Role of proteomics in the investigation of pulmonary fibrosis

References

• The diagnosis, assessment and treatment of diffuse parenchymal lung disease in adults. Introduction. Thorax54(Suppl.1), S1–S14 (1999).
   PubMed Web of Science ®Google Scholar
• Flaherty KR, Mumford JA, Murray S et al. Prognostic implications of physiologic and radiographic changes in idiopathic interstitial pneumonia. Am. J. Respir. Crit. Care Med.168(5), 543–548 (2003).
   PubMed Web of Science ®Google Scholar
• Collard HR, King TE Jr, Bartelson BB, Vourlekis JS, Schwarz MI, Brown KK. Changes in clinical and physiologic variables predict survival in idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med.168(5), 538–542 (2003).
   PubMed Web of Science ®Google Scholar
• Lama VN, Flaherty KR, Toews GB et al. Prognostic value of desaturation during a 6-minute walk test in idiopathic interstitial pneumonia. Am. J. Respir. Crit. Care Med.168(9), 1084–1090 (2003).
   PubMed Web of Science ®Google Scholar
• Thannickal VJ, Toews GB, White ES, Lynch JP III, Martinez FJ. Mechanisms of pulmonary fibrosis. Annu. Rev. Med.55, 395–417 (2004).
   PubMed Web of Science ®Google Scholar
• American Thoracic Society/European Respiratory Society International Multidisciplinary Consensus Classification of the Idiopathic Interstitial Pneumonias. Am. J. Respir. Crit. Care Med.165(2), 277–304 (2002).
   PubMedGoogle Scholar
• Katzenstein AL, Myers JL. Idiopathic pulmonary fibrosis: clinical relevance of pathologic classification. Am. J. Respir. Crit. Care Med.157(4 Pt 1), 1301–1315 (1998).
   PubMed Web of Science ®Google Scholar
• Raghu G, Brown KK, Bradford WZ et al. A placebo-controlled trial of interferon γ-1b in patients with idiopathic pulmonary fibrosis. N. Engl. J. Med.350(2), 125–133 (2004).
   PubMed Web of Science ®Google Scholar
• Raghu G, Johnson WC, Lockhart D, Mageto Y. Treatment of idiopathic pulmonary fibrosis with a new antifibrotic agent, pirfenidone: results of a prospective, open-label Phase II study. Am. J. Respir. Crit. Care Med.159(4 Pt 1), 1061–1069 (1999).
   PubMed Web of Science ®Google Scholar
• Azuma A, Nukiwa T, Tsuboi E et al. Double-blind, placebo-controlled trial of pirfenidone in patients with idiopathic pulmonary fibrosis. Am. J. Respir. Crit. Care Med.171(9), 1040–1047 (2005).
   PubMed Web of Science ®Google Scholar
• Demedts M, Behr J, Buhl R et al. High-dose acetylcysteine in idiopathic pulmonary fibrosis. N. Engl. J. Med.353(21), 2229–2242 (2005).
   PubMed Web of Science ®Google Scholar
• Robbins SL, Cotran RS. Chapter 16: The Lung. In: Robbins Pathologic Basis of Disease. Kumar V, Collins T (Eds). Saunders WB Co Ltd., PA, USA 726–738 (1999).
   Google Scholar
• Edell ES. Future therapeutic procedures. Chest Surg. Clin. N. Am.6(2), 381–395 (1996).
   Google Scholar
• Winterbauer RH, Lammert J, Selland M, Wu R, Corley D, Springmeyer SC. Bronchoalveolar lavage cell populations in the diagnosis of sarcoidosis. Chest104(2), 352–361 (1993).
   PubMed Web of Science ®Google Scholar
• Costabel U. Sensitivity and specificity of BAL findings in sarcoidosis. Sarcoidosis9(Suppl.1), S211–S214 (1992).
   Google Scholar
• Lenz AG, Meyer B, Weber H, Maier K. Two-dimensional electrophoresis of dog bronchoalveolar lavage fluid proteins. Electrophoresis11(6), 510–513 (1990).
   Google Scholar
• Lindahl M, Stahlbom B, Svartz J, Tagesson C. Protein patterns of human nasal and bronchoalveolar lavage fluids analyzed with two-dimensional gel electrophoresis. Electrophoresis19(18), 3222–3229 (1998).
   PubMed Web of Science ®Google Scholar
• Wattiez R, Hermans C, Cruyt C, Bernard A, Falmagne P. Human bronchoalveolar lavage fluid protein two-dimensional database: study of interstitial lung diseases. Electrophoresis21(13), 2703–2712 (2000).
   PubMed Web of Science ®Google Scholar
• Bell DY, Hook GE. Pulmonary alveolar proteinosis: analysis of airway and alveolar proteins. Am. Rev. Respir. Dis.119(6), 979–990 (1979).
   PubMed Web of Science ®Google Scholar
• Lenz AG, Meyer B, Costabel U, Maier K. Bronchoalveolar lavage fluid proteins in human lung disease: analysis by two-dimensional electrophoresis. Electrophoresis14(3), 242–244 (1993).
   PubMedGoogle Scholar
• Wattiez R, Hermans C, Bernard A, Lesur O, Falmagne P. Human bronchoalveolar lavage fluid: two-dimensional gel electrophoresis, amino acid microsequencing and identification of major proteins. Electrophoresis20(7), 1634–1645 (1999).
   PubMed Web of Science ®Google Scholar
• Noel-Georis I, Bernard A, Falmagne P, Wattiez R. Proteomics as the tool to search for lung disease markers in bronchoalveolar lavage. Dis. Markers17(4), 271–284 (2001).
   PubMed Web of Science ®Google Scholar
• Noel-Georis I, Bernard A, Falmagne P, Wattiez R. Database of bronchoalveolar lavage fluid proteins. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.771(1–2), 221–236 (2002).
   PubMed Web of Science ®Google Scholar
• Wattiez R, Falmagne P. Proteomics of bronchoalveolar lavage fluid. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.815(1–2), 169–178 (2005).
   PubMedGoogle Scholar
• 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. Electrophoresis23(19), 3434–3444 (2002).
   PubMed Web of Science ®Google Scholar
• 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. Proteomics5(10), 2612–2618 (2005).
   PubMed Web of Science ®Google Scholar
• 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. Proteomics5(5), 1423–1430 (2005).
   PubMed Web of Science ®Google Scholar
• Sabounchi-Schutt F, Astrom J, Eklund A, Grunewald J, Bjellqvist B. Detection and identification of human bronchoalveolar lavage proteins using narrow-range immobilized pH gradient DryStrip and the paper bridge sample application method. Electrophoresis22(9), 1851–1860 (2001).
   PubMed Web of Science ®Google Scholar
• Sabounchi-Schutt F, Astrom J, Hellman U, Eklund A, Grunewald J. Changes in bronchoalveolar lavage fluid proteins in sarcoidosis: a proteomics approach. Eur. Respir. J.21(3), 414–420 (2003).
   Web of Science ®Google Scholar
• 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(10), 1145–1154 (2006).
   PubMed Web of Science ®Google Scholar
• Malmström J, Westergren-Thorsson G, Marko-Varga G. A proteomic approach to mimic fibrosis disease evolvement by an in vitro cell line. Electrophoresis22(9), 1776–1784 (2001).
   PubMed Web of Science ®Google Scholar
• Malmström J, Larsen K, Malmström L et al. Proteome annotations and identifications of the human pulmonary fibroblast. J. Proteome Res.3(3), 525–537 (2004).
   PubMed Web of Science ®Google Scholar
• Malmstrom J, Larsen K, Malmstrom L et al. Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: mapping the nuclear proteome of human fibroblasts. Electrophoresis24(21), 3806–3814 (2003).
   PubMed Web of Science ®Google Scholar
• Sabounchi-Schutt F, Mikko M, Eklund A, Grunewald J, Astrom J. Serum protein pattern in sarcoidosis analysed by a proteomics approach. Sarcoidosis Vasc. Diffuse Lung Dis.21(3), 182–190 (2004).
   PubMed Web of Science ®Google Scholar
• Song Z, Marzilli L, Greenlee BM et al. Mycobacterial catalase-peroxidase is a tissue antigen and target of the adaptive immune response in systemic sarcoidosis. J. Exp. Med.201(5), 755–767 (2005).
   PubMed Web of Science ®Google Scholar
• Jordana M, Dolovich M, Newhouse M. Lung epithelial permeability in sarcoidosis. Sarcoidosis4(2), 116–121 (1987).
   Google Scholar
• Hirsch J, Hansen KC, Burlingame AL, Matthay MA. Proteomics: current techniques and potential applications to lung disease. Am. J. Physiol. Lung Cell Mol. Physiol.287(1), L1–L23 (2004).
   Web of Science ®Google Scholar
• Anderson NL, Anderson NG. The human plasma proteome: history, character, and diagnostic prospects. Mol. Cell. Proteomics1(11), 845–867 (2002).
   PubMed Web of Science ®Google Scholar
• Boggs SE. Protein profiling in respiratory disease: techniques and impact. Expert Rev. Proteomics1(1), 29–36 (2004).
   PubMed Web of Science ®Google Scholar
• Malmstrom J, Larsen K, Hansson L et al. Proteoglycan and proteome profiling of central human pulmonary fibrotic tissue utilizing miniaturized sample preparation: a feasibility study. Proteomics2(4), 394–404 (2002).
   PubMed Web of Science ®Google Scholar
• Larsen K, Macleod D, Nihlberg K et al. Specific haptoglobin expression in bronchoalveolar lavage during differentiation of circulating fibroblast progenitor cells in mild asthma. J. Proteome Res.5(6), 1479–1483 (2006).
   PubMed Web of Science ®Google Scholar
• Larsen K, Tufvesson E, Malmstrom J et al. Presence of activated mobile fibroblasts in bronchoalveolar lavage from patients with mild asthma. Am. J. Respir. Crit. Care Med.170(10), 1049–1056 (2004).
   Google Scholar
• Larsen K, Malmstrom J, Wildt M et al. Functional and phenotypical comparison of myofibroblasts derived from biopsies and bronchoalveolar lavage in mild asthma and scleroderma. Respir. Res.7, 11 (2006).
   PubMed Web of Science ®Google Scholar
• Scheja A, Larsen K, Todorova L et al. BAL fluid derived fibroblasts differ from biopsy derived fibroblasts in systemic sclerosis. Eur. Respir. J.29(3) 446–452 (2006).
   Google Scholar
• Nihlberg K, Larsen K, Hultgardh-Nilsson A, Malmstrom A, Bjermer L, Westergren-Thorsson G. Tissue fibrocytes in patients with mild asthma: a possible link to thickness of reticular basement membrane? Respir. Res.7, 50 (2006).
   PubMedGoogle Scholar
• Wasinger VC, Cordwell SJ, Cerpa-Poljak A et al. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis16(7), 1090–1094 (1995).
   PubMed Web of Science ®Google Scholar
• Wilkins MR, Sanchez JC, Gooley AA et al. Progress with proteome projects: why all proteins expressed by a genome should be identified and how to do it. Biotechnol. Genet. Eng. Rev.13, 19–50 (1996).
   PubMed Web of Science ®Google Scholar
• Wu WW, Wang G, Baek SJ, Shen RF. Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, Using 2D Gel- or LC-MALDI TOF/TOF. J. Proteome Res.5(3), 651–658 (2006).
   PubMed Web of Science ®Google Scholar
• Plymoth A, Lofdahl CG, Ekberg-Jansson A et al. Human bronchoalveolar lavage: biofluid analysis with special emphasis on sample preparation. Proteomics3(6), 962–972 (2003).
   PubMed Web of Science ®Google Scholar
• Bowler RP, Duda B, Chan ED et al. Proteomic analysis of pulmonary edema fluid and plasma in patients with acute lung injury. Am. J. Physiol. Lung Cell Mol. Physiol.286(6), L1095–L1104 (2004).
   PubMed Web of Science ®Google Scholar
• Magi B, Bargagli E, Bini L, Rottoli P. Proteome analysis of bronchoalveolar lavage in lung diseases. Proteomics6(23), 6354–6369 (2006).
   PubMed Web of Science ®Google Scholar
• Westbrook JA, Wheeler JX, Wait R, Welson SY, Dunn MJ. The human heart proteome: Two-dimensional maps using narrow-range immobilised pH gradients. Electrophoresis27(8), 1547–1555 (2006).
   Google Scholar
• McGregor E, Dunn MJ. Proteomics of the heart: unraveling disease. Circ. Res.98(3), 309–321 (2006).
   PubMed Web of Science ®Google Scholar
• Patton WF. Detection technologies in proteome analysis. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.771(1–2), 3–31 (2002).
   PubMed Web of Science ®Google Scholar
• Unlu M, Morgan ME, Minden JS. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis18(11), 2071–2077 (1997).
   PubMed Web of Science ®Google Scholar
• Lilley KS, Friedman DB. All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev. Proteomics1(4), 401–409 (2004).
   PubMed Web of Science ®Google Scholar
• Greenlee KJ, Corry DB, Engler DA et al. Proteomic identification of in vivo substrates for matrix metalloproteinases 2 and 9 reveals a mechanism for resolution of inflammation. J. Immunol.177(10), 7312–7321 (2006).
   PubMed Web of Science ®Google Scholar
• Gorg A, Weiss W, Dunn MJ. Current two-dimensional electrophoresis technology for proteomics. Proteomics4(12), 3665–3685 (2004).
   PubMed Web of Science ®Google Scholar
• Ge Y, Rajkumar L, Guzman RC, Nandi S, Patton WF, Agnew BJ. Multiplexed fluorescence detection of phosphorylation, glycosylation, and total protein in the proteomic analysis of breast cancer refractoriness. Proteomics4(11), 3464–3467 (2004).
   PubMed Web of Science ®Google Scholar
• Wu J, Kobayashi M, Sousa EA et al. Differential proteomic analysis of bronchoalveolar lavage fluid in asthmatics following segmental antigen challenge. Mol. Cell. Proteomics4(9), 1251–1264 (2005).
   PubMed Web of Science ®Google Scholar
• Tang HY, Ali-Khan N, Echan LA, Levenkova N, Rux JJ, Speicher DW. A novel four-dimensional strategy combining protein and peptide separation methods enables detection of low-abundance proteins in human plasma and serum proteomes. Proteomics5(13), 3329–3342 (2005).
   PubMed Web of Science ®Google Scholar
• Michel PE, Crettaz D, Morier P et al. Proteome analysis of human plasma and amniotic fluid by off-gel isoelectric focusing followed by nano-LC-MS/MS. Electrophoresis27(5–6), 1169–1181 (2006).
   PubMed Web of Science ®Google Scholar
• Wu L, Han DK. Overcoming the dynamic range problem in mass spectrometry-based shotgun proteomics. Expert Rev. Proteomics3(6), 611–619 (2006).
   PubMed Web of Science ®Google Scholar
• Schnapp LM, Donohoe S, Chen J et al. Mining the acute respiratory distress syndrome proteome: identification of the insulin-like growth factor (IGF)/IGF-binding protein-3 pathway in acute lung injury. Am. J. Pathol.169(1), 86–95 (2006).
   PubMed Web of Science ®Google Scholar
• 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(10), 994–999 (1999).
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell. Proteomics3(12), 1154–1169 (2004).
   PubMed Web of Science ®Google Scholar
• Julka S, Regnier FE. Recent advancements in differential proteomics based on stable isotope coding. Brief. Funct. Genomic. Proteomic.4(2), 158–177 (2005).
   PubMedGoogle Scholar
• Candiano G, Bruschi M, Pedemonte N et al. Proteomic analysis of the airway surface liquid: modulation by proinflammatory cytokines. Am. J. Physiol. Lung Cell Mol. Physiol.292(1), L185–L198 (2007).
   Google Scholar
• Cahill DJ. Protein and antibody arrays and their medical applications. J. Immunol. Methods250(1–2), 81–91 (2001).
   PubMed Web of Science ®Google Scholar
• Haab BB. Applications of antibody array platforms. Curr. Opin. Biotechnol.17(4), 415–421 (2006).
   PubMed Web of Science ®Google Scholar