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Sunata K, Miyata J, Kawashima Y, Konno R, Ishikawa M, Hasegawa Y, Onozato R, Otsu Y, Matsuyama E, Sasaki H, Okuzumi S, Mochimaru T, Masaki K, Kabata H, Kawana A, Arita M, Fukunaga K. Multiomics analysis identified IL-4-induced IL1RL1 high eosinophils characterized by prominent cysteinyl leukotriene metabolism. J Allergy Clin Immunol 2024:S0091-6749(24)00741-3. [PMID: 39067484 DOI: 10.1016/j.jaci.2024.07.012] [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: 03/17/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Clinical studies have demonstrated that IL-4, a type 2 cytokine, plays an important role in the pathogenesis of chronic rhinosinusitis and eosinophilic asthma. However, the direct effect of IL-4 on eosinophils remains unclear. OBJECTIVE We aimed to elucidate the inflammatory effects of IL-4 on the functions of human eosinophils. METHODS A multiomics analysis comprising transcriptomics, proteomics, lipidomics, quantitative RT-PCR, and flow cytometry was performed by using blood eosinophils from healthy subjects stimulated with IL-4, IL-5, or a combination thereof. RESULTS Transcriptomic and proteomic analyses revealed that both IL-4 and IL-5 upregulate the expression of γ-gultamyl transferase 5, a fatty acid-metabolizing enzyme that converts leukotriene C4 into leukotriene D4. In addition, IL-4 specifically upregulates the expression of IL-1 receptor-like 1 (IL1RL1), a receptor for IL-33 and transglutaminase-2. Additional transcriptomic analysis of cells stimulated with IL-13 revealed altered gene expression profiles, characterized by the upregulation of γ-gultamyl transferase 5, transglutaminase-2, and IL1RL1. The IL-13-induced changes were not totally different from the IL-4-induced changes. Lipidomic analysis revealed that IL-5 and IL-4 additively increased the extracellular release of leukotriene D4. In vitro experiments revealed that STAT6 and IL-4 receptor-α control the expression of these molecules in the presence of IL-4 and IL-13. Analysis of eosinophils derived from patients with allergic disorders indicated the involvement of IL-4 and IL-13 at the inflamed sites. CONCLUSIONS IL-4 induces the proallergic phenotype of IL1RL1high eosinophils, with prominent cysteinyl leukotriene metabolism via STAT6. These cellular changes represent potential therapeutic targets for chronic rhinosinusitis and eosinophilic asthma.
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Affiliation(s)
- Keeya Sunata
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | - Jun Miyata
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan; Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan; Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan.
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Yoshinori Hasegawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Chiba, Japan
| | - Ryuta Onozato
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yo Otsu
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Emiko Matsuyama
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hisashi Sasaki
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Shinichi Okuzumi
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Takao Mochimaru
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan; Department of Respiratory Medicine, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Katsunori Masaki
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hiroki Kabata
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Akihiko Kawana
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Saitama, Japan
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan; Graduate School of Medical Life Science, Yokohama City University, Kanagawa, Japan; Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan; Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
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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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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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Song MA, Mori KM, McElroy JP, Freudenheim JL, Weng DY, Reisinger SA, Brasky TM, Wewers MD, Shields PG. Accelerated epigenetic age, inflammation, and gene expression in lung: comparisons of smokers and vapers with non-smokers. Clin Epigenetics 2023; 15:160. [PMID: 37821974 PMCID: PMC10568901 DOI: 10.1186/s13148-023-01577-8] [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: 03/11/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Cigarette smoking and aging are the main risk factors for pulmonary diseases, including cancer. Epigenetic aging may explain the relationship between smoking, electronic cigarette vaping, and pulmonary health. No study has examined smoking and vaping-related epigenetic aging in relation to lung biomarkers. METHODS Lung epigenetic aging measured by DNA methylation (mAge) and its acceleration (mAA) was assessed in young (age 21-30) electronic cigarette vapers (EC, n = 14, including 3 never-smoking EC), smokers (SM, n = 16), and non-EC/non-SM (NS, n = 39). We investigated relationships of mAge estimates with chronological age (Horvath-mAge), lifespan/mortality (Grim-mAge), telomere length (TL-mAge), smoking/EC history, urinary biomarkers, lung cytokines, and transcriptome. RESULTS Compared to NS, EC and SM had significantly older Grim-mAge, shorter TL-mAge, significantly accelerated Grim-mAge and decelerated TL-mAge. Among SM, Grim-mAA was associated with nicotine intake and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL). For EC, Horvath-mAA was significantly correlated with puffs per day. Overall, cytokines (IL-1β, IL-6, and IL-8) and 759 transcripts (651 unique genes) were significantly associated with Grim-mAA. Grim-mAA-associated genes were highly enriched in immune-related pathways and genes that play a role in the morphology and structures of cells/tissues. CONCLUSIONS Faster lung mAge for SM is consistent with prior studies of blood. Faster lung mAge for EC compared to NS indicates possible adverse pulmonary effects of EC on biological aging. Our findings support further research, particularly on epigenetic markers, on effects of smoking and vaping on pulmonary health. Given that most EC are former smokers, further study is needed to understand unique effects of electronic cigarettes on biological aging.
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Affiliation(s)
- Min-Ae Song
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 404 Cunz Hall, 1841 Neil Ave., Columbus, OH, 43210, USA.
| | - Kellie M Mori
- Division of Environmental Health Sciences, College of Public Health, The Ohio State University, 404 Cunz Hall, 1841 Neil Ave., Columbus, OH, 43210, USA
| | - Joseph P McElroy
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Jo L Freudenheim
- Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Daniel Y Weng
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Sarah A Reisinger
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Theodore M Brasky
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Mark D Wewers
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
| | - Peter G Shields
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH, USA
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5
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Mebratu YA, Soni S, Rosas L, Rojas M, Horowitz JC, Nho R. The aged extracellular matrix and the profibrotic role of senescence-associated secretory phenotype. Am J Physiol Cell Physiol 2023; 325:C565-C579. [PMID: 37486065 PMCID: PMC10511170 DOI: 10.1152/ajpcell.00124.2023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an irreversible and fatal lung disease that is primarily found in the elderly population, and several studies have demonstrated that aging is the major risk factor for IPF. IPF is characterized by the presence of apoptosis-resistant, senescent fibroblasts that generate an excessively stiff extracellular matrix (ECM). The ECM profoundly affects cellular functions and tissue homeostasis, and an aberrant ECM is closely associated with the development of lung fibrosis. Aging progressively alters ECM components and is associated with the accumulation of senescent cells that promote age-related tissue dysfunction through the expression of factors linked to a senescence-associated secretary phenotype (SASP). There is growing evidence that SASP factors affect various cell behaviors and influence ECM turnover in lung tissue through autocrine and/or paracrine signaling mechanisms. Since life expectancy is increasing worldwide, it is important to elucidate how aging affects ECM dynamics and turnover via SASP and thereby promotes lung fibrosis. In this review, we will focus on the molecular properties of SASP and its regulatory mechanisms. Furthermore, the pathophysiological process of ECM remodeling by SASP factors and the influence of an altered ECM from aged lungs on the development of lung fibrosis will be highlighted. Finally, recent attempts to target ECM alteration and senescent cells to modulate fibrosis will be introduced.NEW & NOTEWORTHY Aging is the most prominent nonmodifiable risk factor for various human diseases including Idiopathic pulmonary fibrosis. Aging progressively alters extracellular matrix components and is associated with the accumulation of senescent cells that promote age-related tissue dysfunction. In this review, we will discuss the pathological impact of aging and senescence on lung fibrosis via senescence-associated secretary phenotype factors and potential therapeutic approaches to limit the progression of lung fibrosis.
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Affiliation(s)
- Yohannes A Mebratu
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Sourabh Soni
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Lorena Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Jeffrey C Horowitz
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
| | - Richard Nho
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, The Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, United States
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6
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Fang H, Liu Y, Yang Q, Han S, Zhang H. Prognostic Biomarkers Based on Proteomic Technology in COPD: A Recent Review. Int J Chron Obstruct Pulmon Dis 2023; 18:1353-1365. [PMID: 37408604 PMCID: PMC10319291 DOI: 10.2147/copd.s410387] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common heterogeneous respiratory disease which is characterized by persistent and incompletely reversible airflow limitation. Due to the heterogeneity and phenotypic complexity of COPD, traditional diagnostic methods provide limited information and pose a great challenge to clinical management. In recent years, with the development of omics technologies, proteomics, metabolomics, transcriptomics, etc., have been widely used in the study of COPD, providing great help to discover new biomarkers and elucidate the complex mechanisms of COPD. In this review, we summarize the prognostic biomarkers of COPD based on proteomic studies in recent years and evaluate their association with COPD prognosis. Finally, we present the prospects and challenges of COPD prognostic-related studies. This review is expected to provide cutting-edge evidence in prognostic evaluation of clinical patients with COPD and to inform future proteomic studies on prognostic biomarkers of COPD.
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Affiliation(s)
- Hanyu Fang
- Beijing University of Chinese Medicine, Beijing, 100029, People’s Republic of China
| | - Ying Liu
- The Second Health and Medical Department, China-Japan Friendship Hospital, Beijing, 100029, People’s Republic of China
| | - Qiwen Yang
- Beijing University of Chinese Medicine, Beijing, 100029, People’s Republic of China
| | - Siyu Han
- Beijing University of Chinese Medicine, Beijing, 100029, People’s Republic of China
| | - Hongchun Zhang
- Beijing University of Chinese Medicine, Beijing, 100029, People’s Republic of China
- The Second Health and Medical Department, China-Japan Friendship Hospital, Beijing, 100029, People’s Republic of China
- Department of Traditional Chinese Medicine for Pulmonary Diseases, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, 100029, People’s Republic of China
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7
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Guo T, He C, Venado A, Zhou Y. Extracellular Matrix Stiffness in Lung Health and Disease. Compr Physiol 2022; 12:3523-3558. [PMID: 35766837 PMCID: PMC10088466 DOI: 10.1002/cphy.c210032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The extracellular matrix (ECM) provides structural support and imparts a wide variety of environmental cues to cells. In the past decade, a growing body of work revealed that the mechanical properties of the ECM, commonly known as matrix stiffness, regulate the fundamental cellular processes of the lung. There is growing appreciation that mechanical interplays between cells and associated ECM are essential to maintain lung homeostasis. Dysregulation of ECM-derived mechanical signaling via altered mechanosensing and mechanotransduction pathways is associated with many common lung diseases. Matrix stiffening is a hallmark of lung fibrosis. The stiffened ECM is not merely a sequelae of lung fibrosis but can actively drive the progression of fibrotic lung disease. In this article, we provide a comprehensive view on the role of matrix stiffness in lung health and disease. We begin by summarizing the effects of matrix stiffness on the function and behavior of various lung cell types and on regulation of biomolecule activity and key physiological processes, including host immune response and cellular metabolism. We discuss the potential mechanisms by which cells probe matrix stiffness and convert mechanical signals to regulate gene expression. We highlight the factors that govern matrix stiffness and outline the role of matrix stiffness in lung development and the pathogenesis of pulmonary fibrosis, pulmonary hypertension, asthma, chronic obstructive pulmonary disease (COPD), and lung cancer. We envision targeting of deleterious matrix mechanical cues for treatment of fibrotic lung disease. Advances in technologies for matrix stiffness measurements and design of stiffness-tunable matrix substrates are also explored. © 2022 American Physiological Society. Compr Physiol 12:3523-3558, 2022.
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Affiliation(s)
- Ting Guo
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Alabama, USA.,Department of Respiratory Medicine, the Second Xiangya Hospital, Central-South University, Changsha, Hunan, China
| | - Chao He
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Alabama, USA
| | - Aida Venado
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Yong Zhou
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Alabama, USA
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8
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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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9
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Burgess JK, Harmsen MC. Chronic lung diseases: entangled in extracellular matrix. Eur Respir Rev 2022; 31:31/163/210202. [PMID: 35264410 DOI: 10.1183/16000617.0202-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 12/17/2021] [Indexed: 01/10/2023] Open
Abstract
The extracellular matrix (ECM) is the scaffold that provides structure and support to all organs, including the lung; however, it is also much more than this. The ECM provides biochemical and biomechanical cues to cells that reside or transit through this micro-environment, instructing their responses. The ECM structure and composition changes in chronic lung diseases; how such changes impact disease pathogenesis is not as well understood. Cells bind to the ECM through surface receptors, of which the integrin family is one of the most widely recognised. The signals that cells receive from the ECM regulate their attachment, proliferation, differentiation, inflammatory secretory profile and survival. There is extensive evidence documenting changes in the composition and amount of ECM in diseased lung tissues. However, changes in the topographical arrangement, organisation of the structural fibres and stiffness (or viscoelasticity) of the matrix in which cells are embedded have an undervalued but strong impact on cell phenotype. The ECM in diseased lungs also changes in physical and biomechanical ways that drive cellular responses. The characteristics of these environments alter cell behaviour and potentially orchestrate perpetuation of lung diseases. Future therapies should target ECM remodelling as much as the underlying culprit cells.
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Affiliation(s)
- Janette K Burgess
- University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, Groningen, The Netherlands .,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, KOLFF Institute - REGENERATE, Groningen, The Netherlands
| | - Martin C Harmsen
- University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, KOLFF Institute - REGENERATE, Groningen, The Netherlands
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10
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He N, Liu X, Vegter AR, Evans TIA, Gray JS, Guo J, Moll SR, Guo LJ, Luo M, Ma N, Sun X, Liang B, Yan Z, Feng Z, Qi L, Joshi AS, Shahin W, Yi Y, Gibson-Corley KN, Hoffman EA, Wang K, Mueller C, Engelhardt JF, Rosen BH. Ferret models of alpha-1 antitrypsin deficiency develop lung and liver disease. JCI Insight 2022; 7:e143004. [PMID: 35104244 PMCID: PMC8983124 DOI: 10.1172/jci.insight.143004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 01/28/2022] [Indexed: 11/19/2022] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is the most common genetic cause and risk factor for chronic obstructive pulmonary disease, but the field lacks a large-animal model that allows for longitudinal assessment of pulmonary function. We hypothesized that ferrets would model human AATD-related lung and hepatic disease. AAT-knockout (AAT-KO) and PiZZ (E342K, the most common mutation in humans) ferrets were generated and compared with matched controls using custom-designed flexiVent modules to perform pulmonary function tests, quantitative computed tomography (QCT), bronchoalveolar lavage (BAL) proteomics, and alveolar morphometry. Complete loss of AAT (AAT-KO) led to increased pulmonary compliance and expiratory airflow limitation, consistent with obstructive lung disease. QCT and morphometry confirmed emphysema and airspace enlargement, respectively. Pathway analysis of BAL proteomics data revealed inflammatory lung disease and impaired cellular migration. The PiZ mutation resulted in altered AAT protein folding in the liver, hepatic injury, and reduced plasma concentrations of AAT, and PiZZ ferrets developed obstructive lung disease. In summary, AAT-KO and PiZZ ferrets model the progressive obstructive pulmonary disease seen in AAT-deficient patients and may serve as a platform for preclinical testing of therapeutics including gene therapy.
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Affiliation(s)
- Nan He
- Department of Anatomy and Cell Biology
| | | | | | | | | | | | | | | | | | | | | | - Bo Liang
- Department of Anatomy and Cell Biology
| | | | | | - Lisi Qi
- Department of Anatomy and Cell Biology
| | | | | | - Yaling Yi
- Department of Anatomy and Cell Biology
| | | | | | - Kai Wang
- Department of Biostatistics, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Christian Mueller
- Department of Pediatrics, University of Massachusetts Medical Center, Worcester, Massachusetts, USA
| | - John F. Engelhardt
- Department of Anatomy and Cell Biology
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
| | - Bradley H. Rosen
- Department of Anatomy and Cell Biology
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa, USA
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11
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Rayavara K, Kurosky A, Hosakote YM. Respiratory syncytial virus infection induces the release of transglutaminase 2 from human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 2022; 322:L1-L12. [PMID: 34704843 PMCID: PMC8721898 DOI: 10.1152/ajplung.00013.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Respiratory syncytial virus (RSV) is an important human pathogen that causes severe lower respiratory tract infections in young children, the elderly, and the immunocompromised, yet no effective treatments or vaccines are available. The precise mechanism underlying RSV-induced acute airway disease and associated sequelae are not fully understood; however, early lung inflammatory and immune events are thought to play a major role in the outcome of the disease. Moreover, oxidative stress responses in the airways play a key role in the pathogenesis of RSV. Oxidative stress has been shown to elevate cytosolic calcium (Ca2+) levels, which in turn activate Ca2+-dependent enzymes, including transglutaminase 2 (TG2). Transglutaminase 2 is a multifunctional cross-linking enzyme implicated in various physiological and pathological conditions; however, its involvement in respiratory virus-induced airway inflammation is largely unknown. In this study, we demonstrated that RSV-induced oxidative stress promotes enhanced activation and release of TG2 from human lung epithelial cells as a result of its translocation from the cytoplasm and subsequent release into the extracellular space, which was mediated by Toll-like receptor (TLR)-4 and NF-κB pathways. Antioxidant treatment significantly inhibited RSV-induced TG2 extracellular release and activation via blocking viral replication. Also, treatment of RSV-infected lung epithelial cells with TG2 inhibitor significantly reduced RSV-induced matrix metalloprotease activities. These results suggested that RSV-induced oxidative stress activates innate immune receptors in the airways, such as TLRs, that can activate TG2 via the NF-κB pathway to promote cross-linking of extracellular matrix proteins, resulting in enhanced inflammation.
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Affiliation(s)
- Kempaiah Rayavara
- 1Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas
| | - Alexander Kurosky
- 2Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, Texas
| | - Yashoda M. Hosakote
- 1Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, Texas
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12
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Zhang YH, Hoopmann MR, Castaldi PJ, Simonsen KA, Midha MK, Cho MH, Criner GJ, Bueno R, Liu J, Moritz RL, Silverman EK. Lung proteomic biomarkers associated with chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2021; 321:L1119-L1130. [PMID: 34668408 PMCID: PMC8715017 DOI: 10.1152/ajplung.00198.2021] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/27/2021] [Accepted: 10/15/2021] [Indexed: 11/22/2022] Open
Abstract
Identifying protein biomarkers for chronic obstructive pulmonary disease (COPD) has been challenging. Most previous studies have used individual proteins or preselected protein panels measured in blood samples. Mass spectrometry proteomic studies of lung tissue have been based on small sample sizes. We used mass spectrometry proteomic approaches to discover protein biomarkers from 150 lung tissue samples representing COPD cases and controls. Top COPD-associated proteins were identified based on multiple linear regression analysis with false discovery rate (FDR) < 0.05. Correlations between pairs of COPD-associated proteins were examined. Machine learning models were also evaluated to identify potential combinations of protein biomarkers related to COPD. We identified 4,407 proteins passing quality controls. Twenty-five proteins were significantly associated with COPD at FDR < 0.05, including interleukin 33, ferritin (light chain and heavy chain), and two proteins related to caveolae (CAV1 and CAVIN1). Multiple previously reported plasma protein biomarkers for COPD were not significantly associated with proteomic analysis of COPD in lung tissue, although RAGE was borderline significant. Eleven pairs of top significant proteins were highly correlated (r > 0.8), including several strongly correlated with RAGE (EHD2 and CAVIN1). Machine learning models using Random Forests with the top 5% of protein biomarkers demonstrated reasonable accuracy (0.707) and area under the curve (0.714) for COPD prediction. Mass spectrometry-based proteomic analysis of lung tissue is a promising approach for the identification of biomarkers for COPD.
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Affiliation(s)
- Yu-Hang Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Gerard J Criner
- Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jiangyuan Liu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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13
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Xiao C, Cheng S, Lin H, Weng Z, Peng P, Zeng D, Du X, Zhang X, Yang Y, Liang Y, Huang R, Chen C, Wang L, Wu H, Li R, Wang X, Zhang R, Yang Z, Li X, Cao X, Yang W. Isoforskolin, an adenylyl cyclase activator, attenuates cigarette smoke-induced COPD in rats. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2021; 91:153701. [PMID: 34438230 DOI: 10.1016/j.phymed.2021.153701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is characterized by limited airflow due to pulmonary and alveolar abnormalities from exposure to cigarette smoke (CS). Current therapeutic drugs are limited and the development of novel treatments to prevent disease progression is challenging. Isoforskolin (ISOF) from the plant Coleus forskohlii is an effective activator of adenylyl cyclase (AC) isoforms. Previously we found ISOF could attenuate acute lung injury in animal models, while the effect of ISOF on COPD has not been elucidated. PURPOSE In this study, we aimed to evaluate the efficacy of ISOF on COPD and reveal its potential mechanisms. METHODS A rat model of COPD was established by long-term exposure to CS, then the rats were orally administered with ISOF (0.5, 1 and 2 mg/kg). The pulmonary function, lung morphology, inflammatory cells and cytokines in serum or bronchoalveolar lavage fluid (BALF) were evaluated. Transcriptomics, proteomics and network pharmacology analysis were utilized to identify potential mechanisms of ISOF. Droplet digital PCR was used to detect the mRNA expression of AC1-10 in donor lung tissues. AC activation was determined in recombinant human embryonic kidney 293 (HEK293) cells stably expressing human AC isoforms. In addition, ISOF caused trachea relaxation ex vivo were assessed in isolated trachea rings from guinea pigs. RESULTS ISOF significantly ameliorated pathological damage of lung tissue and improved pulmonary function in COPD rats. ISOF treatment decreased the number of inflammatory cells in peripheral blood, and also the levels of pro-inflammatory cytokines in serum and BALF. Consistent with omics-based analyses, ISOF markedly downregulated the mTOR level in lung tissue. Flow cytometry analysis revealed that ISOF treatment reduced the ratio of Th17/Treg cells in peripheral blood. Furthermore, the expression levels of AC1 and AC2 are relatively higher than other AC isoforms in normal lung tissues, and ISOF could potently activate AC1 and AC2 in vitro and significantly relax isolated guinea pig trachea. CONCLUSION Collectively, our studies suggest that ISOF exerts its anti-COPD effect by improving lung function, anti-inflammation and trachea relaxation, which may be related to AC activation, mTOR signaling and Th17/Treg balance.
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Affiliation(s)
- Chuang Xiao
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Sha Cheng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Haochang Lin
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Zhiying Weng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Peihua Peng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Deyou Zeng
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Xiaohua Du
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Xiujuan Zhang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Yaqing Yang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Yaping Liang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Rong Huang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Chen Chen
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Lueli Wang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Hongxiang Wu
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China
| | - Runfeng Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Xinhua Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Rongping Zhang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China.
| | - Xian Li
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
| | - Xue Cao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming 650500, China.
| | - Weimin Yang
- School of Pharmaceutical Science and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming 650500, China.
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14
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Chen L, Liu S, Xiao L, Chen K, Tang J, Huang C, Luo W, Ferrandon D, Lai K, Li Z. An initial assessment of the involvement of transglutaminase2 in eosinophilic bronchitis using a disease model developed in C57BL/6 mice. Sci Rep 2021; 11:11946. [PMID: 34099759 PMCID: PMC8184915 DOI: 10.1038/s41598-021-90950-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/12/2021] [Indexed: 11/09/2022] Open
Abstract
The detailed pathogenesis of eosinophilic bronchitis (EB) remains unclear. Transglutaminase 2 (TG2) has been implicated in many respiratory diseases including asthma. Herein, we aim to assess preliminarily the relationship of TG2 with EB in the context of the development of an appropriate EB model through ovalbumin (OVA) sensitization and challenge in the C57BL/6 mouse strain. Our data lead us to propose a 50 μg dose of OVA challenge as appropriate to establish an EB model in C57BL/6 mice, whereas a challenge with a 400 μg dose of OVA significantly induced asthma. Compared to controls, TG2 is up-regulated in the airway epithelium of EB mice and EB patients. When TG2 activity was inhibited by cystamine treatment, there were no effects on airway responsiveness; in contrast, the lung pathology score and eosinophil counts in bronchoalveolar lavage fluid were significantly increased whereas the cough frequency was significantly decreased. The expression levels of interleukin (IL)-4, IL-13, IL-6, mast cell protease7 and the transient receptor potential (TRP) ankyrin 1 (TRPA1), TRP vanilloid 1 (TRPV1) were significantly decreased. These data open the possibility of an involvement of TG2 in mediating the increased cough frequency in EB through the regulation of TRPA1 and TRPV1 expression. The establishment of an EB model in C57BL/6 mice opens the way for a genetic investigation of the involvement of TG2 and other molecules in this disease using KO mice, which are often generated in the C57BL/6 genetic background.
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Affiliation(s)
- Lan Chen
- Sino-French Hoffmann Institute, Guangzhou, China
| | - Shuyan Liu
- Sino-French Hoffmann Institute, Guangzhou, China
| | - Linzhuo Xiao
- Sino-French Hoffmann Institute, Guangzhou, China
| | - Kanyao Chen
- Sino-French Hoffmann Institute, Guangzhou, China
| | | | - Chuqin Huang
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Wei Luo
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
| | - Dominique Ferrandon
- Sino-French Hoffmann Institute, Guangzhou, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China
- Université de Strasbourg, M3I UPR9022 du CNRS, 67000, Strasbourg, France
| | - Kefang Lai
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China.
| | - Zi Li
- Sino-French Hoffmann Institute, Guangzhou, China.
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, Guangzhou Medical University, Guangzhou, China.
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15
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Lu HH, Zeng HH, Chen Y. Early chronic obstructive pulmonary disease: A new perspective. Chronic Dis Transl Med 2021; 7:79-87. [PMID: 34136767 PMCID: PMC8180470 DOI: 10.1016/j.cdtm.2021.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Indexed: 01/10/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a respiratory disease with a high incidence, mortality, and disability rate. Because there are few symptoms in the early stages of COPD, diagnosis and treatment are seriously insufficient. It is necessary to find effective clues for early COPD diagnosis and provide appropriate interventions. Several studies suggest that small airway disease is the earliest stage of COPD because it is correlated with subsequent development of airflow obstruction. However, there are currently no globally accepted criteria for defining early COPD. This study mainly introduced risk factors, definition, diagnosis, and treatment of early COPD from a new perspective.
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Affiliation(s)
- Huan-Huan Lu
- Department of Respiratory and Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan 410011, China
| | - Hui-Hui Zeng
- Department of Respiratory and Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan 410011, China
| | - Yan Chen
- Department of Respiratory and Critical Care Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China
- Diagnosis and Treatment Center of Respiratory Disease, Central South University, Changsha, Hunan 410011, China
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16
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Shotgun Proteomics of Isolated Urinary Extracellular Vesicles for Investigating Respiratory Impedance in Healthy Preschoolers. Molecules 2021; 26:molecules26051258. [PMID: 33652646 PMCID: PMC7956503 DOI: 10.3390/molecules26051258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/08/2021] [Accepted: 02/18/2021] [Indexed: 01/04/2023] Open
Abstract
Urine proteomic applications in children suggested their potential in discriminating between healthy subjects from those with respiratory diseases. The aim of the current study was to combine protein fractionation, by urinary extracellular vesicle isolation, and proteomics analysis in order to establish whether different patterns of respiratory impedance in healthy preschoolers can be characterized from a protein fingerprint. Twenty-one 3-5-yr-old healthy children, representative of 66 recruited subjects, were selected: 12 late preterm (LP) and 9 full-term (T) born. Children underwent measurement of respiratory impedance through Forced Oscillation Technique (FOT) and no significant differences between LP and T were found. Unbiased clustering, based on proteomic signatures, stratified three groups of children (A, B, C) with significantly different patterns of respiratory impedance, which was slightly worse in group A than in groups B and C. Six proteins (Tripeptidyl peptidase I (TPP1), Cubilin (CUBN), SerpinA4, SerpinF1, Thy-1 membrane glycoprotein (THY1) and Angiopoietin-related protein 2 (ANGPTL2)) were identified in order to type the membership of subjects to the three groups. The differential levels of the six proteins in groups A, B and C suggest that proteomic-based profiles of urinary fractionated exosomes could represent a link between respiratory impedance and underlying biological profiles in healthy preschool children.
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17
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Bchir S, Boumiza S, Ben Nasr H, Garrouch A, Kallel I, Tabka Z, Chahed K. Impact of cathepsin D activity and C224T polymorphism (rs17571) on chronic obstructive pulmonary disease: correlations with oxidative and inflammatory markers. Clin Exp Med 2021; 21:457-465. [PMID: 33611777 DOI: 10.1007/s10238-021-00692-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
BACKGROUND Cathepsin D (CTSD) is an aspartyl proteinase that plays an important role in protein degradation, antigen processing and apoptosis. It has been associated with several pathologies such as cancer, Alzheimer's disease and inflammatory disorders. Its function in lung diseases remains, however, controversial. In the current study, we determined CTSD activity in serum of patients with chronic obstructive pulmonary disease (COPD) and evaluated the correlations between this proteinase and inflammatory and oxidative parameters. We also investigated the impact of a CTSD C224T polymorphism on enzyme activity and clinicopathological parameters. METHODS Our population included 211 healthy controls and 138 patients with COPD. CTSD activity, MMPs (-1/-7/-12), cytokines (IL-6, TNF-α), malondialdehyde (MDA), nitric oxide and peroxynitrite levels were measured in patients and controls using standard methods. Genotyping of CTSD C224T polymorphism was determined using PCR-RFLP. RESULTS Our results showed an increased CTSD activity in COPD patients compared to healthy controls (4.87 [3.99-6.07] vs. 3.94 [2.91-5.84], respectively, p < 0.001). COPD smokers presented also a higher CTSD activity when compared to nonsmokers (4.91[3.98-6.18] vs. 4.65[4.16-5.82], respectively, p = 0.01), while no differences were found when subjects were compared according to their GOLD stages. The activity of this proteinase was not dependent on the C224T polymorphism because we did not found any influence of this SNP on proteinase activity among patients and controls. Furthermore, our data provide the first evidence of the interrelationships between CTSD activity and both MMPs and TNF-α levels (MMP-1[r = - 0.4; p = 0.02], MMP-7[r = 0.37; p = 0.04], MMP-12[r = 0.43; p = 0.02], TNF-α [r = 0.89, p = 0.001]) in COPD smokers. There were no correlations, however, between CTSD activity and oxidative stress parameters in controls and patients. CONCLUSION Our findings suggest that CTSD could be a relevant marker for COPD disease. Alteration of CTSD activity may be related to increased MMPs and TNF-α levels, particularly in COPD smokers.
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Affiliation(s)
- Sarra Bchir
- Laboratoire de Recherche LR19ES09, Physiologie de L'Exercice Et Physiopathologie : de L'Intégré Au Moléculaire Biologie, Médecine Et Santé, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia.
| | - Soumaya Boumiza
- Laboratoire de Recherche LR19ES09, Physiologie de L'Exercice Et Physiopathologie : de L'Intégré Au Moléculaire Biologie, Médecine Et Santé, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Hela Ben Nasr
- Laboratoire de Recherche LR19ES09, Physiologie de L'Exercice Et Physiopathologie : de L'Intégré Au Moléculaire Biologie, Médecine Et Santé, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia.,Institut Des Sciences Infirmières, Sousse, Tunisia
| | | | - Imen Kallel
- Laboratoire de Recherche Toxicologie Microbiologie Environnementale Et Santé LR17ES06, Faculté Des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
| | - Zouhair Tabka
- Laboratoire de Recherche LR19ES09, Physiologie de L'Exercice Et Physiopathologie : de L'Intégré Au Moléculaire Biologie, Médecine Et Santé, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia
| | - Karim Chahed
- Laboratoire de Recherche LR19ES09, Physiologie de L'Exercice Et Physiopathologie : de L'Intégré Au Moléculaire Biologie, Médecine Et Santé, Faculté de Médecine de Sousse, Université de Sousse, Sousse, Tunisia.,Faculté Des Sciences de Sfax, Université de Sfax, Sfax, Tunisia
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18
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Singanayagam A, Glanville N, Cuthbertson L, Bartlett NW, Finney LJ, Turek E, Bakhsoliani E, Calderazzo MA, Trujillo-Torralbo MB, Footitt J, James PL, Fenwick P, Kemp SV, Clarke TB, Wedzicha JA, Edwards MR, Moffatt M, Cookson WO, Mallia P, Johnston SL. Inhaled corticosteroid suppression of cathelicidin drives dysbiosis and bacterial infection in chronic obstructive pulmonary disease. Sci Transl Med 2020; 11:11/507/eaav3879. [PMID: 31462509 DOI: 10.1126/scitranslmed.aav3879] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 02/12/2019] [Accepted: 07/23/2019] [Indexed: 12/11/2022]
Abstract
Bacterial infection commonly complicates inflammatory airway diseases such as chronic obstructive pulmonary disease (COPD). The mechanisms of increased infection susceptibility and how use of the commonly prescribed therapy inhaled corticosteroids (ICS) accentuates pneumonia risk in COPD are poorly understood. Here, using analysis of samples from patients with COPD, we show that ICS use is associated with lung microbiota disruption leading to proliferation of streptococcal genera, an effect that could be recapitulated in ICS-treated mice. To study mechanisms underlying this effect, we used cellular and mouse models of streptococcal expansion with Streptococcus pneumoniae, an important pathogen in COPD, to demonstrate that ICS impairs pulmonary clearance of bacteria through suppression of the antimicrobial peptide cathelicidin. ICS impairment of pulmonary immunity was dependent on suppression of cathelicidin because ICS had no effect on bacterial loads in mice lacking cathelicidin (Camp -/-) and exogenous cathelicidin prevented ICS-mediated expansion of streptococci within the microbiota and improved bacterial clearance. Suppression of pulmonary immunity by ICS was mediated by augmentation of the protease cathepsin D. Collectively, these data suggest a central role for cathepsin D/cathelicidin in the suppression of antibacterial host defense by ICS in COPD. Therapeutic restoration of cathelicidin to boost antibacterial immunity and beneficially modulate the lung microbiota might be an effective strategy in COPD.
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Affiliation(s)
- Aran Singanayagam
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK.
| | - Nicholas Glanville
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Leah Cuthbertson
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Nathan W Bartlett
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK.,Faculty of Health and Medicine and Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW 2305, Australia
| | - Lydia J Finney
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Elena Turek
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Eteri Bakhsoliani
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK
| | | | | | - Joseph Footitt
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Phillip L James
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Peter Fenwick
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Samuel V Kemp
- Royal Brompton Hospital, Fulham Road, London SW2 6NP, UK
| | - Thomas B Clarke
- MRC Centre for Molecular Bacteriology and Infection, Department of Medicine, Imperial College London, London SW7 2AZ, UK
| | - Jadwiga A Wedzicha
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Michael R Edwards
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Miriam Moffatt
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - William O Cookson
- National Heart and Lung Institute, Brompton Campus, Imperial College London, London SW3 6LY, UK
| | - Patrick Mallia
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Sebastian L Johnston
- National Heart and Lung Institute, St Mary's Campus, Imperial College London, London W2 1PG, UK.
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19
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Gao J, Törölä T, Li CX, Ohlmeier S, Toljamo T, Nieminen P, Hattori N, Pulkkinen V, Iwamoto H, Mazur W. Sputum Vitamin D Binding Protein (VDBP) GC1S/1S Genotype Predicts Airway Obstruction: A Prospective Study in Smokers with COPD. Int J Chron Obstruct Pulmon Dis 2020; 15:1049-1059. [PMID: 32546996 PMCID: PMC7237691 DOI: 10.2147/copd.s234464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 04/20/2020] [Indexed: 12/14/2022] Open
Abstract
Introduction The vitamin D binding protein (VDBP, also known as GC-globulin) and vitamin D deficiency have been associated with chronic obstructive pulmonary disease (COPD). rs7041 and rs4588 are two single nucleotide polymorphisms of the VDBP gene, including three common allelic variants (GC1S, GC1F and GC2). Previous studies primarily assessed the serum levels of vitamin D and VDBP in COPD. However, less is known regarding the impact of the local release of VDBP on COPD lung function. Thus, we examined the association of sputum and plasma VDBP with lung function at baseline and at four years, and examined potential genetic polymorphism interactions. Methods The baseline levels of sputum VDBP, plasma VDBP and plasma 25-OH vitamin D, as well as the GC rs4588 and rs7041 genotypes, were assessed in a 4-year Finnish follow-up cohort (n = 233) of non-smokers, and smokers with and without COPD. The associations between the VDBP levels and the longitudinal decline of lung function were further analysed. Results High frequencies of the haplotypes in rs7041/rs4588 were homozygous GC1S/1S (42.5%). Higher sputum VDBP levels in stage I and stage II COPD were observed only in carriers with GC1S/1S genotype when compared with non-smokers (p = 0.034 and p = 0.002, respectively). Genotype multivariate regression analysis indicated that the baseline sputum VDBP and FEV1/FVC ratio at baseline independently predicted FEV1% at follow-up. Discussion and Conclusion The baseline sputum VDBP expression was elevated in smokers with COPD among individuals with the GC1S/1S genotype, and predicted follow-up airway obstruction. Our results suggest that the GC polymorphism should be considered when exploring the potential of VDBP as a biomarker for COPD.
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Affiliation(s)
- Jing Gao
- Heart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tanja Törölä
- Heart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Chuan-Xing Li
- Pulmonomics Group, Respiratory Medicine Unit, Department of Medicine & Centre for Molecular Medicine, Karolinska Institute, Stockholm, Sweden
| | - Steffen Ohlmeier
- Proteomics Core Facility, Biocentre Oulu, Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Tuula Toljamo
- Department of Pulmonary Medicine, Lapland Central Hospital, Rovaniemi, Finland
| | - Pentti Nieminen
- Medical Informatics and Statistics Group, University of Oulu, Oulu, Finland
| | - Noboru Hattori
- Department of Molecular and Internal Medicine, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Ville Pulkkinen
- Heart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hiroshi Iwamoto
- Department of Molecular and Internal Medicine, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Witold Mazur
- Heart and Lung Centre, Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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20
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Abstract
Alpha-1 antitrypsin (AAT) protects the lung by inhibiting neutrophil proteinases, but AAT has many other non-proteolytic functions that are anti-inflammatory, antiviral and homeostatic. Approximately 1 in 1600 to 1 in 5000 people have the homozygous Z mutation, which causes AAT misfolding, accumulation in (predominantly) liver cells and low circulating levels of AAT, leading to AAT deficiency (AATD). AATD is classically a disease of neutrophilic inflammation, with an aggressive and damaging innate immune response contributing to emphysema and other pathologies. AATD is one of the most common genetic disorders but considerably under-recognised. Most patients are diagnosed later in life, by which time they may have accumulated significant lung, liver and multisystem damage. Disease presentation is heterogeneous and not fully explained by deficiency levels alone or exposure to cigarette smoking. This suggests other factors influence AATD-associated pathological processes. Aging itself is associated with organ dysfunction, including emphysema and airflow obstruction, inflammation, altered immune cell responses (termed immunosenescence) and a loss of proteostasis. Many of these processes are present in AATD but at an earlier age and more advanced stage compared with chronological aging alone. Augmentation therapy does not completely abrogate the manifold disease processes present in AATD. New approaches are needed. There is emerging evidence that both age- and AATD-related disease processes are amenable to correction by targeting proteostasis, autophagy, immunosenescence and epigenetic factors. This review explores the impact of the aging process on AATD presentation and discusses novel therapeutic strategies to mitigate low levels of AAT or misfolded AAT in an aging host.
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21
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Horan MP, Hoffmann P, Briggs MT, Condina M, Herbert S, Ito J, Rodger A, McKay M, Maltby D, Crossett B, Abudulai LN, Clarke MW, Badrick T. An external quality assurance trial to assess mass spectrometry protein testing facilities for identifying multiple human peptides. Anal Bioanal Chem 2019; 411:6575-6581. [PMID: 31384985 DOI: 10.1007/s00216-019-02047-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/11/2019] [Accepted: 07/22/2019] [Indexed: 12/13/2022]
Abstract
The application of proteomic liquid chromatography mass spectrometry (LC-MS) for identifying proteins and peptides associated with human disease is rapidly growing in clinical diagnostics. However, the ability to accurately and consistently detect disease-associated peptides remains clinically uncertain. Variability in diagnostic testing occurs in part due to the absence of appropriate reference testing materials and standardised clinical guidelines for proteomic testing. In addition, multiple proteomic testing pipelines have not been fully assessed through external quality assurance (EQA). This trial was therefore devised to evaluate the performance of a small number of mass spectrometry (MS) testing facilities to (i) evaluate the EQA material for potential usage in a proteomic quality assurance program, and to (ii) identify key problem areas associated with human peptide testing. Five laboratories were sent six peptide reference testing samples formulated to contain a total of 35 peptides in differing ratios of light (natural) to heavy (labelled) peptides. Proficiency assessment of laboratory data used a modified approach to similarity and dissimilarity testing that was based on Bray-Curtis and Sorensen indices. Proficiency EQA concordant consensus values could not be derived from the assessed data since none of the laboratories correctly identified all reference testing peptides in all samples. However, the produced data may be reflective of specific inter-laboratory differences for detecting multiple peptides since no two testing pipelines used were the same for any laboratory. In addition, laboratory feedback indicated that peptide filtering of the reference material was a common key problem area prior to analysis. These data highlight the importance of an EQA programme for identifying underlying testing issues so that improvements can be made and confidence for clinical diagnostic analysis can be attained.
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Affiliation(s)
- Martin P Horan
- Royal College of Pathologists of Australasia Quality Assurance Programs, Molecular Genetics, 8 Herbert Street, St Leonard's, Sydney, NSW, 2065, Australia.
| | - Peter Hoffmann
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, GPO Box 2471, Adelaide, SA, 5001, Australia
| | - Matthew T Briggs
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, GPO Box 2471, Adelaide, SA, 5001, Australia
| | - Mark Condina
- Future Industries Institute, Mawson Lakes Campus, University of South Australia, GPO Box 2471, Adelaide, SA, 5001, Australia
| | - Shane Herbert
- Proteomics International Pty Ltd, QEII Medical Centre, 6 Verdun Street, Perth, WA, 6009, Australia
| | - Jason Ito
- Proteomics International Pty Ltd, QEII Medical Centre, 6 Verdun Street, Perth, WA, 6009, Australia
| | - Alison Rodger
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, 4 Wally's Walk, Sydney, NSW, 2109, Australia
| | - Matthew McKay
- Australian Proteome Analysis Facility, Department of Molecular Sciences, Macquarie University, 4 Wally's Walk, Sydney, NSW, 2109, Australia
| | - David Maltby
- Sydney Mass Spectrometry, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Ben Crossett
- Sydney Mass Spectrometry, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Laila N Abudulai
- Metabolomics Australia, Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia.,The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Michael W Clarke
- Metabolomics Australia, Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, Perth, WA, 6009, Australia.,The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Tony Badrick
- Royal College of Pathologists of Australasia Quality Assurance Programs, Molecular Genetics, 8 Herbert Street, St Leonard's, Sydney, NSW, 2065, Australia
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22
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Sun P, Ye R, Wang C, Bai S, Zhao L. Identification of proteomic signatures associated with COPD frequent exacerbators. Life Sci 2019; 230:1-9. [DOI: 10.1016/j.lfs.2019.05.047] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/18/2019] [Indexed: 10/26/2022]
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23
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Kobos L, Teimouri Sendesi SM, Whelton AJ, Boor BE, Howarter JA, Shannahan J. In vitro toxicity assessment of emitted materials collected during the manufacture of water pipe plastic linings. Inhal Toxicol 2019; 31:131-146. [PMID: 31187656 DOI: 10.1080/08958378.2019.1621966] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Objectives: US water infrastructure is in need of widespread repair due to age-related deterioration. Currently, the cured-in-place (CIPP) procedure is the most common method for water pipe repair. This method involves the on-site manufacture of a new polymer composite plastic liner within the damaged pipe. The CIPP process can release materials resulting in occupational and public health concerns. To understand hazards associated with CIPP-related emission exposures, an in vitro toxicity assessment was performed. Materials and Methods: Mouse alveolar epithelial and alveolar macrophage cell lines and condensates collected at 3 worksites utilizing styrene-based resins were utilized for evaluations. All condensate samples were normalized based on the major emission component, styrene. Further, a styrene-only exposure group was used as a control to determine mixture related toxicity. Results: Cytotoxicity differences were observed between worksite samples, with the CIPP worksite 4 sample inducing the most cell death. A proteomic evaluation was performed, which demonstrated styrene-, worksite-, and cell-specific alterations. This examination of protein expression changes determined potential biomarkers of exposure including transglutaminase 2, advillin, collagen type 1, perilipin-2, and others. Pathway analysis of exposure-induced proteomic alterations identified MYC and p53 to be regulators of cellular responses. Protein changes were also related to pathways involved in cell damage, immune response, and cancer. Conclusions: Together these findings demonstrate potential risks associated with the CIPP procedure as well as variations between worksites regarding emissions and toxicity. Our evaluation identified biological pathways that require a future evaluation and also demonstrates that exposure assessment of CIPP worksites should examine multiple chemical components beyond styrene, as many cellular responses were styrene-independent.
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Affiliation(s)
- Lisa Kobos
- a School of Health Sciences, College of Human and Health Sciences , Purdue University , West Lafayette , IN , USA
| | - Seyedeh Mahboobeh Teimouri Sendesi
- b Lyles School of Civil Engineering and Division of Environmental and Ecological Engineering , College of Engineering, Purdue University , West Lafayette , IN , USA
| | - Andrew J Whelton
- b Lyles School of Civil Engineering and Division of Environmental and Ecological Engineering , College of Engineering, Purdue University , West Lafayette , IN , USA
| | - Brandon E Boor
- b Lyles School of Civil Engineering and Division of Environmental and Ecological Engineering , College of Engineering, Purdue University , West Lafayette , IN , USA
| | - John A Howarter
- c Division of Environmental and Ecological Engineering, and School of Materials Engineering, College of Engineering , Purdue University , West Lafayette , IN , USA
| | - Jonathan Shannahan
- a School of Health Sciences, College of Human and Health Sciences , Purdue University , West Lafayette , IN , USA
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24
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Quantitative proteomic profiling of extracellular matrix and site-specific collagen post-translational modifications in an in vitro model of lung fibrosis. Matrix Biol Plus 2019; 1:100005. [PMID: 33543004 PMCID: PMC7852317 DOI: 10.1016/j.mbplus.2019.04.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/21/2022] Open
Abstract
Lung fibrosis is characterized by excessive deposition of extracellular matrix (ECM), in particular collagens, by fibroblasts in the interstitium. Transforming growth factor-β1 (TGF-β1) alters the expression of many extracellular matrix (ECM) components produced by fibroblasts, but such changes in ECM composition as well as modulation of collagen post-translational modification (PTM) levels have not been comprehensively investigated. Here, we performed mass spectrometry (MS)-based proteomics analyses to assess changes in the ECM deposited by cultured lung fibroblasts from idiopathic pulmonary fibrosis (IPF) patients upon stimulation with transforming growth factor β1 (TGF-β1). In addition to the ECM changes commonly associated with lung fibrosis, MS-based label-free quantification revealed profound effects on enzymes involved in ECM crosslinking and turnover as well as multiple positive and negative feedback mechanisms of TGF-β1 signaling. Notably, the ECM changes observed in this in vitro model correlated significantly with ECM changes observed in patient samples. Because collagens are subject to multiple PTMs with major implications in disease, we implemented a new bioinformatic platform to analyze MS data that allows for the comprehensive mapping and site-specific quantitation of collagen PTMs in crude ECM preparations. These analyses yielded a comprehensive map of prolyl and lysyl hydroxylations as well as lysyl glycosylations for 15 collagen chains. In addition, site-specific PTM analysis revealed novel sites of prolyl-3-hydroxylation and lysyl glycosylation in type I collagen. Interestingly, the results show, for the first time, that TGF-β1 can modulate prolyl-3-hydroxylation and glycosylation in a site-specific manner. Taken together, this proof of concept study not only reveals unanticipated TGF-β1 mediated regulation of collagen PTMs and other ECM components but also lays the foundation for dissecting their key roles in health and disease. The proteomic data has been deposited to the ProteomeXchange Consortium via the MassIVE partner repository with the data set identifier MSV000082958. Quantitative proteomics of TGF-β-induced changes in ECM composition and collagen PTM in pulmonary fibroblasts TGF-β promotes crosslinking and turnover as well as complex feedback mechanisms that alter fibroblast ECM homeostasis. A novel bioinformatic workflow for MS data analysis enabled global mapping and quantitation of known and novel collagen PTMs Quantitative assessment of prolyl-3-hydroxylation site occupancy and lysine-O-glycosylation microheterogeneity TGF-β1 modulates collagen PTMs in a site-specific manner that may favor collagen accumulation in lung fibrosis
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Key Words
- 3-HyP, 3-hydroxyproline
- 4-HyP, 4-hydroxyproline
- AGC, automatic gain control
- ANXA11, annexin A11
- BGN, biglycan
- COL1A1, collagen-I alpha 1 chain
- Collagen
- Collagen post-translational modifications
- DCN, decorin
- ECM, extracellular matrix
- Extracellular matrix
- FN1, fibronectin 1
- G-HyK, galactosylhydroxylysine
- GG-HyK, glucosylgalactosylhydroxylysine
- HyK, hydroxylysine
- HyP, hydroxyproline
- ILD, interstitial lung disease
- IPF, idiopathic pulmonary fibrosis
- LH, lysyl hydroxylase
- LOX(L), lysyl oxidase(-like)
- LTBP2, latent-transforming growth factor β -binding protein 2
- Lysyl glycosylation
- Lysyl hydroxylation
- P3H, prolyl-3-hydroxylase
- P4H, prolyl-4-hydroxylase
- PAI1, plasminogen activator inhibitor 1
- PCA, principal component analysis
- PLOD (LH), procollagen-lysine,2-oxoglutarate 5-dioxygenases (lysyl hydroxylases)
- PTM, post-translational modification
- Prolyl hydroxylation
- Pulmonary fibrosis
- SEMA7A, semaphorin 7a
- TGF-β, transforming growth factor β
- TGM2, transglutaminase 1
- Transforming growth factor-β
- VCAN, versican
- Xaa, Xaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- Yaa, Yaa position in the Gly-Xaa-Yaa repeat in triple-helical collagen
- α-SMA, α-smooth muscle actin
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25
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Aydindogan E, Penque D, Zoidakis J. Systematic review on recent potential biomarkers of chronic obstructive pulmonary disease. Expert Rev Mol Diagn 2018; 19:37-45. [DOI: 10.1080/14737159.2018.1559054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Eda Aydindogan
- Department of Biochemistry, Institute of Natural Sciences, Ege University, Izmir, Turkey
| | - Deborah Penque
- Laboratory of Proteomics, Human Genetics Department, Instituto Nacional de Saúde Dr Ricardo Jorge, Lisboa, Portugal
- ToxOmics- Centre of Toxicogenomics and Human Health, Universidade Nova de Lisboa, Lisboa, Portugal
| | - Jerome Zoidakis
- Department of Biotechnology, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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26
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Cardoso AL, Fernandes A, Aguilar-Pimentel JA, de Angelis MH, Guedes JR, Brito MA, Ortolano S, Pani G, Athanasopoulou S, Gonos ES, Schosserer M, Grillari J, Peterson P, Tuna BG, Dogan S, Meyer A, van Os R, Trendelenburg AU. Towards frailty biomarkers: Candidates from genes and pathways regulated in aging and age-related diseases. Ageing Res Rev 2018; 47:214-277. [PMID: 30071357 DOI: 10.1016/j.arr.2018.07.004] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 07/08/2018] [Accepted: 07/10/2018] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Use of the frailty index to measure an accumulation of deficits has been proven a valuable method for identifying elderly people at risk for increased vulnerability, disease, injury, and mortality. However, complementary molecular frailty biomarkers or ideally biomarker panels have not yet been identified. We conducted a systematic search to identify biomarker candidates for a frailty biomarker panel. METHODS Gene expression databases were searched (http://genomics.senescence.info/genes including GenAge, AnAge, LongevityMap, CellAge, DrugAge, Digital Aging Atlas) to identify genes regulated in aging, longevity, and age-related diseases with a focus on secreted factors or molecules detectable in body fluids as potential frailty biomarkers. Factors broadly expressed, related to several "hallmark of aging" pathways as well as used or predicted as biomarkers in other disease settings, particularly age-related pathologies, were identified. This set of biomarkers was further expanded according to the expertise and experience of the authors. In the next step, biomarkers were assigned to six "hallmark of aging" pathways, namely (1) inflammation, (2) mitochondria and apoptosis, (3) calcium homeostasis, (4) fibrosis, (5) NMJ (neuromuscular junction) and neurons, (6) cytoskeleton and hormones, or (7) other principles and an extensive literature search was performed for each candidate to explore their potential and priority as frailty biomarkers. RESULTS A total of 44 markers were evaluated in the seven categories listed above, and 19 were awarded a high priority score, 22 identified as medium priority and three were low priority. In each category high and medium priority markers were identified. CONCLUSION Biomarker panels for frailty would be of high value and better than single markers. Based on our search we would propose a core panel of frailty biomarkers consisting of (1) CXCL10 (C-X-C motif chemokine ligand 10), IL-6 (interleukin 6), CX3CL1 (C-X3-C motif chemokine ligand 1), (2) GDF15 (growth differentiation factor 15), FNDC5 (fibronectin type III domain containing 5), vimentin (VIM), (3) regucalcin (RGN/SMP30), calreticulin, (4) PLAU (plasminogen activator, urokinase), AGT (angiotensinogen), (5) BDNF (brain derived neurotrophic factor), progranulin (PGRN), (6) α-klotho (KL), FGF23 (fibroblast growth factor 23), FGF21, leptin (LEP), (7) miRNA (micro Ribonucleic acid) panel (to be further defined), AHCY (adenosylhomocysteinase) and KRT18 (keratin 18). An expanded panel would also include (1) pentraxin (PTX3), sVCAM/ICAM (soluble vascular cell adhesion molecule 1/Intercellular adhesion molecule 1), defensin α, (2) APP (amyloid beta precursor protein), LDH (lactate dehydrogenase), (3) S100B (S100 calcium binding protein B), (4) TGFβ (transforming growth factor beta), PAI-1 (plasminogen activator inhibitor 1), TGM2 (transglutaminase 2), (5) sRAGE (soluble receptor for advanced glycosylation end products), HMGB1 (high mobility group box 1), C3/C1Q (complement factor 3/1Q), ST2 (Interleukin 1 receptor like 1), agrin (AGRN), (6) IGF-1 (insulin-like growth factor 1), resistin (RETN), adiponectin (ADIPOQ), ghrelin (GHRL), growth hormone (GH), (7) microparticle panel (to be further defined), GpnmB (glycoprotein nonmetastatic melanoma protein B) and lactoferrin (LTF). We believe that these predicted panels need to be experimentally explored in animal models and frail cohorts in order to ascertain their diagnostic, prognostic and therapeutic potential.
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27
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Norman KC, Moore BB, Arnold KB, O’Dwyer DN. Proteomics: Clinical and research applications in respiratory diseases. Respirology 2018; 23:993-1003. [PMID: 30105802 PMCID: PMC6234509 DOI: 10.1111/resp.13383] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/05/2018] [Accepted: 07/19/2018] [Indexed: 12/27/2022]
Abstract
The proteome is the study of the protein content of a definable component of an organism in biology. However, the tissue-specific expression of proteins and the varied post-translational modifications, splice variants and protein-protein complexes that may form, make the study of protein a challenging yet vital tool in answering many of the unanswered questions in medicine and biology to date. Indeed, the spatial, temporal and functional composition of proteins in the human body has proven difficult to elucidate for many years. Given the effect of microRNA and epigenetic regulation on silencing and enhancing gene transcription, the study of protein arguably provides more accurate information on homeostasis and perturbation in health and disease. There have been significant advances in the field of proteomics in recent years, with new technologies and platforms available to the research community. In this review, we briefly discuss some of these new technologies and developments in the context of respiratory disease. We also discuss the types of data science approaches to analyses and interpretation of the large volumes of data generated in proteomic studies. We discuss the application of these technologies with regard to respiratory disease and highlight the potential for proteomics in generating major advances in the understanding of respiratory pathophysiology into the future.
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Affiliation(s)
- Katy C. Norman
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - Bethany B. Moore
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, USA
| | - Kelly B. Arnold
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, USA
| | - David N. O’Dwyer
- Department of Internal Medicine, Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, USA
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28
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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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29
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Fernández-Blanco JA, Fakih D, Arike L, Rodríguez-Piñeiro AM, Martínez-Abad B, Skansebo E, Jackson S, Root J, Singh D, McCrae C, Evans CM, Åstrand A, Ermund A, Hansson GC. Attached stratified mucus separates bacteria from the epithelial cells in COPD lungs. JCI Insight 2018; 3:120994. [PMID: 30185674 DOI: 10.1172/jci.insight.120994] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/31/2018] [Indexed: 02/02/2023] Open
Abstract
The respiratory tract is normally kept essentially free of bacteria by cilia-mediated mucus transport, but in chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF), bacteria and mucus accumulates instead. To address the mechanisms behind the mucus accumulation, the proteome of bronchoalveolar lavages from COPD patients and mucus collected in an elastase-induced mouse model of COPD was analyzed, revealing similarities with each other and with the protein content in colonic mucus. Moreover, stratified laminated sheets of mucus were observed in airways from patients with CF and COPD and in elastase-exposed mice. On the other hand, the mucus accumulation in the elastase model was reduced in Muc5b-KO mice. While mucus plugs were removed from airways by washing with hypertonic saline in the elastase model, mucus remained adherent to epithelial cells. Bacteria were trapped on this mucus, whereas, in non-elastase-treated mice, bacteria were found on the epithelial cells. We propose that the adherence of mucus to epithelial cells observed in CF, COPD, and the elastase-induced mouse model of COPD separates bacteria from the surface cells and, thus, protects the respiratory epithelium.
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Affiliation(s)
- Joan Antoni Fernández-Blanco
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden.,Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - Dalia Fakih
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Liisa Arike
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Elin Skansebo
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Sonya Jackson
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - James Root
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - Dave Singh
- Medicines Evaluation Unit, University of Manchester, Manchester, United Kingdom
| | - Christopher McCrae
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, Gothenburg, Sweden
| | | | - Annika Åstrand
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca Gothenburg, Gothenburg, Sweden
| | - Anna Ermund
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
| | - Gunnar C Hansson
- Department of Medical Biochemistry, University of Gothenburg, Gothenburg, Sweden
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30
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Mižíková I, Pfeffer T, Nardiello C, Surate Solaligue DE, Steenbock H, Tatsukawa H, Silva DM, Vadász I, Herold S, Pease RJ, Iismaa SE, Hitomi K, Seeger W, Brinckmann J, Morty RE. Targeting transglutaminase 2 partially restores extracellular matrix structure but not alveolar architecture in experimental bronchopulmonary dysplasia. FEBS J 2018; 285:3056-3076. [PMID: 29935061 DOI: 10.1111/febs.14596] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/12/2018] [Accepted: 06/21/2018] [Indexed: 12/21/2022]
Abstract
The generation, maturation and remodelling of the extracellular matrix (ECM) are essential for the formation of alveoli during lung development. Alveoli formation is disturbed in preterm infants that develop bronchopulmonary dysplasia (BPD), where collagen fibres are malformed, and perturbations to lung ECM structures may underlie BPD pathogenesis. Malformed ECM structures might result from abnormal protein cross-linking, in part attributable to the increased expression and activity of transglutaminase 2 (TGM2) that have been noted in affected patient lungs, as well as in hyperoxia-based BPD animal models. The objective of the present study was to assess whether TGM2 plays a causal role in normal and aberrant lung alveolarization. Targeted deletion of Tgm2 in C57BL/6J mice increased septal thickness and reduced gas-exchange surface area in otherwise normally developing lungs. During aberrant lung alveolarization that occurred under hyperoxic conditions, collagen structures in Tgm2-/- mice were partially protected from the impact of hyperoxia, where normal dihydroxylysinonorleucine and hydroxylysylpiridinoline collagen cross-link abundance was restored; however, the lung alveolar architecture remained abnormal. Inhibition of transglutaminases (including TGM2) with cysteamine appreciably reduced transglutaminase activity in vivo, as assessed by Nε -(γ-l-glutamyl)-l-lysine abundance and TGM catalytic activity, and restored normal dihydroxylysinonorleucine and hydroxylysylpiridinoline collagen cross-link abundance under pathological conditions. Furthermore, a moderate improvement in alveoli size and gas-exchange surface density was noted in cysteamine-treated mouse lungs in which BPD was modelled. These data indicate that TGM2 plays a role in normal lung alveolarization, and contributes to the formation of aberrant ECM structures during disordered lung alveolarization.
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Affiliation(s)
- Ivana Mižíková
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - Tilman Pfeffer
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - Claudio Nardiello
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - David E Surate Solaligue
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - Heiko Steenbock
- Institute of Virology and Cell Biology, University of Lübeck, Germany
| | - Hideki Tatsukawa
- Graduate School of Pharmaceutical Sciences, Nagoya University, Japan
| | - Diogo M Silva
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - István Vadász
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - Susanne Herold
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - Richard J Pease
- Leeds Institute for Cardiovascular and Metabolic Medicine, University of Leeds, UK
| | - Siiri E Iismaa
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Kiyotaka Hitomi
- Graduate School of Pharmaceutical Sciences, Nagoya University, Japan
| | - Werner Seeger
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
| | - Jürgen Brinckmann
- Institute of Virology and Cell Biology, University of Lübeck, Germany.,Department of Dermatology, University of Lübeck, Germany
| | - Rory E Morty
- Department of Lung Development and Remodelling, Max Planck Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Giessen, Germany, Bad Nauheim, Germany.,Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Germany
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31
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Hussell T, Lui S, Jagger C, Morgan D, Brand O. The consequence of matrix dysfunction on lung immunity and the microbiome in COPD. Eur Respir Rev 2018; 27:27/148/180032. [PMID: 29950305 DOI: 10.1183/16000617.0032-2018] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 06/12/2018] [Indexed: 12/23/2022] Open
Abstract
The pulmonary extracellular matrix (ECM) is a complex network of proteins which primarily defines tissue architecture and regulates various biochemical and biophysical processes. It is a dynamic system comprising two main structures (the interstitial matrix and the basement membrane) which undergo continuous, yet highly regulated, remodelling. This remodelling process is essential for tissue homeostasis and uncontrolled regulation can lead to pathological states including chronic obstructive pulmonary disease (COPD). Altered expression of ECM proteins, as observed in COPD, can contribute to the degradation of alveolar walls and thickening of the small airways which can cause limitations in airflow. Modifications in ECM composition can also impact immune cell migration and retention in the lung with migrating cells becoming entrapped in the diseased airspaces. Furthermore, ECM changes affect the lung microbiome, aggravating and advancing disease progression. A dysbiosis in bacterial diversity can lead to infection, inducing epithelial injury and pro-inflammatory reactions. Here we review the changes noted in the different ECM components in COPD and discuss how an imbalance in microbial commensalism can impact disease development.
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Affiliation(s)
- Tracy Hussell
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
| | - Sylvia Lui
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
| | - Christopher Jagger
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
| | - David Morgan
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
| | - Oliver Brand
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
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32
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Tan HW, Xu YM, Wu DD, Lau ATY. Recent insights into human bronchial proteomics - how are we progressing and what is next? Expert Rev Proteomics 2018; 15:113-130. [PMID: 29260600 DOI: 10.1080/14789450.2017.1417847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The human respiratory system is highly prone to diseases and complications. Many lung diseases, including lung cancer (LC), tuberculosis (TB), and chronic obstructive pulmonary disease (COPD) have been among the most common causes of death worldwide. Cystic fibrosis (CF), the most common genetic disease in Caucasians, has adverse impacts on the lungs. Bronchial proteomics plays a significant role in understanding the underlying mechanisms and pathogenicity of lung diseases and provides insights for biomarker and therapeutic target discoveries. Areas covered: We overview the recent achievements and discoveries in human bronchial proteomics by outlining how some of the different proteomic techniques/strategies are developed and applied in LC, TB, COPD, and CF. Also, the future roles of bronchial proteomics in predictive proteomics and precision medicine are discussed. Expert commentary: Much progress has been made in bronchial proteomics. Owing to the advances in proteomics, we now have better ability to isolate proteins from desired cellular compartments, greater protein separation methods, more powerful protein detection technologies, and more sophisticated bioinformatic techniques. These all contributed to our further understanding of lung diseases and for biomarker and therapeutic target discoveries.
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Affiliation(s)
- Heng Wee Tan
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Yan-Ming Xu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Dan-Dan Wu
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
| | - Andy T Y Lau
- a Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics , Shantou University Medical College , Shantou , People's Republic of China
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33
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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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34
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Metabolomic similarities between bronchoalveolar lavage fluid and plasma in humans and mice. Sci Rep 2017; 7:5108. [PMID: 28698669 PMCID: PMC5505974 DOI: 10.1038/s41598-017-05374-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 05/30/2017] [Indexed: 12/22/2022] Open
Abstract
This observational study catalogues the overlap in metabolites between matched bronchoalveolar lavage fluid (BALF) and plasma, identifies the degree of congruence between these metabolomes in human and mouse, and determines how molecules may change in response to cigarette smoke (CS) exposure. Matched BALF and plasma was collected from mice (ambient air or CS-exposed) and humans (current or former smokers), and analyzed using mass spectrometry. There were 1155 compounds in common in all 4 sample types; fatty acyls and glycerophospholipids strongly overlapped between groups. In humans and mice, more than half of the metabolites present in BALF were also present in plasma. Mouse BALF and human BALF had a strong positive correlation with 2040 metabolites in common, suggesting that mouse models can be used to interrogate human lung metabolome changes. While power was affected by small sample size in the mouse study, the BALF metabolome appeared to be more affected by CS than plasma. CS-exposed mice showed increased plasma and BALF glycerolipids and glycerophospholipids. This is the first report cataloguing the metabolites present across mouse and human, BALF and plasma. Findings are relevant to translational studies where mouse models are used to examine human disease, and where plasma may be interrogated in lieu of BALF or lung tissue.
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35
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Fujii K, Nakamura H, Nishimura T. Recent mass spectrometry-based proteomics for biomarker discovery in lung cancer, COPD, and asthma. Expert Rev Proteomics 2017; 14:373-386. [PMID: 28271730 DOI: 10.1080/14789450.2017.1304215] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Lung cancer and related diseases have been one of the most common causes of deaths worldwide. Genomic-based biomarkers may hardly reflect the underlying dynamic molecular mechanism of functional protein interactions, which is the center of a disease. Recent developments in mass spectrometry (MS) have made it possible to analyze disease-relevant proteins expressed in clinical specimens by proteomic challenges. Areas covered: To understand the molecular mechanisms of lung cancer and its subtypes, chronic obstructive pulmonary disease (COPD), asthma and others, great efforts have been taken to identify numerous relevant proteins by MS-based clinical proteomic approaches. Since lung cancer is a multifactorial disease that is biologically associated with asthma and COPD among various lung diseases, this study focused on proteomic studies on biomarker discovery using various clinical specimens for lung cancer, COPD, and asthma. Expert commentary: MS-based exploratory proteomics utilizing clinical specimens, which can incorporate both experimental and bioinformatic analysis of protein-protein interaction and also can adopt proteogenomic approaches, makes it possible to reveal molecular networks that are relevant to a disease subgroup and that could differentiate between drug responders and non-responders, good and poor prognoses, drug resistance, and so on.
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Affiliation(s)
- Kiyonaga Fujii
- a Department of Translational Medicine Informatics , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan
| | - Haruhiko Nakamura
- a Department of Translational Medicine Informatics , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan.,b Department of Chest Surgery , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan
| | - Toshihide Nishimura
- a Department of Translational Medicine Informatics , St. Marianna University School of Medicine, Miyamae-ku , Kawasaki , Japan
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36
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Prakash YS. Emerging concepts in smooth muscle contributions to airway structure and function: implications for health and disease. Am J Physiol Lung Cell Mol Physiol 2016; 311:L1113-L1140. [PMID: 27742732 DOI: 10.1152/ajplung.00370.2016] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/06/2016] [Indexed: 12/15/2022] Open
Abstract
Airway structure and function are key aspects of normal lung development, growth, and aging, as well as of lung responses to the environment and the pathophysiology of important diseases such as asthma, chronic obstructive pulmonary disease, and fibrosis. In this regard, the contributions of airway smooth muscle (ASM) are both functional, in the context of airway contractility and relaxation, as well as synthetic, involving production and modulation of extracellular components, modulation of the local immune environment, cellular contribution to airway structure, and, finally, interactions with other airway cell types such as epithelium, fibroblasts, and nerves. These ASM contributions are now found to be critical in airway hyperresponsiveness and remodeling that occur in lung diseases. This review emphasizes established and recent discoveries that underline the central role of ASM and sets the stage for future research toward understanding how ASM plays a central role by being both upstream and downstream in the many interactive processes that determine airway structure and function in health and disease.
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Affiliation(s)
- Y S Prakash
- Departments of Anesthesiology, and Physiology & Biomedical Engineering, Mayo Clinic, Rochester, Minnesota
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37
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Kangas SM, Ohlmeier S, Sormunen R, Jouhilahti EM, Peltonen S, Peltonen J, Heape AM. An approach to comprehensive genome and proteome expression analyses in Schwann cells and neurons during peripheral nerve myelin formation. J Neurochem 2016; 138:830-44. [PMID: 27364987 DOI: 10.1111/jnc.13722] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/09/2016] [Accepted: 06/27/2016] [Indexed: 12/01/2022]
Abstract
Peripheral nerve myelination is a complex event resulting from spatially and temporally regulated reciprocal interactions between the neuron and myelin-forming Schwann cells. The dynamic process and the protein functional modules and networks that operate throughout the myelination process are poorly understood because of a lack of methodologies suitable for observing specific changes in the Schwann cell/neuron-unit. The identification of the precise roles for the proteins participating in the functional modules and networks that participate in the myelination process is hindered by the cellular and molecular complexity of the nervous tissue itself. We have developed an approach based on a myelinating dorsal root ganglion explant model that allows distinguishing clear, reproducible and predictable differences between the biochemical properties and the genomic and proteomic expression profiles of both cellular components of the Schwann cell/neuron unit at different stages of the myelination process. This model, derived from E13.5 C57BL/6J mouse embryos, is sufficiently robust for use in identifying the protein functional networks and modules related to peripheral nerve myelin formation. The genomic expression profiles of the selected neuronal, Schwann cell and myelin-specific proteins in the cultures reflect in vivo profiles reported in the literature, and the structural and ultrastructural properties of the myelin, as well as the myelination schedule of the cultures, closely resemble those observed in peripheral nerves in situ. The RNA expression data set is available through NCBI gene expression omnibus accession GSE60345. We have developed a reproducible and robust cell culture-based approach, accompanied by a genome-wide expression data set, which allows studying myelination in the peripheral nervous system at the proteomic and transcriptomic levels in Schwann cells and neurons. Myelinating dorsal root explant cultures, prepared from C57BL/6J mouse embryos, present distinct developmental stages comparable to those observed in a peripheral nerve in situ. This model can be used for identifying the protein functional networks and modules related to peripheral nerve myelin formation.
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Affiliation(s)
- Salla M Kangas
- Cancer and Translational Medicine Research Unit (Anatomy and Cell Biology), University of Oulu, Oulu, Finland.
| | - Steffen Ohlmeier
- Proteomics Core Facility, Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Raija Sormunen
- Biocenter Oulu and Departments of Pathology, University of Oulu, Oulu, Finland
| | - Eeva-Mari Jouhilahti
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sirkku Peltonen
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
| | - Juha Peltonen
- Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Anthony M Heape
- Cancer and Translational Medicine Research Unit (Anatomy and Cell Biology), University of Oulu, Oulu, Finland.
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38
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Ghosh N, Dutta M, Singh B, Banerjee R, Bhattacharyya P, Chaudhury K. Transcriptomics, proteomics and metabolomics driven biomarker discovery in COPD: an update. Expert Rev Mol Diagn 2016; 16:897-913. [PMID: 27267972 DOI: 10.1080/14737159.2016.1198258] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Diagnosis of chronic obstructive pulmonary disease (COPD), characterized by progressive irreversible airflow limitation, remains a challenge. Lack of sensitive diagnostic markers and alternative treatments have limited patients' survival rate. Herein, we provide for clinicians and scientists a comprehensive review on the various omics platforms used to investigate COPD. AREAS COVERED This review consists of articles from PubMed (2009-2016) as well as views of the contributing authors. The review highlights the need for COPD biomarker identification and also provides an update on promising candidate markers identified in various biological fluids using omics technologies. Expert commentary: The multi-omics approach holds promise for the development of robust early stage COPD diagnostic markers, screening of high-risk population, and also improved prognosis which could lead to personalized medicine in future. Various factors regulating an omics study including sample size, control selection, disease phenotyping, usage of complementary techniques and result replication in omics-based research are outlined.
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Affiliation(s)
- Nilanjana Ghosh
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Mainak Dutta
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Brajesh Singh
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
| | - Rintu Banerjee
- b Department of Agricultural & Food Engineering , Indian Institute of Technology Kharagpur , Kharagpur , India
| | | | - Koel Chaudhury
- a School of Medical Science and Technology , Indian Institute of Technology Kharagpur , Kharagpur , India
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