High-resolution mass spectrometry proteomics for the identification of candidate plasma protein biomarkers for chronic obstructive pulmonary disease

References

• Agusti A, MacNee W, Donaldson K, Cosio M. (2003). Hypothesis: does COPD have an autoimmune component? Thorax 58:832–4.
   PubMed Web of Science ®Google Scholar
• Agusti A, Soriano JB. (2008). COPD as a systemic disease. COPD 5:133–8.
   PubMedGoogle Scholar
• Anthonisen NR, Connett JE, Kiley JP, Altose MD, Bailey WC, Buist AS, Conway WA Jr, Enright PL, Kanner RE, O’Hara P et al. (1994). Effects of smoking intervention and the use of an inhaled anticholinergic bronchodilator on the rate of decline of FEV1. The Lung Health Study. JAMA 272:1497–505.
   PubMed Web of Science ®Google Scholar
• Anthonisen NR, Connett JE, Murray RP. (2002). Smoking and lung function of Lung Health Study participants after 11 years. Am J Respir Crit Care Med 166:675–9.
   PubMed Web of Science ®Google Scholar
• Barnes PJ, Shapiro SD, Pauwels RA. (2003). Chronic obstructive pulmonary disease: molecular and cellular mechanisms. Eur Respir J 22:672–88.
   PubMed Web of Science ®Google Scholar
• Benjamini Y, Hochberg Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J Roy Stat Soc B 57:289–300.
   Web of Science ®Google Scholar
• Bolger MS, Ross DS, Jiang H, Frank MM, Ghio AJ, Schwartz DA, Wright JR. (2007). Complement levels and activity in the normal and LPS-injured lung. Am J Physiol Lung Cell Mol Physiol 292: L748–59.
   PubMed Web of Science ®Google Scholar
• Bolton CE, Evans M, Ionescu AA, Edwards SM, Morris RH, Dunseath G, Luzio SD, Owens DR, Shale DJ. (2007). Insulin resistance and inflammation – a further systemic complication of COPD. COPD 4:121–6.
   PubMedGoogle Scholar
• Carpenter SL, Mathew P. (2008). Alpha2-antiplasmin and its deficiency: fibrinolysis out of balance. Haemophilia 14:1250–4.
   PubMed Web of Science ®Google Scholar
• Celli BR, Cote CG, Marin JM, Casanova C, Montes de Oca M, Mendez RA, Pinto Plata V, Cabral HJ. (2004). The body-mass index airflow obstruction dyspnea and exercise capacity index in chronic obstructive pulmonary disease. N Engl J Med 350:1005–12.
   PubMed Web of Science ®Google Scholar
• Choolani M, Narasimhan K, Kolla V, Hahn S. (2009). Proteomic technologies for prenatal diagnostics: advances and challenges ahead. Expert Rev Proteomics 6:87–101.
   PubMed Web of Science ®Google Scholar
• Chung KF. (2001). Cytokines in chronic obstructive pulmonary disease. Eur Respir J (Suppl. 34):50s–59s.
   Google Scholar
• Elias JE, Gygi SP. (2007). Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nature Methods 4(3):207–214.
   Google Scholar
• Ezzati M, Lopez AD. (2003). Estimates of global mortality attributable to smoking in 2000. Lancet 362:847–52.
   PubMed Web of Science ®Google Scholar
• Fabbri LM, Luppi F, Beghe B, Rabe KF. (2008). Complex chronic comorbidities of COPD. Eur Respir J 31:204–12.
   PubMed Web of Science ®Google Scholar
• Fabbri LM, Rabe KF. (2007). From COPD to chronic systemic inflammatory syndrome? Lancet 370:797–9.
   PubMed Web of Science ®Google Scholar
• Fay WP, Garg N, Sunkar M. (2007). Vascular functions of the plasminogen activation system. Arterioscler Thromb Vasc Biol 27:1231–7.
   PubMed Web of Science ®Google Scholar
• Feghali-Bostwick CA, Gadgil AS, Otterbein LE, Pilewski JM, Stoner MW, Csizmadia E, Zhang Y, Sciurba FC, Duncan SR. (2008). Autoantibodies in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 177:156–63.
   PubMed Web of Science ®Google Scholar
• Fu Q, Van Eyk JE. (2006). Proteomics and heart disease: identifying biomarkers of clinical utility. Expert Rev Proteomics 3:237–49.
   PubMed Web of Science ®Google Scholar
• Furie B, & Furie BC. (2005). Thrombus formation in vivo. J Clin Invest 115:3355–62.
   PubMed Web of Science ®Google Scholar
• Hersh CP, DeMeo DL, Silverman EK. (2008). National Emphysema Treatment Trial state of the art: genetics of emphysema. Proc Am Thorac Soc 5:486–93.
   Google Scholar
• Hogg JC. (2006). Why does airway inflammation persist after the smoking stops? Thorax 61:96–7.
   PubMed Web of Science ®Google Scholar
• Hou Y, Okada K, Okamoto C, Ueshima S, Matsuo O. (2008). Alpha2-antiplasmin is a critical regulator of angiotensin II-mediated vascular remodeling. Arterioscler Thromb Vasc Biol 28(7):1257–62.
   Google Scholar
• Ishii T, Matsuse T, Teramoto S, Matsui H, Hosoi T, Fukuchi Y, Ouchi Y. (2000). Association between alpha-1-antichymotrypsin polymorphism and susceptibility to chronic obstructive pulmonary disease. Eur J Clin Invest 30:543–8.
   PubMed Web of Science ®Google Scholar
• Jacot W, Lhermitte L, Dossat N, Pujol JL, Molinari N, Daures JP, Maudelonde T, Mange A, Solassol J. (2008). Serum proteomic profiling of lung cancer in high-risk groups and determination of clinical outcomes. J Thorac Oncol 3:840–50.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. (2008). KEGG for linking genomes to life and the environment. Nucleic Acids Res 36(database issue):D480–4.
   Google Scholar
• Kanehisa M, Goto S. (2000). KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28:27–30.
   PubMed Web of Science ®Google Scholar
• Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, Katayama T, Araki M, Hirakawa M. (2006). From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res 34(database issue):D354–7.
   PubMed Web of Science ®Google Scholar
• Karadag F, Karul AB, Cildag O, Yilmaz M, Ozcan H. (2008). Biomarkers of systemic inflammation in stable and exacerbation phases of COPD. Lung 186:403–9.
   PubMed Web of Science ®Google Scholar
• Kumar R, Singh VP, Baker KM. (2008). The intracellular renin-angiotensin system: implications in cardiovascular remodeling. Curr Opin Nephrol Hypertens 17:168–73.
   PubMed Web of Science ®Google Scholar
• Lalouel JM, Rohrwasser A, Terreros D, Morgan T, Ward K. (2001). Angiotensinogen in essential hypertension: from genetics to nephrology. J Am Soc Nephrol 12:606–15.
   Google Scholar
• Lappalainen U, Whitsett JA, Wert SE, Tichelaar JW, Bry K. (2005). Interleukin-1beta causes pulmonary inflammation emphysema and airway remodeling in the adult murine lung. Am J Respir Cell Mol Biol 32:311–18.
   PubMed Web of Science ®Google Scholar
• Lee JM, Kang YR, Park SH, Cha SI, Kim JS, Kang HK, Lee WK, Kim MJ, Kim CH, Kim NS, Jung TH, Park JY. (2008). Polymorphisms in interleukin-1B and its receptor antagonist genes and the risk of chronic obstructive pulmonary disease in a Korean population: a case–control study. Respir Med 102:1311–20.
   Google Scholar
• Lee PS, Waxman AB, Cotich KL, Chung SW, Perrella MA, Stossel TP. (2007). Plasma gelsolin is a marker and therapeutic agent in animal sepsis. Crit Care Med 35:849–55.
   PubMed Web of Science ®Google Scholar
• Li X, Gong Y, Wang Y, Wu S, Cai Y, He P, Lu Z, Ying W, Zhang Y, Jiao L, He H, Zhang Z, He F, Zhao X, Qian X. (2005). Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project. Proteomics 5:3423–41.
   PubMed Web of Science ®Google Scholar
• Mannino DM, Homa DM, Akinbami LJ, Ford ES, Redd SC. (2002). Chronic obstructive pulmonary disease surveillance – United States 1971–2000. MMWR Surveill Summ 51:1–16.
   PubMed Web of Science ®Google Scholar
• Marcovina S, Packard CJ. (2006). Measurement and meaning of apolipoprotein AI and apolipoprotein B plasma levels. J Intern Med 259:437–46.
   PubMed Web of Science ®Google Scholar
• Markiewski MM, Lambris JD. (2007). The role of complement in inflammatory diseases from behind the scenes into the spotlight. Am J Pathol 171:715–27.
   PubMed Web of Science ®Google Scholar
• Meng Z, Veenstra TD. (2007). Proteomic analysis of serum plasma and lymph for the identification of biomarkers. Proteomics Clin Appl 1:747–57.
   PubMed Web of Science ®Google Scholar
• Navabi A, Mather DE, Bernier J, Spaner DM, Atlin GN. (2009). QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses. Theor Appl Genet 118:347–58.
   Google Scholar
• Omenn GS, States DJ, Adamski M, Blackwell TW, Menon R, Hermjakob H, Apweiler R, Haab BB, Simpson RJ, Eddes JS, et al. (2005). Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups generating a core dataset of 3020 proteins and a publicly-available database. Proteomics 5:3226–245.
   PubMed Web of Science ®Google Scholar
• Pinto-Plata V, Toso J, Lee K, Park D, Bilello J, Mullerova H, De Souza MM, Vessey R, Celli B. (2007). Profiling serum biomarkers in patients with COPD: associations with clinical parameters. Thorax 62:595–601.
   PubMed Web of Science ®Google Scholar
• Poller W, Faber JP, Scholz S, Weidinger S, Bartholome K, Olek K, Eriksson S. (1992). Mis-sense mutation of alpha 1-antichymotrypsin gene associated with chronic lung disease. Lancet 339:1538.
   PubMed Web of Science ®Google Scholar
• Qin X, Swertfeger DK, Zheng S, Hui DY, Tso P. (1998). Apolipoprotein AIV: a potent endogenous inhibitor of lipid oxidation. Am J Physiol 274:H1836–40.
   Google Scholar
• Rabe KF, Hurd S, Anzueto A, Barnes PJ, Buist SA, Calverley P, Fukuchi Y, Jenkins C, Rodriguez-Roisin R, van Weel C, Zielinski J. (2007). Global strategy for the diagnosis management and prevention of chronic obstructive pulmonary disease: GOLD executive summary. Am J Respir Crit Care Med 176:532–55.
   PubMed Web of Science ®Google Scholar
• Rahman I, Morrison D, Donaldson K, MacNee W. (1996). Systemic oxidative stress in asthma COPD and smokers. Am J Respir Crit Care Med 154:1055–60.
   PubMed Web of Science ®Google Scholar
• Ribeiro-Oliveira A, Jr Nogueira, AI, Pereira RM, Boas WW, Dos Santos RA, Simoes e Silva AC. (2008). The renin–angiotensin system and diabetes: an update. Vasc Health Risk Manag 4:787–803.
   PubMedGoogle Scholar
• Rosenberg RD, Bauer KA. (1987). Thrombosis in inherited deficiencies of antithrombin protein C and protein S. Hum Pathol 18:253.
   PubMed Web of Science ®Google Scholar
• Rosenzweig CN, Zhang Z, Sun X, Sokoll LJ, Osborne K, Partin AW, Chan DW. (2009). Predicting prostate cancer biochemical recurrence using a panel of serum proteomic biomarkers. J Urol 181:1407–14.
   PubMed Web of Science ®Google Scholar
• Sevenoaks M, J, & Stockley R. A. (2006). Chronic obstructive pulmonary disease inflammation and co-morbidity – a common inflammatory phenotype? Respir Res 7:70.
   PubMed Web of Science ®Google Scholar
• Soriano JB, Sin DD, Zhang X, Camp PG, Anderson JA, Anthonisen NR, Buist AS, Burge PS, Calverley PM, Connett JE, Petersson S, Postma DS, Szafranski W, Vestbo J. (2007). A pooled analysis of FEV1 decline in COPD patients randomized to inhaled corticosteroids or placebo. Chest 131:682–9.
   PubMed Web of Science ®Google Scholar
• Stockley RA. (2007). Biomarkers in COPD: time for a deep breath. Thorax 62:657–60.
   PubMed Web of Science ®Google Scholar
• Storey JD, Tibshirani R. (2003a). Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol 224:149–57.
   Google Scholar
• Storey JD, Tibshirani R. (2003b). Statistical significance for genomewide studies. Proc Natl Acad Sci U S A 100:9440–5.
   PubMed Web of Science ®Google Scholar
• Tapson VF. (2005). The role of smoking in coagulation and thromboembolism in chronic obstructive pulmonary disease. Proc Am Thorac Soc 2:71–7.
   PubMedGoogle Scholar
• Tiengo A, Fadini GP, Avogaro A. (2008). The metabolic syndrome diabetes and lung dysfunction. Diabetes Metab 34:447–54.
   PubMed Web of Science ®Google Scholar
• van den Oord EJ. (2005). Controlling false discoveries in candidate gene studies. Mol Psychiatry 10:230–1.
   Google Scholar
• Vivanco F, Martin-Ventura JL, Duran MC, Barderas MG, Blanco-Colio L, Darde VM, Mas S, Meilhac O, Michel JB, Tunon J, Egido J. (2005). Quest for novel cardiovascular biomarkers by proteomic analysis. J Proteome Res 4:1181–91.
   PubMedGoogle Scholar
• Voelkel NF, Cool CD. (2003). Pulmonary vascular involvement in chronic obstructive pulmonary disease. Eur Respir J (Suppl. 46):28s–32s.
   Google Scholar
• Voelkel NF, Douglas IS, Nicolls M. (2007). Angiogenesis in chronic lung disease. Chest 131:874–9.
   PubMedGoogle Scholar
• Walter RE, Wilk JB, Larson MG, Vasan RS, Keaney JF Jr, Lipinska I, O’Connor GT, Benjamin EJ. (2008). Systemic inflammation and COPD: the Framingham Heart Study. Chest 133:19–25.
   PubMed Web of Science ®Google Scholar
• Watson L, Vonk JM, Lofdahl CG, Pride NB, Pauwels RA, Laitinen LA, Schouten JP, Postma DS. (2006). Predictors of lung function and its decline in mild to moderate COPD in association with gender: results from the Euroscop study. Respir Med 100:746–53.
   PubMed Web of Science ®Google Scholar
• Wilk JB, Walter RE, Laramie JM, Gottlieb DJ, O’Connor GT. (2007). Framingham Heart Study genome-wide association: results for pulmonary function measures. BMC Med Genet 8 (Suppl. 1):S8.
   Google Scholar
• Wouters EF, Creutzberg EC, Schols AM. (2002). Systemic effects in COPD. Chest 121 (Suppl.):127S–30S.
   Google Scholar
• Yanbaeva DG, Dentener MA, Creutzberg EC, Wesseling G, Wouters EF. (2007). Systemic effects of smoking. Chest 131:1557–66.
   PubMed Web of Science ®Google Scholar