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      Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation

      research-article
      1 , 2 , , 2 , 3 , 2 , 3 , 4 , 5 , 2 , 3 , 6 , 6 , 7 , 2 , 3 , 8 , 2 , 3 , 9 , 10 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 1 , 35 , 36 , 36 , 2 , 3 , 3 , 37 , 38 , 23 , 23 , 13 , 22 , 1 , 2 , 3 , 38 , 2 , 3 39
      The European Respiratory Journal
      European Respiratory Society

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          Abstract

          Rationale

          Asthma phenotyping requires novel biomarker discovery.

          Objectives

          To identify plasma biomarkers associated with asthma phenotypes by application of a new proteomic panel to samples from two well-characterised cohorts of severe (SA) and mild-to-moderate (MMA) asthmatics, COPD subjects and healthy controls (HCs).

          Methods

          An antibody-based array targeting 177 proteins predominantly involved in pathways relevant to inflammation, lipid metabolism, signal transduction and extracellular matrix was applied to plasma from 525 asthmatics and HCs in the U-BIOPRED cohort, and 142 subjects with asthma and COPD from the validation cohort BIOAIR. Effects of oral corticosteroids (OCS) were determined by a 2-week, placebo-controlled OCS trial in BIOAIR, and confirmed by relation to objective OCS measures in U-BIOPRED.

          Results

          In U-BIOPRED, 110 proteins were significantly different, mostly elevated, in SA compared to MMA and HCs. 10 proteins were elevated in SA versus MMA in both U-BIOPRED and BIOAIR (alpha-1-antichymotrypsin, apolipoprotein-E, complement component 9, complement factor I, macrophage inflammatory protein-3, interleukin-6, sphingomyelin phosphodiesterase 3, TNF receptor superfamily member 11a, transforming growth factor-β and glutathione S-transferase). OCS treatment decreased most proteins, yet differences between SA and MMA remained following correction for OCS use. Consensus clustering of U-BIOPRED protein data yielded six clusters associated with asthma control, quality of life, blood neutrophils, high-sensitivity C-reactive protein and body mass index, but not Type-2 inflammatory biomarkers. The mast cell specific enzyme carboxypeptidase A3 was one major contributor to cluster differentiation.

          Conclusions

          The plasma proteomic panel revealed previously unexplored yet potentially useful Type-2-independent biomarkers and validated several proteins with established involvement in the pathophysiology of SA.

          Abstract

          Application of new proteomic panel in two established European asthma cohorts identifies plasma proteins associated with disease severity independently of Type-2 inflammation, suggesting potentially useful novel biomarkers and therapeutic targets. https://bit.ly/3jtTq5m

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          Most cited references46

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          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

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            ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

            Summary: Unsupervised class discovery is a highly useful technique in cancer research, where intrinsic groups sharing biological characteristics may exist but are unknown. The consensus clustering (CC) method provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset. ConsensusClusterPlus implements the CC method in R and extends it with new functionality and visualizations including item tracking, item-consensus and cluster-consensus plots. These new features provide users with detailed information that enable more specific decisions in unsupervised class discovery. Availability: ConsensusClusterPlus is open source software, written in R, under GPL-2, and available through the Bioconductor project (http://www.bioconductor.org/). Contact: mwilkers@med.unc.edu Supplementary Information: Supplementary data are available at Bioinformatics online.
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              Feature Selection with theBorutaPackage

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                Author and article information

                Journal
                Eur Respir J
                Eur Respir J
                ERJ
                erj
                The European Respiratory Journal
                European Respiratory Society
                0903-1936
                1399-3003
                February 2022
                17 February 2022
                : 59
                : 2
                : 2100142
                Affiliations
                [1 ]Dept of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
                [2 ]Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
                [3 ]Centre for Allergy Research, Karolinska Institutet, Stockholm, Sweden
                [4 ]PEXA AB, Gothenburg, Sweden
                [5 ]Knowles Consulting, Stevenage Bioscience Catalyst, Stevenage, UK
                [6 ]Dept of Laboratory Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
                [7 ]Dept of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Solna, Sweden
                [8 ]Dept of Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
                [9 ]Dept of Internal Medicine, Asthma and Allergy, Medical University of Lodz, University of Lodz, Lodz, Poland
                [10 ]European Institute for Systems Biology and Medicine, Lyon, France
                [11 ]Dept of Clinical Science, University of Bergen, Bergen, Norway
                [12 ]Dept of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
                [13 ]Dept of Respiratory Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
                [14 ]Dept of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
                [15 ]Assistance Publique des Hôpitaux de Marseille, Clinique des Bronches, Allergies et Sommeil, Aix Marseille Université, Marseille, France
                [16 ]COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
                [17 ]Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester; Manchester Academic Health Science Centre and NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
                [18 ]Respiratory Medicine Dept and Asthma Centre, Athens Chest Hospital “Sotiria”, University of Athens, Athens, Greece
                [19 ]Dept for Pulmonary Medicine, University Hospital and University of Bern, Bern, Switzerland
                [20 ]Institute for Research and Biomedical Innovation, Italian National Research Council, Palermo, Italy
                [21 ]Dept of Pulmonology, Semmelweis University, Budapest, Hungary
                [22 ]NIHR Southampton Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, and Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
                [23 ]National Heart and Lung Institute, Imperial College London, London, UK
                [24 ]Dept of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
                [25 ]Dept of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
                [26 ]Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
                [27 ]Dept of Pharmacology, Università Cattolica del Sacro Cuore, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
                [28 ]Dept of Internal Medicine, Jagiellonian University Medical College, Krakow, Poland
                [29 ]Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
                [30 ]Division of lnternal and Cardiorespiratory Medicine, University of Ferrara, Ferrara, Italy
                [31 ]Dept of Internal Medicine, Christian Albrechts University Kiel, Kiel, Germany
                [32 ]Dept of Public Health and Clinical Medicine, Umeå University, Umeå, Sweden
                [33 ]Respiratory Research Unit, University of Nottingham, Nottingham, UK
                [34 ]Dept of Thoracic Medicine, Medical School, University of Crete, Heraklion, Crete, Greece
                [35 ]Dept of Neuroscience, Karolinska Institutet, Stockholm, Sweden
                [36 ]Respiratory Therapeutic Unit, GlaxoSmithKline, London, UK
                [37 ]Dept of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
                [38 ]Dept of Respiratory Medicine and Allergy, Karolinska University Hospital, Stockholm, Sweden
                [39 ]The collaborating members of the U-BIOPRED and the BIOAIR study groups are listed in the Acknowledgements section
                Author notes
                Corresponding author: Maria Sparreman Mikus ( maria.mikus@ 123456ki.se )
                Author information
                https://orcid.org/0000-0001-8518-0095
                https://orcid.org/0000-0002-4412-2080
                https://orcid.org/0000-0002-4524-1663
                https://orcid.org/0000-0002-9949-6012
                https://orcid.org/0000-0003-0619-7927
                https://orcid.org/0000-0002-3149-9444
                https://orcid.org/0000-0003-4106-8469
                https://orcid.org/0000-0002-8113-0653
                https://orcid.org/0000-0003-2101-8843
                https://orcid.org/0000-0002-4657-8532
                Article
                ERJ-00142-2021
                10.1183/13993003.00142-2021
                8850689
                34737220
                223ed438-4580-49a8-9850-db90fa1dbc40
                Copyright ©The authors 2022.

                This version is distributed under the terms of the Creative Commons Attribution Non-Commercial Licence 4.0. For commercial reproduction rights and permissions contact permissions@ersnet.org

                History
                : 15 January 2021
                : 24 June 2021
                Funding
                Funded by: Swedish MRC
                Funded by: Swedish Asthma and Allergy Association’s Research Foundation
                Funded by: Sixth Framework Programme, doi 10.13039/100011103;
                Award ID: FOOD‐CT‐2004‐506378
                Funded by: ChAMP (Centre for Allergy Research Highlights Asthma Markers of Phenotype) consortium which is funded by the Swedish Foundation for Strategic Research, the Karolinska Institutet, AstraZeneca & Science for Life Laboratory Joint Research Collaboration, and the Vårdal Foundation
                Funded by: Innovative Medicines Initiative, doi 10.13039/501100010767;
                Award ID: 115010
                Award ID: 831434
                Funded by: Fifth Framework Programme, doi 10.13039/100011104;
                Award ID: QLG1‐CT‐2000‐01185
                Funded by: Stockholm County Council Research Funds (ALF)
                Funded by: Karolinska Institutet, doi 10.13039/501100004047;
                Funded by: Hjärt-Lungfonden, doi 10.13039/501100003793;
                Funded by: Bernard Osher Initiative for Severe Asthma
                Categories
                Original Research Articles
                Asthma
                2

                Respiratory medicine
                Respiratory medicine

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