NIHRDataInsights/HRCSData huggingface dataset:
Title: MRC/FAPESP - bilateral agreement: Multiple-epitope vaccine to confer serotype-independent protection against pneumonia
Funder: Medical Research Council

Abstract: Invasive pneumococcal disease is a leading cause of morbidity and premature mortality around the world. Although current vaccination strategies are effective, they have major limitations such as low levels of protection against pneumonia and serotype replacement. We have conducted extensive basic laboratory and clinical translational research that has substantially improved our understanding of the limitations of current vaccines and provided insights into new approaches for vaccine development. We now propose a collaborative project between BI and LSTM that draws on previous successful projects to identify targets for a completely new type of pneumonia vaccine that will confer serotype-independent protection against pneumonia. Pneumococcal surface protein A (PspA) and Pneumococcal surface protein C (PspC) are among the most promising vaccine candidates but they exhibit antigen variability. We will describe the entire range of PspA and PspC peptides in peptide arrays that will be probed with serum from immunized mice and adults exposed to pneumococci during experimental carriage to identify optimal cross-reacting epitopes to be included in a multiple-epitope vaccine. We will test the protective potential of this vaccine in murine models and serum cross-reactivity in in vitro assays. We will confirm induction of cellular responses in immunized mice and the presence of multiple-epitope antigen specific CD4 T cells in healthy adults and pneumonia patients after ex-vivo stimulation. We will determine responses to vaccine associated with protection from experimental human pneumococcal carriage and with susceptibility to pneumonia disease. These experiments will add a novel approach to protein vaccine discovery and knowledge regarding optimal vaccination strategy for mucosal protection.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Characterisation of uptake and sub-cellular transit of human serum trypanolytic factors by Trypanosoma brucei
Funder: Medical Research Council

Abstract: African trypanosomes are transmitted by the tsetse fly and circulate in the bloodstream of their host. They cause Human African Trypanosomiasis and nagana in livestock. Humans have an innate immunity to many African trypanosomes, including T. b. brucei, mediated by TLF1/2. The human infective forms, T. b. gambiense and T. b. rhodesiense, evade this by reduced TLF1 uptake and expression of SRA, respectively. Several questions remain: how does TLF2 enter the cell; how does TLF transit the endocytic system; which parasite proteins are essential and what are their roles in TLF efficacy; and, what other routes to TLF resistance exist? Initial sequencing of a T. b. brucei RNAi library selected in normal human serum (NHS) identified the TLF1-receptor and a lysosomal protein, validating the approach. Inhibitor of cysteine peptidase (ICP) and three previously uncharacterised proteins were also identified, including a pH regulator and a transmembrane protein. High throughput sequencing will identify all the RNAi inserts in the selected library. 'Hits' will be subjected to a comparative bioinformatic analysis using the genome sequences: T. b. brucei, T. congolense, T. vivax (sensitive) and T. b. gambiense (resistant). Standard techniques will be used to confirm any variations and to test their role in the T. b. brucei lab-adapted strain. 'Hits' representative of functional categories will be characterised using stemloop RNAi, TLF uptake/ transit assays, epitope-tagging and tandem affinity purification. The role of ICP/cathepsins in TLF efficacy will be analysed by cathepsin stemloop RNAi in an icp null cell line. The pH regulator will be characterised by epitope-tagging, stemloop RNAi, and genetic dissection of the pH regulatory domain. A panel of antibodies will be raised against key proteins identified in these analyses, enabling the translation of the findings into tools for diagnosis and characterisation of African trypanosome isolates of known and unknown NHS sensitivity.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Development and testing of novel recombinant pnemococcal glyconjugate vaccines
Funder: Medical Research Council

Abstract: Streptococcus pneumoniae causes pneumonia, septicaemia and meningitis, and globally one million children die of pneumococcal disease each year. Current pneumococcal glycoconjugate vaccines require both purification of the capsule glycan from the pathogen and its chemical coupling to a suitable protein carrier. These are costly and only protect against some S. pneumoniae serotypes, which can promote capsule switching and vaccine escape strains. The Wren group has pioneered an approach termed bacterial Protein Glycan Coupling Technology (PGCT) whereby combinations of recombinant protein/glycan structures are produced in E. coli exploiting a toolbox of bacterial oligosaccharyltransferases. This recombinant approach promises maximum flexibility in terms of glycoconjugate design that should produce an unlimited and purified supply of vaccine at low cost. The Mitchell group has demonstrated that inactivated pneumolysin protein can provide a mucosal immune response against a broad range of pneumococci, but requires a boost to produce a lasting response. Additionally other conserved protein candidates have been shown to be effective in the murine infection model. We hypothesise that addition of a capsule determinant(s) to a protein carrier would produce a "best of both worlds" pneumococcal vaccine in terms of efficacy and protection range. The capsule(s) will be enzymatically coupled to six conserved pneumococcal protein or fusion protein vaccine candidates. In this study, we will combine the expertise to engineer recombinant glycoconjugate vaccines using PGCT and test for protection in the pneumococcal murine infection model. The study will produce a novel serotype-independent pneumococcal glycoconjugate vaccine that will induce cellular and humoral immunity. The successful production of glycoconjugate vaccines using PGCT should have wide applications to construct further S. pneumoniae glycoconjugate vaccines and vaccines diverse pathogens.


Research activity codes: 3.4 VACCINES
Health categories: INFECTION
Title: Defining the metabolic phenotype of intracellular Mycobacterium tuberculosis
Funder: Medical Research Council

Abstract: Despite decades of research many aspects of the biology of Mycobacterium tuberculosis remain unclear and this is reflected in the antiquated tools available to treat and prevent tuberculosis and consequently this disease remains a serious public health problem. Important discoveries linking the ability to metabolise specific substrates intracellularly within a macrophage to virulence have identified energy metabolism as a theoretically very powerful therapeutic target for tuberculosis. However the identity of the carbon sources and major metabolic pathways used by intracellular M. tuberculosis is poorly defined. The goal of this research is to identify the key carbon substrates and pathways ustilised by M. tuberculosis during intraphagosomal growth. We will perform comprehensive 13C-isotopologue profiling analysis of wild type and mutant strains of this pathogen in order to identify the different carbon sources which are contributing to the intracellular nutrition of M. tuberculosis. In parallel we will investigate the metabolic pathways required for consumption of these carbon sources under defined conditions in vitro using 13C-metabolic flux analysis. We will also perform transcriptomic analysis of intracellular M. tuberculosis in order to indirectly monitor metabolism. All of this data will then be used to constrain genome scale metabolic networks in order to define the metabolic phenotype of intracellular M. tuberculosis.


Research activity codes: 2.2 FACTORS RELATING TO PHYSICAL ENVIRONMENT;2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Structure-function analysis of Type IV secretion systems by cryo-electron microscopy
Funder: Medical Research Council

Abstract: Pathogenicity of bacteria is closely linked to secretion machineries which provide and secure both transportation and injection of toxic molecules into target cells. Among several secretion systems existing in bacteria, the type IV secretion (T4S) systems are exceptionally adaptable to different conditions in bacteria. All known T4S systems are evolutionary related: they have similar major components and share a common requirement for proteins that utilize ATP as an energy source to drive transport of macromolecules. T4S systems are huge dynamic macromolecular complexes that comprise 12 proteins VirB1-11, and VirD4. The assembly is powered by three ATPases: VirD4, VirB11 and VirB4, which interact with each other. It has been shown that the ATPases promote substrate transfer; however, very little is known concerning the details of their interactions with a substrate, and with the core of T4S systems In this study we aim to reveal structures of the T4S system core complexed with individual ATPases VirB4, VirD4, and VirB11, and their complexes with additional components VirB3 and VirB8. That will help us to understand principles of interactions between the components and to trace the signalling pathway within the T4S system. To reveal a structural basis of the T4SS function we will combine methods of structural cryo electron microscopy, crystallography, NMR, and bioinformatics. All available atomic structures (VirB11 ATPase, VirD4 ATPase, VirB8 and VirB10 periplasmic domains, and the OM complex) will be docked into the electron density maps to identify locations of the protein components and their conformational changes upon binding. T4S system activity will be monitored by specially designed T4S system assay based on conjugation. The essential feature of our research programme is that cell microbiological approaches that form the basis of T4S infectivity studies are complementing our structural biology work to address crucial questions in the infection process.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: Developing and refining methods of analysing malaria genetic data obtained from infected human blood samples.
Funder: Medical Research Council

Abstract: The easiest method of obtaining malaria genetic data from natural transmission settings is by genotyping infected human blood samples. There are two major methodological issues in analysing these data. Firstly, we can only identify alleles as being present or absent in the blood sample so that, for example, if a blood sample contains 5 malaria clones and both wildtype and mutant alleles are detected at a locus, it is impossible to discern if that human infection contains 1,2,3 or 4 mutant clones; this precludes estimating population allele frequencies by simple counting. The second problem is that we may detect several alleles at different genetic positions in the same blood sample but we cannot always recover the individual malaria multi-locus haplotypes. These issues become extremely important when trying to assess the level of drug resistance in the malaria populations but have more general application in understanding the genetic epidemiology of malaria transmission. We have developed maximum likelihood (ML) methods to infer allele and haplotype frequencies from infected blood samples but these need to be updated to reflect different assumptions about malaria genetic epidemiology (for example, the possibility of co-transmission of genetically-related clones), to reflect differences in data structure (for example, the number of clones in a human blood sample, the MOI, may not be reported), and to reflect differing assay sensitivities and the presence of genotyping errors in the field datasets. We will address these issues by extending the ML approach and developing a parallel Bayesian approach.


Research activity codes: 8.4 RESEARCH DESIGN AND METHODOLOGIES (HEALTH SERVICES);2.5 RESEARCH DESIGN AND METHODOLOGIES (AETIOLOGY)
Health categories: INFECTION
Title: MICA: Development of a Clostridium difficile Vaccine
Funder: Medical Research Council

Abstract: Clostridium difficile (CD) is the most common cause of nosocomial antibiotic associated diarrhea in the UK. The leading vaccines currently under development are based on parenteral delivery of toxoids, which generate strong systemic Ab responses but weak mucosal responses. Moreover, protection is found only to primary infection and not to relapse. We have very good evidence that an additional spore-associated colonization factor (CotE) exists in CD and use of this protein in a vaccine formulation will produce a more robust CD vaccine. The CotE antigen will be used in vaccination approaches either in combination with existing toxoids using parenteral delivery or in combination with bacterial (B. subtilis) spores. B. subtilis spores that express the C-terminus of toxoid A (CDTA) have been shown to confer 75% protection to both primary infection and full protection to relapse in hamsters following oral immunization. Mucosal immunity (sIgA) is of paramount importance for robust protection and decolonisation. We have previously demonstrated this can be achieved using mucosal delivery of B. subtilis spores. We will co-express CotE with CDTA using B. subtilis spores and evaluate immunity and protection (primary & relapse) using mouse and hamster models of infection. The project will identify delivery routes (oral & sub-lingual) as well as live vs killed bacterial spores and we will validate a more robust vaccine that protects against hypervirulent CD strains. We will also evaluate CotE in parenteral toxoid-based vaccines and so provide two validated vaccination approaches, a parenteral vaccine that will be superior to those under current development and a mucosal vaccine that is heat-stable and potentially more patient friendly. Our strategy is to develop a new and innovative vaccine for this disease. The inclusion of a major vaccine company in this proposal could provide a route to long-term exploitation.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Clinical assessment of a novel simian adenovirus-vectored influenza vaccine designed to induce broadly protective immunity
Funder: Medical Research Council

Abstract: A vaccine against influenza that induced protective T cell responses against conserved internal antigens could provide lasting immunity against not only human seasonal influenza, but also other subtypes currently found in avian species or swine which threaten to cause a new influenza pandemic. Adenoviruses are the ideal vector for such a vaccine as they induce broad, potent and well-maintained T cell responses after a single vaccination, so could be used to confer broad immunity rapidly. They can also boost pre-existing T cell responses acquired by prior exposure to influenza that have since declined to non-protective levels in adults or the elderly. We have constructed a replication-deficient simian adenovirus-vectored vaccine expressing conserved influenza antigens, completed manufacture in preparation for clinical trials, and will conduct a dose-escalation during Q2-Q3 2012. The first clinical study proposed here will test vaccination with the new simian adenovirus-vectored vaccine and the existing MVA-vectored vaccine in a crossover design that allows comparison of the two vaccines as well as heterologous prime-boost immunisation with two different boosting intervals. A second clinical trial will test safety and immunogenicity of the adenovirus-vectored vaccine in volunteers aged over 50 years. The MVA-vectored vaccine has already been shown to provide protection against infection in an influenza Phase IIa challenge study, and comparing the two vaccines at the same time in the same population will provide a clear understanding of the relative immunogenicity of the vaccines. At the completion of the study, sufficient information will have been gathered to enable efficacy testing of the adenovirus vectored vaccine to proceed, either as a Phase IIa influenza challenge study or a Phase IIb field efficacy study, leading to Phase III studies and licensure if successful.


Research activity codes: 4.3 INFLUENCES AND IMPACT;6.1 PHARMACEUTICALS
Health categories: INFECTION
Title: NANOHAT: Development of a safer and more effective sleeping sickness drug.
Funder: Medical Research Council

Abstract: Human African trypanosomiasis (HAT or sleeping sickness) is a potentially fatal disease caused by the parasite Trypanosoma brucei sspp. The disease has two stages - a haemolymphatic stage after the bite of an infected tsetse fly, followed by a central nervous system (CNS) stage where the parasite penetrates the brain, causing death if left untreated. The blood-brain barrier (BBB) makes the CNS stage difficult to treat because it prevents 99% of all known compounds from entering the brain, including some anti-HAT drugs. Those that do enter the brain are toxic compounds in their own right and have serious side effects. Pentamidine is a less toxic blood stage drug, which our research has shown has a limited ability to cross the BBB due to its removal by efflux transporters. Furthermore transporters are considered essential in the mode of action of pentamidine against trypanosomes. The objective of this multi-disciplinary study is to use nanotechnology to both improve the delivery of pentamidine to the brain and trypanosomes, whilst reducing its side effects.


Research activity codes: 5.1 PHARMACEUTICALS
Health categories: INFECTION
Title: Modulation of innate defences in the neonatal gastrointestinal tract by colonizing neuropathogenic Escherichia coli
Funder: Medical Research Council

Abstract: Neonatal bacterial sepsis and meningitis are severe, life-threatening infections that are difficult to control by prophylaxis; further, they do not always respond to aggressive combination antibiotic therapy. One of the major causative agents, Escherichia coli K1, is acquired at birth, colonizes the immature neonatal GI tract and may translocate into the blood circulation prior to invasion of the central nervous system. Many aspects of E. coli K1 pathogenesis are unclear, but there is strong evidence that systemic infection is determined by the capacity of the neuropathogen to escape from the lumen of the gut into the circulation. Key features of the infection can be replicated in the neonatal rat. In contrast to infection-resistant animals, the physical and chemical barriers to translocation in the GI tract of infection-susceptible neonatal rats are not fully formed: protective mucin layers in the small intestine and colon are less substantial and the population of alpha-defensin-secreting Paneth cells is small. I have recently obtained evidence that colonizing E. coli K1 bacteria do not stimulate the synthesis of the alpha-defensins Defa24 and Defa-rs1 in susceptible rats but do so in non-susceptible animals. Further, the expression of Trefoil factor 2 (Tff2), a peptide associated with maturation and stability of the mucin barrier, is substantially down-regulated by E. coli K1 in susceptible neonates. I will evaluate the hypothesis that dysregulation of functional barrier development in the neonate by colonizing E. coli K1 allows translocation of the neuropathogen from the gut to the circulation and is the basis of susceptibility to systemic infection. As oral administration of trefoil factor peptides accelerates repair of GI mucosal lesions, infection-susceptible rat neonates will be dosed with recombinant Tff2 to determine if this intervention can provide protection against systemic infection and form the basis of a novel approach to prophylaxis of the disease.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION
Title: The impact of maternal infection with Mycobacterium tuberculosis on the infant response to BCG immunisation
Funder: Medical Research Council

Abstract: We propose that the poor effectiveness of BCG in sub-Saharan Africa may be due to maternal Mycobacterium tuberculosis (M.tb) infection, which is endemic in this setting. If maternal M.tb infection influences the infant response to BCG, the timing, magnitude, or quality of the BCG-specific immune response may be altered in infants of M.tb-infected women compared to those without such exposure. Such effects may be manifested as a delayed peak in response to BCG immunisation, or a lower overall recruitment of BCG-specific immune cells in the priming phase, leading to a lower set point of BCG-specific immunological memory, and as differences in the effector response profile. We will therefore conduct longitudinal studies to examine the timing, magnitude and quality of the initial response to BCG immunisation, and will follow infants to age one year in order to assess the establishment of BCG-specific immunological memory. To investigate the effects of maternal M.tb infection, we will compare these parameters between infants of mothers infected with M.tb, and infants of uninfected mothers, in Uganda. We will also explore mechanisms by which such effects may be mediated by studying differences in dendritic cell profiles, mRNA-Seq profiles and in circulating molecules - such as chemokines and cytokines - that may control the immunological milieu and hence, ultimately, effector cell function. To investigate whether maternal M.tb infection contributes significantly to the association between latitude and response to BCG immunisation we will compare infant responses between Uganda and the UK and assess whether differences are qualitatively similar to those between infants of mothers with and without M.tb infection.


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