Proteomic approaches for studying human parenchymal lung diseases

Expert Review of Proteomics

Volumn 6, Issue 6, 2009, Pages 619-629

  Kinnula, Vuokko L ^a   Ishikawa, Nobuhisa ^a,b   Bergmann, Ulrich ^c   Ohlmeier, Steffen ^c  

^a UNIVERSITY OF HELSINKI   (Finland)

^b HIROSHIMA UNIVERSITY   (Japan)

^c UNIVERSITY OF OULU   (Finland)

Author keywords

2DE; Bronchoalveolar lavage fluid; Chronic obstructive pulmonary disease; Emphysema; Idiopathic pulmonary fibrosis; Induced sputum; Lung tissue; Mass spectrometry; Proteomics; SELDI

Indexed keywords

BIOLOGICAL MARKER; CALGRANULIN A; CALGRANULIN B; PROTEIN; SALBUTAMOL; SODIUM CHLORIDE;

AIRWAY OBSTRUCTION; BLOOD SAMPLING; BRONCHUS BIOPSY; CHRONIC OBSTRUCTIVE LUNG DISEASE; CLINICAL FEATURE; CLINICAL PRACTICE; DIFFERENTIAL DIAGNOSIS; DISEASE COURSE; DISEASE SEVERITY; EMPHYSEMA; ENZYME LINKED IMMUNOSORBENT ASSAY; FIBROSING ALVEOLITIS; HUMAN; INTERSTITIAL PNEUMONIA; LASER CAPTURE MICRODISSECTION; LIQUID CHROMATOGRAPHY; LUNG DISEASE; LUNG FIBROSIS; LUNG INJURY; LUNG LAVAGE; LUNG PARENCHYMA; MASS SPECTROMETRY; MORBIDITY; MORTALITY; PARENCHYMAL LUNG DISEASE; PATHOGENESIS; PROTEIN ANALYSIS; PROTEOMICS; REVIEW; RISK FACTOR; SMOKING; SPUTUM CULTURE; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TREATMENT RESPONSE; TWO DIMENSIONAL ELECTROPHORESIS; TWO DIMENSIONAL GEL ELECTROPHORESIS; WESTERN BLOTTING;

HUMANS; LUNG; LUNG DISEASES, INTERSTITIAL; PROTEOMICS;

EID: 74049163804     PISSN: 14789450     EISSN: 17448387     Source Type: Journal    
DOI: 10.1586/epr.09.80     Document Type: Review

References (62)

1. Alban A, David SO, Bjorkesten L et al. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3, 36-44 (2003).
2. Kondo T, Seike M, Mori Y, Fujii K, Yamada T, Hirohashi S. Application of sensitive fluorescent dyes in linkage of laser microdissection and two-dimensional gel electrophoresis as a cancer proteomic study tool. Proteomics 3, 1758-1766 (2003).
3. Wu J, Kobayashi M, Sousa EA et al. Differential proteomic analysis of bronchoalveolar lavage fluid in asthmatics following segmental antigen challenge. Mol. Cell. Proteomics 4, 1251-1264 (2005).
4. Plymoth A, Yang Z, Löfdahl CG et al. Rapid proteome analysis of bronchoalveolar lavage samples of lifelong smokers and never-smokers by micro-scale liquid chromatography and mass spectrometry. Clin. Chem. 52, 671-679 (2006).
5. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999 (1999).
6. Ross PL, Huang YLN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using aminereactive isobaric tagging reagents. Mol. Cell. Proteomics 3, 1154-1169 (2004).
7. Pinto-Plata V, Toso J, Lee K et al. Profiling serum biomarkers in patients with COPD: associations with clinical parameters. Thorax 62, 595-601 (2007). • Antibody-based protein chip technology and correlation with clinical parameters to identify potential biomarkers for chronic obstructive pulmonary disease (COPD).
8. Tang N, Tornatore P, Weinberger SR. Current developments in SELDI affinity technology. Mass Spectrom. Rev. 23, 34-44 (2004).
9. American Thoracic Society; European Respiratory Society. American Thoracic Society/European Respiratory Society International Multidisciplinary Consensus Classification of the Idiopathic Interstitial Pneumonias. This joint statement of the American Thoracic Society (ATS), and the European Respiratory Society (ERS) was adopted by the ATS board of directors, June 2001 and by the ERS Executive Committee, June 2001. Am. J. Respir. Crit. Care Med. 165, 277-304 (2002). •• International consensus statement for the classification of idiopathic interstitial pneumonias (IIPs).
10. Rabe KF, Beghé B, Luppi F, Fabbri LM. Update in chronic obstructive pulmonary disease 2006. Am. J. Respir. Crit. Care Med. 175, 1222-1232 (2007).
11. Rabe KF, Hurd S, Anzueto A et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am. J. Respir. Crit. Care Med. 176, 532-555 (2007). •• Comprehensive review on COPD.
12. Bringardner BD, Baran CP, Eubank TD, Marsh CB. The role of inf lammation in the pathogenesis of idiopathic pulmonary fibrosis. Antioxid. Redox. Signal. 10, 287-301 (2008).
13. Demedts M, Behr J, Buhl R et al. High-dose acetylcysteine in idiopathic pulmonary f ibrosis. N. Engl. J. Med. 353, 2229-2242 (2005).
14. Kinnula VL, Fattman CL, Tan RJ, Oury TD. Oxidative stress in pulmonary fibrosis: a possible role for redox modulatory therapy. Am. J. Respir. Crit. Care Med. 172, 417-422 (2005). • Overview of the role of oxidative stress in idiopathic pulmonary fibrosis (IPF).
15. Koli K, Myllärniemi M, Keski-Oja J, Kinnula VL. Transforming growth factor-beta activation in the lung: focus on fibrosis and reactive oxygen species. Antioxid. Redox Signal. 10, 333-342 (2008).
16. Wells AU, Hogaboam CM. Update in diffuse parenchymal lung disease 2007. Am. J. Respir. Crit. Care Med. 177, 580-584 (2008).
17. Salvi SS, Barnes PJ. Chronic obstructive pulmonary disease in non-smokers. Lancet 374, 733-742 (2009).
18. Hogg JC, Chu F, Utokaparch S et al. The nature of small-airway obstruction in chronic obstructive pulmonary disease. N. Engl. J. Med. 350, 2645-2653 (2004).
19. Gauldie J, Kolb M, Ask K et al. Smad3 signaling involved in pulmonary fibrosis and emphysema. Proc. Am. Thorac. Soc. 3, 696-702 (2006).
20. Leppäranta O, Myllärniemi M, Salmenkivi K, Kinnula VL, Keski-Oja J, Koli K. Reduced phosphorylation of the TGF-b signal transducer Smad2 in emphysematous human lung. COPD 4, 234-241 (2009).
21. Fabbri LM, Rabe KF. From COPD to chronic systemic inflammatory syndrome? Lancet 370, 797-799 (2007).
22. Louhelainen N, Rytilä P, Haahtela T, Kinnula VL, Djukanović R. Persistence of oxidant and protease burden in the airways after smoking cessation. BMC Pulm. Med. 9, 25 (2009).
23. Tashkin DP, Celli B, Senn S et al. A 4-year trial of tiotropium in chronic obstructive pulmonary disease. N. Engl. J. Med. 359, 1543-1554 (2008).
24. Marko-Varga G, Lindberg H, Löfdahl CG et al. Discovery of biomarker candidates within disease by protein profiling: principles and concepts. J. Proteome Res. 4, 1200-1212 (2005).
25. Kelsen SG, Duan X, Ji R, Perez O, Liu C, Merali S. Cigarette smoke induces an unfolded protein response in the human lung: a proteomic approach. Am. J. Respir. Cell. Mol. Biol. 38, 541-550 (2008).
26. Ohlmeier S, Vuolanto M, Toljamo T et al. Proteomics of human lung tissue identifies surfactant protein A as a marker of chronic obstructive pulmonary disease. J. Proteome Res. 7, 5125-5132 (2008). • First proteomic study (2DE) on COPD biomarkers in lung tissue.
27. Lee EJ, In KH, Kim JH et al. Proteomic analysis in lung tissue of smokers and COPD patients. Chest 135, 344-352 (2009).
28. Kelly MM, Leigh R, Gilpin SE et al. Cell-specific gene expression in patients with usual interstitial pneumonia. Am. J. Respir. Crit. Care. Med.174, 557-565 (2006).
29. Björhall K, Miliotis T, Davidsson P. Comparison of different depletion strategies for improved resolution in proteomic analysis of human serum samples. Proteomics 5, 307-317 (2005).
30. Bozinovski S, Hutchinson A, Thompson M et al. Serum amyloid A is a biomarker of acute exacerbations of chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 177, 269-278 (2008).
31. Bowler RP, Canham ME, Ellison MC. Surface enhanced laser desorption/ ionization (SELDI) time-of-flight mass spectrometry to identify patients with chronic obstructive pulmonary disease. COPD 3, 41-50 (2006).
32. Casado B, Iadarola P, Luisetti M, Kussmann M. Proteomics-based diagnosis of chronic obstructive pulmonary disease: the hunt for new markers. Expert Rev. Proteomics 5(5), 693-704 (2008).
33. Miller I, Eberini I, Gianazza E. Proteomics of lung physiopathology. Proteomics 8, 5053-5073 (2008).
34. Magi B, Bargagli E, Bini L, Rottoli P. Proteome analysis of bronchoalveolar lavage in lung diseases. Proteomics 6, 6354-6369 (2006).
35. Merkel D, Rist W, Seither P, Weith A, Lenter MC. Proteomic study of human bronchoalveolar lavage fluids from smokers with chronic obstructive pulmonary disease by combining surface-enhanced laser desorption/ionization-mass spectrometry profiling with mass spectrometric protein identification. Proteomics 5, 2972-2980 (2005).
36. Kriegova E, Melle C, Kolek V et al. Protein profiles of bronchoalveolar lavage fluid from patients with pulmonary sarcoidosis. Am. J. Respir. Crit. Care Med. 173, 1145-1154 (2006).
37. de Torre C, Ying SX, Munson PJ, Meduri GU, Suffredini AF. Proteomic analysis of inflammatory biomarkers in bronchoalveolar lavage. Proteomics 6, 3949-3957 (2006).
38. Djukanović R, Sterk PJ, Fahy JV, Hargreave FE. Standardised methodology of sputum induction and processing. Eur. Respir. J . 37, S1-S2 (2002).
39. Thornton DJ, Sheehan JK. From mucins to mucus: toward a more coherent understanding of this essential barrier. Proc. Am. Thorac. Soc. 1, 54-61 (2004).
40. Nicholas B, Skipp P, Mould R et al. Shotgun proteomic analysis of humaninduced sputum. Proteomics 6, 4390-4401 (2006). • First proteomic study of induced sputum, including an optimized sputum preparation.
41. Casado B, Iadarola P, Pannell LK et al. Protein expression in sputum of smokers and chronic obstructive pulmonary disease patients: a pilot study by CapLC-ESI-QTOF. J. Proteome Res. 6, 4615-4623 (2007). • Proteomic study that investigated protein content in induced sputum of nonsmokers, healthy smokers and patients with chronic bronchitis, COPD and COPD with emphysema.
42. Gray RD, MacGregor G, Noble D et al. Sputum proteomics in inflammatory and suppurative respiratory diseases. Am. J. Respir. Crit. Care Med. 178, 444-452 (2008).
43. Lenz AG, Meyer B, Costabel U, Maier K. Bronchoalveolar lavage fluid proteins in human lung disease: analysis by two-dimensional electrophoresis. Electrophoresis 14, 242-244 (1993).
44. Wattiez R, Hermans C, Cruyt C, Bernard A, Falmagne P. Human bronchoalveolar lavage fluid protein two-dimensional database: study of interstitial lung diseases. Electrophoresis 21, 2703-2712 (2000).
45. Magi B, Bini L, Perari MG et al. Bronchoalveolar lavage fluid protein composition in patients with sarcoidosis and idiopathic pulmonary fibrosis: a two-dimensional electrophoretic study. Electrophoresis 23, 3434-3444 (2002).
46. Rottoli P, Magi B, Perari MG et al. Cytokine profile and proteome analysis in bronchoalveolar lavage of patients with sarcoidosis, pulmonary fibrosis associated with systemic sclerosis and idiopathic pulmonary fibrosis. Proteomics 5, 1423-1430 (2005). • 2DE study of bronchoalveolar lavage fluid identifies a large number of proteins in sarcoidosis and IPF.
47. Bargagli E, Olivieri C, Prasse A et al. Calgranulin B (S100A9) levels in bronchoalveolar lavage fluid of patients with interstitial lung diseases. Inflammation 31, 351-354 (2008).
48. Bargagli E, Olivieri C, Nikiforakis N et al. Analysis of macrophage migration inhibitory factor (MIF) in patients with idiopathic pulmonary fibrosis. Respir. Physiol. Neurobiol. 167, 261-267 (2009).
49. Rottoli P, Magi B, Cianti R et al. Carbonylated proteins in bronchoalveolar lavage of patients with sarcoidosis, pulmonary fibrosis associated with systemic sclerosis and idiopathic pulmonary fibrosis. Proteomics 5, 2612-2618 (2005).
50. Travis WD, Hunninghake G, King TE Jr et al. Idiopathic nonspecific interstitial pneumonia: report of an American Thoracic Society project. Am. J. Respir. Crit. Care Med. 177, 1338-1347 (2008).
51. Selman M, Pardo A, Barrera L et al. Gene expression profiles distinguish idiopathic pulmonary fibrosis from hypersensitivity pneumonitis. Am. J. Respir. Crit. Care. Med. 173, 188-198 (2006).
52. Yang IV, Burch LH, Steele MP et al. Gene expression profiling of familial and sporadic interstitial pneumonia. Am. J. Respir. Crit. Care. Med. 175, 45-54 (2007).
53. Bons JA, Drent M, Bouwman FG et al. Potential biomarkers for diagnosis of sarcoidosis using proteomics in serum. Respir. Med. 101, 1687-1695 (2007).
54. Silva E, Bourin S, Sabounchi-Schütt F et al. A quantitative proteomic analysis of soluble bronchoalveolar fluid proteins from patients with sarcoidosis and chronic beryllium disease. Sarcoidosis Vasc. Diffuse Lung Dis. 24, 24-32 (2007).
55. Archimandriti DT, Dalavanga YA, Cianti R et al. Proteome analysis of bronchoalveolar lavage in individuals from Metsovo, nonoccupationally exposed to asbestos. J. Proteome Res. 8, 860-869 (2009).
56. Petrak J, Ivanek R, Toman O et al. Déjà vu in proteomics. A hit parade of repeatedly identified differentially expressed proteins. Proteomics 8, 1744-1749 (2008).
57. Wang P, Bouwman FG, Mariman EC. Generally detected proteins in comparative proteomics-a matter of cellular stress response? Proteomics 9, 2955-2966 (2009).
58. Kubota K, Wakabayashi K, Matsuoka T. Proteome analysis of secreted proteins during osteoclast differentiation using two different methods: two-dimensional electrophoresis and isotope-coded affinity tags analysis with two-dimensional chromatography. Proteomics 3, 616-626 (2003).
59. Schmidt F, Donahoe S, Hagens K et al. Complementary analysis of the Mycobacterium tuberculosis proteome by two-dimensional electrophoresis and isotope-coded affinity tag technology. Mol. Cell. Proteomics 3, 24-42 (2004).
60. Valaskovic GA, Kelleher NL, McLafferty FW. Attomole protein characterization by capillary electrophoresis-mass spectrometry. Science 273, 1199-1202 (1996).
61. Macek B, Waanders LF, Olsen JV, Mann M. Top-down protein sequencing and MS3 on a hybrid linear quadrupole ion trap-orbitrap mass spectrometer. Mol. Cell. Proteomics 5, 949-958 (2006).
62. Ocak S, Chaurand P, Massion PP. Mass spectrometry-based proteomic profiling of lung cancer. Proc. Am. Thorac. Soc. 6, 159-170 (2009).