A Proteomics-Based Analysis of Blood Biomarkers for the Diagnosis of COPD Acute Exacerbation

References

• Vogelmeier CF, Criner GJ, Martinez FJ, et al. Global strategy for the diagnosis, management, and prevention of chronic obstructive lung disease 2017 report: GOLD executive summary. Eur Respir J. 2017;49(3):1700214. doi:10.1183/13993003.00214-2017
   PubMed Web of Science ®Google Scholar
• Adeloye D, Chua S, Lee C, et al. Global and regional estimates of COPD prevalence: systematic review and meta-analysis. J Glob Health. 2015;5(2):020415. doi:10.7189/jogh.05.020415
   PubMed Web of Science ®Google Scholar
• Decramer M, Janssens W, Miravitlles M. Chronic obstructive pulmonary disease. Lancet. 2012;379(9823):1341–1351. doi:10.1016/S0140-6736(11)60968-9
   PubMed Web of Science ®Google Scholar
• Mouronte-Roibás C, Leiro-Fernández V, Fernández-Villar A, Botana-Rial M, Ramos-Hernández C, Ruano-Ravina A. COPD, emphysema and the onset of lung cancer. A systematic review. Cancer Lett. 2016;382(2):240–244. doi:10.1016/j.canlet.2016.09.002
   PubMed Web of Science ®Google Scholar
• Mohsenzadegan M, Peng RW, Roudi R. Dendritic cell/cytokine-induced killer cell-based immunotherapy in lung cancer: what we know and future landscape. J Cell Physiol. 2020;235(1):74–86. doi:10.1002/jcp.28977
   PubMed Web of Science ®Google Scholar
• Zhu J, Li R, Tiselius E, et al. Immunotherapy (excluding checkpoint inhibitors) for stage I to III non-small cell lung cancer treated with surgery or radiotherapy with curative intent. Cochrane Database Syst Rev. 2017;12(12):Cd011300. doi:10.1002/14651858.CD011300.pub2
   PubMedGoogle Scholar
• Wedzicha JA, Seemungal TA. COPD exacerbations: defining their cause and prevention. Lancet. 2007;370(9589):786–796. doi:10.1016/S0140-6736(07)61382-8
   PubMed Web of Science ®Google Scholar
• Anthonisen NR, Manfreda J, Warren CP, Hershfield ES, Harding GK, Nelson NA. Antibiotic therapy in exacerbations of chronic obstructive pulmonary disease. Ann Intern Med. 1987;106(2):196–204. doi:10.7326/0003-4819-106-2-196
   PubMed Web of Science ®Google Scholar
• Murtagh E, Heaney L, Gingles J, et al. Prevalence of obstructive lung disease in a general population sample: the NICECOPD study. Eur J Epidemiol. 2005;20(5):443–453. doi:10.1007/s10654-005-1248-8
   PubMed Web of Science ®Google Scholar
• 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. 2007;176(6):532–555. doi:10.1164/rccm.200703-456SO
   PubMed Web of Science ®Google Scholar
• Kim V, Aaron SD. What is a COPD exacerbation? Current definitions, pitfalls, challenges and opportunities for improvement. Eur Respir J. 2018;52(5):1801261. doi:10.1183/13993003.01261-2018
   PubMed Web of Science ®Google Scholar
• Trigueros Carrero JA. How should we define and classify exacerbations in chronic obstructive pulmonary disease? Expert Rev Respir Med. 2013;7(2 Suppl):33–41. doi:10.1586/ers.13.16
   PubMed Web of Science ®Google Scholar
• Regan EA, Hersh CP, Castaldi PJ, et al. Omics and the search for blood biomarkers in chronic obstructive pulmonary disease: insights from COPDGene. Am J Respir Cell Mol Biol. 2019;61(2):143–149. doi:10.1165/rcmb.2018-0245PS
   PubMed Web of Science ®Google Scholar
• Sidhaye VK, Nishida K, Martinez FJ. Precision medicine in COPD: where are we and where do we need to go? Eur Respir Rev. 2018;27(149):180022. doi:10.1183/16000617.0022-2018
   PubMed Web of Science ®Google Scholar
• Leung JM, Chen V, Hollander Z, et al. COPD exacerbation biomarkers validated using multiple reaction monitoring mass spectrometry. PLoS One. 2016;11(8):e0161129. doi:10.1371/journal.pone.0161129
   PubMed Web of Science ®Google Scholar
• Devanarayan V, Scholand MB, Hoidal J, et al. Identification of distinct plasma biomarker signatures in patients with rapid and slow declining forms of COPD. COPD. 2010;7(1):51–58. doi:10.3109/15412550903499530
   PubMedGoogle Scholar
• Ruan W, Wu M, Shi L, et al. Serum levels of IGFBP7 are elevated during acute exacerbation in COPD patients. Int J Chron Obstruct Pulmon Dis. 2017;12:1775–1780. doi:10.2147/COPD.S132652
   PubMed Web of Science ®Google Scholar
• Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol. 2018;14(8):e8126. doi:10.15252/msb.20178126
   PubMed Web of Science ®Google Scholar
• Narasimhan M, Kannan S, Chawade A, Bhattacharjee A, Govekar R. Clinical biomarker discovery by SWATH-MS based label-free quantitative proteomics: impact of criteria for identification of differentiators and data normalization method. J Transl Med. 2019;17(1):184. doi:10.1186/s12967-019-1937-9
   PubMedGoogle Scholar
• Lin Q, Tan HT, Chung MCM. Next generation proteomics for clinical biomarker detection using SWATH-MS. Methods Mol Biol. 2019;1977:3–15.
   PubMedGoogle Scholar
• Anjo SI, Santa C, Manadas B. SWATH-MS as a tool for biomarker discovery: from basic research to clinical applications. Proteomics. 2017;17(3–4):1600278. doi:10.1002/pmic.201600278
   Web of Science ®Google Scholar
• Jylha A, Nattinen J, Aapola U, et al. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. Clin Proteomics. 2018;15:24. doi:10.1186/s12014-018-9201-5
   PubMed Web of Science ®Google Scholar
• Celli BR, Barnes PJ. Exacerbations of chronic obstructive pulmonary disease. Eur Respir J. 2007;29(6):1224–1238. doi:10.1183/09031936.00109906
   PubMed Web of Science ®Google Scholar
• Rodriguez-Roisin R. Toward a consensus definition for COPD exacerbations. Chest. 2000;117(5 Suppl 2):398s–401s. doi:10.1378/chest.117.5_suppl_2.398S
   PubMed Web of Science ®Google Scholar
• HaileMariam M, Eguez RV, Singh H, et al. S-trap, an ultrafast sample-preparation approach for shotgun proteomics. J Proteome Res. 2018;17(9):2917–2924. doi:10.1021/acs.jproteome.8b00505
   PubMed Web of Science ®Google Scholar
• Escher C, Reiter L, MacLean B, et al. Using iRT, a normalized retention time for more targeted measurement of peptides. Proteomics. 2012;12(8):1111–1121. doi:10.1002/pmic.201100463
   PubMed Web of Science ®Google Scholar
• Zhu T, Zhu Y, Xuan Y, et al. DPHL: a DIA pan-human protein mass spectrometry library for robust biomarker discovery. Genomics Proteomics Bioinformatics. 2020;18(2):104–119. doi:10.1016/j.gpb.2019.11.008
   PubMed Web of Science ®Google Scholar
• Zimmermann MT, Kabat B, Grill DE, Kennedy RB, Poland GA. RITAN: rapid integration of term annotation and network resources. PeerJ. 2019;7:e6994. doi:10.7717/peerj.6994
   PubMed Web of Science ®Google Scholar
• Hoofnagle AN, Whiteaker JR, Carr SA, et al. Recommendations for the generation, quantification, storage, and handling of peptides used for mass spectrometry-based assays. Clin Chem. 2016;62(1):48–69. doi:10.1373/clinchem.2015.250563
   PubMed Web of Science ®Google Scholar
• Chen H, Wang D, Bai C, Wang X. Proteomics-based biomarkers in chronic obstructive pulmonary disease. J Proteome Res. 2010;9(6):2798–2808. doi:10.1021/pr100063r
   PubMed Web of Science ®Google Scholar
• Haddad A, Wilson AM. Biochemistry, Complement. StatPearls. Treasure Island (FL): StatPearls Publishing Copyright © 2020, StatPearls Publishing LLC.; 2020.
   Google Scholar
• Perera WR, Hurst JR, Wilkinson TM, et al. Inflammatory changes, recovery and recurrence at COPD exacerbation. Eur Respir J. 2007;29(3):527–534. doi:10.1183/09031936.00092506
   PubMed Web of Science ®Google Scholar
• Levels JHM, Pajkrt D, Schultz M, et al. Alterations in lipoprotein homeostasis during human experimental endotoxemia and clinical sepsis. Biochimica et Biophysica Acta. 2007;1771(12):1429–1438. doi:10.1016/j.bbalip.2007.10.001
   PubMed Web of Science ®Google Scholar
• Pruzanski W, Stefanski E, de Beer FC, de Beer MC, Ravandi A, Kuksis A. Comparative analysis of lipid composition of normal and acute-phase high density lipoproteins. J Lipid Res. 2000;41(7):1035–1047. doi:10.1016/S0022-2275(20)32007-1
   PubMed Web of Science ®Google Scholar
• Khovidhunkit W, Memon RA, Feingold KR, Grunfeld C. Infection and inflammation-induced proatherogenic changes of lipoproteins. J Infect Dis. 2000;181(Suppl 3):S462–472. doi:10.1086/315611
   PubMed Web of Science ®Google Scholar
• Chen H, Li Z, Dong L, Wu Y, Shen H, Chen Z. Lipid metabolism in chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2019;14:1009–1018. doi:10.2147/COPD.S196210
   PubMed Web of Science ®Google Scholar
• Chan SMH, Selemidis S, Bozinovski S, Vlahos R. Pathobiological mechanisms underlying metabolic syndrome (MetS) in chronic obstructive pulmonary disease (COPD): clinical significance and therapeutic strategies. Pharmacol Ther. 2019;198:160–188.
   PubMed Web of Science ®Google Scholar
• Baffi CW, Wood L, Winnica D, et al. Metabolic syndrome and the lung. Chest. 2016;149(6):1525–1534. doi:10.1016/j.chest.2015.12.034
   PubMed Web of Science ®Google Scholar
• Regueiro V, Campos MA, Morey P, et al. Lipopolysaccharide-binding protein and CD14 are increased in the bronchoalveolar lavage fluid of smokers. Eur Respir J. 2009;33(2):273–281. doi:10.1183/09031936.00087708
   PubMed Web of Science ®Google Scholar
• Groenewegen KH, Postma DS, Hop WC, Wielders PL, Schlösser NJ, Wouters EF. Increased systemic inflammation is a risk factor for COPD exacerbations. Chest. 2008;133(2):350–357. doi:10.1378/chest.07-1342
   PubMed Web of Science ®Google Scholar
• Dentener MA, Creutzberg EC, Schols AM, et al. Systemic anti-inflammatory mediators in COPD: increase in soluble interleukin 1 receptor II during treatment of exacerbations. Thorax. 2001;56(9):721–726. doi:10.1136/thorax.56.9.721
   PubMed Web of Science ®Google Scholar
• Zhu HZ, Zhou WJ, Wan YF, Ge K, Lu J, Jia CK. Downregulation of orosomucoid 2 acts as a prognostic factor associated with cancer-promoting pathways in liver cancer. World J Gastroenterol. 2020;26(8):804–817. doi:10.3748/wjg.v26.i8.804
   PubMed Web of Science ®Google Scholar
• Uysal P, Uzun H. Relationship between circulating Serpina3g, matrix metalloproteinase-9, and tissue inhibitor of metalloproteinase-1 and −2 with chronic obstructive pulmonary disease severity. Biomolecules. 2019;9(2):62. doi:10.3390/biom9020062
   PubMed Web of Science ®Google Scholar
• Hazari YM, Bashir A, Habib M, et al. Alpha-1-antitrypsin deficiency: genetic variations, clinical manifestations and therapeutic interventions. Mutat Res. 2017;773:14–25. doi:10.1016/j.mrrev.2017.03.001
   PubMed Web of Science ®Google Scholar
• Takei N, Suzuki M, Makita H, et al. Serum alpha-1 antitrypsin levels and the clinical course of chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis. 2019;14:2885–2893. doi:10.2147/COPD.S225365
   PubMed Web of Science ®Google Scholar
• Prins HJ, Duijkers R, van der Valk P, et al. CRP-guided antibiotic treatment in acute exacerbations of COPD in hospital admissions. Eur Respir J. 2019;53(5):1802014. doi:10.1183/13993003.02014-2018
   PubMed Web of Science ®Google Scholar