Host Cell Transcriptome Profile during Wild-Type and Attenuated Dengue Virus Infection

PLoS Neglected Tropical Diseases

Volumn 7, Issue 3, 2013, Pages

  Sessions, October M ^a   Tan, Ying ^a   Goh, Kenneth C ^a   Liu, Yujing ^a,b   Tan, Patrick ^a   Rozen, Steve ^a   Ooi, Eng Eong ^a  

^a DUKE NUS MEDICAL SCHOOL   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

RNA ISOFORM; TRANSCRIPTOME;

ALGORITHM; ALTERNATIVE RNA SPLICING; ARTICLE; CONTROLLED STUDY; DENGUE; DENGUE VIRUS 1; DNA LIBRARY; FLUORESCENCE MICROSCOPY; GENE EXPRESSION; HUMAN; HUMAN CELL; IMMUNE RESPONSE; IMMUNOFLUORESCENCE TEST; NONHUMAN; PREDICTION; REAL TIME POLYMERASE CHAIN REACTION; REGULATORY MECHANISM; RNA SEQUENCE; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

EID: 84875980690     PISSN: 19352727     EISSN: 19352735     Source Type: Journal    
DOI: 10.1371/journal.pntd.0002107     Document Type: Article

References (55)

1. Kyle JL, Harris E, (2008) Global spread and persistence of dengue. Annu Rev Microbiol 62: 71-92.
2. Wilder-Smith A, Ooi EE, Vasudevan SG, Gubler DJ, (2010) Update on dengue: epidemiology, virus evolution, antiviral drugs, and vaccine development. Curr Infect Dis Rep 12: 157-164.
3. Beatty ME, Beutels P, Meltzer MI, Shepard DS, Hombach J, et al. (2011) Health economics of dengue: a systematic literature review and expert panel's assessment. Am J Trop Med Hyg 84: 473-488.
4. Carrasco LR, Lee LK, Lee VJ, Ooi EE, Shepard DS, et al. (2011) Economic impact of dengue illness and the cost-effectiveness of future vaccination programs in Singapore. PLoS Negl Trop Dis 5: e1426.
5. Gubler DJ, (2004) The changing epidemiology of yellow fever and dengue, 1900 to 2003: full circle? Comp Immunol Microbiol Infect Dis 27: 319-330.
6. Normile D, (2007) Tropical diseases. Hunt for dengue vaccine heats up as the disease burden grows. Science 317: 1494-1495.
7. Shepard DS, Suaya JA, Halstead SB, Nathan MB, Gubler DJ, et al. (2004) Cost-effectiveness of a pediatric dengue vaccine. Vaccine 22: 1275-1280.
8. Suaya JA, Shepard DS, Siqueira JB, Martelli CT, Lum LC, et al. (2009) Cost of dengue cases in eight countries in the Americas and Asia: a prospective study. Am J Trop Med Hyg 80: 846-855.
9. Fernandez-Garcia MD, Mazzon M, Jacobs M, Amara A, (2009) Pathogenesis of flavivirus infections: using and abusing the host cell. Cell Host Microbe 5: 318-328.
10. Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, et al. (2008) RNA interference screen for human genes associated with West Nile virus infection. Nature 455: 242-245.
11. Sessions OM, Barrows NJ, Souza-Neto JA, Robinson TJ, Hershey CL, et al. (2009) Discovery of insect and human dengue virus host factors. Nature 458: 1047-1050.
12. Balas C, Kennel A, Deauvieau F, Sodoyer R, Arnaud-Barbe N, et al. (2011) Different innate signatures induced in human monocyte-derived dendritic cells by wild-type dengue 3 virus, attenuated but reactogenic dengue 3 vaccine virus, or attenuated nonreactogenic dengue 1-4 vaccine virus strains. J Infect Dis 203: 103-108.
13. Becerra A, Warke RV, Martin K, Xhaja K, de Bosch N, et al. (2009) Gene expression profiling of dengue infected human primary cells identifies secreted mediators in vivo. Journal of medical virology 81: 1403-1411.
14. Conceicao TM, El-Bacha T, Villas-Boas CS, Coello G, Ramirez J, et al. (2010) Gene expression analysis during dengue virus infection in HepG2 cells reveals virus control of innate immune response. The Journal of infection 60: 65-75.
15. Fink J, Gu F, Ling L, Tolfvenstam T, Olfat F, et al. (2007) Host gene expression profiling of dengue virus infection in cell lines and patients. PLoS Negl Trop Dis 1: e86.
16. Hoang LT, Lynn DJ, Henn M, Birren BW, Lennon NJ, et al. (2010) The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults. J Virol 84: 12982-12994.
17. Liew KJ, Chow VT, (2006) Microarray and real-time RT-PCR analyses of a novel set of differentially expressed human genes in ECV304 endothelial-like cells infected with dengue virus type 2. Journal of virological methods 131: 47-57.
18. Loke P, Hammond SN, Leung JM, Kim CC, Batra S, et al. (2010) Gene expression patterns of dengue virus-infected children from nicaragua reveal a distinct signature of increased metabolism. PLoS Negl Trop Dis 4: e710.
19. Long HT, Hibberd ML, Hien TT, Dung NM, Van Ngoc T, et al. (2009) Patterns of gene transcript abundance in the blood of children with severe or uncomplicated dengue highlight differences in disease evolution and host response to dengue virus infection. J Infect Dis 199: 537-546.
20. Moreno-Altamirano MM, Romano M, Legorreta-Herrera M, Sanchez-Garcia FJ, Colston MJ, (2004) Gene expression in human macrophages infected with dengue virus serotype-2. Scandinavian journal of immunology 60: 631-638.
21. Nascimento EJ, Braga-Neto U, Calzavara-Silva CE, Gomes AL, Abath FG, et al. (2009) Gene expression profiling during early acute febrile stage of dengue infection can predict the disease outcome. PloS one 4: e7892.
22. Nasirudeen AM, Liu DX, (2009) Gene expression profiling by microarray analysis reveals an important role for caspase-1 in dengue virus-induced p53-mediated apoptosis. Journal of medical virology 81: 1069-1081.
23. Silveira GF, Meyer F, Delfraro A, Mosimann AL, Coluchi N, et al. (2011) Dengue virus type 3 isolated from a fatal case with visceral complications induces enhanced proinflammatory responses and apoptosis of human dendritic cells. J Virol 85: 5374-5383.
24. Simmons CP, Popper S, Dolocek C, Chau TN, Griffiths M, et al. (2007) Patterns of host genome-wide gene transcript abundance in the peripheral blood of patients with acute dengue hemorrhagic fever. J Infect Dis 195: 1097-1107.
25. Tolfvenstam T, Lindblom A, Schreiber MJ, Ling L, Chow A, et al. (2011) Characterization of early host responses in adults with dengue disease. BMC infectious diseases 11: 209.
26. Ubol S, Masrinoul P, Chaijaruwanich J, Kalayanarooj S, Charoensirisuthikul T, et al. (2008) Differences in global gene expression in peripheral blood mononuclear cells indicate a significant role of the innate responses in progression of dengue fever but not dengue hemorrhagic fever. J Infect Dis 197: 1459-1467.
27. Umareddy I, Pluquet O, Wang QY, Vasudevan SG, Chevet E, et al. (2007) Dengue virus serotype infection specifies the activation of the unfolded protein response. Virol J 4: 91.
28. Villas-Boas CS, Conceicao TM, Ramirez J, Santoro AB, Da Poian AT, et al. (2009) Dengue virus-induced regulation of the host cell translational machinery. Brazilian journal of medical and biological research = Revista brasileira de pesquisas medicas e biologicas/Sociedade Brasileira de Biofisica [et al] 42: 1020-1026.
29. Warke RV, Xhaja K, Martin KJ, Fournier MF, Shaw SK, et al. (2003) Dengue virus induces novel changes in gene expression of human umbilical vein endothelial cells. J Virol 77: 11822-11832.
30. Blencowe BJ, (2006) Alternative splicing: new insights from global analyses. Cell 126: 37-47.
31. Matlin AJ, Clark F, Smith CW, (2005) Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 6: 386-398.
32. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y, (2008) RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18: 1509-1517.
33. Wang Z, Gerstein M, Snyder M, (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
34. Bhamarapravati N, Yoksan S. (1997) Live attenuated tetravalent dengue vaccine. In: Gubler DJ, Kuno G., editor. Dengue and Dengue Hemorrhagic Fever. Wallingford, UK: CAB International. pp. 367-378.
35. Halstead SB, Marchette NJ, (2003) Biologic properties of dengue viruses following serial passage in primary dog kidney cells: studies at the University of Hawaii. Am J Trop Med Hyg 69: 5-11.
36. Schreiber MJ, Holmes EC, Ong SH, Soh HS, Liu W, et al. (2009) Genomic epidemiology of a dengue virus epidemic in urban Singapore. J Virol 83: 4163-4173.
37. Tissera HA, Ooi EE, Gubler DJ, Tan Y, Logendra B, et al. (2011) New dengue virus type 1 genotype in Colombo, Sri Lanka. Emerg Infect Dis 17: 2053-2055.
38. Malewicz B, Jenkin HM, (1979) Development of dengue virus plaques under serum-free overlay medium. J Clin Microbiol 9: 609-614.
39. Gubler DJ, Kuno G, Sather GE, Velez M, Oliver A, (1984) Mosquito cell cultures and specific monoclonal antibodies in surveillance for dengue viruses. Am J Trop Med Hyg 33: 158-165.
40. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28: 511-515.
41. Katz Y, Wang ET, Airoldi EM, Burge CB, (2010) Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods 7: 1009-1015.
42. Trapnell C, Pachter L, Salzberg SL, (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
43. Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, et al. (2008) Alternative isoform regulation in human tissue transcriptomes. Nature 456: 470-476.
44. Deluca DS, Levin JZ, Sivachenko A, Fennell T, Nazaire MD, et al. (2012) RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28: 1530-1532.
45. Pulendran B, Ahmed R, (2011) Immunological mechanisms of vaccination. Nat Immunol 12: 509-517.
46. Huang HY, Chien CH, Jen KH, Huang HD, (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res 34: W429-434.
47. Le Breton M, Meyniel-Schicklin L, Deloire A, Coutard B, Canard B, et al. (2011) Flavivirus NS3 and NS5 proteins interaction network: a high-throughput yeast two-hybrid screen. BMC Microbiol 11: 234.
48. Li Q, Brass AL, Ng A, Hu Z, Xavier RJ, et al. (2009) A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc Natl Acad Sci U S A 106: 16410-16415.
49. Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, et al. (2009) A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe 5: 298-307.
50. Ward AM, Bidet K, Yinglin A, Ler SG, Hogue K, et al. (2011) Quantitative mass spectrometry of DENV-2 RNA-interacting proteins reveals that the DEAD-box RNA helicase DDX6 binds the DB1 and DB2 3′ UTR structures. RNA Biol 8: 1173-1186.
51. Le Sommer C, Barrows NJ, Bradrick SS, Pearson JL, Garcia-Blanco MA, (2012) G protein-coupled receptor kinase 2 promotes flaviviridae entry and replication. PLoS Negl Trop Dis 6: e1820.
52. Pena J, Harris E, (2011) Dengue virus modulates the unfolded protein response in a time-dependent manner. J Biol Chem 286: 14226-14236.
53. Yu CY, Hsu YW, Liao CL, Lin YL, (2006) Flavivirus infection activates the XBP1 pathway of the unfolded protein response to cope with endoplasmic reticulum stress. J Virol 80: 11868-11880.
54. Huang CY, Butrapet S, Pierro DJ, Chang GJ, Hunt AR, et al. (2000) Chimeric dengue type 2 (vaccine strain PDK-53)/dengue type 1 virus as a potential candidate dengue type 1 virus vaccine. J Virol 74: 3020-3028.
55. Sabchareon A, Wallace D, Sirivichayakul C, Limkittikul K, Chanthavanich P, et al. (2012) Protective efficacy of the recombinant, live-attenuated, CYD tetravalent dengue vaccine in Thai schoolchildren: a randomised, controlled phase 2b trial. Lancet 380: 1559-1567.