will integrate our studies on the cross-linked network of PG, following a multi-pronged approach that will involve the detailed genetic, biochemical and structural characterisation of key M. tuberculosis PG biosynthetic enzymes. Addressing these topics will provide fundamental knowledge on M. tuberculosis cell envelope assembly. In addition, it is anticipated that the above basic functional and structural studies will ultimately prove useful in the identification and detailed mode of action studies of inhibitors, emerging from whole cell 'hit-to-lead' screening studies, such as benzothiazinones (BTZ). All of the above investigations will exploit the full power of a multi-disciplinary approach using biochemistry, chemistry, immunology and molecular biology.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Epidemiological and statistical research on health problems of developing countries: MRC Tropical Epidemiology Group
Funder: Medical Research Council

Abstract: We will conduct epidemiological research on HIV, TB, malaria and other diseases of public health importance in developing countries with an emphasis on randomised intervention trials. In HIV, we will conduct the first trial of the impact of a test-and-treat intervention on HIV incidence in Africa, implementation research on scale-up of male circumcision, and RCTs to reduce early mortality among patients with low CD4 counts and to evaluate different treatment strategies for cryptococcal meningitis. In TB, we will complete a trial of a four-month pulmonary TB treatment regimen. We will extend our research on treatment strategies for TB and HIV co-infection, including trials to compare 3 treatment strategies in ARV-naïve TB/HIV patients, a CRT to assess the effect of a point-of-care TB test-and-treat algorithm on early mortality in HIV-infected patients accessing ART; and a CRT of the impact of TB diagnosis by Xpert MTB/RIF on mortality and time-to-initiation of treatment. Malaria research will build on previous work on Seasonal Malaria Chemoprevention (SMC), to evaluate effectiveness of delivery through routine health services, to monitor for adverse effects and to determine the effectiveness of adding SMC to existing control strategies for malaria. We will continue to evaluate multi-component malaria control on Bioko Island, and will develop new collaborations to assess the role of the RTS,S vaccine if licensed. We will continue trials on lay-health worker interventions to treat common mental disorders, on the beneficial and adverse effects of helminths and antihelmintics on other conditions and of the effectiveness of pneumococcal vaccines. Methodological work will include spatial analysis of spill-over effects in CRTs, and evaluation and prediction of vaccine impact. Finally, we will continue to build research capacity in Africa, including development of the MRC-supported Mwanza Intervention Trials Unit and our programme of TEG training fellowships.


Research activity codes: 6.1 PHARMACEUTICALS;6.4 SURGERY
Health categories: INFECTION
Title: Stratified Medicine to Optimise Treatment for Hepatitis C Virus Infection
Funder: Medical Research Council

Abstract: HCV infects 300,000 people within the UK and is an MRC priority research area. We have developed a flexible and dynamic UK wide consortium(STOP-HCV) that will use patient stratification to optimise treatment of infected patients. The consortium builds on existing cutting edge clinical and scientific expertise, in genuine partnership with industry, supported by NIHR infrastructure. Our overarching aim is to define and develop a deeper understanding of patient strata and to develop prognostic models so that rational treatment strategies can be deployed. In a new era of novel Directly Acting Antiviral (DAA) therapies, treating only a subset of patients with DAA will cost the NHS an estimated £96 million/year with an expected overall treatment failure rate of 30%. Moreover, 40% of patients receiving DAAs would respond to current cheaper therapies. Therefore, refined patient stratification will be of enormous clinical and economic benefit. A focus of our program will be study of HCV genotype-3 infection, highly prevalent in the UK, with a characteristic clinical phenotype, and a high relapse rate with standard therapy. We will also focus on difficult-to-treat patient groups such as those with cirrhosis and those co-infected with HIV, where optimal management pathways will be of particular benefit in patients. Our consortium is underpinned by HCV Research UK, a network of 18 UK centres biobanking samples from 10,000 HCV infected patients, linked to a state-of-the-art clinical database. The consortium has been purposefully constructed to support rational enquiry and will be divided into integrated themes including cohort development, host and viral genomics, immune phenotyping and biomarker evaluation. The program is supported by health economic, methodological, statistical, and bioinformatics expertise. The STOP-HCV consortium draws together UK expertise in collaborative working to ensure stratification at a national level for the optimal treatment of patients with HCV


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY);2.6 RESOURCES AND INFRASTRUCTURE (AETIOLOGY);6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Phase I/II trial of lentiviral vector mediated gene therapy for Adenosine Deaminase deficiency
Funder: Medical Research Council

Abstract: Patients will be selected based on the following inclusion and exclusion criteria: Inclusion criteria 1. Diagnosis of ADA-SCID confirmed by DNA sequencing OR by confirmed absence of <3% of ADA enzymatic activity in peripheral blood or (for neonates) in umbilical cord blood erythrocytes and/or leucocytes or in cultured fetal cells derived from either chorionic villus biopsy or amniocentesis, prior to institution of PEG-ADA replacement therapy 2. Patients who lack a fully HLA-matched family donor 3. Patients < 5yrs of age 4. Parental/guardian signed informed consent Exclusion criteria 1. Cytogenetic abnormalities on peripheral blood 2. Evidence of infection with HIV-1&2, hepatitis B, HCV 3. Evidence of active malignant disease 4. Known sensitivity to busulfan PEG-ADA therapy will be stopped 1-2 weeks prior to the gene therapy procedure. For the transduction protocol, CD34+ cells will be purified either from autologous bone marrow or from G-CSF mobilised PBMCs recovered by leukapheresis. Patient conditioning will be initiated immediately after bone marrow or PBMC collection and will consist of Busulfan i.v. (total dosage 4mg/kg). Patients will not proceed to conditioning if the harvest is <1 x 106 CD34+ cells/kg. In these patients, PEG-ADA will be restarted and patients will be withdrawn from the study. After purification, CD34+ cells will be transduced with the lentiviral vector in established protocols, then evaluated for sterility, cell count, and viability, and immediately infused into patients. Other tests for safety including testing for RCLs will be performed on reinfused cells and results will be recorded retrospectively. If after 180 days there is no evidence of the transgene in PBMCs by qPCR or there is no evidence of T cell recovery, then patients will re-start PEG-ADA and will be withdrawn from the study. Patients will be followed-up on study at 1 month, 6 weeks, 3, 6, 9, 12, 18, 24, 30 and 36 months post gene therapy.


Research activity codes: 6.2 CELLULAR AND GENE THERAPIES
Health categories: INFECTION
Title: Structural and molecular investigations of membrane-embedded pilus assembly nanomachines in Gram-negative bacterial pathogens
Funder: Medical Research Council

Abstract: This proposal aims to understand the mechanism of pilus assembly by two systems: the chaperone-usher (CU) pilus and the type IV pilus (TFP) assembly systems. Both systems are of significant biomedical importance: CU pili have been intensely characterised in uropathogenic E. coli, where they play well defined roles in host tissue recognition and adhesion; the role of TFP pili has been characterised in a number of bacterial pathogens including Neisseria meningitis, the TFP system of which we propose to study. Our research programme aims to determine the structure of these assembly systems and carry out a detailed biochemical and biophysical characterisation of their mechanism. To carry out the proposed research, we will use a multidisciplinary approach combining molecular biological, biochemical, and biophysical methods such as X-ray crystallography, and cryo Electron Microscopy (EM) to gain structural information, and fluorescence resonance energy transfer (FRET) to gain dynamic information on domain/protein motions during pilus biogenesis. For the CU pilus assembly system, we have derived a general model for system-mediated pilus biogenesis, which we propose here to investigate by solving additional structures to further characterise the properties of the system, and by fluorescence spectroscopy to analyse the details of protein and domain motions during pilus assembly. For the TFP assembly system, which is at a less advanced stage of structural knowledge, we will first determine the structure of the assembly system either by EM or X-ray crystallography. Next, we will study the recruitment of pilus subunits to the assembly system. Once these two objectives are fulfilled, we will aim to investigate the detailed mechanism of TFP biogenesis using solution biophysics methods similar to the ones used to dissect the mechanism of CU pilus assembly. In both cases, we will seek to exploit our detailed knowledge to design inhibitors of pilus biogenesis.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: EspO orthologs and NleF: type III secretion system effectors of enteric pathogens that modulate apoptosis and inflammation
Funder: Medical Research Council

Abstract: 1. The effector proteins will be over-produced in E. coli either individually or through co-expression and purified using our standard protocol. Purified proteins and their interactions will be characterised biochemically and biophysically using native-PAGE, SEC-MALS and ITC. Proteins and their stable complexes will be subject to crystallisation experiments. Crystals will be screened for their diffraction quality using our in-house X-ray setup before data collection at the diamond synchrotron radiation source. Phase information will be obtained either through molecular replacement or Se-Met derivatised crystals and MAD phasing. 2. We will use protein-protein interaction assays (e.g. co-IP, column pull-down and yeast two hybrid) together with proteome analysis of co-IP material to identify the entire signalling complexes formed by the effectors and their cellular targets during infection and transfection. 3. We will generate inducible, stable, effector cells lines and use them for localisation and functional studies during infection and trasfection by employing conventional cell biology and microscopy techniques (immunofluorescent and immungold EM). We will also use other cell types (including polarised epithelial cells and macrophages) to study the role of the effectors and their target proteins in pathogen-host interaction. 4. We will use wild type and isogenic effector mutants (S. Typhimurium and the EPEC/EHEC-like mouse pathogen Citrobacter rodentium), expressing bioluminescent or fluorescent reporters to study infection dynamics and clearance in real time and 3D using the IVIS technology. We will use histology and immunoflorescent staining to study the localisation of the effectors' targets in healthy and infected tissues. We will use immunohistochemistry and cytokine qRT-PCR to measure host immune responses and knockout mice infected with bioluminescent bacteria to determine the role of the effectors' targets on the infection.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Regulation of clonality in a natural retrovirus infection
Funder: Medical Research Council

Abstract: Objectives i) To identify and quantify the genetic and epigenetic factors that determine the number, abundance and spontaneous proviral expression of HTLV-1-infected T cell clones in asymptomatic carriers and patients with HTLV-1 diseases; ii) To test mechanistic hypotheses on the regulation of HTLV-1 proviral latency in naturally-infected T cells. Methods & experimental approach i) Materials: genomic DNA from primary peripheral blood mononuclear cells from subjects with HTLV-1 infection. Methods: High-throughput mapping and quantification of proviral integration sites in the genome (350 gDNA samples per Illumina HiSeq 2000 flow-cell). Laboratory protocols, work flow and sequences of primers and linkers are given in Gillet et al 2011. Bioinformatic, mathematical and statistical techniques are outlined in Gillet et al 2011 and extended in Berry et al 2012 (Bioinformatics 28, 755-762). ii) Materials: Fresh primary PBMCs from HTLV-1+ subjects; HTLV-1+ CD4+ T cell clones isolated from PBMCs by limiting dilution; HTLV-1+ T cell lines. Methods: Chromatin immunoprecipitation (ChIP) to localize and quantify binding to chromatin of host proteins involved in regulating gene expression (RNA Pol II, cohesin etc) and epigenetic markers (H3K9Me3 etc). Electrophoretic mobility shift assay (EMSA) to confirm binding of proteins to proviral DNA. Chromosome conformation capture (3C) to detect and map chromatin loops formed between proviral DNA and host chromatin. Flow-sorting of cells according to stage of cell cycle. iii) Generalized linear models; logistic regression; ordinary differential equations; standard parametric & non-parametric statistics. Application & exploitation We are developing a rapid, semi-quantitative assay of clonality for use in clinical management of ATLL.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Proteolysis and life cycle progression in Leishmania
Funder: Medical Research Council

Abstract: This multidisciplinary research programme will exploit state-of-the-art techniques in parasite genetic manipulation, genomics, quantitative proteomics and molecular parasitology and will lead to the elucidation of key mechanisms that enable Leishmania to undergo the cellular remodelling required for successful life cycle transition. We will 1. use standard molecular genetics and biochemistry approaches to the study of a few selected Leishmania peptidases. 2. develop a new approach for genetic manipulation of Leishmania using a modified cre-lox system - this will allow the investigation of essential peptidases in both promastigotes and amastigotes. 3. apply quantitative proteomics (such as SILAC and TAILS) to identify secreted peptidases (potential virulence factors) and peptidase substrates in Leishmania. 4. Use high content cell imaging to carry out phenotype-directed, peptidase-wide or kinome-wide RNAi screens using specific reporter lines. This will identify protein kinases involved in regulating key cellular processes such as autophagy, endocytosis and differentiation. 5. Use high content cell imaging to carry out novel, target-based and phenotype-directed screens with kinase focussed or peptidase-focussed chemical libraries. This will identify hits suitable for further drug discovery efforts, as well as chemical tools for investigating protein kinase or peptidase function. 6. Sequence 150-250 clinical isolates of Leishmania from the Sudan and then use an in house bioinformatics pipeline to identify structural variation that might contribute to disease tropism.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: Human cytomegalovirus: changes in the latently infected cell as chemotherapeutic and immunological targets for antiviral therapy
Funder: Medical Research Council

Abstract: Human cytomegalovirus (HCMV) primary infection of the immunocompetent is asymptomatic. However, infection of individuals with compromised or immature immune systems can be life threatening. Furthermore, HCMV persists for the lifetime of the host which, at least in part, is due to the ability of HCMV to avoid immunesurveillance and, ultimately,establish a latent infection. Cellular latency is defined as genome carriage with viral transcription limited to a few latency-associated genes and no infectious virus production. Consequently, current therapies targeting HCMV replication will not target the latent virus. However, viral reactivation from latency is a major cause of disease in immune suppressed transplant patients. Furthermore, there is increasing evidence associating HCMV with long-term diseases (i.e. atherosclerosis, chronic graft rejection and neoplasias) with reactivation of latent HCMV likely to be a major source of virus. Consequently, therapeutics that target latently infected cells could have far reaching clinical implications. Work from our laboratory has been instrumental in identifying a subset of viral genes expressed during HCMV latency, the host immune responses to these latency-associated antigens,and how these genes modify the latently infected cell.In the case of expression of viral UL138 during latency, we have already identified changes in the latently infected cell mediated by UL138 expression allowing them to be targeted chemotherapeutically. We propose to build on this work and comprehensively analyse the effects of expression of additional viral latency-associated genes on the cell and the immune response. Such analyses will allow a more comprehensive understanding of how this human pathogen persists for the lifetime of the host and also identify additional changes in the latently infected cell which can be further exploited for chemotherapeutic and immunological targets to lead to credible strategies aimed at eliminating latent virus.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS;2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT
Health categories: INFECTION
Title: MICA: Study of disease mechanisms in enteric fever to characterise innate & adaptive immunity in mucosa & blood in controlled human infection model
Funder: Medical Research Council

Abstract: Vaccines for S. enterica currently under development are based on the S. Typhi and S. Paratyphi C Vi polysaccaharide capsule. However, enteric fever caused by S. Paratyphi A (which does not carry Vi) and for which there is currently no vaccine, has risen in the past decade and accounts for more than 50% of cases in some areas. Design and evaluation of effective vaccines is limited by a gap in understanding the mechanisms of susceptibility to capsulate and non-capsulate typhoidal Salmonellae. To fill this knowledge gap we will extend a controlled human infection model (developed by us in Oxford) with S. Typhi to infection with S. Paratyphi by challenging volunteers previously exposed to S. Typhi with either S. Typhi or S. Paratyphi. We will be able to relate responses in a controlled human infection model to natural protection, and use this for potential vaccine antigen discovery. We aim to: A) identify the systemic and mucosal location of bacteria to determine potential for humoral and cellular protection; B) compare innate responses to S. Typhi and Paratyphi in peripheral blood and mucosa in individuals resistant and susceptible to infection; C) define the phenotype and antigen specificities of B cell and T cells responses against the two pathogens to identify correlates of protection against reinfection; D) identify CD1 restricted Salmonella derived lipid antigens that are conserved between different Salmonella strains and which may be used as T cell antigens for alternative vaccination strategies. Our findings will be further validated in naturally exposed individuals in the Mucosal Research Unit within the Wellcome Trust Major Overseas Unit in Malawi. This programme will give new insights into the innate and adaptive immune responses and the pathogenesis of human infection with the bacteria that cause enteric fever. It will provide important correlates of protection that will facilitate the design and optimisation of novel vaccination strategies.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The dynamics and control of infectious diseases close to elimination
Funder: Medical Research Council

Abstract: We are currently lacking methods to analyse infectious disease at high levels of vaccination coverage. In that scenario, assumptions of random mixing break down, and notions such as herd immunity and critical community size need to be reconsidered. The objective of this project is to develop new statistical methods to analyse infectious diseases at the fringe of elimination. This will be linked to a topic of great current public health importance, the ongoing spread of measles in Europe. More specifically, I will 1) extend existing methods for inferring transmission trees from time series of case data to link outbreaks on a continental scale, taking into account genotype and sequence data and vaccination uptake; 2) extend methods for inferring transmission parameters from outbreak size distributions to take into account distribution of genotypes and sequence data, to map measles risk in different parts of Europe; 3) develop inference methods for fitting network models with different distributions of susceptibility to observed outbreak patterns.


Research activity codes: 2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION