Searching for biomarkers of chronic obstructive pulmonary disease using proteomics: The current state

Detection of proteins which may be potential biomarkers of disorders represents a big step forward in understanding the molecular mechanisms that underlie pathological processes. In this context proteomics plays the important role of opening a path for the identification of molecular signatures that can potentially assist in early diagnosis of several clinical disturbances. Aim of this report is to provide an overview of the wide variety of proteomic strategies that have been applied to the investigation of chronic obstructive pulmonary disease (COPD), a severe disorder that causes an irreversible damage to the lungs and for which there is no cure yet. The results in this area published over the past decade show that proteomics indeed has the ability of monitoring alterations in expression profiles of proteins from fluids/tissues of patients affected by COPD and healthy controls. However, these data also suggest that proteomics, while being an attractive tool for the identification of novel pathological mediators of COPD, remains a technique mainly generated and developed in research laboratories. Great efforts dedicated to the validation of these biological signatures will result in the proof of their clinical utility.

[1]  A. Amin,et al.  Treatment patterns for patients hospitalized with chronic obstructive pulmonary disease , 2018, American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists.

[2]  S. Ohlmeier,et al.  Elevated sputum BPIFB1 levels in smokers with chronic obstructive pulmonary disease: a longitudinal study. , 2015, American journal of physiology. Lung cellular and molecular physiology.

[3]  S. Ohlmeier,et al.  Proteomics of human lung tissue identifies surfactant protein A as a marker of chronic obstructive pulmonary disease. , 2008, Journal of proteome research.

[4]  Ming Xu,et al.  Identification of thyroxine-binding globulin as a candidate plasma marker of chronic obstructive pulmonary disease , 2017, International journal of chronic obstructive pulmonary disease.

[5]  J. Bandow,et al.  Improved image analysis workflow for 2‐D gels enables large‐scale 2‐D gel‐based proteomics studies – COPD biomarker discovery study , 2008, Proteomics.

[6]  I. Rahman,et al.  Hemoglobin α and β are ubiquitous in the human lung, decline in idiopathic pulmonary fibrosis but not in COPD , 2010, Respiratory research.

[7]  P. Iadarola,et al.  Spit it out! How could the sputum proteome aid clinical research into pulmonary diseases? , 2017, Expert review of proteomics.

[8]  T. Nishimura,et al.  Recent mass spectrometry-based proteomics for biomarker discovery in lung cancer, COPD, and asthma , 2017, Expert review of proteomics.

[9]  Fabio Ferrari,et al.  Proteomic analysis of exhaled breath condensate from single patients with pulmonary emphysema associated to alpha1-antitrypsin deficiency. , 2008, Journal of proteomics.

[10]  S D Varfolomeev,et al.  [Proteomic analysis of exhaled breath condensate for diagnosis of pathologies of the respiratory system]. , 2015, Biomeditsinskaia khimiia.

[11]  B. Nicholas,et al.  Induced sputum: a window to lung pathology. , 2009, Biochemical Society transactions.

[12]  S. Kjellqvist,et al.  Gender differences in the bronchoalveolar lavage cell proteome of patients with chronic obstructive pulmonary disease. , 2013, The Journal of allergy and clinical immunology.

[13]  I. Kema,et al.  The role of liquid chromatography-tandem mass spectrometry in the clinical laboratory. , 2012, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[14]  D. Postma,et al.  Proteomics of epithelial lining fluid obtained by bronchoscopic microprobe sampling. , 2011, Methods in molecular biology.

[15]  C. Bai,et al.  Alterations of plasma inflammatory biomarkers in the healthy and chronic obstructive pulmonary disease patients with or without acute exacerbation. , 2012, Journal of proteomics.

[16]  K. R. Chapman,et al.  Epidemiology and costs of chronic obstructive pulmonary disease , 2006, European Respiratory Journal.

[17]  G. Paone,et al.  Blood and sputum biomarkers in COPD and asthma: a review. , 2016, European review for medical and pharmacological sciences.

[18]  E. Kunter,et al.  Effect of Corticosteroids on Hemostasis and Pulmonary Arterial Pressure during Chronic Obstructive Pulmonary Disease Exacerbation , 2006, Respiration.

[19]  L. Wood,et al.  Identification of novel diagnostic biomarkers for asthma and chronic obstructive pulmonary disease. , 2011, American journal of respiratory and critical care medicine.

[20]  J. Dalton,et al.  Proteomic Analysis of Extracellular HMGB1 Identifies Binding Partners and Exposes Its Potential Role in Airway Epithelial Cell Homeostasis. , 2018, Journal of proteome research.

[21]  Ming Xu,et al.  Fetuin-B (FETUB): a Plasma Biomarker Candidate Related to the Severity of Lung Function in COPD , 2016, Scientific Reports.

[22]  J. Lammers,et al.  Proteomic profiling of peripheral blood neutrophils identifies two inflammatory phenotypes in stable COPD patients , 2017, Respiratory Research.

[23]  P. Howarth,et al.  Identification of lipocalin and apolipoprotein A1 as biomarkers of chronic obstructive pulmonary disease. , 2010, American journal of respiratory and critical care medicine.

[24]  A. Lindberg,et al.  Proteolytic biomarkers are related to prognosis in COPD- report from a population-based cohort , 2018, Respiratory Research.

[25]  R. Banerjee,et al.  Transcriptomics, proteomics and metabolomics driven biomarker discovery in COPD: an update , 2016, Expert review of molecular diagnostics.

[26]  L. Teran,et al.  Personalized Medicine in Respiratory Disease: Role of Proteomics. , 2016, Advances in protein chemistry and structural biology.

[27]  N. Taniguchi,et al.  Fucosylated surfactant protein-D is a biomarker candidate for the development of chronic obstructive pulmonary disease. , 2015, Journal of proteomics.

[28]  K. Rabe,et al.  Five good reasons to read (and cite) the ERJ , 2008, European Respiratory Journal.

[29]  L. Pannell,et al.  Protein networks in induced sputum from smokers and COPD patients , 2015, International journal of chronic obstructive pulmonary disease.

[30]  M. T. Santini,et al.  Structural alterations in erythrocytes from patients with chronic obstructive pulmonary disease. , 1997, Haemostasis.

[31]  Eun Joo Lee,et al.  Proteomic analysis in lung tissue of smokers and COPD patients. , 2009, Chest.

[32]  Alan D. Lopez,et al.  The global burden of disease, 1990–2020 , 1998, Nature Medicine.

[33]  A. Mangoni,et al.  Plasma Proteomic Signatures in Early Chronic Obstructive Pulmonary Disease , 2018, Proteomics. Clinical applications.

[34]  R. Stockley Biomarkers in chronic obstructive pulmonary disease: confusing or useful? , 2014, International journal of chronic obstructive pulmonary disease.

[35]  Q. Hu,et al.  Large-scale, ion-current-based proteomics investigation of bronchoalveolar lavage fluid in chronic obstructive pulmonary disease patients. , 2014, Journal of proteome research.

[36]  J. Takeda,et al.  New bronchoscopic microsample probe to measure the biochemical constituents in epithelial lining fluid of patients with acute respiratory distress syndrome , 2001, Critical care medicine.

[37]  Michael Vogeser,et al.  A decade of HPLC-MS/MS in the routine clinical laboratory--goals for further developments. , 2008, Clinical biochemistry.

[38]  Xiangdong Wang,et al.  Selection of AECOPD-specific immunomodulatory biomarkers by integrating genomics and proteomics with clinical informatics , 2018, Cell Biology and Toxicology.

[39]  R. Savino,et al.  Asthma and COPD proteomics: Current approaches and future directions , 2015, Proteomics. Clinical applications.

[40]  S. Ohlmeier,et al.  Sputum proteomics identifies elevated PIGR levels in smokers and mild-to-moderate COPD. , 2012, Journal of proteome research.

[41]  Liangliang Sun,et al.  Over 4100 protein identifications from a Xenopus laevis fertilized egg digest using reversed‐phase chromatographic prefractionation followed by capillary zone electrophoresis–electrospray ionization–tandem mass spectrometry analysis , 2016, Proteomics.

[42]  D. Postma,et al.  Proteomic analysis of human epithelial lining fluid by microfluidics‐based nanoLC‐MS/MS: A feasibility study , 2013, Electrophoresis.

[43]  P. Montuschi,et al.  Liquid chromatography-mass spectrometry measurement of leukotrienes in asthma and other respiratory diseases. , 2014, Journal of chromatography. B, Analytical technologies in the biomedical and life sciences.

[44]  S. Ohlmeier,et al.  Biomarkers in Lung Diseases : from Pathogenesis to Prediction to New Therapies Lung tissue proteomics identifies elevated transglutaminase 2 levels in stable chronic obstructive pulmonary disease , 2016 .

[45]  Jun Wang,et al.  Bioinformatics-based identification of potential microRNA biomarkers in frequent and non-frequent exacerbators of COPD , 2018, International journal of chronic obstructive pulmonary disease.

[46]  Å. Wheelock,et al.  Long-term smoking alters abundance of over half of the proteome in bronchoalveolar lavage cell in smokers with normal spirometry, with effects on molecular pathways associated with COPD , 2018, Respiratory Research.

[47]  Jason Liao,et al.  Proteomic profiling of human plasma by iTRAQ reveals down-regulation of ITI-HC3 and VDBP by cigarette smoking. , 2011, Journal of proteome research.

[48]  T. Franz,et al.  Respiratory proteomics: from descriptive studies to personalized medicine. , 2015, Journal of proteome research.

[49]  C. Tinelli,et al.  Profiling the Proteome of Exhaled Breath Condensate in Healthy Smokers and COPD Patients by LC-MS/MS , 2012, International journal of molecular sciences.

[50]  B. Himes,et al.  Using omics approaches to understand pulmonary diseases , 2017, Respiratory Research.

[51]  Kelly A. Jones,et al.  Assessment of two immunodepletion methods: off-target effects and variations in immunodepletion efficiency may confound plasma proteomics. , 2012, Journal of proteome research.

[52]  Giovanna E Carpagnano,et al.  Peptidome profiling of induced sputum by mesoporous silica beads and MALDI‐TOF MS for non‐invasive biomarker discovery of chronic inflammatory lung diseases , 2011, Proteomics.

[53]  L. Pannell,et al.  Protein expression in sputum of smokers and chronic obstructive pulmonary disease patients: a pilot study by CapLC-ESI-Q-TOF. , 2007, Journal of proteome research.

[54]  Marinos Elia,et al.  Influence of deprivation on health care use, health care costs, and mortality in COPD , 2018, International journal of chronic obstructive pulmonary disease.

[55]  Richard D. Smith,et al.  Proteomic biomarkers in plasma that differentiate rapid and slow decline in lung function in adult cigarette smokers with chronic obstructive pulmonary disease (COPD) , 2010, Analytical and bioanalytical chemistry.

[56]  H. Salehi,et al.  Chronic obstructive pulmonary disease: MicroRNAs and exosomes as new diagnostic and therapeutic biomarkers , 2018, Journal of research in medical sciences : the official journal of Isfahan University of Medical Sciences.

[57]  T. Veenstra,et al.  Profiling the erythrocyte membrane proteome isolated from patients diagnosed with chronic obstructive pulmonary disease. , 2012, Journal of proteomics.

[58]  F. Hargreave,et al.  The use of cellular and molecular biomarkers to manage COPD exacerbations , 2017, Expert review of respiratory medicine.

[59]  D. Halpin,et al.  Chronic obstructive pulmonary disease guidelines in Europe: a look into the future , 2018, Respiratory Research.

[60]  M. Strlič,et al.  Depletion of high-abundance proteins from human plasma using a combination of an affinity and pseudo-affinity column. , 2009, Journal of chromatography. A.

[61]  B. McManus,et al.  COPD Exacerbation Biomarkers Validated Using Multiple Reaction Monitoring Mass Spectrometry , 2016, PloS one.

[62]  B. Garcia,et al.  Proteomics , 2011, Journal of biomedicine & biotechnology.

[63]  M. Neurath,et al.  RAGE Mediates a Novel Proinflammatory Axis A Central Cell Surface Receptor for S100/Calgranulin Polypeptides , 1999, Cell.

[64]  L. Paz-Ares,et al.  Identification of proteomic signatures associated with lung cancer and COPD. , 2013, Journal of proteomics.

[65]  S. Ohlmeier,et al.  Proteomic studies on receptor for advanced glycation end product variants in idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease , 2010, Proteomics. Clinical applications.

[66]  R. M. Ford Allergy in asthma , 1982 .

[67]  Fabio Ferrari,et al.  From micellar electrokinetic chromatography to liquid chromatography‐mass spectrometry: Revisiting the way of analyzing human fluids for the search of desmosines, putative biomarkers of chronic obstructive pulmonary disease , 2014, Electrophoresis.

[68]  A. Fernández-Villar,et al.  Reliability and usefulness of spirometry performed during admission for COPD exacerbation , 2018, PloS one.

[69]  D. Porteous,et al.  SELDI-TOF biomarker signatures for cystic fibrosis, asthma and chronic obstructive pulmonary disease. , 2010, Clinical biochemistry.

[70]  Per Broberg,et al.  Protein expression patterns associated with progression of chronic obstructive pulmonary disease in bronchoalveolar lavage of smokers. , 2007, Clinical chemistry.

[71]  C. Brightling Chronic obstructive pulmonary disease phenotypes, biomarkers, and prognostic indicators. , 2016, Allergy and asthma proceedings.

[72]  J. Enghild,et al.  Human skin keratins are the major proteins in exhaled breath condensate , 2008, European Respiratory Journal.

[73]  Charles Auffray,et al.  Application of ’omics technologies to biomarker discovery in inflammatory lung diseases , 2013, European Respiratory Journal.

[74]  Å. Wheelock,et al.  Proteomic profiling of lung immune cells reveals dysregulation of phagocytotic pathways in female-dominated molecular COPD phenotype , 2018, Respiratory Research.

[75]  M. Peitsch,et al.  Alterations in the sputum proteome and transcriptome in smokers and early-stage COPD subjects. , 2015, Journal of proteomics.

[76]  R. Bowler,et al.  Analysis of the Plasma Proteome in COPD: Novel Low Abundance Proteins Reflect the Severity of Lung Remodeling , 2014, COPD.

[77]  R. Savino,et al.  Application of Proteomics and Peptidomics to COPD , 2014, BioMed research international.

[78]  L. Paz-Ares,et al.  Identification of Oxidative Stress Related Proteins as Biomarkers for Lung Cancer and Chronic Obstructive Pulmonary Disease in Bronchoalveolar Lavage , 2013, International journal of molecular sciences.

[79]  P. Barnes,et al.  Chronic obstructive pulmonary disease. , 2000, The New England journal of medicine.

[80]  T. Welte,et al.  Does urinary peptide content differ between COPD patients with and without inherited alpha-1 antitrypsin deficiency? , 2017, International journal of chronic obstructive pulmonary disease.

[81]  D. Porteous,et al.  Sputum proteomics in inflammatory and suppurative respiratory diseases. , 2008, American journal of respiratory and critical care medicine.

[82]  D. Postma,et al.  Susceptibility to COPD: Differential Proteomic Profiling after Acute Smoking , 2014, PloS one.