51
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Li X, Goobie GC, Gregory AD, Kass DJ, Zhang Y. Toll-Interacting Protein in Pulmonary Diseases. Abiding by the Goldilocks Principle. Am J Respir Cell Mol Biol 2021; 64:536-546. [PMID: 33233920 PMCID: PMC8086045 DOI: 10.1165/rcmb.2020-0470tr] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
TOLLIP (Toll-interacting protein) is an intracellular adaptor protein with diverse actions throughout the body. In a context- and cell type–specific manner, TOLLIP can function as an inhibitor of inflammation and endoplasmic-reticulum stress, an activator of autophagy, or a critical regulator of intracellular vacuole trafficking. The distinct functions of this protein have been linked to innate immune responses and lung epithelial-cell apoptosis. TOLLIP genetic variants have been associated with a variety of chronic lung diseases, including idiopathic pulmonary fibrosis, asthma, and primary graft dysfunction after lung transplantation, and with infections, such as tuberculosis, Legionella pneumonia, and respiratory viruses. TOLLIP exists in a delicate homeostatic balance, with both positive and negative effects on the trajectory of pulmonary diseases. This translational review summarizes the genetic and molecular associations that link TOLLIP to the development and progression of noninfectious and infectious pulmonary diseases. We highlight current limitations of in vitro and in vivo models in assessing the role of TOLLIP in these conditions, and we describe future approaches that will enable a more nuanced exploration of the role of TOLLIP in pulmonary conditions. There has been a surge in recent research evaluating the role of this protein in human diseases, but critical mechanistic pathways require further exploration. By understanding its biologic functions in disease-specific contexts, we will be able to determine whether TOLLIP can be therapeutically modulated to treat pulmonary diseases.
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Affiliation(s)
- Xiaoyun Li
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Gillian C Goobie
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; and.,Clinician Investigator Program, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alyssa D Gregory
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Daniel J Kass
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Yingze Zhang
- Dorothy P. and Richard P. Simmons Center for Interstitial Lung Disease, Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania; and
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52
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Oldham JM. Interstitial Lung Abnormalities and Aging Biomarkers: A Mediation. Am J Respir Crit Care Med 2021; 203:1058-1060. [PMID: 33227215 PMCID: PMC8314893 DOI: 10.1164/rccm.202011-4046ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
- Justin M Oldham
- Division of Pulmonary Critical Care and Sleep Medicine University of California at Davis Sacramento, California
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53
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Newton CA, Herzog EL. Molecular Markers and the Promise of Precision Medicine for Interstitial Lung Disease. Clin Chest Med 2021; 42:357-364. [PMID: 34024410 DOI: 10.1016/j.ccm.2021.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Management of patients with interstitial lung disease (ILD) requires accurate classification. However, this process relies on subjective interpretation of nonspecific and overlapping clinical features that could hamper clinical care. The development and implementation of objective biomarkers reflective of specific disease states could facilitate precision-based approaches based on patient-level biology to improve the health of ILD patients. Omics-based studies allow for the seemingly unbiased and highly efficient screening of candidate biomarkers and offer unprecedented opportunities for discovery. This review outlines representative major omics-based discoveries in a well-studied condition, idiopathic pulmonary fibrosis, to develop a roadmap to personalized medicine in ILD.
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Affiliation(s)
- Chad A Newton
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-8558, USA.
| | - Erica L Herzog
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, Yale School of Medicine, Yale University, 300 Cedar Street TAC441S, New Haven, CT 06520-8057, USA
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54
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McErlean P, Bell CG, Hewitt RJ, Busharat Z, Ogger PP, Ghai P, Albers GJ, Calamita E, Kingston S, Molyneaux PL, Beck S, Lloyd CM, Maher TM, Byrne AJ. DNA Methylome Alterations are Associated with Airway Macrophage Differentiation and Phenotype During Lung Fibrosis. Am J Respir Crit Care Med 2021; 204:954-966. [PMID: 34280322 DOI: 10.1164/rccm.202101-0004oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a fatal respiratory disease with no cure. However, knowledge of epigenetics of AMs in IPF are limited. METHODS We undertook DNA methylation profiling using Illumina EPIC (850k) arrays in sorted AMs from Healthy (n=14) and IPF (n=30) donors. Cell-type deconvolution was performed using reference myeloid-cell DNA methylomes. MEASUREMENTS AND MAIN RESULTS Our analysis revealed epigenetic heterogeneity was a key characteristic of IPF-AMs. DNAm 'clock' analysis indicated epigenetic alterations in IPF-AMs was not associated with accelerated ageing. In differential DNAm analysis, we identified numerous differentially methylated positions (DMPs, n=11) and regions (DMRs, n=49) between healthy and IPF AMs respectively. DMPs and DMRs encompassed genes involved in lipid (LPCAT1) and glucose (PFKFB3) metabolism and importantly, DNAm status was associated with disease severity in IPF. CONCLUSIONS Collectively, our data identify that changes in the epigenome are associated with development and function of AMs in the IPF lung.
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Affiliation(s)
- Peter McErlean
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Christopher G Bell
- William Harvey Research Institute, 105713, London, United Kingdom of Great Britain and Northern Ireland
| | - Richard J Hewitt
- National Heart and Lung Institute, Inflammation, Repair & Development, London, United Kingdom of Great Britain and Northern Ireland
| | - Zabreen Busharat
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Patricia P Ogger
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Poonam Ghai
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Gesa J Albers
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
| | - Emily Calamita
- Imperial College London, 4615, London, United Kingdom of Great Britain and Northern Ireland
| | - Shaun Kingston
- Royal Brompton Hospital, 156726, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland
| | - Philip L Molyneaux
- Imperial College London, National Heart and Lung Institute, London, United Kingdom of Great Britain and Northern Ireland
| | - Stephan Beck
- University College London, 4919, London, United Kingdom of Great Britain and Northern Ireland
| | - Clare M Lloyd
- Imperial College, Leukocyte Biology, London, United Kingdom of Great Britain and Northern Ireland
| | - Toby M Maher
- Royal Brompton Hospital, 156726, Interstitial Lung Disease Unit, London, United Kingdom of Great Britain and Northern Ireland;
| | - Adam J Byrne
- Imperial College London, London, United Kingdom of Great Britain and Northern Ireland
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55
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Qin W, Crestani B, Spek CA, Scicluna BP, van der Poll T, Duitman J. Alveolar epithelial TET2 is not involved in the development of bleomycin-induced pulmonary fibrosis. FASEB J 2021; 35:e21599. [PMID: 33913570 DOI: 10.1096/fj.202002686rr] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/26/2021] [Accepted: 03/31/2021] [Indexed: 11/11/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic lung disease of unknown etiology with minimal treatment options. Repetitive alveolar epithelial injury has been suggested as one of the causative mechanisms of this disease. Type 2 alveolar epithelial cells (AEC2) play a crucial role during fibrosis by functioning as stem cells able to repair epithelial damage. The DNA demethylase Tet methylcytosine dioxygenase 2 (TET2) regulates the stemness of multiple types of stem cells, but whether it also affects the stemness of AEC2 during fibrosis remains elusive. To study the role of TET2 in AEC2 during fibrosis, we first determined TET2 protein levels in the lungs of IPF patients and compared TET2 expression in AEC2 of IPF patients and controls using publicly available data sets. Subsequently, pulmonary fibrosis was induced by the intranasal administration of bleomycin to wild-type and AEC2-specific TET2 knockout mice to determine the role of TET2 in vivo. Fibrosis was assessed by hydroxyproline analysis and fibrotic gene expression. Additionally, macrophage recruitment and activation, and epithelial injury were analyzed. TET2 protein levels and gene expression were downregulated in IPF lungs and AEC2, respectively. Bleomycin inoculation induced a robust fibrotic response as indicated by increased hydroxyproline levels and increased expression of pro-fibrotic genes. Additionally, increased macrophage recruitment and both M1 and M2 activation were observed. None of these parameters were, however, affected by AEC2-specific TET2 deficiency. TET2 expression is reduced in IPF, but the absence of TET2 in AEC2 cells does not affect the development of bleomycin-induced pulmonary fibrosis.
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Affiliation(s)
- Wanhai Qin
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Bruno Crestani
- INSERM UMR1152, Medical School Xavier Bichat, Paris, France.,Département Hospitalo-universitaire FIRE (Fibrosis, Inflammation and Remodeling) and LabEx Inflamex, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - C Arnold Spek
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Brendon P Scicluna
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Tom van der Poll
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,Division of Infectious Diseases, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - JanWillem Duitman
- Center for Experimental and Molecular Medicine, Amsterdam UMC, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
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56
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Abstract
Epigenetic modifications are emerging as important regulatory mechanisms of gene expression in lung disease, given that they are influenced by environmental exposures and genetic variants, and that they regulate immune and fibrotic processes. In this review, we introduce these concepts with a focus on the study of DNA methylation and histone modifications and discuss how they have been applied to lung disease, and how they can be applied to sarcoidosis. This information has implications for other exposure and immunologically mediated lung diseases, such as chronic beryllium disease, hypersensitivity pneumonitis, and asbestosis.
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Affiliation(s)
- Iain R Konigsberg
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Lisa A Maier
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, National Jewish Health, Denver, CO, USA
- Dept of Environmental and Occupational Health, Colorado School of Public Health, Aurora, CO, USA
| | - Ivana V Yang
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Dept of Epidemiology, Colorado School of Public Health, Aurora, CO, USA
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57
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Merkt W, Zhou Y, Han H, Lagares D. Myofibroblast fate plasticity in tissue repair and fibrosis: Deactivation, apoptosis, senescence and reprogramming. Wound Repair Regen 2021; 29:678-691. [PMID: 34117675 DOI: 10.1111/wrr.12952] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022]
Abstract
In response to tissue injury, fibroblasts differentiate into professional repair cells called myofibroblasts, which orchestrate many aspects of the normal tissue repair programme including synthesis, deposition and contraction of extracellular matrix proteins, leading to wound closure. Successful tissue repair responses involve termination of myofibroblast activities in order to prevent pathologic fibrotic scarring. Here, we discuss the cellular and molecular mechanisms limiting myofibroblast activities during physiological tissue repair, including myofibroblast deactivation, apoptosis, reprogramming and immune clearance of senescent myofibroblasts. In addition, we summarize pathological mechanisms leading to myofibroblast persistence and survival, a hallmark of fibrotic diseases. Finally, we discuss emerging anti-fibrotic therapies aimed at targeting myofibroblast fate such as senolytics, gene therapy, cellular immunotherapy and CAR-T cells.
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Affiliation(s)
- Wolfgang Merkt
- Fibrosis Research Center, Center for Immunology and Inflammatory Diseases, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Hematology, Oncology and Rheumatology, Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany
| | - Yan Zhou
- Fibrosis Research Center, Center for Immunology and Inflammatory Diseases, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.,Department of Physiology, Xiangya Medical School, Central South University, Changsha, China
| | - Hongwei Han
- Fibrosis Research Center, Center for Immunology and Inflammatory Diseases, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Lagares
- Fibrosis Research Center, Center for Immunology and Inflammatory Diseases, Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
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58
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Yang Y, Yuan L, Yang M, Du X, Qin L, Wang L, Zhou K, Wu M, He R, Feng J, Xiang Y, Qu X, Liu H, Qin X, Liu C. Aberrant Methylation of Aging-Related Genes in Asthma. Front Mol Biosci 2021; 8:655285. [PMID: 34136532 PMCID: PMC8203316 DOI: 10.3389/fmolb.2021.655285] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
Background: Asthma is a complex pulmonary inflammatory disease which is common among older adults. Aging-related alterations have also been found in structural cells and immune cells of asthma patients. Nonetheless, the underlying mechanism by which differenced aging-related gene contributes to asthma pathology remains unclear. Of note, DNA methylation (DNAm) has been proven to play a critical mechanism for age-related gene expression changes. However, the methylation changes of aging-related genes in asthma patients are still obscure. Methods: First, changes in DNAm and gene expression were detected with multiple targeted bisulfite enrichment sequencing (MethTarget) and qPCR in peripheral blood of 51 healthy controls (HCs) and 55 asthmatic patients. Second, the correlation between the DNAm levels of specific altered CpG sites and the pulmonary function indicators of asthma patients was evaluated. Last, the receiver operator characteristic (ROC) curve and principal component analysis (PCA) were used to identify the feasibility of the candidate CpG sites as biomarkers for asthma. Results: Compared with HCs, there was a differential mRNA expression for nine aging-related genes in peripheral blood of asthma patients. Besides, the methylation levels of the nine aging-related genes were also altered in asthma patients, and a total of 68 CpG sites were associated with the severity of asthma. Notably, 9 of the 68 CpG sites were significantly associated with pulmonary function parameters. Moreover, ROC curve and PCA analysis showed that the candidate differential methylation sites (DMSs) can be used as potential biomarkers for asthma. Conclusions: In summary, this study confirmed the differentially expressed mRNA and aberrant DNAm level of aging-related genes in asthma patients. DMSs are associated with the clinical evaluation indicators of asthma, which indicate the involvement of aging-related genes in the pathogenesis of asthma and provide some new possible biomarkers for asthma.
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Affiliation(s)
- Yu Yang
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Lin Yuan
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ming Yang
- Centre for Asthma and Respiratory Disease, School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle and Hunter Medical Research Institute, Callaghan, NSW, Australia
| | - Xizi Du
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ling Qin
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Leyuan Wang
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Kai Zhou
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Mengping Wu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Ruoxi He
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Juntao Feng
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Basic and Clinical Research Laboratory of Major Respiratory Diseases, Central South University, Changsha, China
| | - Yang Xiang
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Xiangping Qu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Huijun Liu
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Xiaoqun Qin
- Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China
| | - Chi Liu
- Department of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Xiangya Hospital, Central South University, Changsha, China.,Department of Physiology, School of Basic Medicine Science, Central South University, Changsha, China.,Research Center of China-Africa Infectious Diseases, Xiangya School of Medicine Central South University, Changsha, China
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59
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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: 71] [Impact Index Per Article: 17.8] [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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60
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Nouws J, Wan F, Finnemore E, Roque W, Kim SJ, Bazan I, Li CX, Skold CM, Dai Q, Yan X, Chioccioli M, Neumeister V, Britto CJ, Sweasy J, Bindra R, Wheelock ÅM, Gomez JL, Kaminski N, Lee PJ, Sauler M. MicroRNA miR-24-3p reduces DNA damage responses, apoptosis, and susceptibility to chronic obstructive pulmonary disease. JCI Insight 2021; 6:134218. [PMID: 33290275 PMCID: PMC7934877 DOI: 10.1172/jci.insight.134218] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 12/02/2020] [Indexed: 12/27/2022] Open
Abstract
The pathogenesis of chronic obstructive pulmonary disease (COPD) involves aberrant responses to cellular stress caused by chronic cigarette smoke (CS) exposure. However, not all smokers develop COPD and the critical mechanisms that regulate cellular stress responses to increase COPD susceptibility are not understood. Because microRNAs are well-known regulators of cellular stress responses, we evaluated microRNA expression arrays performed on distal parenchymal lung tissue samples from 172 subjects with and without COPD. We identified miR-24-3p as the microRNA that best correlated with radiographic emphysema and validated this finding in multiple cohorts. In a CS exposure mouse model, inhibition of miR-24-3p increased susceptibility to apoptosis, including alveolar type II epithelial cell apoptosis, and emphysema severity. In lung epithelial cells, miR-24-3p suppressed apoptosis through the BH3-only protein BIM and suppressed homology-directed DNA repair and the DNA repair protein BRCA1. Finally, we found BIM and BRCA1 were increased in COPD lung tissue, and BIM and BRCA1 expression inversely correlated with miR-24-3p. We concluded that miR-24-3p, a regulator of the cellular response to DNA damage, is decreased in COPD, and decreased miR-24-3p increases susceptibility to emphysema through increased BIM and apoptosis.
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Affiliation(s)
- Jessica Nouws
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Feng Wan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Anatomy, Beijing University of Chinese Medicine, Beijing, China
| | - Eric Finnemore
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Willy Roque
- Department of Internal Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - So-Jin Kim
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Isabel Bazan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Chuan-Xing Li
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - C Magnus Skold
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Qile Dai
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, USA
| | - Maurizio Chioccioli
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Veronique Neumeister
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Clemente J Britto
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Joann Sweasy
- Department of Radiation Oncology, University of Arizona College of Medicine, Tucson, Arizona, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Åsa M Wheelock
- Division of Respiratory Medicine and Allergy, Department of Medicine, and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jose L Gomez
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Patty J Lee
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA.,Section of Pulmonary, Allergy, and Critical Care Medicine, Department of Internal Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Maor Sauler
- Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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61
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Hamanaka RB, Mutlu GM. Metabolic requirements of pulmonary fibrosis: role of fibroblast metabolism. FEBS J 2021; 288:6331-6352. [PMID: 33393204 DOI: 10.1111/febs.15693] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 12/27/2022]
Abstract
Fibrosis is a pathologic condition characterized by excessive deposition of extracellular matrix and chronic scaring that can affect every organ system. Organ fibrosis is associated with significant morbidity and mortality, contributing to as many as 45% of all deaths in the developed world. In the lung, many chronic lung diseases may lead to fibrosis, the most devastating being idiopathic pulmonary fibrosis (IPF), which affects approximately 3 million people worldwide and has a median survival of 3.8 years. Currently approved therapies for IPF do not significantly extend lifespan, and thus, there is pressing need for novel therapeutic strategies to treat IPF and other fibrotic diseases. At the heart of pulmonary fibrosis are myofibroblasts, contractile cells with characteristics of both fibroblasts and smooth muscle cells, which are the primary cell type responsible for matrix deposition in fibrotic diseases. Much work has centered around targeting the extracellular growth factors and intracellular signaling regulators of myofibroblast differentiation. Recently, metabolic changes associated with myofibroblast differentiation have come to the fore as targetable mechanisms required for myofibroblast function. In this review, we will discuss the metabolic changes associated with myofibroblast differentiation, as well as the mechanisms by which these changes promote myofibroblast function. We will then discuss the potential for this new knowledge to lead to the development of novel therapies for IPF and other fibrotic diseases.
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Affiliation(s)
- Robert B Hamanaka
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, IL, USA
| | - Gökhan M Mutlu
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, University of Chicago, IL, USA
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62
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Wang Y, Zhang L, Wu GR, Zhou Q, Yue H, Rao LZ, Yuan T, Mo B, Wang FX, Chen LM, Sun F, Song J, Xiong F, Zhang S, Yu Q, Yang P, Xu Y, Zhao J, Zhang H, Xiong W, Wang CY. MBD2 serves as a viable target against pulmonary fibrosis by inhibiting macrophage M2 program. SCIENCE ADVANCES 2021; 7:eabb6075. [PMID: 33277324 PMCID: PMC7775789 DOI: 10.1126/sciadv.abb6075] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/29/2020] [Indexed: 05/22/2023]
Abstract
Despite past extensive studies, the mechanisms underlying pulmonary fibrosis (PF) still remain poorly understood. Here, we demonstrated that lungs originating from different types of patients with PF, including coronavirus disease 2019, systemic sclerosis-associated interstitial lung disease, and idiopathic PF, and from mice following bleomycin (BLM)-induced PF are characterized by the altered methyl-CpG-binding domain 2 (MBD2) expression in macrophages. Depletion of Mbd2 in macrophages protected mice against BLM-induced PF. Mbd2 deficiency significantly attenuated transforming growth factor-β1 (TGF-β1) production and reduced M2 macrophage accumulation in the lung following BLM induction. Mechanistically, Mbd2 selectively bound to the Ship promoter in macrophages, by which it repressed Ship expression and enhanced PI3K/Akt signaling to promote the macrophage M2 program. Therefore, intratracheal administration of liposomes loaded with Mbd2 siRNA protected mice from BLM-induced lung injuries and fibrosis. Together, our data support the possibility that MBD2 could be a viable target against PF in clinical settings.
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Affiliation(s)
- Yi Wang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Lei Zhang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Guo-Rao Wu
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Qing Zhou
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Huihui Yue
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Li-Zong Rao
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guilin Medical University, 212 Renmin Road, Guilin 541000, China
| | - Ting Yuan
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guilin Medical University, 212 Renmin Road, Guilin 541000, China
| | - Biwen Mo
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Guilin Medical University, 212 Renmin Road, Guilin 541000, China
| | - Fa-Xi Wang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Long-Min Chen
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Fei Sun
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Jia Song
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Fei Xiong
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Shu Zhang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Qilin Yu
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Ping Yang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Yongjian Xu
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Jianping Zhao
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China
| | - Huilan Zhang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China.
| | - Weining Xiong
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China.
- Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, Shanghai 200011, China
| | - Cong-Yi Wang
- The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Department of Respiratory and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, 1095 Jiefang Ave., Wuhan 430030, China.
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Bartczak K, Białas AJ, Kotecki MJ, Górski P, Piotrowski WJ. More than a Genetic Code: Epigenetics of Lung Fibrosis. Mol Diagn Ther 2020; 24:665-681. [PMID: 32926347 PMCID: PMC7677145 DOI: 10.1007/s40291-020-00490-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At the end of the last century, genetic studies reported that genetic information is not transmitted solely by DNA, but is also transmitted by other mechanisms, named as epigenetics. The well-described epigenetic mechanisms include DNA methylation, biochemical modifications of histones, and microRNAs. The role of altered epigenetics in the biology of various fibrotic diseases is well-established, and recent advances demonstrate its importance in the pathogenesis of pulmonary fibrosis-predominantly referring to idiopathic pulmonary fibrosis, the most lethal of the interstitial lung diseases. The deficiency in effective medications suggests an urgent need to better understand the underlying pathobiology. This review summarizes the current knowledge concerning epigenetic changes in pulmonary fibrosis and associations of these changes with several cellular pathways of known significance in its pathogenesis. It also designates the most promising substances for further research that may bring us closer to new therapeutic options.
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Affiliation(s)
- Krystian Bartczak
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland.
| | - Adam J Białas
- Department of Pathobiology of Respiratory Diseases, The Medical University of Lodz, Lodz, Poland
| | - Mateusz J Kotecki
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Paweł Górski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
| | - Wojciech J Piotrowski
- Department of Pneumology and Allergology, The Medical University of Lodz, Kopcińskiego 22, 90-153, Lodz, Poland
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Goobie GC, Nouraie M, Zhang Y, Kass DJ, Ryerson CJ, Carlsten C, Johannson KA. Air Pollution and Interstitial Lung Diseases: Defining Epigenomic Effects. Am J Respir Crit Care Med 2020; 202:1217-1224. [PMID: 32569479 PMCID: PMC7605178 DOI: 10.1164/rccm.202003-0836pp] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Affiliation(s)
- Gillian C. Goobie
- Department of Human Genetics, Graduate School of Public Health and
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Yingze Zhang
- Department of Human Genetics, Graduate School of Public Health and
- Department of Medicine and
| | | | - Christopher J. Ryerson
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada; and
| | - Christopher Carlsten
- Division of Respiratory Medicine, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, British Columbia, Canada; and
| | - Kerri A. Johannson
- Division of Respiratory Medicine, Department of Medicine, University of Calgary, Calgary, Alberta, Canada
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Research Advances on DNA Methylation in Idiopathic Pulmonary Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:73-81. [PMID: 32949391 DOI: 10.1007/978-981-15-4494-1_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic complex lung disease with no specific treatment and poor prognosis, characterized by the pulmonary progressive fibrosis and dysfunctions that lead to respiratory failure. Several factors may impact the progress of IPF, including age, cigarette smoking, and dusts, of which genetic and epigenetic factors mainly contribute to lung tissue fibrosis. DNA methylation is one of epigenetic processes that occur in many diseases and regulate chromosomal and extrachromosomal DNA functions in response to environmental exposures. The methylation plays pivotal roles in regulation of gene expression to facilitate the formation of fibroblastic foci and lung fibrosis. This chapter will describe alterations and effects of the DNA methylation on gene expression, the potential application of DNA methylation as a biomarker, and significance as therapeutic targets. Those understanding will provide us new insight into the treatment and prognosis of IPF.
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Glass DS, Grossfeld D, Renna HA, Agarwala P, Spiegler P, Kasselman LJ, Glass AD, DeLeon J, Reiss AB. Idiopathic pulmonary fibrosis: Molecular mechanisms and potential treatment approaches. Respir Investig 2020; 58:320-335. [PMID: 32487481 DOI: 10.1016/j.resinv.2020.04.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 03/17/2020] [Accepted: 04/13/2020] [Indexed: 06/11/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive disease with high mortality that commonly occurs in middle-aged and older adults. IPF, characterized by a decline in lung function, often manifests as exertional dyspnea and cough. Symptoms result from a fibrotic process driven by alveolar epithelial cells that leads to increased migration, proliferation, and differentiation of lung fibroblasts. Ultimately, the differentiation of fibroblasts into myofibroblasts, which synthesize excessive amounts of extracellular matrix proteins, destroys the lung architecture. However, the factors that induce the fibrotic process are unclear. Diagnosis can be a difficult process; the gold standard for diagnosis is the multidisciplinary conference. Practical biomarkers are needed to improve diagnostic and prognostic accuracy. High-resolution computed tomography typically shows interstitial pneumonia with basal and peripheral honeycombing. Gas exchange and diffusion capacity are impaired. Treatments are limited, although the anti-fibrotic drugs pirfenidone and nintedanib can slow the progression of the disease. Lung transplantation is often contraindicated because of age and comorbidities, but it improves survival when successful. The incidence and prevalence of IPF has been increasing and there is an urgent need for improved therapies. This review covers the detailed cellular and molecular mechanisms underlying IPF progression as well as current treatments and cutting-edge research into new therapeutic targets.
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Affiliation(s)
- Daniel S Glass
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - David Grossfeld
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Heather A Renna
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Priya Agarwala
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Peter Spiegler
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Lora J Kasselman
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Amy D Glass
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Joshua DeLeon
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
| | - Allison B Reiss
- Department of Medicine and Winthrop Research Institute, NYU Long Island School of Medicine and NYU Winthrop Hospital, Mineola, NY, USA.
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Schoeff SS, Shi X, Young WG, Whited CW, Soni RS, Liu P, Ong IM, Dailey SH, Welham NV. Proteomic and Genomic Methylation Signatures of Idiopathic Subglottic Stenosis. Laryngoscope 2020; 131:E540-E546. [PMID: 32619300 DOI: 10.1002/lary.28851] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 12/29/2022]
Abstract
OBJECTIVE Idiopathic subglottic stenosis (iSGS) is a chronic inflammatory condition that causes dyspnea and affects middle-aged women of White race and non-Latino or Hispanic ethnicity. To better characterize its phenotype and pathogenesis, we assessed the proteomic and genomic methylation signatures of subglottic tissue collected from iSGS patients compared to controls. STUDY DESIGN Molecular analysis of clinical biospecimens. METHODS We collected subglottic tissue biopsies from 12 patients during direct laryngoscopy, immediately prior to surgical treatment of iSGS; as well as from 4 age-, sex-, and race/ethnicity-matched control patients undergoing other direct laryngoscopic procedures. We isolated protein and genomic DNA, acquired proteomic data using label-free quantitative mass spectrometry techniques, and acquired genome-wide methylation data using bisulfite conversion and a microarray platform. We compared molecular profiles across the iSGS and control groups, and with respect to clinical course in the iSGS group. Eight of the 12 iSGS patients underwent subsequent blood collection and plasma isolation for further assessment. RESULTS Proteomic analysis revealed 42 differentially abundant proteins in the iSGS biopsies compared to controls, inferring enrichment of biological pathways associated with early wound healing, innate immunity, matrix remodeling, and metabolism. Proteome-based hierarchical clustering organized patients into two iSGS and one control subgroups. Methylation analysis revealed five hypermethylated genes in the iSGS biopsies compared to controls, including the biotin recycling enzyme biotinidase (BTD). Follow-up analysis showed elevated plasma BTD activity in iSGS patients compared to both controls and published normative data. CONCLUSION iSGS exhibits distinct proteomic and genomic methylation signatures. These signatures expand current understanding of the iSGS phenotype, support the possibility of disease subgroups, and should inform the direction of future experimental studies. LEVEL OF EVIDENCE Not applicable Laryngoscope, 131:E540-E546, 2021.
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Affiliation(s)
- Stephen S Schoeff
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Xudong Shi
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - William G Young
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Chad W Whited
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Resha S Soni
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Peng Liu
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Irene M Ong
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A.,Department of Obstetrics and Gynecology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Seth H Dailey
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
| | - Nathan V Welham
- Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, U.S.A
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Parimon T, Yao C, Stripp BR, Noble PW, Chen P. Alveolar Epithelial Type II Cells as Drivers of Lung Fibrosis in Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2020; 21:E2269. [PMID: 32218238 PMCID: PMC7177323 DOI: 10.3390/ijms21072269] [Citation(s) in RCA: 253] [Impact Index Per Article: 50.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/15/2020] [Accepted: 03/19/2020] [Indexed: 12/19/2022] Open
Abstract
: Alveolar epithelial type II cells (AT2) are a heterogeneous population that have critical secretory and regenerative roles in the alveolus to maintain lung homeostasis. However, impairment to their normal functional capacity and development of a pro-fibrotic phenotype has been demonstrated to contribute to the development of idiopathic pulmonary fibrosis (IPF). A number of factors contribute to AT2 death and dysfunction. As a mucosal surface, AT2 cells are exposed to environmental stresses that can have lasting effects that contribute to fibrogenesis. Genetical risks have also been identified that can cause AT2 impairment and the development of lung fibrosis. Furthermore, aging is a final factor that adds to the pathogenic changes in AT2 cells. Here, we will discuss the homeostatic role of AT2 cells and the studies that have recently defined the heterogeneity of this population of cells. Furthermore, we will review the mechanisms of AT2 death and dysfunction in the context of lung fibrosis.
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Affiliation(s)
- Tanyalak Parimon
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Changfu Yao
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Barry R Stripp
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Paul W Noble
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Peter Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Women’s Guild Lung Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
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Wang Y, Xiao H, Zhao F, Li H, Gao R, Yan B, Ren J, Yang J. Decrypting the crosstalk of noncoding RNAs in the progression of IPF. Mol Biol Rep 2020; 47:3169-3179. [PMID: 32180083 DOI: 10.1007/s11033-020-05368-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/29/2020] [Indexed: 12/16/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is an agnogenic, rare, and lethal disease, with high mortality and poor prognosis and a median survival time as short as 3 to 5 years after diagnosis. No effective therapeutic drugs are still not available not only in clinical practice, but also in preclinical phases. To better and deeper understand pulmonary fibrosis will provide more effective strategies for therapy. Mounting evidence suggests that noncoding RNAs (ncRNAs) and their interactions may contribute to lung fibrosis; however, the mechanisms underlying their roles are largely unknown. In this review, we systematically summarized the recent advances regarding the crucial roles of long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and circular RNAs (circRNAs) and crosstalk among them in the development of IPF. The perspective for related genes was well highlighted. In summary, ncRNA and their interactions play a key regulatory part in the progression of IPF and are bound to provide us with new diagnostic and therapeutic targets.
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Affiliation(s)
- Yujuan Wang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Han Xiao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Fenglian Zhao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Han Li
- 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
| | - Bingdi Yan
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Jin Ren
- 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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Otoupalova E, Smith S, Cheng G, Thannickal VJ. Oxidative Stress in Pulmonary Fibrosis. Compr Physiol 2020; 10:509-547. [PMID: 32163196 DOI: 10.1002/cphy.c190017] [Citation(s) in RCA: 163] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oxidative stress has been linked to various disease states as well as physiological aging. The lungs are uniquely exposed to a highly oxidizing environment and have evolved several mechanisms to attenuate oxidative stress. Idiopathic pulmonary fibrosis (IPF) is a progressive age-related disorder that leads to architectural remodeling, impaired gas exchange, respiratory failure, and death. In this article, we discuss cellular sources of oxidant production, and antioxidant defenses, both enzymatic and nonenzymatic. We outline the current understanding of the pathogenesis of IPF and how oxidative stress contributes to fibrosis. Further, we link oxidative stress to the biology of aging that involves DNA damage responses, loss of proteostasis, and mitochondrial dysfunction. We discuss the recent findings on the role of reactive oxygen species (ROS) in specific fibrotic processes such as macrophage polarization and immunosenescence, alveolar epithelial cell apoptosis and senescence, myofibroblast differentiation and senescence, and alterations in the acellular extracellular matrix. Finally, we provide an overview of the current preclinical studies and clinical trials targeting oxidative stress in fibrosis and potential new strategies for future therapeutic interventions. © 2020 American Physiological Society. Compr Physiol 10:509-547, 2020.
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Affiliation(s)
- Eva Otoupalova
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Sam Smith
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Guangjie Cheng
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Victor J Thannickal
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Lee E, Kang MJ, Kim JH, Lee SH, Lee SY, Cho HJ, Yoon J, Jung S, Park Y, Oh DK, Hong SB, Hong SJ. NOTCH1 Pathway is Involved in Polyhexamethylene Guanidine-Induced Humidifier Disinfectant Lung Injuries. Yonsei Med J 2020; 61:186-191. [PMID: 31997628 PMCID: PMC6992453 DOI: 10.3349/ymj.2020.61.2.186] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/29/2019] [Accepted: 12/26/2019] [Indexed: 12/17/2022] Open
Abstract
An outbreak of fatal humidifier disinfectant lung injuries (HDLI) occurred in Korea. Human studies on mechanisms underlying HDLI have yet to be conducted. This study aimed to investigate methylation changes and their potential role in HDLI after exposure to HDs containing polyhexamethylene guanidine-phosphate. DNA methylation analysis was performed in blood samples from 10 children with HDLI and 10 healthy children using Infinium Human MethylationEPIC BeadChip. Transcriptome analysis was performed using lung tissues from 5 children with HDLI and 5 controls. Compared to healthy controls, 92 hypo-methylated and 79 hyper-methylated CpG sites were identified in children with HDLI at the statistical significance level of |Δβ|>0.2 and p<0.05. NOTCH1 was identified as a candidate network hub gene in cases. NOTCH1 transcripts significantly increased in lung tissues from HDLI cases compared to unexposed controls (p=0.05). NOTCH1 may play an important role in pulmonary fibrosis of HDLI.
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Affiliation(s)
- Eun Lee
- Department of Pediatrics, Chonnam National University Hospital, Chonnam National University Medical School, Gwangju, Korea
| | - Mi Jin Kang
- Asan Medical Center, Asan Institute for Life Sciences, Environmental Health Center, Seoul, Korea
| | - Jeong Hyun Kim
- Department of Medicine, University of Ulsan Collage of Medicine, Seoul, Korea
| | - Seung Hwa Lee
- Asan Medical Center, Asan Institute for Life Sciences, Environmental Health Center, Seoul, Korea
| | - So Yeon Lee
- Department of Pediatrics, Childhood Asthma Atopy Center, Environmental Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyun Ju Cho
- Department of Pediatrics, International St. Mary's hospital, Catholic Kwandong University College of Medicine, Incheon, Korea
| | - Jisun Yoon
- Department of Pediatrics, Mediplex Hospital, Incheon, Korea
| | - Sungsu Jung
- Department of Pediatrics, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Yangsoon Park
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Dong Kyu Oh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, Seoul, Korea
| | - Sang Bum Hong
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Soo Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Environmental Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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Whole-Genome DNA Methylation Associated With Differentially Expressed Genes Regulated Anthocyanin Biosynthesis Within Flower Color Chimera of Ornamental Tree Prunus mume. FORESTS 2020. [DOI: 10.3390/f11010090] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is one of the best-studied epigenetic modifications involved in many biological processes. However, little is known about the epigenetic mechanism for flower color chimera of Prunus mume (Japanese apricot, mei). Using bisulfate sequencing and RNA sequencing, we analyzed the white (FBW) and red (FBR) petals collected from an individual tree of Japanese apricot cv. ‘Fuban Tiaozhi’ mei to reveal the different changes in methylation patterns associated with gene expression leading to significant difference in anthocyanins accumulation of FBW (0.012 ± 0.005 mg/g) and FBR (0.078 ± 0.013 mg/g). It was found that gene expression levels were positively correlated with DNA methylation levels within gene-bodies of FBW and FBR genomes; however, negative correlations between gene expression and DNA methylation levels were detected within promoter domains. In general, the methylation level within methylome of FBW was higher; and in total, 4,618 differentially methylated regions (DMRs) and 1,212 differentially expressed genes (DEGs) were detected from FBW vs. FBR. We also identified 82 DMR-associated DEGs, and 13 of them, including PmBAHD, PmCYP450, and PmABC, were playing critical roles in phenylalanine metabolism pathway, glycosyltransferase activity, and ABC transporter. The evidence exhibited DNA methylation may regulate gene expression resulting in flower color chimera of Japanese apricot.
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73
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Wang H, Wang M, Xiao K, Zhang X, Wang P, Xiao S, Qi H, Meng L, Zhang X, Shen F. Bioinformatics analysis on differentially expressed genes of alveolar macrophage in IPF. Exp Lung Res 2019; 45:288-296. [PMID: 31762326 DOI: 10.1080/01902148.2019.1680765] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Objective: This study aimed to explore the differentially expressed genes (DEGs) of pulmonary macrophages in human idiopathic pulmonary fibrosis (IPF) by bioinformatics, and elaborate on IPF on the gene level. Methods: The gene expression profile GSE49072 was downloaded from the gene expression omnibus (GEO) database. Genes of alveolar macrophages between normal volunteers and patients diagnosed as IPF were analyzed by GEO2R tools. Gene ontology (GO) and pathway enrichment analyses of genes were performed in the database for annotation, visualization and integrated discovery (DAVID) database, followed by functional annotation and protein-protein interaction (PPI) network construction in String website. Finally, the results were analyzed in a comprehensive way. Results: A total of 551 DEGs, including 205 down-regulated and 346 up-regulated were identified. The expression of 209875_s_at (secreted phosphoprotein 1, SPP1) and 214146_s_at (pro-platelet basic protein, PPBP) genes are the most significant in upregulated genes. DEGs in the MAPK(mitogen-activated protein kinase) signaling pathway and chemokine signaling pathway play important roles in the development of IPF. Conclusions: The up-regulation of genes such as SPP1 and PPBP affect the secretion of alveolar macrophages, thereby speeding up the process of fibrosis.
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Affiliation(s)
- Huaibin Wang
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, Hebei, P.R. China
| | - Miaomiao Wang
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, Hebei, P.R. China
| | - Kun Xiao
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, Hebei, P.R. China
| | - Xu Zhang
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, Hebei, P.R. China
| | - Peng Wang
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, Hebei, P.R. China
| | - Shuyu Xiao
- Tangshan Center of Disease Control and Prevention, Tangshan, Hebei, P.R. China
| | - Huisheng Qi
- Tangshan Gongren Hospital, Tangshan, Hebei, P.R. China
| | - Lijun Meng
- Department of Environmental and Chemical Engineering, Tangshan College, Tangshan, Hebei, P.R. China
| | - Xiujun Zhang
- College of Psychology, North China University of Science and Technology, Tangshan, Hebei, P.R. China
| | - Fuhai Shen
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan, Hebei, P.R. China
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74
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Tatler AL. Recent advances in the non-invasive assessment of fibrosis using biomarkers. Curr Opin Pharmacol 2019; 49:110-115. [PMID: 31756570 DOI: 10.1016/j.coph.2019.09.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/24/2019] [Indexed: 12/22/2022]
Abstract
Fibrosis can occur in most organs and is characterised by excessive and progressive extracellular matrix deposition and destruction of normal tissue architecture and function. In many cases treatment options are limited. Fibrotic diseases are therefore associated with high morbidity and mortality. Tissue biopsies remain a key part of diagnosing fibrosis; however, due to their invasive nature, tissue biopsies are unsuitable for monitoring disease progression. In some cases, tissue biopsies carry an unacceptable risk of mortality to the patient. Furthermore, assessing fibrosis via tissue biopsy is severely limited by the heterogenetic nature of fibrotic diseases and suffers from both sampling bias and observer variation/bias. The search for less invasive methods of diagnosing and monitoring fibrosis has led to the identification of many new biomarkers, many of which can be measured in serum in a so-called 'liquid biopsy' or can be imaged using state-of-the-art imaging modalities. These approaches have the potential to dramatically improve the diagnosis and monitoring of disease, and improve the design of clinical trials in to novel fibrotic therapies. This review summarises some of the recent advances in identifying novel biomarkers to diagnose and monitor fibrosis non-invasively.
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Affiliation(s)
- Amanda L Tatler
- Nottingham Respiratory Biomedical Research Centre, Division of Respiratory Medicine, School of Medicine, University of Nottingham, United Kingdom.
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75
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Idiopathic Pulmonary Fibrosis Is a Genetic Disease Involving Mucus and the Peripheral Airways. Ann Am Thorac Soc 2019; 15:S192-S197. [PMID: 30431344 DOI: 10.1513/annalsats.201802-144aw] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is localized to the lung, is characterized by a pattern of heterogeneous, subpleural patches of fibrotic, remodeled lung, and is associated with a median survival of 3-5 years after diagnosis. A common gain-of-function MUC5B promoter variant, rs35705950, is the strongest risk factor (genetic and otherwise), accounting for at least 30% of the total risk of developing IPF. The MUC5B promoter variant can be used to identify individuals in the preclinical phase of this progressive disease, and, in the IPF lung, we have found that MUC5B is specifically overexpressed in bronchoalveolar epithelium. Thus, MUC5B represents a key molecule to understand the mechanisms that appear to initiate the fibroproliferative process in the bronchoalveolar epithelium. Moreover, focusing on MUC5B may provide a unique opportunity to define the early molecular events that lead to, and potentially prevent, the development of IPF.
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76
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Yang IV, Konigsberg I, MacPhail K, Li L, Davidson EJ, Mroz PM, Hamzeh N, Gillespie M, Silveira LJ, Fingerlin TE, Maier LA. DNA Methylation Changes in Lung Immune Cells Are Associated with Granulomatous Lung Disease. Am J Respir Cell Mol Biol 2019; 60:96-105. [PMID: 30141971 DOI: 10.1165/rcmb.2018-0177oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Epigenetic marks are likely to explain variability of response to antigen in granulomatous lung disease. The objective of this study was to identify DNA methylation and gene expression changes associated with chronic beryllium disease (CBD) and sarcoidosis in lung cells obtained by BAL. BAL cells from CBD (n = 8), beryllium-sensitized (n = 8), sarcoidosis (n = 8), and additional progressive sarcoidosis (n = 9) and remitting (n = 15) sarcoidosis were profiled on the Illumina 450k methylation and Affymetrix/Agilent gene expression microarrays. Statistical analyses were performed to identify DNA methylation and gene expression changes associated with CBD, sarcoidosis, and disease progression in sarcoidosis. DNA methylation array findings were validated by pyrosequencing. We identified 52,860 significant (P < 0.005 and q < 0.05) CpGs associated with CBD; 2,726 CpGs near 1,944 unique genes have greater than 25% methylation change. A total of 69% of differentially methylated genes are significantly (q < 0.05) differentially expressed in CBD, with many canonical inverse relationships of methylation and expression in genes critical to T-helper cell type 1 differentiation, chemokines and their receptors, and other genes involved in immunity. Testing of these CBD-associated CpGs in sarcoidosis reveals that methylation changes only approach significance, but are methylated in the same direction, suggesting similarities between the two diseases with more heterogeneity in sarcoidosis that limits power with the current sample size. Analysis of progressive versus remitting sarcoidosis identified 15,215 CpGs (P < 0.005 and q < 0.05), but only 801 of them have greater than 5% methylation change, demonstrating that DNA methylation marks of disease progression changes are more subtle. Our study highlights the significance of epigenetic marks in lung immune response in granulomatous lung disease.
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Affiliation(s)
- Ivana V Yang
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,2 Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado.,3 Center for Genes, Environment, and Health
| | - Iain Konigsberg
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | | | - Li Li
- 4 Department of Medicine, and
| | - Elizabeth J Davidson
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | | | | | | | | | - Tasha E Fingerlin
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,3 Center for Genes, Environment, and Health.,5 Department of Biomedical Research, National Jewish Health, Denver, Colorado; and.,6 Department of Biostatistics and Bioinformatics and
| | - Lisa A Maier
- 1 Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,4 Department of Medicine, and.,7 Department of Environmental and Occupational Health, Colorado School of Public Health, Aurora, Colorado
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77
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Jones DL, Haak AJ, Caporarello N, Choi KM, Ye Z, Yan H, Varelas X, Ordog T, Ligresti G, Tschumperlin DJ. TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression. J Cell Sci 2019; 132:jcs.233486. [PMID: 31527052 DOI: 10.1242/jcs.233486] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022] Open
Abstract
Tissue fibrosis is a chronic disease driven by persistent fibroblast activation that has recently been linked to epigenetic modifications. Here, we screened a small library of epigenetic small-molecule modulators to identify compounds capable of inhibiting or reversing TGFβ-mediated fibroblast activation. We identified pracinostat, an HDAC inhibitor, as a potent attenuator of lung fibroblast activation and confirmed its efficacy in patient-derived fibroblasts isolated from fibrotic lung tissue. Mechanistically, we found that HDAC-dependent transcriptional repression was an early and essential event in TGFβ-mediated fibroblast activation. Treatment of lung fibroblasts with pracinostat broadly attenuated TGFβ-mediated epigenetic repression and promoted fibroblast quiescence. We confirmed a specific role for HDAC-dependent histone deacetylation in the promoter region of the anti-fibrotic gene PPARGC1A (PGC1α) in response to TGFβ stimulation. Finally, we identified HDAC7 as a key factor whose siRNA-mediated knockdown attenuates fibroblast activation without altering global histone acetylation. Together, these results provide novel mechanistic insight into the essential role HDACs play in TGFβ-mediated fibroblast activation via targeted gene repression.
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Affiliation(s)
- Dakota L Jones
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew J Haak
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Nunzia Caporarello
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Kyoung M Choi
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University, Boston, MA 02118, USA
| | - Tamas Ordog
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Giovanni Ligresti
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel J Tschumperlin
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
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78
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Negreros M, Hagood JS, Espinoza CR, Balderas-Martínez YI, Selman M, Pardo A. Transforming growth factor beta 1 induces methylation changes in lung fibroblasts. PLoS One 2019; 14:e0223512. [PMID: 31603936 PMCID: PMC6788707 DOI: 10.1371/journal.pone.0223512] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/22/2019] [Indexed: 12/20/2022] Open
Abstract
Idiopathic pulmonary fibrosis is a complex disease of unknown etiology. Environmental factors can affect disease susceptibility via epigenetic effects. Few studies explore global DNA methylation in lung fibroblasts, but none have focused on transforming growth factor beta-1 (TGF-β1) as a potential modifier of the DNA methylome. Here we analyzed changes in methylation and gene transcription in normal and IPF fibroblasts following TGF-β1 treatment. We analyzed the effects of TGF-β1 on primary fibroblasts derived from normal or IPF lungs treated for 24 hours and 5 days using the Illumina 450k Human Methylation array and the Prime View Human Gene Expression Array. TGF-β1 induced an increased number of gene expression changes after short term treatment in normal fibroblasts, whereas greater methylation changes were observed following long term stimulation mainly in IPF fibroblasts. DNA methyltransferase 3 alpha (DMNT3a) and tet methylcytosine dioxygenase 3 (TET3) were upregulated after 5-days TGF-β1 treatment in both cell types, whereas DNMT3a was upregulated after 24h only in IPF fibroblasts. Our findings demonstrate that TGF-β1 induced the upregulation of DNMT3a and TET3 expression and profound changes in the DNA methylation pattern of fibroblasts, mainly in those derived from IPF lungs.
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Affiliation(s)
- Miguel Negreros
- Facultad de Ciencias Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - James S. Hagood
- Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Pulmonology Division, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Celia R. Espinoza
- Department of Pediatrics, Division of Respiratory Medicine, University of California-San Diego, La Jolla, California, United States of America
| | - Yalbi I. Balderas-Martínez
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
- Cátedra CONACyT-INER, Mexico City, Mexico
| | - Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Annie Pardo
- Facultad de Ciencias Universidad Nacional Autónoma de México, Mexico City, Mexico
- * E-mail:
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79
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Wu AC, Kiley JP, Noel PJ, Amur S, Burchard EG, Clancy JP, Galanter J, Inada M, Jones TK, Kropski JA, Loyd JE, Nogee LM, Raby BA, Rogers AJ, Schwartz DA, Sin DD, Spira A, Weiss ST, Young LR, Himes BE. Current Status and Future Opportunities in Lung Precision Medicine Research with a Focus on Biomarkers. An American Thoracic Society/National Heart, Lung, and Blood Institute Research Statement. Am J Respir Crit Care Med 2019; 198:e116-e136. [PMID: 30640517 DOI: 10.1164/rccm.201810-1895st] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Thousands of biomarker tests are either available or under development for lung diseases. In many cases, adoption of these tests into clinical practice is outpacing the generation and evaluation of sufficient data to determine clinical utility and ability to improve health outcomes. There is a need for a systematically organized report that provides guidance on how to understand and evaluate use of biomarker tests for lung diseases. METHODS We assembled a diverse group of clinicians and researchers from the American Thoracic Society and leaders from the National Heart, Lung, and Blood Institute with expertise in various aspects of precision medicine to review the current status of biomarker tests in lung diseases. Experts summarized existing biomarker tests that are available for lung cancer, pulmonary arterial hypertension, idiopathic pulmonary fibrosis, asthma, chronic obstructive pulmonary disease, sepsis, acute respiratory distress syndrome, cystic fibrosis, and other rare lung diseases. The group identified knowledge gaps that future research studies can address to efficiently translate biomarker tests into clinical practice, assess their cost-effectiveness, and ensure they apply to diverse, real-life populations. RESULTS We found that the status of biomarker tests in lung diseases is highly variable depending on the disease. Nevertheless, biomarker tests in lung diseases show great promise in improving clinical care. To efficiently translate biomarkers into tests used widely in clinical practice, researchers need to address specific clinical unmet needs, secure support for biomarker discovery efforts, conduct analytical and clinical validation studies, ensure tests have clinical utility, and facilitate appropriate adoption into routine clinical practice. CONCLUSIONS Although progress has been made toward implementation of precision medicine for lung diseases in clinical practice in certain settings, additional studies focused on addressing specific unmet clinical needs are required to evaluate the clinical utility of biomarkers; ensure their generalizability to diverse, real-life populations; and determine their cost-effectiveness.
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80
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Lee JU, Son JH, Shim EY, Cheong HS, Shin SW, Shin HD, Baek AR, Ryu S, Park CS, Chang HS, Park JS. Global DNA Methylation Pattern of Fibroblasts in Idiopathic Pulmonary Fibrosis. DNA Cell Biol 2019; 38:905-914. [DOI: 10.1089/dna.2018.4557] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Jong-Uk Lee
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Ji-Hye Son
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Eun-Young Shim
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Hyun Sub Cheong
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Republic of Korea
| | - Seung-Woo Shin
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Hyoung Doo Shin
- Department of Genetic Epidemiology, SNP Genetics, Inc., Sogang University, Seoul, Republic of Korea
- Department of Life Science, Sogang University, Seoul, Republic of Korea
| | - Ae Rin Baek
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Seongho Ryu
- Soonchunhyang Institute of Med-Bioscience (SIMS), Soonchunhyang University, Cheonan-Si, Republic of Korea
| | - Choon-Sik Park
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science Major, Soonchunhyang University, Bucheon, Republic of Korea
| | - Jong-Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
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81
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Common Pathogenic Mechanisms Between Idiopathic Pulmonary Fibrosis and Lung Cancer. Chest 2019; 156:383-391. [DOI: 10.1016/j.chest.2019.04.114] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/14/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022] Open
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82
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Hata A, Nakajima T, Matsusaka K, Fukuyo M, Morimoto J, Yamamoto T, Sakairi Y, Rahmutulla B, Ota S, Wada H, Suzuki H, Matsubara H, Yoshino I, Kaneda A. A low DNA methylation epigenotype in lung squamous cell carcinoma and its association with idiopathic pulmonary fibrosis and poorer prognosis. Int J Cancer 2019; 146:388-399. [PMID: 31241180 DOI: 10.1002/ijc.32532] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/09/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022]
Abstract
Patients with idiopathic pulmonary fibrosis (IPF) have higher risk of developing lung cancer, for example, squamous cell carcinoma (SCC), and show poor prognosis, while the molecular basis has not been fully investigated. Here we conducted DNA methylome analysis of lung SCC using 20 SCC samples with/without IPF, and noncancerous lung tissue samples from smokers/nonsmokers, using Infinium HumanMethylation 450K array. SCC was clustered into low- and high-methylation epigenotypes by hierarchical clustering analysis. Genes hypermethylated in SCC significantly included genes targeted by polycomb repressive complex in embryonic stem cells, and genes associated with Gene Ontology terms, for example, "transcription" and "cell adhesion," while genes hypermethylated specifically in high-methylation subgroup significantly included genes associated with "negative regulation of growth." Low-methylation subgroup significantly correlated with IPF (78%, vs. 17% in high-methylation subgroup, p = 0.04), and the correlation was validated by additional Infinium analysis of SCC samples (n = 44 in total), and data from The Cancer Genome Atlas (n = 390). The correlation between low-methylation subgroup and IPF was further validated by quantitative methylation analysis of marker genes commonly hypermethylated in SCC (HOXA2, HOXA9 and PCDHGB6), and markers specifically hypermethylated in high-methylation subgroup (DLEC1, CFTR, MT1M, CRIP3 and ALDH7A1) in 77 SCC cases using pyrosequencing (p = 0.003). Furthermore, low-methylation epigenotype significantly correlated with poorer prognosis among all SCC patients, or among patients without IPF. Multivariate analysis showed that low-methylation epigenotype is an independent predictor of poor prognosis. These may suggest that lung SCC could be stratified into molecular subtypes with distinct prognosis, and low-methylation lung SCC that significantly correlates with IPF shows unfavorable outcome.
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Affiliation(s)
- Atsushi Hata
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takahiro Nakajima
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Keisuke Matsusaka
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.,Department of Genome Research and Development, Kazusa DNA Research Institute, Chiba, Japan
| | - Junichi Morimoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Takayoshi Yamamoto
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yuichi Sakairi
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Ota
- Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Hironobu Wada
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hidemi Suzuki
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Yoshino
- Department of General Thoracic Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
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83
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Chung A, English J, Volkmann ER. Interstitial Lung Disease in Systemic Sclerosis: Lessons Learned from Idiopathic Pulmonary Fibrosis. CURRENT TREATMENT OPTIONS IN RHEUMATOLOGY 2019. [DOI: 10.1007/s40674-019-00121-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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84
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Hao Y, Li D, Xu Y, Ouyang J, Wang Y, Zhang Y, Li B, Xie L, Qin G. Investigation of lipid metabolism dysregulation and the effects on immune microenvironments in pan-cancer using multiple omics data. BMC Bioinformatics 2019; 20:195. [PMID: 31074374 PMCID: PMC6509864 DOI: 10.1186/s12859-019-2734-4] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Lipid metabolism reprogramming is a hallmark for tumor which contributes to tumorigenesis and progression, but the commonality and difference of lipid metabolism among pan-cancer is not fully investigated. Increasing evidences suggest that the alterations in tumor metabolism, including metabolite abundance and accumulation of metabolic products, lead to local immunosuppression in the tumor microenvironment. An integrated analysis of lipid metabolism in cancers from different tissues using multiple omics data may provide novel insight into the understanding of tumorigenesis and progression. Results Through systematic analysis of the multiple omics data from TCGA, we found that the most-widely altered lipid metabolism pathways in pan-cancer are fatty acid metabolism, arachidonic acid metabolism, cholesterol metabolism and PPAR signaling. Gene expression profiles of fatty acid metabolism show commonalities across pan-cancer, while the alteration in cholesterol metabolism and arachidonic acid metabolism differ with tissue origin, suggesting tissue specific lipid metabolism features in different tumor types. An integrated analysis of gene expression, DNA methylation and mutations revealed factors that regulate gene expression, including the differentially methylated sites and mutations of the lipid genes, as well as mutation and differential expression of the up-stream transcription factors for the lipid metabolism pathways. Correlation analysis of the proportion of immune cells in the tumor microenvironment and the expression of lipid metabolism genes revealed immune-related differentially expressed lipid metabolic genes, indicating the potential crosstalk between lipid metabolism and immune response. Genes related to lipid metabolism and immune response that are associated with poor prognosis were discovered including HMGCS2, GPX2 and CD36, which may provide clues for tumor biomarkers or therapeutic targets. Conclusions Our study provides an integrated analysis of lipid metabolism in pan-cancer, highlights the perturbation of key metabolism processes in tumorigenesis and clarificates the regulation mechanism of abnormal lipid metabolism and effects of lipid metabolism on tumor immune microenvironment. This study also provides new clues for biomarkers or therapeutic targets of lipid metabolism in tumors. Electronic supplementary material The online version of this article (10.1186/s12859-019-2734-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yang Hao
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Daixi Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.
| | - Yong Xu
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Jian Ouyang
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Yongkun Wang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Yuqi Zhang
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China.,Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China
| | - Baoguo Li
- School of Medical Instrument and Food Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China.
| | - Guangrong Qin
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, 201203, China. .,Institute for Systems Biology, Seattle, WA, 98109, USA.
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85
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Zhou J, Yi Z, Fu Q. Dynamic decreased expression and hypermethylation of secreted frizzled-related protein 1 and 4 over the course of pulmonary fibrosis in mice. Life Sci 2019; 218:241-252. [PMID: 30586565 DOI: 10.1016/j.lfs.2018.12.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/18/2018] [Accepted: 12/22/2018] [Indexed: 01/08/2023]
Abstract
Aberrantly activated Wnt signaling pathway and dysregulation of extracellular antagonists of Wnt signaling have been revealed in pulmonary fibrosis. In this study we evaluated the expression of secreted frizzled-related proteins (SFRPs) and their aberrant promoter methylation to investigate the involvement of epigenetic regulation in pulmonary fibrosis. The pulmonary fibrosis induced by intratracheal injection of bleomycin (BLM) into mice was adopted. The transcription and relative protein expression of SFRPs were detected at Day 7 (D7), D14, and D21. DNA methylation analysis was performed by methylation-specific polymerase chain reaction (MSP). A DNA methyltransferase (DNMT) inhibitor (5-aza-2'-deoxycytidine; 5-aza) was used for demethylation and the relative β-catenin expression levels were measured to assess overactivity of the canonical Wnt signaling pathway. The transcription and protein expression of SFRP1 significantly decreased at D14 and D21, whereas the transcription and protein expression of SFRP4 significantly decreased at D7 and stayed downregulated until D21. The significantly hypermethylated promoters of SFRP1 and SFRP4 resulted in impaired transcription and decreased expression during pulmonary fibrosis in mice. Besides, reactivation of SFRP1 and SFRP4 by 5-aza reduced β-catenin mRNA and protein expression in vivo and in vitro. Animal experiments confirmed that 5-aza could significantly alleviate bleomycin-induced pulmonary fibrosis in mice. Thus, changes of promoter hypermethylation might downregulate SFRP1 and SFRP4 at different stages of pulmonary fibrosis, and the finding supports the usefulness of DNMT inhibitors, which might effectively reverse activation of β-catenin and reduce pulmonary fibrosis in mice. These data provide a possible new direction in the research on pulmonary fibrosis treatments.
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Affiliation(s)
- Junfei Zhou
- Department of Rheumatology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, PR China
| | - Zheng Yi
- Department of Rheumatology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, PR China.
| | - Qiang Fu
- Department of Rheumatology, The First Affiliated Hospital of University of South China, HengYang 421001, PR China
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86
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Selman M, Martinez FJ, Pardo A. Why Does an Aging Smoker’s Lung Develop Idiopathic Pulmonary Fibrosis and Not Chronic Obstructive Pulmonary Disease? Am J Respir Crit Care Med 2019; 199:279-285. [DOI: 10.1164/rccm.201806-1166pp] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Affiliation(s)
- Moisés Selman
- Instituto Nacional de Enfermedades Respiratorias, Ismael Cosío Villegas, Mexico City, Mexico
| | - Fernando J. Martinez
- Weill Cornell Medicine, New York-Presbyterian Hospital/Weill Cornell Medical Center, New York, New York
- Deputy Editor, AJRCCM; and
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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87
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Affiliation(s)
- Richard K Albert
- From the Departments of Medicine (R.K.A., D.A.S.) and Microbiology and Immunology (D.A.S.), University of Colorado School of Medicine, Aurora
| | - David A Schwartz
- From the Departments of Medicine (R.K.A., D.A.S.) and Microbiology and Immunology (D.A.S.), University of Colorado School of Medicine, Aurora
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88
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Evolving Genomics of Pulmonary Fibrosis. Respir Med 2019. [DOI: 10.1007/978-3-319-99975-3_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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89
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Saito A, Horie M, Micke P, Nagase T. The Role of TGF-β Signaling in Lung Cancer Associated with Idiopathic Pulmonary Fibrosis. Int J Mol Sci 2018; 19:ijms19113611. [PMID: 30445777 PMCID: PMC6275044 DOI: 10.3390/ijms19113611] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/12/2018] [Accepted: 11/14/2018] [Indexed: 12/14/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease of unknown etiology and dismal prognosis. IPF patients are known to have an increased risk of lung cancer and careful decision-making is required for the treatment of lung cancer associated with IPF. Transforming growth factor (TGF)-β signaling plays a central role in tissue fibrosis and tumorigenesis. TGF-β-mediated pathological changes that occur in IPF lung tissue may promote the process of field cancerization and provide the microenvironment favorable to cancer initiation and progression. This review summarizes the current knowledge related to IPF pathogenesis and explores the molecular mechanisms that underlie the occurrence of lung cancer in the background of IPF, with an emphasis on the multifaceted effects of TGF-β signaling.
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Affiliation(s)
- Akira Saito
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Division for Health Service Promotion, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| | - Masafumi Horie
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
- Hastings Center for Pulmonary Research, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185 Uppsala, Sweden.
| | - Takahide Nagase
- Department of Respiratory Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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90
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Huang LH, Kuo HC, Pan CT, Lin YS, Huang YH, Li SC. Multiomics analyses identified epigenetic modulation of the S100A gene family in Kawasaki disease and their significant involvement in neutrophil transendothelial migration. Clin Epigenetics 2018; 10:135. [PMID: 30382880 PMCID: PMC6211403 DOI: 10.1186/s13148-018-0557-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/02/2018] [Indexed: 02/08/2023] Open
Abstract
Background Kawasaki disease (KD) is a prevalent pediatric disease worldwide and can cause coronary artery aneurysm as a severe complication. Typically, DNA methylation is thought to repress the expression of nearby genes. However, the cases in which DNA methylation promotes gene expression have been reported. In addition, globally, to what extent DNA methylation affects gene expression and how it contributes to the pathogenesis of KD are not yet well understood. Methods To address these important biological questions, we enrolled subjects, collected DNA and RNA samples from the subjects’ total white blood cells, and performed DNA methylation (M450K) and gene expression (HTA 2.0) microarray assays. Results By analyzing the variation ratios of CpG beta values (methylation percentage) and gene expression intensities, we first concluded that the CpG markers close (− 1500 bp to + 500 bp) to the transcription start sites had higher variation ratios, reflecting significant regulation capacities. Next, we observed that, globally speaking, gene expression was modestly negatively correlated (correlation rho ≈ − 0.2) with the DNA methylation status of both upstream and downstream CpG markers in the promoter region. Third, we found that specific CpG markers were hypo-methylated in disease samples compared with healthy samples and hyper-methylated in convalescent samples compared with disease samples, promoting and repressing S100A genes’ expressions, respectively. Finally, using an in vitro cell model, we demonstrated that S100A family proteins enhanced leukocyte transendothelial migration in KD. Conclusions This is the first study to integrate genome-wide DNA methylation with gene expression assays in KD and showed that the S100A family plays important roles in the pathogenesis of KD. Electronic supplementary material The online version of this article (10.1186/s13148-018-0557-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lien-Hung Huang
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, 12th Floor, Children's Hospital, No.123, Dapi Rd, Niaosong District, Kaohsiung, 83301, Taiwan
| | - Ho-Chang Kuo
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Cheng-Tsung Pan
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan
| | - Yeong-Shin Lin
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, Taiwan
| | - Ying-Hsien Huang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Kawasaki Disease Center, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital, 12th Floor, Children's Hospital, No.123, Dapi Rd, Niaosong District, Kaohsiung, 83301, Taiwan.
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91
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Sauler M, Lamontagne M, Finnemore E, Herazo-Maya JD, Tedrow J, Zhang X, Morneau JE, Sciurba F, Timens W, Paré PD, Lee PJ, Kaminski N, Bossé Y, Gomez JL. The DNA repair transcriptome in severe COPD. Eur Respir J 2018; 52:1701994. [PMID: 30190272 PMCID: PMC6422831 DOI: 10.1183/13993003.01994-2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 07/25/2018] [Indexed: 02/05/2023]
Abstract
Inadequate DNA repair is implicated in the pathogenesis of chronic obstructive pulmonary disease (COPD). However, the mechanisms that underlie inadequate DNA repair in COPD are poorly understood. We applied an integrative genomic approach to identify DNA repair genes and pathways associated with COPD severity.We measured the transcriptomic changes of 419 genes involved in DNA repair and DNA damage tolerance that occur with severe COPD in three independent cohorts (n=1129). Differentially expressed genes were confirmed with RNA sequencing and used for patient clustering. Clinical and genome-wide transcriptomic differences were assessed following cluster identification. We complemented this analysis by performing gene set enrichment analysis, Z-score and weighted gene correlation network analysis to identify transcriptomic patterns of DNA repair pathways associated with clinical measurements of COPD severity.We found 15 genes involved in DNA repair and DNA damage tolerance to be differentially expressed in severe COPD. K-means clustering of COPD cases based on this 15-gene signature identified three patient clusters with significant differences in clinical characteristics and global transcriptomic profiles. Increasing COPD severity was associated with downregulation of the nucleotide excision repair pathway.Systematic analysis of the lung tissue transcriptome of individuals with severe COPD identified DNA repair responses associated with disease severity that may underlie COPD pathogenesis.
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Affiliation(s)
- Maor Sauler
- Dept of Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Maxime Lamontagne
- Centre de Recherche Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec, QC, Canada
| | - Eric Finnemore
- Dept of Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - John Tedrow
- Dept of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Xuchen Zhang
- Dept of Pathology, Yale School of Medicine, New Haven, CT, USA
| | | | - Frank Sciurba
- Dept of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wim Timens
- Dept of Pathology and Medical Biology, University Medical Center Groningen, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Peter D. Paré
- The University of British Columbia Centre for Heart Lung Innovation, St. Paul’s Hospital, Vancouver, BC, Canada
| | - Patty J. Lee
- Dept of Medicine, Yale School of Medicine, New Haven, CT, USA
| | | | - Yohan Bossé
- Centre de Recherche Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec, QC, Canada
- Dept of Molecular Medicine, Laval University, Quebec, QC, Canada
| | - Jose L. Gomez
- Dept of Medicine, Yale School of Medicine, New Haven, CT, USA
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92
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Li R, Wang Y, Song X, Sun W, Zhang J, Liu Y, Li H, Meng C, Zhang J, Zheng Q, Lv C. Potential regulatory role of circular RNA in idiopathic pulmonary fibrosis. Int J Mol Med 2018; 42:3256-3268. [PMID: 30272257 PMCID: PMC6202105 DOI: 10.3892/ijmm.2018.3892] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 08/02/2018] [Indexed: 12/16/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive type of interstitial pneumonia with unknown causes, poor prognosis and no effective therapy available. Circular RNAs (circRNAs), which serve as potential therapeutic targets and diagnostic biomarkers for certain diseases, represent a recent hotspot in the field of RNA research. In the present study, a total of 67 significantly dysregulated circRNAs were identified in the plasma of IPF patients by using a circRNA microarray. Among these circRNAs, 38 were upregulated, whereas 29 were downregulated. Further validation of the results by polymerase chain reaction analysis indicated that Homo sapiens (hsa)_circRNA_100906, hsa_circRNA_102100 and hsa_circRNA_102348 were significantly upregulated, whereas hsa_circRNA_101225, hsa_circRNA_104780 and hsa_circRNA_101242 were downregulated in plasma samples of IPF patients compared with those in samples from healthy controls. The majority of differentially expressed circRNAs were generated from exonic regions. The host genes of the differentially expressed circRNAs were involved in the regulation of the cell cycle, adherens junctions and RNA transport. The competing endogenous RNA (ceRNA) network of the circRNAs/micro(mi)RNAs/mRNAs indicated that circRNA-protected mRNA participated in transforming growth factor-β1, hypoxia-inducible factor-1, Wnt, Janus kinase, Rho-associated protein kinase, vascular endothelial growth factor, mitogen-activated protein kinase, Hedgehog and nuclear factor κB signalling pathways or functioned as biomarkers for pulmonary fibrosis. Furthermore, luciferase reporter assays confirmed that hsa_circRNA_100906 and hsa_circRNA_102348 directly interact with miR-324-5p and miR-630, respectively, which were downregulated in IPF patients. The present study provided a novel avenue for exploring the underlying molecular mechanisms of IPF disease.
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Affiliation(s)
- Rongrong Li
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
| | - Youlei Wang
- School of Special Education, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Xiaodong Song
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Wenjing Sun
- School of Life Sciences, Ludong University, Yantai, Shandong 264025, P.R. China
| | - Jinjin Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Yuxia Liu
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
| | - Hongbo Li
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
| | - Chao Meng
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Jie Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Qingyin Zheng
- School of Special Education, Binzhou Medical University, Yantai, Shandong 264003, P.R. China
| | - Changjun Lv
- Department of Respiratory Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, Shandong 256602, P.R. China
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93
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Song X, Xu P, Meng C, Song C, Blackwell TS, Li R, Li H, Zhang J, Lv C. lncITPF Promotes Pulmonary Fibrosis by Targeting hnRNP-L Depending on Its Host Gene ITGBL1. Mol Ther 2018; 27:380-393. [PMID: 30528088 DOI: 10.1016/j.ymthe.2018.08.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 08/26/2018] [Accepted: 08/31/2018] [Indexed: 01/27/2023] Open
Abstract
The role of long non-coding RNA (lncRNA) in idiopathic pulmonary fibrosis (IPF) is poorly understood. We found a novel lncRNA-ITPF that was upregulated in IPF. Bioinformatics and in vitro translation verified that lncITPF is an actual lncRNA, and its conservation is in evolution. Northern blot and rapid amplification of complementary DNA ends were used to analyze the full-length sequence of lncITPF. RNA fluorescence in situ hybridization and nucleocytoplasmic separation demonstrated that lncITPF was mainly located in the nucleus. RNA sequencing, chromatin immunoprecipitation (ChIP)-qPCR, CRISPR-Cas9 technology, and promoter activity analysis showed that the fibrotic function of lncITPF depends on its host gene integrin β-like 1 (ITGBL1), but they did not share the same promoter and were not co-transcribed. Luciferase activity, pathway inhibitors, and ChIP-qPCR showed that smad2/3 binds to the lncITPF promoter, and TGF-β1-smad2/3 was the upstream inducer of the fibrotic pathway. Furthermore, RNA-protein pull-down, liquid chromatography-mass spectrometry (LC-MS), and protein-RNA immunoprecipitation showed that lncITPF regulated H3 and H4 histone acetylation in the ITGBL1 promoter by targeting heterogeneous nuclear ribonucleoprotein L. Finally, sh-lncITPF was used to evaluate the therapeutic effect of lncITPF. Clinical analysis showed that lncITPF is associated with the clinicopathological features of IPF patients. Our findings provide a therapeutic target or diagnostic biomarker for IPF.
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Affiliation(s)
- Xiaodong Song
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China
| | - Pan Xu
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Chao Meng
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Chenguang Song
- Department of Respiratory Medicine, Zouping Chinese Medicine Hospital, Binzhou 256602, China
| | | | - Rongrong Li
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Hongbo Li
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China
| | - Jinjin Zhang
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China.
| | - Changjun Lv
- Department of Respiratory Medicine, Affiliated Hospital to Binzhou Medical University, Binzhou 256602, China; Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai 264003, China.
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94
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Dynamic expression of HOPX in alveolar epithelial cells reflects injury and repair during the progression of pulmonary fibrosis. Sci Rep 2018; 8:12983. [PMID: 30154568 PMCID: PMC6113210 DOI: 10.1038/s41598-018-31214-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/14/2018] [Indexed: 01/29/2023] Open
Abstract
Mechanisms of injury and repair in alveolar epithelial cells (AECs) are critically involved in the progression of various lung diseases including idiopathic pulmonary fibrosis (IPF). Homeobox only protein x (HOPX) contributes to the formation of distal lung during development. In adult lung, alveolar epithelial type (AT) I cells express HOPX and lineage-labeled Hopx+ cells give rise to both ATI and ATII cells after pneumonectomy. However, the cell function of HOPX-expressing cells in adult fibrotic lung diseases has not been investigated. In this study, we have established a flow cytometry-based method to evaluate HOPX-expressing cells in the lung. HOPX expression in cultured ATII cells increased over culture time, which was accompanied by a decrease of proSP-C, an ATII marker. Moreover, HOPX expression was increased in AECs from bleomycin-instilled mouse lungs in vivo. Small interfering RNA-based knockdown of Hopx resulted in suppressing ATII-ATI trans-differentiation and activating cellular proliferation in vitro. In IPF lungs, HOPX expression was decreased in whole lungs and significantly correlated to a decline in lung function and progression of IPF. In conclusion, HOPX is upregulated during early alveolar injury and repair process in the lung. Decreased HOPX expression might contribute to failed regenerative processes in end-stage IPF lungs.
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95
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Ma KF, Zhang QX, Cheng TR, Yan XL, Pan HT, Wang J. Substantial Epigenetic Variation Causing Flower Color Chimerism in the Ornamental Tree Prunus mume Revealed by Single Base Resolution Methylome Detection and Transcriptome Sequencing. Int J Mol Sci 2018; 19:E2315. [PMID: 30087265 PMCID: PMC6121637 DOI: 10.3390/ijms19082315] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/29/2018] [Accepted: 08/02/2018] [Indexed: 01/03/2023] Open
Abstract
Epigenetic changes caused by methylcytosine modification participate in gene regulation and transposable element (TE) repression, resulting in phenotypic variation. Although the effects of DNA methylation and TE repression on flower, fruit, seed coat, and leaf pigmentation have been investigated, little is known about the relationship between methylation and flower color chimerism. In this study, we used a comparative methylomic⁻transcriptomic approach to explore the molecular mechanism responsible for chimeric flowers in Prunus mume "Danban Tiaozhi". High-performance liquid chromatography-electrospray ionization mass spectrometry revealed that the variation in white (WT) and red (RT) petal tissues in this species is directly due to the accumulation of anthocyanins, i.e., cyanidin 3,5-O-diglucoside, cyanidin 3-O-glucoside, and peonidin 3-O-glucoside. We next mapped the first-ever generated methylomes of P. mume, and found that 11.29⁻14.83% of the genomic cytosine sites were methylated. We also determined that gene expression was negatively correlated with methylcytosine level in general, and uncovered significant epigenetic variation between WT and RT. Furthermore, we detected differentially methylated regions (DMRs) and DMR-related genes between WT and RT, and concluded that many of these genes, including differentially expressed genes (DEGs) and transcription factor genes, are critical participants in the anthocyanin regulatory pathway. Importantly, some of the associated DEGs harbored TE insertions that were also modified by methylcytosine. The above evidence suggest that flower color chimerism in P. mume is induced by the DNA methylation of critical genes and TEs.
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Affiliation(s)
- Kai-Feng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Qi-Xiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| | - Tang-Ren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Xiao-Lan Yan
- Mei Research Center of China, Wuhan 430074, China.
| | - Hui-Tang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
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96
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Cheng J, Wei D, Ji Y, Chen L, Yang L, Li G, Wu L, Hou T, Xie L, Ding G, Li H, Li Y. Integrative analysis of DNA methylation and gene expression reveals hepatocellular carcinoma-specific diagnostic biomarkers. Genome Med 2018; 10:42. [PMID: 29848370 PMCID: PMC5977535 DOI: 10.1186/s13073-018-0548-z] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/08/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is the one of the most common cancers and lethal diseases in the world. DNA methylation alteration is frequently observed in HCC and may play important roles in carcinogenesis and diagnosis. METHODS Using the TCGA HCC dataset, we classified HCC patients into different methylation subtypes, identified differentially methylated and expressed genes, and analyzed cis- and trans-regulation of DNA methylation and gene expression. To find potential diagnostic biomarkers for HCC, we screened HCC-specific CpGs by comparing the methylation profiles of 375 samples from HCC patients, 50 normal liver samples, 184 normal blood samples, and 3780 samples from patients with other cancers. A logistic regression model was constructed to distinguish HCC patients from normal controls. Model performance was evaluated using three independent datasets (including 327 HCC samples and 122 normal samples) and ten newly collected biopsies. RESULTS We identified a group of patients with a CpG island methylator phenotype (CIMP) and found that the overall survival of CIMP patients was poorer than that of non-CIMP patients. Our analyses showed that the cis-regulation of DNA methylation and gene expression was dominated by the negative correlation, while the trans-regulation was more complex. More importantly, we identified six HCC-specific hypermethylated sites as potential diagnostic biomarkers. The combination of six sites achieved ~ 92% sensitivity in predicting HCC, ~ 98% specificity in excluding normal livers, and ~ 98% specificity in excluding other cancers. Compared with previously published methylation markers, our markers are the only ones that can distinguish HCC from other cancers. CONCLUSIONS Overall, our study systematically describes the DNA methylation characteristics of HCC and provides promising biomarkers for the diagnosis of HCC.
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Affiliation(s)
- Jinming Cheng
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Dongkai Wei
- Basepair biotechnology Co. LTD, Suzhou, China
| | - Yuan Ji
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lingli Chen
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Liguang Yang
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Guang Li
- Basepair biotechnology Co. LTD, Suzhou, China
| | - Leilei Wu
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ting Hou
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Guohui Ding
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Hong Li
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Yixue Li
- Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
- Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China.
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97
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Vukmirovic M, Kaminski N. Impact of Transcriptomics on Our Understanding of Pulmonary Fibrosis. Front Med (Lausanne) 2018; 5:87. [PMID: 29670881 PMCID: PMC5894436 DOI: 10.3389/fmed.2018.00087] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 03/20/2018] [Indexed: 12/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a lethal fibrotic lung disease characterized by aberrant remodeling of the lung parenchyma with extensive changes to the phenotypes of all lung resident cells. The introduction of transcriptomics, genome scale profiling of thousands of RNA transcripts, caused a significant inversion in IPF research. Instead of generating hypotheses based on animal models of disease, or biological plausibility, with limited validation in humans, investigators were able to generate hypotheses based on unbiased molecular analysis of human samples and then use animal models of disease to test their hypotheses. In this review, we describe the insights made from transcriptomic analysis of human IPF samples. We describe how transcriptomic studies led to identification of novel genes and pathways involved in the human IPF lung such as: matrix metalloproteinases, WNT pathway, epithelial genes, role of microRNAs among others, as well as conceptual insights such as the involvement of developmental pathways and deep shifts in epithelial and fibroblast phenotypes. The impact of lung and transcriptomic studies on disease classification, endotype discovery, and reproducible biomarkers is also described in detail. Despite these impressive achievements, the impact of transcriptomic studies has been limited because they analyzed bulk tissue and did not address the cellular and spatial heterogeneity of the IPF lung. We discuss new emerging technologies and applications, such as single-cell RNAseq and microenvironment analysis that may address cellular and spatial heterogeneity. We end by making the point that most current tissue collections and resources are not amenable to analysis using the novel technologies. To take advantage of the new opportunities, we need new efforts of sample collections, this time focused on access to all the microenvironments and cells in the IPF lung.
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Affiliation(s)
- Milica Vukmirovic
- Section of Pulmonary, Critical Care and Sleep Medicine, Precision Pulmonary Medicine Center (P2MED), Yale University School of Medicine, New Haven, CT, United States
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Precision Pulmonary Medicine Center (P2MED), Yale University School of Medicine, New Haven, CT, United States
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98
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Fibrosis: Lessons from OMICS analyses of the human lung. Matrix Biol 2018; 68-69:422-434. [PMID: 29567123 DOI: 10.1016/j.matbio.2018.03.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/16/2018] [Accepted: 03/16/2018] [Indexed: 12/30/2022]
Abstract
In recent decades there has been a significant shift in our understanding of idiopathic pulmonary fibrosis (IPF), a progressive and lethal disorder. While initially much of the mechanistic understanding was derived from hypotheses generated from animal models of disease, in recent decades new insights derived from humans with IPF have taken precedence. This is mainly because of the establishment of large collections of IPF lung tissues and patient cohorts, and the emergence of high throughput profiling technologies collectively termed 'omics' technologies based on their shared suffix. In this review we describe impacts of 'omics' analyses of human IPF samples on our understanding of the disease. In particular, we discuss the results of genomics and transcriptomics studies, as well as proteomics, epigenomics and metabolomics. We then describe how these findings can be integrated in a modified paradigm of human idiopathic pulmonary fibrosis, that introduces the 'hallmarks of aging' as a central theme in the IPF lung. This allows resolution of all the disparate cellular and molecular features in IPF, from the central role of epithelial cells, through the dramatic phenotypic alterations observed in fibroblasts and the numerous aberrations that inflammatory cells exhibit. We end with reiterating a call for renewed efforts to collect and analyze carefully characterized human tissues, in ways that would facilitate implementation of novel technologies for high resolution single cell omics profiling.
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99
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An American Thoracic Society/National Heart, Lung, and Blood Institute Workshop Report: Addressing Respiratory Health Equality in the United States. Ann Am Thorac Soc 2018; 14:814-826. [PMID: 28459618 DOI: 10.1513/annalsats.201702-167ws] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Health disparities related to race, ethnicity, and socioeconomic status persist and are commonly encountered by practitioners of pediatric and adult pulmonary, critical care, and sleep medicine in the United States. To address such disparities and thus progress toward equality in respiratory health, the American Thoracic Society and the National Heart, Lung, and Blood Institute convened a workshop in May of 2015. The workshop participants addressed health disparities by focusing on six topics, each of which concluded with a panel discussion that proposed recommendations for research on racial, ethnic, and socioeconomic disparities in pulmonary, critical care, and sleep medicine. Such recommendations address best practices to advance research on respiratory health disparities (e.g., characterize broad ethnic groups into subgroups known to differ with regard to a disease of interest), risk factors for respiratory health disparities (e.g., study the impact of new tobacco or nicotine products on respiratory diseases in minority populations), addressing equity in access to healthcare and quality of care (e.g., conduct longitudinal studies of the impact of the Affordable Care Act on respiratory and sleep disorders), the impact of personalized medicine on disparities research (e.g., implement large studies of pharmacogenetics in minority populations), improving design and methodology for research studies in respiratory health disparities (e.g., use study designs that reduce participants' burden and foster trust by engaging participants as decision-makers), and achieving equity in the pulmonary, critical care, and sleep medicine workforce (e.g., develop and maintain robust mentoring programs for junior faculty, including local and external mentors). Addressing these research needs should advance efforts to reduce, and potentially eliminate, respiratory, sleep, and critical care disparities in the United States.
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100
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Abstract
Idiopathic Pulmonary Fibrosis (IPF) is a devastating chronic, progressive and irreversible disease that remains refractory to current therapies. Matrix metalloproteinases (MMPs) and their inhibitors, tissue inhibitors of MMPs (TIMPs), have been implicated in the development of pulmonary fibrosis since decades. Coagulation signalling deregulation, which influences several key inflammatory and fibro-proliferative responses, is also essential in IPF pathogenesis, and a growing body of evidence indicates that Protease-Activated Receptors (PARs) inhibition in IPF may be promising for future evaluation. Therefore, proteases and anti-proteases aroused great biomedical interest over the past years, owing to the identification of their potential roles in lung fibrosis. During these last decades, numerous other proteases and anti-proteases have been studied in lung fibrosis, such as matriptase, Human airway trypsin-like protease (HAT), Hepatocyte growth factor activator (HGFA)/HGFA activator inhibitor (HAI) system, Plasminogen activator inhibitor (PAI)-1, Protease nexine (PN)-1, cathepsins, calpains, and cystatin C. Herein, we provide a general overview of the proteases and anti-proteases unbalance during lung fibrogenesis and explore potential therapeutics for IPF.
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