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Ngo LT, Rekowski MJ, Koestler DC, Yorozuya T, Saito A, Azeem I, Harrison A, Demoruelle MK, Boomer J, England BR, Wolters P, Molyneaux PL, Castro M, Lee JS, Solomon JJ, Koronuma K, Washburn MP, Matson SM. Proteomic profiling of bronchoalveolar lavage fluid uncovers protein clusters linked to survival in idiopathic forms of interstitial lung disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.30.24308215. [PMID: 38853991 PMCID: PMC11160891 DOI: 10.1101/2024.05.30.24308215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Idiopathic interstitial pneumonias (IIPs) such as idiopathic pulmonary fibrosis (IPF) and interstitial pneumonia with autoimmune features (IPAF), present diagnostic and therapeutic challenges due to their heterogeneous nature. This study aimed to identify intrinsic molecular signatures within the lung microenvironment of these IIPs through proteomic analysis of bronchoalveolar lavage fluid (BALF). Methods Patients with IIP (n=23) underwent comprehensive clinical evaluation including pre-treatment bronchoscopy and were compared to controls without lung disease (n=5). Proteomic profiling of BALF was conducted using label-free quantitative methods. Unsupervised cluster analyses identified protein expression profiles which were then analyzed to predict survival outcomes and investigate associated pathways. Results Proteomic profiling successfully differentiated IIP from controls. k-means clustering, based on protein expression revealed three distinct IIP clusters, which were not associated with age, smoking history, or baseline pulmonary function. These clusters had unique survival trajectories and provided more accurate survival predictions than the Gender Age Physiology (GAP) index (C-index 0.794 vs. 0.709). The cluster with the worst prognosis featured decreased inflammatory signaling and complement activation, with pathway analysis highlighting altered immune response pathways related to immunoglobulin production and B cell-mediated immunity. Conclusions The unsupervised clustering of BALF proteomics provided a novel stratification of IIP patients, with potential implications for prognostic and therapeutic targeting. The identified molecular phenotypes underscore the diversity within the IIP classification and the potential importance of personalized treatments for these conditions. Future validation in larger, multi-ethnic cohorts is essential to confirm these findings and to explore their utility in clinical decision-making for patients with IIP.
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Affiliation(s)
- Linh T. Ngo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Michaella J. Rekowski
- Department of Cancer Biology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Devin C. Koestler
- Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, USA
| | - Takafumi Yorozuya
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Atsushi Saito
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Imaan Azeem
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Alexis Harrison
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - M. Kristen Demoruelle
- Division of Rheumatology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jonathan Boomer
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Bryant R. England
- Division of Rheumatology & Immunology, University of Nebraska Medical Center, Omaha, NE USA and Veterans Affairs Nebraska-Western Iowa Health Care System, Omaha, NE, USA
| | - Paul Wolters
- Division of Pulmonary and Critical Care Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Joyce S. Lee
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Aurora, CO, USA
| | - Joshua J. Solomon
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health Hospital, Denver, CO
| | - Koji Koronuma
- Department of Respiratory Medicine and Allergology, Sapporo Medical University, Sapporo, Japan
| | - Michael P. Washburn
- Department of Cancer Biology, University of Kansas School of Medicine, Kansas City, KS, USA
| | - Scott M. Matson
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, KS, USA
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Herb M. NADPH Oxidase 3: Beyond the Inner Ear. Antioxidants (Basel) 2024; 13:219. [PMID: 38397817 PMCID: PMC10886416 DOI: 10.3390/antiox13020219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Reactive oxygen species (ROS) were formerly known as mere byproducts of metabolism with damaging effects on cellular structures. The discovery and description of NADPH oxidases (Nox) as a whole enzyme family that only produce this harmful group of molecules was surprising. After intensive research, seven Nox isoforms were discovered, described and extensively studied. Among them, the NADPH oxidase 3 is the perhaps most underrated Nox isoform, since it was firstly discovered in the inner ear. This stigma of Nox3 as "being only expressed in the inner ear" was also used by me several times. Therefore, the question arose whether this sentence is still valid or even usable. To this end, this review solely focuses on Nox3 and summarizes its discovery, the structural components, the activating and regulating factors, the expression in cells, tissues and organs, as well as the beneficial and detrimental effects of Nox3-mediated ROS production on body functions. Furthermore, the involvement of Nox3-derived ROS in diseases progression and, accordingly, as a potential target for disease treatment, will be discussed.
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Affiliation(s)
- Marc Herb
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine, University Hospital Cologne, University of Cologne, 50935 Cologne, Germany;
- German Centre for Infection Research, Partner Site Bonn-Cologne, 50931 Cologne, Germany
- Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases (CECAD), 50931 Cologne, Germany
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3
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Samarelli AV, Tonelli R, Raineri G, Bruzzi G, Andrisani D, Gozzi F, Marchioni A, Costantini M, Fabbiani L, Genovese F, Pinetti D, Manicardi L, Castaniere I, Masciale V, Aramini B, Tabbì L, Rizzato S, Bettelli S, Manfredini S, Dominici M, Clini E, Cerri S. Proteomic profiling of formalin-fixed paraffine-embedded tissue reveals key proteins related to lung dysfunction in idiopathic pulmonary fibrosis. Front Oncol 2024; 13:1275346. [PMID: 38322285 PMCID: PMC10844556 DOI: 10.3389/fonc.2023.1275346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/29/2023] [Indexed: 02/08/2024] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) severely affects the lung leading to aberrant deposition of extracellular matrix and parenchymal stiffness with progressive functional derangement. The limited availability of fresh tissues represents one of the major limitations to study the molecular profiling of IPF lung tissue. The primary aim of this study was to explore the proteomic profiling yield of archived formalin-fixed paraffin-embedded (FFPE) specimens of IPF lung tissues. Methods We further determined the protein expression according to respiratory functional decline at the time of biopsy. The total proteins isolated from 11 FFPE samples of IPF patients compared to 3 FFPE samples from a non-fibrotic lung defined as controls, were subjected to label-free quantitative proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS) and resulted in the detection of about 400 proteins. Results After the pairwise comparison between controls and IPF, functional enrichment analysis identified differentially expressed proteins that were involved in extracellular matrix signaling pathways, focal adhesion and transforming growth factor β (TGF-β) signaling pathways strongly associated with IPF onset and progression. Five proteins were significantly over- expressed in the lung of IPF patients with either advanced disease stage (Stage II) or impaired pulmonary function (FVC<75, DLCO<55) compared to controls; these were lymphocyte cytosolic protein 1 (LCP1), peroxiredoxin-2 (PRDX2), transgelin 2 (TAGLN2), lumican (LUM) and mimecan (OGN) that might play a key role in the fibrogenic processes. Discussion Our work showed that the analysis of FFPE samples was able to identify key proteins that might be crucial for the IPF pathogenesis. These proteins are correlated with lung carcinogenesis or involved in the immune landscape of lung cancer, thus making possible common mechanisms between lung carcinogenesis and fibrosis progression, two pathological conditions at risk for each other in the real life.
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Affiliation(s)
- Anna Valeria Samarelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Roberto Tonelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Giulia Raineri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Giulia Bruzzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Dario Andrisani
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Filippo Gozzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Alessandro Marchioni
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Matteo Costantini
- Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Luca Fabbiani
- Pathology Institute, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
- Immunohistochemistry Lab, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Filippo Genovese
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy
| | - Diego Pinetti
- Centro Interdipartimentale Grandi Strumenti (C.I.G.S.), University of Modena and Reggio Emilia, Modena, Italy
| | - Linda Manicardi
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Ivana Castaniere
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Valentina Masciale
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
- Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Beatrice Aramini
- Division of Thoracic Surgery, Department of Medical and Surgical Sciences-Diagnostic and Specialty Medicine (DIMEC) of the Alma Mater Studiorum, University of Bologna G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy
| | - Luca Tabbì
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Simone Rizzato
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Stefania Bettelli
- Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy
| | - Samantha Manfredini
- Molecular Pathology and Predictive Medicine Unit, Modena Cancer Center, University Hospital of Modena, Modena, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
- Oncology Unit, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Enrico Clini
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
| | - Stefania Cerri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, University Hospital of Modena, Modena, Italy
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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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5
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Kim Y, Kim Y, Lim HJ, Kim DK, Park JH, Oh CM. Integrative single-cell transcriptome analysis provides new insights into post-COVID-19 pulmonary fibrosis and potential therapeutic targets. J Med Virol 2023; 95:e29201. [PMID: 37966390 DOI: 10.1002/jmv.29201] [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: 07/26/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023]
Abstract
The global COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 virus has resulted in a significant number of patients experiencing persistent symptoms, including post-COVID pulmonary fibrosis (PCPF). This study aimed to identify novel therapeutic targets for PCPF using single-cell RNA-sequencing data from lung tissues of COVID-19 patients, idiopathic pulmonary fibrosis (IPF) patients, and a rat transforming growth factor beta-1-induced fibrosis model treated with antifibrotic drugs. Patients with COVID-19 had lower alveolar macrophage counts than healthy controls, whereas patients with COVID-19 and IPF presented with elevated monocyte-derived macrophage counts. A comparative transcriptome analysis showed that macrophages play a crucial role in IPF and COVID-19 development and progression, and fibrosis- and inflammation-associated genes were upregulated in both conditions. Functional enrichment analysis revealed the upregulation of inflammation and proteolysis and the downregulation of ribosome biogenesis. Cholesterol efflux and glycolysis were augmented in both macrophage types. The study suggests that antifibrotic drugs may reverse critical lung fibrosis mediators in COVID-19. The results help clarify the molecular mechanisms underlying pulmonary fibrosis in patients with severe COVID-19 and IPF and highlight the potential efficacy of antifibrotic drugs in COVID-19 therapy. Collectively, all these findings may have significant implications for the development of new treatment strategies for PCPF.
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Affiliation(s)
- Yumin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Yeongmin Kim
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Hyobin Julianne Lim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Dae-Kyum Kim
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ji-Hwan Park
- Korea Bioinformation Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Chang-Myung Oh
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
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Spasovski V, Andjelkovic M, Parezanovic M, Komazec J, Ugrin M, Klaassen K, Stojiljkovic M. The Role of Autophagy and Apoptosis in Affected Skin and Lungs in Patients with Systemic Sclerosis. Int J Mol Sci 2023; 24:11212. [PMID: 37446389 DOI: 10.3390/ijms241311212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/29/2023] [Accepted: 07/01/2023] [Indexed: 07/15/2023] Open
Abstract
Systemic sclerosis (SSc) is a complex autoimmune inflammatory disorder with multiple organ involvement. Skin changes present the hallmark of SSc and coincide with poor prognosis. Interstitial lung diseases (ILD) are the most widely reported complications in SSc patients and the primary cause of death. It has been proposed that the processes of autophagy and apoptosis could play a significant role in the pathogenesis and clinical course of different autoimmune diseases, and accordingly in SSc. In this manuscript, we review the current knowledge of autophagy and apoptosis processes in the skin and lungs of patients with SSc. Profiling of markers involved in these processes in skin cells can be useful to recognize the stage of fibrosis and can be used in the clinical stratification of patients. Furthermore, the knowledge of the molecular mechanisms underlying these processes enables the repurposing of already known drugs and the development of new biological therapeutics that aim to reverse fibrosis by promoting apoptosis and regulate autophagy in personalized treatment approach. In SSc-ILD patients, the molecular signature of the lung tissues of each patient could be a distinctive criterion in order to establish the correct lung pattern, which directly impacts the course and prognosis of the disease. In this case, resolving the role of tissue-specific markers, which could be detected in the circulation using sensitive molecular methods, would be an important step toward development of non-invasive diagnostic procedures that enable early and precise diagnosis and preventing the high mortality of this rare disease.
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Affiliation(s)
- Vesna Spasovski
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Marina Andjelkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Marina Parezanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Jovana Komazec
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Milena Ugrin
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Kristel Klaassen
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
| | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Vojvode Stepe 444a, 11042 Belgrade, Serbia
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Principi L, Ferrini E, Ciccimarra R, Pagani L, Chinello C, Previtali P, Smith A, Villetti G, Zoboli M, Ravanetti F, Stellari FF, Magni F, Piga I. Proteomic Fingerprint of Lung Fibrosis Progression and Response to Therapy in Bleomycin-Induced Mouse Model. Int J Mol Sci 2023; 24:ijms24054410. [PMID: 36901840 PMCID: PMC10002924 DOI: 10.3390/ijms24054410] [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: 12/02/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease characterized by the aberrant accumulation of extracellular matrix in the lungs. nintedanib is one of the two FDA-approved drugs for IPF treatment; however, the exact pathophysiological mechanisms of fibrosis progression and response to therapy are still poorly understood. In this work, the molecular fingerprint of fibrosis progression and response to nintedanib treatment have been investigated by mass spectrometry-based bottom-up proteomics in paraffin-embedded lung tissues from bleomycin-induced (BLM) pulmonary fibrosis mice. Our proteomics results unveiled that (i) samples clustered depending on the tissue fibrotic grade (mild, moderate, and severe) and not on the time course after BLM treatment; (ii) the dysregulation of different pathways involved in fibrosis progression such as the complement coagulation cascades, advanced glycation end products (AGEs) and their receptors (RAGEs) signaling, the extracellular matrix-receptor interaction, the regulation of actin cytoskeleton, and ribosomes; (iii) Coronin 1A (Coro1a) as the protein with the highest correlation when evaluating the progression of fibrosis, with an increased expression from mild to severe fibrosis; and (iv) a total of 10 differentially expressed proteins (padj-value ≤ 0.05 and Fold change ≤-1.5 or ≥1.5), whose abundance varied in the base of the severity of fibrosis (mild and moderate), were modulated by the antifibrotic treatment with nintedanib, reverting their trend. Notably, nintedanib significantly restored lactate dehydrogenase B (Ldhb) expression but not lactate dehydrogenase A (Ldha). Notwithstanding the need for further investigations to validate the roles of both Coro1a and Ldhb, our findings provide an extensive proteomic characterization with a strong relationship with histomorphometric measurements. These results unveil some biological processes in pulmonary fibrosis and drug-mediated fibrosis therapy.
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Affiliation(s)
- Lucrezia Principi
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Erica Ferrini
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | - Roberta Ciccimarra
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | - Lisa Pagani
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Clizia Chinello
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Paolo Previtali
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Andrew Smith
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Gino Villetti
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.p.A., 43122 Parma, Italy
| | - Matteo Zoboli
- Department of Veterinary Science, University of Parma, 43122 Parma, Italy
| | | | - Franco Fabio Stellari
- Experimental Pharmacology & Translational Science Department, Chiesi Farmaceutici S.p.A., 43122 Parma, Italy
- Correspondence: (F.F.S.); (I.P.)
| | - Fulvio Magni
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
| | - Isabella Piga
- Clinical Proteomics and Metabolomics Unit, Department of Medicine and Surgery, University of Milano-Bicocca, 20854 Monza, Italy
- Correspondence: (F.F.S.); (I.P.)
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Dobrinskikh E, Hennessy CE, Kurche JS, Kim E, Estrella AM, Cardwell J, Yang IV, Schwartz DA. Epithelial Endoplasmic Reticulum Stress Enhances the Risk of Muc5b-associated Lung Fibrosis. Am J Respir Cell Mol Biol 2023; 68:62-74. [PMID: 36108173 PMCID: PMC9817917 DOI: 10.1165/rcmb.2022-0252oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 09/15/2022] [Indexed: 02/05/2023] Open
Abstract
The gain-of-function minor allele of the MUC5B (mucin 5B, oligomeric mucus/gel-forming) promoter (rs35705950) is the strongest risk factor for idiopathic pulmonary fibrosis (IPF), a devastating fibrotic lung disease that leads to progressive respiratory failure in adults. We have previously demonstrated that Muc5b overexpression in mice worsens lung fibrosis after bleomycin exposure and have hypothesized that excess Muc5b promotes endoplasmic reticulum (ER) stress and apoptosis, stimulating fibrotic lung injury. Here, we report that ER stress pathway members ATF4 (activating transcription factor 4) and ATF6 coexpress with MUC5B in epithelia of the distal IPF airway and honeycomb cyst and that this is more pronounced in carriers of the gain-of-function MUC5B promoter variant. Similarly, in mice exposed to bleomycin, Muc5b expression is temporally associated with markers of ER stress. Using bulk and single-cell RNA sequencing in bleomycin-exposed mice, we found that pathologic ER stress-associated transcripts Atf4 and Ddit3 (DNA damage inducible transcript 3) were elevated in alveolar epithelia of SFTPC-Muc5b transgenic (SFTPC-Muc5bTg) mice relative to wild-type (WT) mice. Activation of the ER stress response inhibits protein translation for most genes by phosphorylation of Eif2α (eukaryotic translation initiation factor 2 alpha), which prevents guanine exchange by Eif2B and facilitates translation of Atf4. The integrated stress response inhibitor (ISRIB) facilitates interaction of phosphorylated Eif2α with Eif2B, overcoming translation inhibition associated with ER stress and reducing Atf4. We found that a single dose of ISRIB diminished Atf4 translation in SFTPC-Muc5bTg mice after bleomycin injury. Moreover, ISRIB resolved the exaggerated fibrotic response of SFTPC-Muc5bTg mice to bleomycin. In summary, we demonstrate that MUC5B and Muc5b expression is associated with pathologic ER stress and that restoration of normal translation with a single dose of ISRIB promotes lung repair in bleomycin-injured Muc5b-overexpressing mice.
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Affiliation(s)
| | | | - Jonathan S. Kurche
- Department of Medicine
- Pulmonary Section, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, Colorado
| | | | - Alani M. Estrella
- Roy and Diana Vagelos College of Physicians and Surgeons, Columbia University Medical Center, New York, New York; and
| | | | - Ivana V. Yang
- Department of Medicine
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
| | - David A. Schwartz
- Department of Medicine
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado
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Cell-Specific Response of NSIP- and IPF-Derived Fibroblasts to the Modification of the Elasticity, Biological Properties, and 3D Architecture of the Substrate. Int J Mol Sci 2022; 23:ijms232314714. [PMID: 36499041 PMCID: PMC9738992 DOI: 10.3390/ijms232314714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/18/2022] [Accepted: 11/22/2022] [Indexed: 11/26/2022] Open
Abstract
The fibrotic fibroblasts derived from idiopathic pulmonary fibrosis (IPF) and nonspecific interstitial pneumonia (NSIP) are surrounded by specific environments, characterized by increased stiffness, aberrant extracellular matrix (ECM) composition, and altered lung architecture. The presented research was aimed at investigating the effect of biological, physical, and topographical modification of the substrate on the properties of IPF- and NSIP-derived fibroblasts, and searching for the parameters enabling their identification. Soft and stiff polydimethylsiloxane (PDMS) was chosen for the basic substrates, the properties of which were subsequently tuned. To obtain the biological modification of the substrates, they were covered with ECM proteins, laminin, fibronectin, and collagen. The substrates that mimicked the 3D structure of the lungs were prepared using two approaches, resulting in porous structures that resemble natural lung architecture and honeycomb patterns, typical of IPF tissue. The growth of cells on soft and stiff PDMS covered with proteins, traced using fluorescence microscopy, confirmed an altered behavior of healthy and IPF- and NSIP-derived fibroblasts in response to the modified substrate properties, enabling their identification. In turn, differences in the mechanical properties of healthy and fibrotic fibroblasts, determined using atomic force microscopy working in force spectroscopy mode, as well as their growth on 3D-patterned substrates were not sufficient to discriminate between cell lines.
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10
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Korfei M, Mahavadi P, Guenther A. Targeting Histone Deacetylases in Idiopathic Pulmonary Fibrosis: A Future Therapeutic Option. Cells 2022; 11:cells11101626. [PMID: 35626663 PMCID: PMC9139813 DOI: 10.3390/cells11101626] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with limited therapeutic options, and there is a huge unmet need for new therapies. A growing body of evidence suggests that the histone deacetylase (HDAC) family of transcriptional corepressors has emerged as crucial mediators of IPF pathogenesis. HDACs deacetylate histones and result in chromatin condensation and epigenetic repression of gene transcription. HDACs also catalyse the deacetylation of many non-histone proteins, including transcription factors, thus also leading to changes in the transcriptome and cellular signalling. Increased HDAC expression is associated with cell proliferation, cell growth and anti-apoptosis and is, thus, a salient feature of many cancers. In IPF, induction and abnormal upregulation of Class I and Class II HDAC enzymes in myofibroblast foci, as well as aberrant bronchiolar epithelium, is an eminent observation, whereas type-II alveolar epithelial cells (AECII) of IPF lungs indicate a significant depletion of many HDACs. We thus suggest that the significant imbalance of HDAC activity in IPF lungs, with a “cancer-like” increase in fibroblastic and bronchial cells versus a lack in AECII, promotes and perpetuates fibrosis. This review focuses on the mechanisms by which Class I and Class II HDACs mediate fibrogenesis and on the mechanisms by which various HDAC inhibitors reverse the deregulated epigenetic responses in IPF, supporting HDAC inhibition as promising IPF therapy.
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Affiliation(s)
- Martina Korfei
- Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, D-35392 Giessen, Germany; (P.M.); (A.G.)
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), D-35392 Giessen, Germany
- Correspondence: ; Tel.: +49-641-9942425; Fax: +49-641-9942429
| | - Poornima Mahavadi
- Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, D-35392 Giessen, Germany; (P.M.); (A.G.)
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), D-35392 Giessen, Germany
| | - Andreas Guenther
- Biomedical Research Center Seltersberg (BFS), Justus Liebig University Giessen, D-35392 Giessen, Germany; (P.M.); (A.G.)
- Department of Internal Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), D-35392 Giessen, Germany
- Lung Clinic, Evangelisches Krankenhaus Mittelhessen, D-35398 Giessen, Germany
- European IPF Registry and Biobank, D-35392 Giessen, Germany
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11
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Moss BJ, Ryter SW, Rosas IO. Pathogenic Mechanisms Underlying Idiopathic Pulmonary Fibrosis. ANNUAL REVIEW OF PATHOLOGY 2022; 17:515-546. [PMID: 34813355 DOI: 10.1146/annurev-pathol-042320-030240] [Citation(s) in RCA: 183] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pathogenesis of idiopathic pulmonary fibrosis (IPF) involves a complex interplay of cell types and signaling pathways. Recurrent alveolar epithelial cell (AEC) injury may occur in the context of predisposing factors (e.g., genetic, environmental, epigenetic, immunologic, and gerontologic), leading to metabolic dysfunction, senescence, aberrant epithelial cell activation, and dysregulated epithelial repair. The dysregulated epithelial cell interacts with mesenchymal, immune, and endothelial cells via multiple signaling mechanisms to trigger fibroblast and myofibroblast activation. Recent single-cell RNA sequencing studies of IPF lungs support the epithelial injury model. These studies have uncovered a novel type of AEC with characteristics of an aberrant basal cell, which may disrupt normal epithelial repair and propagate a profibrotic phenotype. Here, we review the pathogenesis of IPF in the context of novel bioinformatics tools as strategies to discover pathways of disease, cell-specific mechanisms, and cell-cell interactions that propagate the profibrotic niche.
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Affiliation(s)
- Benjamin J Moss
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
| | - Stefan W Ryter
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA;
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Baylor College of Medicine, Houston, Texas 77030, USA; ,
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12
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Qiu L, Gong G, Wu W, Li N, Li Z, Chen S, Li P, Chen T, Zhao H, Hu C, Fang Z, Wang Y, Liu H, Cui P, Zhang G. A novel prognostic signature for idiopathic pulmonary fibrosis based on five-immune-related genes. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1570. [PMID: 34790776 PMCID: PMC8576669 DOI: 10.21037/atm-21-4545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/02/2021] [Indexed: 01/04/2023]
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a highly fatal lung disease of unknown etiology with a median survival after diagnosis of only 2–3 years. Its poor prognosis is due to the limited therapy options available as well as the lack of effective prognostic indicators. This study aimed to construct a novel prognostic signature for IPF to assist in the personalized management of IPF patients during treatment. Methods Differentially-expressed genes (DEGs) in IPF patients versus healthy individuals were analyzed using the “limma” package of R software. Immune-related genes (IRGs) were obtained from the ImmPort database. Univariate Cox regression analysis was adopted to screen significantly prognostic IRGs for IPF patients. Multiple Cox regression analysis was used to identify optimal prognostic IRGs and construct a prognostic signature. Results Compared with healthy individuals, there were a total of 52 prognosis-related DEGs in the bronchoalveolar lavage (BAL) samples of IPF patients, of which 37 genes were identified as IRGs. Of these, five genes (CXCL14, SLC40A1, RNASE3, CCR3, and RORA) were significantly associated with overall survival (OS) in IPF patients, and were utilized for establishment of the prognostic signature. IPF patients were divided into high- and low-risk groups based on the prognostic signature. Marked differences in the OS probability were observed between high- and low-risk IPF patients. The area under curves (AUCs) of the receiver operating characteristic (ROC) curve for the prognostic signature in the training and validation cohorts were 0.858 and 0.837, respectively. The expression levels between RNASE3 and SLC40A1 (P<0.01, r=0.394), between RORA and CXCL14 (P<0.01, r=−0.355), between CCR3 and CXCL14 (P<0.01, r=0.258), as well as between RNASE3 and CCR3 (P<0.01, r=0.293) were significantly correlated. Conclusions We developed a validated and reproducible IRG-based prognostic signature that should be helpful in the personalized management of patients with IPF, providing new insights into the relationship between the immune system and IPF.
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Affiliation(s)
- Lingxiao Qiu
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China
| | - Gencheng Gong
- 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, China
| | - Wenjuan Wu
- Department of Geriatric Medicine, Henan Provincial People's Hospital, Zhengzhou, China
| | - Nana Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhaonan Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shanshan Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China
| | - Ping Li
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China.,Zhengzhou Key Laboratory for Chronic Respiratory Disease, Zhengzhou, China
| | - Tengfei Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huasi Zhao
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunling Hu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zeming Fang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Wang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hongping Liu
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Panpan Cui
- School of Nursing and Heath, Zhengzhou University, Zhengzhou, China
| | - Guojun Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.,Henan Provincial Medical Key Laboratory for Interstitial Lung Disease and Lung Transplantation, Zhengzhou, China.,Zhengzhou Key Laboratory for Chronic Respiratory Disease, Zhengzhou, China
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13
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Pharmacological targeting of endoplasmic reticulum stress in disease. Nat Rev Drug Discov 2021; 21:115-140. [PMID: 34702991 DOI: 10.1038/s41573-021-00320-3] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2021] [Indexed: 02/08/2023]
Abstract
The accumulation of misfolded proteins in the endoplasmic reticulum (ER) leads to ER stress, resulting in activation of the unfolded protein response (UPR) that aims to restore protein homeostasis. However, the UPR also plays an important pathological role in many diseases, including metabolic disorders, cancer and neurological disorders. Over the last decade, significant effort has been invested in targeting signalling proteins involved in the UPR and an array of drug-like molecules is now available. However, these molecules have limitations, the understanding of which is crucial for their development into therapies. Here, we critically review the existing ER stress and UPR-directed drug-like molecules, highlighting both their value and their limitations.
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14
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Proteomic Analysis Reveals Key Proteins in Extracellular Vesicles Cargo Associated with Idiopathic Pulmonary Fibrosis In Vitro. Biomedicines 2021; 9:biomedicines9081058. [PMID: 34440261 PMCID: PMC8394197 DOI: 10.3390/biomedicines9081058] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 12/29/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, irreversible, and highly fatal disease. It is characterized by the increased activation of both fibroblast and myofibroblast that results in excessive extracellular matrix (ECM) deposition. Extracellular vesicles (EVs) have been described as key mediators of intercellular communication in various pathologies. However, the role of EVs in the development of IPF remains poorly understood. This study aimed to characterize the differentially expressed proteins contained within EVs cargo derived from the fibroblast cell lines LL97A (IPF-1) and LL29 (IPF-2) isolated from lungs bearing IPF as compared to those derived from the fibroblast cell lines CCD8Lu (NL-1) and CCD19Lu (NL-2) isolated from healthy donors. Isolated EVs were subjected to label-free quantitative proteomic analysis by LC-MS/MS, and as a result, 331 proteins were identified. Differentially expressed proteins were obtained after the pairwise comparison, including all experimental groups. A total of 86 differentially expressed proteins were identified in either one or more comparison groups. Of note, proteins involved in fibrogenic processes, such as tenascin-c (TNC), insulin-like-growth-factor-binding protein 7 (IGFBP7), fibrillin-1 (FBN1), alpha-2 collagen chain (I) (COL1A2), alpha-1 collagen chain (I) (COL1A1), and lysyl oxidase homolog 1 (LOXL1), were identified in EVs cargo isolated from IPF cell lines. Additionally, KEGG pathway enrichment analysis revealed that differentially expressed proteins participate in focal adhesion, PI3K-Akt, and ECM–receptor interaction signaling pathways. In conclusion, our findings reveal that proteins contained within EVs cargo might play key roles during IPF pathogenesis.
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15
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Samarelli AV, Tonelli R, Marchioni A, Bruzzi G, Gozzi F, Andrisani D, Castaniere I, Manicardi L, Moretti A, Tabbì L, Cerri S, Beghè B, Dominici M, Clini E. Fibrotic Idiopathic Interstitial Lung Disease: The Molecular and Cellular Key Players. Int J Mol Sci 2021; 22:8952. [PMID: 34445658 PMCID: PMC8396471 DOI: 10.3390/ijms22168952] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/05/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Interstitial lung diseases (ILDs) that are known as diffuse parenchymal lung diseases (DPLDs) lead to the damage of alveolar epithelium and lung parenchyma, culminating in inflammation and widespread fibrosis. ILDs that account for more than 200 different pathologies can be divided into two groups: ILDs that have a known cause and those where the cause is unknown, classified as idiopathic interstitial pneumonia (IIP). IIPs include idiopathic pulmonary fibrosis (IPF), non-specific interstitial pneumonia (NSIP), cryptogenic organizing pneumonia (COP) known also as bronchiolitis obliterans organizing pneumonia (BOOP), acute interstitial pneumonia (AIP), desquamative interstitial pneumonia (DIP), respiratory bronchiolitis-associated interstitial lung disease (RB-ILD), and lymphocytic interstitial pneumonia (LIP). In this review, our aim is to describe the pathogenic mechanisms that lead to the onset and progression of the different IIPs, starting from IPF as the most studied, in order to find both the common and standalone molecular and cellular key players among them. Finally, a deeper molecular and cellular characterization of different interstitial lung diseases without a known cause would contribute to giving a more accurate diagnosis to the patients, which would translate to a more effective treatment decision.
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Affiliation(s)
- Anna Valeria Samarelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Roberto Tonelli
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
- Clinical and Experimental Medicine PhD Program, University of Modena Reggio Emilia, 41100 Modena, Italy
| | - Alessandro Marchioni
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Giulia Bruzzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Filippo Gozzi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
- Clinical and Experimental Medicine PhD Program, University of Modena Reggio Emilia, 41100 Modena, Italy
| | - Dario Andrisani
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
- Clinical and Experimental Medicine PhD Program, University of Modena Reggio Emilia, 41100 Modena, Italy
| | - Ivana Castaniere
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
- Clinical and Experimental Medicine PhD Program, University of Modena Reggio Emilia, 41100 Modena, Italy
| | - Linda Manicardi
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Antonio Moretti
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Luca Tabbì
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Stefania Cerri
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Bianca Beghè
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
| | - Massimo Dominici
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Oncology Unit, University Hospital of Modena, University of Modena and Reggio Emilia, 41100 Modena, Italy
| | - Enrico Clini
- Laboratory of Cell Therapies and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, 41100 Modena, Italy; (A.V.S.); (R.T.); (A.M.); (G.B.); (F.G.); (D.A.); (I.C.); (L.M.); (A.M.); (S.C.); (B.B.); (M.D.)
- Respiratory Diseases Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena Reggio Emilia, 41100 Modena, Italy;
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16
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van de Wetering C, Elko E, Berg M, Schiffers CHJ, Stylianidis V, van den Berge M, Nawijn MC, Wouters EFM, Janssen-Heininger YMW, Reynaert NL. Glutathione S-transferases and their implications in the lung diseases asthma and chronic obstructive pulmonary disease: Early life susceptibility? Redox Biol 2021; 43:101995. [PMID: 33979767 PMCID: PMC8131726 DOI: 10.1016/j.redox.2021.101995] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 04/23/2021] [Accepted: 04/24/2021] [Indexed: 01/01/2023] Open
Abstract
Our lungs are exposed daily to airborne pollutants, particulate matter, pathogens as well as lung allergens and irritants. Exposure to these substances can lead to inflammatory responses and may induce endogenous oxidant production, which can cause chronic inflammation, tissue damage and remodeling. Notably, the development of asthma and Chronic Obstructive Pulmonary Disease (COPD) is linked to the aforementioned irritants. Some inhaled foreign chemical compounds are rapidly absorbed and processed by phase I and II enzyme systems critical in the detoxification of xenobiotics including the glutathione-conjugating enzymes Glutathione S-transferases (GSTs). GSTs, and in particular genetic variants of GSTs that alter their activities, have been found to be implicated in the susceptibility to and progression of these lung diseases. Beyond their roles in phase II metabolism, evidence suggests that GSTs are also important mediators of normal lung growth. Therefore, the contribution of GSTs to the development of lung diseases in adults may already start in utero, and continues through infancy, childhood, and adult life. GSTs are also known to scavenge oxidants and affect signaling pathways by protein-protein interaction. Moreover, GSTs regulate reversible oxidative post-translational modifications of proteins, known as protein S-glutathionylation. Therefore, GSTs display an array of functions that impact the pathogenesis of asthma and COPD. In this review we will provide an overview of the specific functions of each class of mammalian cytosolic GSTs. This is followed by a comprehensive analysis of their expression profiles in the lung in healthy subjects, as well as alterations that have been described in (epithelial cells of) asthmatics and COPD patients. Particular emphasis is placed on the emerging evidence of the regulatory properties of GSTs beyond detoxification and their contribution to (un)healthy lungs throughout life. By providing a more thorough understanding, tailored therapeutic strategies can be designed to affect specific functions of particular GSTs.
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Affiliation(s)
- Cheryl van de Wetering
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands; Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Evan Elko
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Marijn Berg
- Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Caspar H J Schiffers
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands; Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA
| | - Vasili Stylianidis
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands
| | - Maarten van den Berge
- Pulmonology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Martijn C Nawijn
- Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Emiel F M Wouters
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands; Ludwig Boltzmann Institute for Lung Health, Vienna, Austria
| | - Yvonne M W Janssen-Heininger
- Department of Pathology and Laboratory Medicine, University of Vermont College of Medicine, Burlington, VT, USA.
| | - Niki L Reynaert
- Department of Respiratory Medicine, Maastricht University Medical Center+, Maastricht, the Netherlands.
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17
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Behr J, Prasse A, Kreuter M, Johow J, Rabe KF, Bonella F, Bonnet R, Grohe C, Held M, Wilkens H, Hammerl P, Koschel D, Blaas S, Wirtz H, Ficker JH, Neumeister W, Schönfeld N, Claussen M, Kneidinger N, Frankenberger M, Hummler S, Kahn N, Tello S, Freise J, Welte T, Neuser P, Günther A. Pirfenidone in patients with progressive fibrotic interstitial lung diseases other than idiopathic pulmonary fibrosis (RELIEF): a double-blind, randomised, placebo-controlled, phase 2b trial. THE LANCET RESPIRATORY MEDICINE 2021; 9:476-486. [PMID: 33798455 DOI: 10.1016/s2213-2600(20)30554-3] [Citation(s) in RCA: 223] [Impact Index Per Article: 74.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Pirfenidone has been shown to slow disease progression in patients with idiopathic pulmonary fibrosis (IPF). However, there are few treatment options for progressive fibrotic interstitial lung diseases (ILDs)) other than IPF. In view of the pathomechanistic and clinical similarities between IPF and other progressive fibrotic ILDs, we aimed to assess the efficacy and safety of pirfenidone in patients with four non-IPF progressive fibrotic ILDs. METHODS We did a multicentre, double-blind, randomised, placebo-controlled, parallel phase 2b trial (RELIEF) in 17 centres with expertise in ILD in Germany. Eligible participants were patients aged 18-80 years with progressive fibrotic ILD due to four diagnoses: collagen or vascular diseases (ie, connective tissue disease-associated ILDs), fibrotic non-specific interstitial pneumonia, chronic hypersensitivity pneumonitis, or asbestos-induced lung fibrosis. Other eligibility criteria included a forced vital capacity (FVC) of 40-90% predicted, a diffusing capacity of the lung for carbon monoxide of 10-90% predicted, and an annual decline of FVC of at least 5% predicted despite conventional therapy, based on at least three measurements within 6-24 months before enrolment. Patients who had received any previous antifibrotic therapy were excluded. We randomly assigned patients (1:1) to either oral pirfenidone (267 mg three times per day in week 1, 534 mg three times per day in week 2, and 801 mg three times per day thereafter) or matched placebo, added to their ongoing medication. Randomisation was done centrally using permuted block randomisation with varying block sizes stratified by the four diagnostic groups. Patients, investigators, statisticians, monitors, and the study coordinator were masked to treatment assignment until database closure. The placebo-controlled study period was 48 weeks (including up-titration). The primary endpoint was absolute change in percentage of predicted FVC (FVC % predicted) from baseline to week 48 in the intention-to-treat population, with imputation of missing data by the smallest sum of squared differences and attribution of deceased patients to the lowest rank in a rank ANCOVA model. Additionally, we did linear mixed-model repeated measures slope analyses of FVC % predicted longitudinal data over the course of the study as a prespecified sensitivity analysis and post-hoc sensitivity analyses of the primary endpoint in the intention-to-treat population using imputation methods of last observation carried forward [LOCF] and a regression-based multiple imputation procedure. Safety was assessed in all patients who received at least one dose of study medication. This trial is registered with EudraCT 2014-000861-32; DRKS00009822 and is no longer recruiting. FINDINGS Between April 5, 2016, and Oct 4, 2018, we randomly assigned 127 patients to treatment: 64 to pirfenidone, 63 to placebo. After 127 patients had been randomised, the study was prematurely terminated on the basis of an interim analysis for futility triggered by slow recruitment. After 48 weeks and in the overall population of 127 patients, rank ANCOVA with diagnostic group included as a factor showed a significantly lower decline in FVC % predicted in the pirfenidone group compared with placebo (p=0·043); the result was similar when the model was stratified by diagnostic group (p=0·042). A significant treatment effect was also observed when applying the LOCF and multiple imputation methods to analyses of the primary endpoint. The median difference (Hodges-Lehmann estimate) between pirfenidone and placebo groups for the primary endpoint was 1·69 FVC % predicted (95% CI -0·65 to 4·03). In the linear mixed-model repeated measures slope analysis of FVC % predicted, the estimated difference between treatment and placebo groups from baseline to week 48 was 3·53 FVC % predicted (95% CI 0·21 to 6·86) with imputation of deaths as prespecified, or 2·79 FVC % predicted (95% CI 0·03 to 5·54) without imputation. One death (non-respiratory) occurred in the pirfenidone group (2%) and five deaths (three of which were respiratory) occurred in the placebo group (8%). The most frequent serious adverse events in both groups were infections and infestations (five [8%] in the pirfenidone group, ten [16%] in the placebo group); general disorders including disease worsening (two [3%] in the pirfenidone group, seven [11%] in the placebo group); and cardiac disorders (one ([2%] in the pirfenidone group, 5 [8%] in the placebo group). Adverse events (grade 3-4) of nausea (two patients on pirfenidone, two on placebo), dyspnoea (one patient on pirfenidone, one on placebo), and diarrhoea (one patient on pirfenidone) were also observed. INTERPRETATION In view of the premature study termination, results should be interpreted with care. Nevertheless, our data suggest that in patients with fibrotic ILDs other than IPF who deteriorate despite conventional therapy, adding pirfenidone to existing treatment might attenuate disease progression as measured by decline in FVC. FUNDING German Center for Lung Research, Roche Pharma.
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Affiliation(s)
- Jürgen Behr
- Department of Internal Medicine V, University Hospital, Ludwig Maximilian University (LMU) Munich, Member of the German Center for Lung Research (DZL), Munich, Germany; Asklepios Lung Center Gauting, DZL, Munich, Germany.
| | - Antje Prasse
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, Hannover, Germany
| | - Michael Kreuter
- Center for Interstitial And Rare Lung Diseases, Department of Pneumology, Thoraxklinik Heidelberg University Hospital, Heidelberg, Germany
| | - Johannes Johow
- Coordinating Center for Clinical Trials, Philipps University Marburg, Marburg, Member of the German Center for Lung Research, Germany
| | - Klaus F Rabe
- Lung Clinic Grosshansdorf, Grosshansdorf, Germany
| | - Francesco Bonella
- Department of Pulmonary Medicine, Ruhrlandklinik, University Essen, Essen, Germany
| | - Reiner Bonnet
- Zentralklinik Bad Berka, Department of Pulmonary Medicine, Bad Berka, Germany
| | | | - Matthias Held
- Department of Pulmonary Medicine, KWM Missio Clinic, Würzburg, Würzburg, Germany
| | - Heinrike Wilkens
- Department of Pulmonary Medicine, Saarland University Medical Center, Homburg, Germany
| | | | - Dirk Koschel
- Lung Clinic Coswig, University Carl Gustav Carus Dresden, Dresden, Germany
| | - Stefan Blaas
- Donaustauf Hospital, Center for Pneumology, Donaustauf, Germany
| | - Hubert Wirtz
- Department of Pulmonary Medicine, University Hospital Leipzig, Leipzig, Germany
| | - Joachim H Ficker
- Paracelsus Medical University Nuernberg, Nuernberg General Hospital, Nuernberg, Germany
| | - Wolfgang Neumeister
- Department of Pulmonary Medicine, Catholic Clinic Koblenz Montabaur, Koblenz, Germany
| | - Nicolas Schönfeld
- Helios Klinikum Emil von Behring, Lungenklinik Heckeshorn, Berlin, Germany
| | | | - Nikolaus Kneidinger
- Department of Internal Medicine V, University Hospital, Ludwig Maximilian University (LMU) Munich, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Marion Frankenberger
- Comprehensive Pneumology Center, Helmholtz Center Munich, Ludwig Maximilian University Munich, Munich, Germany; Asklepios Clinic Gauting, Munich, Germany
| | - Simone Hummler
- Center for Interstitial And Rare Lung Diseases, Department of Pneumology, Thoraxklinik Heidelberg University Hospital, Heidelberg, Germany
| | - Nicolas Kahn
- Center for Interstitial And Rare Lung Diseases, Department of Pneumology, Thoraxklinik Heidelberg University Hospital, Heidelberg, Germany
| | - Silke Tello
- Center for Interstitial and Rare Lung Diseases, Justus-Liebig University Giessen, Giessen, Germany
| | - Julia Freise
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, Hannover, Germany
| | - Tobias Welte
- Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, Hannover, Germany
| | - Petra Neuser
- Coordinating Center for Clinical Trials, Philipps University Marburg, Marburg, Member of the German Center for Lung Research, Germany
| | - Andreas Günther
- Center for Interstitial and Rare Lung Diseases, Justus-Liebig University Giessen, Giessen, Germany; Member of the German Center for Lung Research and Cardiopulmonary Institute, and Agaplesion Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany
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18
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Piñeiro-Hermida S, Autilio C, Martínez P, Bosch F, Pérez-Gil J, Blasco MA. Telomerase treatment prevents lung profibrotic pathologies associated with physiological aging. J Cell Biol 2021; 219:152010. [PMID: 32777016 PMCID: PMC7659728 DOI: 10.1083/jcb.202002120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/23/2020] [Accepted: 07/17/2020] [Indexed: 02/08/2023] Open
Abstract
Short/dysfunctional telomeres are at the origin of idiopathic pulmonary fibrosis (IPF) in patients mutant for telomere maintenance genes. However, it remains unknown whether physiological aging leads to short telomeres in the lung, thus leading to IPF with aging. Here, we find that physiological aging in wild-type mice leads to telomere shortening and a reduced proliferative potential of alveolar type II cells and club cells, increased cellular senescence and DNA damage, increased fibroblast activation and collagen deposits, and impaired lung biophysics, suggestive of a fibrosis-like pathology. Treatment of both wild-type and telomerase-deficient mice with telomerase gene therapy prevented the onset of lung profibrotic pathologies. These findings suggest that short telomeres associated with physiological aging are at the origin of IPF and that a potential treatment for IPF based on telomerase activation would be of interest not only for patients with telomerase mutations but also for sporadic cases of IPF associated with physiological aging.
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Affiliation(s)
- Sergio Piñeiro-Hermida
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
| | - Chiara Autilio
- Department of Biochemistry and Molecular Biology, Research Institute "Hospital 12 de Octubre (imas12)," Complutense University, Madrid, Spain
| | - Paula Martínez
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
| | - Fátima Bosch
- Center of Animal Biotechnology and Gene Therapy, Department of Biochemistry and Molecular Biology, School of Veterinary Medicine, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jesús Pérez-Gil
- Department of Biochemistry and Molecular Biology, Research Institute "Hospital 12 de Octubre (imas12)," Complutense University, Madrid, Spain
| | - Maria A Blasco
- Telomeres and Telomerase Group, Molecular Oncology Program, Spanish National Cancer Centre, Madrid, Spain
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19
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Bradley KL, Stokes CA, Marciniak SJ, Parker LC, Condliffe AM. Role of unfolded proteins in lung disease. Thorax 2021; 76:92-99. [PMID: 33077618 PMCID: PMC7803888 DOI: 10.1136/thoraxjnl-2019-213738] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 09/18/2020] [Accepted: 09/20/2020] [Indexed: 01/01/2023]
Abstract
The lungs are exposed to a range of environmental toxins (including cigarette smoke, air pollution, asbestos) and pathogens (bacterial, viral and fungal), and most respiratory diseases are associated with local or systemic hypoxia. All of these adverse factors can trigger endoplasmic reticulum (ER) stress. The ER is a key intracellular site for synthesis of secretory and membrane proteins, regulating their folding, assembly into complexes, transport and degradation. Accumulation of misfolded proteins within the lumen results in ER stress, which activates the unfolded protein response (UPR). Effectors of the UPR temporarily reduce protein synthesis, while enhancing degradation of misfolded proteins and increasing the folding capacity of the ER. If successful, homeostasis is restored and protein synthesis resumes, but if ER stress persists, cell death pathways are activated. ER stress and the resulting UPR occur in a range of pulmonary insults and the outcome plays an important role in many respiratory diseases. The UPR is triggered in the airway of patients with several respiratory diseases and in corresponding experimental models. ER stress has been implicated in the initiation and progression of pulmonary fibrosis, and evidence is accumulating suggesting that ER stress occurs in obstructive lung diseases (particularly in asthma), in pulmonary infections (some viral infections and in the setting of the cystic fibrosis airway) and in lung cancer. While a number of small molecule inhibitors have been used to interrogate the role of the UPR in disease models, many of these tools have complex and off-target effects, hence additional evidence (eg, from genetic manipulation) may be required to support conclusions based on the impact of such pharmacological agents. Aberrant activation of the UPR may be linked to disease pathogenesis and progression, but at present, our understanding of the context-specific and disease-specific mechanisms linking these processes is incomplete. Despite this, the ability of the UPR to defend against ER stress and influence a range of respiratory diseases is becoming increasingly evident, and the UPR is therefore attracting attention as a prospective target for therapeutic intervention strategies.
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Affiliation(s)
- Kirsty L Bradley
- Department of Infection, Immunity and Cardiovascular Diseases, The University of Sheffield, Sheffield, UK
| | - Clare A Stokes
- Department of Infection, Immunity and Cardiovascular Diseases, The University of Sheffield, Sheffield, UK
| | | | - Lisa C Parker
- Department of Infection, Immunity and Cardiovascular Diseases, The University of Sheffield, Sheffield, UK
| | - Alison M Condliffe
- Department of Infection, Immunity and Cardiovascular Diseases, The University of Sheffield, Sheffield, UK
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20
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Khan T, Dasgupta S, Ghosh N, Chaudhury K. Proteomics in idiopathic pulmonary fibrosis: the quest for biomarkers. Mol Omics 2021; 17:43-58. [PMID: 33073811 DOI: 10.1039/d0mo00108b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a debilitating chronic progressive and fibrosing lung disease that culminates in the destruction of alveolar integrity and dismal prognosis. Its etiology is unknown and pathophysiology remains unclear. While great advances have been made in elucidating the pathogenesis mechanism, considerable gaps related to information on pathogenetic pathways and key protein targets involved in the clinical course of the disease exist. These issues need to be addressed for better clinical management of this highly challenging disease. Omics approach has revolutionized the entire area of disease understanding and holds promise in its translation to clinical biomarker discovery. This review outlines the contribution of proteomics towards identification of important biomarkers in IPF in terms of their clinical utility, i.e. prognosis, differential diagnosis, disease progression and treatment monitoring. The major dysregulated pathways associated with IPF are also discussed. Based on numerous proteomics studies on human and animal models, it is proposed that IPF pathogenesis involves complex interactions of several pathways such as oxidative stress, endoplasmic reticulum stress, unfolded protein response, coagulation system, inflammation, abnormal wounding, fibroblast proliferation, fibrogenesis and deposition of extracellular matrix. These pathways and their key path-changing mediators need further validation in large well-planned multi-centric trials at various geographical locations for successful development of clinical biomarkers of this confounding disease.
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Affiliation(s)
- Tila Khan
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Sanjukta Dasgupta
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Nilanjana Ghosh
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, 721302, India.
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21
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HSP90 Inhibition and Modulation of the Proteome: Therapeutical Implications for Idiopathic Pulmonary Fibrosis (IPF). Int J Mol Sci 2020; 21:ijms21155286. [PMID: 32722485 PMCID: PMC7432830 DOI: 10.3390/ijms21155286] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023] Open
Abstract
Idiopathic Pulmonary fibrosis (IPF) is a catastrophic disease with poor outcomes and limited pharmacological approaches. Heat shock protein 90 (HSP90) has been recently involved in the wound-healing pathological response that leads to collagen deposition in patients with IPF and its inhibition represents an exciting drug target against the development of pulmonary fibrosis. Under physiological conditions, HSP90 guarantees proteostasis through the refolding of damaged proteins and the degradation of irreversibly damaged ones. Additionally, its inhibition, by specific HSP90 inhibitors (e.g., 17 AAG, 17 DAG, and AUY-922) has proven beneficial in different preclinical models of human disease. HSP90 inhibition modulates a complex subset of kinases and interferes with intracellular signaling pathways and proteome regulation. In this review, we evaluated the current evidence and rationale for the use of HSP90 inhibitors in the treatment of pulmonary fibrosis, discussed the intracellular pathways involved, described the limitations of the current understanding and provided insights for future research.
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22
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Korfei M, MacKenzie B, Meiners S. The ageing lung under stress. Eur Respir Rev 2020; 29:29/156/200126. [DOI: 10.1183/16000617.0126-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/22/2020] [Indexed: 01/10/2023] Open
Abstract
Healthy ageing of the lung involves structural changes but also numerous cell-intrinsic and cell-extrinsic alterations. Among them are the age-related decline in central cellular quality control mechanisms such as redox and protein homeostasis. In this review, we would like to provide a conceptual framework of how impaired stress responses in the ageing lung, as exemplified by dysfunctional redox and protein homeostasis, may contribute to onset and progression of COPD and idiopathic pulmonary fibrosis (IPF). We propose that age-related imbalanced redox and protein homeostasis acts, amongst others (e.g.cellular senescence), as a “first hit” that challenges the adaptive stress-response pathways of the cell, increases the level of oxidative stress and renders the lung susceptible to subsequent injury and disease. In both COPD and IPF, additional environmental insults such as smoking, air pollution and/or infections then serve as “second hits” which contribute to persistently elevated oxidative stress that overwhelms the already weakened adaptive defence and repair pathways in the elderly towards non-adaptive, irremediable stress thereby promoting development and progression of respiratory diseases. COPD and IPF are thus distinct horns of the same devil, “lung ageing”.
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23
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Elko EA, Cunniff B, Seward DJ, Chia SB, Aboushousha R, van de Wetering C, van der Velden J, Manuel A, Shukla A, Heintz NH, Anathy V, van der Vliet A, Janssen-Heininger YMW. Peroxiredoxins and Beyond; Redox Systems Regulating Lung Physiology and Disease. Antioxid Redox Signal 2019; 31:1070-1091. [PMID: 30799628 PMCID: PMC6767868 DOI: 10.1089/ars.2019.7752] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Significance: The lung is a unique organ, as it is constantly exposed to air, and thus it requires a robust antioxidant defense system to prevent the potential damage from exposure to an array of environmental insults, including oxidants. The peroxiredoxin (PRDX) family plays an important role in scavenging peroxides and is critical to the cellular antioxidant defense system. Recent Advances: Exciting discoveries have been made to highlight the key features of PRDXs that regulate the redox tone. PRDXs do not act in isolation as they require the thioredoxin/thioredoxin reductase/NADPH, sulfiredoxin (SRXN1) redox system, and in some cases glutaredoxin/glutathione, for their reduction. Furthermore, the chaperone function of PRDXs, controlled by the oxidation state, demonstrates the versatility in redox regulation and control of cellular biology exerted by this class of proteins. Critical Issues: Despite the long-known observations that redox perturbations accompany a number of pulmonary diseases, surprisingly little is known about the role of PRDXs in the etiology of these diseases. In this perspective, we review the studies that have been conducted thus far to address the roles of PRDXs in lung disease, or experimental models used to study these diseases. Intriguing findings, such as the secretion of PRDXs and the formation of autoantibodies, raise a number of questions about the pathways that regulate secretion, redox status, and immune response to PRDXs. Future Directions: Further understanding of the mechanisms by which individual PRDXs control lung inflammation, injury, repair, chronic remodeling, and cancer, and the importance of PRDX oxidation state, configuration, and client proteins that govern these processes is needed.
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Affiliation(s)
- Evan A Elko
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Brian Cunniff
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - David J Seward
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Shi Biao Chia
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Reem Aboushousha
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Cheryl van de Wetering
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Jos van der Velden
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Allison Manuel
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Arti Shukla
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Nicholas H Heintz
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Vikas Anathy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Yvonne M W Janssen-Heininger
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
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24
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Peripheral blood proteomic profiling of idiopathic pulmonary fibrosis biomarkers in the multicentre IPF-PRO Registry. Respir Res 2019; 20:227. [PMID: 31640794 PMCID: PMC6805665 DOI: 10.1186/s12931-019-1190-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/20/2019] [Indexed: 01/28/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease for which diagnosis and management remain challenging. Defining the circulating proteome in IPF may identify targets for biomarker development. We sought to quantify the circulating proteome in IPF, determine differential protein expression between subjects with IPF and controls, and examine relationships between protein expression and markers of disease severity. Methods This study involved 300 patients with IPF from the IPF-PRO Registry and 100 participants without known lung disease. Plasma collected at enrolment was analysed using aptamer-based proteomics (1305 proteins). Linear regression was used to determine differential protein expression between participants with IPF and controls and associations between protein expression and disease severity measures (percent predicted values for forced vital capacity [FVC] and diffusion capacity of the lung for carbon monoxide [DLco]; composite physiologic index [CPI]). Multivariable models were fit to select proteins that best distinguished IPF from controls. Results Five hundred fifty one proteins had significantly different levels between IPF and controls, of which 47 showed a |log2(fold-change)| > 0.585 (i.e. > 1.5-fold difference). Among the proteins with the greatest difference in levels in patients with IPF versus controls were the glycoproteins thrombospondin 1 and von Willebrand factor and immune-related proteins C-C motif chemokine ligand 17 and bactericidal permeability-increasing protein. Multivariable classification modelling identified nine proteins that, when considered together, distinguished IPF versus control status with high accuracy (area under receiver operating curve = 0.99). Among participants with IPF, 14 proteins were significantly associated with FVC % predicted, 23 with DLco % predicted, 14 with CPI. Four proteins (roundabout homolog-2, spondin-1, polymeric immunoglobulin receptor, intercellular adhesion molecule 5) demonstrated the expected relationship across all three disease severity measures. When considered in pathways analyses, proteins associated with the presence or severity of IPF were enriched in pathways involved in platelet and haemostatic responses, vascular or platelet derived growth factor signalling, immune activation, and extracellular matrix organisation. Conclusions Patients with IPF have a distinct circulating proteome and can be distinguished using a nine-protein profile. Several proteins strongly associate with disease severity. The proteins identified may represent biomarker candidates and implicate pathways for further investigation. Trial registration ClinicalTrials.gov (NCT01915511).
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25
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Moodley YP, Corte TJ, Oliver BG, Glaspole IN, Livk A, Ito J, Peters K, Lipscombe R, Casey T, Tan DBA. Analysis by proteomics reveals unique circulatory proteins in idiopathic pulmonary fibrosis. Respirology 2019; 24:1111-1114. [PMID: 31393655 DOI: 10.1111/resp.13668] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 04/13/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic disease that has a poor 3-year median survival rate with unclear pathophysiology. Radiological features include bibasal, subpleural fibrosis and honeycombing while its pathology is characterized by fibroblastic foci and honeycombing. Proteomic analysis of circulating molecules in plasma may identify factors that characterize IPF and may assist in the diagnosis, prognostication and determination of pathogenic pathways in this condition. METHODS Two independent quantitative proteomic techniques were used, isobaric tags for relative and absolute quantitation (iTRAQ) and multiple reaction monitoring (MRM), to identify differentially expressed plasma proteins in a group of IPF patients in comparison to healthy controls with normal lung function matched for age and gender. RESULTS Five proteins were identified to be differentially expressed in IPF compared to healthy controls (upregulation of platelet basic protein and downregulation of actin, cytoplasmic 2, antithrombin-III, extracellular matrix protein-1 and fibronectin). CONCLUSION This study further validates the combinational use of non-targeted discovery proteomics (iTRAQ) with targeted quantitation by mass spectrometry (MRM) of soluble biomarkers to identify potentially important molecules and pathways for pulmonary diseases such as IPF.
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Affiliation(s)
- Yuben P Moodley
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia.,Department of Respiratory Medicine, Fiona Stanley Hospital, Perth, WA, Australia.,National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia
| | - Tamera J Corte
- National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia.,Department of Respiratory Medicine, Royal Prince Alfred Hospital, Sydney, NSW, Australia.,School of Medicine, University of Sydney, Sydney, NSW, Australia
| | - Brian G Oliver
- Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Ian N Glaspole
- National Health and Medical Research Council Centre of Research Excellence in Pulmonary Fibrosis, University of Sydney, Sydney, NSW, Australia.,Department of Allergy and Respiratory Medicine, The Alfred Hospital, Melbourne, VIC, Australia.,Faculty of Medicine, Monash University, Melbourne, VIC, Australia
| | | | - Jason Ito
- Proteomics International, Perth, WA, Australia
| | | | | | - Tammy Casey
- Proteomics International, Perth, WA, Australia
| | - Dino B A Tan
- School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia.,Stem Cell Unit, Institute for Respiratory Health, Perth, WA, Australia
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Yasuoka H, Garrett SM, Nguyen XX, Artlett CM, Feghali-Bostwick CA. NADPH oxidase-mediated induction of reactive oxygen species and extracellular matrix deposition by insulin-like growth factor binding protein-5. Am J Physiol Lung Cell Mol Physiol 2019; 316:L644-L655. [PMID: 30810066 DOI: 10.1152/ajplung.00106.2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Insulin-like growth factor binding protein-5 (IGFBP-5) induces production of the extracellular matrix (ECM) components collagen and fibronectin both in vitro and in vivo and is overexpressed in patients with fibrosing lung diseases, such as idiopathic pulmonary fibrosis (IPF) and systemic sclerosis (SSc). However, the mechanism by which IGFBP-5 exerts its fibrotic effect is incompletely understood. Recent reports have shown a substantial role of reactive oxygen species (ROS) in fibrosis; thus we hypothesized that IGFBP-5 induces production of ROS to mediate the profibrotic process. In vitro analyses revealed that ROS production was induced by recombinant and adenoviral vector-mediated IGFBP-5 (AdBP5) in a dose- and time-dependent manner, regulated through MEK/ERK and JNK signaling, and primarily mediated by NADPH oxidase (Nox). Silencing IGFBP-5 in SSc and IPF fibroblasts reduced ROS production. The antioxidants diphenyleneiodonium and N-acetylcysteine blocked IGFBP-5-stimulated ECM production in normal, SSc, and IPF human primary lung fibroblasts. In murine fibroblasts lacking critical components of the Nox machinery, AdBP5-stimulated ROS production and fibronectin expression were reduced compared with wild-type fibroblasts. IGFBP-5 stimulated transcriptional expression of Nox3 in human fibroblasts while selective knockdown of Nox3 reduced ROS production by IGFBP-5. Thus IGFBP-5 mediates fibrosis through production of ROS in a Nox-dependent manner.
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Affiliation(s)
- Hidekata Yasuoka
- Department of Internal Medicine, Division of Rheumatology, Fujita Health University School of Medicine , Aichi , Japan
| | - Sara M Garrett
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina , Charleston, South Carolina
| | - Xinh-Xinh Nguyen
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina , Charleston, South Carolina
| | - Carol M Artlett
- Drexel University College of Medicine , Philadelphia, Pennsylvania
| | - Carol A Feghali-Bostwick
- Department of Medicine, Division of Rheumatology and Immunology, Medical University of South Carolina , Charleston, South Carolina
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27
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Tian Y, Li H, Gao Y, Liu C, Qiu T, Wu H, Cao M, Zhang Y, Ding H, Chen J, Cai H. Quantitative proteomic characterization of lung tissue in idiopathic pulmonary fibrosis. Clin Proteomics 2019; 16:6. [PMID: 30774578 PMCID: PMC6364390 DOI: 10.1186/s12014-019-9226-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Idiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease. IPF is characterized by excessive accumulation of the extracellular matrix (ECM) in the alveolar parenchyma and progressive lung scarring. The pathogenesis of IPF and whether the ECM involved in the process remain unknown. Methods To identify potential treatment target and ECM associated proteins that may be involved in the development of IPF, we employed isobaric tag for relative and absolute quantitation (iTRAQ) combined liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to examine protein expression in lung tissues from IPF patients. Results A total of 662 proteins with altered expression (455 upregulated proteins and 207 downregulated proteins) were identified in lung tissue of IPF patients compared with control. KEGG pathway enrichment analysis showed that the altered proteins in lung tissue mainly belonged to the PI3K-Akt signaling, focal adhesion, ECM-receptor interaction, and carbon metabolism pathways. According to the bioinformatic definition of the matrisome, 229 matrisome proteins were identified in lung tissue. These proteins comprised the ECM of lung, of which 104 were core matrisome proteins, and 125 were matrisome-associated proteins. Of the 229 ECM quantified proteins, 56 significantly differentially expressed proteins (19 upregulated proteins and 37 downregulated proteins) were detected in IPF lung tissue samples. In addition to proteins with well-known functions such as COL1A1, SCGB1A1, TAGLN, PSEN2, TSPAN1, CTSB, AGR2, CSPG2, and SERPINB3, we identified several novel ECM proteins with unknown function deposited in IPF lung tissue including LGALS7, ASPN, HSP90AA1 and HSP90AB1. Some of these differentially expressed proteins were further verified using Western blot analysis and immunohistochemical staining. Conclusions This study provides a list of proteomes that were detected in IPF lung tissue by iTRAQ technology combined with LC-MS/MS. The findings of this study will contribute better understanding to the pathogenesis of IPF and facilitate the development of therapeutic targets.
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Affiliation(s)
- Yaqiong Tian
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Hui Li
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Yujuan Gao
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Chuanmei Liu
- 2Department of Respiratory Medicine, Yi Ji Shan Hospital of Wannan Medical College, No. 2 Zheshan West Road, Wuhu, 241001 Anhui People's Republic of China
| | - Ting Qiu
- Department of Respiratory Medicine, KunShan Hospital of Traditional Chinese Medicine, No. 189 Chaoyang Road, Kunshan, 215300 Jiangsu People's Republic of China
| | - Hongyan Wu
- 4Department of Pathology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Mengshu Cao
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Yingwei Zhang
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
| | - Hui Ding
- 5Department of Respiratory Medicine, Yixing People Hospital, Affiliated Jiangsu University, No. 75 Tongzhenguan Road, Yixing, 214200 Jiangsu People's Republic of China
| | - Jingyu Chen
- 6Jiangsu Key Laboratory of Organ Transplantation, Wuxi People's Hospital, Nanjing Medical University, No. 299 Qingyang Road, Wuxi, 214023 Jiangsu People's Republic of China
| | - Hourong Cai
- 1Department of Respiratory Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, No. 321 Zhongshan Road, Nanjing, 210008 Jiangsu People's Republic of China
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28
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Pacifici F, Della Morte D, Capuani B, Pastore D, Bellia A, Sbraccia P, Di Daniele N, Lauro R, Lauro D. Peroxiredoxin6, a Multitask Antioxidant Enzyme Involved in the Pathophysiology of Chronic Noncommunicable Diseases. Antioxid Redox Signal 2019; 30:399-414. [PMID: 29160110 DOI: 10.1089/ars.2017.7427] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
SIGNIFICANCE Chronic noncommunicable diseases (NCDs) are the leading causes of disability and death worldwide. NCDs mainly comprise diabetes mellitus, cardiovascular diseases, chronic obstructive pulmonary disease, cancer, and neurological degenerative diseases, which kill more than 80% of population, especially the elderly, worldwide. Recent Advances: Several recent theories established NCDs as multifactorial diseases, where a combination of genetic, epigenetic, and environmental factors contributes to their pathogenesis. Nevertheless, recent findings suggest that the common factor linking all these pathologies is an increase in oxidative stress and the age-related loss of the antioxidant mechanisms of defense against it. Impairment in mitochondrial homeostasis with consequent deregulation in oxidative stress balance has also been suggested. CRITICAL ISSUES Therefore, antioxidant proteins deserve particular attention for their potential role against NCDs. In particular, peroxiredoxin(Prdx)6 is a unique antioxidant enzyme, belonging to the Prdx family, with double properties, peroxidase and phospholipase activities. Through these activities, Prdx6 has been shown to be a powerful antioxidant enzyme, implicated in the pathogenesis of different NCDs. Recently, we described a phenotype of diabetes mellitus in Prdx6 knockout mice, suggesting a pivotal role of Prdx6 in the pathogenesis of cardiometabolic diseases. FUTURE DIRECTIONS Increasing awareness on the role of antioxidant defenses in the pathogenesis of NCDs may open novel therapeutic approaches to reduce the burden of this pandemic phenomenon. However, knowledge of the role of Prdx6 in NCD prevention and pathogenesis is still not clarified.
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Affiliation(s)
- Francesca Pacifici
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy
| | - David Della Morte
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy .,2 Department of Human Sciences and Quality of Life Promotion, San Raffaele Roma Open University , Rome, Italy
| | - Barbara Capuani
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy
| | - Donatella Pastore
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy
| | - Alfonso Bellia
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy .,3 Policlinico Tor Vergata Foundation, University Hospital , Rome, Italy
| | - Paolo Sbraccia
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy .,3 Policlinico Tor Vergata Foundation, University Hospital , Rome, Italy
| | - Nicola Di Daniele
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy .,3 Policlinico Tor Vergata Foundation, University Hospital , Rome, Italy
| | - Renato Lauro
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy
| | - Davide Lauro
- 1 Department of Systems Medicine, University of Rome Tor Vergata , Rome, Italy .,3 Policlinico Tor Vergata Foundation, University Hospital , Rome, Italy
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29
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Na M, Hong X, Fuyu J, Dingjie X, Sales D, Hui Z, Zhongqiu W, Shifeng L, Xuemin G, Wenchen C, Dan L, Guizhen Z, Bonan Z, Lijuan Z, Shumin L, Ying Z, Jin W, Mingwang R, Summer R, Fang Y. Proteomic profile of TGF-β1 treated lung fibroblasts identifies novel markers of activated fibroblasts in the silica exposed rat lung. Exp Cell Res 2019; 375:1-9. [PMID: 30641040 DOI: 10.1016/j.yexcr.2019.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 10/27/2022]
Abstract
We performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) on control and TGF-β1-exposed rat lung fibroblasts to identify proteins differentially expressed between cell populations. A total of 196 proteins were found to be differentially expressed in response to TGF-β1 treatment. Guided by these results, we next determined whether similar changes in protein expression were detectable in the rat lung after chronic exposure to silica dust. Of the five proteins selected for further analysis, we found that levels of all proteins were markedly increased in the silica-exposed rat lung, including the proteins for the very low density lipoprotein receptor (VLDLR) and the transmembrane (type I) heparin sulfate proteoglycan called syndecan 2 (SDC2). Because VLDLR and SDC2 have not, to our knowledge, been previously linked to the pathobiology of silicosis, we next examined whether knockdown of either gene altered responses to TGF-β1 in MRC-5 lung fibroblasts. Interestingly, we found knockdown of either VLDLR or SDC2 dramatically reduced collagen production to TGF-β1, suggesting that both proteins might play a novel role in myofibroblast biology and pathogenesis of silica-induced pulmonary fibrosis. In summary, our findings suggest that performing LC-MS/MS on TGF-β1 stimulated lung fibroblasts can uncover novel molecular targets of activated myofibroblasts in silica-exposed lung.
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Affiliation(s)
- Mao Na
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Xu Hong
- Medical Research Center, North China University of Science and Technology, Tangshan, China
| | - Jin Fuyu
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Xu Dingjie
- College of Traditional Chinese Medicine, North China University of Science and Technology, Tangshan, China
| | - Dominic Sales
- Center for Translational Medicine, Jane and Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zhang Hui
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Wei Zhongqiu
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Li Shifeng
- Medical Research Center, North China University of Science and Technology, Tangshan, China
| | - Gao Xuemin
- Medical Research Center, North China University of Science and Technology, Tangshan, China
| | - Cai Wenchen
- School of public health, North China University of Science and Technology, Tangshan, China
| | - Li Dan
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Zhang Guizhen
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Zhang Bonan
- School of public health, North China University of Science and Technology, Tangshan, China
| | - Zhang Lijuan
- Medical Research Center, North China University of Science and Technology, Tangshan, China
| | - Li Shumin
- School of public health, North China University of Science and Technology, Tangshan, China
| | - Zhu Ying
- School of public health, North China University of Science and Technology, Tangshan, China
| | - Wang Jin
- Basic Medical College, North China University of Science and Technology, Tangshan, China
| | - Rui Mingwang
- Medical Research Center, North China University of Science and Technology, Tangshan, China
| | - Ross Summer
- Center for Translational Medicine, Jane and Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yang Fang
- Basic Medical College, North China University of Science and Technology, Tangshan, China; School of public health, North China University of Science and Technology, Tangshan, China; The Hebei key laboratory for organ fibrosis research, North China University of Science and Technology, Tangshan, China.
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30
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Herrera J, Forster C, Pengo T, Montero A, Swift J, Schwartz MA, Henke CA, Bitterman PB. Registration of the extracellular matrix components constituting the fibroblastic focus in idiopathic pulmonary fibrosis. JCI Insight 2019; 4:e125185. [PMID: 30626754 PMCID: PMC6485370 DOI: 10.1172/jci.insight.125185] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 11/20/2018] [Indexed: 01/18/2023] Open
Abstract
The extracellular matrix (ECM) in idiopathic pulmonary fibrosis (IPF) drives fibrosis progression; however, the ECM composition of the fibroblastic focus (the hallmark lesion in IPF) and adjacent regions remains incompletely defined. Herein, we serially sectioned IPF lung specimens constructed into tissue microarrays and immunostained for ECM components reported to be deregulated in IPF. Immunostained sections were imaged, anatomically aligned, and 3D reconstructed. The myofibroblast core of the fibroblastic focus (defined by collagen I, α-smooth muscle actin, and procollagen I immunoreactivity) was associated with collagens III, IV, V, and VI; fibronectin; hyaluronan; and versican immunoreactivity. Hyaluronan immunoreactivity was also present at the fibroblastic focus perimeter and at sites where early lesions appear to be forming. Fibrinogen immunoreactivity was often observed at regions of damaged epithelium lining the airspace and the perimeter of the myofibroblast core but was absent from the myofibroblast core itself. The ECM components of the fibroblastic focus were distributed in a characteristic and reproducible manner in multiple patients. This information can inform the development of high-fidelity model systems to dissect mechanisms by which the IPF ECM drives fibrosis progression.
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Affiliation(s)
- Jeremy Herrera
- Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Colleen Forster
- University of Minnesota, Clinical and Translational Science Institute, Minneapolis, Minnesota, USA
| | - Thomas Pengo
- University of Minnesota Informatics Institute, University of Minnesota Twin Cities, Minneapolis, Minnesota, USA
| | - Angeles Montero
- Manchester University Foundation Trust, Department of Histopathology, Manchester, United Kingdom
| | - Joe Swift
- Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Martin A. Schwartz
- Wellcome Centre for Cell-Matrix Research, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom
| | - Craig A. Henke
- University of Minnesota, Department of Medicine, Minneapolis, Minnesota, USA
| | - Peter B. Bitterman
- University of Minnesota, Department of Medicine, Minneapolis, Minnesota, USA
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31
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Sandbo N. Mechanisms of Fibrosis in IPF. Respir Med 2019. [DOI: 10.1007/978-3-319-99975-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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32
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Dickens JA, Malzer E, Chambers JE, Marciniak SJ. Pulmonary endoplasmic reticulum stress-scars, smoke, and suffocation. FEBS J 2019; 286:322-341. [PMID: 29323786 DOI: 10.1111/febs.14381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 12/11/2017] [Accepted: 01/08/2018] [Indexed: 12/14/2022]
Abstract
Protein misfolding within the endoplasmic reticulum (ER stress) can be a cause or consequence of pulmonary disease. Mutation of proteins restricted to the alveolar type II pneumocyte can lead to inherited forms of pulmonary fibrosis, but even sporadic cases of pulmonary fibrosis appear to be strongly associated with activation of the unfolded protein response and/or the integrated stress response. Inhalation of smoke can impair protein folding and may be an important cause of pulmonary ER stress. Similarly, tissue hypoxia can lead to impaired protein homeostasis (proteostasis). But the mechanisms linking smoke and hypoxia to ER stress are only partially understood. In this review, we will examine the role of ER stress in the pathogenesis of lung disease by focusing on fibrosis, smoke, and hypoxia.
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Affiliation(s)
- Jennifer A Dickens
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
| | - Elke Malzer
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
| | - Joseph E Chambers
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
| | - Stefan J Marciniak
- Cambridge Institute for Medical Research (CIMR), University of Cambridge, UK
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33
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Fois AG, Paliogiannis P, Sotgia S, Mangoni AA, Zinellu E, Pirina P, Carru C, Zinellu A. Evaluation of oxidative stress biomarkers in idiopathic pulmonary fibrosis and therapeutic applications: a systematic review. Respir Res 2018; 19:51. [PMID: 29587761 PMCID: PMC5872514 DOI: 10.1186/s12931-018-0754-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/19/2018] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Idiopathic pulmonary fibrosis (IPF), a fatal lung disease of unknown origin, is characterized by chronic and progressive fibrosing interstitial pneumonia which progressively impairs lung function. Oxidative stress is one of the main pathogenic pathways in IPF. The aim of this systematic review was to describe the type of markers of oxidative stress identified in different biological specimens and the effects of antioxidant therapies in patients with IPF. METHODS We conducted a systematic search of publications listed in electronic databases (Pubmed, Web of Science, Scopus and Google Scholar) from inception to October 2017. Two investigators independently reviewed all identified articles to determine eligibility. RESULTS After a substantial proportion of the initially identified articles (n = 554) was excluded because they were duplicates, abstracts, irrelevant, or did not meet the selection criteria, we identified 30 studies. In each study, we critically appraised the type, site (systemic vs. local, e.g. breath, sputum, expired breath condensate, epithelial lining fluid, bronchoalveolar lavage, and lung tissue specimens), and method used for measuring the identified oxidative stress biomarkers. Furthermore, the current knowledge on antioxidant therapies in IPF was summarized. CONCLUSIONS A number of markers of oxidative stress, with individual advantages and limitations, have been described in patients with IPF. Nevertheless, trials of antioxidant treatments have been unable to demonstrate consistent benefits, barring recent pharmacogenomics data suggesting different results in specific genotype subgroups of patients with IPF.
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Affiliation(s)
- Alessandro G Fois
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy. .,Department of Respiratory Diseases, University Hospital Sassari (AOU), Sassari, Italy.
| | | | - Salvatore Sotgia
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Arduino A Mangoni
- Department of Clinical Pharmacology, College of Medicine and Public Health, Flinders University, Adelaide, Australia
| | - Elisabetta Zinellu
- Department of Respiratory Diseases, University Hospital Sassari (AOU), Sassari, Italy
| | - Pietro Pirina
- Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy.,Department of Respiratory Diseases, University Hospital Sassari (AOU), Sassari, Italy
| | - Ciriaco Carru
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Angelo Zinellu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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34
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Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biol 2018; 68-69:422-434. [PMID: 29567123 DOI: 10.1016/j.matbio.2018.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
In recent decades there has been a significant shift in our understanding of idiopathic pulmonary fibrosis (IPF), a progressive and lethal disorder. While initially much of the mechanistic understanding was derived from hypotheses generated from animal models of disease, in recent decades new insights derived from humans with IPF have taken precedence. This is mainly because of the establishment of large collections of IPF lung tissues and patient cohorts, and the emergence of high throughput profiling technologies collectively termed 'omics' technologies based on their shared suffix. In this review we describe impacts of 'omics' analyses of human IPF samples on our understanding of the disease. In particular, we discuss the results of genomics and transcriptomics studies, as well as proteomics, epigenomics and metabolomics. We then describe how these findings can be integrated in a modified paradigm of human idiopathic pulmonary fibrosis, that introduces the 'hallmarks of aging' as a central theme in the IPF lung. This allows resolution of all the disparate cellular and molecular features in IPF, from the central role of epithelial cells, through the dramatic phenotypic alterations observed in fibroblasts and the numerous aberrations that inflammatory cells exhibit. We end with reiterating a call for renewed efforts to collect and analyze carefully characterized human tissues, in ways that would facilitate implementation of novel technologies for high resolution single cell omics profiling.
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35
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Kropski JA, Blackwell TS. Endoplasmic reticulum stress in the pathogenesis of fibrotic disease. J Clin Invest 2018; 128:64-73. [PMID: 29293089 DOI: 10.1172/jci93560] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Eukaryotic cells contain an elegant protein quality control system that is crucial in maintaining cellular homeostasis; however, dysfunction of this system results in endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR). Severe or prolonged ER stress is associated with the development of degenerative and fibrotic disorders in multiple organs, as evidenced by the identification of disease-causing mutations in epithelial-restricted genes that lead to protein misfolding or mistrafficking in familial fibrotic diseases. Emerging evidence implicates ER stress and UPR signaling in a variety of profibrotic mechanisms in individual cell types. In epithelial cells, ER stress can induce apoptosis, inflammatory signaling, and epithelial-mesenchymal transition. In other cell types, ER stress is linked to myofibroblast activation, macrophage polarization, and T cell differentiation. ER stress-targeted therapies have begun to emerge using approaches that range from global enhancement of chaperone function to selective targeting of activated ER stress sensors and other downstream mediators. As the complex regulatory mechanisms of this system are further clarified, there are opportunities to develop new disease-modifying therapeutic strategies in a wide range of chronic fibrotic diseases.
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Affiliation(s)
- Jonathan A Kropski
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
| | - Timothy S Blackwell
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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36
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Nally JE, Schuller S. Proteomic Analysis of Lung Tissue by DIGE. Methods Mol Biol 2018; 1664:167-183. [PMID: 29019133 DOI: 10.1007/978-1-4939-7268-5_14] [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] [Indexed: 06/07/2023]
Abstract
Lungs perform an essential physiological function, mediated by a complex series of events that involve the coordination of multiple cell types to support not only gaseous exchange, but homeostasis and protection from infection. Guinea pigs are an important animal disease model for a number of infectious and noninfectious pulmonary conditions and the availability of a complete genome facilitates comprehensive analysis of tissues using the tools of proteomics. Here, we describe the application of 2-D Difference Gel Electrophoresis (DIGE) to compare, quantify, and identify differential protein expression of proteins in lung tissue from guinea pigs with leptospiral pulmonary hemorrhage syndrome (LPHS) compared to noninfected controls. 2-D DIGE is a powerful technique that provides novel insights into the dynamics of the complex lung proteome during health and disease.
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Affiliation(s)
- Jarlath E Nally
- Infectious Bacterial Diseases, National Animal Disease Center-USDA-ARS, 1920 Dayton Avenue, Ames, IA, 50010, USA.
| | - Simone Schuller
- Division of Small Animal Internal Medicine, Department of Clinical Veterinary Medicine, Vetsuisse Faculty, University of Bern, Länggassstr. 128, 3012, Bern, Switzerland
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37
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Bowler RP, Wendt CH, Fessler MB, Foster MW, Kelly RS, Lasky-Su J, Rogers AJ, Stringer KA, Winston BW. New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2017; 14:1721-1743. [PMID: 29192815 PMCID: PMC5946579 DOI: 10.1513/annalsats.201710-770ws] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This document presents the proceedings from the workshop entitled, "New Strategies and Challenges in Lung Proteomics and Metabolomics" held February 4th-5th, 2016, in Denver, Colorado. It was sponsored by the National Heart Lung Blood Institute, the American Thoracic Society, the Colorado Biological Mass Spectrometry Society, and National Jewish Health. The goal of this workshop was to convene, for the first time, relevant experts in lung proteomics and metabolomics to discuss and overcome specific challenges in these fields that are unique to the lung. The main objectives of this workshop were to identify, review, and/or understand: (1) emerging technologies in metabolomics and proteomics as applied to the study of the lung; (2) the unique composition and challenges of lung-specific biological specimens for metabolomic and proteomic analysis; (3) the diverse informatics approaches and databases unique to metabolomics and proteomics, with special emphasis on the lung; (4) integrative platforms across genetic and genomic databases that can be applied to lung-related metabolomic and proteomic studies; and (5) the clinical applications of proteomics and metabolomics. The major findings and conclusions of this workshop are summarized at the end of the report, and outline the progress and challenges that face these rapidly advancing fields.
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38
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Wu J, Li X, Zhao M, Huang H, Sun W, Gao Y. Early Detection of Urinary Proteome Biomarkers for Effective Early Treatment of Pulmonary Fibrosis in a Rat Model. Proteomics Clin Appl 2017; 11. [DOI: 10.1002/prca.201700103] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 09/12/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Jianqiang Wu
- Department of Pathophysiology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Xundou Li
- Department of Pathophysiology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Mindi Zhao
- Department of Pathophysiology; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - He Huang
- Department of Biochemistry and Molecular Biology; School of Life Sciences; Beijing Normal University; Gene Engineering and Biotechnology Beijing Key Laboratory; Beijing China
| | - Wei Sun
- Core Facility of Instrument; Institute of Basic Medical Sciences; Chinese Academy of Medical Sciences; School of Basic Medicine; Peking Union Medical College; Beijing China
| | - Youhe Gao
- Department of Biochemistry and Molecular Biology; School of Life Sciences; Beijing Normal University; Gene Engineering and Biotechnology Beijing Key Laboratory; Beijing China
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39
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Gibbons MA, Scotton CJ. Delving Deep into the Proteome of Lung Fibrosis Brings Plasma Cells to the Surface. Am J Respir Crit Care Med 2017; 196:1238-1240. [PMID: 28696776 DOI: 10.1164/rccm.201706-1186ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Michael A Gibbons
- 1 Institute of Biomedical and Clinical Science University of Exeter Medical School Exeter, United Kingdom and.,2 Respiratory Department Royal Devon and Exeter NHS Foundation Trust Exeter, United Kingdom
| | - Chris J Scotton
- 1 Institute of Biomedical and Clinical Science University of Exeter Medical School Exeter, United Kingdom and
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40
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Karhadkar TR, Pilling D, Cox N, Gomer RH. Sialidase inhibitors attenuate pulmonary fibrosis in a mouse model. Sci Rep 2017; 7:15069. [PMID: 29118338 PMCID: PMC5678159 DOI: 10.1038/s41598-017-15198-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/23/2017] [Indexed: 01/14/2023] Open
Abstract
Fibrosis involves increasing amounts of scar tissue appearing in a tissue, but what drives this is unclear. In fibrotic lesions in human and mouse lungs, we found extensive desialylation of glycoconjugates, and upregulation of sialidases. The fibrosis-associated cytokine TGF-β1 upregulates sialidases in human airway epithelium cells, lung fibroblasts, and immune system cells. Conversely, addition of sialidases to human peripheral blood mononuclear cells induces accumulation of extracellular TGF-β1, forming what appears to be a sialidase - TGF-β1 - sialidase positive feedback loop. Monocyte-derived cells called fibrocytes also activate fibroblasts, and we found that sialidases potentiate fibrocyte differentiation. A sialylated glycoprotein called serum amyloid P (SAP) inhibits fibrocyte differentiation, and sialidases attenuate SAP function. Injections of the sialidase inhibitors DANA and oseltamivir (Tamiflu) starting either 1 day or 10 days after bleomycin strongly attenuate pulmonary fibrosis in the mouse bleomycin model, and by breaking the feedback loop, cause a downregulation of sialidase and TGF-β1 accumulation. Together, these results suggest that a positive feedback loop involving sialidases potentiates fibrosis, and suggest that sialidase inhibitors could be useful for the treatment of fibrosis.
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Affiliation(s)
- Tejas R Karhadkar
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA
| | - Darrell Pilling
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA
| | - Richard H Gomer
- Department of Biology, Texas A&M University, 301 Old Main Drive, College Station, Texas, 77843-3474, USA.
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Greiffo FR, Eickelberg O, Fernandez IE. Systems medicine advances in interstitial lung disease. Eur Respir Rev 2017; 26:26/145/170021. [PMID: 28954764 DOI: 10.1183/16000617.0021-2017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/15/2017] [Indexed: 01/17/2023] Open
Abstract
Fibrotic lung diseases involve subject-environment interactions, together with dysregulated homeostatic processes, impaired DNA repair and distorted immune functions. Systems medicine-based approaches are used to analyse diseases in a holistic manner, by integrating systems biology platforms along with clinical parameters, for the purpose of understanding disease origin, progression, exacerbation and remission.Interstitial lung diseases (ILDs) refer to a heterogeneous group of complex fibrotic diseases. The increase of systems medicine-based approaches in the understanding of ILDs provides exceptional advantages by improving diagnostics, unravelling phenotypical differences, and stratifying patient populations by predictable outcomes and personalised treatments. This review discusses the state-of-the-art contributions of systems medicine-based approaches in ILDs over the past 5 years.
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Affiliation(s)
- Flavia R Greiffo
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany.,Division of Respiratory Sciences and Critical Care Medicine, Dept of Medicine, University of Colorado, Denver, CO, USA
| | - Isis E Fernandez
- Comprehensive Pneumology Center, Ludwig-Maximilians-Universität, University Hospital Grosshadern and Helmholtz Zentrum München and Member of the German Center for Lung Research, Munich, Germany
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42
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Zhao YD, Yin L, Archer S, Lu C, Zhao G, Yao Y, Wu L, Hsin M, Waddell TK, Keshavjee S, Granton J, de Perrot M. Metabolic heterogeneity of idiopathic pulmonary fibrosis: a metabolomic study. BMJ Open Respir Res 2017; 4:e000183. [PMID: 28883924 PMCID: PMC5531310 DOI: 10.1136/bmjresp-2017-000183] [Citation(s) in RCA: 132] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 11/28/2022] Open
Abstract
Introduction Idiopathic pulmonary fibrosis (IPF) is a chronic and fatal disease of unknown cause characterised by progressive fibrotic formation in lung tissue. We hypothesise that disrupted metabolic pathways in IPF contribute to disease pathogenesis. Methods Metabolomics of human IPF was performed using mass spectroscopy (IPF lung=8; donor lung=8). Gene expression of key metabolic enzymes was measured using microarrays. Of the 108 metabolites whose levels were found altered, 48 were significantly increased, whereas 60 were significantly decreased in IPF samples compared with normal controls. Results Specific metabolic pathways mediating the IPF remodelling were found with a downregulated sphingolipid metabolic pathway but an upregulated arginine pathway in IPF. In addition, disrupted glycolysis, mitochondrial beta-oxidation and tricarboxylic acid cycle, altered bile acid, haem and glutamate/aspartate metabolism were found in IPF samples compared with control. Conclusions Our results show alterations in metabolic pathways for energy consumption during lung structural remodelling, which may contribute to IPF pathogenesis. We believe that this is the first report of simultaneously and systemically measuring changes of metabolites involving nine metabolic pathways in human severe IPF lungs. The measurement of the metabolites may serve in the future diagnosis and prognosis of IPF.
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Affiliation(s)
- Yidan D Zhao
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Li Yin
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Stephen Archer
- Department of Medicine, Queen's University, Kingston, Ontario, Canada
| | - Catherine Lu
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - George Zhao
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Yan Yao
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Licun Wu
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Michael Hsin
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Thomas K Waddell
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - Shaf Keshavjee
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
| | - John Granton
- Division of Respirology, University Health Network, Toronto, Ontario, Canada
| | - Marc de Perrot
- Department of Thoracic Surgery, University Health Network, Toronto, Ontario, Canada
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Evans CM, Fingerlin TE, Schwarz MI, Lynch D, Kurche J, Warg L, Yang IV, Schwartz DA. Idiopathic Pulmonary Fibrosis: A Genetic Disease That Involves Mucociliary Dysfunction of the Peripheral Airways. Physiol Rev 2017; 96:1567-91. [PMID: 27630174 PMCID: PMC5243224 DOI: 10.1152/physrev.00004.2016] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an incurable complex genetic disorder that is associated with sequence changes in 7 genes (MUC5B, TERT, TERC, RTEL1, PARN, SFTPC, and SFTPA2) and with variants in at least 11 novel loci. We have previously found that 1) a common gain-of-function promoter variant in MUC5B rs35705950 is the strongest risk factor (genetic and otherwise), accounting for 30-35% of the risk of developing IPF, a disease that was previously considered idiopathic; 2) the MUC5B promoter variant can potentially be used to identify individuals with preclinical pulmonary fibrosis and is predictive of radiologic progression of preclinical pulmonary fibrosis; and 3) MUC5B may be involved in the pathogenesis of pulmonary fibrosis with MUC5B message and protein expressed in bronchiolo-alveolar epithelia of IPF and the characteristic IPF honeycomb cysts. Based on these considerations, we hypothesize that excessive production of MUC5B either enhances injury due to reduced mucociliary clearance or impedes repair consequent to disruption of normal regenerative mechanisms in the distal lung. In aggregate, these novel considerations should have broad impact, resulting in specific etiologic targets, early detection of disease, and novel biologic pathways for use in the design of future intervention, prevention, and mechanistic studies of IPF.
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Affiliation(s)
- Christopher M Evans
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Tasha E Fingerlin
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Marvin I Schwarz
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - David Lynch
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Jonathan Kurche
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Laura Warg
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - Ivana V Yang
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
| | - David A Schwartz
- Department of Medicine, University of Colorado Denver, School of Medicine, Aurora, Colorado; National Jewish Health, Denver, Colorado; and Department of Immunology, University of Colorado Denver, School of Medicine, Aurora, Colorado
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Knudsen L, Ruppert C, Ochs M. Tissue remodelling in pulmonary fibrosis. Cell Tissue Res 2016; 367:607-626. [PMID: 27981380 DOI: 10.1007/s00441-016-2543-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/19/2016] [Indexed: 12/16/2022]
Abstract
Many lung diseases result in fibrotic remodelling. Fibrotic lung disorders can be divided into diseases with known and unknown aetiology. Among those with unknown aetiology, idiopathic pulmonary fibrosis (IPF) is a common diagnosis. Because of its progressive character leading to a rapid decline in lung function, it is a fatal disease with poor prognosis and limited therapeutic options. Thus, IPF has motivated many studies in the last few decades in order to increase our mechanistic understanding of the pathogenesis of the disease. The current concept suggests an ongoing injury of the alveolar epithelium, an impaired regeneration capacity, alveolar collapse and, finally, a fibroproliferative response. The origin of lung injury remains elusive but a diversity of factors, which will be discussed in this article, has been shown to be associated with IPF. Alveolar epithelial type II (AE2) cells play a key role in lung fibrosis and their crucial role for epithelial regeneration, stabilisation of alveoli and interaction with fibroblasts, all known to be responsible for collagen deposition, will be illustrated. Whereas mechanisms of collagen deposition and fibroproliferation are the focus of many studies in the field, the awareness of other mechanisms in this disease is currently limited to biochemical and imaging studies including quantitative assessments of lung structure in IPF and animal models assigning alveolar collapse and collapse induration crucial roles for the degradation of the lung resulting in de-aeration and loss of surface area. Dysfunctional AE2 cells, instable alveoli and mechanical stress trigger remodelling that consists of collapsed alveoli absorbed by fibrotic tissue (i.e., collapse induration).
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Affiliation(s)
- Lars Knudsen
- Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany. .,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany. .,REBIRTH, Cluster of Excellence, Hannover Medical School, Hannover, Germany.
| | - Clemens Ruppert
- Department of Internal Medicine, Justus-Liebig-University Giessen, Giessen, Germany.,Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg, Giessen, Germany
| | - Matthias Ochs
- Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg Strasse 1, 30625, Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, Hannover, Germany.,REBIRTH, Cluster of Excellence, Hannover Medical School, Hannover, Germany
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45
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Selman M, López-Otín C, Pardo A. Age-driven developmental drift in the pathogenesis of idiopathic pulmonary fibrosis. Eur Respir J 2016; 48:538-52. [DOI: 10.1183/13993003.00398-2016] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 05/13/2016] [Indexed: 12/21/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and usually lethal disease of unknown aetiology. A growing body of evidence supports that IPF represents an epithelial-driven process characterised by aberrant epithelial cell behaviour, fibroblast/myofibroblast activation and excessive accumulation of extracellular matrix with the subsequent destruction of the lung architecture. The mechanisms involved in the abnormal hyper-activation of the epithelium are unclear, but we propose that recapitulation of pathways and processes critical to embryological development associated with a tissue specific age-related stochastic epigenetic drift may be implicated. These pathways may also contribute to the distinctive behaviour of IPF fibroblasts. Genomic and epigenomic studies have revealed that wingless/Int, sonic hedgehog and other developmental signalling pathways are reactivated and deregulated in IPF. Moreover, some of these pathways cross-talk with transforming growth factor-β activating a profibrotic feedback loop. The expression pattern of microRNAs is also dysregulated in IPF and exhibits a similar expression profile to embryonic lungs. In addition, senescence, a process usually associated with ageing, which occurs early in alveolar epithelial cells of IPF lungs, likely represents a conserved programmed developmental mechanism. Here, we review the major developmental pathways that get twisted in IPF, and discuss the connection with ageing and potential therapeutic approaches.
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46
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The Protective Effect of Naringin against Bleomycin-Induced Pulmonary Fibrosis in Wistar Rats. Pulm Med 2016; 2016:7601393. [PMID: 26977316 PMCID: PMC4764747 DOI: 10.1155/2016/7601393] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 12/23/2015] [Accepted: 01/14/2016] [Indexed: 12/22/2022] Open
Abstract
The aim of the current study was to investigate the protective effect of naringin on bleomycin-induced pulmonary fibrosis in rats. Twenty-four Wistar rats randomly divided into four groups (control, bleomycin alone, bleomycin + naringin 40, and bleomycin + naringin 80) were used. Rats were administered a single dose of bleomycin (5 mg/kg; via the tracheal cannula) alone or followed by either naringin 40 mg/kg (orally) or naringin 80 mg/kg (orally) or water (1 mL, orally) for 14 days. Rats and lung tissue were weighed to determine the lung index. TNF-α and IL-1β levels, hydroxyproline content, and malondialdehyde (MDA) levels were assayed. Glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD) activities were determined. Tissue sections were stained with hematoxylin-eosin, Masson's trichrome, and 0.1% toluidine blue. TNF-α, IL-1β, and MDA levels and hydroxyproline content significantly increased (p < 0.01) and GPx and SOD activities significantly decreased in bleomycin group (p < 0.01). Naringin at a dose of 80 mg/kg body weight significantly decreased TNF-α and IL-1β activity, hydroxyproline content, and MDA level (p < 0.01) and increased GPx and SOD activities (p < 0.05). Histological evidence supported the results. These results show that naringin has the potential of reducing the toxic effects of bleomycin and may provide supportive therapy for conventional treatment methods for idiopathic pulmonary fibrosis.
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47
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Personalized Medicine in Respiratory Disease: Role of Proteomics. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2015; 102:115-46. [PMID: 26827604 DOI: 10.1016/bs.apcsb.2015.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Respiratory diseases affect humanity globally, with chronic lung diseases (e.g., asthma, chronic obstructive pulmonary disease, idiopathic pulmonary fibrosis, among others) and lung cancer causing extensive morbidity and mortality. These conditions are highly heterogeneous and require an early diagnosis. However, initial symptoms are nonspecific, and the clinical diagnosis is made late frequently. Over the last few years, personalized medicine has emerged as a medical care approach that uses novel technology aiming to personalize treatments according to the particular patient's medical needs. This review highlights the contributions of proteomics toward the understanding of personalized medicine in respiratory disease and its potential applications in the clinic.
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48
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Ahuja S, Knudsen L, Chillappagari S, Henneke I, Ruppert C, Korfei M, Gochuico BR, Bellusci S, Seeger W, Ochs M, Guenther A, Mahavadi P. MAP1LC3B overexpression protects against Hermansky-Pudlak syndrome type-1-induced defective autophagy in vitro. Am J Physiol Lung Cell Mol Physiol 2015; 310:L519-31. [PMID: 26719147 DOI: 10.1152/ajplung.00213.2015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 12/24/2015] [Indexed: 01/07/2023] Open
Abstract
Hermansky-Pudlak syndrome (HPS) is a rare autosomal recessive disorder, and some patients with HPS develop pulmonary fibrosis, known as HPS-associated interstitial pneumonia (HPSIP). We have previously reported that HPSIP is associated with severe surfactant accumulation, lysosomal stress, and alveolar epithelial cell type II (AECII) apoptosis. Here, we hypothesized that defective autophagy might result in excessive lysosomal stress in HPSIP. Key autophagy proteins, including LC3B lipidation and p62, were increased in HPS1/2 mice lungs. Electron microscopy demonstrated a preferable binding of LC3B to the interior of lamellar bodies in the AECII of HPS1/2 mice, whereas in wild-type mice it was present on the limiting membrane in addition to the interior of the lamellar bodies. Similar observations were noted in human HPS1 lung sections. In vitro knockdown of HPS1 revealed increased LC3B lipidation and p62 accumulation, associated with an increase in proapoptotic caspases. Overexpression of LC3B decreased the HPS1 knockdown-induced p62 accumulation, whereas rapamycin treatment did not show the same effect. We conclude that loss of HPS1 protein results in impaired autophagy that is restored by exogenous LC3B and that defective autophagy might therefore play a critical role in the development and progression of HPSIP.
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Affiliation(s)
- Saket Ahuja
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany
| | - Lars Knudsen
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany; REBIRTH Cluster of Excellence, Hannover, Germany
| | - Shashi Chillappagari
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany; Department of Pediatrics, Justus-Liebig-University, Giessen, Germany
| | - Ingrid Henneke
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany
| | - Clemens Ruppert
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany; Excellence Cluster Cardiopulmonary System (ECCPS), Giessen, Germany
| | - Martina Korfei
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany
| | - Bernadette R Gochuico
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Saverio Bellusci
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany; Excellence Cluster Cardiopulmonary System (ECCPS), Giessen, Germany
| | - Werner Seeger
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany; Excellence Cluster Cardiopulmonary System (ECCPS), Giessen, Germany; Member European IPF Registry/Biobank; and
| | - Matthias Ochs
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in End-Stage and Obstructive Lung Disease Hannover (BREATH), Member of the German Center for Lung Research (DZL), Hannover, Germany; REBIRTH Cluster of Excellence, Hannover, Germany
| | - Andreas Guenther
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany; Excellence Cluster Cardiopulmonary System (ECCPS), Giessen, Germany; Member European IPF Registry/Biobank; and Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany
| | - Poornima Mahavadi
- Department of Internal Medicine, Justus-Liebig University, Giessen, Germany; Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Centre for Lung Research (DZL), Giessen, Germany
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Kulkarni YM, Dutta S, Iyer AKV, Venkatadri R, Kaushik V, Ramesh V, Wright CA, Semmes OJ, Yakisich JS, Azad N. A proteomics approach to identifying key protein targets involved in VEGF inhibitor mediated attenuation of bleomycin-induced pulmonary fibrosis. Proteomics 2015; 16:33-46. [PMID: 26425798 DOI: 10.1002/pmic.201500171] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/07/2015] [Accepted: 09/25/2015] [Indexed: 12/18/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with a life expectancy of less than 5 years post diagnosis for most patients. Poor molecular characterization of IPF has led to insufficient understanding of the pathogenesis of the disease, resulting in lack of effective therapies. In this study, we have integrated a label-free LC-MS based approach with systems biology to identify signaling pathways and regulatory nodes within protein interaction networks that govern phenotypic changes that may lead to IPF. Ingenuity Pathway Analysis of proteins modulated in response to bleomycin treatment identified PI3K/Akt and Wnt signaling as the most significant profibrotic pathways. Similar analysis of proteins modulated in response to vascular endothelial growth factor (VEGF) inhibitor (CBO-P11) treatment identified natural killer cell signaling and PTEN signaling as the most significant antifibrotic pathways. Mechanistic/mammalian target of rapamycin (mTOR) and extracellular signal-regulated kinase (ERK) were identified to be key mediators of pro- and antifibrotic response, where bleomycin (BLM) treatment resulted in increased expression and VEGF inhibitor treatment attenuated expression of mTOR and ERK. Using a BLM mouse model of pulmonary fibrosis and VEGF inhibitor CBO-P11 as a therapeutic measure, we identified a comprehensive set of signaling pathways and proteins that contribute to the pathogenesis of pulmonary fibrosis that can be targeted for therapy against this fatal disease.
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Affiliation(s)
- Yogesh M Kulkarni
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
| | - Sucharita Dutta
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA.,Leroy T. Canoles Jr, Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Anand Krishnan V Iyer
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
| | - Rajkumar Venkatadri
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
| | - Vivek Kaushik
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
| | - Vani Ramesh
- Department of Obstetrics and Gynecology, The Jones Institute for Reproductive Medicine, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Clayton A Wright
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
| | - Oliver John Semmes
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA, USA.,Leroy T. Canoles Jr, Cancer Research Center, Eastern Virginia Medical School, Norfolk, VA, USA
| | - Juan S Yakisich
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
| | - Neelam Azad
- Department of Pharmaceutical Sciences, School of Pharmacy, Hampton University, Hampton, VA, USA
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50
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Birkelbach B, Lutz D, Ruppert C, Henneke I, Lopez-Rodriguez E, Günther A, Ochs M, Mahavadi P, Knudsen L. Linking progression of fibrotic lung remodeling and ultrastructural alterations of alveolar epithelial type II cells in the amiodarone mouse model. Am J Physiol Lung Cell Mol Physiol 2015; 309:L63-75. [PMID: 25957292 DOI: 10.1152/ajplung.00279.2014] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 05/07/2015] [Indexed: 01/08/2023] Open
Abstract
Chronic injury of alveolar epithelial type II cells (AE2 cells) represents a key event in the development of lung fibrosis in animal models and in humans, such as idiopathic pulmonary fibrosis (IPF). Intratracheal delivery of amiodarone to mice results in a profound injury and macroautophagy-dependent apoptosis of AE2 cells. Increased autophagy manifested in AE2 cells by disturbances of the intracellular surfactant. Hence, we hypothesized that ultrastructural alterations of the intracellular surfactant pool are signs of epithelial stress correlating with the severity of fibrotic remodeling. With the use of design-based stereology, the amiodarone model of pulmonary fibrosis in mice was characterized at the light and ultrastructural level during progression. Mean volume of AE2 cells, volume of lamellar bodies per AE2 cell, and mean size of lamellar bodies were correlated to structural parameters reflecting severity of fibrosis like collagen content. Within 2 wk amiodarone leads to an increase in septal wall thickness and a decrease in alveolar numbers due to irreversible alveolar collapse associated with alveolar surfactant dysfunction. Progressive hypertrophy of AE2 cells and increase in mean individual size and total volume of lamellar bodies per AE2 cell were observed. A high positive correlation of these AE2 cell-related ultrastructural changes and the deposition of collagen fibrils within septal walls were established. Qualitatively, similar alterations could be found in IPF samples with mild to moderate fibrosis. We conclude that ultrastructural alterations of AE2 cells including the surfactant system are tightly correlated with the progression of fibrotic remodeling.
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Affiliation(s)
- Bastian Birkelbach
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Member of the German Center for Lung Research (DZL), Germany
| | - Dennis Lutz
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Member of the German Center for Lung Research (DZL), Germany
| | - Clemens Ruppert
- Department of Internal Medicine, Justus-Liebig-University Giessen, Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany; Member of the German Center for Lung Research (DZL), Germany
| | - Ingrid Henneke
- Department of Internal Medicine, Justus-Liebig-University Giessen, Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany; Member of the German Center for Lung Research (DZL), Germany
| | - Elena Lopez-Rodriguez
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Member of the German Center for Lung Research (DZL), Germany
| | - Andreas Günther
- Department of Internal Medicine, Justus-Liebig-University Giessen, Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany; Member of the German Center for Lung Research (DZL), Germany; European IPF Network, Giessen, Germany; Excellence Cluster "Cardiopulmonary System ECCPS," Giessen, Germany; Lung Clinic Waldhof-Elgershausen, Greifenstein, Germany; and
| | - Matthias Ochs
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Member of the German Center for Lung Research (DZL), Germany; REBIRTH Cluster of Excellence, Hannover, Germany
| | - Poornima Mahavadi
- Department of Internal Medicine, Justus-Liebig-University Giessen, Universities of Giessen and Marburg Lung Center (UGMLC), Giessen, Germany; Member of the German Center for Lung Research (DZL), Germany
| | - Lars Knudsen
- Institute of Functional and Applied Anatomy, Hannover Medical School, Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Member of the German Center for Lung Research (DZL), Germany;
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