MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Proceedings of the National Academy of Sciences of the United States of America

Volumn 115, Issue 5, 2018, Pages E1012-E1021

  Menachery, Vineet D ^a,b   Schäfer, Alexandra ^b   Burnum Johnson, Kristin E ^c   Mitchell, Hugh D ^c   Eisfeld, Amie J ^d   Walters, Kevin B ^d,g   Nicora, Carrie D ^c   Purvine, Samuel O ^c   Casey, Cameron P ^c   Monroe, Matthew E ^c   Weitz, Karl K ^c   Stratton, Kelly G ^c   Webb Robertson, Bobbie Jo M ^c   Gralinski, Lisa E ^b   Metz, Thomas O ^c   Smith, Richard D ^c   Waters, Katrina M ^c   Sims, Amy C ^b   Kawaoka, Yoshihiro ^d,e   Baric, Ralph S ^b,f  

^a University of Texas Medical Branch School of Medicine   (United States)

^b IL   (United States)

^c PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^d UNIVERSITY OF WISCONSIN MADISON   (United States)

^e UNIVERSITY OF TOKYO   (Japan)

^f UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^g Southern Research Institute   (United States)

Author keywords

Antigen presentation; Coronavirus; DNA; Epigenetics; Influenza; Methylation

Indexed keywords

GAMMA INTERFERON; HISTONE;

ANTIGEN PRESENTATION; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DOWN REGULATION; EPIGENETIC LANDSCAPE; EPIGENETICS; GENE CONTROL; GENE EXPRESSION; GENETIC REGULATION; HISTONE MODIFICATION; INFLUENZA A (H5N1); INFLUENZA A VIRUS (A INFLUENZA CALIFORNIA 04 2009(H1N1)); INFLUENZA A VIRUS (A INFLUENZA VIETNAM 1203 2004(H1N1)); INFLUENZA A VIRUS (H1N1); INFLUENZA A VIRUS (H5N1); MIDDLE EAST RESPIRATORY SYNDROME; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; SARS CORONAVIRUS; ANIMAL; ANTIGENIC VARIATION; CELL LINE; CHEMISTRY; CHLOROCEBUS AETHIOPS; DOG; GENETIC EPIGENESIS; HUMAN; MAJOR HISTOCOMPATIBILITY COMPLEX; MDCK CELL LINE; MUTATION; OPEN READING FRAME; PATHOGENICITY; VERO CELL LINE;

ANIMALS; ANTIGEN PRESENTATION; ANTIGENIC VARIATION; CELL LINE; CERCOPITHECUS AETHIOPS; DNA METHYLATION; DOGS; DOWN-REGULATION; EPIGENESIS, GENETIC; HISTONES; HUMANS; INFLUENZA A VIRUS, H5N1 SUBTYPE; MADIN DARBY CANINE KIDNEY CELLS; MAJOR HISTOCOMPATIBILITY COMPLEX; MIDDLE EAST RESPIRATORY SYNDROME CORONAVIRUS; MUTATION; OPEN READING FRAMES; PROTEOMICS; VERO CELLS;

EID: 85041174031     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1706928115     Document Type: Article

References (46)

1. Mandl JN, et al. (2015) Reservoir host immune responses to emerging zoonotic viruses. Cell 160:20–35.
2. Kreuder Johnson C, et al. (2015) Spillover and pandemic properties of zoonotic viruses with high host plasticity. Sci Rep 5:14830.
3. Morse SS, et al. (2012) Prediction and prevention of the next pandemic zoonosis. Lancet 380:1956–1965.
4. Sawyer SL, Elde NC (2012) A cross-species view on viruses. Curr Opin Virol 2:561–568.
5. Menachery VD, Baric RS (2013) Bugs in the system. Immunol Rev 255:256–274.
6. Menachery VD, et al. (2014) Pathogenic influenza viruses and coronaviruses utilize similar and contrasting approaches to control interferon-stimulated gene responses. MBio 5:e01174-14.
7. Avgousti DC, et al. (2016) A core viral protein binds host nucleosomes to sequester immune danger signals. Nature 535:173–177.
8. Marazzi I, et al. (2012) Suppression of the antiviral response by an influenza histone mimic. Nature 483:428–433.
9. Lewandowska-Polak A, et al. (2015) Human parainfluenza virus type 3 (HPIV3) induces production of IFNγ and RANTES in human nasal epithelial cells (HNECs). J Inflamm (Lond) 12:16.
10. Pancham K, et al. (2015) Premature infants have impaired airway antiviral IFNγ responses to human metapneumovirus compared to respiratory syncytial virus. Pediatr Res 78:389–394.
11. Tenland E, et al. (2016) Innate immune responses after airway epithelial stimulation with Mycobacterium bovis Bacille-Calmette Guérin. PLoS One 11:e0164431.
12. Siezen CL, et al. (2009) Genetic susceptibility to respiratory syncytial virus bronchiolitis in preterm children is associated with airway remodeling genes and innate immune genes. Pediatr Infect Dis J 28:333–335.
13. Heller NM, et al. (2004) Interferon-gamma inhibits STAT6 signal transduction and gene expression in human airway epithelial cells. Am J Respir Cell Mol Biol 31: 573–582.
14. Zissler UM, et al. (2016) Interleukin-4 and interferon-γ orchestrate an epithelial polarization in the airways. Mucosal Immunol 9:917–926.
15. Scobey T, et al. (2013) Reverse genetics with a full-length infectious cDNA of the Middle East respiratory syndrome coronavirus. Proc Natl Acad Sci USA 110:16157–16162.
16. Chakrabarti AK, et al. (2010) Host gene expression profiling in influenza A virus-infected lung epithelial (A549) cells: A comparative analysis between highly pathogenic and modified H5N1 viruses. Virol J 7:219.
17. Sarmento L, Afonso CL, Estevez C, Wasilenko J, Pantin-Jackwood M (2008) Differential host gene expression in cells infected with highly pathogenic H5N1 avian influenza viruses. Vet Immunol Immunopathol 125:291–302.
18. Wang Z, et al. (2014) Transcriptome analysis of the hippocampus in novel rat model of febrile seizures. PLoS One 9:e95237.
19. Guo Y, Korteweg C, McNutt MA, Gu J (2008) Pathogenetic mechanisms of severe acute respiratory syndrome. Virus Res 133:4–12.
20. Chu H, et al. (2014) Productive replication of Middle East respiratory syndrome coronavirus in monocyte-derived dendritic cells modulates innate immune response. Virology 454–455:197–205.
21. Chu H, et al. (2016) Middle East respiratory syndrome coronavirus efficiently infects human primary T lymphocytes and activates the extrinsic and intrinsic apoptosis pathways. J Infect Dis 213:904–914.
22. Tynell J, et al. (2016) Middle East respiratory syndrome coronavirus shows poor replication but significant induction of antiviral responses in human monocyte-derived macrophages and dendritic cells. J Gen Virol 97:344–355.
23. Summerfield A, McCullough KC (2009) Dendritic cells in innate and adaptive immune responses against influenza virus. Viruses 1:1022–1034.
24. Perrone LA, Plowden JK, García-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.
25. Hatta Y, et al. (2010) Viral replication rate regulates clinical outcome and CD8 T cell responses during highly pathogenic H5N1 influenza virus infection in mice. PLoS Pathog 6:e1001139.
26. Rimmelzwaan GF, Katz JM (2013) Immune responses to infection with H5N1 influenza virus. Virus Res 178:44–52.
27. Arabi YM, et al. (2016) Feasibility of using convalescent plasma immunotherapy for MERS-CoV infection, Saudi Arabia. Emerg Infect Dis 22:1554–1561.
28. Alshukairi AN, et al. (2016) Antibody response and disease severity in healthcare worker MERS survivors. Emerg Infect Dis 22:1113–1115.
29. Smale ST, Tarakhovsky A, Natoli G (2014) Chromatin contributions to the regulation of innate immunity. Annu Rev Immunol 32:489–511.
30. Lieberman PM (2016) Epigenetics and genetics of viral latency. Cell Host Microbe 19: 619–628.
31. Ferrari R, et al. (2014) Adenovirus small E1A employs the lysine acetylases p300/CBP and tumor suppressor Rb to repress select host genes and promote productive virus infection. Cell Host Microbe 16:663–676.
32. Seo YL, Heo S, Jang KL (2015) Hepatitis C virus core protein overcomes H2O2-induced apoptosis by downregulating p14 expression via DNA methylation. J Gen Virol 96:822–832.
33. Verweij MC, et al. (2015) Viral inhibition of the transporter associated with antigen processing (TAP): A striking example of functional convergent evolution. PLoS Pathog 11:e1004743.
34. Aevermann BD, et al. (2014) A comprehensive collection of systems biology data characterizing the host response to viral infection. Sci Data 1:140033.
35. McDermott JE, et al. (2016) The effect of inhibition of PP1 and TNFα signaling on pathogenesis of SARS coronavirus. BMC Syst Biol 10:93.
36. Gralinski LE, et al. (2013) Mechanisms of severe acute respiratory syndrome coronavirus-induced acute lung injury. MBio 4:e00271-13.
37. Sims AC, et al. (2013) Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol 87: 3885–3902.
38. Josset L, et al. (2013) Cell host response to infection with novel human coronavirus EMC predicts potential antivirals and important differences with SARS coronavirus. MBio 4:e00165–e13.
39. Gibbs DL, et al. (2013) Protein co-expression network analysis (ProCoNA). J Clin Bioinforma 3:11.
40. Li C, et al. (2011) Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus. J Virol 85:10955–10967.
41. Yount B, et al. (2003) Reverse genetics with a full-length infectious cDNA of severe acute respiratory syndrome coronavirus. Proc Natl Acad Sci USA 100:12995–13000.
42. Neumann G, et al. (1999) Generation of influenza A viruses entirely from cloned cDNAs. Proc Natl Acad Sci USA 96:9345–9350.
43. Webb-Robertson BJ, et al. (2010) Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data. J Proteome Res 9:5748–5756.
44. Matzke MM, et al. (2011) Improved quality control processing of peptide-centric LC-MS proteomics data. Bioinformatics 27:2866–2872.
45. Webb-Robertson BJ, Matzke MM, Jacobs JM, Pounds JG, Waters KM (2011) A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors. Proteomics 11: 4736–4741.
46. Matzke MM, et al. (2013) A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. Proteomics 13:493–503.