Propagation of respiratory viruses in human airway epithelia reveals persistent virus- specific signatures Manel Essaidi-Laziosi, PhD, Francisco Brito,

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Propagation of respiratory viruses in human airway epithelia reveals persistent virus- specific signatures Manel Essaidi-Laziosi, PhD, Francisco Brito, MSc, Sacha Benaoudia, MSc, Léna Royston, MD, Valeria Cagno, PhD, Mélanie Fernandes-Rocha, Isabelle Piuz, Evgeny Zdobnov, PhD, Song Huang, PhD, Samuel Constant, PhD, Marc-Olivier Boldi, PhD, Laurent Kaiser, MD, Caroline Tapparel, PhD Journal of Allergy and Clinical Immunology Volume 141, Issue 6, Pages 2074-2084 (June 2018) DOI: 10.1016/j.jaci.2017.07.018 Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 1 Virus production at the apical (A) and basal (B) sides of air-liquid interface culture of reconstituted human airway epithelia. Viral RNA loads measured by using qPCR from infected samples collected at the apical (Fig 1, A) or basal (Fig 1, B) side of tissues infected with 9 different respiratory viruses (n ≥ 4) are shown. Each tissue was inoculated apically with 106 RNA copies of the indicated virus and washed 3 times after 4 hours. Samples were then collected from the apical or basal face at the indicated time point. Input, Viral RNA load present in the inoculum for each viral stock; p.i., post-inoculation; Residual, residual bound virus after 3 washes. Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 2 Immunofluorescence of epithelia infected with the indicated respiratory virus. A, Three-dimensional view of noninfected and infected tissues, with ciliated cells stained in green, viruses in red, and cell nuclei in blue. For all viruses, immunofluorescence was performed at day 5 after infection, whereas for H3N2 and EV-D68, immunofluorescence was also done at day 2, as indicated. B, Two-dimensional view of tissues infected with H3N2 at day 5 after infection (virus stained in green, mucus cells in red [Muc5A], basal cells in red [P63], and cell nuclei in blue), with magnification insets of selected regions (*) in each panel. DAPI, 4′-6-Diamidino-2-phenylindole dihydrochloride. Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 3 Effect of infections on epithelia. Viral toxicities calculated from the amount of LDH released by damaged cells in the basal medium (n = 8; A) and TEER (n ≥ 2; B) were measured at days 2 and 5 post infection (p.i.). The 48-hour time point represents LDH accumulated during 48 hours; for later time points, the medium was replaced every day, and data correspond to LDH secretions within the preceding 24 hours. Dotted lines in Fig 3, B, correspond to the established threshold of tissue integrity. *P < .05, **P < .01, and ***P < .001. Asterisks in light gray show statistical significance relative to noninfected tissue, whereas black asterisks show statistical significance compared with all other respiratory viruses at each time point. Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 4 Effect of respiratory viruses on cytokine production. Chemokine (A) and cytokine (B) levels were measured in basal medium 96 hours after infection with the indicated respiratory virus (n = 4). Data correspond to cytokine secretions within the preceding 24 hours. *P < .05, **P < .01, and ***P < .001. Asterisks in light gray show statistical significance relative to noninfected tissue, whereas black asterisks show statistical significance compared with HCoV-OC43. Differences between other viruses are shown with bars. Additional cytokines (IL-33, TGF-β, IL-25, IFN-β, and thymic stromal lymphopoietin [TSLP]) were also tested but either were not significantly induced by viral infections or were not detected in basal medium (Fig E1). Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 5 Effect of respiratory viruses on MCC. Displacement velocity of polystyrene microbeads applied at the apical side of the tissue at 5 dpi with indicated virus is shown (n ≥ 5). ***P < .001 (vs noninfected). Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 6 Virus production at the apical site of air-liquid interface cultures of reconstituted human airway epithelia over a prolonged time period. Viral RNA loads measured by using qPCR from infected samples collected at the apical side of tissues infected with 9 different respiratory viruses are shown. Each tissue was inoculated with 106 RNA copies of the indicated virus, and tissues were washed 3 times after 4 hours; samples were then collected from the apical surface at the indicated time point (n = 4). Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig 7 Comparison between the top 30 most significantly enriched biological processes in tissues infected with RV-C15 and RV-B48 at the indicated time. Circle size represents the number of differentially expressed genes found on that pathway, whereas the color represents the adjusted P value. The top 100 genes showing significant changes in each condition is available in Table E2, as well as the enrichment analysis for gene ontology biological processes (see Table E3) and the reactome pathway (see Table E4). SRP, Signal recognition particle. Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E1 Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E2 Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E3 Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E4 Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions

Fig E5 Journal of Allergy and Clinical Immunology 2018 141, 2074-2084DOI: (10.1016/j.jaci.2017.07.018) Copyright © 2017 American Academy of Allergy, Asthma & Immunology Terms and Conditions