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Zhang H, Hua H, Wang C, Zhu C, Xia Q, Jiang W, Hu X, Zhang Y. Construction of an artificial neural network diagnostic model and investigation of immune cell infiltration characteristics for idiopathic pulmonary fibrosis. BMC Pulm Med 2024; 24:458. [PMID: 39289672 DOI: 10.1186/s12890-024-03249-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 08/29/2024] [Indexed: 09/19/2024] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a severe lung condition, and finding better ways to diagnose and treat the disease is crucial for improving patient outcomes. Our study sought to develop an artificial neural network (ANN) model for IPF and determine the immune cell types that differed between the IPF and control groups. METHODS From the Gene Expression Omnibus (GEO) database, we first obtained IPF microarray datasets. To conduct protein-protein interaction (PPI) networks and enrichment analyses, differentially expressed genes (DEGs) were screened between tissues of patients with IPF and tissues of controls. Afterward, we identified the important feature genes associated with IPF using random forest (RF) analysis, and then constructed and validated a prediction ANN mode. In addition, the proportions of immune cells were quantified using cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) analysis, which was performed on microarray datasets based on gene expression profiling. RESULTS A total of 11 downregulated and 36 upregulated DEGs were identified. PPI networks and enrichment analyses were carried out; the immune system and extracellular matrix were the subjects of the enrichments. Using RF analysis, the significant feature genes LRRC17, COMP, ASPN, CRTAC1, POSTN, COL3A1, PEBP4, IL13RA2, and CA4 were identified. The nine feature gene scores were integrated into the ANN to develop a diagnostic prediction model. The receiver operating characteristic (ROC) curves demonstrated the strong diagnostic ability of the ANN in predicting IPF in the training and testing sets. An analysis of IPF tissues in comparison to normal tissues revealed a reduction in the infiltration of natural killer cells resting, monocytes, macrophages M0, and neutrophils; conversely, the infiltration of T cells CD4 memory resting, mast cells, and macrophages M0 increased. CONCLUSION LRRC17, COMP, ASPN, CRTAC1, POSTN, COL3A1, PEBP4, IL13RA2, and CA4 were determined as key feature genes for IPF. The nine feature genes in the ANN model will be extremely important for diagnosing IPF. It may be possible to use differentiated immune cells from IPF samples in comparison to normal samples as targets for immunotherapy in patients with IPF.
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Affiliation(s)
- Huizhe Zhang
- Department of Respiratory Medicine, Yancheng Hospital of Traditional Chinese Medicine; Yancheng TCM Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, 224005, China
| | - Haibing Hua
- Department of Gastroenterology, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China
| | - Cong Wang
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China
- Research Institute of Respiratory Diseases, Jiangsu Province Clinical Academy of Traditional Chinese Medicine (Jiangyin Branch), Jiangyin, Jiangsu, 214400, China
| | - Chenjing Zhu
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China
- Research Institute of Respiratory Diseases, Jiangsu Province Clinical Academy of Traditional Chinese Medicine (Jiangyin Branch), Jiangyin, Jiangsu, 214400, China
| | - Qingqing Xia
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China
- Research Institute of Respiratory Diseases, Jiangsu Province Clinical Academy of Traditional Chinese Medicine (Jiangyin Branch), Jiangyin, Jiangsu, 214400, China
| | - Weilong Jiang
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China.
- Research Institute of Respiratory Diseases, Jiangsu Province Clinical Academy of Traditional Chinese Medicine (Jiangyin Branch), Jiangyin, Jiangsu, 214400, China.
| | - Xiaodong Hu
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China.
- Research Institute of Respiratory Diseases, Jiangsu Province Clinical Academy of Traditional Chinese Medicine (Jiangyin Branch), Jiangyin, Jiangsu, 214400, China.
| | - Yufeng Zhang
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine; Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, 214400, China.
- Research Institute of Respiratory Diseases, Jiangsu Province Clinical Academy of Traditional Chinese Medicine (Jiangyin Branch), Jiangyin, Jiangsu, 214400, China.
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Bellani S, Molyneaux PL, Maher TM, Spagnolo P. Potential of αvβ6 and αvβ1 integrin inhibition for treatment of idiopathic pulmonary fibrosis. Expert Opin Ther Targets 2024; 28:575-585. [PMID: 38949181 DOI: 10.1080/14728222.2024.2375375] [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: 03/23/2024] [Accepted: 06/28/2024] [Indexed: 07/02/2024]
Abstract
INTRODUCTION Idiopathic pulmonary fibrosis (IPF) is a chronic progressive interstitial lung disease of unknown cause with a dismal prognosis. Nintedanib and Pirfenidone are approved worldwide for the treatment of IPF, but they only slow the rate of functional decline and disease progression. Therefore, there is an urgent need for more efficacious and better tolerated drugs. AREAS COVERED αvβ6 and αvβ1 are two integrins overexpressed in fibrotic tissue, which play a critical role in the development of lung fibrosis. They act by converting transforming growth factor (TGF)-β, one of the most important profibrotic cytokine, in its active form. Here, we summarize and critically discuss the potential of a dual αvβ6/αvβ1 integrin inhibitor for the treatment of IPF. EXPERT OPINION Bexotegrast, a dual αvβ6/αvβ1 integrin inhibitor, has the potential to slow or even halt disease progression in IPF. Indeed, the strong pre-clinical rationale and promising early phase clinical trial data have raised expectations.
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Affiliation(s)
- Serena Bellani
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
| | - Philip L Molyneaux
- National Heart and Lung Institute, Imperial College, London, UK
- Interstitial Lung Disease Unit, Royal Brompton and Harefield Hospitals, London, UK
| | - Toby M Maher
- Hastings Centre for Pulmonary Research and Division of Pulmonary, Critical Care and Sleep Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Padova, Italy
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Guo B, Sun Y, Wang Y, Zhang Y, Zheng Y, Xu S, Yang G, Ren W. Evolutionary genetics of pulmonary anatomical adaptations in deep-diving cetaceans. BMC Genomics 2024; 25:339. [PMID: 38575860 PMCID: PMC10993460 DOI: 10.1186/s12864-024-10263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Cetaceans, having experienced prolonged adaptation to aquatic environments, have undergone evolutionary changes in their respiratory systems. This process of evolution has resulted in the emergence of distinctive phenotypic traits, notably the abundance of elastic fibers and thickened alveolar walls in their lungs, which may facilitate alveolar collapse during diving. This structure helps selective exchange of oxygen and carbon dioxide, while minimizing nitrogen exchange, thereby reducing the risk of DCS. Nevertheless, the scientific inquiry into the mechanisms through which these unique phenotypic characteristics govern the diving behavior of marine mammals, including cetaceans, remains unresolved. RESULTS This study entails an evolutionary analysis of 42 genes associated with pulmonary fibrosis across 45 mammalian species. Twenty-one genes in cetaceans exhibited accelerated evolution, featuring specific amino acid substitutions in 14 of them. Primarily linked to the development of the respiratory system and lung morphological construction, these genes play a crucial role. Moreover, among marine mammals, we identified eight genes undergoing positive selection, and the evolutionary rates of three genes significantly correlated with diving depth. Specifically, the SFTPC gene exhibited convergent amino acid substitutions. Through in vitro cellular experiments, we illustrated that convergent amino acid site mutations in SFTPC contribute positively to pulmonary fibrosis in marine mammals, and the presence of this phenotype can induce deep alveolar collapse during diving, thereby reducing the risk of DCS during diving. CONCLUSIONS The study unveils pivotal genetic signals in cetaceans and other marine mammals, arising through evolution. These genetic signals may influence lung characteristics in marine mammals and have been linked to a reduced risk of developing DCS. Moreover, the research serves as a valuable reference for delving deeper into human diving physiology.
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Affiliation(s)
- Boxiong Guo
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yixuan Sun
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yuehua Wang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Ya Zhang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yu Zheng
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
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Gandhi SA, Min B, Fazio JC, Johannson KA, Steinmaus C, Reynolds CJ, Cummings KJ. The Impact of Occupational Exposures on the Risk of Idiopathic Pulmonary Fibrosis: A Systematic Review and Meta-Analysis. Ann Am Thorac Soc 2024; 21:486-498. [PMID: 38096107 PMCID: PMC10913770 DOI: 10.1513/annalsats.202305-402oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/13/2023] [Indexed: 03/02/2024] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic pulmonary disorder of unknown etiology that is characterized by a usual interstitial pneumonia pattern. Previous meta-analyses have reported associations between occupational exposures and IPF, but higher-quality studies have been published in recent years, doubling the number of studied patients. Objectives: To provide a contemporary and comprehensive assessment of the relationship between occupational exposures and IPF. Methods: We searched PubMed, Embase, and Web of Science through July 2023 to identify all publications on occupational exposure and IPF. We conducted a meta-analysis of the occupational burden, odds ratio (OR), and population attributable fraction (PAF) of exposures. Five exposure categories were analyzed: vapors, gas, dust, and fumes (VGDF); metal dust; wood dust; silica dust; and agricultural dust. A comprehensive bias assessment was performed. The study protocol was registered in the International Prospective Register of Systematic Reviews (identifier CRD42021267808). Results: Our search identified 23,942 publications. Sixteen publications contained relative risks needed to calculate pooled ORs and PAFs, and 12 additional publications reported an occupational burden within a case series. The proportion of cases with occupational exposures to VGDF was 44% (95% confidence interval [CI], 36-53%), with a range of 8-17% within more specific exposure categories. The pooled OR was increased for VGDF at 1.8 (95% CI, 1.3-2.4), with a pooled PAF of 21% (95% CI, 15-28%). ORs and PAFs, respectively, were found to be 1.6 and 7% for metal dust, 1.6 and 3% for wood dust, 1.8 and 14% for agricultural dust, and 1.8 and 4% for silica dust. The pooled ORs and PAFs within specific exposure categories ranged from 1.6 to 1.8 and from 4% to 14%, respectively. We identified some publication bias, but it was not sufficient to diminish the association between occupational exposures and IPF based on sensitivity analysis and bias assessment. Conclusions: Our findings indicate that 21% of IPF cases (or approximately one in five) could be prevented by removal of occupational exposure (alongside a pooled OR of 1.8). Additionally, 44% of patients with IPF report occupational exposure to VGDF. This meta-analysis suggests that a considerable number of cases of IPF are attributable to inhaled occupational exposures and warrant increased consideration in the clinical care of patients and future prevention efforts.
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Affiliation(s)
- Sheiphali A. Gandhi
- Division of Occupational, Environmental, and Climate Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Bohyung Min
- Department of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jane C. Fazio
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of California, Los Angeles, Los Angeles, California
| | | | - Craig Steinmaus
- School of Public Health, University of California, Berkeley, Berkeley, California
| | - Carl J. Reynolds
- Faculty of Medicine, National Heart and Lung Institute, Imperial College of London, London, United Kingdom; and
| | - Kristin J. Cummings
- Occupational Health Branch, California Department of Public Health, Richmond, California
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Xing Q, Liu X, Liu Z, Yan Q, Hu Y, Li W, Peng K. Elucidating the Mechanism of Buyanghuanwu Decoction Acting on Pulmonary Fibrosis Based on Network Pharmacology and Animal Studies. Comb Chem High Throughput Screen 2024; 27:1046-1055. [PMID: 37612869 PMCID: PMC11165711 DOI: 10.2174/1386207326666230823093958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/20/2023] [Accepted: 07/24/2023] [Indexed: 08/25/2023]
Abstract
BACKGROUND AND OBJECTIVE Buyanghuanwu Decoction (BYHWD) is a clinically proven prescription effective in treating pulmonary fibrosis (PF), but the molecular mechanism underlying its action remains unclear. The network pharmacology analysis was performed to elucidate the acting substances and related pathways of BYHWD in treating bleomycin (BLM) induced PF mouse. METHODS First, the pharmacologically active components and corresponding targets in BYHWD were identified through the TCMSP database and literature review. Second, PF-related targets were identified through the DisGeNet database. Then, the components-targets network of BYHWD in PF treatment was constructed using Cytoscape. The DAVID database was used for the enrichment analysis of GO terms and KEGG pathways. At last, the therapeutic effect of BYHWD on BLMinduced PF mice were verified, and the mRNA and protein expression of related targets was determined through RT-PCR and western blotting, respectively. RESULTS The core component-target network contained 58 active components and 147 targets. Thirty-nine core targets were mainly involved in the regulation of biological functions and KEGG pathways, such as the positive regulation of nitric oxide biosynthesis and the TNF signaling pathway. These core targets were obtained through enrichment analysis. Moreover, animal studies revealed that BYHWD down-regulated the mRNA expression levels of TNF, IL-6, IL-1β, and NOS2 and inhibited NF-κB and p38 phosphorylation. CONCLUSION The effects of BYHWD on PF mice are therapeutic, and its anti-PF mechanism mainly involves the effects on inflammatory factors and the NF-κB/p38 pathway.
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Affiliation(s)
- Qichang Xing
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
- Zhou Honghao Research Institute Xiangtan, Xiangtan, Hunan, 411100, China
| | - Xiang Liu
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
- Zhou Honghao Research Institute Xiangtan, Xiangtan, Hunan, 411100, China
| | - Zheng Liu
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
| | - Qingzi Yan
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
| | - Yixiang Hu
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
| | - Wencan Li
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
| | - Ke Peng
- Department of Clinical Pharmacy, Xiangtan Central Hospital, Xiangtan, Hunan, 411100, China
- College of Pharmacy, Changsha Medical College, Changsha, Hunan, 410219, China
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Amin R, Pandey R, Vaishali K, Acharya V, Sinha MK, Kumar N. Therapeutic Approaches for the Treatment of Interstitial Lung Disease: An Exploratory Review on Molecular Mechanisms. Mini Rev Med Chem 2024; 24:618-633. [PMID: 37587813 DOI: 10.2174/1389557523666230816090112] [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: 01/12/2023] [Revised: 05/04/2023] [Accepted: 06/09/2023] [Indexed: 08/18/2023]
Abstract
BACKGROUND Interstitial Lung Diseases (ILDs) are characterized by shortness of breath caused by alveolar wall inflammation and/or fibrosis. OBJECTIVE Our review aims to study the depth of various variants of ILD, diagnostic procedures, pathophysiology, molecular dysfunction and regulation, subject and objective assessment techniques, pharmacological intervention, exercise training and various modes of delivery for rehabilitation. METHOD Articles are reviewed from PubMed and Scopus and search engines. RESULTS ILD is a rapidly progressing disease with a high mortality rate. Each variant has its own set of causal agents and expression patterns. Patients often find it challenging to self-manage due to persistent symptoms and a rapid rate of worsening. The present review elaborated on the pathophysiology, risk factors, molecular mechanisms, diagnostics, and therapeutic approaches for ILD will guide future requirements in the quest for innovative and tailored ILD therapies at the molecular and cellular levels. CONCLUSION The review highlights the rationale for conventional and novel therapeutic approaches for better management of ILD.
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Affiliation(s)
- Revati Amin
- Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, India
| | - Ruchi Pandey
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, 844102, India
| | - K Vaishali
- Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, India
| | - Vishak Acharya
- Department of Pulmonary Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Mangalore, India
| | - Mukesh Kumar Sinha
- Department of Physiotherapy, Manipal College of Health Professions, Manipal Academy of Higher Education, Manipal, India
| | - Nitesh Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Hajipur, Bihar, 844102, India
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Lettieri S, Bertuccio FR, del Frate L, Perrotta F, Corsico AG, Stella GM. The Plastic Interplay between Lung Regeneration Phenomena and Fibrotic Evolution: Current Challenges and Novel Therapeutic Perspectives. Int J Mol Sci 2023; 25:547. [PMID: 38203718 PMCID: PMC10779349 DOI: 10.3390/ijms25010547] [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: 12/13/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Interstitial lung diseases (ILDs) are a heterogeneous group of pulmonary disorders characterized by variable degrees of inflammation, interstitial thickening, and fibrosis leading to distortion of the pulmonary architecture and gas exchange impairment. Among them, idiopathic pulmonary fibrosis (IPF) displays the worst prognosis. The only therapeutic options consist of the two antifibrotic drugs, pirfenidone and nintedanib, which limit fibrosis progression but do not reverse the lung damage. The shift of the pathogenetic paradigm from inflammatory disease to epithelium-derived disease has definitively established the primary role of type II alveolar cells, which lose their epithelial phenotype and acquire a mesenchymal phenotype with production of collagen and extracellular matrix (EMC) deposition. Some predisposing environmental and genetic factors (e.g., smoke, pollution, gastroesophageal reflux, variants of telomere and surfactant genes) leading to accelerated senescence set a pro-fibrogentic microenvironment and contribute to the loss of regenerative properties of type II epithelial cells in response to pathogenic noxae. This review provides a complete overview of the different pathogenetic mechanisms leading to the development of IPF. Then, we summarize the currently approved therapies and the main clinical trials ongoing. Finally, we explore the potentialities offered by agents not only interfering with the processes of fibrosis but also restoring the physiological properties of alveolar regeneration, with a particular focus on potentialities and concerns about cell therapies based on mesenchymal stem cells (MSCs), whose anti-inflammatory and immunomodulant properties have been exploited in other fibrotic diseases, such as graft versus host disease (GVHD) and COVID-19-related ARDS.
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Affiliation(s)
- Sara Lettieri
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesco R. Bertuccio
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Lucia del Frate
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Fabio Perrotta
- Department of Translational Medical Science, University of Campania Luigi Vanvitelli, 80055 Naples, Italy;
| | - Angelo G. Corsico
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giulia M. Stella
- Department of Internal Medicine and Medical Therapeutics, University of Pavia Medical School, 27100 Pavia, Italy; (S.L.); (F.R.B.); (L.d.F.); (A.G.C.)
- Cardiothoracic and Vascular Department, Unit of Respiratory Diseases, IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Liu H, Lai W, Nie H, Shi Y, Zhu L, Yang L, Tian L, Li K, Bian L, Xi Z, Lin B. PM 2.5 triggers autophagic degradation of Caveolin-1 via endoplasmic reticulum stress (ERS) to enhance the TGF-β1/Smad3 axis promoting pulmonary fibrosis. ENVIRONMENT INTERNATIONAL 2023; 181:108290. [PMID: 37924604 DOI: 10.1016/j.envint.2023.108290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/06/2023]
Abstract
Air pollution is highly associated with respiratory diseases. However, the influence and mechanism of particulate matter with aerodynamic equal to or less than 2.5 μm (PM2.5) in lung homeostasis remain unclear. Herein, we demonstrated the induction of pulmonary fibrosis (PF) by PM2.5 exposure. The animal model showed that PM2.5 exposure could activate the oxidative stress and inflammation response, promoting epithelial-mesenchymal transition and accumulation of collagen, high expression of pro-fibrotic factors, and pathological characteristics of fibrosis. The proteomic analysis indicated that PM2.5 exposure decreased the expression of caveolin-1 (Cav-1), and many differential proteins were enriched in the TGF-β1/Smad, endoplasmic reticulum stress (ERS) and autophagy pathways. Combining in vivo and in vitro experiments, it was found that PM2.5 exposure could reduce Cav-1 protein levels and activate TGF-β1/Smad3 signaling pathways through ERS and autophagy pathways, thereby inducing cell apoptosis and promoting pulmonary fibrosis. However, inhibiting ERS could alleviate the occurrence of autophagy, and blocking the autophagy system could increase the level of Cav-1 protein and inhibit TGF- β 1/Smad3 signaling pathway to improve pulmonary fibrosis. Therefore, we demonstrated that the exposure of PM2.5 could enhance the ERS induced-autophagy-mediated Cav-1 degradation, thus activating the TGF-β1/Smad3 axis to promote pneumonocytes apoptosis and overproduction of extracellular matrix (ECM), finally aggravating PF. Moreover, our findings revealed that intermittent exposure to high doses of PM2.5 was more toxic than continuous exposure to low dose.
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Affiliation(s)
- Huanliang Liu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Wenqing Lai
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Huipeng Nie
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Yue Shi
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Lina Zhu
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Linhui Yang
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Lei Tian
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Kang Li
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Liping Bian
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China
| | - Zhuge Xi
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China.
| | - Bencheng Lin
- Tianjin Institute of Environmental and Operational Medicine, Tianjin 300050, China; Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment & Food Safety, Tianjin 300050, China.
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Hollmén M, Laaka A, Partanen JJ, Koskela J, Sutinen E, Kaarteenaho R, Ainola M, Myllärniemi M. KIF15 missense variant is associated with the early onset of idiopathic pulmonary fibrosis. Respir Res 2023; 24:240. [PMID: 37777755 PMCID: PMC10543873 DOI: 10.1186/s12931-023-02540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 09/15/2023] [Indexed: 10/02/2023] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) has an unknown aetiology and limited treatment options. A recent meta-analysis identified three novel causal variants in the TERT, SPDL1, and KIF15 genes. This observational study aimed to investigate whether the aforementioned variants cause clinical phenotypes in a well-characterised IPF cohort. METHODS The study consisted of 138 patients with IPF who were diagnosed and treated at the Helsinki University Hospital and genotyped in the FinnGen FinnIPF study. Data on > 25 clinical parameters were collected by two pulmonologists who were blinded to the genetic data for patients with TERT loss of function and missense variants, SPDL1 and KIF15 missense variants, and a MUC5B variant commonly present in patients with IPF, or no variants were separately analysed. RESULTS The KIF15 missense variant is associated with the early onset of the disease, leading to progression to early-age transplantation or death. In patients with the KIF15 variant, the median age at diagnosis was 54.0 years (36.5-69.5 years) compared with 72.0 years (65.8-75.3 years) in the other patients (P = 0.023). The proportion of KIF15 variant carriers was 9- or 3.6-fold higher in patients aged < 55 or 65 years, respectively. The variants for TERT and MUC5B had similar effects on the patient's clinical course, as previously described. No distinct phenotypes were observed in patients with the SPDL1 variant. CONCLUSIONS Our study indicated the potential of KIF15 to be used in the genetic diagnostics of IPF. Further studies are needed to elucidate the biological mechanisms of KIF15 in IPF.
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Affiliation(s)
- Maria Hollmén
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Atte Laaka
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Juulia J. Partanen
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Jukka Koskela
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Eva Sutinen
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Riitta Kaarteenaho
- Research Unit of Biomedicine and Internal Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Mari Ainola
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
| | - Marjukka Myllärniemi
- Individrug, Heart and Lung Centre, The University of Helsinki and Helsinki University Hospital, Research Programs Unit, Helsinki, Finland
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10
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Enomoto Y, Katsura H, Fujimura T, Ogata A, Baba S, Yamaoka A, Kihara M, Abe T, Nishimura O, Kadota M, Hazama D, Tanaka Y, Maniwa Y, Nagano T, Morimoto M. Autocrine TGF-β-positive feedback in profibrotic AT2-lineage cells plays a crucial role in non-inflammatory lung fibrogenesis. Nat Commun 2023; 14:4956. [PMID: 37653024 PMCID: PMC10471635 DOI: 10.1038/s41467-023-40617-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 07/31/2023] [Indexed: 09/02/2023] Open
Abstract
The molecular etiology of idiopathic pulmonary fibrosis (IPF) has been extensively investigated to identify new therapeutic targets. Although anti-inflammatory treatments are not effective for patients with IPF, damaged alveolar epithelial cells play a critical role in lung fibrogenesis. Here, we establish an organoid-based lung fibrosis model using mouse and human lung tissues to assess the direct communication between damaged alveolar type II (AT2)-lineage cells and lung fibroblasts by excluding immune cells. Using this in vitro model and mouse genetics, we demonstrate that bleomycin causes DNA damage and activates p53 signaling in AT2-lineage cells, leading to AT2-to-AT1 transition-like state with a senescence-associated secretory phenotype (SASP). Among SASP-related factors, TGF-β plays an exclusive role in promoting lung fibroblast-to-myofibroblast differentiation. Moreover, the autocrine TGF-β-positive feedback loop in AT2-lineage cells is a critical cellular system in non-inflammatory lung fibrogenesis. These findings provide insights into the mechanism of IPF and potential therapeutic targets.
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Affiliation(s)
- Yasunori Enomoto
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Department of Regenerative and Infectious Pathology, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Hiroaki Katsura
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takashi Fujimura
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
- Department of Drug Modality Development, Osaka Research Center for Drug Discovery, Otsuka Pharmaceutical Co., Ltd., 5-1-35 Saitoaokita, Minoh, 562-0029, Japan
| | - Akira Ogata
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Saori Baba
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Akira Yamaoka
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Miho Kihara
- Laboratory for Animal Resources and Genetic Engineering (LARGE), RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering (LARGE), RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Osamu Nishimura
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Mitsutaka Kadota
- Laboratory for Phyloinformatics, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Daisuke Hazama
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Yugo Tanaka
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Yoshimasa Maniwa
- Division of Thoracic Surgery, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Tatsuya Nagano
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, 7-5-2 Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
| | - Mitsuru Morimoto
- Laboratory for Lung Development and Regeneration, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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11
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Chen M, Zhang Y, Adams T, Ji D, Jiang W, Wain LV, Cho M, Kaminski N, Zhao H. Integrative analyses for the identification of idiopathic pulmonary fibrosis-associated genes and shared loci with other diseases. Thorax 2023; 78:792-798. [PMID: 36216496 PMCID: PMC10083187 DOI: 10.1136/thorax-2021-217703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 09/16/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Although genome-wide association studies (GWAS) have identified many genomic regions associated with idiopathic pulmonary fibrosis (IPF), the causal genes and functions remain largely unknown. Many single-cell expression data have become available for IPF, and there is increasing evidence suggesting a shared genetic basis between IPF and other diseases. METHODS We conducted integrative analyses to improve the power of GWAS. First, we calculated global and local genetic correlations to identify IPF genetically associated traits and local regions. Then, we prioritised candidate genes contributing to local genetic correlation. Second, we performed transcriptome-wide association analysis (TWAS) of 44 tissues to identify candidate genes whose genetically predicted expression level is associated with IPF. To replicate our findings and investigate the regulatory role of the transcription factors (TF) in identified candidate genes, we first conducted the heritability enrichment analysis in TF binding sites. Then, we examined the enrichment of the TF target genes in cell-type-specific differentially expressed genes (DEGs) identified from single-cell expression data of IPF and healthy lung samples. FINDINGS We identified 12 candidate genes across 13 genomic regions using local genetic correlation, including the POT1 locus (p value=0.00041), which contained variants with protective effects on lung cancer but increasing IPF risk. We identified another 13 novel genes using TWAS. Two TFs, MAFK and SMAD2, showed significant enrichment in both partitioned heritability and cell-type-specific DEGs. INTERPRETATION Our integrative analysis identified new genes for IPF susceptibility and expanded the understanding of the complex genetic architecture and disease mechanism of IPF.
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Affiliation(s)
- Ming Chen
- Biostatistics, Yale University School of Public Health, New Haven, Connecticut, USA
| | - Yiliang Zhang
- Biostatistics, Yale University School of Public Health, New Haven, Connecticut, USA
| | - Taylor Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Dingjue Ji
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Wei Jiang
- Biostatistics, Yale University School of Public Health, New Haven, Connecticut, USA
| | - Louise V Wain
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hongyu Zhao
- Biostatistics, Yale University School of Public Health, New Haven, Connecticut, USA
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
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12
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Cîrjaliu RE, Deacu M, Gherghișan I, Marghescu AȘ, Enciu M, Băltățescu GI, Nicolau AA, Tofolean DE, Arghir OC, Fildan AP. Clinicopathological Outlines of Post-COVID-19 Pulmonary Fibrosis Compared with Idiopathic Pulmonary Fibrosis. Biomedicines 2023; 11:1739. [PMID: 37371834 DOI: 10.3390/biomedicines11061739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
This review brings together the current knowledge regarding the risk factors and the clinical, radiologic, and histological features of both post-COVID-19 pulmonary fibrosis (PCPF) and idiopathic pulmonary fibrosis (IPF), describing the similarities and the disparities between these two diseases, using numerous databases to identify relevant articles published in English through October 2022. This review would help clinicians, pathologists, and researchers make an accurate diagnosis, which can help identify the group of patients selected for anti-fibrotic therapies and future therapeutic perspectives.
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Affiliation(s)
- Roxana-Elena Cîrjaliu
- Department of Pneumology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
- Clinical Emergency "St. Andrew" Hospital of Constanta, 900591 Constanta, Romania
| | - Mariana Deacu
- Clinical Emergency "St. Andrew" Hospital of Constanta, 900591 Constanta, Romania
- Department of Anatomopathology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
| | - Ioana Gherghișan
- Department of Pneumology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
- Pneumology Hospital of Constanta, 900002 Constanta, Romania
| | - Angela-Ștefania Marghescu
- Department of Anatomopathology, "Carol Davila" University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Pneumology Institute "Marius Nasta", 50158 Bucharest, Romania
| | - Manuela Enciu
- Clinical Emergency "St. Andrew" Hospital of Constanta, 900591 Constanta, Romania
- Department of Anatomopathology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
| | - Gabriela Izabela Băltățescu
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology-CEDMOG, "Ovidius" University of Constanta, 900591 Constanta, Romania
| | - Antonela Anca Nicolau
- Center for Research and Development of the Morphological and Genetic Studies of Malignant Pathology-CEDMOG, "Ovidius" University of Constanta, 900591 Constanta, Romania
| | - Doina-Ecaterina Tofolean
- Department of Pneumology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
- Clinical Emergency "St. Andrew" Hospital of Constanta, 900591 Constanta, Romania
| | - Oana Cristina Arghir
- Department of Pneumology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
- Pneumology Hospital of Constanta, 900002 Constanta, Romania
| | - Ariadna-Petronela Fildan
- Department of Pneumology, Faculty of Medicine, "Ovidius" University of Constanta, 900470 Constanta, Romania
- Pneumology Hospital of Constanta, 900002 Constanta, Romania
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13
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Gunatilaka A, Zhang S, Tan WSD, G Stewart A. Anti-fibrotic strategies and pulmonary fibrosis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2023; 98:179-224. [PMID: 37524487 DOI: 10.1016/bs.apha.2023.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) results from the dysregulated process of injury and repair, which promotes scarring of the lung tissue and deposition of collagen-rich extracellular matrix (ECM) components, that make the lung unphysiologically stiff. IPF presents a serious concern as its pathogenesis remains elusive, and current anti-fibrotic treatments are only effective in slowing rather than halting disease progression. The IPF disease pathogenesis is incompletely defined, complex and incorporates interplay between different fibrogenesis signaling pathways. Preclinical IPF experimental models used to validate drug candidates present significant limitations in modeling IPF pathobiology, with their limited time frame, simplicity and inaccurate representation of the disease and the mechanical influences of IPF. Potentially more accurate mimetic disease models that capture the cell-cell and cell-matrix interaction, such as 3D cultures, organoids and precision-cut lung slices (PCLS), may yield more meaningful clinical predictions for drug candidates. Recent advances in developing anti-fibrotic compounds have positioned drug towards targeting components of the fibrogenesis signaling pathway of IPF or the extracellular microenvironment. The major goals in this area of research focus on finding ways to reverse or halt the disease progression by utilizing more disease-relevant experimental models to improve the qualification of potential drug targets for treating pulmonary fibrosis.
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Affiliation(s)
- Avanka Gunatilaka
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, Australia; ARC Centre for Personalised Therapeutics Technologies, The University of Melbourne, Parkville, VIC, Australia
| | - Stephanie Zhang
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, Australia
| | - Wan Shun Daniel Tan
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, Australia
| | - Alastair G Stewart
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC, Australia; ARC Centre for Personalised Therapeutics Technologies, The University of Melbourne, Parkville, VIC, Australia.
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14
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Wang S, Rao W, Hoffman A, Lin J, Li J, Lin T, Liew AA, Vincent M, Mertens TCJ, Karmouty-Quintana H, Crum CP, Metersky ML, Schwartz DA, Davies PJA, Stephan C, Jyothula SSK, Sheshadri A, Suarez EE, Huang HJ, Engelhardt JF, Dickey BF, Parekh KR, McKeon FD, Xian W. Cloning a profibrotic stem cell variant in idiopathic pulmonary fibrosis. Sci Transl Med 2023; 15:eabp9528. [PMID: 37099633 PMCID: PMC10794039 DOI: 10.1126/scitranslmed.abp9528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 02/28/2023] [Indexed: 04/28/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive, irreversible, and rapidly fatal interstitial lung disease marked by the replacement of lung alveoli with dense fibrotic matrices. Although the mechanisms initiating IPF remain unclear, rare and common alleles of genes expressed in lung epithelia, combined with aging, contribute to the risk for this condition. Consistently, single-cell RNA sequencing (scRNA-seq) studies have identified lung basal cell heterogeneity in IPF that might be pathogenic. We used single-cell cloning technologies to generate "libraries" of basal stem cells from the distal lungs of 16 patients with IPF and 10 controls. We identified a major stem cell variant that was distinguished from normal stem cells by its ability to transform normal lung fibroblasts into pathogenic myofibroblasts in vitro and to activate and recruit myofibroblasts in clonal xenografts. This profibrotic stem cell variant, which was shown to preexist in low quantities in normal and even fetal lungs, expressed a broad network of genes implicated in organ fibrosis and showed overlap in gene expression with abnormal epithelial signatures identified in previously published scRNA-seq studies of IPF. Drug screens highlighted specific vulnerabilities of this profibrotic variant to inhibitors of epidermal growth factor and mammalian target of rapamycin signaling as prospective therapeutic targets. This profibrotic stem cell variant in IPF was distinct from recently identified profibrotic stem cell variants in chronic obstructive pulmonary disease and may extend the notion that inappropriate accrual of minor and preexisting stem cell variants contributes to chronic lung conditions.
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Affiliation(s)
- Shan Wang
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | - Wei Rao
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | - Ashley Hoffman
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | - Jennifer Lin
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | - Justin Li
- AccuraScience, Johnston, IA 50131, USA
| | - Tao Lin
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | - Audrey-Ann Liew
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | | | - Tinne C. J. Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Christopher P. Crum
- Department of Pathology, Harvard Medical School and Brigham and Women’s Hospital, Boston, MA 02215, USA
| | - Mark L. Metersky
- Department of Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Connecticut School of Medicine, Farmington, CT 06032, USA
| | - David A. Schwartz
- Departments of Medicine and Microbiology and Immunology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | | | - Clifford Stephan
- Texas A&M Health Institute of Biotechnology, Houston, TX 77030, USA
| | - Soma S. K. Jyothula
- Lung Transplant Center at Memorial Hermann-Texas Medical Center, Houston, TX 77030, USA
| | - Ajay Sheshadri
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik Eddie Suarez
- Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - Howard J. Huang
- Department of Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
| | - John F. Engelhardt
- Department of Anatomy and Cell Biology, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Burton F. Dickey
- Department of Pulmonary Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kalpaj R. Parekh
- Department of Surgery, Division of Cardiothoracic Surgery, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA
| | - Frank D. McKeon
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
| | - Wa Xian
- Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA
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15
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Zhao L, Luo JL, Ali MK, Spiekerkoetter E, Nicolls MR. The Human Respiratory Microbiome: Current Understandings and Future Directions. Am J Respir Cell Mol Biol 2023; 68:245-255. [PMID: 36476129 PMCID: PMC9989478 DOI: 10.1165/rcmb.2022-0208tr] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.
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Affiliation(s)
- Lan Zhao
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California.,VA Palo Alto Health Care System, Palo Alto, California; and
| | - Jun-Li Luo
- The Cancer Research Institute, Hengyang Medical School, University of South China, Hengyang, China
| | - Mohammed Khadem Ali
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California
| | - Edda Spiekerkoetter
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California
| | - Mark R Nicolls
- Division of Pulmonary, Allergy & Critical Care Medicine, Department of Medicine, and.,Vera Moulton Wall Center for Pulmonary Vascular Disease, Stanford University School of Medicine, Stanford, California.,VA Palo Alto Health Care System, Palo Alto, California; and
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16
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Chamorro-Herrero I, Zambrano A. Modeling of Respiratory Diseases Evolving with Fibrosis from Organoids Derived from Human Pluripotent Stem Cells. Int J Mol Sci 2023; 24:ijms24054413. [PMID: 36901843 PMCID: PMC10002124 DOI: 10.3390/ijms24054413] [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: 12/15/2022] [Revised: 02/03/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Respiratory disease is one of the leading causes of morbidity and mortality worldwide. There is no cure for most diseases, which are treated symptomatically. Hence, new strategies are required to deepen the understanding of the disease and development of therapeutic strategies. The advent of stem cell and organoid technology has enabled the development of human pluripotent stem cell lines and adequate differentiation protocols for developing both airways and lung organoids in different formats. These novel human-pluripotent-stem-cell-derived organoids have enabled relatively accurate disease modeling. Idiopathic pulmonary fibrosis is a fatal and debilitating disease that exhibits prototypical fibrotic features that may be, to some extent, extrapolated to other conditions. Thus, respiratory diseases such as cystic fibrosis, chronic obstructive pulmonary disease, or the one caused by SARS-CoV-2 may reflect some fibrotic aspects reminiscent of those present in idiopathic pulmonary fibrosis. Modeling of fibrosis of the airways and the lung is a real challenge due to the large number of epithelial cells involved and interaction with other cell types of mesenchymal origin. This review will focus on the status of respiratory disease modeling from human-pluripotent-stem-cell-derived organoids, which are being used to model several representative respiratory diseases, such as idiopathic pulmonary fibrosis, cystic fibrosis, chronic obstructive pulmonary disease, and COVID-19.
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17
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Zhang Y, Wang C, Xia Q, Jiang W, Zhang H, Amiri-Ardekani E, Hua H, Cheng Y. Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis. Front Med (Lausanne) 2023; 10:1001813. [PMID: 36860337 PMCID: PMC9968813 DOI: 10.3389/fmed.2023.1001813] [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: 08/03/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
Objective This study aimed to identify candidate gene biomarkers associated with immune infiltration in idiopathic pulmonary fibrosis (IPF) based on machine learning algorithms. Methods Microarray datasets of IPF were extracted from the Gene Expression Omnibus (GEO) database to screen for differentially expressed genes (DEGs). The DEGs were subjected to enrichment analysis, and two machine learning algorithms were used to identify candidate genes associated with IPF. These genes were verified in a validation cohort from the GEO database. Receiver operating characteristic (ROC) curves were plotted to assess the predictive value of the IPF-associated genes. The cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) algorithm was used to evaluate the proportion of immune cells in IPF and normal tissues. Additionally, the correlation between the expression of IPF-associated genes and the infiltration levels of immune cells was examined. Results A total of 302 upregulated and 192 downregulated genes were identified. Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed that the DEGs were related to the extracellular matrix and immune responses. COL3A1, CDH3, CEBPD, and GPIHBP1 were identified as candidate biomarkers using machine learning algorithms, and their predictive value was verified in a validation cohort. Additionally, ROC analysis revealed that the four genes had high predictive accuracy. The infiltration levels of plasma cells, M0 macrophages and resting dendritic cells were higher and those of resting natural killer (NK) cells, M1 macrophages and eosinophils were lower in the lung tissues of patients with IPF than in those of healthy individuals. The expression of the abovementioned genes was correlated with the infiltration levels of plasma cells, M0 macrophages and eosinophils. Conclusion COL3A1, CDH3, CEBPD, and GPIHBP1 are candidate biomarkers of IPF. Plasma cells, M0 macrophages and eosinophils may be involved in the development of IPF and may serve as immunotherapeutic targets in IPF.
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Affiliation(s)
- Yufeng Zhang
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, China
| | - Cong Wang
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, China
| | - Qingqing Xia
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, China
| | - Weilong Jiang
- Department of Pulmonary and Critical Care Medicine, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, China
| | - Huizhe Zhang
- Department of Respiratory Medicine, Yancheng Hospital of Traditional Chinese Medicine, Yancheng Hospital Affiliated to Nanjing University of Chinese Medicine, Yancheng, Jiangsu, China
| | - Ehsan Amiri-Ardekani
- Department of Phytopharmaceuticals (Traditional Pharmacy), Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran,*Correspondence: Ehsan Amiri-Ardekani,
| | - Haibing Hua
- Department of Gastroenterology, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin Hospital Affiliated to Nanjing University of Chinese Medicine, Jiangyin, Jiangsu, China,Haibing Hua,
| | - Yi Cheng
- Department of Respiratory Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China,Yi Cheng,
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18
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Ding D, Gao R, Xue Q, Luan R, Yang J. Genomic Fingerprint Associated with Familial Idiopathic Pulmonary Fibrosis: A Review. Int J Med Sci 2023; 20:329-345. [PMID: 36860670 PMCID: PMC9969503 DOI: 10.7150/ijms.80358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe interstitial lung disease; although the recent introduction of two anti-fibrosis drugs, pirfenidone and Nidanib, have resulted in a significant reduction in lung function decline, IPF is still not curable. Approximately 2-20% of patients with IPF have a family history of the disease, which is considered the strongest risk factor for idiopathic interstitial pneumonia. However, the genetic predispositions of familial IPF (f-IPF), a particular type of IPF, remain largely unknown. Genetics affect the susceptibility and progression of f-IPF. Genomic markers are increasingly being recognized for their contribution to disease prognosis and drug therapy outcomes. Existing data suggest that genomics may help identify individuals at risk for f-IPF, accurately classify patients, elucidate key pathways involved in disease pathogenesis, and ultimately develop more effective targeted therapies. Since several genetic variants associated with the disease have been found in f-IPF, this review systematically summarizes the latest progress in the gene spectrum of the f-IPF population and the underlying mechanisms of f-IPF. The genetic susceptibility variation related to the disease phenotype is also illustrated. This review aims to improve the understanding of the IPF pathogenesis and facilitate his early detection.
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Affiliation(s)
- Dongyan Ding
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Rong Gao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Qianfei Xue
- Hospital of Jilin University, Changchun, China
| | - Rumei Luan
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Junling Yang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
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Cerro Chiang G, Parimon T. Understanding Interstitial Lung Diseases Associated with Connective Tissue Disease (CTD-ILD): Genetics, Cellular Pathophysiology, and Biologic Drivers. Int J Mol Sci 2023; 24:ijms24032405. [PMID: 36768729 PMCID: PMC9917355 DOI: 10.3390/ijms24032405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/27/2023] Open
Abstract
Connective tissue disease-associated interstitial lung disease (CTD-ILD) is a collection of systemic autoimmune disorders resulting in lung interstitial abnormalities or lung fibrosis. CTD-ILD pathogenesis is not well characterized because of disease heterogeneity and lack of pre-clinical models. Some common risk factors are inter-related with idiopathic pulmonary fibrosis, an extensively studied fibrotic lung disease, which includes genetic abnormalities and environmental risk factors. The primary pathogenic mechanism is that these risk factors promote alveolar type II cell dysfunction triggering many downstream profibrotic pathways, including inflammatory cascades, leading to lung fibroblast proliferation and activation, causing abnormal lung remodeling and repairs that result in interstitial pathology and lung fibrosis. In CTD-ILD, dysregulation of regulator pathways in inflammation is a primary culprit. However, confirmatory studies are required. Understanding these pathogenetic mechanisms is necessary for developing and tailoring more targeted therapy and provides newly discovered disease biomarkers for early diagnosis, clinical monitoring, and disease prognostication. This review highlights the central CTD-ILD pathogenesis and biological drivers that facilitate the discovery of disease biomarkers.
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Affiliation(s)
- Giuliana Cerro Chiang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Correspondence:
| | - Tanyalak Parimon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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20
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Papiris SA, Kannengiesser C, Borie R, Kolilekas L, Kallieri M, Apollonatou V, Ba I, Nathan N, Bush A, Griese M, Dieude P, Crestani B, Manali ED. Genetics in Idiopathic Pulmonary Fibrosis: A Clinical Perspective. Diagnostics (Basel) 2022; 12:2928. [PMID: 36552935 PMCID: PMC9777433 DOI: 10.3390/diagnostics12122928] [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: 10/14/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Unraveling the genetic background in a significant proportion of patients with both sporadic and familial IPF provided new insights into the pathogenic pathways of pulmonary fibrosis. AIM The aim of the present study is to overview the clinical significance of genetics in IPF. PERSPECTIVE It is fascinating to realize the so-far underestimated but dynamically increasing impact that genetics has on aspects related to the pathophysiology, accurate and early diagnosis, and treatment and prevention of this devastating disease. Genetics in IPF have contributed as no other in unchaining the disease from the dogma of a "a sporadic entity of the elderly, limited to the lungs" and allowed all scientists, but mostly clinicians, all over the world to consider its many aspects and "faces" in all age groups, including its co-existence with several extra pulmonary conditions from cutaneous albinism to bone-marrow and liver failure. CONCLUSION By providing additional evidence for unsuspected characteristics such as immunodeficiency, impaired mucus, and surfactant and telomere maintenance that very often co-exist through the interaction of common and rare genetic variants in the same patient, genetics have created a generous and pluralistic yet unifying platform that could lead to the understanding of the injurious and pro-fibrotic effects of many seemingly unrelated extrinsic and intrinsic offending factors. The same platform constantly instructs us about our limitations as well as about the heritability, the knowledge and the wisdom that is still missing.
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Affiliation(s)
- Spyros A. Papiris
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Caroline Kannengiesser
- Département de Génétique, APHP Hôpital Bichat, Université de Paris, 75018 Paris, France
- INSERM UMR 1152, Université de Paris, 75018 Paris, France
| | - Raphael Borie
- Service de Pneumologie A, INSERM UMR_1152, Centre de Référence des Maladies Pulmonaires Rares, FHU APOLLO, APHP Hôpital Bichat, Sorbonne Université, 75018 Paris, France
| | - Lykourgos Kolilekas
- 7th Pulmonary Department, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece
| | - Maria Kallieri
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Vasiliki Apollonatou
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Ibrahima Ba
- Département de Génétique, APHP Hôpital Bichat, Université de Paris, 75018 Paris, France
| | - Nadia Nathan
- Peditric Pulmonology Department and Reference Centre for Rare Lung Diseases RespiRare, INSERM UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Sorbonne University and APHP, 75012 Paris, France
| | - Andrew Bush
- Paediatrics and Paediatric Respirology, Imperial College, Imperial Centre for Paediatrics and Child Health, Royal Brompton Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Matthias Griese
- Department of Pediatric Pneumology, Dr von Hauner Children’s Hospital, Ludwig-Maximilians-University, German Center for Lung Research, 80337 Munich, Germany
| | - Philippe Dieude
- Department of Rheumatology, INSERM U1152, APHP Hôpital Bichat-Claude Bernard, Université de Paris, 75018 Paris, France
| | - Bruno Crestani
- Service de Pneumologie A, INSERM UMR_1152, Centre de Référence des Maladies Pulmonaires Rares, FHU APOLLO, APHP Hôpital Bichat, Sorbonne Université, 75018 Paris, France
| | - Effrosyni D. Manali
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
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21
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Nagel DJ, Rackow AR, Ku WY, Bell TJ, Sime PJ, Kottmann RM. Cell-Type-Specific Effects of the Ovarian Cancer G-Protein Coupled Receptor (OGR1) on Inflammation and Fibrosis; Potential Implications for Idiopathic Pulmonary Fibrosis. Cells 2022; 11:2540. [PMID: 36010617 PMCID: PMC9406836 DOI: 10.3390/cells11162540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a disease characterized by irreversible lung scarring. The pathophysiology is not fully understood, but the working hypothesis postulates that a combination of epithelial injury and myofibroblast differentiation drives progressive pulmonary fibrosis. We previously demonstrated that a reduction in extracellular pH activates latent TGF-β1, and that TGF-β1 then drives its own activation, creating a feed-forward mechanism that propagates myofibroblast differentiation. Given the important roles of extracellular pH in the progression of pulmonary fibrosis, we sought to identify whether pH mediates other cellular phenotypes independent of TGF-β1. Proton-sensing G-protein coupled receptors are activated by acidic environments, but their role in fibrosis has not been studied. Here, we report that the Ovarian Cancer G-Protein Coupled Receptor1 (OGR1 or GPR68) has dual roles in both promoting and mitigating pulmonary fibrosis. We demonstrate that OGR1 protein expression is significantly reduced in lung tissue from patients with IPF and that TGF-β1 decreases OGR1 expression. In fibroblasts, OGR1 inhibits myofibroblast differentiation and does not contribute to inflammation. However, in epithelial cells, OGR1 promotes epithelial to mesenchymal transition (EMT) and inflammation. We then demonstrate that sub-cellular localization and alternative signaling pathways may be responsible for the differential effect of OGR1 in each cell type. Our results suggest that strategies to selectively target OGR1 expression may represent a novel therapeutic strategy for pulmonary fibrosis.
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Affiliation(s)
- David J. Nagel
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ashley R. Rackow
- Laboratory Medicine, Department of Pathology, Division of Clinical Chemistry, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Wei-Yao Ku
- BMW of North America, Woodcliff Lake, NJ 07675, USA
| | - Tyler J. Bell
- Department of Environmental Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Patricia J. Sime
- Department of Medicine, Virginia Commonwealth University Health System, Richmond, VA 23298, USA
| | - Robert Matthew Kottmann
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
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22
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Wang JY, Young LR. Insights into the Pathogenesis of Pulmonary Fibrosis from Genetic Diseases. Am J Respir Cell Mol Biol 2022; 67:20-35. [PMID: 35294321 PMCID: PMC9273221 DOI: 10.1165/rcmb.2021-0557tr] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/16/2022] [Indexed: 11/24/2022] Open
Abstract
Pulmonary fibrosis is a disease process associated with significant morbidity and mortality, with limited therapeutic options owing to an incomplete understanding of the underlying pathophysiology. Mechanisms driving the fibrotic cascade have been elucidated through studies of rare and common variants in surfactant-related and telomere-related genes in familial and sporadic forms of pulmonary fibrosis, as well as in multisystem Mendelian genetic disorders that present with pulmonary fibrosis. In this translational review, we outline insights into the pathophysiology of pulmonary fibrosis derived from genetic forms of the disease, with a focus on model systems, shared cellular and molecular mechanisms, and potential targets for therapy.
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Affiliation(s)
- Joanna Y. Wang
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Lisa R. Young
- Division of Pulmonary, Allergy, and Critical Care, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania; and
- Division of Pulmonary and Sleep Medicine, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
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23
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Abstract
The lungs are continually subjected to noxious and inert substances, are immunologically active, and are in a constant state of damage and repair. This makes the pulmonary system particularly vulnerable to diseases of aging. Aging can be understood as random molecular damage that is unrepaired and accumulates over time, resulting in cellular defects and tissue dysfunction. The breakdown of cellular mechanisms, including stem cell exhaustion, genomic instability, telomere attrition, epigenetic alteration, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, altered intercellular communication, and changes in the extracellular matrix is thought to advance the aging process itself. Chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and cancers illustrate a pathologic breakdown in these mechanisms beyond normal aging. The immune system becomes less effective with advancing age. There is a low-level state of chronic inflammation termed inflammaging which is thought to be driven by immunosenescence, the changes in the innate and adaptive immune systems with advancing age that lead to dysregulation and decreased effectiveness of the immune system. These processes of aging lead to expected changes in the form and function of the respiratory system, most notably a loss of lung elasticity, decrease in respiratory muscle strength, increase in ventilation-perfusion mismatching, and stiffening of the vasculature. The astute clinician is aware of these expected findings and does not often attribute dyspnea to aging alone. Maintaining a low threshold to investigate for comorbid disease and understanding how pulmonary disease presents differently in the elderly than in younger adults can improve clinical outcomes. © 2022 American Physiological Society. Compr Physiol 12:3509-3522, 2022.
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Affiliation(s)
- Julia Budde
- New York City Health and Hospitals/Metropolitan Hospital, New York, New York, USA
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24
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Abbasi A, Chen C, Gandhi CK, Wu R, Pardo A, Selman M, Floros J. Single Nucleotide Polymorphisms (SNP) and SNP-SNP Interactions of the Surfactant Protein Genes Are Associated With Idiopathic Pulmonary Fibrosis in a Mexican Study Group; Comparison With Hypersensitivity Pneumonitis. Front Immunol 2022; 13:842745. [PMID: 35720392 PMCID: PMC9201215 DOI: 10.3389/fimmu.2022.842745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 05/09/2022] [Indexed: 01/12/2023] Open
Abstract
Surfactant proteins (SPs) are important for normal lung function and innate immunity of the lungs and their genes have been identified with significant genetic variability. Changes in quantity or quality of SPs due to genetic mutations or natural genetic variability may alter their functions and contribute to the host susceptibility for particular diseases. Alternatively, SP single nucleotide polymorphisms (SNPs) can serve as markers to identify disease risk or response to therapies, as shown for other genes in a number of other studies. In the current study, we evaluated associations of SFTP SNPs with idiopathic pulmonary fibrosis (IPF) by studying novel computational models where the epistatic effects (dominant, additive, recessive) of SNP-SNP interactions could be evaluated, and then compared the results with a previously published hypersensitivity pneumonitis (HP) study where the same novel models were used. Mexican Hispanic patients (IPF=84 & HP=75) and 194 healthy control individuals were evaluated. The goal was to identify SP SNPs and SNP-SNP interactions that associate with IPF as well as SNPs and interactions that may be unique to each of these interstitial diseases or common between them. We observed: 1) in terms of IPF, i) three single SFTPA1 SNPs to associate with decreased IPF risk, ii) three SFTPA1 haplotypes to associate with increased IPF risk, and iii) a number of three-SNP interactions to associate with IPF susceptibility. 2) Comparison of IPF and HP, i) three SFTPA1 and one SFTPB SNP associated with decreased risk in IPF but increased risk in HP, and one SFTPA1 SNP associated with decreased risk in both IPF and HP, ii) a number of three-SNP interactions with the same or different effect pattern associated with IPF and/or HP susceptibility, iii) one of the three-SNP interactions that involved SNPs of SFTPA1, SFTPA2, and SFTPD, with the same effect pattern, was associated with a disease-specific outcome, a decreased and increased risk in HP and IPF, respectively. This is the first study that compares the SP gene variants in these two phenotypically similar diseases. Our findings indicate that SNPs of all SFTPs may play an important role in the genetic susceptibility to IPF and HP. Importantly, IPF and HP share some SP genetic variants, suggesting common pathophysiological mechanisms and pathways regarding surfactant biogenesis, but also some differences, highlighting the diverse underlying pathogenic mechanisms between an inflammatory-driven fibrosis (HP) and an epithelial-driven fibrosis (IPF). Alternatively, the significant SNPs identified here, along with SNPs of other genes, could serve as markers to distinguish these two devastating diseases.
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Affiliation(s)
- Ata Abbasi
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran.,Department of Pathology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Chixiang Chen
- Department of Public Health Science, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Chintan K Gandhi
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Rongling Wu
- Department of Public Health Science, Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Moises Selman
- Unidad de Investigación, Instituto Nacional de Enfermedades Respiratorias "Ismael Cosio Villegas", Mexico City, Mexico
| | - Joanna Floros
- Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, PA, United States.,Department of Obstetrics & Gynecology, Pennsylvania State University College of Medicine, Hershey, PA, United States
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25
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Consensus Gene Co-Expression Network Analysis Identifies Novel Genes Associated with Severity of Fibrotic Lung Disease. Int J Mol Sci 2022; 23:ijms23105447. [PMID: 35628257 PMCID: PMC9141193 DOI: 10.3390/ijms23105447] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/07/2022] [Accepted: 05/10/2022] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe fibrotic lung disease characterized by irreversible scarring of the lung parenchyma leading to dyspnea, progressive decline in lung function, and respiratory failure. We analyzed lung transcriptomic data from independent IPF cohorts using weighted gene co-expression network analysis (WGCNA) to identify gene modules based on their preservation status in these cohorts. The consensus gene modules were characterized by leveraging existing clinical and molecular data such as lung function, biological processes, pathways, and lung cell types. From a total of 32 consensus gene modules identified, two modules were found to be significantly correlated with the disease, lung function, and preserved in other IPF datasets. The upregulated gene module was enriched for extracellular matrix, collagen metabolic process, and BMP signaling while the downregulated module consisted of genes associated with tube morphogenesis, blood vessel development, and cell migration. Using a combination of connectivity-based and trait-based significance measures, we identified and prioritized 103 "hub" genes (including 25 secretory candidate biomarkers) by their similarity to known IPF genetic markers. Our validation studies demonstrate the dysregulated expression of CRABP2, a retinol-binding protein, in multiple lung cells of IPF, and its correlation with the decline in lung function.
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26
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Evaluation of Proteasome Inhibitors in the Treatment of Idiopathic Pulmonary Fibrosis. Cells 2022; 11:cells11091543. [PMID: 35563849 PMCID: PMC9099509 DOI: 10.3390/cells11091543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/22/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is the most common form of idiopathic interstitial pneumonia, and it has a worse prognosis than non-small cell lung cancer. The pathomechanism of IPF is not fully understood, but it has been suggested that repeated microinjuries of epithelial cells induce a wound healing response, during which fibroblasts differentiate into myofibroblasts. These activated myofibroblasts express α smooth muscle actin and release extracellular matrix to promote matrix deposition and tissue remodeling. Under physiological conditions, the remodeling process stops once wound healing is complete. However, in the lungs of IPF patients, myofibroblasts re-main active and deposit excess extracellular matrix. This leads to the destruction of alveolar tissue, the loss of lung elastic recoil, and a rapid decrease in lung function. Some evidence has indicated that proteasomal inhibition combats fibrosis by inhibiting the expressions of extracellular matrix proteins and metalloproteinases. However, the mechanisms by which proteasome inhibitors may protect against fibrosis are not known. This review summarizes the current research on proteasome inhibitors for pulmonary fibrosis, and provides a reference for whether proteasome inhibitors have the potential to become new drugs for the treatment of pulmonary fibrosis.
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27
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Chakraborty A, Mastalerz M, Ansari M, Schiller HB, Staab-Weijnitz CA. Emerging Roles of Airway Epithelial Cells in Idiopathic Pulmonary Fibrosis. Cells 2022; 11:cells11061050. [PMID: 35326501 PMCID: PMC8947093 DOI: 10.3390/cells11061050] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 12/24/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal disease with incompletely understood aetiology and limited treatment options. Traditionally, IPF was believed to be mainly caused by repetitive injuries to the alveolar epithelium. Several recent lines of evidence, however, suggest that IPF equally involves an aberrant airway epithelial response, which contributes significantly to disease development and progression. In this review, based on recent clinical, high-resolution imaging, genetic, and single-cell RNA sequencing data, we summarize alterations in airway structure, function, and cell type composition in IPF. We furthermore give a comprehensive overview on the genetic and mechanistic evidence pointing towards an essential role of airway epithelial cells in IPF pathogenesis and describe potentially implicated aberrant epithelial signalling pathways and regulation mechanisms in this context. The collected evidence argues for the investigation of possible therapeutic avenues targeting these processes, which thus represent important future directions of research.
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28
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Decato BE, Leeming DJ, Sand JMB, Fischer A, Du S, Palmer SM, Karsdal M, Luo Y, Minnich A. LPA 1 antagonist BMS-986020 changes collagen dynamics and exerts antifibrotic effects in vitro and in patients with idiopathic pulmonary fibrosis. Respir Res 2022; 23:61. [PMID: 35303880 PMCID: PMC8933988 DOI: 10.1186/s12931-022-01980-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a debilitating lung disease with limited treatment options. A phase 2 trial (NCT01766817) showed that twice-daily treatment with BMS-986020, a lysophosphatidic acid receptor 1 (LPA1) antagonist, significantly decreased the slope of forced vital capacity (FVC) decline over 26 weeks compared with placebo in patients with IPF. This analysis aimed to better understand the impact of LPA1 antagonism on extracellular matrix (ECM)-neoepitope biomarkers and lung function through a post hoc analysis of the phase 2 study, along with an in vitro fibrogenesis model. METHODS Serum levels of nine ECM-neoepitope biomarkers were measured in patients with IPF. The association of biomarkers with baseline and change from baseline FVC and quantitative lung fibrosis as measured with high-resolution computed tomography, and differences between treatment arms using linear mixed models, were assessed. The Scar-in-a-Jar in vitro fibrogenesis model was used to further elucidate the antifibrotic mechanism of BMS-986020. RESULTS In 140 patients with IPF, baseline ECM-neoepitope biomarker levels did not predict FVC progression but was significantly correlated with baseline FVC and lung fibrosis measurements. Most serum ECM-neoepitope biomarker levels were significantly reduced following BMS-986020 treatment compared with placebo, and several of the reductions correlated with FVC and/or lung fibrosis improvement. In the Scar-in-a-Jar in vitro model, BMS-986020 potently inhibited LPA1-induced fibrogenesis. CONCLUSIONS BMS-986020 reduced serum ECM-neoepitope biomarkers, which were previously associated with IPF prognosis. In vitro, LPA promoted fibrogenesis, which was LPA1 dependent and inhibited by BMS-986020. Together these data elucidate a novel antifibrotic mechanism of action for pharmacological LPA1 blockade. Trial registration ClinicalTrials.gov identifier: NCT01766817; First posted: January 11, 2013; https://clinicaltrials.gov/ct2/show/NCT01766817 .
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Affiliation(s)
- Benjamin E Decato
- Research & Early Development, Bristol Myers Squibb, 3401 Princeton Pike, Princeton, NJ, 08648, USA
| | | | | | - Aryeh Fischer
- Research & Early Development, Bristol Myers Squibb, 3401 Princeton Pike, Princeton, NJ, 08648, USA
| | - Shuyan Du
- Research & Early Development, Bristol Myers Squibb, 3401 Princeton Pike, Princeton, NJ, 08648, USA
| | - Scott M Palmer
- Duke University Medical Center, 2085 Msrb2 2 Genome Ct., Durham, NC, 27710, USA
| | - Morten Karsdal
- Nordic Bioscience, Herlev Hovedgade 205-207, 2730 Herlev, Denmark
| | - Yi Luo
- Research & Early Development, Bristol Myers Squibb, 3401 Princeton Pike, Princeton, NJ, 08648, USA
| | - Anne Minnich
- Research & Early Development, Bristol Myers Squibb, 3401 Princeton Pike, Princeton, NJ, 08648, USA.
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29
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Michalski JE, Kurche JS, Schwartz DA. From ARDS to pulmonary fibrosis: the next phase of the COVID-19 pandemic? Transl Res 2022; 241:13-24. [PMID: 34547499 PMCID: PMC8452088 DOI: 10.1016/j.trsl.2021.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 01/08/2023]
Abstract
While the coronavirus disease 19 (COVID-19) pandemic has transformed the medical and scientific communites since it was first reported in late 2019, we are only beginning to understand the chronic health burdens associated with this disease. Although COVID-19 is a multi-systemic disease, the lungs are the primary source of infection and injury, resulting in pneumonia and, in severe cases, acute respiratory distress syndrome (ARDS). Given that pulmonary fibrosis is a well-recognized sequela of ARDS, many have questioned whether COVID-19 survivors will face long-term pulmonary consequences. This review is aimed at integrating our understanding of the pathophysiologic mechanisms underlying fibroproliferative ARDS with our current knowledge of the pulmonary consequences of COVID-19 disease.
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Affiliation(s)
- Jacob E Michalski
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado; Medicine Service, Pulmonary Section, Rocky Mountain Regional VA Medical Center, Aurora, Colorado
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado.
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30
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Zheng P, Sun S, Wang J, Cheng ZJ, Lei KC, Xue M, Zhang T, Huang H, Zhang XD, Sun B. Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis. Cell Mol Life Sci 2022; 79:66. [PMID: 35015148 PMCID: PMC11075137 DOI: 10.1007/s00018-021-04094-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 11/30/2021] [Accepted: 12/15/2021] [Indexed: 12/17/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.
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Affiliation(s)
- Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Shixue Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Jingxian Wang
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Province Key Laboratory of Regenerative Medicine, Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guizhou, 550025, China
| | - Zhangkai Jason Cheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Kuan Cheok Lei
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Mingshan Xue
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Teng Zhang
- Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Huimin Huang
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | | | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Centre for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
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Zhang K, Xu L, Cong YS. Telomere Dysfunction in Idiopathic Pulmonary Fibrosis. Front Med (Lausanne) 2021; 8:739810. [PMID: 34859008 PMCID: PMC8631932 DOI: 10.3389/fmed.2021.739810] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis is an age-dependent progressive and fatal lung disease of unknown etiology, which is characterized by the excessive accumulation of extracellular matrix inside the interstitial layer of the lung parenchyma that leads to abnormal scar architecture and compromised lung function capacity. Recent genetic studies have attributed the pathological genes or genetic mutations associated with familial idiopathic pulmonary fibrosis (IPF) and sporadic IPF to telomere-related components, suggesting that telomere dysfunction is an important determinant of this disease. In this study, we summarized recent advances in our understanding of how telomere dysfunction drives IPF genesis. We highlighted the key role of alveolar stem cell dysfunction caused by telomere shortening or telomere uncapping, which bridged the gap between telomere abnormalities and fibrotic lung pathology. We emphasized that senescence-associated secretory phenotypes, innate immune cell infiltration, and/or inflammation downstream of lung stem cell dysfunction influenced the native microenvironment and local cell signals, including increased transforming growth factor-beta (TGF-β) signaling in the lung, to induce pro-fibrotic conditions. In addition, the failed regeneration of new alveoli due to alveolar stem cell dysfunction might expose lung cells to elevated mechanical tension, which could activate the TGF-β signaling loop to promote the fibrotic process, especially in a periphery-to-center pattern as seen in IPF patients. Understanding the telomere-related molecular and pathophysiological mechanisms of IPF would provide new insights into IPF etiology and therapeutic strategies for this fatal disease.
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Affiliation(s)
- Kexiong Zhang
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Lu Xu
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yu-Sheng Cong
- Key Laboratory of Aging and Cancer Biology of Zhejiang Province, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, China
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Kronborg-White S, Madsen LB, Bendstrup E, Poletti V. PD-L1 Expression in Patients with Idiopathic Pulmonary Fibrosis. J Clin Med 2021; 10:jcm10235562. [PMID: 34884264 PMCID: PMC8658518 DOI: 10.3390/jcm10235562] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/05/2021] [Accepted: 11/15/2021] [Indexed: 01/16/2023] Open
Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is the most common and severe form within the group of idiopathic interstitial pneumonias. It is characterized by repetitive alveolar injury in genetically susceptible individuals and abnormal wound healing, leading to dysregulated bronchiolar proliferation and excessive deposition of extracellular matrix, causing complete architectural distortion and fibrosis. Epithelial-to-mesenchymal transition is considered an important pathogenic event, a phenomenon also observed in various malignant neoplasms, in which tumor cells express programmed death-ligand one (PD-L1). The aim of this study was to assess the presence of PD-L1 in patients with IPF and other interstitial lung diseases (ILDs). Method: Patients with a clinically and radiologically suspected idiopathic interstitial pneumonia or other ILDs undergoing transbronchial cryobiopsy to confirm the diagnosis at the Department of Respiratory Diseases and Allergy, Aarhus University Hospital, were included in this prospective observational study. Cellular membrane PD-L1 expression in epithelial cells was determined using the DAKO PD-L1 IHC 22C3 PharmDx Kit. Results: Membrane-bound PD-L1 (mPD-L1) was found in twelve (28%) of the forty-three patients with IPF and in five (9%) of the fifty-five patients with other ILDs (p = 0.015). When adjusting for age, gender and smoking status, the odds ratio of having IPF when expressing mPD-L1 in alveolar and/or bronchiolar epithelial cells was 4.3 (CI: 1.3–14.3). Conclusion: Expression of mPD-L1 in epithelial cells in the lung parenchymal zones was detected in a consistent subgroup of patients with IPF compared to other interstitial pneumonias. Larger studies are needed to explore the role of mPD-L1 in patients with IPF.
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Affiliation(s)
- Sissel Kronborg-White
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, 8200 Aarhus, Denmark; (E.B.); (V.P.)
- Correspondence:
| | - Line Bille Madsen
- Department of Pathology, Aarhus University Hospital, 8200 Aarhus, Denmark;
| | - Elisabeth Bendstrup
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, 8200 Aarhus, Denmark; (E.B.); (V.P.)
| | - Venerino Poletti
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, 8200 Aarhus, Denmark; (E.B.); (V.P.)
- Department of the Diseases of the Thorax, Ospedale Morgagni, University of Bologna, 47121 Forli, Italy
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Fabbrizzi A, Nannini G, Lavorini F, Tomassetti S, Amedei A. Microbiota and IPF: hidden and detected relationships. SARCOIDOSIS VASCULITIS AND DIFFUSE LUNG DISEASES 2021; 38:e2021028. [PMID: 34744424 PMCID: PMC8552575 DOI: 10.36141/svdld.v38i3.11365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022]
Abstract
Lung microbiota (LM) is an interesting new way to consider and redesign pathogenesis and possible therapeutic approach to many lung diseases, such as idiopathic pulmonary fibrosis (IPF), which is an interstitial pneumonia with bad prognosis. Chronic inflammation is the basis but probably not the only cause of lung fibrosis and although the risk factors are not completely clear, endogenous factors (e.g. gastroesophageal reflux) and environmental factors like cigarette smoking, industrial dusts, and precisely microbial agents could contribute to the IPF development. It is well demonstrated that many bacteria can cause epithelial cell injuries in the airways through induction of a host immune response or by activating flogosis mediators following a chronic, low-level antigenic stimulus. This persistent host response could influence fibroblast responsiveness suggesting that LM may play a role in repetitive alveolar injury in IPF. We reviewed literature regarding not only bacteria but also the role of virome and mycobiome in IPF. In fact, some viruses such as hepatitis C virus or certain fungi could be etiological agents or co-factors in the IPF progress. We aim to illustrate how the cross-talk between different local microbiotas throughout specific axis and immune modulation governed by microorganisms could be at the basis of lung dysfunctions and IPF development. Finally, since the future direction of medicine will be personalized, we suggest that the analysis of LM could be a goal to research new therapies also in IPF.
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Affiliation(s)
- Alessio Fabbrizzi
- Department of Respiratory Physiopathology, Palagi Hospital, Florence, Italy
| | - Giulia Nannini
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Federico Lavorini
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy
| | - Amedeo Amedei
- Department of Clinical and Experimental Medicine, University of Florence, Florence, Italy.,SOD of Interdisciplinary Internal Medicine, Azienda Ospedaliera Universitaria Careggi (AOUC), Florence, Italy
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Yoon HY, Moon SJ, Song JW. Lung Tissue Microbiome Is Associated With Clinical Outcomes of Idiopathic Pulmonary Fibrosis. Front Med (Lausanne) 2021; 8:744523. [PMID: 34733866 PMCID: PMC8559550 DOI: 10.3389/fmed.2021.744523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/20/2021] [Indexed: 12/26/2022] Open
Abstract
Background: Several studies using bronchoalveolar lavage fluid (BALF) reported that lung microbial communities were associated with the development and clinical outcome of idiopathic pulmonary fibrosis (IPF). However, the microbial communities in IPF lung tissues are not well known. This study is aimed to investigate bacterial microbial communities in lung tissues and determine their impact on the clinical outcomes of patients with IPF. Methods: Genomic DNA extracted from lung tissues of patients with IPF (n = 20; 10 non-survivors) and age- and sex-matched controls (n = 20) was amplified using fusion primers targeting the V3 and V4 regions of the 16S RNA genes with indexing barcodes. Results: Mean age of IPF subjects was 63.3 yr, and 65% were male. Alpha diversity indices did not significantly differ between IPF patients and controls, or between IPF non-survivors and survivors. The relative abundance of Lactobacillus, Paracoccus, and Akkermansia was increased, whereas that of Caulobacter, Azonexus, and Undibacterium decreased in patients with IPF compared with that in the controls. A decreased relative abundance of Pelomonas (odds ratio [OR], 0.352, p = 0.027) and Azonexus (OR, 0.013, p = 0.046) was associated with a diagnosis of IPF in the multivariable logistic analysis adjusted by age and gender. Multivariable Cox analysis adjusted for age and forced vital capacity (FVC) revealed that higher relative abundance of Streptococcus (hazard ratio [HR], 1.993, p = 0.044), Sphingomonas (HR, 57.590, p = 0.024), and Clostridium (HR, 37.189, p = 0.038) was independently associated with IPF mortality. The relative abundance of Curvibacter (r = 0.590) and Thioprofundum (r = 0.373) was correlated positively, whereas that of Anoxybacillus (r = -0.509) and Enterococcus (r = -0.593) was correlated inversely with FVC. In addition, the relative abundance of the Aquabacterium (r = 0.616) and Peptoniphilus (r = 0.606) genera was positively correlated, whereas that of the Fusobacterium (r = -0.464) and Phycicoccus (r = -0.495) genera was inversely correlated with distance during the 6-min walking test. Conclusions: The composition of the microbiome in lung tissues differed between patients with IPF and controls and was associated with the diagnosis, mortality, and disease severity of IPF.
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Affiliation(s)
- Hee-Young Yoon
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Su-Jin Moon
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Jin Woo Song
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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Sterclova M, Kishore A, Sikorova K, Skibova J, Petrek M, Vasakova M. Effect of genotype on the disease course in idiopathic pulmonary fibrosis despite antifibrotic treatment. Biomed Rep 2021; 15:87. [PMID: 34589215 PMCID: PMC8444193 DOI: 10.3892/br.2021.1463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 07/06/2021] [Indexed: 11/12/2022] Open
Abstract
A genetic predisposition has been identified in 30% of idiopathic pulmonary fibrosis (IPF) cases. Although it is highly probable that the genotype affects the disease susceptibility and course in almost all patients, the specific genotype goes undetected. The aim of the present study was to explore the effects of variants of the genes encoding interleukin-4 (IL-4), mucin 5B (MUC5B), toll interacting protein (TOLLIP), surfactant protein A (SFPTA), transforming growth factor-β (TGF-β) and transporters associated with antigen processing (TAP1 and TAP2) on the course of IPF. A total of 50 patients with IPF were enrolled, and variants of these genes were assessed. Lung function at the time of diagnosis and after 6, 12 and 18 months, and the number of acute exacerbations and deaths in each observation period were measured. ANOVA was used to test the association between gene polymorphisms and the decrease in lung function. There was no significant effect of the gene polymorphisms on the outcomes of patients up to 6 months during the observation period. After 12 months, an effect of an IL-4 single nucleotide polymorphism (SNP) (rs 2070874) on patient outcomes was observed [relative risk (RR) for T allele: 5.6; 95% confidence interval (CI), 0.79-39.0; P=0.053]. The RR of progression in patients with the IL-4 SNP (rs 2243250) and the CT and TT genotypes was 4.3 (95% CI, 1.1-17.5; P=0.046). A total of 18 months after the diagnosis of IPF, an effect of the TOLLIP polymorphism on patient outcome was detected (rs 111521887; risk allele GC; RR: 7.2; 95% CI, 0.97-53.6; P=0.052). Thus, IL-4 and TOLLIP gene polymorphisms may represent disease course-modifying factors, but not drivers of IPF.
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Affiliation(s)
- Martina Sterclova
- Department of Respiratory Medicine, 1st Medical Faculty of Charles University and Thomayer University Hospital, 140 00 Prague, Czech Republic
| | - Amit Kishore
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, 775 15 Olomouc, Czech Republic
| | - Katerina Sikorova
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, 775 15 Olomouc, Czech Republic.,Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 775 15 Olomouc, Czech Republic
| | - Jelena Skibova
- Department of Biostatistics, Institute of Clinical and Experimental Medicine, 140 00 Prague, Czech Republic
| | - Martin Petrek
- Department of Pathological Physiology, Faculty of Medicine and Dentistry, Palacky University, 775 15 Olomouc, Czech Republic
| | - Martina Vasakova
- Department of Respiratory Medicine, 1st Medical Faculty of Charles University and Thomayer University Hospital, 140 00 Prague, Czech Republic
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Doubkova M, Kriegova E, Littnerova S, Schneiderova P, Sterclova M, Bartos V, Plackova M, Zurkova M, Bittenglova R, Lostaková V, Siskova L, Lisa P, Suldova H, Doubek M, Psikalova J, Snizek T, Musilova P, Vasakova M. DSP rs2076295 variants influence nintedanib and pirfenidone outcomes in idiopathic pulmonary fibrosis: a pilot study. Ther Adv Respir Dis 2021; 15:17534666211042529. [PMID: 34515605 DOI: 10.1177/17534666211042529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The antifibrotic drugs nintedanib and pirfenidone are used for the treatment of idiopathic pulmonary fibrosis (IPF). We analysed the association of common profibrotic polymorphisms in MUC5B (mucin 5B, rs35705950) and DSP (desmoplakin, rs2076295) on antifibrotic treatment outcomes in IPF. METHODS MUC5B rs35705950 and DSP rs2076295 were assessed in IPF patients (n = 210, 139 men/71 women) from the Czech EMPIRE registry and age- or sex-matched healthy individuals (n = 205, 125 men/80 women). Genetic data were collated with overall survival (OS), acute exacerbation episodes, worsening lung function and antifibrotic treatment. RESULTS We confirmed overexpression of the MUC5B rs35705950*T allele (55.2% versus 20.9%, p < 0.001) and the DSP rs2076295*G allele (80.4% versus 68.3%, p < 0.001) in IPF compared with controls. On antifibrotic drugs, lower mortability was observed in IPF patients with DSP G* allele (p = 0.016) and MUC5B T* allele (p = 0.079). Carriers of the DSP rs2076295*G allele benefitted from nintedanib treatment compared with TT genotype by a longer OS [hazard ratio (HR) = 7.99; 95% confidence interval (CI) = 1.56-40.90; p = 0.013] and a slower decline in lung function (HR = 8.51; 95% CI = 1.68-43.14; p = 0.010). Patients with a TT genotype (rs2076295) benefitted from treatment with pirfenidone by prolonged OS (p = 0.040; HR = 0.35; 95% CI = 0.13-0.95) compared with nintedanib treatment. Both associations were confirmed by cross-validation analysis. After stratifying by MUC5B rs35705950*T allele carriage, no difference in treatment outcome was observed for nintedanib or pirfenidone (p = 0.784). In the multivariate model, smoking, age, forced vital capacity (FVC) and DLCO (diffuse lung capacity) at the IPF diagnosis were associated with survival. CONCLUSION Our real-world study showed that IPF patients with MUC5B T* allele or DSP G* allele profit from antifibrotic treatment by lower mortability. Moreover, carriers of the DSP rs2076295*G allele benefit from treatment with nintedanib, and TT genotype from treatment with pirfenidone. MUC5B rs35705950 did not impact the outcome of treatment with either nintedanib or pirfenidone. Our single-registry pilot study should be confirmed with an independent patient cohort.
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Affiliation(s)
- Martina Doubkova
- Department of Pulmonology and Physiology, Faculty of Medicine, Masaryk University and University Hospital Brno, Jihlavská 20, 625 00 Brno, Czech Republic
| | - Eva Kriegova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University in Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Simona Littnerova
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Petra Schneiderova
- Department of Immunology, Faculty of Medicine and Dentistry, Palacky University in Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Martina Sterclova
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Vladimir Bartos
- Department of Pneumology, Faculty of Medicine in Hradec Králové, Charles University, Prague, Czech Republic
| | - Martina Plackova
- Department of Pneumology, Faculty of Medicine, University Hospital in Ostrava, Ostrava, Czech Republic
| | - Monika Zurkova
- Department of Respiratory Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Radka Bittenglova
- Department of Respiratory Diseases, Faculty of Medicine in Pilsen, Charles University and University Hospital Pilsen, Pilsen, Czech Republic
| | - Vladimira Lostaková
- Department of Respiratory Medicine, Faculty of Medicine and Dentistry, Palacky University in Olomouc and University Hospital Olomouc, Olomouc, Czech Republic
| | - Lenka Siskova
- Department of Respiratory Diseases, Tomáš Baťa Regional Hospital, Zlín, Czech Republic
| | - Pavlina Lisa
- Department of Pneumology, Second Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Hana Suldova
- Pulmonary Department, České Budějovice Hospital, Ceske Budejovice, Czech Republic
| | - Michael Doubek
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Jana Psikalova
- PneumoAllergology Department, Kroměříž Hospital, Kromeriz, Czech Republic
| | - Tomas Snizek
- Department of Respiratory Diseases, Jihlava Hospital, Jihlava, Czech Republic
| | - Pavlina Musilova
- Department of Respiratory Diseases, Jihlava Hospital, Jihlava, Czech Republic
| | - Martina Vasakova
- Department of Respiratory Medicine, First Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
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Liu C, He Y. [Research Progress in the Pathogenesis of Idiopathic Pulmonary Fibrosis with Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2021; 23:695-700. [PMID: 32838491 PMCID: PMC7467990 DOI: 10.3779/j.issn.1009-3419.2020.102.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
特发性肺纤维化(idiopathic pulmonary fibrosis, IPF)是一种原因不明,以弥漫性肺泡炎和肺泡结构紊乱最终导致肺间质纤维化为特征的疾病。针对IPF尚无有效的治疗手段,主要以延缓疾病进展、改善患者生活质量为主。而目前IPF合并肺癌(IPF with lung cancer, IPF-LC)的发病率越来越高,致使患者死亡率明显增加、生活质量显著下降。IPF-LC多见于男性、高龄和吸烟者,是一种临床表现缺乏特异性、无明确治疗方案、中位生存期短、预后较差的致死性疾病。目前IPF-LC发病机制及治疗方案尚不明确。本文就目前IPF-LC的危险因素、发病机制、临床特征和治疗的相关研究进展作简要综述。
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Affiliation(s)
- Chunhui Liu
- The First Affiliated Hospital of Xinjiang Medical University, Urumuqi 830000, China
| | - Yuanbing He
- The First Affiliated Hospital of Xinjiang Medical University, Urumuqi 830000, China
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Idiopathic pulmonary fibrosis and systemic sclerosis: pathogenic mechanisms and therapeutic interventions. Cell Mol Life Sci 2021; 78:5527-5542. [PMID: 34145462 PMCID: PMC8212897 DOI: 10.1007/s00018-021-03874-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 05/07/2021] [Accepted: 06/05/2021] [Indexed: 12/19/2022]
Abstract
Fibrotic diseases take a very heavy toll in terms of morbidity and mortality equal to or even greater than that caused by metastatic cancer. In this review, we examine the pathogenesis of fibrotic diseases, mainly addressing triggers for induction, processes that lead to progression, therapies and therapeutic trials. For the most part, we have focused on two fibrotic diseases with lung involvement, idiopathic pulmonary fibrosis, in which the contribution of inflammatory mechanisms may be secondary to non-immune triggers, and systemic sclerosis in which the contribution of adaptive immunity may be predominant.
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Rostami MR, Bradic M. The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis. Mob DNA 2021; 12:14. [PMID: 34108012 PMCID: PMC8191028 DOI: 10.1186/s13100-021-00241-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/26/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are repetitive sequences of viral origin that compose almost half of the human genome. These elements are tightly controlled within cells, and if activated, they can cause changes in both gene regulation and immune viral responses that have been associated with several chronic inflammatory diseases in humans. As oxidants are potent activators of TEs, and because oxidative injury is a major risk factor in relation to idiopathic pulmonary fibrosis (IPF), we hypothesized that TEs might be involved in the regulation of gene expression and so contribute to inflammation in cases of IPF. IPF is a fatal lung disease that involves the gradual replacement of the alveolar tissue with fibrotic scars as well as the accumulation of inflammatory cells in the lower respiratory tract. Although IPF is known to occur as a result of the complex interaction between age, environmental risk factors (i.e., oxidative stress) and genetics, the relative contributions of these factors to the disease remain unclear. To determine whether TEs are associated with IPF, we compared the transcriptional profiles of the genes and TEs of lung cells obtained from both healthy donors and IPF patients. RESULTS We quantified TE and gene expression levels using a published bulk RNA-seq dataset containing 24 subjects (16 donors and eight IPF patients), including three lung-cell types per subject, as well as an scRNA-seq dataset concerning 16 subjects (eight donors and eight IPF patients). We found evidence of TE dysregulation in the alveolar type II lung cells and alveolar macrophages of the IPF patients. In addition, the activation of the LINE1 family of elements in IPF is associated with the increased expression of TE cellular regulators (MOV10, IFI16, SAMHD1, and APOBECG3), interferon-stimulating genes (ISG15, IFI6, IFI27, IFI44, and OAS1), chemokines (CX3CL1 and CXCL9), and interleukins (IL15RA). We also propose that TE derepression might be involved in the regulation of previously reported IPF candidate genes (MUC5B, CHL1, SPP1, and MMP7). CONCLUSION Based on our findings, we propose that TE derepression plays an important role in the regulation of gene expression and can also prompt both the recruitment of inflammatory processes and the disruption of the immunological balance, which can lead to chronic inflammation in IPF.
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Affiliation(s)
- Mahboubeh R Rostami
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Martina Bradic
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Sun S, Huang C, Leng D, Chen C, Zhang T, Lei KC, Zhang XD. Gene fusion of IL7 involved in the regulation of idiopathic pulmonary fibrosis. Ther Adv Respir Dis 2021; 15:1753466621995045. [PMID: 33878985 PMCID: PMC8064517 DOI: 10.1177/1753466621995045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background: Idiopathic pulmonary fibrosis (IPF) is a rare form of immune-mediated interstitial lung disease characterized by progressive pulmonary fibrosis and scarring. The pathogenesis of IPF is still unclear. Gene fusion events exist universally during transcription and show alternated patterns in a variety of lung diseases. Therefore, the comprehension of the function of gene fusion in IPF might shed light on IPF pathogenesis research and facilitate treatment development. Methods: In this study, we included 91 transcriptome datasets from the National Center for Biotechnology Information (NCBI), including 52 IPF patients and 39 healthy controls. We detected fusion events in these datasets and probed gene fusion-associated differential gene expression and functional pathways. To obtain robust results, we corrected the batch bias across different projects. Results: We identified 1550 gene fusion events in all transcriptomes and studied the possible impacts of IL7 = AC083837.1 gene fusion. The two genes locate adjacently in chromosome 8 and share the same promoters. Their fusion is associated with differential expression of 282 genes enriched in six Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 35 functional gene sets. Gene ontology (GO) enrichment analysis shows that IL7 = AC083837.1 gene fusion is associated with the enrichment of 187 gene sets. The co-expression network of interleukin-7 (IL7) indicates that decreased IL7 expression is associated with many pathways that regulate IPF progress. Conclusion: Based on the results, we conclude that IL7 = AC083837.1 gene fusion might exacerbate fibrosis in IPF via enhancing activities of natural killer cell-mediated cytotoxicity, skin cell apoptosis, and vessel angiogenesis, the interaction of which contributes to the development of fibrosis and the deterioration of respiratory function of IPF patients. Our work unveils the possible roles of gene fusion in regulating IPF and demonstrates that gene fusion investigation is a valid approach in probing immunologic mechanisms and searching potential therapeutic targets for treating IPF. The reviews of this paper are available via the supplemental material section.
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Affiliation(s)
- Shixue Sun
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Chen Huang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Dongliang Leng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Chang Chen
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Teng Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Kuan Cheok Lei
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR, China
| | - Xiaohua Douglas Zhang
- CRDA, Faculty of Health Sciences, University of Macau, Avenida de Universidade, Taipa, Macau SAR, China
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41
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de Carvalho ALRT, Liu HY, Chen YW, Porotto M, Moscona A, Snoeck HW. The in vitro multilineage differentiation and maturation of lung and airway cells from human pluripotent stem cell-derived lung progenitors in 3D. Nat Protoc 2021; 16:1802-1829. [PMID: 33649566 PMCID: PMC9460941 DOI: 10.1038/s41596-020-00476-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
Lung and airway epithelial cells generated in vitro from human pluripotent stem cells (hPSCs) have applications in regenerative medicine, modeling of lung disease, drug screening and studies of human lung development. Here, we describe a strategy for directed differentiation of hPSCs into mature lung and airway epithelial cells obtained through maturation of NKX2.1+ hPSC-derived lung progenitors in a 3D matrix of collagen I in the absence of glycogen synthase kinase 3 inhibition. This protocol is an extension of our previously published protocol on the directed differentiation of lung and airway epithelium from hPSCs that modifies the technique and offers additional applications. This protocol is conducted in defined media conditions, has a duration of 50-80 d, does not require reporter lines and results in cultures containing mature alveolar type II and I cells as well as airway basal, ciliated, club and neuroendocrine cells. We also present a flow cytometry strategy to assess maturation in the cultures. Several of these populations, including mature NGFR+ basal cells, can be prospectively isolated by cell sorting and expanded for further investigation.
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Affiliation(s)
- Ana Luisa Rodrigues Toste de Carvalho
- Columbia Center for Human Development, Columbia University
Medical Center, New York, NY 10032, USA,Department of Medicine, Columbia University Medical Center,
New York, NY 10032, USA,Life and Health Sciences Research Institute (ICVS), School
of Medicine, University of Minho, 4710-057 Braga, Portugal,ICVS/3B’s, PT Government Associate Laboratory,
4710-057 Braga/Guimarães, Portugal
| | - Hsiao-Yun Liu
- Columbia Center for Human Development, Columbia University
Medical Center, New York, NY 10032, USA,Department of Medicine, Columbia University Medical Center,
New York, NY 10032, USA
| | - Ya-Wen Chen
- Columbia Center for Human Development, Columbia University
Medical Center, New York, NY 10032, USA,Department of Medicine, Columbia University Medical Center,
New York, NY 10032, USA
| | - Matteo Porotto
- Department of Pediatrics, Columbia University Medical
Center, New York, New York, 10032, United States,Center for Host–Pathogen Interaction, Columbia
University Medical Center, New York, New York, 10032, United States,Department of Experimental Medicine, University of Campania
‘Luigi Vanvitelli’, Italy
| | - Anne Moscona
- Department of Pediatrics, Columbia University Medical
Center, New York, New York, 10032, United States,Center for Host–Pathogen Interaction, Columbia
University Medical Center, New York, New York, 10032, United States,Department of Microbiology & Immunology, Columbia
University Medical Center, New York, New York, 10032, United States,Department of Physiology & Cellular Biophysics,
Columbia University Medical Center, New York, New York, 10032, United States
| | - Hans-Willem Snoeck
- Columbia Center for Human Development, Columbia University
Medical Center, New York, NY 10032, USA,Department of Medicine, Columbia University Medical Center,
New York, NY 10032, USA,Columbia Center for Translational Immunology, Columbia
University Medical Center, New York, NY 10032, USA,Department of Microbiology and Immunology, Columbia
University Medical Center, New York, NY 10032, USA, Correspondence should be addressed to H.W.S
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Liu G, Philp AM, Corte T, Travis MA, Schilter H, Hansbro NG, Burns CJ, Eapen MS, Sohal SS, Burgess JK, Hansbro PM. Therapeutic targets in lung tissue remodelling and fibrosis. Pharmacol Ther 2021; 225:107839. [PMID: 33774068 DOI: 10.1016/j.pharmthera.2021.107839] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/03/2021] [Indexed: 02/07/2023]
Abstract
Structural changes involving tissue remodelling and fibrosis are major features of many pulmonary diseases, including asthma, chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Abnormal deposition of extracellular matrix (ECM) proteins is a key factor in the development of tissue remodelling that results in symptoms and impaired lung function in these diseases. Tissue remodelling in the lungs is complex and differs between compartments. Some pathways are common but tissue remodelling around the airways and in the parenchyma have different morphologies. Hence it is critical to evaluate both common fibrotic pathways and those that are specific to different compartments; thereby expanding the understanding of the pathogenesis of fibrosis and remodelling in the airways and parenchyma in asthma, COPD and IPF with a view to developing therapeutic strategies for each. Here we review the current understanding of remodelling features and underlying mechanisms in these major respiratory diseases. The differences and similarities of remodelling are used to highlight potential common therapeutic targets and strategies. One central pathway in remodelling processes involves transforming growth factor (TGF)-β induced fibroblast activation and myofibroblast differentiation that increases ECM production. The current treatments and clinical trials targeting remodelling are described, as well as potential future directions. These endeavours are indicative of the renewed effort and optimism for drug discovery targeting tissue remodelling and fibrosis.
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Affiliation(s)
- Gang Liu
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Ashleigh M Philp
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia; St Vincent's Medical School, UNSW Medicine, UNSW, Sydney, NSW, Australia
| | - Tamera Corte
- Royal Prince Alfred Hospital, Camperdown, NSW, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mark A Travis
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, Manchester Academic Health Sciences Centre and Wellcome Trust Centre for Cell-Matrix Research, University of Manchester, Manchester, United Kingdom
| | - Heidi Schilter
- Pharmaxis Ltd, 20 Rodborough Road, Frenchs Forest, Sydney, NSW, Australia
| | - Nicole G Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia
| | - Chris J Burns
- Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mathew S Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Sukhwinder S Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS, Australia
| | - Janette K Burgess
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Department of Pathology and Medical Biology, Groningen, The Netherlands; Woolcock Institute of Medical Research, Discipline of Pharmacology, The University of Sydney, Sydney, NSW, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, NSW, Australia.
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Pardo A, Selman M. The Interplay of the Genetic Architecture, Aging, and Environmental Factors in the Pathogenesis of Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 64:163-172. [PMID: 32946290 DOI: 10.1165/rcmb.2020-0373ps] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic fibrosing lung disease of indeterminate etiology and limited therapeutic options. The initiation, development, and progression of IPF are influenced by genetic predisposition, aging, and host and environmental factors, but the magnitude of the contribution of each of them and the sequence of the pathogenic events are uncertain. Current evidence indicates that accumulated environmental exposures in a genetically predisposed individual, usually over 60 years of age, leads to phenotypic and functional alterations of the lung epithelium. Aberrant activation of epithelial cells results, through a complex release of numerous mediators, in the local expansion of peculiar subsets of aggressive fibroblasts and myofibroblasts, which are crucial effector cells of fibrotic remodeling and loss of the normal lung architecture and function. Progressive increase of the mechanical stiffness activates cell-autonomous and matrix-dependent processes contributing to the perpetuation of the fibrotic response. This Perspective provides an integral overview of the major risk factors underpinning the pathogenesis of IPF, including gene variants, aging alterations, environmental factors, host risk factors, and epigenetic reprogramming.
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Affiliation(s)
- Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, México City, Mexico; and
| | - Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias "Ismael Cosío Villegas," México City, Mexico
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44
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Role of various imbalances centered on alveolar epithelial cell/fibroblast apoptosis imbalance in the pathogenesis of idiopathic pulmonary fibrosis. Chin Med J (Engl) 2021; 134:261-274. [PMID: 33522725 PMCID: PMC7846426 DOI: 10.1097/cm9.0000000000001288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
There have been recent extensive studies and rapid advancement on the pathogenesis underlying idiopathic pulmonary fibrosis (IPF), and intricate pathogenesis of IPF has been suggested. The purpose of this study was to clarify the logical relationship between these mechanisms. An extensive search was undertaken of the PubMed using the following keywords: “etiology,” “pathogenesis,” “alveolar epithelial cell (AEC),” “fibroblast,” “lymphocyte,” “macrophage,” “epigenomics,” “histone,” acetylation,” “methylation,” “endoplasmic reticulum stress,” “mitochondrial dysfunction,” “telomerase,” “proteases,” “plasminogen,” “epithelial-mesenchymal transition,” “oxidative stress,” “inflammation,” “apoptosis,” and “idiopathic pulmonary fibrosis.” This search covered relevant research articles published up to April 30, 2020. Original articles, reviews, and other articles were searched and reviewed for content; 240 highly relevant studies were obtained after screening. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors: environmental exposures affect epigenetic marks; epigenetic processes translate environmental exposures into the regulation of chromatin; epigenetic processes shape gene expression profiles; in turn, an individual's genetic background determines epigenetic marks; finally, these genetic and epigenetic factors act in concert to dysregulate gene expression in IPF lung tissue. The pathogenesis of IPF involves various imbalances including endoplasmic reticulum, telomere length homeostasis, mitochondrial dysfunction, oxidant/antioxidant imbalance, Th1/Th2 imbalance, M1–M2 polarization of macrophages, protease/antiprotease imbalance, and plasminogen activation/inhibition imbalance. These affect each other, promote each other, and ultimately promote AEC/fibroblast apoptosis imbalance directly or indirectly. Excessive AEC apoptosis and impaired apoptosis of fibroblasts contribute to fibrosis. IPF is likely the result of complex interactions between environmental, genetic, and epigenetic factors. The pathogenesis of IPF involves various imbalances centered on AEC/fibroblast apoptosis imbalance.
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Nemoto M, Zaizen Y, Kataoka K, Kuroda K, Tabata K, Bychkov A, Sumikawa H, Johkoh T, Aoshima M, Kondoh Y, Fukuoka J. Histologic factors associated with nintedanib efficacy in patients with idiopathic pulmonary fibrosis. PLoS One 2021; 16:e0245147. [PMID: 33411718 PMCID: PMC7790243 DOI: 10.1371/journal.pone.0245147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/22/2020] [Indexed: 12/25/2022] Open
Abstract
Background Histopathologic factors predictive of nintedanib efficacy in idiopathic pulmonary fibrosis have not been studied. We aimed to describe the characteristics, focusing on histopathology, of idiopathic pulmonary fibrosis patients who did and did not respond to nintedanib. Methods This study retrospectively examined the clinicoradiopathologic features of 40 consecutive patients with surgical lung biopsy-confirmed idiopathic pulmonary fibrosis treated with nintedanib. Additionally, we compared the histopathologic scoring of 21 microscopic features between patients with functional or radiological progression and those with non-progression during 12 months of treatment. Results The histopathologic evaluation showed edematous changes in the interlobular septum as the only histologic finding observed more frequently in patients with both functional and radiological progression than in those without (58% vs. 14%, P = 0.007 and 50% vs. 0%, P = 0.003, respectively). Regarding per-year change, patients with edematous changes in the interlobular septum showed greater progression in median changes in spared area (-12%, interquartile range: [-25%–-5%], vs. -3% [-7%–0%], P = 0.004) and reticular shadow (7% [3%–13%], vs. 0% [0%–5%], P = 0.041) on computed tomography. Functional and radiological progression-free survival were shorter in patients with edematous changes in the interlobular septum than in those without (6.6 months, 95% confidence interval: [5.9–25.3], vs. event <50%, [12.1–Not available], P = 0.0009, and 6.1 months, [5.2–6.6] vs. 14.5 months [7.8–not available], P<0.0001). Conclusions Edematous changes in the interlobular septum may indicate poor nintedanib efficacy in idiopathic pulmonary fibrosis. Further studies are needed to validate these findings and address the mechanism behind ECIS.
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Affiliation(s)
- Masahiro Nemoto
- Department of Pulmonary Medicine, Kameda Medical Center, Kamogawa, Japan
- Department of Immunology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yoshiaki Zaizen
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kensuke Kataoka
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Japan
| | - Kishio Kuroda
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Kazuhiro Tabata
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Andrey Bychkov
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Pathology, Kameda Medical Center, Kamogawa, Japan
| | - Hiromitsu Sumikawa
- Department of Diagnostic Radiology, Sakai City Medical Center, Sakai, Japan
| | - Takeshi Johkoh
- Department of Radiology, Kinki Central Hospital of Mutual Aid Association of Public School Teachers, Itami, Japan
| | - Masahiro Aoshima
- Department of Pulmonary Medicine, Kameda Medical Center, Kamogawa, Japan
| | - Yasuhiro Kondoh
- Department of Respiratory Medicine and Allergy, Tosei General Hospital, Seto, Japan
| | - Junya Fukuoka
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Pathology, Kameda Medical Center, Kamogawa, Japan
- * E-mail:
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Michalski JE, Schwartz DA. Genetic Risk Factors for Idiopathic Pulmonary Fibrosis: Insights into Immunopathogenesis. J Inflamm Res 2021; 13:1305-1318. [PMID: 33447070 PMCID: PMC7801923 DOI: 10.2147/jir.s280958] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis is an etiologically complex interstitial lung disease characterized by progressive scarring of the lungs with a subsequent decline in lung function. While much of the pathogenesis of IPF still remains unclear, it is now understood that genetic variation accounts for at least one-third of the risk of developing the disease. The single-most validated and most significant risk factor, genetic or otherwise, is a gain-of-function promoter variant in the MUC5B gene. While the functional impact of these IPF risk variants at the cellular and tissue levels are areas of active investigation, there is a growing body of evidence that these genetic variants may influence disease pathogenesis through modulation of innate immune processes.
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Affiliation(s)
- Jacob E Michalski
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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Aghaei M, Dastghaib S, Aftabi S, Aghanoori MR, Alizadeh J, Mokarram P, Mehrbod P, Ashrafizadeh M, Zarrabi A, McAlinden KD, Eapen MS, Sohal SS, Sharma P, Zeki AA, Ghavami S. The ER Stress/UPR Axis in Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Life (Basel) 2020; 11:1. [PMID: 33374938 PMCID: PMC7821926 DOI: 10.3390/life11010001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
Cellular protein homeostasis in the lungs is constantly disrupted by recurrent exposure to various external and internal stressors, which may cause considerable protein secretion pressure on the endoplasmic reticulum (ER), resulting in the survival and differentiation of these cell types to meet the increased functional demands. Cells are able to induce a highly conserved adaptive mechanism, known as the unfolded protein response (UPR), to manage such stresses. UPR dysregulation and ER stress are involved in numerous human illnesses, such as metabolic syndrome, fibrotic diseases, and neurodegeneration, and cancer. Therefore, effective and specific compounds targeting the UPR pathway are being considered as potential therapies. This review focuses on the impact of both external and internal stressors on the ER in idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) and discusses the role of the UPR signaling pathway activation in the control of cellular damage and specifically highlights the potential involvement of non-coding RNAs in COPD. Summaries of pathogenic mechanisms associated with the ER stress/UPR axis contributing to IPF and COPD, and promising pharmacological intervention strategies, are also presented.
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Affiliation(s)
- Mahmoud Aghaei
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 8174673461, Iran
| | - Sanaz Dastghaib
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran; (S.D.); (P.M.)
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
| | - Sajjad Aftabi
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Medical Physics Department, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Mohamad-Reza Aghanoori
- Division of Neurodegenerative Disorders, St Boniface Hospital Albrechtsen Research Centre, University of Manitoba, Winnipeg, MB R2H 2A6, Canada;
- Department of Internal Medicine, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Javad Alizadeh
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Pooneh Mokarram
- Department of Clinical Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran; (S.D.); (P.M.)
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
| | - Parvaneh Mehrbod
- Influenza and Respiratory Viruses Department, Pasteur Institute of Iran, Tehran 1316943551, Iran;
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, 34956 Istanbul, Turkey;
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey;
| | - Ali Zarrabi
- Sabanci University Nanotechnology Research and Application Center (SUNUM), Tuzla, 34956 Istanbul, Turkey;
| | - Kielan Darcy McAlinden
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston 7250, Tasmania, Australia; (K.D.M.); (M.S.E.); (S.S.S.)
| | - Mathew Suji Eapen
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston 7250, Tasmania, Australia; (K.D.M.); (M.S.E.); (S.S.S.)
| | - Sukhwinder Singh Sohal
- Respiratory Translational Research Group, Department of Laboratory Medicine, School of Health Sciences, University of Tasmania, Launceston 7250, Tasmania, Australia; (K.D.M.); (M.S.E.); (S.S.S.)
| | - Pawan Sharma
- Center for Translational Medicine, Jane & Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA 19107, USA;
| | - Amir A. Zeki
- Davis School of Medicine, Department of Internal Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, UC Davis Lung Center, University of California, Davis, CA 95616, USA;
- Veterans Affairs Medical Center, Mather, CA 95655, USA
| | - Saeid Ghavami
- Department of Human Anatomy and Cell Science, Rady Faculty of Health Sciences, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (M.A.); (S.A.); (J.A.)
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz 7134845794, Iran
- Research Institute of Oncology and Hematology, Cancer Care Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Biology of Breathing Theme, Children Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
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Skibba M, Drelich A, Poellmann M, Hong S, Brasier AR. Nanoapproaches to Modifying Epigenetics of Epithelial Mesenchymal Transition for Treatment of Pulmonary Fibrosis. Front Pharmacol 2020; 11:607689. [PMID: 33384604 PMCID: PMC7770469 DOI: 10.3389/fphar.2020.607689] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/09/2020] [Indexed: 12/11/2022] Open
Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a chronically progressive interstitial lung that affects over 3 M people worldwide and rising in incidence. With a median survival of 2-3 years, IPF is consequently associated with high morbidity, mortality, and healthcare burden. Although two antifibrotic therapies, pirfenidone and nintedanib, are approved for human use, these agents reduce the rate of decline of pulmonary function but are not curative and do not reverse established fibrosis. In this review, we discuss the prevailing epithelial injury hypothesis, wherein pathogenic airway epithelial cell-state changes known as Epithelial Mesenchymal Transition (EMT) promotes the expansion of myofibroblast populations. Myofibroblasts are principal components of extracellular matrix production that result in airspace loss and mortality. We review the epigenetic transition driving EMT, a process produced by changes in histone acetylation regulating mesenchymal gene expression programs. This mechanistic work has focused on the central role of bromodomain-containing protein 4 in mediating EMT and myofibroblast transition and initial preclinical work has provided evidence of efficacy. As nanomedicine presents a promising approach to enhancing the efficacy of such anti-IPF agents, we then focus on the state of nanomedicine formulations for inhalable delivery in the treatment of pulmonary diseases, including liposomes, polymeric nanoparticles (NPs), inorganic NPs, and exosomes. These nanoscale agents potentially provide unique properties to existing pulmonary therapeutics, including controlled release, reduced systemic toxicity, and combination delivery. NP-based approaches for pulmonary delivery thus offer substantial promise to modify epigenetic regulators of EMT and advance treatments for IPF.
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Affiliation(s)
- Melissa Skibba
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
| | - Adam Drelich
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States
| | - Michael Poellmann
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States
| | - Seungpyo Hong
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, United States
- Carbone Cancer Center, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
- Yonsei Frontier Lab, Department of Pharmacy, Yonsei University, Seoul, South Korea
| | - Allan R. Brasier
- Department of Medicine, University of Wisconsin-Madison School of Medicine and Public Health (SMPH), Madison, WI, United States
- Institute for Clinical and Translational Research (ICTR), University of Wisconsin-Madison, Madison, WI, United States
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Mishra S, Shah MI, Udhaya Kumar S, Thirumal Kumar D, Gopalakrishnan C, Al-Subaie AM, Magesh R, George Priya Doss C, Kamaraj B. Network analysis of transcriptomics data for the prediction and prioritization of membrane-associated biomarkers for idiopathic pulmonary fibrosis (IPF) by bioinformatics approach. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 123:241-273. [PMID: 33485486 DOI: 10.1016/bs.apcsb.2020.10.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a rare yet crucial persistent lung disorder that actuates scarring of lung tissues, which makes breathing difficult. Smoking, environmental pollution, and certain viral infections could initiate lung scarring. However, the molecular mechanism involved in IPF remains elusive. To develop an efficient therapeutic arsenal against IPF, it is vital to understand the pathology and deviations in biochemical pathways that lead to disorder. In this study, we availed network analysis and other computational pipelines to delineate the prominent membrane proteins as diagnostic biomarkers and therapeutic targets for IPF. This study yielded a significant role of glycosaminoglycan binding, endothelin, and GABA-B receptor signaling pathway in IPF pathogenesis. Furthermore, ADCY8, CRH, FGB, GPR17, MCHR1, NMUR1, and SAA1 genes were found to be immensely involved with IPF, and the enrichment pathway analysis suggests that most of the pathways were corresponding to membrane transport and signal transduction functionalities. This analysis could help in better understanding the molecular mechanism behind IPF to develop an efficient therapeutic target or biomarkers for IPF.
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Affiliation(s)
- Smriti Mishra
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India; Navipoint Health India Pvt Ltd, Moula-Ali, Hyderabad, Telangana, India
| | - Mohammad Imran Shah
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh, India; Navipoint Health India Pvt Ltd, Moula-Ali, Hyderabad, Telangana, India
| | - S Udhaya Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - D Thirumal Kumar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | | | - Abeer Mohammed Al-Subaie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - R Magesh
- Faculty of Biomedical Sciences, Technology & Research, Department of Biotechnology, Sri Ramachandra University, Chennai, Tamil Nadu, India
| | - C George Priya Doss
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Balu Kamaraj
- Department of Neuroscience Technology, College of Applied Medical Sciences in Jubail, Imam Abdulrahman Bin Faisal University, Jubail, Saudi Arabia
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Rackow AR, Nagel DJ, McCarthy C, Judge J, Lacy S, Freeberg MAT, Thatcher TH, Kottmann RM, Sime PJ. The self-fulfilling prophecy of pulmonary fibrosis: a selective inspection of pathological signalling loops. Eur Respir J 2020; 56:13993003.00075-2020. [PMID: 32943406 PMCID: PMC7931159 DOI: 10.1183/13993003.00075-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/01/2020] [Indexed: 12/28/2022]
Abstract
Pulmonary fibrosis is a devastating, progressive disease and carries a prognosis worse than most cancers. Despite ongoing research, the mechanisms that underlie disease pathogenesis remain only partially understood. However, the self-perpetuating nature of pulmonary fibrosis has led several researchers to propose the existence of pathological signalling loops. According to this hypothesis, the normal wound-healing process becomes corrupted and results in the progressive accumulation of scar tissue in the lung. In addition, several negative regulators of pulmonary fibrosis are downregulated and, therefore, are no longer capable of inhibiting these feed-forward loops. The combination of pathological signalling loops and loss of a checks and balances system ultimately culminates in a process of unregulated scar formation. This review details specific signalling pathways demonstrated to play a role in the pathogenesis of pulmonary fibrosis. The evidence of detrimental signalling loops is elucidated with regard to epithelial cell injury, cellular senescence and the activation of developmental and ageing pathways. We demonstrate where these loops intersect each other, as well as common mediators that may drive these responses and how the loss of pro-resolving mediators may contribute to the propagation of disease. By focusing on the overlapping signalling mediators among the many pro-fibrotic pathways, it is our hope that the pulmonary fibrosis community will be better equipped to design future trials that incorporate the redundant nature of these pathways as we move towards finding a cure for this unrelenting disease.
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Affiliation(s)
- Ashley R Rackow
- Dept of Environmental Medicine, University of Rochester Medical Center, Rochester, NY, USA.,Authors contributed equally to this work
| | - David J Nagel
- Division of Pulmonary Diseases and Critical Care, University of Rochester Medical Center, Rochester, NY, USA.,Authors contributed equally to this work
| | | | | | - Shannon Lacy
- US Army of Veterinary Corps, Fort Campbell, KY, USA
| | | | - Thomas H Thatcher
- Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
| | - R Matthew Kottmann
- Division of Pulmonary Diseases and Critical Care, University of Rochester Medical Center, Rochester, NY, USA
| | - Patricia J Sime
- Division of Pulmonary Diseases and Critical Care, University of Rochester Medical Center, Rochester, NY, USA.,Department of Medicine, Virginia Commonwealth University, Richmond, VA, USA
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