Influenza Virus-Specific CD8+ T Cells -Longevity, Cross-Reactivity and Viral Evasion

Influenza Virus-specific CD8+ T Cells -longevity, cross-reactivity and viral evasion- Carolien van de Sandt The research described in this thesis was conducted at the ErasmusMC Viroscience department, Rotterdam, the Netherlands and was performed within the framework of the Erasmus Postgraduate School Molecular Medicine. Financial support for the printing of this thesis was provided by: MoneYou, Mabtech, Immudex (MHC Dextramers), Cirion Foundation, Greiner Bio-One, BD Biosciences, Zeiss and GR instruments. ISBN: 978-94-6295-416-8 Cover art: Carolien van de Sandt and Wesley Vroegh Other art: Carolien van de Sandt Print: Uitgeverij BOXPress || Proefschriftmaken.nl © C.E. van de Sandt, 2015 All rights reserved. No part of this thesis may be reproduced or transmitted, in any form or by any means, without the permission of the author. Influenza Virus-specific CD8+ T Cells -longevity, cross-reactivity and viral evasion- Influenzavirus-specifieke CD8+ T-cellen -levensduur, kruis-reactiviteit en virale ontwijking- Proefschrift ter verkrijging van de graad van doctor aan de Erasmus Universiteit Rotterdam op gezag van de rector magnificus Prof.dr. H.A.P. Pols en volgens besluit van het College voor Promoties. De openbare verdediging zal plaatsvinden op vrijdag 22 januari 2016 om 11:30 uur door Carolien Emma van de Sandt geboren te Enschede Promotiecommissie: Promotoren: Prof.dr. G.F. Rimmelzwaan Prof.dr. A.D.M.E. Osterhaus Overige leden: Prof.dr. R.A.M. Fouchier Prof.dr. R.W. Hendriks Prof.dr. F. Ossendorp -If you never try, you will never know- Contents Chapter 1 General introduction 9 Partially based on: Viruses, 2012 and Future Microbiology, 2015 Chapter 2 Influenza B virus-specific CD8+ T-lymphocytes strongly cross- 41 react with viruses of the opposing influenza B lineage Journal of General Virology, 2015 Chapter 3 Human cytotoxic T lymphocytes directed to seasonal influenza 61 A viruses cross-react with the newly emerging H7N9 virus Journal of Virology, 2014 Chapter 4 Human influenza A virus-specific CD8+ T cell response is 77 long-lived Journal of Infectious Disease, 2015 Chapter 5 Differential recognition of influenza A viruses by58-66 M1 87 epitope-specific CD8+ T cells is determined by extra-epitopic amino acid residues Journal of Virology, in press Chapter 6 Novel G3/DT adjuvant promotes the induction of protective T 109 cell responses after vaccination with a seasonal trivalent inacti- vated split-virion influenza vaccine Vaccine, 2014 Chapter 7 Summarizing discussion 127 Chapter 8 References 139 Chapter 9 Nederlandse samenvatting 165 Chapter 10 Dankwoord 173 Chapter 11 About the author 179 Curriculum Vitae 181 PhD Portfolio 182 Publications 185 CHAPTER 1: General introduction Partially based on: Evasion of influenza A viruses from innate and adaptive immune responses Carolien E. van de Sandt, Joost H.C.M. Kreijtz and Guus F. Rimmelzwaan Viruses, 2012, 4, 1438-1476 And Influenza B viruses: Not to be discounted Carolien E. van de Sandt, Rogier Bodewes, Guus F. Rimmelzwaan and Rory D. de Vries Future Microbiology, 2015, 10, 1447-1465 General introduction Chapter 1 Chapter Influenza A and B viruses Influenza viruses that belong to the family of Orthomyxoviridae, which consists of six genera: Isavirus, Thogoto virus and influenza virus A, B, C and D. Influenza viruses have a diameter of 80-120nm and are distinguished bases on their surface glycoproteins, membrane channel proteins and their genome size [1]. Influenza A viruses are further classified based on the antigenic properties of their surface glycoproteins: hemagglutinin (HA) and neuraminidase (NA). Thus far, 18 HA subtypes (H1-H18) and 11 NA subtypes (N1-N11) have been identified [2-5]. Although influenza B viruses are not subdivided into subtypes, two genetically and antigenically distinct lineages can be discriminated based on the HA surface glycoprotein, namely the B/Yamaga- ta lineage and the B/Victoria lineage [6]. The nomenclature of influenza viruses is based on the type / host of origin (except human) / isolation site (geographically) / strain number / year of isolation and is followed by the description of the antigenic subtype, e.g. A/Chicken/Netherlands/1/2003 (H7N7) or B/Netherlands/455/2011 (B/Victoria lineage). Figure 1 Schematic overview of an influenza A virus particle and gene segments Structure and proteins of influenza A and B viruses Influenza virus particles are enveloped and have a single stranded negative sense RNA genome that is divided over eight separate gene segments (Figure 1). The influenza A genome encodes for 17 proteins, the influenza B genome encodes for 11 proteins [2, 7] an overview of these differences in protein expression can be found in table 1. The eight RNA gene segments are encapsidated by nucleoproteins (NP), and are associated with the polymerase basic protein 1 (PB1) and PB2 and polymerase acidic protein (PA), which together form the ribonuleoprotein (RNP) complex [8, 9]. The polymerase proteins initiate replication of the viral RNA (vRNA) and transcription into messenger RNA (mRNA) [2, 8]. The viral envelope is a lipid bilayer derived from 10 General introduction Chapter 1 Chapter Table 1 Molecular differences between influenza A and B viruses 1 2 RNA Influenza A Influenza B segment Protein Length (AA) Protein Length (AA) Function Component of RNA polymerase; 1 PB2 759 PB2 770 Cap-binding Catalytical subunit of RNA polymerase; PB1 757 PB1 752 Role RNA chain elongation Pro-apoptotic activity, regulate innate PB1-F2* 873 immune responses, interact with PB1 to 2 regulate polymerase activity N-terminally truncated version PB1; interacts with polymerase complex PB1-N40* 718 subunits, balance PB1 and PB1-F2 expression, exact function unknown Component of RNA polymerase; PA 716 PA 726 Cap-snatching endonuclease subunit Modulates host gene expression, PA-X* 613 negative virulence regulator 3 N-terminally truncated version PA; PA-N155* 568 function unknown N-terminally truncated version PA; PA-N182* 535 function unknown Surface glycoprotein; receptor binding 4 HA 550 HA 584 and membrane fusion; antigenic determinant Encapsidation of viral genomic RNA; 5 NP 498 NP 560 RNA synthesis, nuclear import vRNA Surface glycoprotein; neuraminidase NA 454 NA 486 activity, release novel virus particles 6 after budding; antigenic determinant NB* 100 Ion channel activity; function unknown M1§ 252 M1 248 Role viral assembly, budding Ion channel activity; essential for M2† 97 BM2Δ 109 7 uncoating, role virus budding M2 isoform with alternative M42†3 99 ectodomain, ion channel activity; functionally complement/replace M2 Regulation viral RNA polymerase com- NS1§ 230 NS1§ 281 plex, interfere with antiviral state cell † NS2/ Role nuclear export RNP, regulate NS2/NEP 121 † 122 8 NEP transcription and replication NS1 isoform with an internal deletion; function unknown, possible NS3†3 174 role host adaptation and overcoming the species barrier 1 On basis of A/PuertoRico/8/1934; 2 On bases of B/Lee/1940; 3 Depending on the isolate * Alternate ORF; Δ Additional ORF, § Unspliced mRNA; † Spliced mRNA Adapted from [2, 7], additional information from [10-13]. 11 General introduction Chapter 1 Chapter the host membrane and its inner surface is lined by matrix protein 1 (M1) which has an important role in viral assembly and budding [13-15]. Two major surface glycoprotein, HA and NA, are located on the outer surface of the viral envelope. HA protein is initially synthesized as a polypeptide precursor (HA0) which requires proteolytic cleavage by host cell proteases into HA1 and HA2 in order to become functionally active [16]. HA1 mainly forms the globular head region of the HA protein and encompasses the receptor-binding pocket, needed for attachment of the virus particle to the host cell [17, 18]. The HA2 represents the trans membrane (envelope) stem region of the HA protein and is essential for pH-dependent fusion of the viral envelope with the endosomal vesicle [19-21]. NA on the other hand has an important role in viral release from infected cells as it acts as a receptor-destroying enzyme that cleaves host cell sialic acid residues [22]. Matrix protein 2 (M2) is the result of alternative splicing of the matrix mRNA in case of influenza A viruses, whereas the M gene segment of influenza B viruses encompasses an additional open reading frame (ORF) directly subsequent of the M1 ORF that encodes for the BM2 protein [2, 7]. Both M2 proteins function as a transmembrane (envelope) ion channel [10, 23]. Although the M2 proteins of influenza A and B viruses are comparable in their function they differ in their respective size. Also the influenza A virus M2 channel pore is lined with hydrophobic amino acids while influenza B virus BM2 channel pores are lined with polar serines. As a result, only influenza A viruses are inhibited by the antiviral drug amantadine [10]. In addition, the M2 protein of influenza A viruses was described to have a role in virus budding [13]. A minority of the influenza A viruses express an additional ion channel protein called M42 which also results from alternative splicing of the matrix mRNA. The M42 protein represents an isoform of the M2 protein that encompasses an alternative ectodomain and was shown to functionally complement or replace the M2 protein and was demonstrated to support viral replication [24]. The expression of the highly conserved NB protein, encoded by an additional ORF in the NA gene segment, is unique for influenza B viruses. Since this protein shows ion channel activity it was long thought that the NB protein was a functional analogue of the influenza A virus M2 ion channel protein (reviewed in [11]). This theory was challenged by a study that demonstrated that NB ion channel activity was not essential for influenza B virus replication in vitro [25]. The true function of the NB protein remains to be established [11]. Besides the expression of structural proteins, several nonstructural proteins are expressed.

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