Quantitative proteomics of bronchoalveolar lavage fluid in idiopathic pulmonary fibrosis

Journal of Proteome Research

Volumn 14, Issue 2, 2015, Pages 1238-1249

  Foster, Matthew W ^a,b   Morrison, Lake D ^a   Todd, Jamie L ^a   Snyder, Laurie D ^a   Thompson, J Will ^b   Soderblom, Erik J ^b   Plonk, Kelly ^b   Weinhold, Kent J ^b   Townsend, Robert ^c   Minnich, Anne ^c   Moseley, M Arthur ^b  

^a Cleveland Clinic Main Campus   (United States)

^b DUKE UNIVERSITY MEDICAL CENTER   (United States)

^c BRISTOL MYERS SQUIBB   (United States)

Author keywords

airway lining fluid; CRAC1; immunodepletion; label free; PEDF; targeted proteomics

Indexed keywords

BONE MORPHOGENETIC PROTEIN 4; CARCINOEMBRYONIC ANTIGEN RELATED CELL ADHESION MOLECULE 6; CCL18 CHEMOKINE; CHEMOKINE; CXCL7 CHEMOKINE; EOTAXIN 2; LIPOCALIN 1; MATRILYSIN; MUCIN 5AC; MUCIN 5B; OSTEOPONTIN; PIGMENT EPITHELIUM DERIVED FACTOR; PROTEIN; STABLE ISOTOPE; UNCLASSIFIED DRUG; VINCULIN;

ADULT; AGED; ARTICLE; CONTROLLED STUDY; EOSINOPHIL; FIBROSING ALVEOLITIS; HUMAN; LIQUID CHROMATOGRAPHY; LUNG FIBROBLAST; LUNG LAVAGE; NEUTROPHIL; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEOMICS; REVERSED PHASE LIQUID CHROMATOGRAPHY; TANDEM MASS SPECTROMETRY; ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY; UPREGULATION; BRONCHOALVEOLAR LAVAGE FLUID; METABOLISM; REPRODUCIBILITY;

BRONCHOALVEOLAR LAVAGE FLUID; ELECTROPHORESIS, POLYACRYLAMIDE GEL; HUMANS; IDIOPATHIC PULMONARY FIBROSIS; PROTEOMICS; REPRODUCIBILITY OF RESULTS; TANDEM MASS SPECTROMETRY;

EID: 84922596181     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr501149m     Document Type: Article

References (79)

1. Wells, A. U. The revised ATS/ERS/JRS/ALAT diagnostic criteria for idiopathic pulmonary fibrosis (IPF)-practical implications Respir. Res. 2013, 14 (Suppl 1) S2
2. Wuyts, W. A.; Agostini, C.; Antoniou, K. M.; Bouros, D.; Chambers, R. C.; Cottin, V.; Egan, J. J.; Lambrecht, B. N.; Lories, R.; Parfrey, H.; Prasse, A.; Robalo-Cordeiro, C.; Verbeken, E.; Verschakelen, J. A.; Wells, A. U.; Verleden, G. M. The pathogenesis of pulmonary fibrosis: a moving target Eur. Respir. J. 2013, 41 (5) 1207-18
3. Selman, M.; Pardo, A. Update in diffuse parenchymal lung disease 2012 Am. J. Respir. Crit. Care Med. 2013, 187 (9) 920-5
4. Seeger, W.; Adir, Y.; Barbera, J. A.; Champion, H.; Coghlan, J. G.; Cottin, V.; De Marco, T.; Galie, N.; Ghio, S.; Gibbs, S.; Martinez, F. J.; Semigran, M. J.; Simonneau, G.; Wells, A. U.; Vachiery, J. L. Pulmonary hypertension in chronic lung diseases J. Am. Coll. Cardiol. 2013, 62 (25 Suppl) D109-16
5. Kistler, K. D.; Nalysnyk, L.; Rotella, P.; Esser, D. Lung transplantation in idiopathic pulmonary fibrosis: a systematic review of the literature BMC Pulm. Med. 2014, 14, 139
6. Richeldi, L.; du Bois, R. M.; Raghu, G.; Azuma, A.; Brown, K. K.; Costabel, U.; Cottin, V.; Flaherty, K. R.; Hansell, D. M.; Inoue, Y.; Kim, D. S.; Kolb, M.; Nicholson, A. G.; Noble, P. W.; Selman, M.; Taniguchi, H.; Brun, M.; Le Maulf, F.; Girard, M.; Stowasser, S.; Schlenker-Herceg, R.; Disse, B.; Collard, H. R.; Investigators, I. T. Efficacy and safety of nintedanib in idiopathic pulmonary fibrosis N. Engl. J. Med. 2014, 370 (22) 2071-82
7. King, T. E., Jr.; Bradford, W. Z.; Castro-Bernardini, S.; Fagan, E. A.; Glaspole, I.; Glassberg, M. K.; Gorina, E.; Hopkins, P. M.; Kardatzke, D.; Lancaster, L.; Lederer, D. J.; Nathan, S. D.; Pereira, C. A.; Sahn, S. A.; Sussman, R.; Swigris, J. J.; Noble, P. W.; Group, A. S. A phase 3 trial of pirfenidone in patients with idiopathic pulmonary fibrosis N. Engl. J. Med. 2014, 370 (22) 2083-92
8. Borensztajn, K.; Crestani, B.; Kolb, M. Idiopathic pulmonary fibrosis: from epithelial injury to biomarkers - insights from the bench side Respiration 2013, 86 (6) 441-52
9. Blackwell, T. S.; Tager, A. M.; Borok, Z.; Moore, B. B.; Schwartz, D. A.; Anstrom, K. J.; Bar-Joseph, Z.; Bitterman, P.; Blackburn, M. R.; Bradford, W.; Brown, K. K.; Chapman, H. A.; Collard, H. R.; Cosgrove, G. P.; Deterding, R.; Doyle, R.; Flaherty, K. R.; Garcia, C. K.; Hagood, J. S.; Henke, C. A.; Herzog, E.; Hogaboam, C. M.; Horowitz, J. C.; King, T. E., Jr.; Loyd, J. E.; Lawson, W. E.; Marsh, C. B.; Noble, P. W.; Noth, I.; Sheppard, D.; Olsson, J.; Ortiz, L. A.; O'Riordan, T. G.; Oury, T. D.; Raghu, G.; Roman, J.; Sime, P. J.; Sisson, T. H.; Tschumperlin, D.; Violette, S. M.; Weaver, T. E.; Wells, R. G.; White, E. S.; Kaminski, N.; Martinez, F. J.; Wynn, T. A.; Thannickal, V. J.; Eu, J. P. Future directions in idiopathic pulmonary fibrosis research. An NHLBI workshop report Am. J. Respir. Crit. Care Med. 2014, 189 (2) 214-22
10. Cosgrove, G. P.; Brown, K. K.; Schiemann, W. P.; Serls, A. E.; Parr, J. E.; Geraci, M. W.; Schwarz, M. I.; Cool, C. D.; Worthen, G. S. Pigment epithelium-derived factor in idiopathic pulmonary fibrosis: a role in aberrant angiogenesis Am. J. Respir. Crit. Care Med. 2004, 170 (3) 242-51
11. Kaminski, N.; Rosas, I. O. Gene expression profiling as a window into idiopathic pulmonary fibrosis pathogenesis: can we identify the right target genes? Proc. Am. Thorac. Soc. 2006, 3 (4) 339-44
12. Selman, M.; Pardo, A.; Barrera, L.; Estrada, A.; Watson, S. R.; Wilson, K.; Aziz, N.; Kaminski, N.; Zlotnik, A. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis Am. J. Respir. Crit. Care Med. 2006, 173 (2) 188-98
13. Boon, K.; Bailey, N. W.; Yang, J.; Steel, M. P.; Groshong, S.; Kervitsky, D.; Brown, K. K.; Schwarz, M. I.; Schwartz, D. A. Molecular phenotypes distinguish patients with relatively stable from progressive idiopathic pulmonary fibrosis (IPF) PLoS One 2009, 4 (4) e5134
14. Konishi, K.; Gibson, K. F.; Lindell, K. O.; Richards, T. J.; Zhang, Y.; Dhir, R.; Bisceglia, M.; Gilbert, S.; Yousem, S. A.; Song, J. W.; Kim, D. S.; Kaminski, N. Gene expression profiles of acute exacerbations of idiopathic pulmonary fibrosis Am. J. Respir. Crit. Care Med. 2009, 180 (2) 167-75
15. Meltzer, E. B.; Barry, W. T.; D'Amico, T. A.; Davis, R. D.; Lin, S. S.; Onaitis, M. W.; Morrison, L. D.; Sporn, T. A.; Steele, M. P.; Noble, P. W. Bayesian probit regression model for the diagnosis of pulmonary fibrosis: proof-of-principle BMC Med. Genomics 2011, 4, 70
16. Yang, I. V.; Coldren, C. D.; Leach, S. M.; Seibold, M. A.; Murphy, E.; Lin, J.; Rosen, R.; Neidermyer, A. J.; McKean, D. F.; Groshong, S. D.; Cool, C.; Cosgrove, G. P.; Lynch, D. A.; Brown, K. K.; Schwarz, M. I.; Fingerlin, T. E.; Schwartz, D. A. Expression of cilium-associated genes defines novel molecular subtypes of idiopathic pulmonary fibrosis Thorax 2013, 68 (12) 1114-21
17. Vuga, L. J.; Milosevic, J.; Pandit, K.; Ben-Yehudah, A.; Chu, Y.; Richards, T.; Sciurba, J.; Myerburg, M.; Zhang, Y.; Parwani, A. V.; Gibson, K. F.; Kaminski, N. Cartilage oligomeric matrix protein in idiopathic pulmonary fibrosis PLoS One 2013, 8 (12) e83120
18. Emblom-Callahan, M. C.; Chhina, M. K.; Shlobin, O. A.; Ahmad, S.; Reese, E. S.; Iyer, E. P.; Cox, D. N.; Brenner, R.; Burton, N. A.; Grant, G. M.; Nathan, S. D. Genomic phenotype of non-cultured pulmonary fibroblasts in idiopathic pulmonary fibrosis Genomics 2010, 96 (3) 134-45
19. Lindahl, G. E.; Stock, C. J.; Shi-Wen, X.; Leoni, P.; Sestini, P.; Howat, S. L.; Bou-Gharios, G.; Nicholson, A. G.; Denton, C. P.; Grutters, J. C.; Maher, T. M.; Wells, A. U.; Abraham, D. J.; Renzoni, E. A. Microarray profiling reveals suppressed interferon stimulated gene program in fibroblasts from scleroderma-associated interstitial lung disease Respir. Res. 2013, 14, 80
20. Yu, G.; Kovkarova-Naumovski, E.; Jara, P.; Parwani, A.; Kass, D.; Ruiz, V.; Lopez-Otin, C.; Rosas, I. O.; Gibson, K. F.; Cabrera, S.; Ramirez, R.; Yousem, S. A.; Richards, T. J.; Chensny, L. J.; Selman, M.; Kaminski, N.; Pardo, A. Matrix metalloproteinase-19 is a key regulator of lung fibrosis in mice and humans Am. J. Respir. Crit. Care Med. 2012, 186 (8) 752-62
21. Herazo-Maya, J. D.; Noth, I.; Duncan, S. R.; Kim, S.; Ma, S. F.; Tseng, G. C.; Feingold, E.; Juan-Guardela, B. M.; Richards, T. J.; Lussier, Y.; Huang, Y.; Vij, R.; Lindell, K. O.; Xue, J.; Gibson, K. F.; Shapiro, S. D.; Garcia, J. G.; Kaminski, N. Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis Sci. Transl. Med. 2013, 5 (205) 205ra136
22. Wattiez, R.; Hermans, C.; Cruyt, C.; Bernard, A.; Falmagne, P. Human bronchoalveolar lavage fluid protein two-dimensional database: study of interstitial lung diseases Electrophoresis 2000, 21 (13) 2703-12
23. Rottoli, P.; Magi, B.; Perari, M. G.; Liberatori, S.; Nikiforakis, N.; Bargagli, E.; Cianti, R.; Bini, L.; Pallini, V. Cytokine profile and proteome analysis in bronchoalveolar lavage of patients with sarcoidosis, pulmonary fibrosis associated with systemic sclerosis and idiopathic pulmonary fibrosis Proteomics 2005, 5 (5) 1423-30
24. Bargagli, E.; Olivieri, C.; Prasse, A.; Bianchi, N.; Magi, B.; Cianti, R.; Bini, L.; Rottoli, P.; Calgranulin, B. (S100A9) levels in bronchoalveolar lavage fluid of patients with interstitial lung diseases Inflammation 2008, 31 (5) 351-4
25. Foster, M. W.; Thompson, J. W.; Que, L. G.; Yang, I. V.; Schwartz, D. A.; Moseley, M. A.; Marshall, H. E. Proteomic analysis of human bronchoalveolar lavage fluid after subsgemental exposure J. Proteome Res. 2013, 12 (5) 2194-205
26. Raghu, G.; Collard, H. R.; Egan, J. J.; Martinez, F. J.; Behr, J.; Brown, K. K.; Colby, T. V.; Cordier, J. F.; Flaherty, K. R.; Lasky, J. A.; Lynch, D. A.; Ryu, J. H.; Swigris, J. J.; Wells, A. U.; Ancochea, J.; Bouros, D.; Carvalho, C.; Costabel, U.; Ebina, M.; Hansell, D. M.; Johkoh, T.; Kim, D. S.; King, T. E., Jr.; Kondoh, Y.; Myers, J.; Muller, N. L.; Nicholson, A. G.; Richeldi, L.; Selman, M.; Dudden, R. F.; Griss, B. S.; Protzko, S. L.; Schunemann, H. J.; Fibrosis, A. E. J. A. C. o. I. P. An official ATS/ERS/JRS/ALAT statement: idiopathic pulmonary fibrosis: evidence-based guidelines for diagnosis and management Am. J. Respir. Crit. Care Med. 2011, 183 (6) 788-824
27. Hoos, M. D.; Richardson, B. M.; Foster, M. W.; Everhart, A.; Thompson, J. W.; Moseley, M. A.; Colton, C. A. Longitudinal study of differential protein expression in an Alzheimer's mouse model lacking inducible nitric oxide synthase J. Proteome Res. 2013, 12 (10) 4462-77
28. Reidel, B.; Thompson, J. W.; Farsiu, S.; Moseley, M. A.; Skiba, N. P.; Arshavsky, V. Y. Proteomic profiling of a layered tissue reveals unique glycolytic specializations of photoreceptor cells Mol. Cell Proteomics 2011, 10 (3) M110 002469
29. MacLean, B.; Tomazela, D. M.; Shulman, N.; Chambers, M.; Finney, G. L.; Frewen, B.; Kern, R.; Tabb, D. L.; Liebler, D. C.; MacCoss, M. J., Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 2010, 26, (7), 966-8.
30. Winterbauer, R. H.; Wu, R.; Springmeyer, S. C. Fractional analysis of the 120-ml bronchoalveolar lavage. Determination of the best specimen for diagnosis of sarcoidosis Chest 1993, 104 (2) 344-51
31. Rennard, S. I.; Ghafouri, M.; Thompson, A. B.; Linder, J.; Vaughan, W.; Jones, K.; Ertl, R. F.; Christensen, K.; Prince, A.; Stahl, M. G. Fractional processing of sequential bronchoalveolar lavage to separate bronchial and alveolar samples Am. Rev. Respir. Dis. 1990, 141 (1) 208-17
32. Limper, A. H.; Specks, U.; Brutinel, W. M.; Martin, W. J., 2nd; Rohrbach, M. S. Interlobar variation in the recovery of bronchoalveolar lavage fluid, cell populations, and angiotensin-converting enzyme in normal volunteers J. Lab Clin. Med. 1993, 121 (6) 785-91
33. Foster, M. W.; Thompson, J. W.; Que, L. G.; Yang, I. V.; Schwartz, D. A.; Moseley, M. A.; Marshall, H. E., Proteomic Analysis of Human Bronchoalveolar Lavage Fluid after Subsgemental Exposure. J. Proteome Res. 2013.
34. Voynow, J. A.; Young, L. R.; Wang, Y.; Horger, T.; Rose, M. C.; Fischer, B. M. Neutrophil elastase increases MUC5AC mRNA and protein expression in respiratory epithelial cells Am. J. Physiol. 1999, 276 (5 Pt 1) L835-43
35. Burgel, P. R.; Lazarus, S. C.; Tam, D. C.; Ueki, I. F.; Atabai, K.; Birch, M.; Nadel, J. A. Human eosinophils induce mucin production in airway epithelial cells via epidermal growth factor receptor activation J. Immunol. 2001, 167 (10) 5948-54
36. Schwartz, D. A.; Helmers, R. A.; Dayton, C. S.; Merchant, R. K.; Hunninghake, G. W. Determinants of bronchoalveolar lavage cellularity in idiopathic pulmonary fibrosis J. Appl. Physiol. (1985) 1991, 71 (5) 1688-93
37. Kinder, B. W.; Brown, K. K.; Schwarz, M. I.; Ix, J. H.; Kervitsky, A.; King, T. E., Jr. Baseline BAL neutrophilia predicts early mortality in idiopathic pulmonary fibrosis Chest 2008, 133 (1) 226-32
38. Nath, J.; Gallin, J. I. Ionic requirements and subcellular localization of tubulin tyrosinolation in human polymorphonuclear leukocytes J. Immunol. 1986, 136 (2) 628-35
39. Nath, J.; Flavin, M.; Gallin, J. I. Tubulin tyrosinolation in human polymorphonuclear leukocytes: studies in normal subjects and in patients with the Chediak-Higashi syndrome J. Cell Biol. 1982, 95 (2 Pt 1) 519-26
40. Nath, J.; Powledge, A.; Wright, D. G. Studies of signal transduction in the respiratory burst-associated stimulation of fMet-Leu-Phe-induced tubulin tyrosinolation and phorbol 12-myristate 13-acetate-induced posttranslational incorporation of tyrosine into multiple proteins in activated neutrophils and HL-60 cells J. Biol. Chem. 1989, 264 (2) 848-55
41. Hallgren, R.; Bjermer, L.; Lundgren, R.; Venge, P. The eosinophil component of the alveolitis in idiopathic pulmonary fibrosis. Signs of eosinophil activation in the lung are related to impaired lung function Am. Rev. Respir. Dis. 1989, 139 (2) 373-7
42. Reynolds, H. Y.; Fulmer, J. D.; Kazmierowski, J. A.; Roberts, W. C.; Frank, M. M.; Crystal, R. G. Analysis of cellular and protein content of broncho-alveolar lavage fluid from patients with idiopathic pulmonary fibrosis and chronic hypersensitivity pneumonitis J. Clin. Invest. 1977, 59 (1) 165-75
43. Pesci, A.; Ricchiuti, E.; Ruggiero, R.; De Micheli, A. Bronchoalveolar lavage in idiopathic pulmonary fibrosis: what does it tell us? Respir. Med. 2010, 104 (Suppl 1) S70-3
44. Fujimoto, K.; Kubo, K.; Yamaguchi, S.; Honda, T.; Matsuzawa, Y. Eosinophil activation in patients with pulmonary fibrosis Chest 1995, 108 (1) 48-54
45. Willems, S.; Verleden, S. E.; Vanaudenaerde, B. M.; Wynants, M.; Dooms, C.; Yserbyt, J.; Somers, J.; Verbeken, E. K.; Verleden, G. M.; Wuyts, W. A. Multiplex protein profiling of bronchoalveolar lavage in idiopathic pulmonary fibrosis and hypersensitivity pneumonitis Ann. Thorac Med. 2013, 8 (1) 38-45
46. Korthagen, N. M.; Nagtegaal, M. M.; van Moorsel, C. H.; Kazemier, K. M.; van den Bosch, J. M.; Grutters, J. C. MRP14 is elevated in the bronchoalveolar lavage fluid of fibrosing interstitial lung diseases Clin. Exp. Immunol. 2010, 161 (2) 342-7
47. Pardo, A.; Gibson, K.; Cisneros, J.; Richards, T. J.; Yang, Y.; Becerril, C.; Yousem, S.; Herrera, I.; Ruiz, V.; Selman, M.; Kaminski, N. Up-regulation and profibrotic role of osteopontin in human idiopathic pulmonary fibrosis PLoS Med. 2005, 2 (9) e251
48. Schaberg, T.; Orzechowski, K.; Oesterling, C.; Lode, H.; Schuppan, D. Simultaneous measurement of collagen type-VI-related antigen and procollagen type-III-N-propeptide levels in bronchoalveolar lavage Eur. Respir. J. 1994, 7 (7) 1221-6
49. Prasse, A.; Probst, C.; Bargagli, E.; Zissel, G.; Toews, G. B.; Flaherty, K. R.; Olschewski, M.; Rottoli, P.; Muller-Quernheim, J. Serum CC-chemokine ligand 18 concentration predicts outcome in idiopathic pulmonary fibrosis Am. J. Respir. Crit. Care Med. 2009, 179 (8) 717-23
50. Rosas, I. O.; Richards, T. J.; Konishi, K.; Zhang, Y.; Gibson, K.; Lokshin, A. E.; Lindell, K. O.; Cisneros, J.; Macdonald, S. D.; Pardo, A.; Sciurba, F.; Dauber, J.; Selman, M.; Gochuico, B. R.; Kaminski, N. MMP1 and MMP7 as potential peripheral blood biomarkers in idiopathic pulmonary fibrosis PLoS Med. 2008, 5 (4) e93
51. Zhang, Y.; Kaminski, N. Biomarkers in idiopathic pulmonary fibrosis Curr. Opin. Pulm. Med. 2012, 18 (5) 441-6
52. Chapin, C.; Bailey, N. A.; Gonzales, L. W.; Lee, J. W.; Gonzalez, R. F.; Ballard, P. L. Distribution and surfactant association of carcinoembryonic cell adhesion molecule 6 in human lung Am. J. Physiol. Lung Cell. Mol. Physiol. 2012, 302 (2) L216-25
53. Kolla, V.; Gonzales, L. W.; Bailey, N. A.; Wang, P.; Angampalli, S.; Godinez, M. H.; Madesh, M.; Ballard, P. L. Carcinoembryonic cell adhesion molecule 6 in human lung: regulated expression of a multifunctional type II cell protein Am. J. Physiol. Lung Cell. Mol. Physiol. 2009, 296 (6) L1019-30
54. Yang, I. V.; Luna, L. G.; Cotter, J.; Talbert, J.; Leach, S. M.; Kidd, R.; Turner, J.; Kummer, N.; Kervitsky, D.; Brown, K. K.; Boon, K.; Schwarz, M. I.; Schwartz, D. A.; Steele, M. P. The peripheral blood transcriptome identifies the presence and extent of disease in idiopathic pulmonary fibrosis PLoS One 2012, 7 (6) e37708
55. Khalil, N.; O'Connor, R. Idiopathic pulmonary fibrosis: current understanding of the pathogenesis and the status of treatment CMAJ 2004, 171 (2) 153-60
56. Katzenstein, A. L.; Myers, J. L. Idiopathic pulmonary fibrosis: clinical relevance of pathologic classification Am. J. Respir. Crit. Care Med. 1998, 157 (4 Pt 1) 1301-15
57. Travis, W. D.; Costabel, U.; Hansell, D. M.; King, T. E., Jr.; Lynch, D. A.; Nicholson, A. G.; Ryerson, C. J.; Ryu, J. H.; Selman, M.; Wells, A. U.; Behr, J.; Bouros, D.; Brown, K. K.; Colby, T. V.; Collard, H. R.; Cordeiro, C. R.; Cottin, V.; Crestani, B.; Drent, M.; Dudden, R. F.; Egan, J.; Flaherty, K.; Hogaboam, C.; Inoue, Y.; Johkoh, T.; Kim, D. S.; Kitaichi, M.; Loyd, J.; Martinez, F. J.; Myers, J.; Protzko, S.; Raghu, G.; Richeldi, L.; Sverzellati, N.; Swigris, J.; Valeyre, D. An official American Thoracic Society/European Respiratory Society statement: Update of the international multidisciplinary classification of the idiopathic interstitial pneumonias Am. J. Respir. Crit. Care Med. 2013, 188 (6) 733-48
58. Enomoto, N.; Suda, T.; Kato, M.; Kaida, Y.; Nakamura, Y.; Imokawa, S.; Ida, M.; Chida, K. Quantitative analysis of fibroblastic foci in usual interstitial pneumonia Chest 2006, 130 (1) 22-9
59. Lung Genomics Research Consortium. http://www.lung-genomics.org/.
60. Steck, E.; Braun, J.; Pelttari, K.; Kadel, S.; Kalbacher, H.; Richter, W. Chondrocyte secreted CRTAC1: a glycosylated extracellular matrix molecule of human articular cartilage Matrix Biol. 2007, 26 (1) 30-41
61. Myllarniemi, M.; Vuorinen, K.; Pulkkinen, V.; Kankaanranta, H.; Aine, T.; Salmenkivi, K.; Keski-Oja, J.; Koli, K.; Kinnula, V. Gremlin localization and expression levels partially differentiate idiopathic interstitial pneumonia severity and subtype J. Pathol. 2008, 214 (4) 456-63
62. Koli, K.; Myllarniemi, M.; Vuorinen, K.; Salmenkivi, K.; Ryynanen, M. J.; Kinnula, V. L.; Keski-Oja, J. Bone morphogenetic protein-4 inhibitor gremlin is overexpressed in idiopathic pulmonary fibrosis Am. J. Pathol. 2006, 169 (1) 61-71
63. Farkas, L.; Farkas, D.; Gauldie, J.; Warburton, D.; Shi, W.; Kolb, M. Transient overexpression of Gremlin results in epithelial activation and reversible fibrosis in rat lungs Am. J. Respir. Cell Mol. Biol. 2011, 44 (6) 870-8
64. Myllarniemi, M.; Lindholm, P.; Ryynanen, M. J.; Kliment, C. R.; Salmenkivi, K.; Keski-Oja, J.; Kinnula, V. L.; Oury, T. D.; Koli, K. Gremlin-mediated decrease in bone morphogenetic protein signaling promotes pulmonary fibrosis Am. J. Respir. Crit. Care Med. 2008, 177 (3) 321-9
65. Jablonska, E.; Markart, P.; Zakrzewicz, D.; Preissner, K. T.; Wygrecka, M. Transforming growth factor-beta1 induces expression of human coagulation factor XII via Smad3 and JNK signaling pathways in human lung fibroblasts J. Biol. Chem. 2010, 285 (15) 11638-51
66. Navaratnam, V.; Fogarty, A. W.; McKeever, T.; Thompson, N.; Jenkins, G.; Johnson, S. R.; Dolan, G.; Kumaran, M.; Pointon, K.; Hubbard, R. B., Presence of a prothrombotic state in people with idiopathic pulmonary fibrosis: a population-based case-control study. Thorax 2013.
67. Mani, D. R.; Abbatiello, S. E.; Carr, S. A. Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics BMC Bioinformatics 2012, 13 (Suppl 16) S9
68. Kohan, M.; Puxeddu, I.; Reich, R.; Levi-Schaffer, F.; Berkman, N. Eotaxin-2/CCL24 and eotaxin-3/CCL26 exert differential profibrogenic effects on human lung fibroblasts Ann. Allergy Asthma Immunol. 2010, 104 (1) 66-72
69. Casale, T. B.; Trapp, S.; Zehr, B.; Hunninghake, G. W. Bronchoalveolar lavage fluid histamine levels in interstitial lung diseases Am. Rev. Respir. Dis. 1988, 138 (6) 1604-8
70. Ziegenhagen, M. W.; Zabel, P.; Zissel, G.; Schlaak, M.; Muller-Quernheim, J. Serum level of interleukin 8 is elevated in idiopathic pulmonary fibrosis and indicates disease activity Am. J. Respir Crit. Care Med. 1998, 157 (3 Pt 1) 762-8
71. Ashitani, J.; Mukae, H.; Taniguchi, H.; Ihi, T.; Kadota, J.; Kohno, S.; Matsukura, S. Granulocyte-colony stimulating factor levels in bronchoalveolar lavage fluid from patients with idiopathic pulmonary fibrosis Thorax 1999, 54 (11) 1015-20
72. Phelps, D. S.; Umstead, T. M.; Mejia, M.; Carrillo, G.; Pardo, A.; Selman, M. Increased surfactant protein-A levels in patients with newly diagnosed idiopathic pulmonary fibrosis Chest 2004, 125 (2) 617-25
73. Kasabova, M.; Joulin-Giet, A.; Lecaille, F.; Saidi, A.; Marchand-Adam, S.; Lalmanach, G. Human cystatin C: a new biomarker of idiopathic pulmonary fibrosis? Proteomics Clin. Appl. 2014, 8 (5-6) 447-53
74. Korthagen, N. M.; van Moorsel, C. H.; Barlo, N. P.; Ruven, H. J.; Kruit, A.; Heron, M.; van den Bosch, J. M.; Grutters, J. C. Serum and BALF YKL-40 levels are predictors of survival in idiopathic pulmonary fibrosis Respir. Med. 2011, 105 (1) 106-13
75. Nakayama, S.; Mukae, H.; Ishii, H.; Kakugawa, T.; Sugiyama, K.; Sakamoto, N.; Fujii, T.; Kadota, J.; Kohno, S. Comparison of BALF concentrations of ENA-78 and IP10 in patients with idiopathic pulmonary fibrosis and nonspecific interstitial pneumonia Respir. Med. 2005, 99 (9) 1145-51
76. Nguyen, E. V.; Gharib, S. A.; Crothers, K.; Chow, Y. H.; Park, D. R.; Goodlett, D. R.; Schnapp, L. M. Proteomic landscape of bronchoalveolar lavage fluid in human immunodeficiency virus infection Am. J. Physiol. Lung Cell. Mol. Physiol. 2014, 306 (1) L35-42
77. Huang, Y. J.; Lynch, S. V.; Wiener-Kronish, J. P. From microbe to microbiota: considering microbial community composition in infections and airway diseases Am. J. Respir. Crit. Care Med. 2012, 185 (7) 691-2
78. Segal, L. N.; Alekseyenko, A. V.; Clemente, J. C.; Kulkarni, R.; Wu, B.; Chen, H.; Berger, K. I.; Goldring, R. M.; Rom, W. N.; Blaser, M. J.; Weiden, M. D. Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation Microbiome 2013, 1 (1) 19
79. Sharma, V.; Eckels, J.; Taylor, G. K.; Shulman, N. J.; Stergachis, A. B.; Joyner, S. A.; Yan, P.; Whiteaker, J. R.; Halusa, G. N.; Schilling, B.; Gibson, B. W.; Colangelo, C. M.; Paulovich, A. G.; Carr, S. A.; Jaffe, J. D.; MacCoss, M. J.; MacLean, B. Panorama: a targeted proteomics knowledge base J. Proteome Res. 2014, 13 (9) 4205-10