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Weise DO, Kruk ME, Higgins L, Markowski TW, Jagtap PD, Mehta S, Mickelson A, Parker LL, Wendt CH, Griffin TJ. An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples. Clin Proteomics 2023; 20:14. [PMID: 37005570 PMCID: PMC10068177 DOI: 10.1186/s12014-023-09404-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 03/13/2023] [Indexed: 04/04/2023] Open
Abstract
BACKGROUND Clinical bronchoalveolar lavage fluid (BALF) samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease. However, mass spectrometry (MS)-based proteomic analysis of BALF is challenged by the dynamic range of protein abundance, and potential for interfering contaminants. A robust, MS-based proteomics compatible sample preparation workflow for BALF samples, including those of small and large volume, would be useful for many researchers. RESULTS We have developed a workflow that combines high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, that is compatible with either qualitative or quantitative MS-based proteomic analysis. The workflow includes a value-added collection of endogenous peptides for peptidomic analysis of BALF samples, if desired, as well as amenability to offline semi-preparative or microscale fractionation of complex peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis. We demonstrate the effectiveness of this workflow on BALF samples collected from COPD patients, including for smaller sample volumes of 1-5 mL that are commonly available from the clinic. We also demonstrate the repeatability of the workflow as an indicator of its utility for quantitative proteomic studies. CONCLUSIONS Overall, our described workflow consistently provided high quality proteins and tryptic peptides for MS analysis. It should enable researchers to apply MS-based proteomics to a wide-variety of studies focused on BALF clinical specimens.
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Affiliation(s)
- Danielle O Weise
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Monica E Kruk
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Todd W Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Pratik D Jagtap
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Subina Mehta
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Alan Mickelson
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
| | - Laurie L Parker
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Christine H Wendt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Medical School, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System, Minneapolis, MN, USA
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
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2
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Zhu Y, Esnault S, Ge Y, Jarjour NN, Brasier AR. Airway fibrin formation cascade in allergic asthma exacerbation: implications for inflammation and remodeling. Clin Proteomics 2022; 19:15. [PMID: 35590254 PMCID: PMC9117591 DOI: 10.1186/s12014-022-09351-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Airway remodeling in patients with asthma, which leads to a decline in pulmonary function, is likely the result of repeated exacerbations often provoked by aeroallergen exposures. Aeroallegen exposure triggers a stereotypic response orchestrated by growth factor cytokines and other protein mediators. This results in a late-phase allergic reaction characterized by vascular permeability, recruitment of activated leukocytes, and activation of structural cells of the airway. The spectrum of protein mediators and their functions are incompletely understood. METHODS Bronchoalveolar lavage fluid (BALF) samples were obtained from 12 volunteers who exhibited robust eosinophilic recruitment following segmental bronchial provocation with allergen (SBP-Ag). We systematically identified and quantified proteins in BALF using high-performance liquid chromatography-high-resolution mass spectrometry (LC-MS/MS) followed by pathway analysis and correlations with airway physiology. RESULTS Pairwise analysis of protein abundance in BALF pre- vs post-SBP-Ag revealed that 55 proteins were upregulated and 103 proteins were downregulated. We observed enrichment of groups of proteins mapping to hemostasis/fibrin clot, platelet activation, lipoprotein assembly, neutrophil degranulation proteins, and acute-phase inflammation-airway remodeling pathways. The abundances of F2 and Fibrinogen γ (FGG) correlated with eosinophil numbers, whereas SERPINA3 negatively correlated with change in FeNO. The coagulation proteins F2 and KNG negatively correlated with FN1 an index of airway remodeling. Interestingly, patients with lower FEV1 showed distinct allergen-induced patterns of 8 BALF proteins, including MUC1, alarmins (HSPB1), and actin polymerization factors. CONCLUSIONS Protein abundance of the fibrin formation cascade, platelet activation and remodeling are associated with late-phase leukocyte numbers and markers of remodeling. Patients with lower FEV1 have distinct dynamic responses to allergen.
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Affiliation(s)
- Yanlong Zhu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Stephane Esnault
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, 53705, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Nizar N Jarjour
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, 53705, USA
| | - Allan R Brasier
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, 715 Highland Ave, Madison, WI, 53705, USA.
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3
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Covarrubias-Zambrano O, Motamedi M, Ameredes BT, Tian B, Calhoun WJ, Zhao Y, Brasier AR, Kalubowilage M, Malalasekera AP, Yapa AS, Wang H, Culbertson CT, Troyer DL, Bossmann SH. Optical biosensing of markers of mucosal inflammation. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2021; 40:102476. [PMID: 34743019 DOI: 10.1016/j.nano.2021.102476] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 09/13/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023]
Abstract
We report the design and adaptation of iron/iron oxide nanoparticle-based optical nanobiosensors for enzymes or cytokine/chemokines that are established biomarkers of lung diseases. These biomarkers comprise ADAM33, granzyme B, MMP-8, neutrophil elastase, arginase, chemokine (C-C motif) ligand 20 and interleukin-6. The synthesis of nanobiosensors for these seven biomarkers, their calibration with commercially available enzymes and cytokines/chemokines, as well as their validation using bronchoalveolar lavage (BAL) obtained from a mouse model of TLR3-mediated inflammation are discussed here. Exhaled Breath Condensate (EBC) is a minimally invasive approach for sampling airway fluid in the diagnosis and management of various lung diseases in humans (e.g., asthma, COPD and viral infections). We report the proof-of-concept of using human EBC in conjunction with nanobiosensors for diagnosis/monitoring airway inflammation. These findings suggest that, with nanosensor technology, human EBC can be utilized as a liquid biopsy to monitor inflammation/remodeling in lung disease.
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Affiliation(s)
| | - Massoud Motamedi
- Center for Biomedical Engineering, University of Texas Medical Branch, Galveston, TX, USA
| | - Bill T Ameredes
- Institute for Translational Sciences and Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX
| | - Bing Tian
- Institute for Translational Sciences and Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX
| | - William J Calhoun
- Institute for Translational Sciences and Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX
| | - Yingxin Zhao
- Institute for Translational Sciences and Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX
| | - Allan R Brasier
- Institute for Clinical and Translational Research, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI
| | | | - Aruni P Malalasekera
- Department of Chemistry, Southwestern College, 100 College Street, Winfield, KS, USA
| | - Asanka S Yapa
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | - Hongwang Wang
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | | | - Deryl L Troyer
- Department of Anatomy & Physiology, Kansas State University, Manhattan, KS, USA
| | - Stefan H Bossmann
- Department of Chemistry, Kansas State University, Manhattan, KS, USA; The University of Kansas Medical Center, Department of Cancer Biology and The University of Kansas Cancer Center, Kansas City, KS, USA.
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4
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Ivanova O, Richards LB, Vijverberg SJ, Neerincx AH, Sinha A, Sterk PJ, Maitland‐van der Zee AH. What did we learn from multiple omics studies in asthma? Allergy 2019; 74:2129-2145. [PMID: 31004501 DOI: 10.1111/all.13833] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/25/2019] [Accepted: 04/12/2019] [Indexed: 12/13/2022]
Abstract
More than a decade has passed since the finalization of the Human Genome Project. Omics technologies made a huge leap from trendy and very expensive to routinely executed and relatively cheap assays. Simultaneously, we understood that omics is not a panacea for every problem in the area of human health and personalized medicine. Whilst in some areas of research omics showed immediate results, in other fields, including asthma, it only allowed us to identify the incredibly complicated molecular processes. Along with their possibilities, omics technologies also bring many issues connected to sample collection, analyses and interpretation. It is often impossible to separate the intrinsic imperfection of omics from asthma heterogeneity. Still, many insights and directions from applied omics were acquired-presumable phenotypic clusters of patients, plausible biomarkers and potential pathways involved. Omics technologies develop rapidly, bringing improvements also to asthma research. These improvements, together with our growing understanding of asthma subphenotypes and underlying cellular processes, will likely play a role in asthma management strategies.
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Affiliation(s)
- Olga Ivanova
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Levi B. Richards
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Susanne J. Vijverberg
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anne H. Neerincx
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anirban Sinha
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Peter J. Sterk
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
| | - Anke H. Maitland‐van der Zee
- Department of Respiratory Medicine, Amsterdam University Medical Centres (AUMC) University of Amsterdam Amsterdam the Netherlands
- Department of Paediatric Pulmonology Amsterdam UMC/ Emma Children's Hospital Amsterdam the Netherlands
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5
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Ferraro VA, Zanconato S, Baraldi E, Carraro S. Nitric Oxide and Biological Mediators in Pediatric Chronic Rhinosinusitis and Asthma. J Clin Med 2019; 8:jcm8111783. [PMID: 31731479 PMCID: PMC6912805 DOI: 10.3390/jcm8111783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND In the context of the so-called unified airway theory, chronic rhinosinusitis (CRS) and asthma may coexist. The inflammation underlying these conditions can be studied through the aid of biomarkers. Main body: We described the main biological mediators that have been studied in pediatric CRS and asthma, and, according to the available literature, we reported their potential role in the diagnosis and management of these conditions. As for CRS, we discussed the studies that investigated nasal nitric oxide (nNO), pendrin, and periostin. As for asthma, we discussed the role of fractional exhaled nitric oxide (feNO), the role of periostin, and that of biological mediators measured in exhaled breath condensate (EBC) and exhaled air (volatile organic compounds, VOCs). CONCLUSION Among non-invasive biomarkers, nNO seems the most informative in CRS and feNO in asthma. Other biological mediators seem promising, but further studies are needed before they can be applied in clinical practice.
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Kasaian MT, Lee J, Brennan A, Danto SI, Black KE, Fitz L, Dixon AE. Proteomic analysis of serum and sputum analytes distinguishes controlled and poorly controlled asthmatics. Clin Exp Allergy 2018; 48:814-824. [PMID: 29665127 DOI: 10.1111/cea.13151] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 03/11/2018] [Accepted: 03/28/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND A major goal of asthma therapy is to achieve disease control, with maintenance of lung function, reduced need for rescue medication, and prevention of exacerbation. Despite current standard of care, up to 70% of patients with asthma remain poorly controlled. Analysis of serum and sputum biomarkers could offer insights into parameters associated with poor asthma control. OBJECTIVE To identify signatures as determinants of asthma disease control, we performed proteomics using Olink proximity extension analysis. METHODS Up to 3 longitudinal serum samples were collected from 23 controlled and 25 poorly controlled asthmatics. Nine of the controlled and 8 of the poorly controlled subjects also provided 2 longitudinal sputum samples. The study included an additional cohort of 9 subjects whose serum was collected within 48 hours of asthma exacerbation. Two separate pre-defined Proseek Multiplex panels (INF and CVDIII) were run to quantify 181 separate protein analytes in serum and sputum. RESULTS Panels consisting of 9 markers in serum (CCL19, CCL25, CDCP1, CCL11, FGF21, FGF23, Flt3L, IL-10Rβ, IL-6) and 16 markers in sputum (tPA, KLK6, RETN, ADA, MMP9, Chit1, GRN, PGLYRP1, MPO, HGF, PRTN3, DNER, PI3, Chi3L1, AZU1, and OPG) distinguished controlled and poorly controlled asthmatics. The sputum analytes were consistent with a pattern of neutrophil activation associated with poor asthma control. The serum analyte profile of the exacerbation cohort resembled that of the controlled group rather than that of the poorly controlled asthmatics, possibly reflecting a therapeutic response to systemic corticosteroids. CONCLUSIONS AND CLINICAL RELEVANCE Proteomic profiles in serum and sputum distinguished controlled and poorly controlled asthmatics, and were maintained over time. Findings support a link between sputum neutrophil markers and loss of asthma control.
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Affiliation(s)
- M T Kasaian
- Inflammation and Immunology Research Unit, Pfizer, Cambridge, Massachusetts, USA
| | - J Lee
- Early Clinical Development, Pfizer, Cambridge, Massachusetts, USA
| | - A Brennan
- Inflammation and Immunology Research Unit, Pfizer, Cambridge, Massachusetts, USA
| | - S I Danto
- Inflammation and Immunology Research Unit, Pfizer, Cambridge, Massachusetts, USA
| | - K E Black
- Department of Medicine, University of Vermont, Burlington, Vermont, USA
| | - L Fitz
- Early Clinical Development, Pfizer, Cambridge, Massachusetts, USA
| | - A E Dixon
- Department of Medicine, University of Vermont, Burlington, Vermont, USA
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7
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Maroto R, Zhao Y, Jamaluddin M, Popov VL, Wang H, Kalubowilage M, Zhang Y, Luisi J, Sun H, Culbertson CT, Bossmann SH, Motamedi M, Brasier AR. Effects of storage temperature on airway exosome integrity for diagnostic and functional analyses. J Extracell Vesicles 2017; 6:1359478. [PMID: 28819550 PMCID: PMC5556670 DOI: 10.1080/20013078.2017.1359478] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 07/16/2017] [Indexed: 11/23/2022] Open
Abstract
Background: Extracellular vesicles contain biological molecules specified by cell-type of origin and modified by microenvironmental changes. To conduct reproducible studies on exosome content and function, storage conditions need to have minimal impact on airway exosome integrity. Aim: We compared surface properties and protein content of airway exosomes that had been freshly isolated vs. those that had been treated with cold storage or freezing. Methods: Mouse bronchoalveolar lavage fluid (BALF) exosomes purified by differential ultracentrifugation were analysed immediately or stored at +4°C or -80°C. Exosomal structure was assessed by dynamic light scattering (DLS), transmission electron microscopy (TEM) and charge density (zeta potential, ζ). Exosomal protein content, including leaking/dissociating proteins, were identified by label-free LC-MS/MS. Results: Freshly isolated BALF exosomes exhibited a mean diameter of 95 nm and characteristic morphology. Storage had significant impact on BALF exosome size and content. Compared to fresh, exosomes stored at +4°C had a 10% increase in diameter, redistribution to polydisperse aggregates and reduced ζ. Storage at -80°C produced an even greater effect, resulting in a 25% increase in diameter, significantly reducing the ζ, resulting in multilamellar structure formation. In fresh exosomes, we identified 1140 high-confidence proteins enriched in 19 genome ontology biological processes. After storage at room temperature, 848 proteins were identified. In preparations stored at +4°C, 224 proteins appeared in the supernatant fraction compared to the wash fractions from freshly prepared exosomes; these proteins represent exosome leakage or dissociation of loosely bound "peri-exosomal" proteins. In preparations stored at -80°C, 194 proteins appeared in the supernatant fraction, suggesting that distinct protein groups leak from exosomes at different storage temperatures. Conclusions: Storage destabilizes the surface characteristics, morphological features and protein content of BALF exosomes. For preservation of the exosome protein content and representative functional analysis, airway exosomes should be analysed immediately after isolation.
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Affiliation(s)
- Rosario Maroto
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
| | - Yingxin Zhao
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | - Mohammad Jamaluddin
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | | | - Hongwang Wang
- Department of Chemistry, Kansas State University, Manhattan, KS, USA
| | | | - Yueqing Zhang
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | - Jonathan Luisi
- Center for Biomedical Engineering, UTMB, Galveston, TX, USA
| | - Hong Sun
- Department of Internal Medicine, UTMB, Galveston, TX, USA
| | | | | | | | - Allan R. Brasier
- Sealy Center for Molecular Medicine, University of Texas Medical Branch (UTMB), Galveston, TX, USA
- Institute for Translational Sciences, UTMB, Galveston, TX, USA
- Department of Internal Medicine, UTMB, Galveston, TX, USA
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8
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Diao W, Shen N, Du Y, Sun X, Liu B, Xu M, He B. Identification of thyroxine-binding globulin as a candidate plasma marker of chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis 2017; 12:1549-1564. [PMID: 28579773 PMCID: PMC5448702 DOI: 10.2147/copd.s137806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Biomarkers for the management of chronic obstructive pulmonary disease (COPD) are limited. The aim of this study was to explore new plasma biomarkers in patients with COPD. Thyroxine-binding globulin (THBG) was initially identified by proteomics in a discovery panel and subsequently verified by enzyme-linked immunosorbent assay in another verification panel with a 1-year follow-up. THBG levels were elevated in patients with COPD (9.2±2.3 μg/mL) compared to those of the controls (6.6±2.0 μg/mL). Receiver operating characteristic curves suggested that THBG was able to slightly differentiate between patients with COPD and controls (area under the curve [AUC]: 0.814) and performed better if combined with fibrinogen (AUC: 0.858). THBG was more capable of distinguishing Global Initiative for Obstructive Lung Disease stages I–III and IV (AUC: 0.851) compared with fibrinogen (AUC 0.582). THBG levels were negatively associated with predicted percentage forced expiratory volume in 1 s and positively related to predicted percentage residual volume, RV/percentage total lung capacity, and percentage low-attenuation area. COPD patients with higher baseline THBG levels had a greater risk of acute exacerbation (AE) than those with lower THBG levels (P=0.014, by Kaplan–Meier curve; hazard ratio: 4.229, by Cox proportional hazards model). In summary, THBG is a potential plasma biomarker of COPD and can assist in the management of stable stage and AEs in COPD patients.
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Affiliation(s)
| | | | | | | | | | - Ming Xu
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital.,Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, People's Republic of China
| | - Bei He
- Department of Respiratory Medicine
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9
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Kononikhin AS, Fedorchenko KY, Ryabokon AM, Starodubtseva NL, Popov IA, Zavialova MG, Anaev EC, Chuchalin AG, Varfolomeev SD, Nikolaev EN. Proteomic analysis of exhaled breath condensate for diagnostics of respiratory system diseases. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2016. [DOI: 10.1134/s1990750816030069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Jiang C, Yu H, Sun Q, Zhu W, Xu J, Gao N, Zhang R, Liu L, Wu X, Yang X, Meng L, Lu S. Extracellular microRNA-21 and microRNA-26a increase in body fluids from rats with antigen induced pulmonary inflammation and children with recurrent wheezing. BMC Pulm Med 2016; 16:50. [PMID: 27075111 PMCID: PMC4831091 DOI: 10.1186/s12890-016-0216-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 04/05/2016] [Indexed: 12/18/2022] Open
Abstract
Background This study aims to find out whether extracellular miRNAs is implicated in recurrent childhood wheezing with asthmatic risk. Methods One hundred and forty children of Chinese Han population were recruited for this study. Plasma and intracellular miRNAs from children with recurrent wheezing and rats with antigen induced pulmonary inflammation (AIPI) were detected by using reverse transcription-quantitative PCR. Differential leukocytes in blood were automatically counted. Total IgE was detected by enzyme-linked immunosorbent assay. Clinical implication in diagnosis was evaluated using receiver operating characteristic curves. Results The increase of plasma miR-21 and miR-26a was screened out from 11 candidate miRNAs and validated in wheezing children. The level of expression for both miRNAs were comparable in different age and gender. Plasma miR-21 was more preferable to miR-26a and total IgE for diagnosis. Plasma miR-21 and miR-26a levels were not significantly correlated with various leukocyte counts or miRNA expression in blood cells. In acute and chronic AIPI rats, miR-21 levels increased in both plasma and lavaged lung compared with control. Moreover, circulating miR-21 and miR-26a levels were highly positively correlated with infiltrated cell counts in bronchoalveolar lavage fluid of AIPI rats. Conclusions Circulating miR-21 and miR-26a increase in wheezing children and AIPI rats. This not only manifests their strong clinical implication in recurrent childhood wheezing with asthma risk, but also provides novel insights into the role of extracellular miRNAs during development of airway inflammation and recurrent wheezing. Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0216-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Congshan Jiang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Hongchuan Yu
- Department of Respiratory Medicine, Xi'an Children Hospital, Xi'an, Shaanxi, PR China
| | - Qingzhu Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Wenhua Zhu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Jing Xu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Ning Gao
- Department of Clinical Laboratory, the Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Rui Zhang
- Department of Bone and Joint Diseases, Xi'an Honghui Hospital, Xi'an, Shaanxi, PR China
| | - Li Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Xiaoying Wu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Xudong Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China.,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China
| | - Liesu Meng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China. .,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China.
| | - Shemin Lu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, West Yanta Road No.76, Xi'an, Shaanxi, PR China. .,Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University), Ministry of Education, Xi'an, Shaanxi, PR China.
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11
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Kononikhin AS, Fedorchenko KY, Ryabokon AM, Starodubtseva NL, Popov IA, Zavialova MG, Anaev EC, Chuchalin AG, Varfolomeev SD, Nikolaev EN. [Proteomic analysis of exhaled breath condensate for diagnosis of pathologies of the respiratory system]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:777-80. [PMID: 26716752 DOI: 10.18097/pbmc20156106777] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Study of the proteomic composition of exhaled breath condensate (EBC), is a promising non-invasive method for the diagnosis of the respiratory tract diseases in patients. In this study the EBC proteomic composition of the 79 donors, including patients with different pathologies of the respiratory system has been investigated. Cytoskeletal keratins type II (1, 2, 3, 4, 5, 6) and cytoskeletal keratins the type I (9, 10, 14, 15, 16) were invariant for all samples. Analyzing the frequency of occurrence of proteins in different groups of examined patients, several categories of protein have been recognized: found in all pathologies (Dermcidin, Alpha-1-microglobulin, SHROOM3), found in several pathologies (CSTA, LCN1, JUP, PIP, TXN), and specific for a single pathology (PRDX1, Annexin A1/A2). The EBC analysis by HPLC-MS/MS can be used to identify potential protein markers characteristic for pathologies such as chronic obstructive pulmonary disease (PRDX1) and pneumonia (Annexin A1/A2).
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Affiliation(s)
- A S Kononikhin
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia; Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - K Yu Fedorchenko
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - A M Ryabokon
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - N L Starodubtseva
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia; Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - I A Popov
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia; Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - M G Zavialova
- Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - E C Anaev
- Research Institute of Pulmonology, Moscow, Russia
| | | | - S D Varfolomeev
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia; Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia
| | - E N Nikolaev
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
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12
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Republished: Respiratory microbiota: addressing clinical questions, informing clinical practice. Postgrad Med J 2015; 91:463-70. [PMID: 26304986 PMCID: PMC4552901 DOI: 10.1136/postgradmedj-2014-205826rep] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/30/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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13
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Exhaled Breath Condensate: Technical and Diagnostic Aspects. ScientificWorldJournal 2015; 2015:435160. [PMID: 26106641 PMCID: PMC4461795 DOI: 10.1155/2015/435160] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/21/2015] [Indexed: 01/18/2023] Open
Abstract
Purpose. The aim of this study was to evaluate the 30-year progress of research on exhaled breath condensate in a disease-based approach. Methods. We searched PubMed/Medline, ScienceDirect, and Google Scholar using the following keywords: exhaled breath condensate (EBC), biomarkers, pH, asthma, gastroesophageal reflux (GERD), smoking, COPD, lung cancer, NSCLC, mechanical ventilation, cystic fibrosis, pulmonary arterial hypertension (PAH), idiopathic pulmonary fibrosis, interstitial lung diseases, obstructive sleep apnea (OSA), and drugs. Results. We found 12600 related articles in total in Google Scholar, 1807 in ScienceDirect, and 1081 in PubMed/Medline, published from 1980 to October 2014. 228 original investigation and review articles were eligible. Conclusions. There is rapidly increasing number of innovative articles, covering all the areas of modern respiratory medicine and expanding EBC potential clinical applications to other fields of internal medicine. However, the majority of published papers represent the results of small-scale studies and thus current knowledge must be further evaluated in large cohorts. In regard to the potential clinical use of EBC-analysis, several limitations must be pointed out, including poor reproducibility of biomarkers and absence of large surveys towards determination of reference-normal values. In conclusion, contemporary EBC-analysis is an intriguing achievement, but still in early stage when it comes to its application in clinical practice.
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14
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Terracciano R, Pelaia G, Preianò M, Savino R. Asthma and COPD proteomics: current approaches and future directions. Proteomics Clin Appl 2015; 9:203-20. [PMID: 25504544 DOI: 10.1002/prca.201400099] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/26/2014] [Accepted: 12/08/2014] [Indexed: 12/25/2022]
Abstract
Although asthma and chronic obstructive pulmonary disease COPD represent the two most common chronic respiratory diseases worldwide, the mechanisms underlying their pathobiology need to be further elucidated. Presently, differentiation of asthma and COPD are largely based on clinical and lung function parameters. However, the complexity of these multifactorial diseases may lead to misclassification and to inappropriate management strategies. Recently, tremendous progress in MS has extended the sensitivity, accuracy, and speed of analysis, enabling the identification of thousands of proteins per experiment. Beyond identification, MS has also greatly implemented quantitation issues allowing to assess qualitative-quantitative differences in protein profiles of different samples, in particular diseased versus normal. Herein, we provide a summary of recent proteomics-based investigations in the field of asthma/COPD, highlighting major issues related to sampling and processing procedures for proteomic analyses of specific airway and parenchymal specimens (induced sputum, exhaled breath condensate, epithelial lining fluid, bronchoalveolar and nasal lavage fluid), as well as blood-derived specimen (plasma and serum). Within such a context, together with current difficulties and limitations mainly due to lack of general standardization in preanalytical sampling procedure, our discussion will focus on the challenges and possible benefits of proteomic studies in phenotypic stratification of asthma and COPD.
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Affiliation(s)
- Rosa Terracciano
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
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15
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Rogers GB, Shaw D, Marsh RL, Carroll MP, Serisier DJ, Bruce KD. Respiratory microbiota: addressing clinical questions, informing clinical practice. Thorax 2015; 70:74-81. [PMID: 25035125 PMCID: PMC4283665 DOI: 10.1136/thoraxjnl-2014-205826] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 06/23/2014] [Indexed: 12/23/2022]
Abstract
Over the last decade, technological advances have revolutionised efforts to understand the role played by microbes in airways disease. With the application of ever more sophisticated techniques, the literature has become increasingly inaccessible to the non-specialist reader, potentially hampering the translation of these gains into improvements in patient care. In this article, we set out the key principles underpinning microbiota research in respiratory contexts and provide practical guidance on how best such studies can be designed, executed and interpreted. We examine how an understanding of the respiratory microbiota both challenges fundamental assumptions and provides novel clinical insights into lung disease, and we set out a number of important targets for ongoing research.
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Affiliation(s)
- Geraint B Rogers
- SAHMRI Infection and Immunity Theme, School of Medicine, Flinders University, Adelaide, Australia
| | - Dominick Shaw
- Nottingham Respiratory Research Unit, University of Nottingham, Nottingham City Hospital, Nottingham, Notts, UK
| | - Robyn L Marsh
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mary P Carroll
- Cystic Fibrosis Unit, Southampton University Hospitals NHS Trust, Southampton, UK
| | - David J Serisier
- Immunity, Infection, and Inflammation Program, Mater Research Institute, University of Queensland, and Translational Research Institute, Woolloongabba, Queensland, Australia
- Department of Respiratory Medicine, Mater Adult Hospital, South Brisbane, Australia
| | - Kenneth D Bruce
- King's College London, Institute of Pharmaceutical Science, London, UK
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16
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Pathak RR, Davé V. Integrating omics technologies to study pulmonary physiology and pathology at the systems level. Cell Physiol Biochem 2014; 33:1239-60. [PMID: 24802001 PMCID: PMC4396816 DOI: 10.1159/000358693] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2014] [Indexed: 12/13/2022] Open
Abstract
Assimilation and integration of "omics" technologies, including genomics, epigenomics, proteomics, and metabolomics has readily altered the landscape of medical research in the last decade. The vast and complex nature of omics data can only be interpreted by linking molecular information at the organismic level, forming the foundation of systems biology. Research in pulmonary biology/medicine has necessitated integration of omics, network, systems and computational biology data to differentially diagnose, interpret, and prognosticate pulmonary diseases, facilitating improvement in therapy and treatment modalities. This review describes how to leverage this emerging technology in understanding pulmonary diseases at the systems level -called a "systomic" approach. Considering the operational wholeness of cellular and organ systems, diseased genome, proteome, and the metabolome needs to be conceptualized at the systems level to understand disease pathogenesis and progression. Currently available omics technology and resources require a certain degree of training and proficiency in addition to dedicated hardware and applications, making them relatively less user friendly for the pulmonary biologist and clinicians. Herein, we discuss the various strategies, computational tools and approaches required to study pulmonary diseases at the systems level for biomedical scientists and clinical researchers.
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Affiliation(s)
- Ravi Ramesh Pathak
- Morsani College of Medicine, Department of Pathology and Cell Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
| | - Vrushank Davé
- Morsani College of Medicine, Department of Pathology and Cell Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL USA
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