Specific mutations in H5N1 mainly impact the magnitude and velocity of the host response in mice

详细信息    查看全文

• 作者：Nicolas Tchitchek (7)
  Amie J Eisfeld (8)
  Jennifer Tisoncik-Go (7)
  Laurence Josset (7)
  Lisa E Gralinski (9)
  Christophe Bécavin (7)
  Susan C Tilton (8)
  Bobbie-Jo Webb-Robertson (8)
  Martin T Ferris (9)
  Allison L Totura (9)
  Chengjun Li (8)
  Gabriele Neumann (8)
  Thomas O Metz (8)
  Richard D Smith (8)
  Katrina M Waters (8)
  Ralph Baric (9)
  Yoshihiro Kawaoka (8)
  Michael G Katze (7) (9)
  
• 关键词：Influenza ; Host ; Response ; Kinetics ; Magnitude ; Velocity ; Transcriptomics ; Proteomics ; Multidimensional ; Scaling
• 刊名：BMC Systems Biology
• 出版年：2013
• 出版时间：December 2013
• 年：2013
• 卷：7
• 期：1
• 全文大小：1054KB
• 参考文献：1. Herfst S, Schrauwen EJA, Linster M, Chutinimitkul S, de Wit E, Munster VJ, Sorrell EM, Bestebroer TM, Burke DF, Smith DJ, Rimmelzwaan GF, Osterhaus ADME, Fouchier RAM: class="a-plus-plus">Airborne transmission of influenza A/H5N1 virus between ferrets. / Science (New York, NY) 2012, class="a-plus-plus">336:1534-541. class="external" href="http://dx.doi.org/10.1126/science.1213362">CrossRef
  2. Imai M, Watanabe T, Hatta M, Das SC, Ozawa M, Shinya K, Zhong G, Hanson A, Katsura H, Watanabe S, Li C, Kawakami E, Yamada S, Kiso M, Suzuki Y, Maher EA, Neumann G, Kawaoka Y: class="a-plus-plus">Experimental adaptation of an influenza H5 HA confers respiratory droplet transmission to a reassortant H5 HA/H1N1 virus in ferrets. / Nature 2012, class="a-plus-plus">486:420-28.
  3. Russell CA, Fonville JM, Brown AEX, Burke DF, Smith DL, James SL, Herfst S, van Boheemen S, Linster M, Schrauwen EJ, Katzelnick L, Mosterín A, Kuiken T, Maher E, Neumann G, Osterhaus ADME, Kawaoka Y, Fouchier RAM, Smith DJ: class="a-plus-plus">The potential for respiratory droplet-transmissible A/H5N1 influenza virus to evolve in a mammalian host. / Science (New York, NY) 2012, class="a-plus-plus">336:1541-547. class="external" href="http://dx.doi.org/10.1126/science.1222526">CrossRef
  4. Hatta M, Gao P, Halfmann P, Kawaoka Y: class="a-plus-plus">Molecular basis for high virulence of Hong Kong H5N1 influenza A viruses. / Science (New York, NY) 2001, class="a-plus-plus">293:1840-842. class="external" href="http://dx.doi.org/10.1126/science.1062882">CrossRef
  5. Hatta M, Hatta Y, Kim JH, Watanabe S, Shinya K, Nguyen T, Lien PS, Le QM, Kawaoka Y: class="a-plus-plus">Growth of H5N1 influenza A viruses in the upper respiratory tracts of mice. / PLoS Pathog 2007, class="a-plus-plus">3:1374-379. class="external" href="http://dx.doi.org/10.1371/journal.ppat.0030133">CrossRef
  6. Cilloniz C, Pantin-Jackwood MJ, Ni C, Goodman AG, Peng X, Proll SC, Carter VS, Rosenzweig ER, Szretter KJ, Katz JM, Korth MJ, Swayne DE, Tumpey TM, Katze MG: class="a-plus-plus">Lethal dissemination of H5N1 influenza virus is associated with dysregulation of inflammation and lipoxin signaling in a mouse model of infection. / J Virol 2010, class="a-plus-plus">84:7613-624. class="external" href="http://dx.doi.org/10.1128/JVI.00553-10">CrossRef
  7. Stieneke-Gr?ber A, Vey M, Angliker H, Shaw E, Thomas G, Roberts C, Klenk HD, Garten W: class="a-plus-plus">Influenza virus hemagglutinin with multibasic cleavage site is activated by furin, a subtilisin-like endoprotease. / EMBO J 1992, class="a-plus-plus">11:2407-414.
  8. Bosch FX, Orlich M, Klenk HD, Rott R: class="a-plus-plus">The structure of the hemagglutinin, a determinant for the pathogenicity of influenza viruses. / Virology 1979, class="a-plus-plus">95:197-07. class="external" href="http://dx.doi.org/10.1016/0042-6822(79)90414-8">CrossRef
  9. Horimoto T, Kawaoka Y: class="a-plus-plus">Reverse genetics provides direct evidence for a correlation of hemagglutinin cleavability and virulence of an avian influenza A virus. / J Virol 1994, class="a-plus-plus">68:3120-128.
  10. Boivin S, Cusack S, Ruigrok RWH, Hart DJ: class="a-plus-plus">Influenza A virus polymerase: structural insights into replication and host adaptation mechanisms. / J Biol Chem 2010, class="a-plus-plus">285:28411-8417. class="external" href="http://dx.doi.org/10.1074/jbc.R110.117531">CrossRef
  11. Fornek JL, Gillim-Ross L, Santos C, Carter V, Ward JM, Cheng LI, Proll S, Katze MG, Subbarao K: class="a-plus-plus">A single-amino-acid substitution in a polymerase protein of an H5N1 influenza virus is associated with systemic infection and impaired T-cell activation in mice. / J Virol 2009, class="a-plus-plus">83:11102-1115. class="external" href="http://dx.doi.org/10.1128/JVI.00994-09">CrossRef
  12. Gack MU, Albrecht RA, Urano T, Inn K-S, Huang I-C, Carnero E, Farzan M, Inoue S, Jung JU, García-Sastre A: class="a-plus-plus">Influenza A virus NS1 targets the ubiquitin ligase TRIM25 to evade recognition by the host viral RNA sensor RIG-I. / Cell Host Microbe 2009, class="a-plus-plus">5:439-49. class="external" href="http://dx.doi.org/10.1016/j.chom.2009.04.006">CrossRef
  13. Hale BG, Randall RE, Ortín J, Jackson D: class="a-plus-plus">The multifunctional NS1 protein of influenza A viruses. / J Gen Virol 2008,class="a-plus-plus">89(Pt 10)class="a-plus-plus">:2359-376. class="external" href="http://dx.doi.org/10.1099/vir.0.2008/004606-0">CrossRef
  14. Chen Z, Li Y, Krug RM: class="a-plus-plus">Influenza A virus NS1 protein targets poly(A)-binding protein II of the cellular 3-end processing machinery. / EMBO J 1999, class="a-plus-plus">18:2273-283. class="external" href="http://dx.doi.org/10.1093/emboj/18.8.2273">CrossRef
  15. Nemeroff ME, Barabino SM, Li Y, Keller W, Krug RM: class="a-plus-plus">Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 3’end formation of cellular pre-mRNAs. / Mol Cell 1998, class="a-plus-plus">1:991-000. class="external" href="http://dx.doi.org/10.1016/S1097-2765(00)80099-4">CrossRef
  16. Schmolke M, Manicassamy B, Pena L, Sutton T, Hai R, Varga ZT, Hale BG, Steel J, Pérez DR, García-Sastre A: class="a-plus-plus">Differential contribution of PB1-F2 to the virulence of highly pathogenic H5N1 influenza A virus in mammalian and avian species. / PLoS Pathog 2011, class="a-plus-plus">7:e1002186. class="external" href="http://dx.doi.org/10.1371/journal.ppat.1002186">CrossRef
  17. Smith AM, Adler FR, McAuley JL, Gutenkunst RN, Ribeiro RM, McCullers JA, Perelson AS: class="a-plus-plus">Effect of 1918 PB1-F2 expression on influenza A virus infection kinetics. / PLoS Comput Biol 2011, class="a-plus-plus">7:e1001081. class="external" href="http://dx.doi.org/10.1371/journal.pcbi.1001081">CrossRef
  18. Ozawa M, Basnet S, Burley LM, Neumann G, Hatta M, Kawaoka Y: class="a-plus-plus">Impact of amino acid mutations in PB2, PB1-F2, and NS1 on the replication and pathogenicity of pandemic (H1N1) 2009 influenza viruses. / J Virol 2011, class="a-plus-plus">85:4596-601. class="external" href="http://dx.doi.org/10.1128/JVI.00029-11">CrossRef
  19. McAuley JL, Chipuk JE, Boyd KL, Van De Velde N, Green DR, McCullers JA: class="a-plus-plus">PB1-F2 proteins from H5N1 and 20 century pandemic influenza viruses cause immunopathology. / PLoS Pathog 2010, class="a-plus-plus">6:e1001014. class="external" href="http://dx.doi.org/10.1371/journal.ppat.1001014">CrossRef
  20. Conenello GM, Tisoncik JR, Rosenzweig E, Varga ZT, Palese P, Katze MG: class="a-plus-plus">A single N66S mutation in the PB1-F2 protein of influenza A virus increases virulence by inhibiting the early interferon response in vivo. / J Virol 2011, class="a-plus-plus">85:652-62. class="external" href="http://dx.doi.org/10.1128/JVI.01987-10">CrossRef
  21. Le Goffic R, Bouguyon E, Chevalier C, Vidic J, Da Costa B, Leymarie O, Bourdieu C, Decamps L, Dhorne-Pollet S, Delmas B: class="a-plus-plus">Influenza A virus protein PB1-F2 exacerbates IFN-beta expression of human respiratory epithelial cells. / J Immunol 2010, class="a-plus-plus">185:4812-823. class="external" href="http://dx.doi.org/10.4049/jimmunol.0903952">CrossRef
  22. Itoh Y, Shinya K, Kiso M, Watanabe T, Sakoda Y, Hatta M, Muramoto Y, Tamura D, Sakai-Tagawa Y, Noda T, Sakabe S, Imai M, Hatta Y, Watanabe S, Li C, Yamada S, Fujii K, Murakami S, Imai H, Kakugawa S, Ito M, Takano R, Iwatsuki-Horimoto K, Shimojima M, Horimoto T, Goto H, Takahashi K, Makino A, Ishigaki H, Nakayama M, / et al.: class="a-plus-plus">In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses. / Nature 2009, class="a-plus-plus">460:1021-025.
  23. Kestler HA, Müller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN: class="a-plus-plus">VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. / BMC Bioinformatics 2008, class="a-plus-plus">9:67. class="external" href="http://dx.doi.org/10.1186/1471-2105-9-67">CrossRef
  24. Alter O, Brown PO, Botstein D: class="a-plus-plus">Singular value decomposition for genome-wide expression data processing and modeling. / Proc Natl Acad Sci USA 2000, class="a-plus-plus">97:10101-0106. class="external" href="http://dx.doi.org/10.1073/pnas.97.18.10101">CrossRef
  25. Watanabe T, Tisoncik-Go J, Tchitchek N, Watanabe S, Benecke AG, Katze MG, Kawaoka Y: class="a-plus-plus">1918 influenza virus hemagglutinin (HA) and the viral RNA polymerase complex enhance viral pathogenicity, but only HA induces aberrant host responses in mice. / J Virol 2013, class="a-plus-plus">87:5239-254. class="external" href="http://dx.doi.org/10.1128/JVI.02753-12">CrossRef
  26. Hatta Y, Hershberger K, Shinya K, Proll SC, Dubielzig RR, Hatta M, Katze MG, Kawaoka Y, Suresh M: class="a-plus-plus">Viral replication rate regulates clinical outcome and CD8 T cell responses during highly pathogenic H5N1 influenza virus infection in mice. / PLoS Pathog 2010, class="a-plus-plus">6:e1001139. class="external" href="http://dx.doi.org/10.1371/journal.ppat.1001139">CrossRef
  27. Imai Y, Kuba K, Neely GG, Yaghubian-Malhami R, Perkmann T, van Loo G, Ermolaeva M, Veldhuizen R, Leung YHC, Wang H, Liu H, Sun Y, Pasparakis M, Kopf M, Mech C, Bavari S, Peiris JSM, Slutsky AS, Akira S, Hultqvist M, Holmdahl R, Nicholls J, Jiang C, Binder CJ, Penninger JM: class="a-plus-plus">Identification of oxidative stress and Toll-like receptor 4 signaling as a key pathway of acute lung injury. / Cell 2008, class="a-plus-plus">133:235-49. class="external" href="http://dx.doi.org/10.1016/j.cell.2008.02.043">CrossRef
  28. Kruskal JB, Wish M: class="a-plus-plus">Multidimensional Scaling. / Methods 1978, class="a-plus-plus">116:463-04.
  29. Bécavin C, Tchitchek N, Mintsa-Eya C, Lesne A, Benecke A: class="a-plus-plus">Improving the efficiency of multidimensional scaling in the analysis of high-dimensional data using singular value decomposition. / Bioinformatics (Oxford, England) 2011, class="a-plus-plus">27:1413-421. class="external" href="http://dx.doi.org/10.1093/bioinformatics/btr143">CrossRef
  30. de Berg M, Cheong O, van Kreveld M, Overmars M: / Computational Geometry: Algorithms and Applications. 3rd edition. Santa Clara, CA, USA: Springer-Verlag TELOS; 2008.
  31. Billharz R, Zeng H, Proll SC, Korth MJ, Lederer S, Albrecht R, Goodman AG, Rosenzweig E, Tumpey TM, García-Sastre A, Katze MG: class="a-plus-plus">The NS1 protein of the 1918 pandemic influenza virus blocks host interferon and lipid metabolism pathways. / J Virol 2009, class="a-plus-plus">83:10557-0570. class="external" href="http://dx.doi.org/10.1128/JVI.00330-09">CrossRef
  32. Peiris JSM, Yu WC, Leung CW, Cheung CY, Ng WF, Nicholls JM, Ng TK, Chan KH, Lai ST, Lim WL, Yuen KY, Guan Y: class="a-plus-plus">Re-emergence of fatal human influenza A subtype H5N1 disease. / Lancet 2004, class="a-plus-plus">363:617-19. class="external" href="http://dx.doi.org/10.1016/S0140-6736(04)15595-5">CrossRef
  33. Tisoncik JR, Korth MJ, Simmons CP, Farrar J, Martin TR, Katze MG: class="a-plus-plus">Into the eye of the cytokine storm. / Microbiology and molecular biology reviews: MMBR 2012, class="a-plus-plus">76:16-2. class="external" href="http://dx.doi.org/10.1128/MMBR.05015-11">CrossRef
  34. Go JT, Belisle SE, Tchitchek N, Tumpey TM, Ma W, Richt JA, Safronetz D, Feldmann H, Katze MG: class="a-plus-plus">2009 pandemic H1N1 influenza virus elicits similar clinical course but differential host transcriptional response in mouse, macaque, and swine infection models. / BMC Genomics 2012, class="a-plus-plus">13:627. class="external" href="http://dx.doi.org/10.1186/1471-2164-13-627">CrossRef
  35. Josset L, Tisoncik-Go J, Katze MG: class="a-plus-plus">Moving H5N1 studies into the era of systems biology. / Virus Res 2013. doi:10.1016/j.virusres.2013.02.011
  36. Garbis S, Lubec G, Fountoulakis M: class="a-plus-plus">Limitations of current proteomics technologies. / J Chromatogr A 2005, class="a-plus-plus">1077:1-8. class="external" href="http://dx.doi.org/10.1016/j.chroma.2005.04.059">CrossRef
  37. Chang ST, Tchitchek N, Ghosh D, Benecke A, Katze MG: class="a-plus-plus">A chemokine gene expression signature derived from meta-analysis predicts the pathogenicity of viral respiratory infections. / BMC Syst Biol 2011, class="a-plus-plus">5:202. class="external" href="http://dx.doi.org/10.1186/1752-0509-5-202">CrossRef
  38. Pommerenke C, Wilk E, Srivastava B, Schulze A, Novoselova N, Geffers R, Schughart K: class="a-plus-plus">Global transcriptome analysis in influenza-infected mouse lungs reveals the kinetics of innate and adaptive host immune responses. / PLoS One 2012, class="a-plus-plus">7:e41169. class="external" href="http://dx.doi.org/10.1371/journal.pone.0041169">CrossRef
  39. Cheung CY, Chan EY, Krasnoselsky A, Purdy D, Navare AT, Bryan JT, Leung CKL, Hui KPY, Peiris JSM, Katze MG: class="a-plus-plus">H5N1 virus causes significant perturbations in host proteome very early in influenza virus-infected primary human monocyte-derived macrophages. / J Infect Dis 2012, class="a-plus-plus">206:640-45. class="external" href="http://dx.doi.org/10.1093/infdis/jis423">CrossRef
  40. Lum PY, Singh G, Lehman A, Ishkanov T, Vejdemo-Johansson M, Alagappan M, Carlsson J, Carlsson G: class="a-plus-plus">Extracting insights from the shape of complex data using topology. / Sci Rep 2013, class="a-plus-plus">3:1236. class="external" href="http://dx.doi.org/10.1038/srep01236">CrossRef
  41. Norman C: class="a-plus-plus">2011 International Science & Engineering Visualization Challenge. / Science (New York, NY) 2012, class="a-plus-plus">335:525-35. class="external" href="http://dx.doi.org/10.1126/science.335.6068.525">CrossRef
  42. Fox P, Hendler J: class="a-plus-plus">Changing the equation on scientific data visualization. / Science (New York, NY) 2011, class="a-plus-plus">331:705-08. class="external" href="http://dx.doi.org/10.1126/science.1197654">CrossRef
  43. Aderem A, Adkins JN, Ansong C, Galagan J, Kaiser S, Korth MJ, Law GL, McDermott JG, Proll SC, Rosenberger C, Schoolnik G, Katze MG: class="a-plus-plus">A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm. / mBio 2011, class="a-plus-plus">2:e00325-0. class="external" href="http://dx.doi.org/10.1128/mBio.00325-10">CrossRef
  44. Neumann G, Watanabe T, Ito H, Watanabe S, Goto H, Gao P, Hughes M, Perez DR, Donis R, Hoffmann E, Hobom G, Kawaoka Y: class="a-plus-plus">Generation of influenza A viruses entirely from cloned cDNAs. / Proc Natl Acad Sci U S A 1999, class="a-plus-plus">96:9345-350. class="external" href="http://dx.doi.org/10.1073/pnas.96.16.9345">CrossRef
  45. Watanabe T, Watanabe S, Kim JH, Hatta M, Kawaoka Y: class="a-plus-plus">Novel approach to the development of effective H5N1 influenza A virus vaccines: use of M2 cytoplasmic tail mutants. / J Virol 2008, class="a-plus-plus">82:2486-492. class="external" href="http://dx.doi.org/10.1128/JVI.01899-07">CrossRef
  46. Reed Muench H: class="a-plus-plus">A simple method of estimating fifty per cent edpoints. / Am J Epidemiol 1938, class="a-plus-plus">27:493-97.
  47. Kawakami E, Watanabe T, Fujii K, Goto H, Watanabe S, Noda T, Kawaoka Y: class="a-plus-plus">Strand-specific real-time RT-PCR for distinguishing influenza vRNA, cRNA, and mRNA. / J Virol Methods 2011, class="a-plus-plus">173:1-. class="external" href="http://dx.doi.org/10.1016/j.jviromet.2010.12.014">CrossRef
  48. Yang YH, Dudoit S, Luu P, Speed TP: class="a-plus-plus">Normalization for cDNA microarray data. In / Microarrays Optical Technologies and Informatics. Volume 4266 Edited by: Bittner ML, Chen Y, Dorsel AN, Dougherty ER. 2001, 141-52. class="external" href="http://dx.doi.org/10.1117/12.427982">CrossRef
  49. Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP: class="a-plus-plus">Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. / Nucleic Acids Res 2002, class="a-plus-plus">30:e15. class="external" href="http://dx.doi.org/10.1093/nar/30.4.e15">CrossRef
  50. Smyth GK, Speed T: class="a-plus-plus">Normalization of cDNA microarray data. / Methods (San Diego, Calif) 2003, class="a-plus-plus">31:265-73. class="external" href="http://dx.doi.org/10.1016/S1046-2023(03)00155-5">CrossRef
  51. Smyth GK: class="a-plus-plus">Limma: linear models for microarray data. / Bioinformat Comput Biol Solutions using R and Bioconductor 2005, class="a-plus-plus">1:397-20. class="external" href="http://dx.doi.org/10.1007/0-387-29362-0_23">CrossRef
  52. R Development Core Team R: / R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing; 2011:409.
  53. Metz TO, Jacobs JM, Gritsenko MA, Fontès G, Qian W-J, Camp DG, Poitout V, Smith RD: class="a-plus-plus">Characterization of the human pancreatic islet proteome by two-dimensional LC/MS/MS. / J Proteome Res 2006, class="a-plus-plus">5:3345-354. class="external" href="http://dx.doi.org/10.1021/pr060322n">CrossRef
  54. Zimmer JSD, Monroe ME, Qian W-J, Smith RD: class="a-plus-plus">Advances in proteomics data analysis and display using an accurate mass and time tag approach. / Mass Spectrom Rev 2006, class="a-plus-plus">25:450-82. class="external" href="http://dx.doi.org/10.1002/mas.20071">CrossRef
  55. Livesay EA, Tang K, Taylor BK, Buschbach MA, Hopkins DF, LaMarche BL, Zhao R, Shen Y, Orton DJ, Moore RJ, Kelly RT, Udseth HR, Smith RD: class="a-plus-plus">Fully automated four-column capillary LC-MS system for maximizing throughput in proteomic analyses. / Anal Chem 2008, class="a-plus-plus">80:294-02. class="external" href="http://dx.doi.org/10.1021/ac701727r">CrossRef
  56. Eng JK, Mccormack AL, Yates JR: class="a-plus-plus">An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. / J Am Soc Mass Spectrom 1994, class="a-plus-plus">5:976-89. class="external" href="http://dx.doi.org/10.1016/1044-0305(94)80016-2">CrossRef
  57. Elias JE, Gygi SP: class="a-plus-plus">Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. / Nat Methods 2007, class="a-plus-plus">4:207-14. class="external" href="http://dx.doi.org/10.1038/nmeth1019">CrossRef
  58. Petritis K, Kangas LJ, Ferguson PL, Anderson GA, Pasa-Toli? L, Lipton MS, Auberry KJ, Strittmatter EF, Shen Y, Zhao R, Smith RD: class="a-plus-plus">Use of artificial neural networks for the accurate prediction of peptide liquid chromatography elution times in proteome analyses. / Anal Chem 2003, class="a-plus-plus">75:1039-048. class="external" href="http://dx.doi.org/10.1021/ac0205154">CrossRef
  59. Kiebel GR, Auberry KJ, Jaitly N, Clark DA, Monroe ME, Peterson ES, Toli? N, Anderson GA, Smith RD: class="a-plus-plus">PRISM: a data management system for high-throughput proteomics. / Proteomics 2006, class="a-plus-plus">6:1783-790. class="external" href="http://dx.doi.org/10.1002/pmic.200500500">CrossRef
  60. Jaitly N, Mayampurath A, Littlefield K, Adkins JN, Anderson GA, Smith RD: class="a-plus-plus">Decon2LS: an open-source software package for automated processing and visualization of high resolution mass spectrometry data. / BMC Bioinformatics 2009, class="a-plus-plus">10:87. class="external" href="http://dx.doi.org/10.1186/1471-2105-10-87">CrossRef
  61. Monroe ME, Toli? N, Jaitly N, Shaw JL, Adkins JN, Smith RD: class="a-plus-plus">VIPER: an advanced software package to support high-throughput LC-MS peptide identification. / Bioinformatics (Oxford, England) 2007, class="a-plus-plus">23:2021-023. class="external" href="http://dx.doi.org/10.1093/bioinformatics/btm281">CrossRef
  62. Webb-Robertson B-JM, McCue LA, Waters KM, Matzke MM, Jacobs JM, Metz TO, Varnum SM, Pounds JG: class="a-plus-plus">Combined statistical analyses of peptide intensities and peptide occurrences improves identification of significant peptides from MS-based proteomics data. / J Proteome Res 2010, class="a-plus-plus">9:5748-756. class="external" href="http://dx.doi.org/10.1021/pr1005247">CrossRef
  63. Matzke MM, Waters KM, Metz TO, Jacobs JM, Sims AC, Baric RS, Pounds JG, Webb-Robertson B-JM: class="a-plus-plus">Improved quality control processing of peptide-centric LC-MS proteomics data. / Bioinformatics (Oxford, England) 2011, class="a-plus-plus">27:2866-872. class="external" href="http://dx.doi.org/10.1093/bioinformatics/btr479">CrossRef
  64. Webb-Robertson B-JM, Matzke MM, Jacobs JM, Pounds JG, Waters KM: class="a-plus-plus">A statistical selection strategy for normalization procedures in LC-MS proteomics experiments through dataset-dependent ranking of normalization scaling factors. / Proteomics 2011, class="a-plus-plus">11:4736-741. class="external" href="http://dx.doi.org/10.1002/pmic.201100078">CrossRef
  65. Matzke MM, Brown JN, Gritsenko MA, Metz TO, Pounds JG, Rodland KD, Shukla AK, Smith RD, Waters KM, McDermott JE, Webb-Robertson B-J: class="a-plus-plus">A comparative analysis of computational approaches to relative protein quantification using peptide peak intensities in label-free LC-MS proteomics experiments. / Proteomics 2013, class="a-plus-plus">13:493-03. class="external" href="http://dx.doi.org/10.1002/pmic.201200269">CrossRef
  66. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB: class="a-plus-plus">Missing value estimation methods for DNA microarrays. / Bioinformatics (Oxford, England) 2001, class="a-plus-plus">17:520-25. class="external" href="http://dx.doi.org/10.1093/bioinformatics/17.6.520">CrossRef
  67. Wong J: class="a-plus-plus">Imputation: imputation. / R package version 2.0.1 2013.
  68. Tchitchek N, Dzib JFG, Targat B, Noth S, Benecke A, Lesne A: class="a-plus-plus">CDS: a fold-change based statistical test for concomitant identification of distinctness and similarity in gene expression analysis. / Genomics Proteomics Bioinformatics 2012, class="a-plus-plus">10:127-35. class="external" href="http://dx.doi.org/10.1016/j.gpb.2012.06.002">CrossRef
  69. Fisher RA: class="a-plus-plus">On the interpretation of χ2 from contingency tables, and the calculation of P. / J Roy St Soc 1922, class="a-plus-plus">85:87-4. class="external" href="http://dx.doi.org/10.2307/2340521">CrossRef
  
• 作者单位：Nicolas Tchitchek (7)
  Amie J Eisfeld (8)
  Jennifer Tisoncik-Go (7)
  Laurence Josset (7)
  Lisa E Gralinski (9)
  Christophe Bécavin (7)
  Susan C Tilton (8)
  Bobbie-Jo Webb-Robertson (8)
  Martin T Ferris (9)
  Allison L Totura (9)
  Chengjun Li (8)
  Gabriele Neumann (8)
  Thomas O Metz (8)
  Richard D Smith (8)
  Katrina M Waters (8)
  Ralph Baric (9)
  Yoshihiro Kawaoka (8)
  Michael G Katze (7) (9)
  
  7. Unité des Interactions Bactéries-Cellules, Institut Pasteur, 75015, Paris, France
  8. Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
  9. Washington National Primate Research Center, University of Washington, Seattle, WA, USA
  

文摘

Background Influenza infection causes respiratory disease that can lead to death. The complex interplay between virus-encoded and host-specific pathogenicity regulators -and the relative contributions of each toward viral pathogenicity -is not well-understood. Results By analyzing a collection of lung samples from mice infected by A/Vietnam/1203/2004 (H5N1; VN1203), we characterized a signature of transcripts and proteins associated with the kinetics of the host response. Using a new geometrical representation method and two criteria, we show that inoculation concentrations and four specific mutations in VN1203 mainly impact the magnitude and velocity of the host response kinetics, rather than specific sets of up- and down- regulated genes. We observed analogous kinetic effects using lung samples from mice infected with A/California/04/2009 (H1N1), and we show that these effects correlate with morbidity and viral titer. Conclusions We have demonstrated the importance of the kinetics of the host response to H5N1 pathogenesis and its relationship with clinical disease severity and virus replication. These kinetic properties imply that time-matched comparisons of ‘omics profiles to viral infections give limited views to differentiate host-responses. Moreover, these results demonstrate that a fast activation of the host-response at the earliest time points post-infection is critical for protective mechanisms against fast replicating viruses.