Identification of common biological pathways and drug targets across multiple respiratory viruses based on human host gene expression analysis

PLoS ONE

Volumn 7, Issue 3, 2012, Pages

  Smith, Steven B ^a,b   Dampier, William ^c   Tozeren, Aydin ^c   Brown, James R ^b   Magid Slav, Michal ^b  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b GLAXOSMITHKLINE   (United States)

^c DREXEL UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABATACEPT; ADALIMUMAB; AMRINONE; ARSENIC TRIOXIDE; BLOOD CLOTTING FACTOR 7A; CANAKINUMAB; CAPTOPRIL; CHLOROQUINE; CLENBUTEROL; DANAZOL; ETANERCEPT; INFLIXIMAB; IRBESARTAN; ISOPRENALINE; IXABEPILONE; MARIMASTAT; MESSENGER RNA; MINOCYCLINE; PARKIN; PRANLUKAST; THALIDOMIDE; THYMOCYTE ANTIBODY; UBIQUITIN; ANTIVIRUS AGENT; PROTEASOME; UBIQUITIN PROTEIN LIGASE;

ARTICLE; CASP1 GENE; CMMP9 GENE; CONTROLLED STUDY; COXSACKIE VIRUS; CYTOMEGALOVIRUS; DISEASE COURSE; F3 GENE; GENE EXPRESSION PROFILING; GENE SEQUENCE; HUMAN; HUMAN CELL; IL1B GENE; IMMUNE RESPONSE; INFLUENZA VIRUS A; METAPNEUMOVIRUS; MICROARRAY ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PARKINSON DISEASE; RESPIRATORY SYNCYTIAL PNEUMOVIRUS; RESPIRATORY VIRUS; RHINOVIRUS; SARS CORONAVIRUS; TNF GENE; VIRUS CELL INTERACTION; VIRUS GENE; VIRUS IDENTIFICATION; VIRUS INFECTION; DNA MICROARRAY; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETIC DATABASE; GENETICS; HOST PATHOGEN INTERACTION; METABOLISM; MOLECULARLY TARGETED THERAPY; PHYSIOLOGY; QUALITY CONTROL; RESPIRATORY SYNCYTIAL VIRUS INFECTION; SIGNAL TRANSDUCTION; VIROLOGY;

COXSACKIEVIRUS; CYTOMEGALOVIRUS; INFLUENZA A VIRUS; RESPIRATORY SYNCYTIAL VIRUS; RHINOVIRUS; SARS CORONAVIRUS;

ANTIVIRAL AGENTS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, VIRAL; HOST-PATHOGEN INTERACTIONS; HUMANS; MOLECULAR TARGETED THERAPY; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROTEASOME ENDOPEPTIDASE COMPLEX; QUALITY CONTROL; RESPIRATORY SYNCYTIAL VIRUS INFECTIONS; RESPIRATORY SYNCYTIAL VIRUSES; RNA, MESSENGER; SIGNAL TRANSDUCTION; UBIQUITIN; UBIQUITIN-PROTEIN LIGASES;

EID: 84863243471     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0033174     Document Type: Article

References (116)

1. Nichols GW, Peck Campbell AJ, Boeckh M, (2008) Respiratory Viruses Other than Influenza Virus: Impact and Therapeutic Advances. Clin Biol Rev 21: 274-290.
2. Shrestha SS, Swerdlow DL, Borse RH, Prabhu VS, Finelli L, et al. (2011) Estimating the burden of 2009 pandemic influenza A (H1N1) in the United States (April 2009-April 2010). Clin Infect Dis 52 (Suppl 1): S75-S82 ciq012 [pii];10.1093/cid/ciq012 [doi].
3. Meissner HC, Bocchini JA, Brady MT, Hall CB, Kimberlin DW, et al. (2009) The role of immunoprophylaxis in the reduction of disease attributable to respiratory syncytial virus. Pediatrics 124: 1676-1679 124/6/1676 [pii];10.1542/peds.2009-2346 [doi].
4. Bezerra PG, Britto MC, Correia JB, Duarte MC, Fonceca AM, et al. (2011) Viral and atypical bacterial detection in acute respiratory infection in children under five years. PLoS One 6: e18928 10.1371/journal.pone.0018928 [doi].
5. Cassino L, Benetti S, Fay F, Tanno H, Quarleri J, (2011) Unsuccessful therapy with adefovir and entecavir-tenofovir in a patient with chronic hepatitis B infection with previous resistance to lamivudine: a fourteen-year evolution of hepatitis B virus mutations. BMC Infect Dis 11: 178 1471-2334-11-178 [pii];10.1186/1471-2334-11-178 [doi].
6. Bonavia A, Franti M, Pusateri KE, Kuhen K, Seepersaud M, et al. (2011) Identification of broad-spectrum antiviral compounds and assessment of the druggability of their target for efficacy against respiratory syncytial virus (RSV). Proc Natl Acad Sci U S A 108: 6739-6744 1017142108 [pii];10.1073/pnas.1017142108 [doi].
7. Zhu Q, McAuliffe JM, Patel NK, Palmer-Hill FJ, Yang CF, et al. (2011) Analysis of respiratory syncytial virus preclinical and clinical variants resistant to neutralization by monoclonal antibodies palivizumab and/or motavizumab. J Infect Dis 203: 674-682 jiq100 [pii];10.1093/infdis/jiq100 [doi].
8. [Anonymous], (2011) Weekly epidemiological record:Recommended composition of influenza virus vaccines for use in the 2011-2012 northern hemisphere influenza season. pp. 81-92.
9. Oslund KL, Baumgarth N, (2011) Influenza-induced innate immunity: regulators of viral replication, respiratory tract pathology & adaptive immunity. Future Virol 6: 951-962.
10. Torchinsky MB, Garaude J, Blander JM, (2010) Infection and apoptosis as a combined inflammatory trigger. Curr Opin Immunol 22: 55-62 S0952-7915(10)00004-X [pii];10.1016/j.coi.2010.01.003 [doi].
11. Nagy PD, Pogany J, (2011) The dependence of viral RNA replication on co-opted host factors. Nat Rev Microbiol pp. nrmicro2692 [pii];10.1038/nrmicro2692 [doi].
12. Sayama K, Kajiya K, Sugawara K, Sato S, Hirakawa S, et al. (2010) Inflammatory mediator TAK1 regulates hair follicle morphogenesis and anagen induction shown by using keratinocyte-specific TAK1-deficient mice. PLoS One 5 e11275. 10.1371/journal.pone.0011275 [doi].
13. Rincon M, Anguita J, Nakamura T, Fikrig E, Flavell RA, (1997) Interleukin (IL)-6 directs the differentiation of IL-4-producing CD4+ T cells. J Exp Med 185: 461-469.
14. Subauste MC, Jacoby DB, Richards SM, Proud D, (1995) Infection of a human respiratory epithelial cell line with rhinovirus. Induction of cytokine release and modulation of susceptibility to infection by cytokine exposure. J Clin Invest 96: 549-557 10.1172/JCI118067 [doi].
15. Einarsson O, Geba GP, Zhu Z, Landry M, Elias JA, (1996) Interleukin-11: stimulation in vivo and in vitro by respiratory viruses and induction of airways hyperresponsiveness. J Clin Invest 97: 915-924 10.1172/JCI118514 [doi].
16. Churchill L, Friedman B, Schleimer RP, Proud D, (1992) Production of granulocyte-macrophage colony-stimulating factor by cultured human tracheal epithelial cells. Immunology 75: 189-195.
17. Tan SL, Ganji G, Paeper B, Proll S, Katze MG, (2007) Systems biology and the host response to viral infection. Nat Biotechnol 25: 1383-1389 nbt1207-1383 [pii];10.1038/nbt1207-1383 [doi].
18. Diedrich CR, Flynn JL, (2011) HIV-1/mycobacterium tuberculosis coinfection immunology: how does HIV-1 exacerbate tuberculosis? Infect Immun 79: 1407-1417 IAI.01126-10 [pii];10.1128/IAI.01126-10 [doi].
19. Piggott DA, Karakousis PC, (2011) Timing of antiretroviral therapy for HIV in the setting of TB treatment. Clin Dev Immunol 2011: 103917 10.1155/2011/103917 [doi].
20. Padhy BM, Gupta YK, (2011) Drug repositioning: Re-investigating existing drugs for new therapeutic indications. J Postgrad Med 57: 153-160 jpgm_2011_57_2_153_81870 [pii];10.4103/0022-3859.81870 [doi].
21. Brown JR, Magid-Slav M, Sanseau P, Rajpal DK, (2011) Computational biology approaches for selecting host-pathogen drug targets. Drug Discov Today 16: 229-236 S1359-6446(11)00026-2 [pii];10.1016/j.drudis.2011.01.008 [doi].
22. McGarvey PB, Huang H, Mazumder R, Zhang J, Chen Y, et al. (2009) Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets. PLoS One 4: e7162 10.1371/journal.pone.0007162 [doi].
23. Schwegmann A, Brombacher F, (2008) Host-directed drug targeting of factors hijacked by pathogens. Sci Signal 1: re8 scisignal.129re8 [pii];10.1126/scisignal.129re8 [doi].
24. Luo MH, Hannemann H, Kulkarni AS, Schwartz PH, O'Dowd JM, et al. (2010) Human cytomegalovirus infection causes premature and abnormal differentiation of human neural progenitor cells. J Virol 84: 3528-3541 JVI.02161-09 [pii];10.1128/JVI.02161-09 [doi].
25. Browne EP, Wing B, Coleman D, Shenk T, (2001) Altered cellular mRNA levels in human cytomegalovirus-infected fibroblasts: viral block to the accumulation of antiviral mRNAs. J Virol 75: 12319-12330 10.1128/JVI.75.24.12319-12330.2001 [doi].
26. Thornburg NJ, Shepherd B, Crowe JE Jr, (2010) Transforming growth factor beta is a major regulator of human neonatal immune responses following respiratory syncytial virus infection. J Virol 84: 12895-12902 JVI.01273-10 [pii];10.1128/JVI.01273-10 [doi].
27. Knoblach T, Grandel B, Seiler J, Nevels M, Paulus C, (2011) Human Cytomegalovirus IE1 Protein Elicits a Type II Interferon-Like Host Cell Response That Depends on Activated STAT1 but Not Interferon-gamma. PLoS Pathog 7: e1002016 10.1371/journal.ppat.1002016 [doi].
28. Lee SM, Chan RW, Gardy JL, Lo CK, Sihoe AD, et al. (2010) Systems-level comparison of host responses induced by pandemic and seasonal influenza A H1N1 viruses in primary human type I-like alveolar epithelial cells in vitro. Respir Res 11: 147 1465-9921-11-147 [pii];10.1186/1465-9921-11-147 [doi].
29. Overington J, (2009) ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBL-EBI). Interview by Wendy A. Warr. J Comput Aided Mol Des 23: 195-198 10.1007/s10822-009-9260-9 [doi].
30. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res 36: D901-D906 gkm958 [pii];10.1093/nar/gkm958 [doi].
31. Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, et al. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res 34: D668-D672 34/suppl_1/D668 [pii];10.1093/nar/gkj067 [doi].
32. The Jackson Laboratory (2011) Mouse Mutant Resource Web Site.
33. Dawany NB, Tozeren A, (2010) Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. BMC Bioinformatics 11: 483 1471-2105-11-483 [pii];10.1186/1471-2105-11-483 [doi].
34. Dawany NB, Dampier WN, Tozeren A, (2011) Large-scale integration of microarray data reveals genes and pathways common to multiple cancer types. Int J Cancer 128: 2881-2891 10.1002/ijc.25854 [doi].
35. Kauffmann A, Huber W, (2010) Microarray data quality control improves the detection of differentially expressed genes. Genomics 95: 138-142 S0888-7543(10)00004-2 [pii];10.1016/j.ygeno.2010.01.003 [doi].
36. Eierhoff T, Hrincius ER, Rescher U, Ludwig S, Ehrhardt C, (2010) The epidermal growth factor receptor (EGFR) promotes uptake of influenza A viruses (IAV) into host cells. PLoS Pathog 6 10.1371/journal.ppat.1001099 [doi].
37. Tung WH, Hsieh HL, Lee IT, Yang CM, (2011) Enterovirus 71 modulates a COX-2/PGE2/cAMP-dependent viral replication in human neuroblastoma cells: role of the c-Src/EGFR/p42/p44 MAPK/CREB signaling pathway. J Cell Biochem 112: 559-570 10.1002/jcb.22946 [doi].
38. Tung WH, Hsieh HL, Lee IT, Yang CM, (2011) Enterovirus 71 induces integrin beta1/EGFR-Rac1-dependent oxidative stress in SK-N-SH cells: role of HO-1/CO in viral replication(1). J Cell Physiol 10.1002/jcp.22677 [doi].
39. Yoshikawa T, Hill T, Li K, Peters CJ, Tseng CT, (2009) Severe acute respiratory syndrome (SARS) coronavirus-induced lung epithelial cytokines exacerbate SARS pathogenesis by modulating intrinsic functions of monocyte-derived macrophages and dendritic cells. J Virol 83: 3039-3048 JVI.01792-08 [pii];10.1128/JVI.01792-08 [doi].
40. Soukup JM, Becker S, (2003) Role of monocytes and eosinophils in human respiratory syncytial virus infection in vitro. Clin Immunol 107: 178-185 S152166160300038X [pii].
41. Banchereau J, Bazan F, Blanchard D, Briere F, Galizzi JP, et al. (1994) The CD40 antigen and its ligand. Annu Rev Immunol 12: 881-922 10.1146/annurev.iy.12.040194.004313 [doi].
42. Barbe F, Atanasova K, Van RK, (2011) Cytokines and acute phase proteins associated with acute swine influenza infection in pigs. Vet J 187: 48-53 S1090-0233(09)00488-2 [pii];10.1016/j.tvjl.2009.12.012 [doi].
43. Senft AP, Taylor RH, Lei W, Campbell SA, Tipper JL, et al. (2010) Respiratory syncytial virus impairs macrophage IFN-alpha/beta- and IFN-gamma-stimulated transcription by distinct mechanisms. Am J Respir Cell Mol Biol 42: 404-414 2008-0229OC [pii];10.1165/rcmb.2008-0229OC [doi].
44. Critchley-Thorne RJ, Yan N, Nacu S, Weber J, Holmes SP, et al. (2007) Down-regulation of the interferon signaling pathway in T lymphocytes from patients with metastatic melanoma. PLoS Med 4: e176 06-PLME-RA-0927R2 [pii];10.1371/journal.pmed.0040176 [doi].
45. Maedler K, Dharmadhikari G, Schumann DM, Storling J, (2009) Interleukin-1 beta targeted therapy for type 2 diabetes. Expert Opin Biol Ther 9: 1177-1188 10.1517/14712590903136688 [doi].
46. Gonzalez-Navajas JM, Lee J, David M, Raz E, (2012) Immunomodulatory functions of type I interferons. Nat Rev Immunol nri3133 [pii];10.1038/nri3133 [doi].
47. Chaugule VK, Burchell L, Barber KR, Sidhu A, Leslie SJ, et al. (2011) Autoregulation of Parkin activity through its ubiquitin-like domain. EMBO J 30: 2853-2867 emboj2011204 [pii];10.1038/emboj.2011.204 [doi].
48. Zhang Y, Gao J, Chung KK, Huang H, Dawson VL, et al. (2000) Parkin functions as an E2-dependent ubiquitin-protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1. Proceeding of the National Academy of Sciences of the United States of America 97: 13354-13359.
49. Ren Y, Zhao J, Feng J, (2003) Parkin binds to alpha/beta tubulin and increases their ubiquitination and degradation. The Journal of Neuroscience 23: 3316-3324.
50. Shimura H, Schlossmacher MG, Hattori N, Frosch MP, Trockenbacher A, et al. (2001) Ubiquitination of a new form of alpha-synuclein by parkin from human brain: implications for Parkinson's disease. Science 293: 263-269 10.1126/science.1060627 [doi];1060627 [pii].
51. Chung KK, Zhang Y, Lim KL, Tanaka Y, Huang H, et al. (2001) Parkin ubiquitinates the alpha-synuclein-interacting protein, synphilin-1: implications for Lewy-body formation in Parkinson disease. Nat Med 7: 1144-1150 10.1038/nm1001-1144 [doi];nm1001-1144 [pii].
52. Takahashi R, Imai Y, (2003) Pael receptor, endoplasmic reticulum stress, and Parkinson's disease. J Neurol 250 (Suppl 3): III25-III29 10.1007/s00415-003-1305-8 [doi].
53. Staropoli JF, McDermott C, Martinat C, Schulman B, Demireva E, et al. (2003) Parkin is a component of an SCF-like ubiquitin ligase complex and protects postmitotic neurons from kainate excitotoxicity. Neuron 37: 735-749 S0896627303000849 [pii].
54. Kahns S, Kalai M, Jakobsen LD, Clark BF, Vandenabeele P, et al. (2003) Caspase-1 and caspase-8 cleave and inactivate cellular parkin. J Biol Chem 278: 23376-23380 10.1074/jbc.M300495200 [doi];M300495200 [pii].
55. Jiang X, Chen ZJ, (2011) The role of ubiquitylation in immune defence and pathogen evasion. Nat Rev Immunol 12: 35-48 nri3111 [pii];10.1038/nri3111 [doi].
56. Zhang D, Zhang DE, (2011) Interferon-stimulated gene 15 and the protein ISGylation system. J Interferon Cytokine Res 31: 119-130 10.1089/jir.2010.0110 [doi].
57. Jang H, Boltz D, Sturm-Ramirez K, Shepherd KR, Jiao Y, et al. (2009) Highly pathogenic H5N1 influenza virus can enter the central nervous system and induce neuroinflammation and neurodegeneration. Proc Natl Acad Sci U S A 106: 14063-14068 0900096106 [pii];10.1073/pnas.0900096106 [doi].
58. Rohn TT, Catlin LW, (2011) Immunolocalization of influenza a virus and markers of inflammation in the human Parkinson's disease brain. PLoS One 6: e20495 10.1371/journal.pone.0020495 [doi];PONE-D-11-03510 [pii].
59. Jang H, Boltz DA, Webster RG, Smeyne RJ, (2009) Viral parkinsonism. Biochim Biophys Acta 1792: 714-721 S0925-4439(08)00156-7 [pii];10.1016/j.bbadis.2008.08.001 [doi].
60. Cookson MR, Lockhart PJ, McLendon C, O'Farrell C, Schlossmacher M, et al. (2003) RING finger 1 mutations in Parkin produce altered localization of the protein. Hum Mol Genet 12: 2957-2965 10.1093/hmg/ddg328 [doi];ddg328 [pii].
61. Gu WJ, Corti O, Araujo F, Hampe C, Jacquier S, et al. (2003) The C289G and C418R missense mutations cause rapid sequestration of human Parkin into insoluble aggregates. Neurobiol Dis 14: 357-364 S0969996103001529 [pii].
62. Wang C, Tan JM, Ho MW, Zaiden N, Wong SH, et al. (2005) Alterations in the solubility and intracellular localization of parkin by several familial Parkinson's disease-linked point mutations. J Neurochem 93: 422-431 JNC3023 [pii];10.1111/j.1471-4159.2005.03023.x [doi].
63. Ali S, Vollaard AM, Widjaja S, Surjadi C, van d V, et al. (2006) PARK2/PACRG polymorphisms and susceptibility to typhoid and paratyphoid fever. Clin Exp Immunol 144: 425-431 CEI3087 [pii];10.1111/j.1365-2249.2006.03087.x [doi].
64. Mira MT, Alcais A, Nguyen VT, Moraes MO, Di FC, et al. (2004) Susceptibility to leprosy is associated with PARK2 and PACRG. Nature 427: 636-640 10.1038/nature02326 [doi];nature02326 [pii].
65. Landau YE, Grisaru-Soen G, Reif S, Fattal-Valevski A, (2011) Pediatric Neurologic Complications Associated With Influenza A H1N1. Pediatr Neurol 44: 47-51 S0887-8994(10)00385-1 [pii];10.1016/j.pediatrneurol.2010.08.011 [doi].
66. Toovey S, (2008) Influenza-associated central nervous system dysfunction: a literature review. Travel Med Infect Dis 6: 114-124 S1477-8939(08)00048-3 [pii];10.1016/j.tmaid.2008.03.003 [doi].
67. Nakamura Y, Ikeda K, Yoshii Y, Ito H, Hirayama T, et al. (2011) Influenza-associated Monophasic Neuromyelitis Optica. Intern Med 50: 1605-1609 JST.JSTAGE/internalmedicine/50.5027 [pii].
68. Esmon CT, Xu J, Lupu F, (2011) Innate immunity and coagulation. J Thromb Haemost 9 (Suppl 1): 182-188 10.1111/j.1538-7836.2011.04323.x [doi].
69. Menu P, Vince JE, (2011) The NLRP3 inflammasome in health and disease: the good, the bad and the ugly. Clin Exp Immunol 10.1111/j.1365-2249.2011.04440.x [doi].
70. Luna T, Santos SB, Nascimento M, Porto MA, Muniz AL, et al. (2011) Effect of TNF-alpha production inhibitors on the production of pro-inflammatory cytokines by peripheral blood mononuclear cells from HTLV-1-infected individuals. Braz J Med Biol Res 44: 1134-1140 S0100-879X2011007500140 [pii].
71. Riccioni G, Bucciarelli T, Mancini B, Di IC, D'Orazio N, (2007) Antileukotriene drugs: clinical application, effectiveness and safety. Curr Med Chem 14: 1966-1977.
72. Ichiyama T, Kajimoto M, Hasegawa M, Hashimoto K, Matsubara T, et al. (2007) Cysteinyl leukotrienes enhance tumour necrosis factor-alpha-induced matrix metalloproteinase-9 in human monocytes/macrophages. Clin Exp Allergy 37: 608-614 CEA2692 [pii];10.1111/j.1365-2222.2007.02692.x [doi].
73. Tomari S, Matsuse H, Machida I, Kondo Y, Kawano T, et al. (2003) Pranlukast, a cysteinyl leukotriene receptor 1 antagonist, attenuates allergen-specific tumour necrosis factor alpha production and nuclear factor kappa B nuclear translocation in peripheral blood monocytes from atopic asthmatics. Clin Exp Allergy 33: 795-801 1656 [pii].
74. Giroir BP, Beutler B, (1992) Effect of amrinone on tumor necrosis factor production in endotoxic shock. Circ Shock 36: 200-207.
75. Matsumori A, (1997) The use of cytokine inhibitors. A new therapeutic insight into heart failure. Int J Cardiol 62 (Suppl 1): S3-12.
76. Crocker IC, Townley RG, Khan MM, (1996) Phosphodiesterase inhibitors suppress proliferation of peripheral blood mononuclear cells and interleukin-4 and-5 secretion by human T-helper type 2 cells. Immunopharmacology 31: 223-235.
77. Essayan DM, Huang SK, Kagey-Sobotka A, Lichtenstein LM, (1997) Differential efficacy of lymphocyte- and monocyte-selective pretreatment with a type 4 phosphodiesterase inhibitor on antigen-driven proliferation and cytokine gene expression. J Allergy Clin Immunol 99: 28-37 S0091674997000079 [pii].
78. Szczypka M, Obminska-Mrukowicz B, (2010) Modulating effects of nonselective and selective phosphodiesterase inhibitors on lymphocyte subsets and humoral immune response in mice. Pharmacol Rep 62: 1148-1158.
79. Verghese MW, McConnell RT, Strickland AB, Gooding RC, Stimpson SA, et al. (1995) Differential regulation of human monocyte-derived TNF alpha and IL-1 beta by type IV cAMP-phosphodiesterase (cAMP-PDE) inhibitors. J Pharmacol Exp Ther 272: 1313-1320.
80. Nemeth ZH, Szabo C, Hasko G, Salzman AL, Vizi ES, (1997) Effect of the phosphodiesterase III inhibitor amrinone on cytokine and nitric oxide production in immunostimulated J774.1 macrophages. Eur J Pharmacol 339: 215-221 S0014-2999(97)01392-7 [pii].
81. Ikemura T, Schwarze J, Makela M, Kanehiro A, Joetham A, et al. (2000) Type 4 phosphodiesterase inhibitors attenuate respiratory syncytial virus-induced airway hyper-responsiveness and lung eosinophilia. J Pharmacol Exp Ther 294: 701-706.
82. Voss A, Gescher K, Hensel A, Nacken W, Kerkhoff C, (2011) Double-stranded RNA induces MMP-9 gene expression in HaCaT keratinocytes by tumor necrosis factor-alpha. Inflamm Allergy Drug Targets 10: 171-179 IA-DT# 61 [pii].
83. Li W, Shen HH, (2007) Effect of respiratory syncytial virus on the activity of matrix metalloproteinase in mice. Chin Med J (Engl) 120: 5-11.
84. Yoo HG, Shin BA, Park JS, Lee KH, Chay KO, et al. (2002) IL-1beta induces MMP-9 via reactive oxygen species and NF-kappaB in murine macrophage RAW 264.7 cells. Biochem Biophys Res Commun 298: 251-256 S0006291X02024312 [pii].
85. Menu E, Muller-Trutwin MC, Pancino G, Saez-Cirion A, Bain C, et al. (2005) First Dominique Dormont International Conference on "Host-pathogen interactions in chronic infections- viral and host determinants of HCV, HCMV, and HIV infections". Retrovirology 2: 24 1742-4690-2-24 [pii];10.1186/1742-4690-2-24 [doi].
86. Husain M, Harrod KS, (2011) Enhanced acetylation of alpha-tubulin in influenza A virus infected epithelial cells. FEBS Lett 585: 128-132 S0014-5793(10)00928-2 [pii];10.1016/j.febslet.2010.11.023 [doi].
87. Tsueng G, Tabor-Godwin JM, Gopal A, Ruller CM, Deline S, et al. (2011) Coxsackievirus preferentially replicates and induces cytopathic effects in undifferentiated neural progenitor cells. J Virol 85: 5718-5732 JVI.02261-10 [pii];10.1128/JVI.02261-10 [doi].
88. Best SM, (2008) Viral subversion of apoptotic enzymes: escape from death row. Annu Rev Microbiol 62: 171-192 10.1146/annurev.micro.62.081307.163009 [doi].
89. Jonasch E, Haluska FG, (2001) Interferon in oncological practice: review of interferon biology, clinical applications, and toxicities. Oncologist 6: 34-55.
90. Hertzog P, Forster S, Samarajiwa S, (2011) Systems biology of interferon responses. J Interferon Cytokine Res 31: 5-11 10.1089/jir.2010.0126 [doi].
91. Pearson K, (1901) On lines and planes of closest fit to systems of points in space. Phil Mag pp. 559-572.
92. Hotelling H, (1933) Analysis of a complex of statistical variables into principal components. J Educ Psychol 24: 417-520.
93. Jolliffe TI, (2002) Principal Component Analysis Springer.
94. Chen K, (2006) Microarray Data analysis using Arraystudio.
95. Omicsoft (2011) Array Studio, version 4.1.1.58 [computer program]. Research Triangle Park, NC, USA.
96. Johnston G, (2011) SAS Software to Fit the Generalized Linear Model.
97. Ekins S, Nikolsky Y, Bugrim A, Kirillov E, Nikolskaya T, (2007) Pathway mapping tools for analysis of high content data. Methods Mol Biol 356: 319-350 1-59745-217-3:319 [pii].
98. Nikolsky Y, Kirillov E, Zuev R, Rakhmatulin E, Nikolskaya T, (2009) Functional analysis of OMICs data and small molecule compounds in an integrated "knowledge-based" platform. Methods Mol Biol 563: 177-196 10.1007/978-1-60761-175-2_10 [doi].
99. Draghici S, Khatri P, Martins RP, Ostermeier GC, Krawetz SA, (2003) Global functional profiling of gene expression. Genomics 81: 98-104 S0888754302000216 [pii].
100. Antoine Lucas (10 A.D.) Another Multidimensional Analysis Package, version.
101. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, et al. (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17: 520-525.
102. The MathWorks I, (2010) MATLAB, version 7.11 [computer program] Massachusetts.
103. Bolton EE, Wang Y, Thiessen PA, Bryant SH, (2008) PubChem: Integrated Platform of Small Molecules and Biological Activities. Ann Reports in Comp Chem 4.
104. Nogalski MT, Chan G, Stevenson EV, Gray S, Yurochko AD, (2011) Human cytomegalovirus-regulated paxillin in monocytes links cellular pathogenic motility to the process of viral entry. J Virol 85: 1360-1369 JVI.02090-10 [pii];10.1128/JVI.02090-10 [doi].
105. Mezger M, Bonin M, Kessler T, Gebhardt F, Einsele H, et al. (2009) Toll-like receptor 3 has no critical role during early immune response of human monocyte-derived dendritic cells after infection with the human cytomegalovirus strain TB40E. Viral Immunol 22: 343-351 10.1089/vim.2009.0011 [doi].
106. Chan G, Nogalski MT, Bentz GL, Smith MS, Parmater A, et al. (2010) PI3K-dependent upregulation of Mcl-1 by human cytomegalovirus is mediated by epidermal growth factor receptor and inhibits apoptosis in short-lived monocytes. J Immunol 184: 3213-3222 jimmunol.0903025 [pii];10.4049/jimmunol.0903025 [doi].
107. Reghunathan R, Jayapal M, Hsu LY, Chng HH, Tai D, et al. (2005) Expression profile of immune response genes in patients with Severe Acute Respiratory Syndrome. BMC Immunol 6: 2 1471-2172-6-2 [pii];10.1186/1471-2172-6-2 [doi].
108. Yoshikawa T, Hill TE, Yoshikawa N, Popov VL, Galindo CL, et al. (2010) Dynamic innate immune responses of human bronchial epithelial cells to severe acute respiratory syndrome-associated coronavirus infection. PLoS One 5: e8729 10.1371/journal.pone.0008729 [doi].
109. Hsu AC, Barr I, Hansbro PM, Wark PA, (2010) Human influenza is more effective than avian influenza at antiviral suppression in airway cells. Am J Respir Cell Mol Biol 44: 906-913.
110. Zaas AK, Chen M, Varkey J, Veldman T, Hero AO III, et al. (2009) Gene expression signatures diagnose influenza and other symptomatic respiratory viral infections in humans. Cell Host Microbe 6: 207-217 S1931-3128(09)00251-0 [pii];10.1016/j.chom.2009.07.006 [doi].
111. Lee SM, Gardy JL, Cheung CY, Cheung TK, Hui KP, et al. (2009) Systems-level comparison of host-responses elicited by avian H5N1 and seasonal H1N1 influenza viruses in primary human macrophages. PLoS One 4: e8072 10.1371/journal.pone.0008072 [doi].
112. Proud D, Turner RB, Winther B, Wiehler S, Tiesman JP, et al. (2008) Gene expression profiles during in vivo human rhinovirus infection: insights into the host response. Am J Respir Crit Care Med 178: 962-968 200805-670OC [pii];10.1164/rccm.200805-670OC [doi].
113. Bochkov YA, Hanson KM, Keles S, Brockman-Schneider RA, Jarjour NN, et al. (2010) Rhinovirus-induced modulation of gene expression in bronchial epithelial cells from subjects with asthma. Mucosal Immunol 3: 69-80 mi2009109 [pii];10.1038/mi.2009.109 [doi].
114. Bao X, Sinha M, Liu T, Hong C, Luxon BA, et al. (2008) Identification of human metapneumovirus-induced gene networks in airway epithelial cells by microarray analysis. Virology 374: 114-127 S0042-6822(07)00850-1 [pii];10.1016/j.virol.2007.12.024 [doi].
115. Mayer AK, Muehmer M, Mages J, Gueinzius K, Hess C, et al. (2007) Differential recognition of TLR-dependent microbial ligands in human bronchial epithelial cells. J Immunol 178: 3134-3142 178/5/3134 [pii].
116. Huang YC, Li Z, Hyseni X, Schmitt M, Devlin RB, et al. (2008) Identification of gene biomarkers for respiratory syncytial virus infection in a bronchial epithelial cell line. Genomic Med 2: 113-125 10.1007/s11568-009-9080-y [doi].