A comparison of host gene expression signatures associated with infection in vitro by the Makona and Ecran (Mayinga) variants of Ebola virus

Scientific Reports

Volumn 7, Issue , 2017, Pages

  Bosworth, Andrew ^a,b   Dowall, Stuart D ^a,b   Garcia Dorival, Isabel ^c   Rickett, Natasha Y ^b,c   Bruce, Christine B ^a   Matthews, David A ^d   Fang, Yongxiang ^c   Aljabr, Waleed ^c   Kenny, John ^c   Nelson, Charlotte ^c   Laws, Thomas R ^e   Williamson, E Diane ^e   Stewart, James P ^c   Carroll, Miles W ^a,b   Hewson, Roger ^a,b   Hiscox, Julian A ^b,c  

^a PUBLIC HEALTH ENGLAND   (United Kingdom)

^b The National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections at University College London in partnership with UK Health Security Agency   (United Kingdom)

^c UNIVERSITY OF LIVERPOOL   (United Kingdom)

^d UNIVERSITY OF BRISTOL   (United Kingdom)

^e DEFENCE SCIENCE AND TECHNOLOGY LABORATORY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME;

A-549 CELL LINE; COMPARATIVE STUDY; EBOLAVIRUS; GENE EXPRESSION PROFILING; GROWTH, DEVELOPMENT AND AGING; HOST PATHOGEN INTERACTION; HUMAN; HUMAN RESPIRATORY SYNCYTIAL VIRUS; SEQUENCE ANALYSIS;

A549 CELLS; EBOLAVIRUS; GENE EXPRESSION PROFILING; HOST-PATHOGEN INTERACTIONS; HUMANS; RESPIRATORY SYNCYTIAL VIRUS, HUMAN; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 85014099864     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep43144     Document Type: Article

References (54)

1. W. H. O. E. R. Team. Ebola virus disease in West Africa-the first 9 months of the epidemic and forward projections. N Engl J Med 371, 1481-1495 (2014).
2. J. H. Kuhn. Filoviruses. A compendium of 40 years of epidemiological, clinical, and laboratory studies. Arch Virol Suppl 20, 13-360 (2008).
3. S. K. Gire et al. Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak. Science 345, 1369-1372 (2014).
4. M. W. Carroll et al. Temporal and spatial analysis of the 2014-2015 Ebola virus outbreak in West Africa. Nature (2015).
5. M. Andrea et al. Delayed Disease Progression in Cynomolgus Macaques Infected with Ebola Virus Makona Strain. Emerging Infectious Disease journal 21 (2015).
6. H. Hofmann-Winkler, K. Gnirß, F. Wrensch & S. Pöhlmann. Comparative Analysis of Host Cell Entry of Ebola Virus From Sierra Leone, 2014, and Zaire, 1976. The Journal of Infectious Diseases 212, S172-S180 (2015).
7. Richard A. Urbanowicz et al. Human Adaptation of Ebola Virus during the West African Outbreak. Cell 167, 1079-1087 e1075 (2016).
8. J. C. Kash et al. Global suppression of the host antiviral response by Ebola- and Marburgviruses: increased antagonism of the type I interferon response is associated with enhanced virulence. J Virol 80, 3009-3020 (2006).
9. C. Cilloniz et al. Functional genomics reveals the induction of inflammatory response and metalloproteinase gene expression during lethal Ebola virus infection. J Virol 85, 9060-9068 (2011).
10. C. F. Basler & G. K. Amarasinghe. Evasion of interferon responses by Ebola and Marburg viruses. J Interferon Cytokine Res 29, 511-520 (2009).
11. B. K. Dove et al. A quantitative proteomic analysis of lung epithelial (A549) cells infected with 2009 pandemic influenza A virus using stable isotope labelling with amino acids in cell culture. PROTEOMICS 12, 1431-1436 (2012).
12. O. Noyori, E. Nakayama, J. Maruyama, R. Yoshida & A. Takada. Suppression of Fas-mediated apoptosis via steric shielding by filovirus glycoproteins. Biochem Biophys Res Commun 441, 994-998 (2013).
13. J. Olejnik et al. Ebola virus does not block apoptotic signaling pathways. J Virol 87, 5384-5396 (2013).
14. H. Reed & A. Muench. Simple Method of Estimating Fifty Percent Endpoints. Am. J. Epidemiol. 27, 493-497 (1938).
15. D. C. Munday et al. Quantitative proteomic analysis of A549 cells infected with human respiratory syncytial virus. Mol Cell Proteomics 9, 2438-2459 (2010).
16. A. R. Trombley et al. Comprehensive panel of real-time TaqMan polymerase chain reaction assays for detection and absolute quantification of filoviruses, arenaviruses, and New World hantaviruses. The American journal of tropical medicine and hygiene 82, 954-960 (2010).
17. W. Aljabr et al. Investigating the Influence of Ribavirin on Human Respiratory Syncytial Virus RNA Synthesis by Using a High-Resolution Transcriptome Sequencing Approach. J Virol 90, 4876-4888 (2016).
18. M. Martin. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17, 10 (2011).
19. D. Kim et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology 14, R36 (2013).
20. B. Langmead & S. Salzberg. Fast gapped-read alignment with Bowtie 2. Nature methods 9, 357-359 (2012).
21. M. Robinson, D. McCarthy & G. Smyth. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England) 26, 139-140 (2010).
22. H. C. Chiu, H. Hannemann, K. J. Heesom, D. A. Matthews & A. D. Davidson. High-throughput quantitative proteomic analysis of dengue virus type 2 infected A549 cells. PLoS One 9, e93305 (2014).
23. E. Frumence et al. The South Pacific epidemic strain of Zika virus replicates efficiently in human epithelial A549 cells leading to IFN-beta production and apoptosis induction. Virology 493, 217-226 (2016).
24. P. F. Simon et al. Avian influenza viruses that cause highly virulent infections in humans exhibit distinct replicative properties in contrast to human H1N1 viruses. Sci Rep 6, 24154 (2016).
25. W. Wu et al. Characterization of the interaction between human respiratory syncytial virus and the cell cycle in continuous cell culture and primary human airway epithelial cells. J Virol 85, 10300-10309 (2011).
26. C. F. Spiropoulou et al. RIG-I activation inhibits ebolavirus replication. Virology 392, 11-15 (2009).
27. M. J. Martínez et al. Role of Ebola Virus VP30 in Transcription Reinitiation. Journal of Virology 82, 12569-12573 (2008).
28. J. Wynne et al. Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis. Genome Biology 15, 532 (2014).
29. S. D. Dowall et al. Elucidating variations in the nucleotide sequence of Ebola virus associated with increasing pathogenicity. Genome Biol 15, 540 (2014).
30. J. A. Nelder & R. W. M. Wedderburn. Generalized Linear Models. Journal of the Royal Statistical Society. Series A (General) 135, 370-384 (1972).
31. M. R. Edwards et al. Differential Regulation of Interferon Responses by Ebola and Marburg Virus VP35 Proteins. Cell Rep 14, 1632-1640 (2016).
32. B. C. Yen & C. F. Basler. Effects of Filovirus IFN Antagonists on Responses of Human Monocyte-Derived Dendritic Cells to RNA virus infection. J Virol (2016).
33. C. F. Basler et al. The Ebola virus VP35 protein inhibits activation of interferon regulatory factor 3. J Virol 77, 7945-7956 (2003).
34. A. L. Hartman et al. Inhibition of IRF-3 activation by VP35 is critical for the high level of virulence of ebola virus. J Virol 82, 2699-2704 (2008).
35. P. A. Ilinykh et al. Different Temporal Effects of Ebola Virus VP35 and VP24 Proteins on Global Gene Expression in Human Dendritic Cells. Journal of Virology 89, 7567-7583 (2015).
36. L. Hilton et al. The NPro Product of Bovine Viral Diarrhea Virus Inhibits DNA Binding by Interferon Regulatory Factor 3 and Targets It for Proteasomal Degradation. Journal of Virology 80, 11723-11732 (2006).
37. D. Sarhan et al. Dendritic cell regulation of NK-cell responses involves lymphotoxin-alpha, IL-12, and TGF-beta. Eur J Immunol 45, 1783-1793 (2015).
38. J. E. Carette et al. Ebola virus entry requires the cholesterol transporter Niemann-Pick C1. Nature 477, 340-343 (2011).
39. W. S. Garver et al. Niemann-Pick C1 protein regulates cholesterol transport to the trans-Golgi network and plasma membrane caveolae. Journal of Lipid Research 43, 579-589 (2002).
40. Y. Boehmann, S. Enterlein, A. Randolf & E. Muhlberger. A reconstituted replication and transcription system for Ebola virus Reston and comparison with Ebola virus Zaire. Virology 332, 406-417 (2005).
41. K. Brauburger et al. Analysis of the highly diverse gene borders in Ebola virus reveals a distinct mechanism of transcriptional regulation. J Virol 88, 12558-12571 (2014).
42. V. Wahl-Jensen et al. Ebola virion attachment and entry into human macrophages profoundly effects early cellular gene expression. PLoS Negl Trop Dis 5, e1359 (2011).
43. J. R. Francica, M. K. Matukonis & P. Bates. Requirements for cell rounding and surface protein down-regulation by Ebola virus glycoprotein. Virology 383, 237-247 (2009).
44. M. Bray & T. W. Geisbert. Ebola virus: the role of macrophages and dendritic cells in the pathogenesis of Ebola hemorrhagic fever. Int J Biochem Cell Biol 37, 1560-1566 (2005).
45. N. Shrestha et al. Eukaryotic Initiation Factor 2 (eIF2) Signaling Regulates Proinflammatory Cytokine Expression and Bacterial Invasion. Journal of Biological Chemistry 287, 28738-28744 (2012).
46. L. Hunt et al. Clinical presentation, biochemical, and haematological parameters and their association with outcome in patients with Ebola virus disease: an observational cohort study. Lancet Infect Dis 15, 1292-1299 (2015).
47. X. Liu et al. Transcriptomic signatures differentiate survival from fatal outcomes in humans infected with Ebola virus. Genome Biology (2016).
48. A. Bakre et al. Respiratory syncytial virus modifies microRNAs regulating host genes that affect virus replication. J Gen Virol 93, 2346-2356 (2012).
49. T. Bian, J. D. Gibbs, C. Orvell & F. Imani. Respiratory syncytial virus matrix protein induces lung epithelial cell cycle arrest through a p53 dependent pathway. PLoS One 7, e38052 (2012).
50. J. D. Gibbs, D. M. Ornoff, H. A. Igo, J. Y. Zeng & F. Imani. Cell cycle arrest by transforming growth factor beta1 enhances replication of respiratory syncytial virus in lung epithelial cells. J Virol 83, 12424-12431 (2009).
51. N. Wauquier, P. Becquart, C. Padilla, S. Baize & E. M. Leroy. Human fatal zaire ebola virus infection is associated with an aberrant innate immunity and with massive lymphocyte apoptosis. PLoS Negl Trop Dis 4 (2010).
52. M. Hacke et al. Inhibition of Ebola virus glycoprotein-mediated cytotoxicity by targeting its transmembrane domain and cholesterol. Nature Communications 6, 7688 (2015).
53. J. C. Kash et al. Global Suppression of the Host Antiviral Response by Ebola- and Marburgviruses: Increased Antagonism of the Type I Interferon Response Is Associated with Enhanced Virulence. Journal of Virology 80, 3009-3020 (2006).
54. R. Weiss et al. Interleukin-24 inhibits influenza A virus replication in vitro through induction of toll-like receptor 3 dependent apoptosis. Antiviral Res 123, 93-104 (2015).