The Network aims to promote multi-disciplinary approaches to address challenging vaccine-related questions. This page contains a curated list of publications that highlight high-impact and collaborative approaches.

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  • Journal article
    Kirk PDW, Huvet M, Melamed A, Maertens GNE, Bangham CRMet al., 2016,

    Retroviruses integrate into a shared, non-palindromic DNA motif

    , Nature Microbiology, Vol: 2, Pages: 1-6, ISSN: 2058-5276

    Many DNA-binding factors, such as transcription factors, form oligomeric complexes with structural symmetry that bind to palindromic DNA sequences1. Palindromic consensus nucleotide sequences are also found at the genomic integration sites of retroviruses2,​3,​4,​5,​6 and other transposable elements7,​8,​9, and it has been suggested that this palindromic consensus arises as a consequence of the structural symmetry in the integrase complex2,3. However, we show here that the palindromic consensus sequence is not present in individual integration sites of human T-cell lymphotropic virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1), but arises in the population average as a consequence of the existence of a non-palindromic nucleotide motif that occurs in approximately equal proportions on the plus strand and the minus strand of the host genome. We develop a generally applicable algorithm to sort the individual integration site sequences into plus-strand and minus-strand subpopulations, and use this to identify the integration site nucleotide motifs of five retroviruses of different genera: HTLV-1, HIV-1, murine leukaemia virus (MLV), avian sarcoma leucosis virus (ASLV) and prototype foamy virus (PFV). The results reveal a non-palindromic motif that is shared between these retroviruses.

  • Journal article
    Bayer Santos E, Durkin CH, Rigano L, Kupz A, Alix E, Cerny O, Jennings E, Liu M, Ryan A, Lapaque N, Kaufmann S, Holden D, Robb Cet al., 2016,

    The Salmonella effector SteD mediates MARCH8-1 dependent ubiquitination of MHC II molecules and inhibits T cell activation

    , Cell Host & Microbe, Vol: 20, Pages: 584-595, ISSN: 1934-6069

    The SPI-2 type III secretion system (T3SS) of intracellular Salmonella enterica translocates effector proteins into mammalian cells. Infection of antigen-presenting cells results in SPI-2 T3SS-dependent ubiquitination and reduction of surface-localized mature MHC class II (mMHCII). We identify the effector SteD as required and sufficient for this process. In Mel Juso cells, SteD localized to the Golgi network and vesicles containing the E3 ubiquitin ligase MARCH8 and mMHCII. SteD caused MARCH8-dependent ubiquitination and depletion of surface mMHCII. One of two transmembrane domains and the C-terminal cytoplasmic region of SteD mediated binding to MARCH8 and mMHCII, respectively. Infection of dendritic cells resulted in SteD-dependent depletion of surface MHCII, the co-stimulatory molecule B7.2, and suppression of T cell activation. SteD also accounted for suppression of T cell activation during Salmonella infection of mice. We propose that SteD is an adaptor, forcing inappropriate ubiquitination of mMHCII by MARCH8 and thereby suppressing T cell activation.

  • Journal article
    Ale A, Crepin VF, Collins, Constantinou N, Habibzay, Babtie AC, Frankel G, Stumpf MPet al., 2016,

    Model of host-pathogen Interaction dynamics links In vivo optical imaging and immune responses

    , Infection and Immunity, Vol: 85, ISSN: 1098-5522

    Tracking disease progression in vivo is essential for the development of treatments against bacterial infection. Optical imaging has become a central tool for in vivo tracking of bacterial population development and therapeutic response. For a precise understanding of in vivo imaging results in terms of disease mechanisms derived from detailed postmortem observations, however, a link between the two is needed. Here, we develop a model that provides that link for the investigation of Citrobacter rodentium infection, a mouse model for enteropathogenic Escherichia coli (EPEC). We connect in vivo disease progression of C57BL/6 mice infected with bioluminescent bacteria, imaged using optical tomography and X-ray computed tomography, to postmortem measurements of colonic immune cell infiltration. We use the model to explore changes to both the host immune response and the bacteria and to evaluate the response to antibiotic treatment. The developed model serves as a novel tool for the identification and development of new therapeutic interventions.

  • Journal article
    Thurston T, Matthews S, Jennings E, Alix E, Shao F, Shenoy A, Birrell M, Holden Det al., 2016,

    Growth inhibition of cytosolic Salmonella by caspase-1 and caspase-11 precedes host cell death

    , Nature Communications, Vol: 7, ISSN: 2041-1723

    Sensing bacterial products in the cytosol of mammalian cells by NOD-like receptors leads to the activation of caspase-1 inflammasomes, and the production of the pro-inflammatory cytokines interleukin (IL)-18 and IL-1β. In addition, mouse caspase-11 (represented in humans by its orthologs, caspase-4 and caspase-5) detects cytosolic bacterial LPS directly. Activation of caspase-1 and caspase-11 initiates pyroptotic host cell death that releases potentially harmful bacteria from the nutrient-rich host cell cytosol into the extracellular environment. Here we use single cell analysis and time-lapse microscopy to identify a subpopulation of host cells, in which growth of cytosolic Salmonella Typhimurium is inhibited independently or prior to the onset of cell death. The enzymatic activities of caspase-1 and caspase-11 are required for growth inhibition in different cell types. Our results reveal that these proteases have important functions beyond the direct induction of pyroptosis and proinflammatory cytokine secretion in the control of growth and elimination of cytosolic bacteria.

  • Journal article
    Pollard DJ, Young JC, Covarelli V, Herrera-León S, Connor TR, Fookes M, Walker D, Echeita A, Thomson NR, Berger CN, Frankel Get al., 2016,

    The type III secretion system effector SeoC of Salmonella enterica subspecies salamae and arizonae ADP-ribosylates Src and inhibits opsono-phagocytosis

    , Infection and Immunity, Vol: 84, Pages: 3618-3628, ISSN: 1098-5522

    Salmonella spp. utilize type III secretion systems (T3SS) to translocate effectors into the cytosol of mammalian host cells, subverting cell signaling and facilitating the onset of gastroenteritis. In this study we compared a draft genome assembly of S. enterica subsp. salamae strain 3588/07 (S. salamae) against the genomes of S. enterica subsp. enterica serovar Typhimurium strain LT2 and S. bongori strain 12419. S. salamae encode the Salmonella pathogenicity island (SPI)-1; SPI-2 and the locus of enterocyte effacement (LEE) T3SSs. Though several key S. Typhimurium effector genes are missing (e.g. avrA, sopB and sseL), S. salamae invades HeLa cells and contain homologues of S. bongori sboK and sboC, which we named seoC. SboC and SeoC are homologues of EspJ from enteropathogenic and enterohaemorrhagic E. coli (EPEC and EHEC), which inhibits Src kinase-dependent phagocytosis by ADP-ribosylation. By screening 73 clinical and environmental Salmonella isolates we identified EspJ homologues in S. bongori, S. salamae and S. enterica subsp. arizonae (S. arizonae). The β-lactamase TEM-1 reporter system showed that SeoC is translocated by the SPI-1 T3SS. All the Salmonella SeoC/SboC homologues ADP-ribosylate Src E310 in vitro. Ectopic expression of SeoC/SboC inhibited phagocytosis of IgG-opsonized bead into Cos-7 cells stably expressing GFP-FcγRIIa. Concurrently, S. salamae infection of J774.A1 macrophages inhibited phagocytosis of beads, in a seoC dependent manner. These results show that S. bongori, S. salamae and S. arizonae share features of the infection strategy of extracellular pathogens EPEC and EHEC and sheds light on the complexities of the T3SS effector repertoires of Enterobacteriaceae.

  • Journal article
    Crepin VF, Collins JW, Habibzay M, Frankel Get al., 2016,

    Citrobacter rodentium mouse model of bacterial infection.

    , Nature Protocols, Vol: 11, Pages: 1851-1876, ISSN: 1754-2189

    Infection of mice with Citrobacter rodentium is a robust model to study bacterial pathogenesis, mucosal immunology, the health benefits of probiotics and the role of the microbiota during infection. C. rodentium was first isolated by Barthold from an outbreak of mouse diarrhea in Yale University in 1972 and was 'rediscovered' by Falkow and Schauer in 1993. Since then the use of the model has proliferated, and it is now the gold standard for studying virulence of the closely related human pathogens enteropathogenic and enterohemorrhagic Escherichia coli (EPEC and EHEC, respectively). Here we provide a detailed protocol for various applications of the model, including bacterial growth, site-directed mutagenesis, mouse inoculation (from cultured cells and after cohabitation), monitoring of bacterial colonization, tissue extraction and analysis, immune responses, probiotic treatment and microbiota analysis. The main protocol, from mouse infection to clearance and analysis of tissues and host responses, takes ∼5 weeks to complete.

  • Journal article
    Furniss RCD, Slater S, Frankel G, Clements Aet al., 2016,

    Enterohaemorrhagic E. coli modulates an ARF6:Rab35 signalling axis to prevent recycling endosome maturation during infection

    , Journal of Molecular Biology, Vol: 428, Pages: 3399-3407, ISSN: 1089-8638

    Enteropathogenic and enterohaemorrhagic Escherichia coli (EPEC/EHEC) manipulate a plethora of host cell processes to establish infection of the gut mucosa. This manipulation is achieved via the injection of bacterial effector proteins into host cells using a Type III secretion system. We have previously reported that the conserved EHEC and EPEC effector EspG disrupts recycling endosome function, reducing cell surface levels of host receptors through accumulation of recycling cargo within the host cell. Here we report that EspG interacts specifically with the small GTPases ARF6 and Rab35 during infection. These interactions target EspG to endosomes and prevent Rab35-mediated recycling of cargo to the host cell surface. Furthermore, we show that EspG has no effect on Rab35-mediated uncoating of newly formed endosomes, and instead leads to the formation of enlarged EspG/TfR/Rab11 positive, EEA1/Clathrin negative stalled recycling structures. Thus, this paper provides a molecular framework to explain how EspG disrupts recycling whilst also reporting the first known simultaneous targeting of ARF6 and Rab35 by a bacterial pathogen.

  • Journal article
    Saso A, Kampmann B, 2016,

    Vaccination against respiratory syncytial virus in pregnancy: a suitable tool to combat global infant morbidity and mortality?

    , Lancet Infectious Diseases, Vol: 16, Pages: e153-e163, ISSN: 1473-3099

    Respiratory syncytial virus (RSV) is the most important viral cause of pneumonia in early childhood (ie, younger than 2 years), responsible for high infant morbidity and mortality worldwide. It is widely accepted that an effective vaccine against RSV would have a major impact on child health globally. Despite the setbacks of the clinical trials in the 1960s, there has been a recent and significant revival of interest in vaccines against RSV, with several promising candidates undergoing evaluation. In this Review, we describe the epidemiological and immunological background to RSV infection and subsequently focus on the promising pipeline of RSV vaccine development. We discuss the potential for implementation of a safe and immunogenic RSV vaccine within the context of global health and with regards to a range of strategies, including vaccination of women during pregnancy, which is likely to emerge as a beneficial and feasible public health tool. This approach would provide interim protection to vulnerable, RSV-naive infants and other high risk groups, in which the burden of admission to hospital and death is greatest. Extending research and implementation from resource-rich to resource-poor settings is required to enhance our understanding of RSV immunity and inform vaccine development and delivery strategies for all settings. We summarise key outstanding issues for researchers and policy makers to understand the interplay of biological and non-biological factors affecting design and distribution of a successful RSV vaccine globally.

  • Journal article
    Clarke E, Saidu Y, Adetifa JU, Adigweme I, Hydara MB, Bashorun AO, Moneke-Anyanwoke N, Umesi A, Roberts E, Cham PM, Okoye ME, Brown KE, Niedrig M, Chowdhury PR, Clemens R, Bandyopadhyay AS, Mueller J, Jeffries DJ, Kampmann Bet al., 2016,

    Safety and immunogenicity of inactivated poliovirus vaccine when given with measles–rubella combined vaccine and yellow fever vaccine and when given via different administration routes: a phase 4, randomised, non-inferiority trial in The Gambia

    , Lancet Global Health, Vol: 4, Pages: e534-e547, ISSN: 2214-109X

    BACKGROUND: The introduction of the inactivated poliovirus vaccine (IPV) represents a crucial step in the polio eradication endgame. This trial examined the safety and immunogenicity of IPV given alongside the measles-rubella and yellow fever vaccines at 9 months and when given as a full or fractional dose using needle and syringe or disposable-syringe jet injector. METHODS: We did a phase 4, randomised, non-inferiority trial at three periurban government clinics in west Gambia. Infants aged 9-10 months who had already received oral poliovirus vaccine were randomly assigned to receive the IPV, measles-rubella, and yellow fever vaccines, singularly or in combination. Separately, IPV was given as a full intramuscular or fractional intradermal dose by needle and syringe or disposable-syringe jet injector at a second visit. The primary outcomes were seroprevalence rates for poliovirus 4-6 weeks post-vaccination and the rate of seroconversion between baseline and post-vaccination serum samples for measles, rubella, and yellow fever; and the post-vaccination antibody titres generated against each component of the vaccines. We did a per-protocol analysis with a non-inferiority margin of 10% for poliovirus seroprevalence and measles, rubella, and yellow fever seroconversion, and (1/3) log2 for log2-transformed antibody titres. This trial is registered with, number NCT01847872. FINDINGS: Between July 10, 2013, and May 8, 2014, we assessed 1662 infants for eligibility, of whom 1504 were enrolled into one of seven groups for vaccine interference and one of four groups for fractional dosing and alternative route of administration. The rubella and yellow fever antibody titres were reduced by co-administration but the seroconversion rates achieved non-inferiority in both cases (rubella, -4·5% [95% CI -9·5 to -0·1]; yellow fever, 1·2% [-2·9 to 5·5]). Measles and poliovirus responses were unaffected (measles, 6·8%

  • Journal article
    Satou Y, Miyazato P, Ishihara Y, Yaguchi H, Melamed A, Miura M, Fukuda A, Nosaka K, Watanabe T, Rowan A, Nakao M, Bangham Cet al., 2016,

    The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome

    , Proceedings of the National Academy of Sciences of the United States of America, Vol: 113, Pages: 3054-3059, ISSN: 0027-8424

    Human T-lymphotropic virus type 1 (HTLV-1) is a retrovirus thatcauses malignant and inflammatory diseases in 10% of infectedpeople. A typical host has between 104and 105clones of HTLV-1-infected T lymphocytes, each clone distinguished by the genomicintegration site of the single-copy HTLV-1 provirus. TheHBZgeneis constitutively expressed from the minus strand of the provirus,whereas plus-strand expression, required for viral propagation touninfected cells, is suppressed or intermittentin vivo, allowingescape from host immune surveillance. It remains unknown whatregulates this pattern of proviral transcription and latency. Herewe show that CTCF, a key regulator of chromatin structure andfunction, binds to the provirus at a sharp border in epigeneticmodifications in the pX region of the HTLV-1 provirus, in T cellsnaturally infected with HTLV-1. CTCF is a zinc-finger protein thatbinds to an insulator region in genomic DNA and plays a funda-mental role in controlling higher-order chromatin structure andgene expression in vertebrate cells. We show that CTCF boundto HTLV-1 acts as an enhancer blocker, regulates HTLV-1 mRNAsplicing, and forms long-distance interactions with flanking hostchromatin. CTCF binding sites have been propagated through-out the genome by transposons in certain primate lineages, butCTCF binding has not previously been described in present-dayexogenous retroviruses. The presence of an ectopic CTCF bindingsite introduced by the retrovirus in tens of thousands of genomiclocations has the potential to cause widespread abnormalities inhost cell chromatin structure and gene expression.

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