Host gene expression and respiratory syncytial virus infection

Current Topics in Microbiology and Immunology

Volumn 372, Issue , 2013, Pages 193-209

  Tripp, Ralph A ^a   Mejias, Asuncion ^b,c   Ramilo, Octavio ^b,c  

^a UNIVERSITY OF GEORGIA   (United States)

^b NATIONWIDE CHILDREN S HOSPITAL   (United States)

^c OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SHORT HAIRPIN RNA; SMALL INTERFERING RNA; TRANSCRIPTOME;

ARTICLE; BACTERIAL INFECTION; EXPERIMENTAL INFECTION; GENE EXPRESSION; GENETIC ASSOCIATION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; HUMAN; IMMUNE EVASION; IMMUNE RESPONSE; IMMUNOPATHOGENESIS; INFECTION RESISTANCE; INFECTION SENSITIVITY; INNATE IMMUNITY; MIXED INFECTION; NONHUMAN; PRIORITY JOURNAL; RESPIRATORY SYNCYTIAL VIRUS INFECTION; RESPIRATORY TRACT INFECTION; RNA INTERFERENCE; VIRUS IMMUNITY; VIRUS REPLICATION; VIRUS VIRULENCE;

ANIMALS; GENE EXPRESSION REGULATION; GENOME-WIDE ASSOCIATION STUDY; HOST-PATHOGEN INTERACTIONS; HUMANS; IMMUNITY, INNATE; MICE; RESPIRATORY SYNCYTIAL VIRUS INFECTIONS; RESPIRATORY SYNCYTIAL VIRUS VACCINES; RESPIRATORY SYNCYTIAL VIRUS, HUMAN; RNA INTERFERENCE; RNA, SMALL INTERFERING; TRANSCRIPTOME; VIRUS REPLICATION;

EID: 84892746515     PISSN: 0070217X     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-642-38919-1_10     Document Type: Article

References (60)

1. Alvisi G, Rawlinson SM, Ghildyal R, Ripalti A, Jans DA (2008) Regulated nucleocytoplasmic trafficking of viral gene products: a therapeutic target? Biochim Biophys Acta 1784:213-227
2. Aza-Blanc P, Cooper CL, Wagner K, Batalov S, Deveraux QL, Cooke MP (2003) Identification of modulators of TRAIL-induced apoptosis via RNAi-based phenotypic screening. Mol Cell 12:627-637
3. Bakre A, Mitchell P, Coleman JK, Jones LP, Saavedra G, Teng M, Tompkins SM, Tripp RA. (2012) Respiratory syncytial virus modifies microRNAs regulating host genes that affect virus replication. J Gen Virol 93(11):2346-2356
4. Banchereau R, Jordan-Villegas A, Ardura M, Mejias A, Baldwin N, Xu H, Saye E, Rossello-Urgell J, Nguyen P, Blankenship D, Creech CB, Pascual V, Banchereau J, Chaussabel D, Ramilo O (2012) Host immune transcriptional profiles reflect the variability in clinical disease manifestations in patients with Staphylococcus aureus infections. PLoS ONE 7:e34390
5. Berry MP, Graham CM, McNab FW, Xu Z, Bloch SA, Oni T, Wilkinson KA, Banchereau R, Skinner J, Wilkinson RJ, Quinn C, Blankenship D, Dhawan R, Cush JJ, Mejias A, Ramilo O, Kon OM, Pascual V, Banchereau J, Chaussabel D, O'Garra A (2010) An interferon-inducible neutrophil-driven blood transcriptional signature in human tuberculosis. Nature 466:973-977
6. Brummelkamp TR, Bernards R, Agami R (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296:550-553
7. Bushman FD, Malani N, Fernandes J, D'Orso I, Cagney G, Diamond TL, Zhou H, Hazuda DJ, Espeseth AS, Konig R, Bandyopadhyay S, Ideker T, Goff SP, Krogan NJ, Frankel AD, Young JA, Chanda SK (2009) Host cell factors in HIV replication: meta-analysis of genome-wide studies. PLoS Pathog 5:e1000437
8. Chaussabel D, Allman W, Mejias A, Chung W, Bennett L, Ramilo O, Pascual V, Palucka AK, Banchereau J (2005) Analysis of significance patterns identifies ubiquitous and diseasespecific gene-expression signatures in patient peripheral blood leukocytes. Ann N Y Acad Sci 1062:146-154
9. Chaussabel D, Quinn C, Shen J, Patel P, Glaser C, Baldwin N, Stichweh D, Blankenship D, Li L, Munagala I, Bennett L, Allantaz F, Mejias A, Ardura M, Kaizer E, Monnet L, Allman W, Randall H, Johnson D, Lanier A, Punaro M, Wittkowski KM, White P, Fay J, Klintmalm G, Ramilo O, Palucka AK, Banchereau J, Pascual V (2008) A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus. Immunity 29:150-164
10. Chaussabel D, Pascual V, Banchereau J (2010) Assessing the human immune system through blood transcriptomics. BMC Biol 8:84
11. Cullen BR (2006) Enhancing and confirming the specificity of RNAi experiments. Nat Methods 3:677-681
12. Dupuy LC, Dobson S, Bitko V, Barik S (1999) Casein kinase 2-mediated phosphorylation of respiratory syncytial virus phosphoprotein P is essential for the transcription elongation activity of the viral polymerase; phosphorylation by casein kinase 1 occurs mainly at Ser (215) and is without effect. J Virol 73:8384-8392
13. Fjaerli HO, Bukholm G, Krog A, Skjaeret C, Holden M, Nakstad B (2006) Whole blood gene expression in infants with respiratory syncytial virus bronchiolitis. BMC Infect Dis 6:175
14. Fjaerli HO, Bukholm G, Skjaeret C, Holden M, Nakstad B (2007) Cord blood gene expression in infants hospitalized with respiratory syncytial virus bronchiolitis. J Infect Dis 196:394-404
15. Ghildyal R, Ho A, Wagstaff KM, Dias MM, Barton CL, Jans P, Bardin P, Jans DA (2005) Nuclear import of the respiratory syncytial virus matrix protein is mediated by importin beta1 independent of importin alpha. Biochemistry 44:12887-12895
16. Ghildyal R, Ho A, Dias M, Soegiyono L, Bardin PG, Tran KC, Teng MN, Jans DA (2009) The respiratory syncytial virus matrix protein possesses a Crm1-mediated nuclear export mechanism. J Virol 83:5353-5362
17. Ghildyal R, Jans DA, Bardin PG, Mills J (2012) Protein-protein interactions in RSV assembly: potential targets for attenuating RSV strains. Infect Disord Drug Targets 12:103-109
18. Gobert GN (2010) Better understanding of anti-schistosomal strategies through microarray analysis. Infect Disord Drug Targets 10:251-257
19. Gonzalez LC (2012) Protein microarrays, biosensors, and cell-based methods for secretome-wide extracellular protein-protein interaction mapping. Methods 57(4):448-458
20. Graham BS (2011) Biological challenges and technological opportunities for respiratory syncytial virus vaccine development. Immunol Rev 239:149-166
21. Graham BS, Perkins MD, Wright PF, Karzon DT (1988) Primary respiratory syncytial virus infection in mice. J Med Virol 26:153-162
22. Houzet L, Jeang KT (2011) Genome-wide screening using RNA interference to study host factors in viral replication and pathogenesis. Exp Biol Med (Maywood) 236:962-967
23. Huang YC, Li Z, Hyseni X, Schmitt M, Devlin RB, Karoly ED, Soukup JM (2008) Identification of gene biomarkers for respiratory syncytial virus infection in a bronchial epithelial cell line. Genomic Med 2:113-125
24. Hussell T, Georgiou A, Sparer TE, Matthews S, Pala P, Openshaw PJ (1998) Host genetic determinants of vaccine-induced eosinophilia during respiratory syncytial virus infection. J Immunol 161:6215-6222
25. Ioannidis I, McNally B, Willette M, Peeples ME, Chaussabel D, Durbin JE, Ramilo O, Mejias A, Flano E (2012) Plasticity and virus specificity of the airway epithelial cell immune response during respiratory virus infection. J Virol 86:5422-5436
26. Jafari M, Soltani M, Naahidi S, Karunaratne DN, Chen P (2012) Nonviral approach for targeted nucleic acid delivery. Curr Med Chem 19:197-208
27. Janssen R, Pennings J, Hodemaekers H, Buisman A, Van Oosten M, De Rond L, Ozturk K, Dormans J, Kimman T, Hoebee B (2007) Host transcription profiles upon primary respiratory syncytial virus infection. J Virol 81:5958-5967
28. Karlas A, Machuy N, Shin Y, Pleissner KP, Artarini A, Heuer D, Becker D, Khalil H, Ogilvie LA, Hess S, Maurer AP, Muller E, Wolff T, Rudel T, Meyer TF (2010) Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication. Nature 463:818-822
29. Kimpton J, Emerman M (1992) Detection of replication-competent and pseudotyped human immunodeficiency virus with a sensitive cell line on the basis of activation of an integrated beta-galactosidase gene. J Virol 66:2232-2239
30. Konig R, Stertz S, Zhou Y, Inoue A, Hoffmann HH, Bhattacharyya S, Alamares JG, Tscherne DM, Ortigoza MB, Liang Y, Gao Q, Andrews SE, Bandyopadhyay S, De Jesus P, Tu BP, Pache L, Shih C, Orth A, Bonamy G, Miraglia L, Ideker T, Garcia-Sastre A, Young JA, Palese P, Shaw ML, Chanda SK (2010) Human host factors required for influenza virus replication. Nature 463:813-817
31. Krausz E (2007) High-content siRNA screening. Mol BioSyst 3:232-240
32. Leroy Q, Raoult D (2010) Review of microarray studies for host-intracellular pathogen interactions. J Microbiol Methods 81:81-95
33. Martinez I, Lombardia L, Garcia-Barreno B, Dominguez O, Melero JA (2007) Distinct gene subsets are induced at different time points after human respiratory syncytial virus infection of A549 cells. J Gen Virol 88:570-581
34. Medzhitov R, Janeway CA Jr (1997) Innate immunity: the virtues of a nonclonal system of recognition. Cell 91:295-298
35. Medzhitov R, Janeway C Jr (2000) Innate immune recognition: mechanisms and pathways. Immunol Rev 173:89-97
36. Mejias A, Dimo B, Jordan-Villegas A, Jartti T, Zu X, Suarez N, Banchereau J, Chaussabel D, Ramilo O (2012) Respiratory syncytial virus infection induces a unique gene expression profile that correlates with disease severity. In: 8th annual respiratory syncytial virus symposium, Santa Fe, NM
37. Meliopoulos VA, Andersen LE, Birrer KF, Simpson KJ, Lowenthal JW, Bean AG, Stambas J Stewart CR, Tompkins SM, Van Beusechem VW, Fraser I, Mhlanga M, Barichievy S, Smith Q, Leake D, Karpilow J, Buck A, Jona G, Tripp RA (2012) Host gene targets for novel influenza therapies elucidated by high-throughput RNA interference screens. FASEB J 26:1372-1386
38. Miller MB, Tang YW (2009) Basic concepts of microarrays and potential applications in clinical microbiology. Clin Microbiol Rev 22:611-633
39. Min JY, Subbarao K (2010) Cellular targets for influenza drugs. Nat Biotechnol 28:239-240
40. Monsurro V, Marincola FM (2011) Microarray analysis for a comprehensive immunologicalstatus evaluation during cancer vaccine immune monitoring. J Biomed Biotechnol 2011:307297
41. Moss EG (2001) RNA interference: it's a small RNA world. Curr Biol 11:R772-R775
42. Oyelaran O, Gildersleeve JC (2007) Application of carbohydrate array technology to antigen discovery and vaccine development. Expert Rev Vaccines 6:957-969
43. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16:948-958
44. Pan Q, Van Der Laan LJ, Janssen HL, Peppelenbosch MP (2012) A dynamic perspective of RNAi library development. Trends Biotechnol 30:206-215
45. Pankla R, Buddhisa S, Berry M, Blankenship DM, Bancroft GJ, Banchereau J, Lertmemongkolchai G, Chaussabel D (2009) Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis. Genome Biol 10:R127
46. Pennings JL, Schuurhof A, Hodemaekers HM, Buisman A, De Rond LC, Widjojoatmodjo MN, Luytjes W, Kimpen JL, Bont L, Janssen R (2011) Systemic signature of the lung response to respiratory syncytial virus infection. PLoS ONE 6:e21461
47. Prince GA, Horswood RL, Berndt J, Suffin SC, Chanock RM (1979) Respiratory syncytial virus infection in inbred mice. Infect Immun 26:764-766
48. Ramilo O, Allman W, Chung W, Mejias A, Ardura M, Glaser C, Wittkowski KM, Piqueras B, Banchereau J, Palucka AK, Chaussabel D (2007) Gene expression patterns in blood leukocytes discriminate patients with acute infections. Blood 109:2066-2077
49. Segovia J, Sabbah A, Mgbemena V, Tsai SY, Chang TH, Berton MT, Morris IR, Allen IC, Ting JP, Bose S (2012) TLR2/MyD88/NF-kappaB pathway, reactive oxygen species, potassium efflux activates NLRP3/ASC inflammasome during respiratory syncytial virus infection. PLoS ONE 7:e29695
50. Stark JM, Barmada MM, Winterberg AV, Majumber N, Gibbons WJ Jr, Stark MA, Sartor MA, Medvedovic M, Kolls J, Bein K, Mailaparambil B, Krueger M, Heinzmann A, Leikauf GD, Prows DR (2009) Genomewide association analysis of respiratory syncytial virus infection in mice. J Virol 84:2257-2269
51. Stark JM, McDowell SA, Koenigsknecht V, Prows DR, Leikauf JE, Le Vine AM, Leikauf GD (2002) Genetic susceptibility to respiratory syncytial virus infection in inbred mice. J Med Virol 67:92-100
52. Schuurhof A, Bont L, Pennings JL, Hodemaekers HM, Wester PW, Buisman A, De Rond LC, Widjojoatmodjo MN, Luytjes W, Kimpen JL, Janssen R (2010) Gene expression differences in lungs of mice during secondary immune responses to respiratory syncytial virus infection. J Virol 84:9584-9594
53. Tayyari F, Hegele RG (2012) Identifying targets in the hunt for effective respiratory syncytial virus interventions. Expert rev respir med 6:215-222
54. Tijsterman M, Plasterk RH (2004) Dicers at RISC; the mechanism of RNAi. Cell 117:1-3
55. Tiscornia G, Singer O, Ikawa M, Verma IM (2003) A general method for gene knockdown in mice by using lentiviral vectors expressing small interfering RNA. Proc Natl Acad Sci USA 100:1844-1848
56. Tripp RA, Oshansky C, Alvarez R (2005) Cytokines and respiratory syncytial virus infection. Proc Am Thorac Soc 2:147-149
57. Uttamchandani M, Neo JL, Ong BN, Moochhala S (2009) Applications of microarrays in pathogen detection and biodefence. Trends Biotechnol 27:53-61
58. Van Diepen A, Brand HK, Sama I, Lambooy LH, Van Den Heuvel LP, Van Der Well L, Huynen M, Osterhaus AD, Andeweg AC, Hermans PW Quantitative proteome profiling of respiratory virus-infected lung epithelial cells. J Proteomics 73:1680-1693
59. Zaas AK, Chen M, Varkey J, Veldman T, Hero AO 3rd, Lucas J, Huang Y, Turner R, Gilbert A, Lambkin-Williams R, Oien 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
60. Ziauddin J, Sabatini DM (2001) Microarrays of cells expressing defined cDNAs. Nature 411:107-110