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Research Paper

Type I interferon related genes are common genes on the early stage after vaccination by meta-analysis of microarray data

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Pages 739-745 | Received 28 Aug 2014, Accepted 14 Dec 2014, Published online: 03 Apr 2015

References

  • Pulendran B, Li S, Nakaya HI. Systems vaccinology. Immunity 2010; 33:516-29; PMID:21029962; http://dx.doi.org/10.1016/j.immuni.2010.10.006
  • Nakaya HI, Wrammert J, Lee EK, Racioppi L, Marie-Kunze S, Haining WN, Means AR, Kasturi SP, Khan N, Li GM, et al. Systems biology of vaccination for seasonal influenza in humans. Nat Immunol 2011; 12:786-95; PMID:21743478; http://dx.doi.org/10.1038/ni.2067
  • Querec TD, Akondy RS, Lee EK, Cao W, Nakaya HI, Teuwen D, Pirani A, Gernert K, Deng J, Marzolf B, et al. Systems biology approach predicts immunogenicity of the yellow fever vaccine in humans. Nat Immunol 2009; 10:116-25; PMID:19029902; http://dx.doi.org/10.1038/ni.1688
  • Gaucher D, Therrien R, Kettaf N, Angermann BR, Boucher G, Filali-Mouhim A, Moser JM, Mehta RS, Drake DR, 3rd, Castro E, et al. Yellow fever vaccine induces integrated multilineage and polyfunctional immune responses. J Exp Med 2008; 205:3119-131; PMID:19047440; http://dx.doi.org/10.1084/jem.20082292
  • Ramasamy A, Mondry A, Holmes CC, Altman DG. Key issues in conducting a meta-analysis of gene expression microarray datasets. PLoS Med 2008; 5:e184; PMID:18767902
  • Pulendran B, Ahmed R. Translating innate immunity into immunological memory: implications for vaccine development. Cell 2006; 124:849-63; PMID:16497593; http://dx.doi.org/10.1016/j.cell.2006.02.019
  • Steinman RM. Dendritic cells in vivo: a key target for a new vaccine science. Immunity 2008, 29:319-24; PMID:18799140; http://dx.doi.org/10.1016/j.immuni.2008.08.001
  • Coffman RL, Sher A, Seder RA. Vaccine adjuvants: putting innate immunity to work. Immunity 2010; 33:492-503; PMID:21029960; http://dx.doi.org/10.1016/j.immuni.2010.10.002
  • Iwasaki A, Medzhitov R. Regulation of adaptive immunity by the innate immune system. Science 2010; 327:291-5; PMID:20075244; http://dx.doi.org/10.1126/science.1183021
  • Campain A, Yang YH. Comparison study of microarray meta-analysis methods. BMC Bioinformatics 2010; 11:408-18; PMID:20678237; http://dx.doi.org/10.1186/1471-2105-11-408
  • Garcia-Pineres AJ, Hildesheim A, Dodd L, Kemp TJ, Yang J, Fullmer B, Harro C, Lowy DR, Lempicki RA, Pinto LA. Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients. J Immunol 2009; 182:1706-29; PMID:19155521; http://dx.doi.org/10.4049/jimmunol.182.3.1706
  • Rhodes DR, Barrette TR, Rubin MA, Ghosh D, Chinnaiyan AM. Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. Cancer Res 2002; 62:4427-33; PMID:12154050
  • Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 2004; 14:1085-94; PMID:15173114; http://dx.doi.org/10.1101/gr.1910904
  • Pilarsky C, Wenzig M, Specht T, Saeger HD, Grutzmann R. Identification and validation of commonly overexpressed genes in solid tumors by comparison of microarray data. Neoplasia 2004; 6:744-50; PMID:15720800; http://dx.doi.org/10.1593/neo.04277
  • Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. Large-scale meta-analysis of cancer microarray data identifies common transcriptional profiles of neoplastic transformation and progression. Proc Natl Acad Sci U S A 2004; 101:9309-14; PMID:15184677; http://dx.doi.org/10.1073/pnas.0401994101
  • Wang J, Coombes KR, Highsmith WE, Keating MJ, Abruzzo LV. Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies. Bioinformatics 2004; 20:3166-78; PMID:15231529; http://dx.doi.org/10.1093/bioinformatics/bth381
  • Grutzmann R, Boriss H, Ammerpohl O, Luttges J, Kalthoff H, Schackert HK, Kloppel G, Saeger HD, Pilarsky C. Meta-analysis of microarray data on pancreatic cancer defines a set of commonly dysregulated genes. Oncogene 2005; 24:5079-88; PMID:15897887; http://dx.doi.org/10.1038/sj.onc.1208696
  • Mehra R, Varambally S, Ding L, Shen R, Sabel MS, Ghosh D, Chinnaiyan AM, Kleer CG. Identification of GATA3 as a breast cancer prognostic marker by global gene expression meta-analysis. Cancer Res 2005; 65:11259-64; PMID:16357129; http://dx.doi.org/10.1158/0008-5472.CAN-05-2495
  • Bianchi F, Nuciforo P, Vecchi M, Bernard L, Tizzoni L, Marchetti A, Buttitta F, Felicioni L, Nicassio F, Di Fiore PP. Survival prediction of stage I lung adenocarcinomas by expression of 10 genes. J Clin Invest 2007; 117:3436-44; PMID:17948124; http://dx.doi.org/10.1172/JCI32007
  • Kim SY, Kim JH, Lee HS, Noh SM, Song KS, Cho JS, Jeong HY, Kim WH, Yeom YI, Kim NS et al. Meta- and gene set analysis of stomach cancer gene expression data. Mol Cells 2007; 24:200-9; PMID:17978572
  • Silva GL, Junta CM, Mello SS, Garcia PS, Rassi DM, Sakamoto-Hojo ET, Donadi EA, Passos GA. Profiling meta-analysis reveals primarily gene coexpression concordance between systemic lupus erythematosus and rheumatoid arthritis. Ann N Y Acad Sci 2007; 1110:33-46; PMID:17911418; http://dx.doi.org/10.1196/annals.1423.005
  • Obermoser G, Presnell S, Domico K, Xu H, Wang Y, Anguiano E, Thompson-Snipes L, Ranganathan R, Zeitner B, Bjork A, et al. Systems scale interactive exploration reveals quantitative and qualitative differences in response to influenza and pneumococcal vaccines. Immunity 2013; 38:831-44; PMID:23601689; http://dx.doi.org/10.1016/j.immuni.2012.12.008
  • Vahey MT, Wang Z, Kester KE, Cummings J, Heppner DG, Jr., Nau ME, Ofori-Anyinam O, Cohen J, Coche T, Ballou WR, et al. Expression of genes associated with immunoproteasome processing of major histocompatibility complex peptides is indicative of protection with adjuvanted RTS,S malaria vaccine. J Infect Dis 2010; 201:580-9; PMID:20078211; http://dx.doi.org/10.1086/650310
  • Palfree RG, LeClair KP, Bothwell A, Hammerling U. cDNA characterization of an Ly-6.2 gene expressed in BW5147 tumor cells. Immunogenetics 1987; 26:389-91; PMID:2822573; http://dx.doi.org/10.1007/BF00343712
  • Codias EK, Malek TR. Regulation of B lymphocyte responses to IL-4 and IFN-gamma by activation through Ly-6A/E molecules. J Immunol 1990; 144:2197-204; PMID:2107254
  • Henrik Gad H, Paulous S, Belarbi E, Diancourt L, Drosten C, Kummerer BM, Plate AE, Caro V, Despres P. The E2-E166K substitution restores Chikungunya virus growth in OAS3 expressing cells by acting on viral entry. Virology 2012; 434:27-37; PMID:22889614
  • Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, Bieniasz P, Rice CM. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 2011; 472:481-5; PMID:21478870; http://dx.doi.org/10.1038/nature09907
  • Xiao H, Killip MJ, Staeheli P, Randall RE, Jackson D. The human interferon-induced MxA protein inhibits early stages of influenza A virus infection by retaining the incoming viral genome in the cytoplasm. J Virol 2013; 87:13053-8; PMID:24049170; http://dx.doi.org/10.1128/JVI.02220-13
  • Bloch DB, Li P, Bloch EG, Berenson DF, Galdos RL, Arora P, Malhotra R, Wu C, Yang W. LMKB/MARF1 localizes to mRNA processing bodies, interacts with Ge-1, and regulates IFI44L gene expression. PLoS One 2014; 9:e94784; PMID:24755989; http://dx.doi.org/10.1371/journal.pone.0094784
  • Park GH, Kim KY, Cho SW, Cheong JY, Yu GI, Shin DH, Kwack KB. Association between Interferon-Inducible Protein 6 (IFI6) Polymorphisms and Hepatitis B Virus Clearance. Genomics Inform 2013; 11:15-23; PMID:23613678; http://dx.doi.org/10.5808/GI.2013.11.1.15
  • Garcia-Pineres AJ, Hildesheim A, Dodd L, Kemp TJ, Yang J, Fullmer B, Harro C, Lowy DR, Lempicki RA, Pinto LA. Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients. J Immunol 2009; 182:1706-29; PMID:19155521; http://dx.doi.org/10.4049/jimmunol.182.3.1706
  • Sadler AJ, Williams BR. Interferon-inducible antiviral effectors. Nat Rev Immunol 2008; 8:559-68; PMID:18575461; http://dx.doi.org/10.1038/nri2314
  • Kochs G, Haller O. Interferon-induced human MxA GTPase blocks nuclear import of Thogoto virus nucleocapsids. Proc Natl Acad Sci U S A 1999; 96:2082-6; PMID:10051598; http://dx.doi.org/10.1073/pnas.96.5.2082
  • Accola MA, Huang B, Al Masri A, McNiven MA. The antiviral dynamin family member, MxA, tubulates lipids and localizes to the smooth endoplasmic reticulum. J Biol Chem 2002; 277:21829-35; PMID:11916975; http://dx.doi.org/10.1074/jbc.M201641200
  • Kerr IM, Brown RE, Hovanessian AG. Nature of inhibitor of cell-free protein synthesis formed in response to interferon and double-stranded RNA. Nature 1977; 268:540-2; PMID:196217; http://dx.doi.org/10.1038/268540a0
  • Rebouillat D, Hovanessian AG. The human 2',5'-oligoadenylate synthetase family: interferon-induced proteins with unique enzymatic properties. J Interferon Cytokine Res 1999; 19:295-308; PMID:10334380; http://dx.doi.org/10.1089/107999099313992
  • Clemens MJ, Vaquero CM. Inhibition of protein synthesis by double-stranded RNA in reticulocyte lysates: evidence for activation of an endoribonuclease. Biochem Biophys Res Commun 1978; 83:59-68; PMID:212051; http://dx.doi.org/10.1016/0006-291X(78)90397-2
  • Roberts WK, Hovanessian A, Brown RE, Clemens MJ, Kerr IM. Interferon-mediated protein kinase and low-molecular-weight inhibitor of protein synthesis. Nature 1976; 264:477-80; PMID:1004583; http://dx.doi.org/10.1038/264477a0
  • Yuan W, Krug RM. Influenza B virus NS1 protein inhibits conjugation of the interferon (IFN)-induced ubiquitin-like ISG15 protein. EMBO J 2001; 20:362-71; PMID:11157743; http://dx.doi.org/10.1093/emboj/20.3.362
  • Takeuchi T, Iwahara S, Saeki Y, Sasajima H, Yokosawa H. Link between the ubiquitin conjugation system and the ISG15 conjugation system: ISG15 conjugation to the UbcH6 ubiquitin E2 enzyme. J Biochem 2005; 138:711-9; PMID:16428300; http://dx.doi.org/10.1093/jb/mvi172
  • Zhao C, Beaudenon SL, Kelley ML, Waddell MB, Yuan W, Schulman BA, Huibregtse JM, Krug RM. The UbcH8 ubiquitin E2 enzyme is also the E2 enzyme for ISG15, an IFN-alpha/beta-induced ubiquitin-like protein. Proc Natl Acad Sci U S A 2004; 101:7578-82; PMID:15131269; http://dx.doi.org/10.1073/pnas.0402528101
  • Lenschow DJ, Giannakopoulos NV, Gunn LJ, Johnston C, O'Guin AK, Schmidt RE, Levine B, Virgin HW, 4th. Identification of interferon-stimulated gene 15 as an antiviral molecule during Sindbis virus infection in vivo. J Virol 2005; 79:13974-83; PMID:16254333; http://dx.doi.org/10.1128/JVI.79.22.13974-13983.2005
  • Osiak A, Utermohlen O, Niendorf S, Horak I, Knobeloch KP. ISG15, an interferon-stimulated ubiquitin-like protein, is not essential for STAT1 signaling and responses against vesicular stomatitis and lymphocytic choriomeningitis virus. Mol Cell Biol 2005; 25:6338-45; PMID:16024773; http://dx.doi.org/10.1128/MCB.25.15.6338-6345.2005
  • Best SM, Morris KL, Shannon JG, Robertson SJ, Mitzel DN, Park GS, Boer E, Wolfinbarger JB, Bloom ME. Inhibition of interferon-stimulated JAK-STAT signaling by a tick-borne flavivirus and identification of NS5 as an interferon antagonist. J Virol 2005; 79:12828-39; PMID:16188985; http://dx.doi.org/10.1128/JVI.79.20.12828-12839.2005
  • Yu S, Chen J, Wu M, Chen H, Kato N, Yuan Z. Hepatitis B virus polymerase inhibits RIG-I- and Toll-like receptor 3-mediated beta interferon induction in human hepatocytes through interference with interferon regulatory factor 3 activation and dampening of the interaction between TBK1/IKKepsilon and DDX3. J Gen Virol 2010; 91:2080-90; PMID:20375222; http://dx.doi.org/10.1099/vir.0.020552-0
  • Munoz-Jordan JL, Sanchez-Burgos GG, Laurent-Rolle M, Garcia-Sastre A. Inhibition of interferon signaling by dengue virus. Proc Natl Acad Sci U S A 2003; 100:14333-8; PMID:14612562; http://dx.doi.org/10.1073/pnas.2335168100
  • Caignard G, Bourai M, Jacob Y, Tangy F, Vidalain PO. Inhibition of IFN-alpha/beta signaling by two discrete peptides within measles virus V protein that specifically bind STAT1 and STAT2. Virology 2009; 383:112-20; PMID:19007958; http://dx.doi.org/10.1016/j.virol.2008.10.014
  • Schlender J, Hornung V, Finke S, Gunthner-Biller M, Marozin S, Brzozka K, Moghim S, Endres S, Hartmann G, Conzelmann KK. Inhibition of toll-like receptor 7- and 9-mediated alpha/beta interferon production in human plasmacytoid dendritic cells by respiratory syncytial virus and measles virus. J Virol 2005; 79:5507-15; PMID:15827165; http://dx.doi.org/10.1128/JVI.79.9.5507-5515.2005
  • Parlato S, Bruni R, Fragapane P, Salerno D, Marcantonio C, Borghi P, Tataseo P, Ciccaglione AR, Presutti C, Romagnoli G et al. IFN-alpha regulates Blimp-1 expression via miR-23a and miR-125b in both monocytes-derived DC and pDC. PLoS One 2013; 8:e72833; PMID: 23977359
  • Coro ES, Chang WL, Baumgarth N. Type I IFN receptor signals directly stimulate local B cells early following influenza virus infection. J Immunol 2006; 176:4343-51; PMID:16547272; http://dx.doi.org/10.4049/jimmunol.176.7.4343
  • Le Bon A, Thompson C, Kamphuis E, Durand V, Rossmann C, Kalinke U, Tough DF. Cutting edge:enhancement of antibody responses through direct stimulation of B and T cells by type I IFN. J Immunol 2006; 176:2074-8; PMID:16455962; http://dx.doi.org/10.4049/jimmunol.176.4.2074
  • Kim D, Martinez-Sobrido L, Choi C, Petroff N, Garcia-Sastre A, Niewiesk S, Carsillo T. Induction of type I interferon secretion through recombinant Newcastle disease virus expressing measles virus hemagglutinin stimulates antibody secretion in the presence of maternal antibodies. J Virol 2011; 85:200-7; PMID:20962092; http://dx.doi.org/10.1128/JVI.01624-10
  • Jego G, Palucka AK, Blanck JP, Chalouni C, Pascual V, Banchereau J. Plasmacytoid dendritic cells induce plasma cell differentiation through type I interferon and interleukin 6. Immunity 2003; 19:225-34; PMID:12932356; http://dx.doi.org/10.1016/S1074-7613(03)00208-5
  • Wang Y, Tong X, Zhang J, Ye X. The complement C1qA enhances retinoic acid-inducible gene-I-mediated immune signalling. Immunology 2012; 136:78-85; PMID:22260551; http://dx.doi.org/10.1111/j.1365-2567.2012.03561.x
  • Max EE, Korsmeyer SJ. Human J chain gene. Structure and expression in B lymphoid cells. J Exp Med 1985; 161:832-49; PMID:2984306
  • R Development Core Team 2006 R: A language and enviroment for statistical computing. Vienna, Austria:R Foundation for Statistical Computing.
  • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004; 5:R80; PMID:15461798
  • Li C, Hung Wong W. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biol 2001; 2:RESEARCH0032; PMID:11532216
  • Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A 2001; 98:5116-21; PMID:11309499; http://dx.doi.org/10.1073/pnas.091062498
  • Mao Q, Cheng T, Zhu F, Li J, Wang Y, Li Y, Gao F, Yang L, Yao X, Shao J, et al. The cross-neutralizing activity of enterovirus 71 subgenotype c4 vaccines in healthy chinese infants and children. PLoS One 2013; 8:e79599; PMID:24260259
  • Liang Z, Mao Q, Gao Q, Li X, Dong C, Yu X, Yao X, Li F, Yin W, Li Q, et al. Establishing China's national standards of antigen content and neutralizing antibody responses for evaluation of enterovirus 71 (EV71) vaccines. Vaccine 2011; 29:9668-74; PMID:22015395; http://dx.doi.org/10.1016/j.vaccine.2011.10.018
  • Liu L, Zhang Y, Wang J, Zhao H, Jiang L, Che Y, Shi H, Li R, Mo Z, Huang T, et al. Study of the integrated immune response induced by an inactivated EV71 vaccine. PLoS One 2013; 8:e54451; PMID:23372725; http://dx.doi.org/10.1371/journal.pone.0054451

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