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Mazio C, Scognamiglio LS, Casale C, Panzetta V, Urciuolo F, Galietta LJV, Imparato G, Netti PA. A functional 3D full-thickness model for comprehending the interaction between airway epithelium and connective tissue in cystic fibrosis. Biomaterials 2024; 308:122546. [PMID: 38552367 DOI: 10.1016/j.biomaterials.2024.122546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/22/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Patients with cystic fibrosis (CF) experience severe lung disease, including persistent infections, inflammation, and irreversible fibrotic remodeling of the airways. Although therapy with transmembrane conductance regulator (CFTR) protein modulators reached optimal results in terms of CFTR rescue, lung transplant remains the best line of care for patients in an advanced stage of CF. Indeed, chronic inflammation and tissue remodeling still represent stumbling blocks during treatment, and underlying mechanisms are still unclear. Nowadays, animal models are not able to fully replicate clinical features of the human disease and the conventional in vitro models lack a stromal compartment undergoing fibrotic remodeling. To address this gap, we show the development of a 3D full-thickness model of CF with a human bronchial epithelium differentiated on a connective airway tissue. We demonstrated that the epithelial cells not only underwent mucociliary differentiation but also migrated in the connective tissue and formed gland-like structures. The presence of the connective tissue stimulated the pro-inflammatory behaviour of the epithelium, which activated the fibroblasts embedded into their own extracellular matrix (ECM). By varying the composition of the model with CF epithelial cells and a CF or healthy connective tissue, it was possible to replicate different moments of CF disease, as demonstrated by the differences in the transcriptome of the CF epithelium in the different conditions. The possibility to faithfully represent the crosstalk between epithelial and connective in CF through the full thickness model, along with inflammation and stromal activation, makes the model suitable to better understand mechanisms of disease genesis, progression, and response to therapy.
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Affiliation(s)
- Claudia Mazio
- Istituto Italiano di Tecnologia-IIT, Center for Advanced Biomaterials for Healthcare, Largo Barsanti e Matteucci 53, 80125, Napoli, Italy
| | - Laura Sara Scognamiglio
- Istituto Italiano di Tecnologia-IIT, Center for Advanced Biomaterials for Healthcare, Largo Barsanti e Matteucci 53, 80125, Napoli, Italy
| | - Costantino Casale
- Interdisciplinary Research Centre on Biomaterials-CRIB, University of Napoli Federico II, P.le Tecchio 80, 80125, Napoli, Italy
| | - Valeria Panzetta
- Interdisciplinary Research Centre on Biomaterials-CRIB, University of Napoli Federico II, P.le Tecchio 80, 80125, Napoli, Italy; Department of Chemical, Materials and Industrial Production Engineering-DICMAPI, University of Naples Federico II, P.le Tecchio 80, 80125, Naples, Italy
| | - Francesco Urciuolo
- Interdisciplinary Research Centre on Biomaterials-CRIB, University of Napoli Federico II, P.le Tecchio 80, 80125, Napoli, Italy; Department of Chemical, Materials and Industrial Production Engineering-DICMAPI, University of Naples Federico II, P.le Tecchio 80, 80125, Naples, Italy
| | - Luis J V Galietta
- Telethon Institute of Genetics and Medicine-TIGEM, Via Campi Flegrei 34, 80078, Pozzuoli, NA, Italy
| | - Giorgia Imparato
- Istituto Italiano di Tecnologia-IIT, Center for Advanced Biomaterials for Healthcare, Largo Barsanti e Matteucci 53, 80125, Napoli, Italy.
| | - Paolo A Netti
- Istituto Italiano di Tecnologia-IIT, Center for Advanced Biomaterials for Healthcare, Largo Barsanti e Matteucci 53, 80125, Napoli, Italy; Interdisciplinary Research Centre on Biomaterials-CRIB, University of Napoli Federico II, P.le Tecchio 80, 80125, Napoli, Italy; Department of Chemical, Materials and Industrial Production Engineering-DICMAPI, University of Naples Federico II, P.le Tecchio 80, 80125, Naples, Italy
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2
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Perea L, Faner R, Chalmers JD, Sibila O. Pathophysiology and genomics of bronchiectasis. Eur Respir Rev 2024; 33:240055. [PMID: 38960613 PMCID: PMC11220622 DOI: 10.1183/16000617.0055-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30-40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
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Affiliation(s)
- Lidia Perea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Oriol Sibila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
- Respiratory Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
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3
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Yao Y, Yang Y, Wang J, Yu P, Guo J, Dong L, Wang C, Liu P, Zhang Y, Song X. Proteomic and metabolomic proof of concept for unified airways in chronic rhinosinusitis and asthma. Ann Allergy Asthma Immunol 2024; 132:713-722.e4. [PMID: 38382675 DOI: 10.1016/j.anai.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/28/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
BACKGROUND The pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) with comorbid asthma remains unclear. OBJECTIVE To assess upper and lower airway unity and identify a possible common pathogenesis in CRSwNP with asthma. METHODS This study analyzed the expression of proteins and metabolites in nasal lavage fluid cells (NLFCs) and induced sputum cells (ISCs). Differentially expressed proteins and their function-related metabolites in the upper and lower airways of patients having CRSwNP with or without asthma were identified; relevant signaling pathways were analyzed, and key pathway-related proteins were identified. Parallel reaction monitoring was used to verify these target proteins. RESULTS Protein or metabolite expression between NLFCs and ISCs was highly correlated and conservative on the basis of expression profiles and weighted gene coexpression network analysis. There were 17 differentially coexpressed proteins and their function-related 13 metabolites that were identified in the NLFCs and ISCs of CRSwNP, whereas 11 proteins and 11 metabolites were identified in CRSwNP with asthma. An asthma pathway was involved in the copathogenesis of upper and lower airways in whether CRSwNP or CRSwNP with asthma. The asthma pathway-related proteins proteoglycan 2 and eosinophil peroxidase, as the core of the protein-metabolism interaction networks between the upper and lower airways, were both highly coexpressed in NLFCs and ISCs in patients having either CRSwNP or CRSwNP with asthma by parallel reaction monitoring validation. CONCLUSION Proteomics and metabolomics reveal upper and lower airway unity. Asthma pathway-related proteins proteoglycan 2 and eosinophil peroxidase from the upper airway could be used to assess the potential risk of lower airway dysfunction in CRSwNP.
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Affiliation(s)
- Yao Yao
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Yujuan Yang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Jianwei Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Pengyi Yu
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Jing Guo
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Luchao Dong
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Cai Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Pengfei Liu
- Shanghai Applied Protein Technology Co, Ltd, Shanghai, People's Republic of China
| | - Yu Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China
| | - Xicheng Song
- Department of Otorhinolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, Shandong, People's Republic of China; Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai, Shandong, People's Republic of China.
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Ngo LT, Rekowski MJ, Koestler DC, Yorozuya T, Saito A, Azeem I, Harrison A, Demoruelle MK, Boomer J, England BR, Wolters P, Molyneaux PL, Castro M, Lee JS, Solomon JJ, Koronuma K, Washburn MP, Matson SM. Proteomic profiling of bronchoalveolar lavage fluid uncovers protein clusters linked to survival in idiopathic forms of interstitial lung disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.30.24308215. [PMID: 38853991 PMCID: PMC11160891 DOI: 10.1101/2024.05.30.24308215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Idiopathic interstitial pneumonias (IIPs) such as idiopathic pulmonary fibrosis (IPF) and interstitial pneumonia with autoimmune features (IPAF), present diagnostic and therapeutic challenges due to their heterogeneous nature. This study aimed to identify intrinsic molecular signatures within the lung microenvironment of these IIPs through proteomic analysis of bronchoalveolar lavage fluid (BALF). Methods Patients with IIP (n=23) underwent comprehensive clinical evaluation including pre-treatment bronchoscopy and were compared to controls without lung disease (n=5). Proteomic profiling of BALF was conducted using label-free quantitative methods. Unsupervised cluster analyses identified protein expression profiles which were then analyzed to predict survival outcomes and investigate associated pathways. Results Proteomic profiling successfully differentiated IIP from controls. k-means clustering, based on protein expression revealed three distinct IIP clusters, which were not associated with age, smoking history, or baseline pulmonary function. These clusters had unique survival trajectories and provided more accurate survival predictions than the Gender Age Physiology (GAP) index (C-index 0.794 vs. 0.709). The cluster with the worst prognosis featured decreased inflammatory signaling and complement activation, with pathway analysis highlighting altered immune response pathways related to immunoglobulin production and B cell-mediated immunity. Conclusions The unsupervised clustering of BALF proteomics provided a novel stratification of IIP patients, with potential implications for prognostic and therapeutic targeting. The identified molecular phenotypes underscore the diversity within the IIP classification and the potential importance of personalized treatments for these conditions. Future validation in larger, multi-ethnic cohorts is essential to confirm these findings and to explore their utility in clinical decision-making for patients with IIP.
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Affiliation(s)
- Linh T. Ngo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Michaella J. Rekowski
- Department of Cancer Biology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Takafumi Yorozuya
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Atsushi Saito
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Imaan Azeem
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Alexis Harrison
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - M. Kristen Demoruelle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jonathan Boomer
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Bryant R. England
- Division of Rheumatology & Immunology, University of Nebraska Medical Center, Omaha, NE USA and Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, USA
| | - Paul Wolters
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Joyce S. Lee
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Aurora, CO, USA
| | - Joshua J. Solomon
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health Hospital, Denver, CO
| | - Koji Koronuma
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Michael P. Washburn
- Department of Cancer Biology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Scott M. Matson
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
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5
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Abrami M, Biasin A, Tescione F, Tierno D, Dapas B, Carbone A, Grassi G, Conese M, Di Gioia S, Larobina D, Grassi M. Mucus Structure, Viscoelastic Properties, and Composition in Chronic Respiratory Diseases. Int J Mol Sci 2024; 25:1933. [PMID: 38339210 PMCID: PMC10856136 DOI: 10.3390/ijms25031933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
The respiratory mucus, a viscoelastic gel, effectuates a primary line of the airway defense when operated by the mucociliary clearance. In chronic respiratory diseases (CRDs), such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF), the mucus is overproduced and its solid content augments, changing its structure and viscoelastic properties and determining a derangement of essential defense mechanisms against opportunistic microbial (virus and bacteria) pathogens. This ensues in damaging of the airways, leading to a vicious cycle of obstruction and infection responsible for the harsh clinical evolution of these CRDs. Here, we review the essential features of normal and pathological mucus (i.e., sputum in CF, COPD, and asthma), i.e., mucin content, structure (mesh size), micro/macro-rheology, pH, and osmotic pressure, ending with the awareness that sputum biomarkers (mucins, inflammatory proteins and peptides, and metabolites) might serve to indicate acute exacerbation and response to therapies. There are some indications that old and novel treatments may change the structure, viscoelastic properties, and biomarker content of sputum; however, a wealth of work is still needed to embrace these measures as correlates of disease severity in association with (or even as substitutes of) pulmonary functional tests.
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Affiliation(s)
- Michela Abrami
- Department of Engineering and Architecture, University of Trieste, Via Valerio 6/A, I-34127 Trieste, Italy; (M.A.); (A.B.); (M.G.)
| | - Alice Biasin
- Department of Engineering and Architecture, University of Trieste, Via Valerio 6/A, I-34127 Trieste, Italy; (M.A.); (A.B.); (M.G.)
| | - Fabiana Tescione
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, P.le E. Fermi 1, I-80055 Portici, Italy; (F.T.); (D.L.)
| | - Domenico Tierno
- Clinical Department of Medical, Surgical and Health Sciences, Cattinara University Hospital, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.)
| | - Barbara Dapas
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy;
| | - Annalucia Carbone
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 121, I-71122 Foggia, Italy; (A.C.); (S.D.G.)
| | - Gabriele Grassi
- Clinical Department of Medical, Surgical and Health Sciences, Cattinara University Hospital, University of Trieste, Strada di Fiume 447, I-34149 Trieste, Italy; (D.T.); (G.G.)
| | - Massimo Conese
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 121, I-71122 Foggia, Italy; (A.C.); (S.D.G.)
| | - Sante Di Gioia
- Department of Clinical and Experimental Medicine, University of Foggia, Via Napoli 121, I-71122 Foggia, Italy; (A.C.); (S.D.G.)
| | - Domenico Larobina
- Institute of Polymers, Composites and Biomaterials, National Research Council of Italy, P.le E. Fermi 1, I-80055 Portici, Italy; (F.T.); (D.L.)
| | - Mario Grassi
- Department of Engineering and Architecture, University of Trieste, Via Valerio 6/A, I-34127 Trieste, Italy; (M.A.); (A.B.); (M.G.)
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O’Farrell HE, Kok HC, Goel S, Chang AB, Yerkovich ST. Endotypes of Paediatric Cough-Do They Exist and Finding New Techniques to Improve Clinical Outcomes. J Clin Med 2024; 13:756. [PMID: 38337450 PMCID: PMC10856076 DOI: 10.3390/jcm13030756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Chronic cough is a common symptom of many childhood lung conditions. Given the phenotypic heterogeneity of chronic cough, better characterization through endotyping is required to provide diagnostic certainty, precision therapies and to identify pathobiological mechanisms. This review summarizes recent endotype discoveries in airway diseases, particularly in relation to children, and describes the multi-omic approaches that are required to define endotypes. Potential biospecimens that may contribute to endotype and biomarker discoveries are also discussed. Identifying endotypes of chronic cough can likely provide personalized medicine and contribute to improved clinical outcomes for children.
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Affiliation(s)
- Hannah E. O’Farrell
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Hing Cheong Kok
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Department of Paediatrics, Sabah Women and Children’s Hospital, Kota Kinabalu 88996, Sabah, Malaysia
| | - Suhani Goel
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
| | - Anne B. Chang
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
- Department of Respiratory and Sleep Medicine, Queensland Children’s Hospital, Brisbane, QLD 4101, Australia
| | - Stephanie T. Yerkovich
- NHMRC Centre for Research Excellence in Paediatric Bronchiectasis (AusBREATHE), Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0810, Australia; (H.C.K.); (A.B.C.); (S.T.Y.)
- Australian Centre for Health Services Innovation, Queensland University of Technology, Brisbane, QLD 4000, Australia;
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Xuan N, Zhao J, Kang Z, Cui W, Tian BP. Neutrophil extracellular traps and their implications in airway inflammatory diseases. Front Med (Lausanne) 2024; 10:1331000. [PMID: 38283037 PMCID: PMC10811107 DOI: 10.3389/fmed.2023.1331000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024] Open
Abstract
Neutrophil extracellular traps (NETs) are essential for immune defense and have been increasingly recognized for their role in infection and inflammation. In the context of airway inflammatory diseases, there is growing evidence suggesting the involvement and significance of NETs. This review aims to provide an overview of the formation mechanisms and components of NETs and their impact on various airway inflammatory diseases, including acute lung injury/ARDS, asthma, chronic obstructive pulmonary disease (COPD) and cystic fibrosis. By understanding the role of NETs in airway inflammation, we can gain valuable insights into the underlying pathogenesis of these diseases and identify potential targets for future therapeutic strategies that either target NETs formation or modulate their harmful effects. Further research is warranted to elucidate the complex interactions between NETs and airway inflammation and to develop targeted therapies that can effectively mitigate their detrimental effects while preserving their beneficial functions in host defense.
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Affiliation(s)
- Nanxia Xuan
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Zhao
- Department of Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, China
| | - Zhiying Kang
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Cui
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bao-ping Tian
- Department of Critical Care Medicine, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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8
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Rezaeeyan H, Arabfard M, Rasouli HR, Shahriary A, Gh BFNM. Evaluation of common protein biomarkers involved in the pathogenesis of respiratory diseases with proteomic methods: A systematic review. Immun Inflamm Dis 2023; 11:e1090. [PMID: 38018577 PMCID: PMC10659759 DOI: 10.1002/iid3.1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 09/22/2023] [Accepted: 11/04/2023] [Indexed: 11/30/2023] Open
Abstract
AIM Respiratory disease (RD) is one of the most common diseases characterized by lung dysfunction. Many diagnostic mechanisms have been used to identify the pathogenic agents of responsible for RD. Among these, proteomics emerges as a valuable diagnostic method for pinpointing the specific proteins involved in RD pathogenesis. Therefore, in this study, for the first time, we examined the protein markers involved in the pathogenesis of chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), asthma, bronchiolitis obliterans (BO), and chemical warfare victims exposed to mustard gas, using the proteomics method as a systematic study. MATERIALS AND METHODS A systematic search was performed up to September 2023 on several databases, including PubMed, Scopus, ISI Web of Science, and Cochrane. In total, selected 4246 articles were for evaluation according to the criteria. Finally, 119 studies were selected for this systematic review. RESULTS A total of 13,806 proteins were identified, 6471 in COPD, 1603 in Asthma, 5638 in IPF, three in BO, and 91 in mustard gas exposed victims. Alterations in the expression of these proteins were observed in the respective diseases. After evaluation, the results showed that 31 proteins were found to be shared among all five diseases. CONCLUSION Although these 31 proteins regulate different factors and molecular pathways in all five diseases, they ultimately lead to the regulation of inflammatory pathways. In other words, the expression of some proteins in COPD and mustard-exposed patients increases inflammatory reactions, while in IPF, they cause lung fibrosis. Asthma, causes allergic reactions due to T-cell differentiation toward Th2.
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Affiliation(s)
- Hadi Rezaeeyan
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion MedicineIranian Blood Transfusion Organization (IBTO)TehranIran
| | - Masoud Arabfard
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - Hamid R. Rasouli
- Trauma Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Alireza Shahriary
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
| | - B. Fatemeh Nobakht M. Gh
- Chemical Injuries Research Center, Systems Biology and Poisonings InstituteBaqiyatallah University of Medical SciencesTehranIran
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9
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Martinu T, Todd JL, Gelman AE, Guerra S, Palmer SM. Club Cell Secretory Protein in Lung Disease: Emerging Concepts and Potential Therapeutics. Annu Rev Med 2023; 74:427-441. [PMID: 36450281 PMCID: PMC10472444 DOI: 10.1146/annurev-med-042921-123443] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Club cell secretory protein (CCSP), also known as secretoglobin 1A1 (gene name SCGB1A1), is one of the most abundant proteins in the lung, primarily produced by club cells of the distal airway epithelium. At baseline, CCSP is found in large concentrations in lung fluid specimens and can also be detected in the blood and urine. Obstructive lung diseases are generally associated with reduced CCSP levels, thought to be due to decreased CCSP production or club cell depletion. Conversely, several restrictive lung diseases have been found to have increased CCSP levels both in the lung and in the circulation, likely related to club cell dysregulation as well as increasedlung permeability. Recent studies demonstrate multiple mechanisms by which CCSP dampens acute and chronic lung inflammation. Given these anti-inflammatory effects, CCSP represents a novel potential therapeutic modality in lung disease.
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Affiliation(s)
- Tereza Martinu
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada;
- Division of Respirology, Department of Medicine, University Health Network, Toronto, Ontario, Canada
- Toronto Lung Transplant Program, Ajmera Transplant Centre, University Health Network, Toronto, Ontario, Canada
| | - Jamie L Todd
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Andrew E Gelman
- Department of Surgery, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, Arizona, USA
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Scott M Palmer
- Division of Pulmonary, Allergy and Critical Care, Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
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10
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Maher RE, Barrett E, Beynon RJ, Harman VM, Jones AM, McNamara PS, Smith JA, Lord RW. The relationship between lung disease severity and the sputum proteome in cystic fibrosis. Respir Med 2022; 204:107002. [DOI: 10.1016/j.rmed.2022.107002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 09/17/2022] [Accepted: 09/24/2022] [Indexed: 10/31/2022]
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11
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Zhai J, Emond MJ, Spangenberg A, Stern DA, Vasquez MM, Blue EE, Buckingham KJ, Sherrill DL, Halonen M, Gibson RL, Rosenfeld M, Sagel SD, Bamshad MJ, Morgan WJ, Guerra S. Club cell secretory protein and lung function in children with cystic fibrosis. J Cyst Fibros 2022; 21:811-820. [PMID: 35367162 PMCID: PMC9509401 DOI: 10.1016/j.jcf.2022.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/18/2022] [Accepted: 03/14/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Club cell secretory protein (CC16) exerts anti-inflammatory functions in lung disease. We sought to determine the relation of serum CC16 deficits and genetic variants that control serum CC16 to lung function among children with cystic fibrosis (CF). METHODS We used longitudinal data from CF children (EPIC Study) with no positive cultures for Pseudomonas aeruginosa prior to enrollment. Circulating levels of CC16 and an inflammatory score (generated from CRP, SAA, calprotectin, G-CSF) were compared between participants with the lowest and highest FEV1 levels in adolescence (LLF and HLF groups, respectively; N = 130-per-group). Single nucleotide variants (SNVs) in the SCGB1A1, EHF-APIP loci were tested for association with circulating CC16 and with decline of FEV1 and FEV1/FVC% predicted levels between ages 7-16 using mixed models. RESULTS Compared with the HLF group, the LLF group had lower levels of CC16 (geometric means: 8.2 vs 6.5 ng/ml, respectively; p = 0.0002) and higher levels of the normalized inflammatory score (-0.21 vs 0.21, p = 0.0007). Participants in the lowest CC16 and highest inflammation tertile had the highest odds for having LLF (p<0.0001 for comparison with participants in the highest CC16 and lowest inflammation tertile). Among seven SNVs associated with circulating CC16, the top SNV rs3741240 was associated with decline of FEV1/FVC and, marginally, FEV1 (p = 0.003 and 0.025, respectively; N = 611 participants, 20,801 lung function observations). CONCLUSIONS Serum CC16 deficits are strongly associated with severity of CF lung disease and their effects are additive with systemic inflammation. The rs3741240 A allele is associated with low circulating CC16 and, possibly, accelerated lung function decline in CF.
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Affiliation(s)
- Jing Zhai
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Mary J Emond
- Department of Biostatistics, University of Washington, Seattle, WA, United States
| | - Amber Spangenberg
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Debra A Stern
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Monica M Vasquez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Elizabeth E Blue
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, United States; Brotman-Baty Institute for Precision Medicine, Seattle, WA, United States
| | - Kati J Buckingham
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Duane L Sherrill
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Marilyn Halonen
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States
| | - Ronald L Gibson
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Margaret Rosenfeld
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, United States
| | - Scott D Sagel
- Department of Pediatrics, Children's Hospital Colorado and University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Michael J Bamshad
- Brotman-Baty Institute for Precision Medicine, Seattle, WA, United States; Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, United States; Department of Genome Sciences, University of Washington, Seattle, WA, United States
| | - Wayne J Morgan
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States; Department of Pediatrics, University of Arizona, Tucson, AZ, United States.
| | - Stefano Guerra
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States; Department of Medicine, University of Arizona, Tucson, AZ, United States.
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12
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Barta I, Paska C, Antus B. Sputum Cytokine Profiling in COPD: Comparison Between Stable Disease and Exacerbation. Int J Chron Obstruct Pulmon Dis 2022; 17:1897-1908. [PMID: 36017119 PMCID: PMC9397440 DOI: 10.2147/copd.s364982] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/21/2022] [Indexed: 12/03/2022] Open
Abstract
Purpose Cytokines are extracellular signaling proteins that have been widely implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). Here, we investigated cytokine expression both at the mRNA and protein level in the sputum of healthy individuals, stable COPD patients, and those experiencing a severe acute exacerbation (AECOPD) requiring hospitalization. Patients and Methods Sputum was collected in 19 healthy controls, 25 clinically stable COPD patients, and 31 patients with AECOPD. In AECOPD patients sample collection was performed both at the time of hospital admission and at discharge following treatment. Sputum supernatant was analyzed by an antibody microarray detecting 120 cytokines simultaneously, while the mRNA expression of 14 selected cytokines in sputum cells was investigated by real-time PCR (qPCR). Results Proteomic analysis identified interleukin (IL)-6 and growth-regulated oncogene (GRO)α as the only sputum cytokines that were differentially expressed between stable COPD patients and healthy controls. At the onset of AECOPD, several cytokines exhibited altered sputum expression compared to stable COPD. Recovery from AECOPD induced significant changes in the sputum cytokine protein profile; however, the length of hospitalization was insufficient for most cytokines to return to stable levels. With regard to gene expression analysis by qPCR, we found that bone morphogenetic protein (BMP)-4 was up-regulated, while IL-1α, monokine-induced by interferon-γ (MIG), and BMP-6 were down-regulated at the mRNA level in patients with AECOPD compared to stable disease. Conclusion The sputum cytokine signature of AECOPD differs from that of stable COPD. Protein level changes are asynchronous with changes in gene expression at the mRNA level in AECOPD. The observation that the levels of most cytokines do not stabilize with acute treatment of AECOPD suggests a prolonged effect of exacerbation on the status of COPD patients.
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Affiliation(s)
- Imre Barta
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Csilla Paska
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary
| | - Balazs Antus
- Department of Pathophysiology, National Koranyi Institute of Pulmonology, Budapest, Hungary.,Department of Pulmonology, National Koranyi Institute of Pulmonology, Budapest, Hungary
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13
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D’Amato M, Iadarola P, Viglio S. Proteomic Analysis of Human Sputum for the Diagnosis of Lung Disorders: Where Are We Today? Int J Mol Sci 2022; 23:ijms23105692. [PMID: 35628501 PMCID: PMC9144372 DOI: 10.3390/ijms23105692] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 05/13/2022] [Accepted: 05/18/2022] [Indexed: 02/07/2023] Open
Abstract
The identification of markers of inflammatory activity at the early stages of pulmonary diseases which share common characteristics that prevent their clear differentiation is of great significance to avoid misdiagnosis, and to understand the intrinsic molecular mechanism of the disorder. The combination of electrophoretic/chromatographic methods with mass spectrometry is currently a promising approach for the identification of candidate biomarkers of a disease. Since the fluid phase of sputum is a rich source of proteins which could provide an early diagnosis of specific lung disorders, it is frequently used in these studies. This report focuses on the state-of-the-art of the application, over the last ten years (2011-2021), of sputum proteomics in the investigation of severe lung disorders such as COPD; asthma; cystic fibrosis; lung cancer and those caused by COVID-19 infection. Analysis of the complete set of proteins found in sputum of patients affected by these disorders has allowed the identification of proteins whose levels change in response to the organism's condition. Understanding proteome dynamism may help in associating these proteins with alterations in the physiology or progression of diseases investigated.
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Affiliation(s)
- Maura D’Amato
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
| | - Paolo Iadarola
- Department of Biology and Biotechnologies “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy
- Correspondence:
| | - Simona Viglio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; (M.D.); (S.V.)
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14
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Hull RC, Huang JTJ, Barton AK, Keir HR, Ellis H, Cookson WOC, Moffatt MF, Loebinger MR, Chalmers JD. Sputum Proteomics in Nontuberculous Mycobacterial Lung Disease. Chest 2022; 161:1180-1191. [PMID: 34838525 DOI: 10.1016/j.chest.2021.11.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/30/2021] [Accepted: 11/06/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Nontuberculous mycobacterial (NTM) infections are difficult to diagnose and treat. Biomarkers to identify patients with active infection or at risk of disease progression would have clinical utility. Sputum is the most frequently used matrix for the diagnosis of NTM lung disease. RESEARCH QUESTION Can sputum proteomics be used to identify NTM-associated inflammatory profiles in sputum? STUDY DESIGN AND METHODS Patients with NTM lung disease and a matched cohort of patients with COPD, bronchiectasis (BE), and cystic fibrosis (CF) without NTM lung disease were enrolled from two hospitals in the United Kingdom. Liquid chromatography-tandem mass spectrometry was used to identify proteomic biomarkers associated with underlying diagnosis (COPD, BE, and CF), the presence of NTM lung disease defined according to American Thoracic Society/Infectious Diseases Society of America criteria, and severity of NTM. A subset of patients receiving guideline-concordant NTM treatment were studied to identify protein changes associated with treatment response. RESULTS This study analyzed 95 sputum samples from 55 subjects (BE, n = 21; COPD, n = 19; CF, n = 15). Underlying disease and infection with Pseudomonas aeruginosa were the strongest drivers of sputum protein profiles. Comparing protein abundance in COPD, BE, and CF found that 12 proteins were upregulated in CF compared with COPD, including MPO, AZU1, CTSG, CAT, and RNASE3, with 21 proteins downregulated, including SCGB1A1, IGFBP2, SFTPB, GC, and CFD. Across CF, BE, and COPD, NTM infection (n = 15) was not associated with statistically significant differences in sputum protein profiles compared with those without NTM. Two proteins associated with iron chelation were significantly downregulated in severe NTM disease. NTM treatment was associated with heterogeneous changes in the sputum protein profile. Patients with NTM and a decrease in immune response proteins had a subjective symptomatic improvement. INTERPRETATION Sputum proteomics identified candidate biomarkers of NTM severity and treatment response. However, underlying lung disease and typical bacterial pathogens such as P aeruginosa are also key determinants of the sputum proteomic profile.
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Affiliation(s)
- Rebecca C Hull
- Department of Infection, Immunity and Cardiovascular Diseases, University of Sheffield, Sheffield, United Kingdom; Florey Institute, University of Sheffield, Sheffield, United Kingdom
| | - Jeffrey T J Huang
- Division of Systems Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Alun K Barton
- Division of Systems Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Holly R Keir
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom
| | - Huw Ellis
- Royal Brompton and Harefield NHS Foundation Trust, London, England; National Heart and Lung Institute, Imperial College, London, England
| | - William O C Cookson
- Royal Brompton and Harefield NHS Foundation Trust, London, England; National Heart and Lung Institute, Imperial College, London, England
| | - Miriam F Moffatt
- Royal Brompton and Harefield NHS Foundation Trust, London, England; National Heart and Lung Institute, Imperial College, London, England
| | - Michael R Loebinger
- Royal Brompton and Harefield NHS Foundation Trust, London, England; National Heart and Lung Institute, Imperial College, London, England
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, University of Dundee, Ninewells Hospital and Medical School, Dundee, Scotland, United Kingdom.
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15
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Keir HR, Chalmers JD. Neutrophil extracellular traps in chronic lung disease: implications for pathogenesis and therapy. Eur Respir Rev 2022; 31:31/163/210241. [PMID: 35197267 PMCID: PMC9488971 DOI: 10.1183/16000617.0241-2021] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 12/20/2022] Open
Abstract
Neutrophilic inflammation has a key role in the pathophysiology of multiple chronic lung diseases. The formation of neutrophil extracellular traps (NETs) has emerged as a key mechanism of disease in neutrophilic lung diseases including asthma, COPD, cystic fibrosis and, most recently, bronchiectasis. NETs are large, web-like structures composed of DNA and anti-microbial proteins that are able to bind pathogens, prevent microbial dissemination and degrade bacterial virulence factors. The release of excess concentrations of proteases, antimicrobial proteins, DNA and histones, however, also leads to tissue damage, impaired mucociliary clearance, impaired bacterial killing and increased inflammation. A number of studies have linked airway NET formation with greater disease severity, increased exacerbations and overall worse disease outcomes across the spectrum of airway diseases. Treating neutrophilic inflammation has been challenging in chronic lung disease because of the delicate balance between reducing inflammation and increasing the risk of infections through immunosuppression. Novel approaches to suppressing NET formation or the associated inflammation are in development and represent an important therapeutic target. This review will discuss the relationship between NETs and the pathophysiology of cystic fibrosis, asthma, COPD and bronchiectasis, and explore the current and future development of NET-targeting therapies. NETs contribute to the pathophysiology of chronic lung disease. Immunomodulating therapies that may reduce inflammatory mediators and NET formation, without compromising bacterial clearance, offer a new treatment path for patients. https://bit.ly/3fyJC6I
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Affiliation(s)
- Holly R Keir
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, UK
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, Dundee, UK
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16
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Shao D, Huang L, Wang Y, Cui X, Li Y, Wang Y, Ma Q, Du W, Cui J. HBFP: a new repository for human body fluid proteome. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6395039. [PMID: 34642750 PMCID: PMC8516408 DOI: 10.1093/database/baab065] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/23/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022]
Abstract
Body fluid proteome has been intensively studied as a primary source for disease
biomarker discovery. Using advanced proteomics technologies, early research
success has resulted in increasingly accumulated proteins detected in different
body fluids, among which many are promising biomarkers. However, despite a
handful of small-scale and specific data resources, current research is clearly
lacking effort compiling published body fluid proteins into a centralized and
sustainable repository that can provide users with systematic analytic tools. In
this study, we developed a new database of human body fluid proteome (HBFP) that
focuses on experimentally validated proteome in 17 types of human body fluids.
The current database archives 11 827 unique proteins reported by 164
scientific publications, with a maximal false discovery rate of 0.01 on both the
peptide and protein levels since 2001, and enables users to query, analyze and
download protein entries with respect to each body fluid. Three unique features
of this new system include the following: (i) the protein annotation page
includes detailed abundance information based on relative qualitative measures
of peptides reported in the original references, (ii) a new score is calculated
on each reported protein to indicate the discovery confidence and (iii) HBFP
catalogs 7354 proteins with at least two non-nested uniquely mapping peptides of
nine amino acids according to the Human Proteome Project Data Interpretation
Guidelines, while the remaining 4473 proteins have more than two unique peptides
without given sequence information. As an important resource for human protein
secretome, we anticipate that this new HBFP database can be a powerful tool that
facilitates research in clinical proteomics and biomarker discovery. Database URL:https://bmbl.bmi.osumc.edu/HBFP/
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Affiliation(s)
- Dan Shao
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA.,Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China.,Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Lan Huang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Yan Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Xueteng Cui
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yufei Li
- Department of Computer Science and Technology, Changchun University, 6543 Weixing Road, Changchun 130022, China
| | - Yao Wang
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qin Ma
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, 310G Lincoln tower, 1800 cannon drive, Columbus, OH 43210, USA
| | - Wei Du
- Key Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Juan Cui
- Department of Computer Science and Engineering, University of Nebraska-Lincoln, 122E Avery Hall, 1144 T St., Lincoln, NE 68588, USA
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17
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Dasgupta A, Chakraborty R, Saha B, Suri H, Singh P, Raj A, Taneja B, Dash D, Sengupta S, Agrawal A. Sputum Protein Biomarkers in Airway Diseases: A Pilot Study. Int J Chron Obstruct Pulmon Dis 2021; 16:2203-2215. [PMID: 34349506 PMCID: PMC8326773 DOI: 10.2147/copd.s306035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 05/04/2021] [Indexed: 01/31/2023] Open
Abstract
Background Chronic mucous hypersecretion (CMH or chronic bronchitis) per se or when associated with chronic inflammatory airway diseases such as asthma or chronic obstructive pulmonary disease (COPD) has several adverse clinical consequences. The sputum fluid phase has several candidate proteins including mucins which have the potential of being therapeutic targets, but has not yet been explored in-depth. This study aimed at exploring the profile of sputum proteins in various airway diseases. Methods Sputum from thirty-one patients with various airway diseases was collected and the fluid phase analyzed by LC-MS/MS and subsequently by sequential window acquisition of all theoretical fragments ion spectra (SWATH) (n = 15) for protein quantitation. Hierarchical clustering and functional grouping were performed. Results A total of 185 proteins were quantitated by SWATH of which 21 proteins were identified which could distinguish between the clinical phenotypes by hierarchical clustering. Functional protein clustering revealed 4 groups: those that are inflammation related, oxidative stress related, mucin related and a cytoskeletal and calcium related group. The levels of eight proteins (Azurocidin1, Neutrophil defensin 3, Lactotransferrin, Calmodulin 3, Coronin1A, Mucin 5B, Mucin 5AC and BPI fold containing family B1) were significantly altered (relative to mean) in exacerbator prone subjects compared to nonexacerbators. Another simple but useful metric which emerged from this study was total protein concentration in sputum which was significantly higher in frequent exacerbators. Conclusion Sputum proteins can detect the various airway disease clinical phenotypes. Total protein concentration and eight other proteins are biomarkers for frequent exacerbators. The clinical and therapeutic implications of the functional groups of proteins need further evaluation.
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Affiliation(s)
- Angira Dasgupta
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India.,B R Singh Hospital and Centre for Medical Education and Research, Kolkata, West Bengal, India
| | - Rahul Chakraborty
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
| | | | - Himanshi Suri
- Institute of Genomics and Integrative Biology, New Delhi, India
| | - Praveen Singh
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
| | - Anurag Raj
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
| | - Bhupesh Taneja
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
| | - Debasis Dash
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
| | - Shantanu Sengupta
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
| | - Anurag Agrawal
- Institute of Genomics and Integrative Biology, New Delhi, India.,Academy of Scientific and Innovative Research, CSIR-HRDG, Ghaziabad, Uttar Pradesh, 201002, India
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18
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Perkins TN, Oury TD. The perplexing role of RAGE in pulmonary fibrosis: causality or casualty? Ther Adv Respir Dis 2021; 15:17534666211016071. [PMID: 34275342 PMCID: PMC8293846 DOI: 10.1177/17534666211016071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease in which most patients die within 3 years of diagnosis. With an unknown etiology, IPF results in progressive fibrosis of the lung parenchyma, diminishing normal lung function, which results in respiratory failure, and eventually, death. While few therapies are available to reduce disease progression, patients continue to advance toward respiratory failure, leaving lung transplantation the only viable option for survival. As incidence and mortality rates steadily increase, the need for novel therapeutics is imperative. The receptor for advanced glycation endproducts (RAGE) is most highly expressed in the lungs and plays a significant role in a number of chronic lung diseases. RAGE has long been linked to IPF; however, confounding data from both human and experimental studies have left an incomplete and perplexing story. This review examines the present understanding of the role of RAGE in human and experimental models of IPF, drawing parallels to recent advances in RAGE biology. Moreover, this review discusses the role of RAGE in lung injury response, type 2 immunity, and cellular senescence, and how such mechanisms may relate to RAGE as both a biomarker of disease progression and potential therapeutic target in IPF.The reviews of this paper are available via the supplemental material section.
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Affiliation(s)
- Timothy N Perkins
- Department of Pathology, University of Pittsburgh School of Medicine, 3550 Terrace Street, S-784 Scaife Hall, Pittsburgh, PA 15261, USA
| | - Tim D Oury
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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19
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Abstract
Bronchiectasis is a complex, heterogeneous disorder defined by both a radiological abnormality of permanent bronchial dilatation and a clinical syndrome. There are multiple underlying causes including severe infections, mycobacterial disease, autoimmune conditions, hypersensitivity disorders, and genetic conditions. The pathophysiology of disease is understood in terms of interdependent concepts of chronic infection, inflammation, impaired mucociliary clearance, and structural lung damage. Neutrophilic inflammation is characteristic of the disease, with elevated levels of harmful proteases such as neutrophil elastase associated with worse outcomes. Recent data show that neutrophil extracellular trap formation may be the key mechanism leading to protease release and severe bronchiectasis. Despite the dominant of neutrophilic disease, eosinophilic subtypes are recognized and may require specific treatments. Neutrophilic inflammation is associated with elevated bacterial loads and chronic infection with organisms such as Pseudomonas aeruginosa. Loss of diversity of the normal lung microbiota and dominance of proteobacteria such as Pseudomonas and Haemophilus are features of severe bronchiectasis and link to poor outcomes. Ciliary dysfunction is also a key feature, exemplified by the rare genetic syndrome of primary ciliary dyskinesia. Mucus symptoms arise through goblet cell hyperplasia and metaplasia and reduced ciliary function through dyskinesia and loss of ciliated cells. The contribution of chronic inflammation, infection, and mucus obstruction leads to progressive structural lung damage. The heterogeneity of the disease is the most challenging aspect of management. An understanding of the pathophysiology of disease and their biomarkers can help to guide personalized medicine approaches utilizing the concept of "treatable traits."
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Affiliation(s)
- Holly R Keir
- Scottish Centre for Respiratory Research, University of Dundee, Dundee, United Kingdom
| | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Dundee, United Kingdom
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20
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Tanaka K, Enomoto N, Hozumi H, Isayama T, Naoi H, Aono Y, Katsumata M, Yasui H, Karayama M, Suzuki Y, Furuhashi K, Fujisawa T, Inui N, Nakamura Y, Suda T. Serum S100A8 and S100A9 as prognostic biomarkers in acute exacerbation of idiopathic pulmonary fibrosis. Respir Investig 2021; 59:827-836. [PMID: 34154976 DOI: 10.1016/j.resinv.2021.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/16/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
BACKGROUND Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) is a devastating and life-threatening condition during its clinical course. Biomarkers for precisely anticipating the prognosis of AE-IPF remain to be fully established. The objective of this study was to clarify whether S100A8 and S100A9, which are calcium-binding proteins mainly produced by activated neutrophils, are significant prognostic biomarkers in AE-IPF. METHODS Thirty-seven patients with AE-IPF who were diagnosed and treated at our hospital were retrospectively evaluated. The serum levels of S100A8 and S100A9 were measured using enzyme-linked immunosorbent assay, and the relationships between these levels and clinical parameters or prognosis were evaluated. RESULTS The serum levels of S100A8 (median 386.5 ng/mL) and S100A9 (median 60.2 ng/mL) in patients with AE-IPF were significantly higher than those in age-matched healthy controls and in patients at IPF diagnosis (p < 0.001 for all combinations). The serum levels of S100A8 negatively correlated with percent forced vital capacity (r = -0.356, p = 0.049) and positively correlated with peripheral white blood cell number (r = 0.509, p = 0.002). Immunohistochemical staining of autopsy lung specimens showed that neutrophils, present mainly in the alveolar septum, were positive for S100A8 and S100A9. Patients with AE-IPF with higher levels of S100A8 or S100A9 showed significantly worse 3-month survival than those with lower levels (log-rank test, both p = 0.028). Finally, in multivariate analysis, the serum levels of both S100A8 and S100A9 were significant prognostic factors (hazard ratio 4.032, p = 0.023 and hazard ratio 4.327, p = 0.012). CONCLUSION The serum levels of S100A8 and S100A9 at AE were significant prognostic biomarkers in patients with AE-IPF.
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Affiliation(s)
- Kazuki Tanaka
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Noriyuki Enomoto
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan; Health Administration Center, Hamamatsu University School of Medicine, Hamamatsu, Japan.
| | - Hironao Hozumi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takuya Isayama
- Medical & Biological Laboratories Co., Ltd., Nagoya, Japan
| | - Hyogo Naoi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuya Aono
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Mineo Katsumata
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hideki Yasui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Masato Karayama
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuzo Suzuki
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuki Furuhashi
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tomoyuki Fujisawa
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Naoki Inui
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan; Department of Clinical Pharmacology and Therapeutics, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yutaro Nakamura
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Takafumi Suda
- Second Division, Department of Internal Medicine, Hamamatsu University School of Medicine, Hamamatsu, Japan
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21
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Calprotectin-Mediated Zinc Chelation Inhibits Pseudomonas aeruginosa Protease Activity in Cystic Fibrosis Sputum. J Bacteriol 2021; 203:e0010021. [PMID: 33927050 DOI: 10.1128/jb.00100-21] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pseudomonas aeruginosa induces pathways indicative of low zinc availability in the cystic fibrosis (CF) lung environment. To learn more about P. aeruginosa zinc access in CF, we grew P. aeruginosa strain PAO1 directly in expectorated CF sputum. The P. aeruginosa Zur transcriptional repressor controls the response to low intracellular zinc, and we used the NanoString methodology to monitor levels of Zur-regulated transcripts, including those encoding a zincophore system, a zinc importer, and paralogs of zinc containing proteins that do not require zinc for activity. Zur-controlled transcripts were induced in sputum-grown P. aeruginosa compared to those grown in control cultures but not if the sputum was amended with zinc. Amendment of sputum with ferrous iron did not reduce expression of Zur-regulated genes. A reporter fusion to a Zur-regulated promoter had variable activity in P. aeruginosa grown in sputum from different donors, and this variation inversely correlated with sputum zinc concentrations. Recombinant human calprotectin (CP), a divalent-metal binding protein released by neutrophils, was sufficient to induce a zinc starvation response in P. aeruginosa grown in laboratory medium or zinc-amended CF sputum, indicating that CP is functional in the sputum environment. Zinc metalloproteases comprise a large fraction of secreted zinc-binding P. aeruginosa proteins. Here, we show that recombinant CP inhibited both LasB-mediated casein degradation and LasA-mediated lysis of Staphylococcus aureus, which was reversible with added zinc. These studies reveal the potential for CP-mediated zinc chelation to posttranslationally inhibit zinc metalloprotease activity and thereby affect the protease-dependent physiology and/or virulence of P. aeruginosa in the CF lung environment. IMPORTANCE The factors that contribute to worse outcomes in individuals with cystic fibrosis (CF) with chronic Pseudomonas aeruginosa infections are not well understood. Therefore, there is a need to understand environmental factors within the CF airway that contribute to P. aeruginosa colonization and infection. We demonstrate that growing bacteria in CF sputum induces a zinc starvation response that inversely correlates with sputum zinc levels. Additionally, both calprotectin and a chemical zinc chelator inhibit the proteolytic activities of LasA and LasB proteases, suggesting that extracellular zinc chelators can influence proteolytic activity and thus P. aeruginosa virulence and nutrient acquisition in vivo.
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22
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Chatziparasidis G, Kantar A. Calprotectin: An Ignored Biomarker of Neutrophilia in Pediatric Respiratory Diseases. CHILDREN-BASEL 2021; 8:children8060428. [PMID: 34063831 PMCID: PMC8223968 DOI: 10.3390/children8060428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/18/2021] [Accepted: 05/19/2021] [Indexed: 12/20/2022]
Abstract
Calprotectin (CP) is a non-covalent heterodimer formed by the subunits S100A8 (A8) and S100A9 (A9). When neutrophils become activated, undergo disruption, or die, this abundant cytosolic neutrophil protein is released. By fervently chelating trace metal ions that are essential for bacterial development, CP plays an important role in human innate immunity. It also serves as an alarmin by controlling the inflammatory response after it is released. Extracellular concentrations of CP increase in response to infection and inflammation, and are used as a biomarker of neutrophil activation in a variety of inflammatory diseases. Although it has been almost 40 years since CP was discovered, its use in daily pediatric practice is still limited. Current evidence suggests that CP could be used as a biomarker in a variety of pediatric respiratory diseases, and could become a valuable key factor in promoting diagnostic and therapeutic capacity. The aim of this study is to re-introduce CP to the medical community and to emphasize its potential role with the hope of integrating it as a useful adjunct, in the practice of pediatric respiratory medicine.
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Affiliation(s)
| | - Ahmad Kantar
- Pediatric Asthma and Cough Centre, Instituti Ospedalieri Bergamaschi, University and Research Hospitals, 24046 Bergamo, Italy
- Correspondence:
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23
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Perkins TN, Donnell ML, Oury TD. The axis of the receptor for advanced glycation endproducts in asthma and allergic airway disease. Allergy 2021; 76:1350-1366. [PMID: 32976640 DOI: 10.1111/all.14600] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 08/31/2020] [Accepted: 09/14/2020] [Indexed: 12/11/2022]
Abstract
Asthma is a generalized term that describes a scope of distinct pathologic phenotypes of variable severity, which share a common complication of reversible airflow obstruction. Asthma is estimated to affect almost 400 million people worldwide, and nearly ten percent of asthmatics have what is considered "severe" disease. The majority of moderate to severe asthmatics present with a "type 2-high" (T2-hi) phenotypic signature, which pathologically is driven by the type 2 cytokines Interleukin-(IL)-4, IL-5, and IL-13. However, "type 2-low" (T2-lo) phenotypic signatures are often associated with more severe, steroid-refractory neutrophilic asthma. A wide range of clinical and experimental studies have found that the receptor for advanced glycation endproducts (RAGE) plays a significant role in the pathogenesis of asthma and allergic airway disease (AAD). Current experimental data indicates that RAGE is a critical mediator of the type 2 inflammatory reactions which drive the development of T2-hi AAD. However, clinical studies demonstrate that increased RAGE ligands and signaling strongly correlate with asthma severity, especially in severe neutrophilic asthma. This review presents an overview of the current understandings of RAGE in asthma pathogenesis, its role as a biomarker of disease, and future implications for mechanistic studies, and potential therapeutic intervention strategies.
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Affiliation(s)
- Timothy N. Perkins
- Department of Pathology University of Pittsburgh School of Medicine Pittsburgh PA USA
| | - Mason L. Donnell
- Department of Pathology University of Pittsburgh School of Medicine Pittsburgh PA USA
| | - Tim D. Oury
- Department of Pathology University of Pittsburgh School of Medicine Pittsburgh PA USA
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24
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Dao TL, Hoang VT, Ly TDA, Lagier JC, Baron SA, Raoult D, Parola P, Courjon J, Marty P, Chaudet H, Gautret P. Sputum proteomic analysis for distinguishing between pulmonary tuberculosis and non-tuberculosis using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS): preliminary results. Clin Microbiol Infect 2021; 27:1694.e1-1694.e6. [PMID: 33711448 DOI: 10.1016/j.cmi.2021.02.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 11/24/2022]
Abstract
OBJECTIVES The aim was to evaluate the feasibility and diagnostic contribution of protein profiling using matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) applied to sputum to diagnose pulmonary tuberculosis. METHODS Sputum samples collected from patients suspected of having pulmonary tuberculosis were analysed using MALDI-TOF MS. Using the differentially expressed protein peaks, we compared three groups of patients, including those with confirmed pulmonary tuberculosis (PTB), those without tuberculosis but with a lower respiratory tract infection (non-TB LRTI) and those without tuberculosis and without an LRTI (non-TB controls). RESULTS A total of 102 patients included 35 PTB, 36 non-TB LRTI and 31 non-TB controls. The model differentiated between the PTB patients and the non-TB controls using the 25 most differentially expressed protein peaks, with a sensitivity of 97%, 95% CI 85-100%, and a specificity of 77%, 95% CI 59-90%. The model distinguished the PTB patients from the non-TB LRTI patients using the ten most differentially expressed protein peaks, with a sensitivity of 80%, 95% CI 63-92%, and a specificity of 89%, 95% CI 74-97%. We observed that the negative predictive value of MALDI-TOF MS sputum analysis was higher (96%, 95% CI 80-100%) than that of direct sputum microscopic examination and sputum culture (78%, 95% CI 62-89%) for non-TB controls. When MALDI-TOF MS sputum analysis and direct microscopic examination were combined, the negative predictive value reached 94%, 95% CI 80-99%, for non-TB LRTI patients. DISCUSSION These results suggest that MALDI-TOF MS sputum analysis coupled with microscopic examination could be used as a screening tool for diagnosing pulmonary TB.
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Affiliation(s)
- Thi Loi Dao
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Van Thuan Hoang
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France; Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | - Tran Duc Anh Ly
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Jean Christophe Lagier
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - Sophie Alexandra Baron
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - Didier Raoult
- IHU-Méditerranée Infection, Marseille, France; Aix Marseille Université, IRD, AP-HM, MEPHI, Marseille, France
| | - Philippe Parola
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Johan Courjon
- Université Côte d'Azur, U1065, Centre Méditerranéen de Médecine Moléculaire, C3M, Virulence Microbienne et Signalisation Inflammatoire, Inserm, Nice, France; Infectiologie, Hôpital de l'Archet, Centre Hospitalier Universitaire de Nice, Nice, France
| | - Pierre Marty
- Université Côte d'Azur, Inserm, C3M, Nice, France; Parasitologie-Mycologie, Centre Hospitalier Universitaire l'Archet, Nice, France
| | - Hervé Chaudet
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Philippe Gautret
- Aix Marseille Université, IRD, AP-HM, SSA, VITROME, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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25
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Sputum Proteome Signatures of Mechanically Ventilated Intensive Care Unit Patients Distinguish Samples with or without Anti-pneumococcal Activity. mSystems 2021; 6:6/2/e00702-20. [PMID: 33653939 PMCID: PMC8546979 DOI: 10.1128/msystems.00702-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mechanically ventilated patients are at risk of contracting pneumonia. Therefore, these patients often receive prophylactic systemic antimicrobial therapy. Intriguingly however, a previous study showed that antimicrobial activity in bronchoalveolar aspirates (here referred to as “sputa”) from ventilated patients was only partially explained by antibiotic therapy. Here we report that sputa from these patients presented distinct proteome signatures depending on the presence or absence of antimicrobial activity. Moreover, we show that the same distinction applied to antibodies against Streptococcus pneumoniae, which is a major causative agent of pneumonia. Specifically, the investigated sputa that inhibited growth of S. pneumoniae, while containing subinhibitory levels of the antibiotic cefotaxime, presented elevated levels of proteins implicated in innate immune defenses, including complement and apolipoprotein-associated proteins. In contrast, S. pneumoniae-inhibiting sputa with relatively high cefotaxime concentrations or noninhibiting sputa contained higher levels of proteins involved in inflammatory responses, such as neutrophil elastase-associated proteins. In an immunoproteomics analysis, 18 out of 55 S. pneumoniae antigens tested showed significantly increased levels of IgGs in inhibiting sputa. Hence, proteomics and immunoproteomics revealed elevated levels of antimicrobial host proteins or S. pneumoniae antigen-specific IgGs in pneumococcal growth-inhibiting sputa, thus explaining their anti-pneumococcal activity. IMPORTANCE Respiratory pathogens like Streptococcus pneumoniae can cause severe pneumonia. Nonetheless, mechanically ventilated intensive care patients, who have a high risk of contracting pneumonia, rarely develop pneumococcal pneumonia. This suggests the presence of potentially protective antimicrobial agents in their lung environment. Our present study shows for the first time that bronchoalveolar aspirates, “sputa,” of ventilated patients in a Dutch intensive care unit were characterized by three distinct groups of proteome abundance signatures that can explain their anti-pneumococcal activity. Importantly, this anti-pneumococcal sputum activity was related either to elevated levels of antimicrobial host proteins or to antibiotics and S. pneumoniae-specific antibodies. Further, the sputum composition of some patients changed over time. Therefore, we conclude that our study may provide a novel tool to measure changes that are indicative of infection-related conditions in the lungs of mechanically ventilated patients.
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26
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Kotsiou OS, Papagiannis D, Papadopoulou R, Gourgoulianis KI. Calprotectin in Lung Diseases. Int J Mol Sci 2021; 22:ijms22041706. [PMID: 33567747 PMCID: PMC7915440 DOI: 10.3390/ijms22041706] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/31/2021] [Accepted: 02/04/2021] [Indexed: 12/14/2022] Open
Abstract
Calprotectin (CLP) is a heterodimer formed by two S-100 calcium-binding cytosolic proteins, S100A8 and S100A9. It is a multifunctional protein expressed mainly by neutrophils and released extracellularly by activated or damaged cells mediating a broad range of physiological and pathological responses. It has been more than 20 years since the implication of S100A8/A9 in the inflammatory process was shown; however, the evaluation of its role in the pathogenesis of respiratory diseases or its usefulness as a biomarker for the appropriate diagnosis and prognosis of lung diseases have only gained attention in recent years. This review aimed to provide current knowledge regarding the potential role of CLP in the pathophysiology of lung diseases and describe how this knowledge is, up until now, translated into daily clinical practice. CLP is involved in numerous cellular processes in lung health and disease. In addition to its anti-microbial functions, CLP also serves as a molecule with pro- and anti-tumor properties related to cell survival and growth, angiogenesis, DNA damage response, and the remodeling of the extracellular matrix. The findings of this review potentially introduce CLP in daily clinical practice within the spectrum of respiratory diseases.
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Affiliation(s)
- Ourania S. Kotsiou
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece;
- Department of Nursing, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece;
- Correspondence:
| | - Dimitrios Papagiannis
- Department of Nursing, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece;
| | - Rodanthi Papadopoulou
- Human Nutrition, School of Medicine, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow Royal Infirmary, Glasgow G31 2ER, UK;
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27
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Gillan JL, Davidson DJ, Gray RD. Targeting cystic fibrosis inflammation in the age of CFTR modulators: focus on macrophages. Eur Respir J 2020; 57:13993003.03502-2020. [PMID: 33303535 DOI: 10.1183/13993003.03502-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/18/2020] [Indexed: 11/05/2022]
Abstract
Cystic fibrosis (CF) is a life-shortening, multi-organ, autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The most prominent clinical manifestation in CF is the development of progressive lung disease characterised by an intense, chronic inflammatory airway response that culminates in respiratory failure and, ultimately, death. In recent years, a new class of therapeutics that have the potential to correct the underlying defect in CF, known as CFTR modulators, have revolutionised the field. Despite the exciting success of these drugs, their impact on airway inflammation, and its long-term consequences, remains undetermined. In addition, studies querying the absolute requirement for infection as a driver of CF inflammation have challenged the traditional consensus on CF pathogenesis, and also emphasise the need to prioritise complementary anti-inflammatory treatments in CF. Macrophages, often overlooked in CF research despite their integral role in other chronic inflammatory pathologies, have increasingly become recognised as key players in the initiation, perpetuation and resolution of CF lung inflammation, perhaps as a direct result of CFTR dysfunction. These findings suggest that macrophages may be an important target for novel anti-inflammatory interventional strategies to effectively treat CF lung function decline. This review will consider evidence for the efficacy of anti-inflammatory drugs in the treatment of CF, the potential role of macrophages, and the significance of targeting these pathways at a time when rectifying the basic defect in CF, through use of novel CFTR modulator therapies, is becoming increasingly viable.
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Affiliation(s)
- Jonathan L Gillan
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK
| | - Donald J Davidson
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK
| | - Robert D Gray
- University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, Edinburgh, UK
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28
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Guerrero CR, Maier LA, Griffin TJ, Higgins L, Najt CP, Perlman DM, Bhargava M. Application of Proteomics in Sarcoidosis. Am J Respir Cell Mol Biol 2020; 63:727-738. [PMID: 32804537 DOI: 10.1165/rcmb.2020-0070ps] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 08/17/2020] [Indexed: 02/03/2023] Open
Abstract
Sarcoidosis is a multisystem disease with heterogeneity in manifestations and outcomes. System-level studies leveraging "omics" technologies are expected to define mechanisms contributing to sarcoidosis heterogeneous manifestations and course. With improvements in mass spectrometry (MS) and bioinformatics, it is possible to study protein abundance for a large number of proteins simultaneously. Contemporary fast-scanning MS enables the acquisition of spectral data for deep coverage of the proteins with data-dependent or data-independent acquisition MS modes. Studies leveraging MS-based proteomics in sarcoidosis have characterized BAL fluid (BALF), alveolar macrophages, plasma, and exosomes. These studies identified several differentially expressed proteins, including protocadherin-2 precursor, annexin A2, pulmonary surfactant A2, complement factors C3, vitamin-D-binding protein, cystatin B, and amyloid P, comparing subjects with sarcoidosis with control subjects. Other studies identified ceruloplasmin, complement factors B, C3, and 1, and others with differential abundance in sarcoidosis compared with other interstitial lung diseases. Using quantitative proteomics, most recent studies found differences in PI3K/Akt/mTOR, MAP kinase, pluripotency-associated transcriptional factor, and hypoxia response pathways. Other studies identified increased clathrin-mediated endocytosis and Fcγ receptor-mediated phagocytosis pathways in sarcoidosis alveolar macrophages. Although studies in mixed BAL and blood cells or plasma are limited, some of the changes in lung compartment are detected in the blood cells and plasma. We review proteomics for sarcoidosis with a focus on the existing MS data acquisition strategies, bioinformatics for spectral data analysis to infer protein identity and quantity, unique aspects about biospecimen collection and processing for lung-related proteomics, and proteomics studies conducted to date in sarcoidosis.
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Affiliation(s)
- Candance R Guerrero
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - Lisa A Maier
- Division of Environmental and Occupational Health Sciences, National Jewish Health, Denver, Colorado
| | - Timothy J Griffin
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - Charles P Najt
- Department of Biochemistry, Molecular Biology, and Biophysics, College of Biological Sciences and
| | - David M Perlman
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota; and
| | - Maneesh Bhargava
- Division of Pulmonary, Critical Care, and Sleep Medicine, University of Minnesota, Minneapolis, Minnesota; and
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29
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Lee YG, Hong J, Lee PH, Lee J, Park SW, Kim D, Jang AS. Serum Calprotectin Is a Potential Marker in Patients with Asthma. J Korean Med Sci 2020; 35:e362. [PMID: 33169556 PMCID: PMC7653171 DOI: 10.3346/jkms.2020.35.e362] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/24/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Calprotectin is the major cytosolic protein in neutrophil granulocytes. Although asthma is known to cause eosinophilic inflammation, some patients with asthma have non-eosinophilic inflammation, which is characterized by local neutrophilic inflammation. The aim of this study was to assess calprotectin expression levels in a mouse model of asthma, and to observe the relationship of serum calprotectin level and clinical variables in patients with asthma. METHODS Mice were sensitized and challenged with 10 μg and 20 μg of Aspergillus fumigatus, respectively; mice treated with saline were used as a control. The levels of calprotectin were determined using enzyme-linked immunosorbent assay, immunoblotting, and immunohistochemical analysis. The serum levels of calprotectin were also assessed in patients with asthma. The relationship between calprotectin and clinicopathological characteristics was determined. RESULTS Calprotectin, S100A8, and S100A9 expression was elevated in the mouse lungs, calprotectin levels were higher in the serum of patients with asthma (n = 33) compared with those of healthy individuals (n = 28). Calprotectin levels correlated with forced expiratory volume in one second/forced vital capacity (r = -0.215, P = 0.043), smoke amount (r = 0.413, P = 0.017), body mass index (r = -0.445, P = 0.000), and blood neutrophil percentage (r = 0.300, P = 0.004) in patients with asthma. CONCLUSION Our data suggest that calprotectin could potentially be used as a biomarker for asthma.
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Affiliation(s)
- Yun Gi Lee
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Jisu Hong
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Pureun Haneul Lee
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Junehyuk Lee
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Sung Woo Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - DoJin Kim
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - An Soo Jang
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea.
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30
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Hardisty GR, Law SM, Carter S, Grogan B, Singh PK, McKone EF, Gray RD. Ivacaftor modifies cystic fibrosis neutrophil phenotype in subjects with R117H residual function CFTR mutations. Eur Respir J 2020; 57:13993003.02161-2020. [PMID: 32855222 PMCID: PMC7817919 DOI: 10.1183/13993003.02161-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 07/30/2020] [Indexed: 11/05/2022]
Abstract
CFTR modulation leads to changes in neutrophil phenotype even in patients with residual function CFTR mutationshttps://bit.ly/2EUk7xH
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Affiliation(s)
- Gareth R Hardisty
- University of Edinburgh, Centre for Inflammation Research, Edinburgh, UK
| | - Sheonagh M Law
- University of Edinburgh, Centre for Inflammation Research, Edinburgh, UK
| | - Suzanne Carter
- St Vincent's Hospital, University College Dublin, Dublin, Ireland
| | - Brenda Grogan
- St Vincent's Hospital, University College Dublin, Dublin, Ireland
| | - Pradeep K Singh
- Dept of Microbiology, University of Washington School of Medicine, Seattle, WA, USA
| | - Edward F McKone
- St Vincent's Hospital, University College Dublin, Dublin, Ireland
| | - Robert D Gray
- University of Edinburgh, Centre for Inflammation Research, Edinburgh, UK
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31
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Houston CJ, Taggart CC, Downey DG. The role of inflammation in cystic fibrosis pulmonary exacerbations. Expert Rev Respir Med 2020; 14:889-903. [PMID: 32544353 DOI: 10.1080/17476348.2020.1778469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Cystic Fibrosis pulmonary exacerbations are critical events in the lives of people with CF that have deleterious effects on lung function, quality of life, and life expectancy. There are significant unmet needs in the management of exacerbations. We review here the associated inflammatory changes that underlie these events and are of interest for the development of biomarkers of exacerbation. AREAS COVERED Inflammatory responses in CF are abnormal and contribute to a sustained proinflammatory lung microenvironment, abundant in proinflammatory mediators and deficient in counter-regulatory mediators that terminate and resolve inflammation. There is increasing interest in these inflammatory pathways to discover novel biomarkers for pulmonary exacerbation management. In this review, we explore the inflammatory changes occurring during intravenous antibiotic therapy for exacerbation and how they may be applied as biomarkers to guide exacerbation therapy. A literature search was conducted using the PubMed database in February 2020. EXPERT OPINION Heterogeneity in inflammatory responses to treatment of a pulmonary exacerbation, a disease process with complex pathophysiology, limits the clinical utility of individual biomarkers. Biomarker panels may be a more successful strategy to capture informative changes within the CF population to improve pulmonary exacerbation management and outcomes.
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Affiliation(s)
- Claire J Houston
- Airway Innate Immunity Group (Aiir), Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast , Northern Ireland
| | - Clifford C Taggart
- Airway Innate Immunity Group (Aiir), Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast , Northern Ireland
| | - Damian G Downey
- Wellcome Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast , Northern Ireland.,Northern Ireland Regional Adult CF Centre, Belfast Health and Social Care Trust , Belfast, UK
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32
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Palmer LD, Maloney KN, Boyd KL, Goleniewska AK, Toki S, Maxwell CN, Chazin WJ, Peebles RS, Newcomb DC, Skaar EP. The Innate Immune Protein S100A9 Protects from T-Helper Cell Type 2-mediated Allergic Airway Inflammation. Am J Respir Cell Mol Biol 2020; 61:459-468. [PMID: 30943376 DOI: 10.1165/rcmb.2018-0217oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Calprotectin is a heterodimer of the proteins S100A8 and S100A9, and it is an abundant innate immune protein associated with inflammation. In humans, calprotectin transcription and protein abundance are associated with asthma and disease severity. However, mechanistic studies in experimental asthma models have been inconclusive, identifying both protective and pathogenic effects of calprotectin. To clarify the role of calprotectin in asthma, calprotectin-deficient S100A9-/- and wild-type (WT) C57BL/6 mice were compared in a murine model of allergic airway inflammation. Mice were intranasally challenged with extracts of the clinically relevant allergen, Alternaria alternata (Alt Ext), or PBS every third day over 9 days. On Day 10, BAL fluid and lung tissue homogenates were harvested and allergic airway inflammation was assessed. Alt Ext challenge induced release of S100A8/S100A9 to the alveolar space and increased protein expression in the alveolar epithelium of WT mice. Compared with WT mice, S100A9-/- mice displayed significantly enhanced allergic airway inflammation, including production of IL-13, CCL11, CCL24, serum IgE, eosinophil recruitment, and airway resistance and elastance. In response to Alt Ext, S100A9-/- mice accumulated significantly more IL-13+IL-5+CD4+ T-helper type 2 cells. S100A9-/- mice also accumulated a significantly lower proportion of CD4+ T regulatory (Treg) cells in the lung that had significantly lower expression of CD25. Calprotectin enhanced WT Treg cell suppressive activity in vitro. Therefore, this study identifies a role for the innate immune protein, S100A9, in protection from CD4+ T-helper type 2 cell hyperinflammation in response to Alt Ext. This protection is mediated, at least in part, by CD4+ Treg cell function.
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Affiliation(s)
- Lauren D Palmer
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
| | - K Nichole Maloney
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
| | - Kelli L Boyd
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
| | - A Kasia Goleniewska
- Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Shinji Toki
- Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - C Noel Maxwell
- Department of Biochemistry and.,Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - Walter J Chazin
- Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Department of Biochemistry and.,Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee
| | - R Stokes Peebles
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Dawn C Newcomb
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and.,Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee; and
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology.,Vanderbilt Institute for Infection, Immunology and Inflammation, and
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Availability of Zinc Impacts Interactions between Streptococcus sanguinis and Pseudomonas aeruginosa in Coculture. J Bacteriol 2020; 202:JB.00618-19. [PMID: 31685535 DOI: 10.1128/jb.00618-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 10/23/2019] [Indexed: 12/22/2022] Open
Abstract
Airway infections associated with cystic fibrosis (CF) are polymicrobial. We reported previously that clinical isolates of Pseudomonas aeruginosa promote the growth of a variety of streptococcal species. To explore the mechanistic basis of this interaction, we performed a genetic screen to identify mutants of Streptococcus sanginuis SK36 whose growth was no longer enhanced by P. aeruginosa PAO1. Mutations in the zinc uptake systems of S. sanguinis SK36 reduced growth of these strains by 1 to 3 logs compared to that of wild-type S. sanguinis SK36 when grown in coculture with P. aeruginosa PAO1, and exogenous zinc (0.1 to 10 μM) rescued the coculture defect of zinc uptake mutants of S. sanguinis SK36. Zinc uptake mutants of S. sanguinis SK36 had no obvious growth defect in monoculture. Consistent with competition for zinc driving coculture dynamics, S. sanguinis SK36 grown in coculture with P. aeruginosa showed increased expression of zinc uptake genes compared to that of S. sanguinis grown alone. Strains of P. aeruginosa PAO1 defective in zinc transport also supported ∼2-fold more growth by S. sanguinis compared to that in coculture with wild-type P. aeruginosa PAO1. An analysis of 118 CF sputum samples revealed that total zinc levels varied from ∼5 to 145 μM. At relatively low zinc levels, Pseudomonas and Streptococcus spp. were found in approximately equal abundance; at higher zinc levels, we observed a decline in relative abundance of Streptococcus spp., perhaps as a result of increasing zinc toxicity. Together, our data indicate that the relative abundances of these microbes in the CF airway may be impacted by zinc levels.IMPORTANCE Polymicrobial infections in CF cases likely impact patient health, but the mechanism(s) underlying such interactions is poorly understood. Here, we show using an in vitro model system that interactions between Pseudomonas and Streptococcus are modulated by zinc availability, and clinical data are consistent with this model. Together with previous studies, our work supports a role for metal homeostasis as a key factor driving microbial interactions.
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Sreejit G, Flynn MC, Patil M, Krishnamurthy P, Murphy AJ, Nagareddy PR. S100 family proteins in inflammation and beyond. Adv Clin Chem 2020; 98:173-231. [PMID: 32564786 DOI: 10.1016/bs.acc.2020.02.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The S100 family proteins possess a variety of intracellular and extracellular functions. They interact with multiple receptors and signal transducers to regulate pathways that govern inflammation, cell differentiation, proliferation, energy metabolism, apoptosis, calcium homeostasis, cell cytoskeleton and microbial resistance. S100 proteins are also emerging as novel diagnostic markers for identifying and monitoring various diseases. Strategies aimed at targeting S100-mediated signaling pathways hold a great potential in developing novel therapeutics for multiple diseases. In this chapter, we aim to summarize the current knowledge about the role of S100 family proteins in health and disease with a major focus on their role in inflammatory conditions.
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Affiliation(s)
| | - Michelle C Flynn
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Mallikarjun Patil
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, Schools of Medicine and Engineering, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Andrew J Murphy
- Division of Immunometabolism, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Immunology, Monash University, Melbourne, VIC, Australia
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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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Manni ML, Alcorn JF. Calprotectin-g the Lung during Type 2 Allergic Airway Inflammation. Am J Respir Cell Mol Biol 2019; 61:405-407. [PMID: 31046403 PMCID: PMC6775944 DOI: 10.1165/rcmb.2019-0125ed] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Michelle L Manni
- Department of PediatricsUPMC Children's Hospital of PittsburghPittsburgh, Pennsylvania
| | - John F Alcorn
- Department of PediatricsUPMC Children's Hospital of PittsburghPittsburgh, Pennsylvania
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Terracciano R, Preianò M, Maggisano G, Pelaia C, Savino R. Hexagonal Mesoporous Silica as a Rapid, Efficient and Versatile Tool for MALDI-TOF MS Sample Preparation in Clinical Peptidomics Analysis: A Pilot Study. Molecules 2019; 24:molecules24122311. [PMID: 31234484 PMCID: PMC6631377 DOI: 10.3390/molecules24122311] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 11/25/2022] Open
Abstract
Improvement in high-throughput MALDI-TOF MS analysis requires practical and efficient sample preparation protocols for high acquisition rates. The use of hexagonal mesoporous silica (HMS) sorbents in combination with MALDI-TOF MS was explored as a versatile tool for peptidomic profiling of clinical specimens difficult to process, but considered important sources of disease biomarkers: synovial fluid and sputum. A rapid and efficient procedure, based on dispersive solid-phase extraction of peptides using commercially available wormhole mesostructured HMS, was tested for: a) pre-concentration of standard peptides in serially diluted solution up to the sub-nanomolar range; b) peptidome profiling of sputum and synovial fluid. The use of HMS, as dispersed sponges, significantly amplified the peptidic repertoire of sputum and synovial fluid by excluding from the adsorptive process large size proteins, which mask and/or suppress peptidome signals. The protocol proposed, as dispersive solid phase extraction, ensures good analytical performances. Moreover, it is economical and rapid, as it avoids the use of less reproducible and prolonged sample preparation procedures, such as the use of ultrafiltration filter devices. These findings may contribute to defining a high-throughput screening MS-based platform for monitoring key peptidic features of difficult to analyse bodily fluids in a clinical setting.
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Affiliation(s)
- Rosa Terracciano
- Department of Health Sciences, University "Magna Græcia", 88100 Catanzaro, Italy.
| | | | - Giuseppina Maggisano
- Department of Health Sciences, University "Magna Græcia", 88100 Catanzaro, Italy.
| | - Corrado Pelaia
- Department of Medical and Surgical Sciences, University "Magna Græcia", 88100 Catanzaro, Italy.
| | - Rocco Savino
- Department of Health Sciences, University "Magna Græcia", 88100 Catanzaro, Italy.
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Liou TG, Adler FR, Argel N, Asfour F, Brown PS, Chatfield BA, Daines CL, Durham D, Francis JA, Glover B, Heynekamp T, Hoidal JR, Jensen JL, Keogh R, Kopecky CM, Lechtzin N, Li Y, Lysinger J, Molina O, Nakamura C, Packer KA, Poch KR, Quittner AL, Radford P, Redway AJ, Sagel SD, Sprandel S, Taylor-Cousar JL, Vroom JB, Yoshikawa R, Clancy JP, Elborn JS, Olivier KN, Cox DR. Prospective multicenter randomized patient recruitment and sample collection to enable future measurements of sputum biomarkers of inflammation in an observational study of cystic fibrosis. BMC Med Res Methodol 2019; 19:88. [PMID: 31027503 PMCID: PMC6485181 DOI: 10.1186/s12874-019-0705-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/11/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Biomarkers of inflammation predictive of cystic fibrosis (CF) disease outcomes would increase the power of clinical trials and contribute to better personalization of clinical assessments. A representative patient cohort would improve searching for believable, generalizable, reproducible and accurate biomarkers. METHODS We recruited patients from Mountain West CF Consortium (MWCFC) care centers for prospective observational study of sputum biomarkers of inflammation. After informed consent, centers enrolled randomly selected patients with CF who were clinically stable sputum producers, 12 years of age and older, without previous organ transplantation. RESULTS From December 8, 2014 through January 16, 2016, we enrolled 114 patients (53 male) with CF with continuing data collection. Baseline characteristics included mean age 27 years (SD = 12), 80% predicted forced expiratory volume in 1 s (SD = 23%), 1.0 prior year pulmonary exacerbations (SD = 1.2), home elevation 328 m (SD = 112) above sea level. Compared with other patients in the US CF Foundation Patient Registry (CFFPR) in 2014, MWCFC patients had similar distribution of sex, age, lung function, weight and rates of exacerbations, diabetes, pancreatic insufficiency, CF-related arthropathy and airway infections including methicillin-sensitive or -resistant Staphylococcus aureus, Pseudomonas aeruginosa, Burkholderia cepacia complex, fungal and non-tuberculous Mycobacteria infections. They received CF-specific treatments at similar frequencies. CONCLUSIONS Randomly-selected, sputum-producing patients within the MWCFC represent sputum-producing patients in the CFFPR. They have similar characteristics, lung function and frequencies of pulmonary exacerbations, microbial infections and use of CF-specific treatments. These findings will plausibly make future interpretations of quantitative measurements of inflammatory biomarkers generalizable to sputum-producing patients in the CFFPR.
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Affiliation(s)
- Theodore G. Liou
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
- Intermountain Pediatric Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113 USA
| | - Frederick R. Adler
- Departments of Mathematics, University of Utah, 155 South 1400 east, JWB 233, Salt Lake City, UT 84112 USA
- School of Biological Sciences, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112 USA
| | - Natalia Argel
- Cystic Fibrosis Center, Phoenix Children’s Hospital, 1919 East Thomas Road, Phoenix, AZ 85016 USA
| | - Fadi Asfour
- Intermountain Pediatric Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113 USA
| | - Perry S. Brown
- St. Luke’s Cystic Fibrosis Center of Idaho, 610 W. Hays Street, Boise, ID 83702 USA
| | - Barbara A. Chatfield
- Intermountain Pediatric Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113 USA
| | - Cori L. Daines
- Division of Pediatric Pulmonary and Sleep Medicine, Department of Pediatrics, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, AZ 85724 USA
| | - Dixie Durham
- St. Luke’s Cystic Fibrosis Center of Idaho, 610 W. Hays Street, Boise, ID 83702 USA
| | - Jessica A. Francis
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
| | - Barbara Glover
- Cystic Fibrosis Center, 3006 S. Maryland Pkwy, Suite #315, Las Vegas, NV 89109 USA
| | - Theresa Heynekamp
- Adult Cystic Fibrosis Program, Division of Pulmonary, Critical Care and Sleep Medicine, DoIM MSC10-5550, 1 University of New Mexico, Albuquerque, NM 87131 USA
| | - John R. Hoidal
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
| | - Judy L. Jensen
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
| | - Ruth Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Room G36, Keppel Street, London, WC1E 7HT UK
| | - Carol M. Kopecky
- Department of Pediatrics, Children’s Hospital Colorado, University of Colorado School of Medicine, 13123 East 16th Avenue, Aurora, CO 80045 USA
| | - Noah Lechtzin
- Division of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, Johns Hopkins University School of Medicine, 601 N. Caroline St, Baltimore, MD 21287 USA
| | - Yanping Li
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
| | - Jerimiah Lysinger
- Montana Cystic Fibrosis Center, Billings Clinic, 2800 10th Avenue N, Billings, MT 59101 USA
| | - Osmara Molina
- Division of Pediatric Pulmonary and Sleep Medicine, Department of Pediatrics, University of Arizona Health Sciences, 1501 N. Campbell Avenue, Room 3301, PO Box 245073, Tucson, AZ 85724 USA
| | - Craig Nakamura
- Cystic Fibrosis Center, 3006 S. Maryland Pkwy, Suite #315, Las Vegas, NV 89109 USA
| | - Kristyn A. Packer
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
| | - Katie R. Poch
- Division of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206 USA
| | - Alexandra L. Quittner
- Former: Department of Psychology, University of Miami, Miami, FL USA
- Present Address: Miami Children’s Research Institute, Nicklaus Children’s Hospital, 3100 SW 62nd Ave, Miami, FL 33155 USA
| | - Peggy Radford
- Cystic Fibrosis Center, Phoenix Children’s Hospital, 1919 East Thomas Road, Phoenix, AZ 85016 USA
| | - Abby J. Redway
- Adult Cystic Fibrosis Program, Division of Pulmonary, Critical Care and Sleep Medicine, DoIM MSC10-5550, 1 University of New Mexico, Albuquerque, NM 87131 USA
| | - Scott D. Sagel
- Department of Pediatrics, Children’s Hospital Colorado, University of Colorado School of Medicine, 13123 East 16th Avenue, Aurora, CO 80045 USA
| | - Shawna Sprandel
- Montana Cystic Fibrosis Center, Billings Clinic, 2800 10th Avenue N, Billings, MT 59101 USA
| | - Jennifer L. Taylor-Cousar
- Division of Pulmonary and Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, 1400 Jackson Street, Denver, CO 80206 USA
- Division of Pulmonology, Department of Pediatrics, National Jewish Health, 1400 Jackson St, Denver, CO 80206 USA
| | - Jane B. Vroom
- Adult Cystic Fibrosis Center, Division of Respiratory, Critical Care and Occupational Pulmonary Medicine, Department of Internal Medicine, University of Utah, 26 North Mario Capecchi Drive, Salt Lake City, UT 84132 USA
- Intermountain Pediatric Cystic Fibrosis Center, Division of Pediatric Pulmonology, Department of Pediatrics, University of Utah, 81 North Mario Capecchi Drive, Salt Lake City, UT 84113 USA
| | - Ryan Yoshikawa
- Cystic Fibrosis Center, 3006 S. Maryland Pkwy, Suite #315, Las Vegas, NV 89109 USA
| | - John P. Clancy
- Division of Pulmonary Medicine, Department of Pediatrics, University of Cincinnati, 3333 Burnet Avenue, Cincinnati, OH 45229-3026 USA
| | - J. Stuart Elborn
- Faculty of Medicine, Health and Life Sciences, Queen’s University Belfast, 90 Lisburn Road, Belfast, BT9 6AG UK
| | - Kenneth N. Olivier
- Laboratory of Chronic Airway Infection, Pulmonary Branch, National Heart Lung and Blood Institute, National Institutes of Health, 10 Center Drive MSC1454, Building 10-CRC, Room 1408A, Bethesda, MD 20892 USA
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Bishwal SC, Das MK, Badireddy VK, Dabral D, Das A, Mahapatra AR, Sahu S, Malakar D, Singh II, Mazumdar H, Patgiri SJ, Deka T, Kapfo W, Liegise K, Kupa RU, Debnath S, Bhowmik R, Debnath R, Behera RK, Pillai MG, Deuri P, Nath R, Khalo KP, Sing WA, Pandit B, Das A, Bhattacharya S, Behera D, Saikia L, Khamo V, Nanda RK. Sputum Proteomics Reveals a Shift in Vitamin D-binding Protein and Antimicrobial Protein Axis in Tuberculosis Patients. Sci Rep 2019; 9:1036. [PMID: 30705350 PMCID: PMC6355791 DOI: 10.1038/s41598-018-37662-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/13/2018] [Indexed: 01/11/2023] Open
Abstract
Existing understanding of molecular composition of sputum and its role in tuberculosis patients is variously limited to its diagnostic potential. We sought to identify infection induced sputum proteome alteration in active/non tuberculosis patients (A/NTB) and their role in altered lung patho-physiology. Out of the study population (n = 118), sputum proteins isolated from discovery set samples (n = 20) was used for an 8-plex isobaric tag for relative and absolute concentration analysis. A minimum set of protein with at least log2(ATB/NTB) >±1.0 in ATB was selected as biosignature and validated in 32 samples. Predictive accuracy was calculated from area under the receiver operating characteristic curve (AUC of ROC) using a confirmatory set (n = 50) by Western blot analysis. Mass spectrometry analysis identified a set of 192 sputum proteins, out of which a signature of β-integrin, vitamin D binding protein:DBP, uteroglobin, profilin and cathelicidin antimicrobial peptide was sufficient to differentiate ATB from NTB. AUC of ROC of the biosignature was calculated to 0.75. A shift in DBP-antimicrobial peptide (AMP) axis in the lungs of tuberculosis patients is observed. The identified sputum protein signature is a promising panel to differentiate ATB from NTB groups and suggest a deregulated DBP-AMP axis in lungs of tuberculosis patients.
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Affiliation(s)
- Subasa C Bishwal
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.,School of Life Sciences, Sambalpur University, JyotiVihar, Sambalpur, India
| | - Mrinal K Das
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Vinod K Badireddy
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Deepti Dabral
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Aleena Das
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Alok R Mahapatra
- School of Life Sciences, Sambalpur University, JyotiVihar, Sambalpur, India
| | - Sukanya Sahu
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - I Ibungo Singh
- Department of Respiratory Medicine, Regional Institute of Medical Sciences, Imphal, India
| | - Himanghsu Mazumdar
- Department of Microbiology, Assam Medical College and Hospital, Dibrugarh, India
| | - Saurav J Patgiri
- Department of Microbiology, Assam Medical College and Hospital, Dibrugarh, India
| | - Trinayan Deka
- Department of Microbiology, Assam Medical College and Hospital, Dibrugarh, India
| | - Wetetsho Kapfo
- Healthcare Laboratory and Research Centre, Naga Hospital Authority Kohima, Nagaland, India
| | - Kevideme Liegise
- Healthcare Laboratory and Research Centre, Naga Hospital Authority Kohima, Nagaland, India
| | - Rukuwe-U Kupa
- Healthcare Laboratory and Research Centre, Naga Hospital Authority Kohima, Nagaland, India
| | - Sanjita Debnath
- Department of Respiratory Medicine, Agartala Government Medical College, Agartala, India
| | - Rajesh Bhowmik
- Department of Respiratory Medicine, Agartala Government Medical College, Agartala, India
| | - Rahul Debnath
- Department of Respiratory Medicine, Agartala Government Medical College, Agartala, India
| | - Rajendra K Behera
- School of Life Sciences, Sambalpur University, JyotiVihar, Sambalpur, India
| | | | - Pranjal Deuri
- Department of Microbiology, Assam Medical College and Hospital, Dibrugarh, India
| | - Reema Nath
- Department of Microbiology, Assam Medical College and Hospital, Dibrugarh, India
| | - K Pewezo Khalo
- Department of Microbiology, Naga Hospital Authority Kohima, Nagaland, India
| | - W Asoka Sing
- Department of Respiratory Medicine, Regional Institute of Medical Sciences, Imphal, India
| | - Bhaswati Pandit
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Anjan Das
- Department of Respiratory Medicine, Agartala Government Medical College, Agartala, India
| | | | - Digambar Behera
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Lahari Saikia
- Department of Microbiology, Assam Medical College and Hospital, Dibrugarh, India
| | - Vinotsole Khamo
- Healthcare Laboratory and Research Centre, Naga Hospital Authority Kohima, Nagaland, India
| | - Ranjan K Nanda
- Translational Health Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India.
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Moon JY, Leitao Filho FS, Shahangian K, Takiguchi H, Sin DD. Blood and sputum protein biomarkers for chronic obstructive pulmonary disease (COPD). Expert Rev Proteomics 2018; 15:923-935. [PMID: 30362838 DOI: 10.1080/14789450.2018.1539670] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) is a heterogeneous set of disorders, characterized by airflow limitation, and reduced lung function. Despite increasing knowledge regarding its pathophysiology, there has been limited advancement in therapeutics and the current treatment strategy is symptom management and prevention of exacerbations. Areas covered: Biomarkers represent important tools for the implementation of precision medicine. As fundamental molecules of all living processes, proteins could provide crucial information about how genes interact with the environment. Proteomics studies could act as important tools in identifying reliable biomarkers to enable a more precise therapeutic approach. In this review, we will explore the most promising blood and sputum protein biomarkers in COPD that have been consistently reported in the literature. Expert commentary: Given the complexity of COPD, no single protein biomarker has been able to improve the outcomes of COPD patients. According to preliminary studies, precision medicine in COPD will likely require a combination of different proteins in a biomarker panel for clinical translation. With advancements in current mass spectrometry techniques, an enhancement in the identification of new biomarkers will be observed, and improvements in sequence database search can fill in potential gaps between biomarker discovery and patient care.
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Affiliation(s)
- Ji-Yong Moon
- a Centre for Heart and Lung Innovation , St. Paul's Hospital & University of British Columbia , Vancouver , Canada.,b Department of Internal Medicine , Hanyang University College of Medicine , Seoul , Korea
| | - Fernando Sergio Leitao Filho
- a Centre for Heart and Lung Innovation , St. Paul's Hospital & University of British Columbia , Vancouver , Canada.,c Division of Pulmonary Medicine, Department of Medicine , Tokai University School of Medicine , Kanagawa , Japan
| | - Kimeya Shahangian
- a Centre for Heart and Lung Innovation , St. Paul's Hospital & University of British Columbia , Vancouver , Canada
| | - Hiroto Takiguchi
- a Centre for Heart and Lung Innovation , St. Paul's Hospital & University of British Columbia , Vancouver , Canada.,d Division of Respiratory Medicine (Department of Medicine) , University of British Columbia , Vancouver , Canada
| | - Don D Sin
- a Centre for Heart and Lung Innovation , St. Paul's Hospital & University of British Columbia , Vancouver , Canada.,d Division of Respiratory Medicine (Department of Medicine) , University of British Columbia , Vancouver , Canada
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41
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Cagnone M, Salvini R, Bardoni A, Fumagalli M, Iadarola P, Viglio S. Searching for biomarkers of chronic obstructive pulmonary disease using proteomics: The current state. Electrophoresis 2018; 40:151-164. [PMID: 30216498 DOI: 10.1002/elps.201800305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 09/10/2018] [Accepted: 09/10/2018] [Indexed: 12/24/2022]
Abstract
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.
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Affiliation(s)
- Maddalena Cagnone
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Roberta Salvini
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Anna Bardoni
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
| | - Marco Fumagalli
- Department of Biology and Biotechnologies "L.Spallanzani", Biochemistry Unit, University of Pavia, Italy
| | - Paolo Iadarola
- Department of Biology and Biotechnologies "L.Spallanzani", Biochemistry Unit, University of Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, Italy
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42
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Intergenic evolution during host adaptation increases expression of the metallophore pseudopaline in Pseudomonas aeruginosa. Microbiology (Reading) 2018; 164:1038-1047. [DOI: 10.1099/mic.0.000687] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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43
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Mastropasqua MC, Lamont I, Martin LW, Reid DW, D'Orazio M, Battistoni A. Efficient zinc uptake is critical for the ability of Pseudomonas aeruginosa to express virulence traits and colonize the human lung. J Trace Elem Med Biol 2018; 48:74-80. [PMID: 29773197 DOI: 10.1016/j.jtemb.2018.03.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 01/31/2018] [Accepted: 03/08/2018] [Indexed: 02/03/2023]
Abstract
We have recently shown that Pseudomonas aeruginosa, an opportunistic pathogen that chronically infects the lungs of patients with cystic fibrosis (CF) and other forms of lung disease, is extremely efficient in recruiting zinc from the environment and that this capability is required for its ability to cause acute lung infections in mice. To verify that P. aeruginosa faces zinc shortage when colonizing the lungs of human patients, we analyzed the expression of three genes that are highly induced under conditions of zinc deficiency (zrmA, dksA2 and rpmE2), in bacteria in the sputum of patients with inflammatory lung disease. All three genes were expressed in all the analyzed sputum samples to a level much higher than that of bacteria grown in zinc-containing laboratory medium, supporting the hypothesis that P. aeruginosa is under zinc starvation during lung infections. We also found that the expression of several virulence traits that play a central role in the ability of P. aeruginosa to colonize the lung is affected by disruption of the most important zinc importing systems. Virulence features dependent on zinc intake include swarming and swimming motility and the ability to form biofilms. Furthermore, alterations in zinc assimilation interfere with the synthesis of the siderophore pyoverdine, suggesting that zinc recruitment could modulate iron uptake and affect siderophore-mediated cell signaling. Our results reveal that zinc uptake is likely to play a key role in the ability of P. aeruginosa to cause chronic lung infections and strongly modulates critical virulence traits of the pathogen. Taking into account the recent discovery that zinc uptake in P. aeruginosa is promoted by the release of a small molecular weight molecule showing high affinity for zinc, our data suggest novel and effective possibilities to control lung infections by these bacteria.
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Affiliation(s)
| | - Iain Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Lois W Martin
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - David W Reid
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia; The Prince Charles Hospital, Brisbane, Queensland, Australia
| | - Melania D'Orazio
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
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44
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Burg D, Schofield JPR, Brandsma J, Staykova D, Folisi C, Bansal A, Nicholas B, Xian Y, Rowe A, Corfield J, Wilson S, Ward J, Lutter R, Fleming L, Shaw DE, Bakke PS, Caruso M, Dahlen SE, Fowler SJ, Hashimoto S, Horváth I, Howarth P, Krug N, Montuschi P, Sanak M, Sandström T, Singer F, Sun K, Pandis I, Auffray C, Sousa AR, Adcock IM, Chung KF, Sterk PJ, Djukanović R, Skipp PJ, The U-Biopred Study Group. Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome. J Proteome Res 2018; 17:2072-2091. [PMID: 29737851 DOI: 10.1021/acs.jproteome.8b00018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of induced sputum supernatant is a minimally invasive approach to study the epithelial lining fluid and, thereby, provide insight into normal lung biology and the pathobiology of lung diseases. We present here a novel proteomics approach to sputum analysis developed within the U-BIOPRED (unbiased biomarkers predictive of respiratory disease outcomes) international project. We present practical and analytical techniques to optimize the detection of robust biomarkers in proteomic studies. The normal sputum proteome was derived using data-independent HDMSE applied to 40 healthy nonsmoking participants, which provides an essential baseline from which to compare modulation of protein expression in respiratory diseases. The "core" sputum proteome (proteins detected in ≥40% of participants) was composed of 284 proteins, and the extended proteome (proteins detected in ≥3 participants) contained 1666 proteins. Quality control procedures were developed to optimize the accuracy and consistency of measurement of sputum proteins and analyze the distribution of sputum proteins in the healthy population. The analysis showed that quantitation of proteins by HDMSE is influenced by several factors, with some proteins being measured in all participants' samples and with low measurement variance between samples from the same patient. The measurement of some proteins is highly variable between repeat analyses, susceptible to sample processing effects, or difficult to accurately quantify by mass spectrometry. Other proteins show high interindividual variance. We also highlight that the sputum proteome of healthy individuals is related to sputum neutrophil levels, but not gender or allergic sensitization. We illustrate the importance of design and interpretation of disease biomarker studies considering such protein population and technical measurement variance.
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Affiliation(s)
- Dominic Burg
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K.,NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - James P R Schofield
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K.,NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Joost Brandsma
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Doroteya Staykova
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K
| | - Caterina Folisi
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K
| | | | - Ben Nicholas
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Yang Xian
- Data Science Institute , Imperial College London , London SW7 2AZ , U.K
| | - Anthony Rowe
- Janssen Research & Development , Buckinghamshire HP12 4DP , U.K
| | | | - Susan Wilson
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Jonathan Ward
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Rene Lutter
- AMC, Department of Experimental Immunology , University of Amsterdam , 1012 WX Amsterdam , The Netherlands.,AMC, Department of Respiratory Medicine , University of Amsterdam , 1012 WX Amsterdam , The Netherlands
| | - Louise Fleming
- Airways Disease , National Heart and Lung Institute, Imperial College, London & Royal Brompton NIHR Biomedical Research Unit , London SW7 2AZ , United Kingdom
| | - Dominick E Shaw
- Respiratory Research Unit , University of Nottingham , Nottingham NG7 2RD , U.K
| | - Per S Bakke
- Institute of Medicine , University of Bergen , 5007 Bergen , Norway
| | - Massimo Caruso
- Department of Clinical and Experimental Medicine Hospital University , University of Catania , 95124 Catania , Italy
| | - Sven-Erik Dahlen
- The Centre for Allergy Research , The Institute of Environmental Medicine, Karolinska Institutet , SE-171 77 Stockholm , Sweden
| | - Stephen J Fowler
- Respiratory and Allergy Research Group , University of Manchester , Manchester M13 9PL , U.K
| | - Simone Hashimoto
- Department of Respiratory Medicine, Academic Medical Centre , University of Amsterdam , 1012 WX Amsterdam , The Netherlands
| | - Ildikó Horváth
- Department of Pulmonology , Semmelweis University , Budapest 1085 , Hungary
| | - Peter Howarth
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Norbert Krug
- Fraunhofer Institute for Toxicology and Experimental Medicine Hannover , 30625 Hannover , Germany
| | - Paolo Montuschi
- Faculty of Medicine , Catholic University of the Sacred Heart , 00168 Rome , Italy
| | - Marek Sanak
- Laboratory of Molecular Biology and Clinical Genetics, Medical College , Jagiellonian University , 31-007 Krakow , Poland
| | - Thomas Sandström
- Department of Medicine, Department of Public Health and Clinical Medicine Respiratory Medicine Unit , Umeå University , 901 87 Umeå , Sweden
| | - Florian Singer
- University Children's Hospital Zurich , 8032 Zurich , Switzerland
| | - Kai Sun
- Data Science Institute , Imperial College London , London SW7 2AZ , U.K
| | - Ioannis Pandis
- Data Science Institute , Imperial College London , London SW7 2AZ , U.K
| | - Charles Auffray
- European Institute for Systems Biology and Medicine, CNRS-ENS-UCBL-INSERM , Université de Lyon , 69007 Lyon , France
| | - Ana R Sousa
- Respiratory Therapeutic Unit, GSK , Stockley Park , Uxbridge UB11 1BT , U.K
| | - Ian M Adcock
- Cell and Molecular Biology Group, Airways Disease Section , National Heart and Lung Institute, Imperial College London , Dovehouse Street , London SW3 6LR , U.K
| | - Kian Fan Chung
- Airways Disease , National Heart and Lung Institute, Imperial College, London & Royal Brompton NIHR Biomedical Research Unit , London SW7 2AZ , United Kingdom
| | - Peter J Sterk
- AMC, Department of Experimental Immunology , University of Amsterdam , 1012 WX Amsterdam , The Netherlands
| | - Ratko Djukanović
- NIHR Southampton Biomedical Research Centre, Clinical and Experimental Sciences, Faculty of Medicine , University of Southampton , Southampton SO16 6YD , U.K
| | - Paul J Skipp
- Centre for Proteomic Research, Biological Sciences , University of Southampton , Southampton SO17 1BJ , U.K
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45
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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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46
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Baralla A, Fois AG, Sotgiu E, Zinellu E, Mangoni AA, Sotgia S, Zinellu A, Pirina P, Carru C. Plasma Proteomic Signatures in Early Chronic Obstructive Pulmonary Disease. Proteomics Clin Appl 2018; 12:e1700088. [DOI: 10.1002/prca.201700088] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 01/15/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Angela Baralla
- Department of Biomedical Sciences; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Alessandro G. Fois
- Department of Clinical and Experimental Medicine; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Elisabetta Sotgiu
- Department of Biomedical Sciences; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Elisabetta Zinellu
- Department of Clinical and Experimental Medicine; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Arduino A. Mangoni
- Department of Clinical Pharmacology; School of Medicine; Flinders University; Adelaide Australia
| | - Salvatore Sotgia
- Department of Biomedical Sciences; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Angelo Zinellu
- Department of Biomedical Sciences; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Pietro Pirina
- Department of Clinical and Experimental Medicine; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
| | - Ciriaco Carru
- Department of Biomedical Sciences; University of Sassari; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
- Quality Control Unit; Azienda Ospedaliero Universitaria di Sassari; Sassari Italy
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47
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Mastropasqua MC, D'Orazio M, Cerasi M, Pacello F, Gismondi A, Canini A, Canuti L, Consalvo A, Ciavardelli D, Chirullo B, Pasquali P, Battistoni A. Growth of Pseudomonas aeruginosa
in zinc poor environments is promoted by a nicotianamine-related metallophore. Mol Microbiol 2017; 106:543-561. [DOI: 10.1111/mmi.13834] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 11/29/2022]
Affiliation(s)
| | - Melania D'Orazio
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - Mauro Cerasi
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | | | - Angelo Gismondi
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - Antonella Canini
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - Lorena Canuti
- Department of Biology; University of Rome Tor Vergata; Rome Italy
| | - Ada Consalvo
- Centro Scienze dell'Invecchiamento e Medicina Traslazionale - CeSI-MeT; Chieti Italy
- Department of Medical, Oral and Biotechnological Sciences; “G. d'Annunzio” University of Chieti-Pescara; Chieti Italy
| | - Domenico Ciavardelli
- Centro Scienze dell'Invecchiamento e Medicina Traslazionale - CeSI-MeT; Chieti Italy
- School of Human and Social Science; “Kore” University of Enna; Enna Italy
| | - Barbara Chirullo
- Department of Food Safety and Veterinary Public Health; Istituto Superiore di Sanità; Rome Italy
| | - Paolo Pasquali
- Department of Food Safety and Veterinary Public Health; Istituto Superiore di Sanità; Rome Italy
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48
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Kan M, Shumyatcher M, Himes BE. Using omics approaches to understand pulmonary diseases. Respir Res 2017; 18:149. [PMID: 28774304 PMCID: PMC5543452 DOI: 10.1186/s12931-017-0631-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Omics approaches are high-throughput unbiased technologies that provide snapshots of various aspects of biological systems and include: 1) genomics, the measure of DNA variation; 2) transcriptomics, the measure of RNA expression; 3) epigenomics, the measure of DNA alterations not involving sequence variation that influence RNA expression; 4) proteomics, the measure of protein expression or its chemical modifications; and 5) metabolomics, the measure of metabolite levels. Our understanding of pulmonary diseases has increased as a result of applying these omics approaches to characterize patients, uncover mechanisms underlying drug responsiveness, and identify effects of environmental exposures and interventions. As more tissue- and cell-specific omics data is analyzed and integrated for diverse patients under various conditions, there will be increased identification of key mechanisms that underlie pulmonary biological processes, disease endotypes, and novel therapeutics that are efficacious in select individuals. We provide a synopsis of how omics approaches have advanced our understanding of asthma, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), idiopathic pulmonary fibrosis (IPF), and pulmonary arterial hypertension (PAH), and we highlight ongoing work that will facilitate pulmonary disease precision medicine.
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Affiliation(s)
- Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
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49
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Pattison SH, Gibson DS, Johnston E, Peacock S, Rivera K, Tunney MM, Pappin DJ, Elborn JS. Proteomic profile of cystic fibrosis sputum cells in adults chronically infected with Pseudomonas aeruginosa. Eur Respir J 2017; 50:50/1/1601569. [DOI: 10.1183/13993003.01569-2016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 03/29/2017] [Indexed: 12/11/2022]
Abstract
Lung disease is the main cause of morbidity and mortality in cystic fibrosis (CF), and involves chronic infection and perturbed immune responses. Tissue damage is mediated mostly by extracellular proteases, but other cellular proteins may also contribute to damage through their effect on cell activities and/or release into sputum fluid by means of active secretion or cell death.We employed MudPIT (multidimensional protein identification technology) to identify sputum cellular proteins with consistently altered abundance in adults with CF, chronically infected with Pseudomonas aeruginosa, compared with healthy controls. Ingenuity Pathway Analysis, Gene Ontology, protein abundance and correlation with lung function were used to infer their potential clinical significance.Differentially abundant proteins relate to Rho family small GTPase activity, immune cell movement/activation, generation of reactive oxygen species, and dysregulation of cell death and proliferation. Compositional breakdown identified high abundance of proteins previously associated with neutrophil extracellular traps. Furthermore, negative correlations with lung function were detected for 17 proteins, many of which have previously been associated with lung injury.These findings expand our current understanding of the mechanisms driving CF lung disease and identify sputum cellular proteins with potential for use as indicators of disease status/prognosis, stratification determinants for treatment prescription or therapeutic targets.
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50
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Finch S, Keir HR, Dicker AJ, Chalmers JD. The past decade in bench research into pulmonary infectious diseases: What do clinicians need to know? Respirology 2017; 22:1062-1072. [PMID: 28657170 DOI: 10.1111/resp.13106] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/07/2017] [Accepted: 05/14/2017] [Indexed: 12/12/2022]
Abstract
Respiratory infections are primarily treated with antibiotics, drugs that are mostly inexpensive and have been widely available since the 1940s and 1950s. Nevertheless, despite antibiotics, the burden of disease in pneumonia, bronchiectasis, cystic fibrosis, COPD and rare respiratory infections remains exceptionally high. There is an urgent need for translational studies to develop new treatments or new biomarkers to improve outcomes in these conditions. The 'translational gaps' between bench science and clinical practice are particularly challenging in respiratory infections. This is partly due to the poor representativeness of animal models of infection to human disease, and a long-term lack of investment into pulmonary infection research. The revolution in genomics and other omics technologies, however, is beginning to unlock clinically important information about the host response to infection, the behaviour of bacterial communities and the development of new antibiotics. It is not possible to review the extensive progress made in the last decade into the pathophysiology of the different respiratory infections and so here, we focus on major technologies that are now changing respiratory infection research, specifically bacterial whole-genome sequencing, the microbiota, personalized medicine with omics technologies, new antibiotic development and host inflammatory cell biology.
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Affiliation(s)
- Simon Finch
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Holly R Keir
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Alison J Dicker
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - James D Chalmers
- Scottish Centre for Respiratory Research, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
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