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Differential pulmonary transcriptomic profiles in murine lungs infected with low and highly virulent influenza H3N2 viruses reveal dysregulation of TREM1 signaling, cytokines, and chemokines

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Abstract

Investigating the relationships between critical influenza viral mutations contributing to increased virulence and host expression factors will shed light on the process of severe pathogenesis from the systems biology perspective. We previously generated a mouse-adapted, highly virulent influenza (HVI) virus through serial lung-to-lung passaging of a human influenza H3N2 virus strain that causes low virulent influenza (LVI) in murine lungs. This HVI virus is characterized by enhanced replication kinetics, severe lung injury, and systemic spread to major organs. Our gene microarray investigations compared the host transcriptomic responses of murine lungs to LVI virus and its HVI descendant at 12, 48, and 96 h following infection. More intense expression of genes associated with cytokine activity, type 1 interferon response, and apoptosis was evident in HVI at all time-points. We highlighted dysregulation of the TREM1 signaling pathway (an amplifier of cytokine production) that is likely to be upregulated in infiltrating neutrophils in HVI-infected lungs. The cytokine gene expression changes were corroborated by elevated levels of multiple cytokine and chemokine proteins in the bronchoalveolar lavage fluid of infected mice, especially at 12 h post-infection. Concomitantly, the downregulation of genes that mediate proliferative, developmental, and metabolic processes likely contributed to the lethality of HVI as well as lack of lung repair. Overall, our comparative transcriptomic study provided insights into key host factors that influence the dynamics, pathogenesis, and outcome of severe influenza.

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References

  • Akeson AL, Greenberg JM, Cameron JE, Thompson FY, Brooks SK, Wiginton D, Whitsett JA (2003) Temporal and spatial regulation of VEGF-A controls vascular patterning in the embryonic lung. Dev Biol 264:443–455

    Article  PubMed  CAS  Google Scholar 

  • Artavanis-Tsakonas S, Rand MD, Lake RJ (1999) Notch signaling: cell fate control and signal integration in development. Science 284:770–776

    Article  PubMed  CAS  Google Scholar 

  • Baskin CR, Bielefeldt-Ohmann H, Tumpey TM, Sabourin PJ, Long JP, García-Sastre A, Tolnay AE, Albrecht R, Pyles JA, Olson PH, Aicher LD, Rosenzweig ER, Murali-Krishna K, Clark EA, Kotur MS, Fornek JL, Proll S, Palermo RE, Sabourin CL, Katze MG (2009) Early and sustained innate immune response defines pathology and death in nonhuman primates infected by highly pathogenic influenza virus. Proc Natl Acad Sci USA 106:3455–3460

    Article  PubMed  CAS  Google Scholar 

  • Bean WJ, Schell M, Katz J, Kawaoka Y, Naeve C, Gorman O, Webster RG (1992) Evolution of the H3 influenza virus hemagglutinin from human and nonhuman hosts. J Virol 66:1129–1138

    PubMed  CAS  Google Scholar 

  • Bermejo-Martin JF, Ortiz de Lejarazu R, Pumarola T, Rello J, Almansa R, Ramírez P, Martin-Loeches I, Varillas D, Gallegos MC, Serón C, Micheloud D, Gomez JM, Tenorio-Abreu A, Ramos MJ, Molina ML, Huidobro S, Sanchez E, Gordón M, Fernández V, Del Castillo A, Marcos MA, Villanueva B, López CJ, Rodríguez-Domínguez M, Galan JC, Cantón R, Lietor A, Rojo S, Eiros JM, Hinojosa C, Gonzalez I, Torner N, Banner D, Leon A, Cuesta P, Rowe T, Kelvin DJ (2009) Th1 and Th17 hypercytokinemia as early host response signature in severe pandemic influenza. Crit Care 13:R201

    Article  PubMed  Google Scholar 

  • Berriz GF, Beaver JE, Cenik C, Tasan M, Roth FP (2009) Next generation software for functional trend analysis. Bioinformatics 25:3043–3044

    Article  PubMed  CAS  Google Scholar 

  • Cameron CM, Cameron MJ, Bermejo-Martin JF, Ran L, Xu L, Turner PV, Ran R, Danesh A, Fang Y, Chan PK, Mytle N, Sullivan TJ, Collins TL, Johnson MG, Medina JC, Rowe T, Kelvin DJ (2008) Gene expression analysis of host innate immune responses during lethal H5N1 infection in ferrets. J Virol 82:11308–11317

    Article  PubMed  CAS  Google Scholar 

  • Chow VT, Tambyah PA, Goh KT (2008) To kill a mocking bird flu? Ann Acad Med 37:451–453

    Google Scholar 

  • Cillóniz C, Shinya K, Peng X, Korth MJ, Proll SC, Aicher LD, Carter VS, Chang JH, Kobasa D, Feldmann F, Strong JE, Feldmann H, Kawaoka Y, Katze MG (2009) Lethal influenza virus infection in macaques is associated with early dysregulation of inflammatory related genes. PLoS Pathog 5:e1000604

    Article  PubMed  Google Scholar 

  • Conn CA, McClellan JL, Maassab HF, Smitka CW, Majde JA, Kluger MJ (1995) Cytokines and the acute phase response to influenza virus in mice. Am J Physiol 268:R78–R84

    PubMed  CAS  Google Scholar 

  • Du P, Kibbe WA, Lin SM (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics 24:1547–1548

    Article  PubMed  CAS  Google Scholar 

  • Ford JW, McVicar DW (2009) TREM and TREM-like receptors in inflammation and disease. Curr Opin Immunol 21:38–46

    Article  PubMed  CAS  Google Scholar 

  • Gibot S (2006) The therapeutic potential of TREM-1 modulation in the treatment of sepsis and beyond. Curr Opin Invest Drugs 7:438–442

    CAS  Google Scholar 

  • Han CY, Subramanian S, Chan CK, Omer M, Chiba T, Wight TN, Chait A (2007) Adipocyte-derived serum amyloid A3 and hyaluronan play a role in monocyte recruitment and adhesion. Diabetes 56:2260–2273

    Article  PubMed  CAS  Google Scholar 

  • Hartshorn KL, Tauber AI (1988) The influenza virus-infected phagocyte. A model of deactivation. Hematol Oncol Clin North Am 2:301–315

    PubMed  CAS  Google Scholar 

  • Hartshorn KL, Reid KB, White MR, Jensenius JC, Morris SM, Tauber AI, Crouch E (1996) Neutrophil deactivation by influenza A viruses: mechanisms of protection after viral opsonization with collectins and hemagglutination-inhibiting antibodies. Blood 87:3450–3461

    PubMed  CAS  Google Scholar 

  • Haselmayer P, Daniel M, Tertilt C, Salih HR, Stassen M, Schild H, Radsak MP (2009) Signaling pathways of the TREM-1 and TLR4-mediated neutrophil oxidative burst. J Innate Immun 1:582–591

    Article  PubMed  CAS  Google Scholar 

  • Horimoto T, Kawaoka Y (2005) Influenza: lessons from past pandemics, warnings from current incidents. Nat Rev Microbiol 3:591–600

    Article  PubMed  CAS  Google Scholar 

  • Johnston JB, Rahman MM, McFadden G (2007) Strategies that modulate inflammasomes: insights from host-pathogen interactions. Semin Immunopathol 29:261–274

    Article  PubMed  CAS  Google Scholar 

  • Kash JC, Basler CF, García-Sastre A, Carter V, Billharz R, Swayne DE, Przygodzki RM, Taubenberger JK, Katze MG, Tumpey TM (2004) Global host immune response: pathogenesis and transcriptional profiling of type A influenza viruses expressing the hemagglutinin and neuraminidase genes from the 1918 pandemic virus. J Virol 78:9499–9511

    Article  PubMed  CAS  Google Scholar 

  • Kash JC, Tumpey TM, Proll SC, Carter V, Perwitasari O, Thomas MJ, Basler CF, Palese P, Taubenberger JK, García-Sastre A, Swayne DE, Katze MG (2006) Genomic analysis of increased host immune and cell death responses induced by 1918 influenza virus. Nature 443:578–581

    PubMed  CAS  Google Scholar 

  • Kim MS, Sweeney TR, Shigenaga JK, Chui LG, Moser A, Grunfeld C, Feingold KR (2007) Tumor necrosis factor and interleukin 1 decrease RXRalpha, PPARalpha, PPARgamma, LXRalpha, and the coactivators SRC-1, PGC-1alpha, and PGC-1beta in liver cells. Metabolism 56:267–279

    Article  PubMed  CAS  Google Scholar 

  • Kobasa D, Jones SM, Shinya K, Kash JC, Copps J, Ebihara H, Hatta Y, Kim JH, Halfmann P, Hatta M, Feldmann F, Alimonti JB, Fernando L, Li Y, Katze MG, Feldmann H, Kawaoka Y (2007) Aberrant innate immune response in lethal infection of macaques with the 1918 influenza virus. Nature 445:319–323

    Article  PubMed  CAS  Google Scholar 

  • Le Cras TD, Spitzmiller RE, Albertine KH, Greenberg JM, Whitsett JA, Akeson AL (2004) VEGF causes pulmonary hemorrhage, hemosiderosis, and air space enlargement in neonatal mice. Am J Physiol Lung Cell Mol Physiol 287:L134–L142

    Article  PubMed  Google Scholar 

  • Lee RM, White MR, Hartshorn KL (2006) Influenza A viruses upregulate neutrophil toll-like receptor 2 expression and function. Scand J Immunol 63:81–89

    Article  PubMed  CAS  Google Scholar 

  • Lee SM, Gardy JL, Cheung CY, Cheung TK, Hui KP, Ip NY, Guan Y, Hancock RE, Peiris JS (2009) Systems-level comparison of host-responses elicited by avian H5N1 and seasonal H1N1 influenza viruses in primary human macrophages. PLoS One 4:e8072

    Article  PubMed  Google Scholar 

  • Louzier V, Raoul W, Leroux A, Branellec D, Caillaud JM, Many H, Levame M, Delclaux C, Adnot S, Maitre B (2004) Adenovirus-mediated fibroblast growth factor 1 expression in the lung induces epithelial cell proliferation: consequences to hyperoxic lung injury in rats. Hum Gene Ther 15:793–804

    Article  PubMed  CAS  Google Scholar 

  • Mallory BP, Mead TJ, Wiginton DA, Kulkarni RM, Greenberg JM, Akeson AL (2006) Lymphangiogenesis in the developing lung promoted by VEGF-A. Microvasc Res 72:62–73

    Article  PubMed  CAS  Google Scholar 

  • Moreb JS, Baker HV, Chang LJ, Amaya M, Lopez MC, Ostmark B, Chou W (2008) ALDH isozymes downregulation affects cell growth, cell motility and gene expression in lung cancer cells. Mol Cancer 7:87

    Article  PubMed  Google Scholar 

  • Narasaraju T, Sim MK, Ng HH, Phoon MC, Shanker N, Lal SK, Chow VTK (2009) Adaptation of human influenza H3N2 virus in a mouse pneumonitis model: insights into viral virulence, tissue tropism and host pathogenesis. Microbes Infect 11:2–11

    Article  PubMed  CAS  Google Scholar 

  • Narasaraju T, Ng HH, Phoon MC, Chow VT (2010) MCP-1 antibody treatment enhances damage and impedes repair of the alveolar epithelium in influenza pneumonitis. Am J Respir Cell Mol Biol 42:732–743

    Article  PubMed  CAS  Google Scholar 

  • Narasaraju T, Yang E, Samy RP, Ng HH, Poh WP, Liew AA, Phoon MC, van Rooijen N, Chow VT (2011) Excessive neutrophils and neutrophil extracellular traps contribute to acute lung injury of influenza pneumonitis. Am J Pathol 179:199–210

    Article  PubMed  CAS  Google Scholar 

  • Neumann G, Noda T, Kawaoka Y (2009) Emergence and pandemic potential of swine-origin H1N1 influenza virus. Nature 459:931–939

    Article  PubMed  CAS  Google Scholar 

  • Osterholm MT (2005) Preparing for the next pandemic. N Engl J Med 352:1839–1842

    Article  PubMed  CAS  Google Scholar 

  • Perrone LA, Plowden JK, Garcia-Sastre A, Katz JM, Tumpey TM (2008) H5N1 and 1918 pandemic influenza virus infection results in early and excessive infiltration of macrophages and neutrophils in the lungs of mice. PLoS Pathog 4:e1000115

    Article  PubMed  Google Scholar 

  • Reid AH, Taubenberger JK, Fanning TG (2004) Evidence of an absence: the genetic origins of the 1918 pandemic influenza virus. Nat Rev Microbiol 2:909–914

    Article  PubMed  CAS  Google Scholar 

  • Reigstad CS, Lundén GO, Felin J, Bäckhed F (2009) Regulation of serum amyloid A3 (SAA3) in mouse colonic epithelium and adipose tissue by the intestinal microbiota. PLoS One 4:e5842

    Article  PubMed  Google Scholar 

  • Rosseau S, Hocke A, Mollenkopf H, Schmeck B, Suttorp N, Kaufmann SH, Zerrahn J (2007) Comparative transcriptional profiling of the lung reveals shared and distinct features of Streptococcus pneumoniae and influenza A virus infection. Immunology 120:380–391

    Article  PubMed  CAS  Google Scholar 

  • Schäfer JR, Kawaoka Y, Bean WJ, Süss J, Senne D, Webster RG (1993) Origin of the pandemic 1957 H2 influenza A virus and the persistence of its possible progenitors in the avian reservoir. Virology 194:781–788

    Article  PubMed  Google Scholar 

  • Storey JD (2002) A direct approach to false discovery rates. J R Statist Soc B 64:479–498

    Article  Google Scholar 

  • Tate MD, Deng YM, Jones JE, Anderson GP, Brooks AG, Reading PC (2009) Neutrophils ameliorate lung injury and the development of severe disease during influenza infection. J Immunol 183:7441–7450

    Article  PubMed  CAS  Google Scholar 

  • Tessarz AS, Cerwenka A (2008) The TREM-1/DAP12 pathway. Immunol Lett 116:111–116

    Article  PubMed  CAS  Google Scholar 

  • Tumpey TM, García-Sastre A, Taubenberger JK, Palese P, Swayne DE, Pantin-Jackwood MJ, Schultz-Cherry S, Solórzano A, Van Rooijen N, Katz JM, Basler CF (2005) Pathogenicity of influenza viruses with genes from the 1918 pandemic virus: functional roles of alveolar macrophages and neutrophils in limiting virus replication and mortality in mice. J Virol 79:14933–14944

    Article  PubMed  CAS  Google Scholar 

  • Wang JP, Bowen GN, Padden C, Cerny A, Finberg RW, Newburger PE, Kurt-Jones EA (2008) Toll-like receptor-mediated activation of neutrophils by influenza A virus. Blood 112:2028–2034

    Article  PubMed  CAS  Google Scholar 

  • Woo PC, Tung ET, Chan KH, Lau CC, Lau SK, Yuen KY (2010) Cytokine profiles induced by the novel swine-origin influenza A/H1N1 virus: implications for treatment strategies. J Infect Dis 201:346–353

    Article  PubMed  CAS  Google Scholar 

  • Yoon M, Madden MC, Barton HA (2006) Developmental expression of aldehyde dehydrogenase in rat: a comparison of liver and lung development. Toxicol Sci 89:386–398

    Article  PubMed  CAS  Google Scholar 

  • Zaas AK, Chen M, Varkey J, Veldman T, Hero AO, Lucas J, Huang Y, Turner R, Gilbert A, Lambkin-Williams R, Øien NC, Nicholson B, Kingsmore S, Carin L, Woods CW, Ginsburg GS (2009) Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 6:207–217

    Article  PubMed  CAS  Google Scholar 

  • Zhang L, Katz JM, Gwinn M, Dowling NF, Khoury MJ (2009) Systems-based candidate genes for human response to influenza infection. Infect Genet Evol 9:1148–1157

    Article  PubMed  CAS  Google Scholar 

  • Zimmerman TL, Thevananther S, Ghose R, Burns AR, Karpen SJ (2006) Nuclear export of retinoid X receptor alpha in response to interleukin-1beta-mediated cell signaling: roles for JNK and SER260. J Biol Chem 281:15434–15440

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Financial support was provided by the National Medical Research Council, Singapore, Microbiology Vaccine Initiative, and Singapore-MIT Alliance. We are grateful to M. C. Phoon and Kelly Lau for technical assistance.

Conflicts of interest

The authors declare no conflicts of interest.

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Authors and Affiliations

  1. Computational and Systems Biology Program, Singapore-MIT Alliance, Singapore, Singapore

    Fransiskus X. Ivan, Jagath C. Rajapakse, Roy E. Welsch, Steve G. Rozen & Vincent T. Chow

  2. BioInformatics Research Centre, Nanyang Technological University, Singapore, Singapore

    Fransiskus X. Ivan & Jagath C. Rajapakse

  3. Infectious Diseases Program, Department of Microbiology, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, 5 Science Drive 2, Kent Ridge, Singapore, 117597, Singapore

    T. Narasaraju, Gordon M. Xiong & Vincent T. Chow

  4. Duke-NUS Graduate Medical School, Singapore, Singapore

    Steve G. Rozen

  5. Massachusetts Institute of Technology, Cambridge, MA, USA

    Roy E. Welsch & Bevin P. Engelward

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  1. Fransiskus X. Ivan
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  2. Jagath C. Rajapakse
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Correspondence to Vincent T. Chow.

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Fig. 1

A summary of overlap between expression of genes exhibiting significant infection, time, and interaction effects as analyzed by two-way ANOVA. (DOCX 49 kb)

Fig. 2

Overall heatmap depicting differentially expressed genes at 12, 48, and 96 h post-infection. Genes include those with an absolute log expression ratio of >0.6 in at least one time-point after low virulent influenza (LVI) and highly virulent influenza (HVI) infection. (DOCX 86 kb)

Fig. 3

Overview of type 1 interferon-stimulated gene expression patterns at 12, 48, and 96 h post-infection with low virulent influenza (LVI) and highly virulent influenza (HVI). (DOCX 252 kb)

Fig. 4

Overview of apoptotic gene expression patterns at 12, 48, and 96 h post-infection with low virulent influenza (LVI) and highly virulent influenza (HVI). (DOCX 202 kb)

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Ivan, F.X., Rajapakse, J.C., Welsch, R.E. et al. Differential pulmonary transcriptomic profiles in murine lungs infected with low and highly virulent influenza H3N2 viruses reveal dysregulation of TREM1 signaling, cytokines, and chemokines. Funct Integr Genomics 12, 105–117 (2012). https://doi.org/10.1007/s10142-011-0247-y

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