Microbiology & Immunology - Theses
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ItemInvestigating the ability of RIG-I agonists to provide protection in mouse and ferret models of respiratory virus infection( 2021)Respiratory infections caused by influenza A virus (IAV) or respiratory syncytial virus (RSV) lead to substantial morbidity and mortality. Treatment options are limited and there is urgent need for the development of efficient therapeutic and prophylactic treatments. Pattern recognition receptors (PRRs) such as the cytoplasmic helicase retinoic-acid-inducible gene I (RIG-I) are part of the innate immune system. RIG-I can be activated by recognition of viral nucleic acids, leading to downstream activation of interferon-stimulated genes (ISGs) and restriction of viral replication. We have used synthetic RNA oligonucleotides to stimulate RIG-I to inhibit replication of respiratory viruses using in vitro and in vivo models of infection. Our in vitro approaches used airway cell lines from humans, mice and ferrets and investigated the effects of RIG-I agonist pre-treatment on subsequent infection with either IAV or RSV. Prophylactic RIG-I agonist treatment induced multiple ISGs and inhibited infection and growth of respiratory viruses in cell lines from each of the different species. In vivo, we utilised mouse and ferret models to study the antiviral potential of RIG-I agonists against IAV and RSV. In mice, we compared animals which do or do not express a functional Mx1 protein and found that a single prophylactic treatment with RIG-I agonist via the intravenous route resulted in ISG induction in the lungs and this correlated with reduced IAV replication. Of interest, these effects were particularly potent and long-lasting in mice expressing a functional Mx1 confirming an important role of Mx1 for RIG-I agonist-induced protection against IAV. In a mouse model of RSV, we found that a single prophylactic treatment with RIG-I agonist resulted in reduced replication of virus in the lung, as observed using bioluminescence imaging of luciferase-labelled RSV as well as plaque assay for infectious virus. Thus, our studies in mouse models indicate that a single pre-treatment with RIG-I agonists resulted in potent inhibition of two very different respiratory viruses. In ferrets, after establishing assays to monitor ISG induction in the blood and in airway tissues, we confirmed that a single intravenous injection of RIG-I agonist induced ISG induction in both peripheral blood mononuclear cells (PBMCs) and the lungs. Moreover, a single treatment prior to infection also resulted in reduced replication of both IAV and RSV in ferret lungs, although this treatment had only negligible effects on virus replication in the nasal tissues. A single treatment to animals with an established IAV infection also resulted in reduced virus titres in the lungs, suggesting its potential as a therapeutic antiviral agent. Myxoma (Mx) proteins are ISGs with potent antiviral effects against IAV. While human and mouse Mx proteins have been studied in detail, ferret Mx proteins have not been characterised. Therefore, we generated different experimental approaches to assess the induction of three endogenous ferret Mx (two splice variants of Mx1 as well as Mx2) in a ferret cell line, as well as in vitro overexpression systems to assess the cellular localisation and antiviral functions of each ferret Mx. Our findings indicate that each ferret Mx localises to the cytoplasm and that particular proteins exhibit antiviral functions against IAV, but not RSV. However, further studies are required to clearly define the antiviral activity of ferret Mx, since our preliminary results indicate that ferret Mx proteins display different antiviral activity following overexpression in human or in ferret cells. Together, studies described in this thesis demonstrate the potential of RIG-I agonists as antiviral treatments against diverse respiratory viruses both in vitro and in vivo and represent an important step towards the development of novel antiviral treatments in humans.
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ItemDynamics and control of T follicular helper cell-dependent and -independent responses to influenza virus infection and immunization( 2020)Seasonal influenza viruses circulate globally and cause recurrent disease in humans. Worldwide, annual epidemics are estimated to cause 1 billion infections, with 3 to 5 million cases of severe illness and 290,000 to 650,000 deaths. Influenza viruses undergo rapid antigenic evolution allowing mutant viruses to escape from host immune responses acquired to parental virus strains. Current seasonal influenza vaccines are effective when vaccine strains are matched with circulating strains. However, there is little to no cross-protection against antigenic variants, emerging pandemic or zoonotic outbreak strains. There is therefore tremendous interest in the development of novel universal vaccines which induce potent, broad and durable antibody responses against most or all influenza viruses. T follicular helper cells are crucial for the generation of high affinity antibodies and the maintenance of B cell memory. But relatively little is known about Tfh in important animal models of influenza. Insights gained from the study of Tfh cell responses will facilitate the design of next generation vaccines against influenza. In this thesis, we first developed an activation-induced marker assay for the identification of antigen specific Tfh cells in mice after influenza virus infection and hemagglutinin protein immunization. We showed that the AIM assay was robust and sensitive for the detection of murine Ag specific Tfh cells by quantifying the upregulation of surface CD154 or CD25 OX40 following either HA peptide pool or whole HA protein stimulation for 18 hours. This murine AIM assay makes it feasible to delineate Ag specific Tfh cells in mice without the need for transgenic mice or MHC II tetramers restricted to specific epitopes. Importantly, Ag specific Tfh cells can be sorted for TCR sequencing or adoptive transfer since AIM assay is a live cell assay. Ferrets are a well established animal model for influenza research and are widely used to investigate the pathogenesis and transmission of influenza viruses and preclinically evaluate the efficacy of influenza vaccines. However, little is known about ferret Tfh cells due to the lack of ferret reactive immunological reagents. To enable the study of ferret Tfh cells, we screened commercial markers of Tfh cells, antiBCL6, CXCR5 and PD1 antibodies, and found two anti-BCL6 antibodies had cross reactivity with lymph node cells from influenza infected ferrets. We also developed two murine monoclonal antibodies against ferret CXCR5 and PD1 using a single B cell PCR based method. We were able to clearly identify Tfh cells in LNs from influenza infected ferrets using these antibodies. The development of ferret Tfh marker antibodies and the identification of ferret Tfh cells will facilitate the assessment of vaccine induced Tfh responses in the ferret model and the design of novel vaccines against influenza infection. HA stem is an attractive target for the development of universal influenza vaccines due to its relatively conserved feature. However, HA stem is poorly immunogenic when administered alone in a soluble form. Immunogen multimerization can enhance the immunogenicity of poor immunogens even in the absence of the help of T cells, which serves as an alternative pathway to improve the immunogenicity of stem without the dependence on Tfh responses. We showed that chemically coupling a peptide derived from the head domain of PR8 HA, P35, with the weakly immunogenic HA stem protein caused aggregation of the HA stem which significantly enhanced stem specific B cell responses independent of Tfh cell help in mice. P35 conjugation represents a new pathway to boost stem specific antibody responses without introducing exotic carrier proteins which will elicit anti carrier responses. Collectively, we investigated Tfh responses to influenza virus infection and immunization in mice and ferrets and explored the effects of immunogen multimerization on humoral immunity in the context limiting Tfh responses to HA stem. An increased understanding of Tfh dependent and independent mechanisms to enhance humoral immune responses will assist developing novel vaccines to prevent the infection of influenza and other viruses.
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ItemAdvancing the ferret as an immunological model to study B-cell responses( 2020)Introduction Influenza is a clinically significant disease, causing 24000-62000 deaths alone in the United States during the 2019-2020 season. While annual vaccines are available, variable efficacies have been reported and annual updates are required due to antigenic drift. Ferrets are a useful model for studying human respiratory viruses and have been widely used to evaluate vaccines and transmission of influenza. Sera from ferrets infected with different influenza strains are used in HI assays as part of strain determination of seasonal influenza vaccines. A key limitation of the ferret model is the paucity of immunological reagents to characterise immune responses and a lack of knowledge regarding the ferret immune system. This PhD thesis aims to advance the ferret as an immunological model to study human respiratory viruses by developing methods and reagents which will enable in-depth interrogation of ferret B-cell responses. Methods While a draft copy of the ferret genome is available, immunoglobulin sequence information is not well-annotated. Hence, we first annotated the ferret genome with immunoglobulin variable, diversity, joining and constant chain genes by inferring homology using human and canine orthologs (Chapter 3). Novel PCR primers targeting 5’- leader, 3’- joining and 3’- constant chain immunoglobulin genes were derived, enabling the recovery of functional, paired heavy and light chain transcript sequences from single sorted ferret B-cells. Ferret immunoglobulin constant sequences were validated by RNA-seq, which enabled the development of ferret IgG expression plasmids. Using this technique, HA-specific B-cell responses were characterised for the first time in ferrets at the transcript level (Chapter 4). Candidate ferret mAbs were derived from the recovered sequences, expressed and screened for HA binding specificity and in-vitro influenza virus neutralisation activity. We noted poor recovery of ferret HA specific mAbs and subsequently sought to improve flow cytometric panels available for ferrets. We established a methodology using previously developed murine single-cell BCR sequencing methods to recover murine anti-ferret mAbs (Chapter 5). First, coding sequences of ferret B and NK-cell reagents were identified on the ferret genome and validated by sequence and structural comparisons with other mammalian homologs. C57BL/6 mice were subsequently immunised with these antigens and candidate mAbs were recovered for examination by ELISA and flow cytometry. Results Ferret variable, diversity, joining and constant chain coding genes were identified on the draft copy of the ferret genome and show good sequence similarity to human and canine variants. Our novel ferret immunoglobulin specific PCR primers enabled the recovery and characterisation of germline ferret immunoglobulin genes from single sorted ferret B-cells. RNA-seq validation of ferret immunoglobulin constant chain genes subsequently enabled the construction of ferret IgG/IgL expression plasmids. This facilitated the expression of chimeric human-ferret CR9114 IgG antibody retaining HA binding specificity. Subsequently, using previously developed trimeric HA probes, clonally expanded sequences were recovered from single sorted HA-specific B-cells derived from infected ferrets. Screening of candidate ferret monoclonal antibodies enabled the identification of two novel antibodies, belonging to the same clonal family showing HA binding specificities. Further examination by HAI and microneutralization assays revealed the ability of the mAbs to neutralise influenza virus in vitro. Viral escape mapping revealed binding epitope to previously reported Sa site of the HA head domain, showing proof of concept for mapping HA epitopes using these recombinant ferret mAbs. We next attempted to improve flow cytometric panels for ferrets which will enhance recovery of ferret immunoglobulin transcripts. As there are currently no mAbs targeting B and NK-cell markers in ferrets, we identified key markers for murine mAb development including CD19, IgD, CD138, NKp46 and LAMP-1. We identified candidate anti-ferret CD19 and IgD mAbs which bound to cognate recombinant antigens by ELISA, validating this method for generating anti-ferret mAbs to improve panels for flow cytometry and confocal microscopy. As the mAbs in this thesis lacked the capacity to resolve ferret cell populations by flow cytometry, we identified and discussed key steps in the process which will inform future use of this approach to develop anti-ferret mAb reagents. Conclusion The body of work presented in this thesis forms the proof of concept of studying antigen-specific B-cell responses at the mAb level in ferrets. Future improvements in tools developed in this thesis and future development of reagents will enable detailed interrogation of the ferret immune system.