Induced sputum proteome in healthy subjects and asthmatic patients

Journal of Allergy and Clinical Immunology

Volumn 128, Issue 6, 2011, Pages

  Gharib, Sina A ^a   Nguyen, Elizabeth V ^a   Lai, Ying ^a   Plampin, Jessica D ^a   Goodlett, David R ^a   Hallstrand, Teal S ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Asthma; exercise induced bronchoconstriction; induced sputum; protein network; shotgun proteomics

Indexed keywords

PROTEOME;

ADULT; AIRWAY REMODELING; ARTICLE; ASTHMA; BRONCHOSPASM; CLINICAL ARTICLE; CONTROLLED STUDY; EXERCISE; FEMALE; HUMAN; MALE; MOLECULAR PATHOLOGY; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEOMICS; SPUTUM ANALYSIS;

EID: 82555166994     PISSN: 00916749     EISSN: 10976825     Source Type: Journal    
DOI: 10.1016/j.jaci.2011.07.053     Document Type: Article

References (74)

1. B. Nicholas, and R. Djukanovic Induced sputum: a window to lung pathology Biochem Soc Trans 37 2009 868 872
2. R.H. Green, C.E. Brightling, S. McKenna, B. Hargadon, D. Parker, and P. Bradding Asthma exacerbations and sputum eosinophil counts: a randomised controlled trial Lancet 360 2002 1715 1721 (Pubitemid 35447900)
3. T.S. Hallstrand, M.M. Wurfel, Y. Lai, Z. Ni, M.H. Gelb, and W.A. Altemeier Transglutaminase 2, a novel regulator of eicosanoid production in asthma revealed by genome-wide expression profiling of distinct asthma phenotypes PLoS One 5 2010 e8583
4. D. Stanescu, A. Sanna, C. Veriter, S. Kostianev, P.G. Calcagni, and L.M. Fabbri Airways obstruction, chronic expectoration, and rapid decline of FEV1 in smokers are associated with increased levels of sputum neutrophils Thorax 51 1996 267 271 (Pubitemid 26086470)
5. E. Fireman, I. Topilsky, J. Greif, Y. Lerman, Y. Schwarz, and A. Man Induced sputum compared to bronchoalveolar lavage for evaluating patients with sarcoidosis and non-granulomatous interstitial lung disease Respir Med 93 1999 827 834
6. S.D. Sagel, M.K. Sontag, J.S. Wagener, R.K. Kapsner, I. Osberg, and F.J. Accurso Induced sputum inflammatory measures correlate with lung function in children with cystic fibrosis J Pediatr 141 2002 811 817 (Pubitemid 35471643)
7. S. Dragonieri, O. Tongoussouva, A. Zanini, A. Imperatori, and A. Spanevello Markers of airway inflammation in pulmonary diseases assessed by induced sputum Monaldi Arch Chest Dis 71 2009 119 126
8. B. Nicholas, P. Skipp, R. Mould, S. Rennard, D.E. Davies, and C.D. O'Connor Shotgun proteomic analysis of human-induced sputum Proteomics 6 2006 4390 4401 (Pubitemid 44277040)
9. R.D. Gray, G. MacGregor, D. Noble, M. Imrie, M. Dewar, and A.C. Boyd Sputum proteomics in inflammatory and suppurative respiratory diseases Am J Respir Crit Care Med 178 2008 444 452
10. J. Chen, S. Ryu, S.A. Gharib, D.R. Goodlett, and L.M. Schnapp Exploration of the normal human bronchoalveolar lavage fluid proteome Proteomics Clin Appl 2 2008 585 595 (Pubitemid 351566265)
11. S.A. Gharib, T. Vaisar, M.L. Aitken, D.R. Park, J.W. Heinecke, and X. Fu Mapping the lung proteome in cystic fibrosis J Proteome Res 8 2009 3020 3028
12. 2 group X overexpression in asthma and bronchial hyperresponsiveness Am J Respir Crit Care Med 176 2007 1072 1078 (Pubitemid 350223752)
13. J. Chen, S. Ryu, S.A. Gharib, D.R. Goodlett, and L.M. Schnapp Exploration of the normal human bronchoalveolar lavage fluid proteome Proteomics Clin Appl 2 2008 585 595 (Pubitemid 351566265)
14. A. Scherl, S.A. Shaffer, G.K. Taylor, H.D. Kulasekara, S.I. Miller, and D.R. Goodlett Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides Anal Chem 80 2008 1182 1191 (Pubitemid 351272354)
15. P.G. Pedrioli, J.K. Eng, R. Hubley, M. Vogelzang, E.W. Deutsch, and B. Raught A common open representation of mass spectrometry data and its application to proteomics research Nat Biotechnol 22 2004 1459 1466 (Pubitemid 39482868)
16. P.J. Kersey, J. Duarte, A. Williams, Y. Karavidopoulou, E. Birney, and R. Apweiler The International Protein Index: an integrated database for proteomics experiments Proteomics 4 2004 1985 1988 (Pubitemid 38880363)
17. A.I. Nesvizhskii, A. Keller, E. Kolker, and R. Aebersold A statistical model for identifying proteins by tandem mass spectrometry Anal Chem 75 2003 4646 4658 (Pubitemid 37082259)
18. H. Liu, R.G. Sadygov, and J.R. Yates 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 76 2004 4193 4201 (Pubitemid 38943698)
19. W. Wang, H. Zhou, H. Lin, S. Roy, T.A. Shaler, and L.R. Hill Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards Anal Chem 75 2003 4818 4826 (Pubitemid 37139783)
20. X. Fu, S.A. Gharib, P.S. Green, M.L. Aitken, D.A. Frazer, and D.R. Park Spectral index for assessment of differential protein expression in shotgun proteomics J Proteome Res 7 2008 845 854
21. Gene Ontology Consortium Creating the gene ontology resource: design and implementation Genome Res 11 2001 1425 1433
22. W. Huang da, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat Protoc 4 2009 44 57
23. B. Zhang, S. Kirov, and J. Snoddy WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Res 33 2005 W741 W748 (Pubitemid 44530021)
24. A.I. Saeed, V. Sharov, J. White, J. Li, W. Liang, and N. Bhagabati TM4: a free, open-source system for microarray data management and analysis Biotechniques 34 2003 374 378 (Pubitemid 36184095)
25. S.E. Calvano, W. Xiao, D.R. Richards, R.M. Felciano, H.V. Baker, and R.J. Cho A network-based analysis of systemic inflammation in humans Nature 437 2005 1032 1037 (Pubitemid 41486985)
26. L.J. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, and J. Muller STRING 8 - a global view on proteins and their functional interactions in 630 organisms Nucleic Acids Res 37 2009 D412 D416
27. K.G. Becker, D.A. Hosack, G. Dennis Jr., R.A. Lempicki, T.J. Bright, and C. Cheadle PubMatrix: a tool for multiplex literature mining BMC Bioinformatics 4 2003 61
28. C.E. Brightling Clinical applications of induced sputum Chest 129 2006 1344 1348
29. B. Zhang, N.C. VerBerkmoes, M.A. Langston, E. Uberbacher, R.L. Hettich, and N.F. Samatova Detecting differential and correlated protein expression in label-free shotgun proteomics J Proteome Res 5 2006 2909 2918 (Pubitemid 44749209)
30. A.M. Vignola, A. Bonanno, A. Mirabella, L. Riccobono, F. Mirabella, and M. Profita Increased levels of elastase and alpha1-antitrypsin in sputum of asthmatic patients Am J Respir Crit Care Med 157 1998 505 511 (Pubitemid 28090542)
31. N. Carpe, I. Mandeville, L. Ribeiro, A. Ponton, J.G. Martin, and A.T. Kho Genetic influences on asthma susceptibility in the developing lung Am J Respir Cell Mol Biol 43 2010 720 730
32. L.C. Chen, Z. Zhang, A.C. Myers, and S.K. Huang Cutting edge: altered pulmonary eosinophilic inflammation in mice deficient for Clara cell secretory 10-kDa protein J Immunol 167 2001 3025 3028 (Pubitemid 32852537)
33. C.H. Hung, L.C. Chen, Z. Zhang, B. Chowdhury, W.L. Lee, and B. Plunkett Regulation of TH2 responses by the pulmonary Clara cell secretory 10-kd protein J Allergy Clin Immunol 114 2004 664 670 (Pubitemid 39194945)
34. H. Wang, X.B. Long, P.P. Cao, N. Wang, Y. Liu, and Y.H. Cui Clara cell 10-kD protein suppresses chitinase 3-like 1 expression associated with eosinophilic chronic rhinosinusitis Am J Respir Crit Care Med 181 2010 908 916
35. N. Shijubo, Y. Itoh, T. Yamaguchi, A. Imada, M. Hirasawa, and T. Yamada Clara cell protein-positive epithelial cells are reduced in small airways of asthmatics Am J Respir Crit Care Med 160 1999 930 933 (Pubitemid 29442033)
36. N. Shijubo, Y. Itoh, T. Yamaguchi, F. Sugaya, M. Hirasawa, and T. Yamada Serum levels of Clara cell 10-kDa protein are decreased in patients with asthma Lung 177 1999 45 52 (Pubitemid 29013440)
37. S.W. Levin, J.D. Butler, U.K. Schumacher, P.D. Wightman, and A.B. Mukherjee Uteroglobin inhibits phospholipase A2 activity Life Sci 38 1986 1813 1819
38. 2 groups IIA and X in the airways and asthma severity Clin Exp Allergy 41 2011 801 810
39. X. Zhang, and J. Kohl A complex role for complement in allergic asthma Expert Rev Clin Immunol 6 2010 269 277
40. M. Wills-Karp Complement activation pathways: a bridge between innate and adaptive immune responses in asthma Proc Am Thorac Soc 4 2007 247 251 (Pubitemid 47036443)
41. A.A. Humbles, B. Lu, C.A. Nilsson, C. Lilly, E. Israel, and Y. Fujiwara A role for the C3a anaphylatoxin receptor in the effector phase of asthma Nature 406 2000 998 1001
42. N. Krug, T. Tschernig, V.J. Erpenbeck, J.M. Hohlfeld, and J. Kohl Complement factors C3a and C5a are increased in bronchoalveolar lavage fluid after segmental allergen provocation in subjects with asthma Am J Respir Crit Care Med 164 2001 1841 1843 (Pubitemid 33152317)
43. H. Kanemitsu, S. Nagasawa, M. Sagai, and Y. Mori Complement activation by diesel exhaust particles (DEP) Biol Pharm Bull 21 1998 129 132 (Pubitemid 28120141)
44. D.M. Walters, P.N. Breysse, B. Schofield, and M. Wills-Karp Complement factor 3 mediates particulate matter-induced airway hyperresponsiveness Am J Respir Cell Mol Biol 27 2002 413 418
45. J.W. Park, C. Taube, A. Joetham, K. Takeda, T. Kodama, and A. Dakhama Complement activation is critical to airway hyperresponsiveness after acute ozone exposure Am J Respir Crit Care Med 169 2004 726 732 (Pubitemid 38338925)
46. M. Shima, and M. Adachi Effects of environmental tobacco smoke on serum levels of acute phase proteins in schoolchildren Prev Med 25 1996 617 624 (Pubitemid 26315235)
47. R.A. Robbins, K.J. Nelson, G.L. Gossman, S. Koyama, and S.I. Rennard Complement activation by cigarette smoke Am J Physiol Lung Cell Mol Physiol 260 1991 L254 L259
48. T.S. Hallstrand, M.W. Moody, M.M. Wurfel, L.B. Schwartz, W.R. Henderson Jr., and M.L. Aitken Inflammatory basis of exercise-induced bronchoconstriction Am J Respir Crit Care Med 172 2005 679 686 (Pubitemid 41324221)
49. N.M. Luscombe, M.M. Babu, H. Yu, M. Snyder, S.A. Teichmann, and M. Gerstein Genomic analysis of regulatory network dynamics reveals large topological changes Nature 431 2004 308 312 (Pubitemid 39265665)
50. S.A. Gharib, W.C. Liles, L.S. Klaff, and W.A. Altemeier Noninjurious mechanical ventilation activates a proinflammatory transcriptional program in the lung Physiol Genomics 37 2009 239 248
51. F.E. Lovegrove, S.A. Gharib, S.N. Patel, C.A. Hawkes, K.C. Kain, and W.C. Liles Expression microarray analysis implicates apoptosis and interferon-responsive mechanisms in susceptibility to experimental cerebral malaria Am J Pathol 171 2007 1894 1903
52. L. Becker, S.A. Gharib, A.D. Irwin, E. Wijsman, T. Vaisar, and J.F. Oram A macrophage sterol-responsive network linked to atherogenesis Cell Metab 11 2010 125 135
53. R.S. Ames, D. Lee, J.J. Foley, A.J. Jurewicz, M.A. Tornetta, and W. Bautsch Identification of a selective nonpeptide antagonist of the anaphylatoxin C3a receptor that demonstrates antiinflammatory activity in animal models J Immunol 166 2001 6341 6348 (Pubitemid 32440767)
54. N. Mizutani, T. Nabe, and S. Yoshino Complement C3a regulates late asthmatic response and airway hyperresponsiveness in mice J Immunol 183 2009 4039 4046
55. S.H. Lee, K.H. Kim, J.M. Kim, S.H. Yoon, T.H. Kim, and S.W. Park Relationship between group-specific component protein and the development of asthma Am J Respir Crit Care Med 2010 [Epub ahead of print]
56. S. Haenen, J.A. Vanoirbeek, V. De Vooght, E. Maes, L. Schoofs, and B. Nemery Proteome analysis of multiple compartments in a mouse model of chemical-induced asthma J Proteome Res 9 2010 5868 5876
57. J. Zhao, I. Endoh, K. Hsu, N. Tedla, Y. Endoh, and C.L. Geczy S100A8 modulates mast cell function and suppresses eosinophil migration in acute asthma Antioxid Redox Signal 14 2011 1589 1600
58. T.S. Hallstrand, M.M. Wurfel, Y. Lai, Z. Ni, M.H. Gelb, and W.A. Altemeier Transglutaminase 2, a novel regulator of eicosanoid production in asthma revealed by genome-wide expression profiling of distinct asthma phenotypes PLoS One 5 2010 e8583
59. 2 group X overexpression in asthma and bronchial hyperresponsiveness Am J Respir Crit Care Med 176 2007 1072 1078 (Pubitemid 350223752)
60. J. Chen, S. Ryu, S.A. Gharib, D.R. Goodlett, and L.M. Schnapp Exploration of the normal human bronchoalveolar lavage fluid proteome Proteomics Clin Appl 2 2008 585 595 (Pubitemid 351566265)
61. A. Scherl, S.A. Shaffer, G.K. Taylor, H.D. Kulasekara, S.I. Miller, and D.R. Goodlett Genome-specific gas-phase fractionation strategy for improved shotgun proteomic profiling of proteotypic peptides Anal Chem 80 2008 1182 1191 (Pubitemid 351272354)
62. P.G. Pedrioli, J.K. Eng, R. Hubley, M. Vogelzang, E.W. Deutsch, and B. Raught A common open representation of mass spectrometry data and its application to proteomics research Nat Biotechnol 22 2004 1459 1466 (Pubitemid 39482868)
63. P.J. Kersey, J. Duarte, A. Williams, Y. Karavidopoulou, E. Birney, and R. Apweiler The International Protein Index: an integrated database for proteomics experiments Proteomics 4 2004 1985 1988 (Pubitemid 38880363)
64. A.I. Nesvizhskii, A. Keller, E. Kolker, and R. Aebersold A statistical model for identifying proteins by tandem mass spectrometry Anal Chem 75 2003 4646 4658 (Pubitemid 37082259)
65. H. Liu, R.G. Sadygov, and J.R. Yates 3rd A model for random sampling and estimation of relative protein abundance in shotgun proteomics Anal Chem 76 2004 4193 4201 (Pubitemid 38943698)
66. W. Wang, H. Zhou, H. Lin, S. Roy, T.A. Shaler, and L.R. Hill Quantification of proteins and metabolites by mass spectrometry without isotopic labeling or spiked standards Anal Chem 75 2003 4818 4826 (Pubitemid 37139783)
67. X. Fu, S.A. Gharib, P.S. Green, M.L. Aitken, D.A. Frazer, and D.R. Park Spectral index for assessment of differential protein expression in shotgun proteomics J Proteome Res 7 2008 845 854
68. S.A. Gharib, T. Vaisar, M.L. Aitken, D.R. Park, J.W. Heinecke, and X. Fu Mapping the lung proteome in cystic fibrosis J Proteome Res 8 2009 3020 3028
69. Gene Ontology Consortium Creating the gene ontology resource: design and implementation Genome Res 11 2001 1425 1433
70. W. Huang da, B.T. Sherman, and R.A. Lempicki Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat Protoc 4 2009 44 57
71. B. Zhang, S. Kirov, and J. Snoddy WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Res 33 2005 W741 W748 (Pubitemid 44530021)
72. A.I. Saeed, V. Sharov, J. White, J. Li, W. Liang, and N. Bhagabati TM4: a free, open-source system for microarray data management and analysis Biotechniques 34 2003 374 378 (Pubitemid 36184095)
73. S.E. Calvano, W. Xiao, D.R. Richards, R.M. Felciano, H.V. Baker, and R.J. Cho A network-based analysis of systemic inflammation in humans Nature 437 2005 1032 1037 (Pubitemid 41486985)
74. L.J. Jensen, M. Kuhn, M. Stark, S. Chaffron, C. Creevey, and J. Muller STRING 8 - a global view on proteins and their functional interactions in 630 organisms Nucleic Acids Res 37 2009 D412 D416