Advances in proteomic techniques for biomarker discovery in COPD

Expert Review of Clinical Immunology

Volumn 7, Issue 1, 2011, Pages 111-123

  Casado, Begoña ^a   Luisetti, Maurizio ^b   Iadarola, Paolo ^b  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

^b UNIVERSITY OF PAVIA   (Italy)

Author keywords

BALF; COPD; exhaled breath; induced sputum; mass spectrometry; proteomics; validation

Indexed keywords

ACTIN; ALBUMIN; APOLIPOPROTEIN A1; BETA TUBULIN; BIOLOGICAL MARKER; CALGRANULIN A; CALGRANULIN B; CALRETICULIN; CATHEPSIN D; COFILIN 1; COLLAGENASE 3; CYTOKERATIN 1; CYTOKERATIN 10; CYTOKERATIN 9; ELONGATION FACTOR 1ALPHA; ELONGATION FACTOR 1BETA; GAMMA INTERFERON; GELSOLIN; GLUCOSE REGULATED PROTEIN 78; GLUTATHIONE TRANSFERASE A2; HEPATOMA DERIVED GROWTH FACTOR; INTERLEUKIN 15; INTERLEUKIN 2; LIPOCORTIN 2; MALATE DEHYDROGENASE; PEROXIREDOXIN 6; PROLINE RICH PROTEIN; PROTEIN DISULFIDE ISOMERASE; TRANSFERRIN; UNINDEXED DRUG;

CHRONIC OBSTRUCTIVE LUNG DISEASE; CYTOTOXIC T LYMPHOCYTE; DISEASE COURSE; FIBROBLAST; GEL ELECTROPHORESIS; HUMAN; LIQUID CHROMATOGRAPHY; LUNG ALVEOLUS; LUNG ALVEOLUS EPITHELIUM; LUNG LAVAGE; MACROPHAGE; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; MONOCYTE; MUCUS SECRETION; NEUTROPHIL; NONHUMAN; PROGNOSIS; PROTEOMICS; REVIEW; SMOKING; SPUTUM; SURFACE ENHANCED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; TH1 CELL;

BIOLOGICAL MARKERS; BRONCHOALVEOLAR LAVAGE FLUID; CHROMATOGRAPHY, LIQUID; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; HUMANS; LUNG; MASS SPECTROMETRY; MIDDLE AGED; PROTEOMICS; PULMONARY DISEASE, CHRONIC OBSTRUCTIVE; SPUTUM;

EID: 78650584003     PISSN: 1744666X     EISSN: None     Source Type: Journal    
DOI: 10.1586/eci.10.75     Document Type: Review

References (98)

1. Barnes PJ. Chronic obstructive pulmonary disease. N. Engl. J. Med. 343, 269-280 (2000).
2. Croxton TL, Weinmann GG, Senior RM et al. Future research directions in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 165, 838-844 (2002).
3. Lopez AD, Murray CC. The global burden of disease, 1990-2020. Nat. Med. 4, 1241-1243 (1998).
4. Stang P, Lydick E, Silberman C et al. The prevalence of COPD: using smoking rates to estimate disease frequency in the general population. Chest 117, 354S-359S (2000).
5. Abboud RT, Vimalanathan S. Pathogenesis of COPD. Part I. The role of protease- antiprotease imbalance in emphysema. Int. J. Tuberc. Lung Dis. 12, 361-367 (2008).
6. Mak JC. Pathogenesis of COPD. Part II. Oxidative-antioxidative imbalance. Int. J. Tuberc. Lung Dis. 12, 368-374 (2008).
7. Roth M. Pathogenesis of COPD. Part III. Inflammation in COPD. Int. J. Tuberc. Lung Dis. 12, 375-380 (2008).
8. Barnes PJ. Genetics and pulmonary medicine. 9. Molecular genetics of chronic obstructive pulmonary disease. Thorax 54, 245-252 (1999).
9. Sandford AJ, Weir TD, Pare PD. Genetic risk factors for chronic obstructive pulmonary disease. Eur. Respir. J. 10, 1380-1391 (1997).
10. Smith CA, Harrison DJ. Association between polymorphism in gene for microsomal epoxide hydrolase and susceptibility to emphysema. Lancet 350, 630-633 (1997).
11. Ezzati M. Indoor air pollution and health in developing countries. Lancet 366, 104-106 (2005).
12. Smith KR, Mehta S. The burden of disease from indoor air pollution in developing countries: comparison of estimates. Int. J. Hyg. Environ. Health 206, 279-289 (2003).
13. Leuenberger P, Schwartz J, Ackermann- Liebrich U et al. Passive smoking exposure in adults and chronic respiratory symptoms (SAPALDIA Study). Swiss Study on Air Pollution and Lung Diseases in Adults, SAPALDIA Team. Am J. Respir. Crit. Care Med. 150, 1222-1228 (1994).
14. Dayal HH, Khuder S, Sharrar R et al. Passive smoking in obstructive respiratory disease in an industrialized urban population. Environ. Res. 65, 161-171 (1994).
15. Barnes PJ, Chowdhury B, Kharitonov SA et al. Pulmonary biomarkers in chronic obstructive pulmonary disease. Am. J. Respir. Crit. Care Med. 174, 6-14 (2006).
16. Barnes PJ, Shapiro SD, Pauwels RA. Chronic obstructive pulmonary disease: molecular and cellular mechanisms. Eur. Respir. J. 22, 672-688 (2003).
17. Barnes PJ. Mediators of chronic obstructive pulmonary disease. Pharmacol. Rev. 56, 515-548 (2004).
18. Franciosi LG, Page CP, Celli BR et al. Markers of disease severity in chronic obstructive pulmonary disease. Pulm. Pharmacol. Ther. 19, 189-199 (2006).
19. Robbins RS. Biology of airway epithelial cells. In: The Lung: Scientific Foundations. Crystal R, West J, Weibel E, Barnes P (Eds). Lippincott-Raven, PA, USA, 453-457 (1996).
20. Shak S. Mucins and lung secretions. In: The Lung: Scientific Foundations. Crystal R, West J, Weibel E, Barnes P (Eds). Lippincott-Raven, PA, USA, 479-486 (1996).
21. Lubman R KKCE. Alveolar epithelial barrier properties. In: The Lung: Scientific Foundations. Crystal R, West J, Weibel E, Barnes P (Eds). Lippincott-Raven, PA, USA, 585-602 (1996).
22. Hawgood S. Surfactant: composition, structure, and metabolism. In: The Lung: Scientific Foundations. Crystal R, West J, Weibel E, Barnes P (Eds). Lippincott-Raven, PA, USA, 557-571 (1996).
23. Lindahl M, Stahlbom B, Tagesson C. Two-dimensional gel electrophoresis of nasal and bronchoalveolar lavage fluids after occupational exposure. Electrophoresis 16, 1199-1204 (1995).
24. Lindahl M, Ekstrom T, Sorensen J et al. Two dimensional protein patterns of bronchoalveolar lavage fluid from nonsmokers, smokers, and subjects exposed to asbestos. Thorax 51, 1028-1035 (1996).
25. Lindahl M, Stahlbom B, Tagesson C. Newly identified proteins in human nasal and bronchoalveolar lavage fluids: potential biomedical and clinical applications. Electrophoresis 20, 3670-3676 (1999).
26. Wattiez R, Hermans C, Bernard A et al. Human bronchoalveolar lavage fluid: two-dimensional gel electrophoresis, amino acid microsequencing and identification of major proteins. Electrophoresis 20, 1634-1645 (1999).
27. Wattiez R, Hermans C, Cruyt C et al. Human bronchoalveolar lavage fluid protein two- dimensional database: study of interstitial lung diseases. Electrophoresis 21, 2703-2712 (2000).
28. Wattiez R, Falmagne P. Proteomics of bronchoalveolar lavage fluid. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 815, 169-178 (2005).
29. Sabounchi-Schutt F, Astrom J, Eklund A et al. Detection and identification of human bronchoalveolar lavage proteins using narrow-range immobilized pH gradient DryStrip and the paper bridge sample application method. Electrophoresis 22, 1851-1860 (2001).
30. Sabounchi-Schutt F, Astrom J, Hellman U et al. Changes in bronchoalveolar lavage fluid proteins in sarcoidosis: a proteomics approach. Eur. Respir. J. 21, 414-420 (2003).
31. 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).
32. 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(5), 1423-1430 (2005).
33. Lindahl M, Stahlbom B, Svartz J et al. Protein patterns of human nasal and bronchoalveolar lavage fluids analyzed with two-dimensional gel electrophoresis. Electrophoresis 19, 3222-3229 (1998).
34. Lomas DA, Silverman EK, Edwards LD et al. Evaluation of serum CC-16 as a biomarker for COPD in the ECLIPSE cohort. Thorax 63, 1058-1063 (2008).
35. Plymoth A, Lofdahl CG, Ekberg-Jansson A et al. Protein expression patterns associated with progression of chronic obstructive pulmonary disease in bronchoalveolar lavage of smokers. Clin. Chem. 53, 636-644 (2007).
36. Plymoth A, Lofdahl CG, Ekberg-Jansson A et al. Human bronchoalveolar lavage: biofluid analysis with special emphasis on sample preparation. Proteomics 3, 962-972 (2003).
37. Link AJ, Eng J, Schieltz DM et al. Direct analysis of protein complexes using mass spectrometry. Nat. Biotechnol. 17, 676-682 (1999).
38. Reynolds HY. Use of bronchoalveolar lavage in humans: past necessity and future imperative. Lung 178, 271-293 (2000).
39. McLachlan A, Borchers M, Velayutham P et al. Characterizing the reproducibility of a protein profiling method for the analysis of mouse bronchoalveolar lavage fluid. J. Proteome Res. 5, 3059-3065 (2006).
40. Merkel D, Rist W, Seither P et al. 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).
41. Plymoth A, Yang Z, Lofdahl 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).
42. Paggiaro PL, Chanez P, Holz O et al. Sputum induction. Eur. Respir. J. 20(Suppl. 37), 3S-8S (2002).
43. Nicholas BL, Skipp P, Mould R et al. Shotgun proteomic analysis of human-induced sputum. Proteomics 6, 4390-4401 (2006).
44. 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-Q-TOF. J. Proteome Res. 6, 4615-4623 (2007).
45. Gevaert K, Van DP, Martens L et al. Diagonal reverse-phase chromatography applications in peptide-centric proteomics: ahead of catalogue-omics? Anal. Biochem. 345, 18-29 (2005).
46. Nicholas BL, Skipp P, Barton S et al. Identification of lipocalin and apolipoprotein a1 as biomarkers of chronic obstructive pulmonary disease. Am J. Respir. Crit. Care Med. 181, 1049-1060 (2010).
47. 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).
48. Pauwels RA, Buist AS, Calverley PM et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive pulmonary disease. NHLBI/ WHO Global Initiative for Chronic Obstructive Lung Disease (GOLD) Workshop summary. Am J. Respir. Crit. Care Med. 163, 1256-1276 (2001).
49. Mutlu GM, Garey KW, Robbins RA et al. Collection and analysis of exhaled breath condensate in humans. Am. J. Respir. Crit. Care Med. 164, 731-737 (2001).
50. Aulak KS, Miyagi M, Yan L et al. Proteomic method identifies proteins nitrated in vivo during inflammatory challenge. Proc. Natl Acad. Sci. USA 98, 12056-12061 (2001).
51. Kurova VS, Anaev EC, Kononikhin AS et al. Proteomics of exhaled breath: methodological nuances and pitfalls. Clin. Chem. Lab. Med. 47, 706-712 (2009).
52. Fumagalli M, Dolcini L, Sala A et al. Proteomic analysis of exhaled breath condansate from single patients with pulmonary emphysema associated to a1-antitrypsin deficiency. J. Proteomics 71, 211-221 (2008).
53. LaBaer J, Ramachandran N. Protein microarrays as tools for functional proteomics. Curr. Opin Chem. Biol. 9, 14-19 (2005).
54. Pinto-Plata V, Toso J, Lee K et al. Use of proteomic patterns of serum biomarkers in patients with chronic obstructive pulmonary disease: correlation with clinical parameters. Proc. Am. Thorac. Soc. 3, 465-466 (2006).
55. Csanky E, Olivova P, Rajnavolgyi E et al. Monoclonal antibody proteomics: discovery and prevalidation of chronic obstructive pulmonary disease biomarkers in a single step. Electrophoresis 28, 4401-4406 (2007).
56. Gao WM, Kuick R, Orchekowski RP et al. Distinctive serum protein profiles involving abundant proteins in lung cancer patients based upon antibody microarray analysis. BMC Cancer 5, 110 (2005).
57. van der Vaart H, Postma DS, Timens W et al. Acute effects of cigarette smoking on inflammation in healthy intermittent smokers. Respir. Res. 6, 22 (2005).
58. de Boer WI, Alagappan VK, Sharma HS. Molecular mechanisms in chronic obstructive pulmonary disease: potential targets for therapy. Cell Biochem. Biophys. 47, 131-148 (2007).
59. Rahman I, Adcock IM. Oxidative stress and redox regulation of lung inflammation in COPD. Eur. Respir. J. 28, 219-242 (2006).
60. Wattiez R, Noel-Georis I, Cruyt C et al. Susceptibility to oxidative stress: proteomic analysis of bronchoalveolar lavage from ozone-sensitive and ozone-resistant strains of mice. Proteomics 3, 658-665 (2003).
61. Barreiro E, Peinado VI, Galdiz JB et al. Cigarette smoke-induced oxidative stress: a role in COPD skeletal muscle dysfunction. Am J. Respir. Crit. Care Med. 182(4), 477-488 (2010).
62. Barreiro E, Gea J, Matar G et al. Expression and carbonylation of creatine kinase in the quadriceps femoris muscles of patients with chronic obstructive pulmonary disease. Am. J. Respir. Cell Mol. Biol. 33, 636-642 (2005).
63. Lehtonen ST, Ohlmeier S, Kaarteenaho- Wiik R et al. Does the oxidative stress in chronic obstructive pulmonary disease cause thioredoxin/peroxiredoxin oxidation? Antioxid. Redox. Signal. 10, 813-819 (2008).
64. Malmstrom J, Westergren-Thorsson G, Marko-Varga G. A proteomic approach to mimic fibrosis disease evolvement by an in vitro cell line. Electrophoresis 22, 1776-1784 (2001).
65. Ying W, Zhang K, Qian X et al. Proteome analysis on an early transformed human bronchial epithelial cell line, BEP2D, after a-particle irradiation. Proteomics 3, 64-72 (2003).
66. Yanagisawa K, Shyr Y, Xu BJ et al. Proteomic patterns of tumour subsets in non-small-cell lung cancer. Lancet 362, 433-439 (2003)
67. Malmstrom J, Larsen K, Malmstrom L et al. Proteome annotations and identifications of the human pulmonary fibroblast. J. Proteome Res. 3, 525-537 (2004).
68. He QY, Yip TT, Li M et al. Proteomic analyses of arsenic-induced cell transformation with SELDI-TOF ProteinChip technology. J. Cell Biochem. 88, 1-8 (2003).
69. Lee EJ, In KH, Kim JH et al. Proteomic analysis in lung tissue of smokers and COPD patients. Chest 135, 344-352 (2008).
70. Kelsen SG, Duan X, Ji R et al. Cigarette smoke induces an unfolded protein response in the human lung: a proteomic approach. Am. J. Respir. Cell Mol. Biol. 38, 541-550 (2008).
71. 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).
72. Nicholas BL, OConnor CD, Diukanovic R. From proteomics to prescription- the search for COPD biomarkers. COPD 6, 298-303 (2009).
73. Cazzola M, Novelli G. Biomarkers in COPD. Pulm. Pharmacol. Ther. 23(6), 493-500 (2010).
74. York TP, van der Oord EJ, Langston TB et al. High-resolution mass spectrometry proteomics for the identification of candidate plasma protein biomarkers for chronic obstructive pulmonary disease. Biomarkers 15, 367-377 (2010).
75. Chen H, Wang D, Bai C et al. Proteomics-based biomarkers in chronic obstructive pulmonary disease. J. Proteome Res. 9(6), 2798-2878 (2010).
76. Gomes-Alves P, Imrie M, Gray RD et al. SELDI-TOF biomarker signatures for cystic fibrosis, asthma, and chronic obstructive pulmonary disease. Clin. Biochem. 43, 168-177 (2010).
77. Maestrelli P, Calcagni PG, Saetta M et al. Integrin upregulation on sputum neutrophils in smokers with chronic airway obstruction. Am J. Respir. Crit. Care Med. 154, 1296-1300 (1996).
78. Vernooy JH, Kucukaycan M, Jacobs JA et al. Local and systemic inflammation in patients with chronic obstructive pulmonary disease: soluble tumor necrosis factor receptors are increased in sputum. Am J. Respir. Crit. Care Med. 166, 1218-1224 (2002).
79. Beeh KM, Beier J, Kornmann O et al. Sputum matrix metalloproteinase-9, tissue inhibitor of metalloprotinease-1, and their molar ratio in patients with chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis and healthy subjects. Respir. Med. 97(6), 634-639 (2003).
80. Cataldo D, Munaut C, Noel A et al. MMP-2- and MMP-9-linked gelatinolytic activity in the sputum from patients with asthma and chronic obstructive pulmonary disease. Int. Arch. Allergy Immunol. 123, 259-267 (2000).
81. Kanazawa H, Shiraishi S, Hirata K et al. Imbalance between levels of nitrogen oxides and peroxynitrite inhibitory activity in chronic obstructive pulmonary disease. Thorax 58, 106-109 (2003).
82. Bonassi S, Neri M, Puntoni R. Validation of biomarkers as early predictors of disease. Mutat. Res. 480-481: 349-358 (2001).
83. Lassere MN, Johnson KR, Boers M et al. Definitions and validation criteria for biomarkers and surrogate endpoints: development and testing of a quantitative hierarchical levels of evidence schema. J. Rheumatol. 34, 607-615 (2007).
84. Lassere MN. The Biomarker-Surrogacy Evaluation Schema: a review of the biomarker surrogate literature and a proposal for a criterion-based, quantitative, multidimensional hierarchical levels of evidence schema for evaluating the status of biomarkers as surrogate endpoints. Stat. Methods Med. Res. 17, 303-340 (2008).
85. Maruvada P, Srivastava S. Joint National Cancer Institute-Food and Drug Administration workshop on research strategies, study designs, and statistical approaches to biomarker validation for cancer diagnosis and detection. Cancer Epidemiol. Biomarkers Prev. 15, 1078-1082 (2006).
86. Weir CJ, Walley RJ. Statistical evaluation of biomarkers as surrogate endpoints: a literature review. Stat. Med. 25, 183-203 (2006).
87. De Gruttola VG, Clax P, DeMets DL et al. Considerations in the evaluation of surrogate endpoints in clinical trials. Summary of a National Institutes of Health workshop. Control Clin. Trials 22, 485-502 (2001).
88. Rifai N, Gillette MA, Carr SA. Protein biomarker discovery and validation: the long and uncertain path to clinical utility. Nat. Biotechnol. 24, 971-983 (2006).
89. van Ommen B, Keijer J, Heil SG et al. Challenging homeostasis to define biomarkers for nutrition related health. Mol. Nutr. Food Res. 53, 795-804 (2009).
90. Gygi SP, Rist B, Gerber SA et al. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994-999 (1999).
91. Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 3, 1154-1169 (2004).
92. Ong SE, Blagoev B, Kratchmarova I et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell Proteomics 1, 376-386 (2002).
93. Mallick P, Schirle M, Chen SS et al. Computational prediction of proteotypic peptides for quantitative proteomics. Nat. Biotechnol. 25, 125-131 (2007).
94. Kirkpatrick DS, Gerber SA, Gygi SP. The absolute quantification strategy: a general procedure for the quantification of proteins and post-translational modifications. Methods 35, 265-273 (2005).
95. Ono M, Shitashige M, Honda K et al. Label-free quantitative proteomics using large peptide data sets generated by nanoflow liquid chromatography and mass spectrometry. Mol. Cell Proteomics 5, 1338-1347 (2006).
96. Picotti P, Rinner O, Stallmach R et al. High-throughput generation of selected reaction monitoring assays for proteins and proteomes. Nat. Methods 7, 43-46 (2010).
97. Minden JS, Dowd SR, Meyer HE et al. Difference gel electrophoresis. Electrophoresis 30, 5156-5161 (2009).
98. Zangar RC, Daly DS, White AM. ELISA microarray technology as a high-throughput system for cancer biomarker validation. Expert Rev. Proteomics 3, 37-44 (2006).