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Wang J, Li K, Hao D, Li X, Zhu Y, Yu H, Chen H. Pulmonary fibrosis: pathogenesis and therapeutic strategies. MedComm (Beijing) 2024; 5:e744. [PMID: 39314887 PMCID: PMC11417429 DOI: 10.1002/mco2.744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 08/31/2024] [Accepted: 09/02/2024] [Indexed: 09/25/2024] Open
Abstract
Pulmonary fibrosis (PF) is a chronic and progressive lung disease characterized by extensive alterations of cellular fate and function and excessive accumulation of extracellular matrix, leading to lung tissue scarring and impaired respiratory function. Although our understanding of its pathogenesis has increased, effective treatments remain scarce, and fibrotic progression is a major cause of mortality. Recent research has identified various etiological factors, including genetic predispositions, environmental exposures, and lifestyle factors, which contribute to the onset and progression of PF. Nonetheless, the precise mechanisms by which these factors interact to drive fibrosis are not yet fully elucidated. This review thoroughly examines the diverse etiological factors, cellular and molecular mechanisms, and key signaling pathways involved in PF, such as TGF-β, WNT/β-catenin, and PI3K/Akt/mTOR. It also discusses current therapeutic strategies, including antifibrotic agents like pirfenidone and nintedanib, and explores emerging treatments targeting fibrosis and cellular senescence. Emphasizing the need for omni-target approaches to overcome the limitations of current therapies, this review integrates recent findings to enhance our understanding of PF and contribute to the development of more effective prevention and management strategies, ultimately improving patient outcomes.
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Affiliation(s)
- Jianhai Wang
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese MedicineTianjin Institute of Respiratory DiseasesTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - Kuan Li
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - De Hao
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
| | - Xue Li
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - Yu Zhu
- Department of Clinical LaboratoryNankai University Affiliated Third Central HospitalTianjinChina
- Department of Clinical LaboratoryThe Third Central Hospital of TianjinTianjin Key Laboratory of Extracorporeal Life Support for Critical DiseasesArtificial Cell Engineering Technology Research Center of TianjinTianjin Institute of Hepatobiliary DiseaseTianjinChina
| | - Hongzhi Yu
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
| | - Huaiyong Chen
- Department of Respiratory MedicineHaihe HospitalTianjin UniversityTianjinChina
- Department of TuberculosisHaihe HospitalTianjin UniversityTianjinChina
- Key Research Laboratory for Infectious Disease Prevention for State Administration of Traditional Chinese MedicineTianjin Institute of Respiratory DiseasesTianjinChina
- Tianjin Key Laboratory of Lung Regenerative Medicine, Haihe HospitalTianjin UniversityTianjinChina
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2
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Baddour NA, Paulin LM, Gassett AJ, Woo H, Hoffman EA, Newell JD, Woodruff PG, Pirozzi CS, Barjaktarevic I, Barr RG, O’Neal W, Han MK, Martinez FJ, Peters SP, Hastie AT, Hansel NN, Ortega VE, Kaufman JD, Sack CS. Air Pollution Exposure and Interstitial Lung Features in SPIROMICS Participants with Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2024; 21:1251-1260. [PMID: 38568439 PMCID: PMC11376362 DOI: 10.1513/annalsats.202308-741oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 04/02/2024] [Indexed: 08/31/2024] Open
Abstract
Rationale: It is unknown whether air pollution is associated with radiographic features of interstitial lung disease in individuals with chronic obstructive pulmonary disease (COPD). Objectives: To determine whether air pollution increases the prevalence of interstitial lung abnormalities (ILA) or percent high-attenuation areas (HAA) on computed tomography (CT) in individuals with a heavy smoking history and COPD. Methods: We performed a cross-sectional study of SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study), focused on current or former smokers with COPD. Ten-year exposure to particulate matter ⩽2.5 μm in aerodynamic diameter (PM2.5), nitrogen oxides (NOx), nitrogen dioxide (NO2), and ozone before enrollment CT (completed between 2010 and 2015) were estimated with validated spatiotemporal models at residential addresses. We applied adjusted multivariable modified Poisson regression and linear regression to investigate associations between pollution exposure and relative risk (RR) of ILA or increased percent HAA (between -600 and -250 Hounsfield units), respectively. We assessed for effect modification by MUC5B-promoter polymorphism (variant allele carriers GT or TT vs. GG at rs3705950), smoking status, sex, and percent emphysema. Results: Among 1,272 participants with COPD assessed for HAA, 424 were current smokers, and 249 were carriers of the variant MUC5B allele. A total of 519 participants were assessed for ILA. We found no association between pollution exposure and ILA or HAA. Associations between pollutant exposures and risk of ILA were modified by the presence of MUC5B polymorphism (P value interaction term for NOx = 0.04 and PM2.5 = 0.05) and smoking status (P value interaction term for NOx = 0.05; NO2 = 0.01; and ozone = 0.05). With higher exposure to NOx and PM2.5, MUC5B variant carriers had an increased risk of ILA (RR per 26 ppb NOx, 2.41; 95% confidence interval [CI], 0.97-6.0; and RR per 4 μg ⋅ m-3 PM2.5, 1.43; 95% CI, 0.93-2.2, respectively). With higher exposure to NO2, former smokers had an increased risk of ILA (RR per 10 ppb, 1.64; 95% CI, 1.0-2.7). Conclusions: Exposure to ambient air pollution was not associated with interstitial features on CT in this population of heavy smokers with COPD. MUC5B modified the association between pollution and ILA, suggesting that gene-environment interactions may influence prevalence of interstitial lung features in COPD.
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Affiliation(s)
| | - Laura M. Paulin
- Department of Medicine, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire
| | | | - Han Woo
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Eric A. Hoffman
- Department of Radiology, University of Iowa, Iowa City, Iowa
| | - John D. Newell
- Department of Radiology, University of Washington, Seattle, Washington
- Department of Radiology, University of Iowa, Iowa City, Iowa
| | - Prescott G. Woodruff
- Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California
| | - Cheryl S. Pirozzi
- Division of Respiratory, Critical Care, and Occupational Pulmonary Medicine, Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Igor Barjaktarevic
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University Medical Center, New York, New York
| | - Wanda O’Neal
- Marsico Lung Institute, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Meilan K. Han
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College, Cornell University, New York, New York
| | - Stephen P. Peters
- Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina; and
| | - Annette T. Hastie
- Section of Pulmonary, Critical Care, Allergy and Immunologic Diseases, Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina; and
| | - Nadia N. Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Victor E. Ortega
- Division of Respiratory Diseases, Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Joel D. Kaufman
- Department of Medicine
- Department of Environmental and Occupational Health Sciences, and
| | - Coralynn S. Sack
- Department of Medicine
- Department of Environmental and Occupational Health Sciences, and
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3
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Adegunsoye A, Kropski JA, Behr J, Blackwell TS, Corte TJ, Cottin V, Glanville AR, Glassberg MK, Griese M, Hunninghake GM, Johannson KA, Keane MP, Kim JS, Kolb M, Maher TM, Oldham JM, Podolanczuk AJ, Rosas IO, Martinez FJ, Noth I, Schwartz DA. Genetics and Genomics of Pulmonary Fibrosis: Charting the Molecular Landscape and Shaping Precision Medicine. Am J Respir Crit Care Med 2024; 210:401-423. [PMID: 38573068 PMCID: PMC11351799 DOI: 10.1164/rccm.202401-0238so] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024] Open
Abstract
Recent genetic and genomic advancements have elucidated the complex etiology of idiopathic pulmonary fibrosis (IPF) and other progressive fibrotic interstitial lung diseases (ILDs), emphasizing the contribution of heritable factors. This state-of-the-art review synthesizes evidence on significant genetic contributors to pulmonary fibrosis (PF), including rare genetic variants and common SNPs. The MUC5B promoter variant is unusual, a common SNP that markedly elevates the risk of early and established PF. We address the utility of genetic variation in enhancing understanding of disease pathogenesis and clinical phenotypes, improving disease definitions, and informing prognosis and treatment response. Critical research gaps are highlighted, particularly the underrepresentation of non-European ancestries in PF genetic studies and the exploration of PF phenotypes beyond usual interstitial pneumonia/IPF. We discuss the role of telomere length, often critically short in PF, and its link to progression and mortality, underscoring the genetic complexity involving telomere biology genes (TERT, TERC) and others like SFTPC and MUC5B. In addition, we address the potential of gene-by-environment interactions to modulate disease manifestation, advocating for precision medicine in PF. Insights from gene expression profiling studies and multiomic analyses highlight the promise for understanding disease pathogenesis and offer new approaches to clinical care, therapeutic drug development, and biomarker discovery. Finally, we discuss the ethical, legal, and social implications of genomic research and therapies in PF, stressing the need for sound practices and informed clinical genetic discussions. Looking forward, we advocate for comprehensive genetic testing panels and polygenic risk scores to improve the management of PF and related ILDs across diverse populations.
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Affiliation(s)
- Ayodeji Adegunsoye
- Pulmonary/Critical Care, and
- Committee on Clinical Pharmacology and Pharmacogenomics, University of Chicago, Chicago, Illinois
| | - Jonathan A. Kropski
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Juergen Behr
- Department of Medicine V, University Hospital, Ludwig Maximilian University of Munich, Munich, Germany
- Comprehensive Pneumology Center Munich, member of the German Center for Lung Research (DZL), Munich, Germany
| | - Timothy S. Blackwell
- Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee
- Department of Veterans Affairs Medical Center, Nashville, Tennessee
| | - Tamera J. Corte
- Centre of Research Excellence in Pulmonary Fibrosis, Camperdown, New South Wales, Australia
- Department of Respiratory and Sleep Medicine, Royal Prince Alfred Hospital, Camperdown, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Vincent Cottin
- National Reference Center for Rare Pulmonary Diseases (OrphaLung), Louis Pradel Hospital, Hospices Civils de Lyon, ERN-LUNG (European Reference Network on Rare Respiratory Diseases), Lyon, France
- Claude Bernard University Lyon, Lyon, France
| | - Allan R. Glanville
- Lung Transplant Unit, St. Vincent’s Hospital Sydney, Sydney, New South Wales, Australia
| | - Marilyn K. Glassberg
- Department of Medicine, Loyola Chicago Stritch School of Medicine, Chicago, Illinois
| | - Matthias Griese
- Department of Pediatric Pneumology, Dr. von Hauner Children’s Hospital, Ludwig-Maximilians-University, German Center for Lung Research, Munich, Germany
| | - Gary M. Hunninghake
- Harvard Medical School, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - Michael P. Keane
- Department of Respiratory Medicine, St. Vincent’s University Hospital and School of Medicine, University College Dublin, Dublin, Ireland
| | - John S. Kim
- Department of Medicine, School of Medicine, and
| | - Martin Kolb
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Toby M. Maher
- Department of Medicine, Keck School of Medicine of University of Southern California, Los Angeles, California
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Justin M. Oldham
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | | | | | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medicine, New York, New York; and
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, University of Virginia, Charlottesville, Virginia
| | - David A. Schwartz
- Department of Medicine, School of Medicine, University of Colorado, Aurora, Colorado
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Gruenwald A, Neururer M, Eidenhammer S, Nerlich A, Popper H. The cGAS-STING pathway drives inflammation in Usual Interstitial Pneumonia, phagocytosis could prevent inflammation but is inhibited by the don't eat me signal CD47. Pathol Res Pract 2024; 260:155432. [PMID: 38944022 DOI: 10.1016/j.prp.2024.155432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 06/21/2024] [Accepted: 06/26/2024] [Indexed: 07/01/2024]
Abstract
BACKGROUND Usual Interstitial Pneumonia (UIP) a fibrosing pneumonia is associated with idiopathic pulmonary fibrosis, chronic autoimmune disease (AID), or hypersensitivity pneumonia. Oxygen radicals, due to tobacco smoke, can damage DNA and might upregulate PARP1. Cytosolic DNA from dying pneumocytes activate cytosolic GMP-AMP-synthase-stimulator of interferon genes (cGAS-STING) pathway and TREX1. Prolonged inflammation induces senescence, which might be inhibited by phagocytosis, eliminating nuclear debris. We aimed to evaluate activation of cGAS-STING-TREX1 pathway in UIP, and if phagocytosis and anti-phagocytosis might counteract inflammation. METHODS 44 cases of UIP with IPF or AID were studied for the expression of cGAS, pSTING, TREX1 and PARP1. LAMP1 and Rab7 expression served as phagocytosis markers. CD47 protecting phagocytosis and p16 to identify senescent cells were also studied. RESULTS Epithelial cells in remodeled areas and macrophages expressed cGAS-pSTING, TREX1; epithelia but not macrophages stained for PARP1. Myofibroblasts, endothelia, and bronchial/bronchiolar epithelial cells were all negative except early myofibroblastic foci expressing cGAS. Type II pneumocytes expressed cGAS and PARP1, but less pSTING. TREX1 although expressed was not activated. Macrophages and many regenerating epithelial cells expressed LAMP1 and Rab7. CD47, the 'don't-eat-me-signal', was expressed by macrophages and epithelial cells including senescence cells within the remodeled areas. CONCLUSIONS The cGAS-STING pathway is activated in macrophages and epithelial cells within remodeled areas. LikelyTREX1 because not activated cannot sufficiently degrade DNA fragments. PARP1 activation points to smoking-induced oxygen radical release, prolonging inflammation and leading to fibrosis. By expressing CD47 epithelial cells within remodeled areas protect themselves from being eliminated by phagocytosis.
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Affiliation(s)
- Alissa Gruenwald
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria
| | - Margarete Neururer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria
| | - Sylvia Eidenhammer
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria
| | - Andreas Nerlich
- Department of Pathology, Clinics München-Bogenhausen, Englschalkinger Straße 77, München 81925, Germany
| | - Helmut Popper
- Diagnostic and Research Institute of Pathology, Medical University of Graz, Austria.
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5
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Dalapati T, Wang L, Jones AG, Cardwell J, Konigsberg IR, Bossé Y, Sin DD, Timens W, Hao K, Yang I, Ko DC. Context-specific eQTLs reveal causal genes underlying shared genetic architecture of critically ill COVID-19 and idiopathic pulmonary fibrosis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.13.24310305. [PMID: 39040187 PMCID: PMC11261970 DOI: 10.1101/2024.07.13.24310305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Most genetic variants identified through genome-wide association studies (GWAS) are suspected to be regulatory in nature, but only a small fraction colocalize with expression quantitative trait loci (eQTLs, variants associated with expression of a gene). Therefore, it is hypothesized but largely untested that integration of disease GWAS with context-specific eQTLs will reveal the underlying genes driving disease associations. We used colocalization and transcriptomic analyses to identify shared genetic variants and likely causal genes associated with critically ill COVID-19 and idiopathic pulmonary fibrosis. We first identified five genome-wide significant variants associated with both diseases. Four of the variants did not demonstrate clear colocalization between GWAS and healthy lung eQTL signals. Instead, two of the four variants colocalized only in cell-type and disease-specific eQTL datasets. These analyses pointed to higher ATP11A expression from the C allele of rs12585036, in monocytes and in lung tissue from primarily smokers, which increased risk of IPF and decreased risk of critically ill COVID-19. We also found lower DPP9 expression (and higher methylation at a specific CpG) from the G allele of rs12610495, acting in fibroblasts and in IPF lungs, and increased risk of IPF and critically ill COVID-19. We further found differential expression of the identified causal genes in diseased lungs when compared to non-diseased lungs, specifically in epithelial and immune cell types. These findings highlight the power of integrating GWAS, context-specific eQTLs, and transcriptomics of diseased tissue to harness human genetic variation to identify causal genes and where they function during multiple diseases.
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Affiliation(s)
- Trisha Dalapati
- Medical Scientist Training Program, Duke University School of Medicine, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Angela G. Jones
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
| | - Jonathan Cardwell
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Iain R. Konigsberg
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec – Université Laval, Department of Molecular Medicine, Québec City, Canada
| | - Don D. Sin
- Center for Heart Lung Innovation, University of British Columbia and St. Paul’s Hospital, Vancouver, BC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Ivana Yang
- Department of Biomedical Informatics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC, USA
- Division of Infectious Diseases, Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Lead contact
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6
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Juge PA, Sparks JA, Gazal S, Ebstein E, Borie R, Debray MP, Kannengiesser C, McDermott GC, Cui J, Hayashi K, Doyle TJ, van Moorsel CHM, van der Vis JJ, Grutters JC, Knevel R, Heckert SL, Vasarmidi E, Antoniou KM, van der Helm van Mil AHM, Boileau C, Crestani B, Dieudé P. RPA3-UMAD1 rs12702634 and rheumatoid arthritis-associated interstitial lung disease in European ancestry. Rheumatol Adv Pract 2024; 8:rkae059. [PMID: 38854416 PMCID: PMC11157136 DOI: 10.1093/rap/rkae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 04/05/2024] [Indexed: 06/11/2024] Open
Abstract
Objective Recently, a genome-wide association study identified an association between RA-associated interstitial lung disease (ILD) and RPA3-UMAD1 rs12702634 in the Japanese population, especially for patients with a usual interstitial pneumonia (UIP) pattern. We aimed to replicate this association in a European population and test for interaction with MUC5B rs35705950. Methods In this genetic case-control association study, patients with RA and ILD and controls with RA and no ILD were included from France, the USA and the Netherlands. Only cases and controls from European genetic ancestries determined by principal components analysis were included in the analyses. RA was defined by the 1987 ACR or 2010 ACR/EULAR criteria and ILD by chest high-resolution CT scan, except in the control dataset from the Netherlands, where the absence of ILD was determined by chart review. Patients were genotyped for RPA3-UMAD1 rs12702634 and MUC5B rs35705950. Associations were tested using logistic regression adjusted for sex, age at RA onset, age at ILD onset or at certified absence of ILD, tobacco smoking status and country of origin. Results Among the 883 patients included, 322 were RA-ILD cases (36.5%). MUC5B rs35705950 was strongly associated with RA-ILD in all datasets {combined adjusted odds ratio [OR] 2.9 [95% CI 2.1, 3.9], P = 1.1 × 10-11. No association between RPA3-UMAD1 rs12702634 and RA-ILD was observed [combined OR 1.2 (95% CI 0.8, 1.6), P = 0.31. No interaction was found between RPA3-UMAD1 rs12702634 and MUC5B rs35705950 (P = 0.70). Conclusion Our findings did not support a contribution of RPA3-UMAD1 rs12702634 to the overall RA-ILD susceptibility in the European population.
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Affiliation(s)
- Pierre-Antoine Juge
- Université de Paris Cité, INSERM UMR 1152, Paris, France
- Service de Rhumatologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Steven Gazal
- Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Esther Ebstein
- Service de Rhumatologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Raphaël Borie
- Université de Paris Cité, INSERM UMR 1152, Paris, France
- Service de Pneumologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | | | - Caroline Kannengiesser
- Université de Paris Cité, INSERM UMR 1152, Paris, France
- Service de Génétique, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Gregory C McDermott
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Keigo Hayashi
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Tracy J Doyle
- Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care, Brigham and Women's Hospital, Boston, MA, USA
| | - Coline H M van Moorsel
- Interstitial Lung Disease Center of Excellence, Department of Pulmonology, St Antonius Hospital, Nieuwegein, The Netherlands
- Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Joanne J van der Vis
- Interstitial Lung Disease Center of Excellence, Department of Pulmonology, St Antonius Hospital, Nieuwegein, The Netherlands
- Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jan C Grutters
- Interstitial Lung Disease Center of Excellence, Department of Pulmonology, St Antonius Hospital, Nieuwegein, The Netherlands
- Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rachel Knevel
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
- Translational & Clinical Research Institute, Newcastle University, UK
| | - Sascha L Heckert
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eirini Vasarmidi
- Laboratory of Molecular and Cellular Pneumonology, Department of Respiratory Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Katerina M Antoniou
- Laboratory of Molecular and Cellular Pneumonology, Department of Respiratory Medicine, School of Medicine, University of Crete, Heraklion, Greece
| | - Annette H M van der Helm van Mil
- Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Rheumatology, Erasmus MC, Rotterdam, The Netherlands
| | - Catherine Boileau
- Service de Génétique, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Bruno Crestani
- Université de Paris Cité, INSERM UMR 1152, Paris, France
- Service de Pneumologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
| | - Philippe Dieudé
- Université de Paris Cité, INSERM UMR 1152, Paris, France
- Service de Rhumatologie, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France
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7
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Tomos I, Roussis I, Matthaiou AM, Dimakou K. Molecular and Genetic Biomarkers in Idiopathic Pulmonary Fibrosis: Where Are We Now? Biomedicines 2023; 11:2796. [PMID: 37893169 PMCID: PMC10604739 DOI: 10.3390/biomedicines11102796] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) represents a chronic progressive fibrotic interstitial lung disease of unknown cause with an ominous prognosis. It remains an unprecedent clinical challenge due to its delayed diagnosis and unpredictable clinical course. The need for accurate diagnostic, prognostic and predisposition biomarkers in everyday clinical practice becomes more necessary than ever to ensure prompt diagnoses and early treatment. The identification of such blood biomarkers may also unravel novel drug targets against IPF development and progression. So far, the role of diverse blood biomarkers, implicated in various pathogenetic pathways, such as in fibrogenesis (S100A4), extracellular matrix remodelling (YKL-40, MMP-7, ICAM-1, LOXL2, periostin), chemotaxis (CCL-18, IL-8), epithelial cell injury (KL-6, SP-A, SP-D), autophagy and unfolded protein response has been investigated in IPF with various results. Moreover, the recent progress in genetics in IPF allows for a better understanding of the underlying disease mechanisms. So far, the causative mutations in pulmonary fibrosis include mutations in telomere-related genes and in surfactant-related genes, markers that could act as predisposition biomarkers in IPF. The aim of this review is to provide a comprehensive overview from the bench to bedside of current knowledge and recent insights on biomarkers in IPF, and to suggest future directions for research. Large-scale studies are still needed to confirm the exact role of these biomarkers.
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Affiliation(s)
- Ioannis Tomos
- 5th Department of Respiratory Medicine, ‘SOTIRIA’ Chest Diseases Hospital of Athens, 11527 Athens, Greece; (I.R.); (A.M.M.); (K.D.)
| | - Ioannis Roussis
- 5th Department of Respiratory Medicine, ‘SOTIRIA’ Chest Diseases Hospital of Athens, 11527 Athens, Greece; (I.R.); (A.M.M.); (K.D.)
| | - Andreas M. Matthaiou
- 5th Department of Respiratory Medicine, ‘SOTIRIA’ Chest Diseases Hospital of Athens, 11527 Athens, Greece; (I.R.); (A.M.M.); (K.D.)
- Laboratory of Molecular and Cellular Pneumonology, Medical School, University of Crete, 714 09 Heraklion, Greece
- Respiratory Physiology Laboratory, Medical School, University of Cyprus, Nicosia 2029, Cyprus
| | - Katerina Dimakou
- 5th Department of Respiratory Medicine, ‘SOTIRIA’ Chest Diseases Hospital of Athens, 11527 Athens, Greece; (I.R.); (A.M.M.); (K.D.)
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8
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Lenders V, Koutsoumpou X, Phan P, Soenen SJ, Allegaert K, de Vleeschouwer S, Toelen J, Zhao Z, Manshian BB. Modulation of engineered nanomaterial interactions with organ barriers for enhanced drug transport. Chem Soc Rev 2023; 52:4672-4724. [PMID: 37338993 DOI: 10.1039/d1cs00574j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
The biomedical use of nanoparticles (NPs) has been the focus of intense research for over a decade. As most NPs are explored as carriers to alter the biodistribution, pharmacokinetics and bioavailability of associated drugs, the delivery of these NPs to the tissues of interest remains an important topic. To date, the majority of NP delivery studies have used tumor models as their tool of interest, and the limitations concerning tumor targeting of systemically administered NPs have been well studied. In recent years, the focus has also shifted to other organs, each presenting their own unique delivery challenges to overcome. In this review, we discuss the recent advances in leveraging NPs to overcome four major biological barriers including the lung mucus, the gastrointestinal mucus, the placental barrier, and the blood-brain barrier. We define the specific properties of these biological barriers, discuss the challenges related to NP transport across them, and provide an overview of recent advances in the field. We discuss the strengths and shortcomings of different strategies to facilitate NP transport across the barriers and highlight some key findings that can stimulate further advances in this field.
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Affiliation(s)
- Vincent Lenders
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium.
| | - Xanthippi Koutsoumpou
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium.
| | - Philana Phan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Stefaan J Soenen
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium.
- NanoHealth and Optical Imaging Group, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium
| | - Karel Allegaert
- Department of Hospital Pharmacy, Erasmus MC University Medical Center, CN Rotterdam, 3015, The Netherlands
- Clinical Pharmacology and Pharmacotherapy, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B3000 Leuven, Belgium
- Leuven Child and Youth Institute, KU Leuven, 3000 Leuven, Belgium
- Woman and Child, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Steven de Vleeschouwer
- Department of Neurosurgery, University Hospitals Leuven, Leuven, Belgium
- Laboratory of Experimental Neurosurgery and Neuroanatomy, Department of Neurosciences, KU Leuven, Leuven, Belgium
- Leuven Brain Institute (LBI), KU Leuven, Leuven, Belgium
| | - Jaan Toelen
- Leuven Child and Youth Institute, KU Leuven, 3000 Leuven, Belgium
- Woman and Child, Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
- Department of Pediatrics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Zongmin Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Bella B Manshian
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, Herestraat 49, B3000 Leuven, Belgium.
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9
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Tomoshige K, Stuart WD, Fink-Baldauf IM, Ito M, Tsuchiya T, Nagayasu T, Yamatsuji T, Okada M, Fukazawa T, Guo M, Maeda Y. FOXA2 Cooperates with Mutant KRAS to Drive Invasive Mucinous Adenocarcinoma of the Lung. Cancer Res 2023; 83:1443-1458. [PMID: 37067057 PMCID: PMC10160002 DOI: 10.1158/0008-5472.can-22-2805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 04/18/2023]
Abstract
The endoderm-lineage transcription factor FOXA2 has been shown to inhibit lung tumorigenesis in in vitro and xenograft studies using lung cancer cell lines. However, FOXA2 expression in primary lung tumors does not correlate with an improved patient survival rate, and the functional role of FOXA2 in primary lung tumors remains elusive. To understand the role of FOXA2 in primary lung tumors in vivo, here, we conditionally induced the expression of FOXA2 along with either of the two major lung cancer oncogenes, EGFRL858R or KRASG12D, in the lung epithelium of transgenic mice. Notably, FOXA2 suppressed autochthonous lung tumor development driven by EGFRL858R, whereas FOXA2 promoted tumor growth driven by KRASG12D. Importantly, FOXA2 expression along with KRASG12D produced invasive mucinous adenocarcinoma (IMA) of the lung, a fatal mucus-producing lung cancer comprising approximately 5% of human lung cancer cases. In the mouse model in vivo and human lung cancer cells in vitro, FOXA2 activated a gene regulatory network involved in the key mucous transcription factor SPDEF and upregulated MUC5AC, whose expression is critical for inducing IMA. Coexpression of FOXA2 with mutant KRAS synergistically induced MUC5AC expression compared with that induced by FOXA2 alone. ChIP-seq combined with CRISPR interference indicated that FOXA2 bound directly to the enhancer region of MUC5AC and induced the H3K27ac enhancer mark. Furthermore, FOXA2 was found to be highly expressed in primary tumors of human IMA. Collectively, this study reveals that FOXA2 is not only a biomarker but also a driver for IMA in the presence of a KRAS mutation. SIGNIFICANCE FOXA2 expression combined with mutant KRAS drives invasive mucinous adenocarcinoma of the lung by synergistically promoting a mucous transcriptional program, suggesting strategies for targeting this lung cancer type that lacks effective therapies.
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Affiliation(s)
- Koichi Tomoshige
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - William D. Stuart
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Iris M. Fink-Baldauf
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Masaoki Ito
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tomoshi Tsuchiya
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Nagayasu
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoki Yamatsuji
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takuya Fukazawa
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yutaka Maeda
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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10
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Peljto AL, Blumhagen RZ, Walts AD, Cardwell J, Powers J, Corte TJ, Dickinson JL, Glaspole I, Moodley YP, Vasakova MK, Bendstrup E, Davidsen JR, Borie R, Crestani B, Dieude P, Bonella F, Costabel U, Gudmundsson G, Donnelly SC, Egan J, Henry MT, Keane MP, Kennedy MP, McCarthy C, McElroy AN, Olaniyi JA, O’Reilly KMA, Richeldi L, Leone PM, Poletti V, Puppo F, Tomassetti S, Luzzi V, Kokturk N, Mogulkoc N, Fiddler CA, Hirani N, Jenkins RG, Maher TM, Molyneaux PL, Parfrey H, Braybrooke R, Blackwell TS, Jackson PD, Nathan SD, Porteous MK, Brown KK, Christie JD, Collard HR, Eickelberg O, Foster EE, Gibson KF, Glassberg M, Kass DJ, Kropski JA, Lederer D, Linderholm AL, Loyd J, Mathai SK, Montesi SB, Noth I, Oldham JM, Palmisciano AJ, Reichner CA, Rojas M, Roman J, Schluger N, Shea BS, Swigris JJ, Wolters PJ, Zhang Y, Prele CMA, Enghelmayer JI, Otaola M, Ryerson CJ, Salinas M, Sterclova M, Gebremariam TH, Myllärniemi M, Carbone RG, Furusawa H, Hirose M, Inoue Y, Miyazaki Y, Ohta K, Ohta S, Okamoto T, Kim DS, Pardo A, Selman M, Aranda AU, Park MS, Park JS, Song JW, Molina-Molina M, Planas-Cerezales L, Westergren-Thorsson G, Smith AV, Manichaikul AW, Kim JS, Rich SS, Oelsner EC, Barr RG, Rotter JI, Dupuis J, O’Connor G, Vasan RS, Cho MH, Silverman EK, Schwarz MI, Steele MP, Lee JS, Yang IV, Fingerlin TE, Schwartz DA. Idiopathic Pulmonary Fibrosis Is Associated with Common Genetic Variants and Limited Rare Variants. Am J Respir Crit Care Med 2023; 207:1194-1202. [PMID: 36602845 PMCID: PMC10161752 DOI: 10.1164/rccm.202207-1331oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/04/2023] [Indexed: 01/06/2023] Open
Abstract
Rationale: Idiopathic pulmonary fibrosis (IPF) is a rare, irreversible, and progressive disease of the lungs. Common genetic variants, in addition to nongenetic factors, have been consistently associated with IPF. Rare variants identified by candidate gene, family-based, and exome studies have also been reported to associate with IPF. However, the extent to which rare variants, genome-wide, may contribute to the risk of IPF remains unknown. Objectives: We used whole-genome sequencing to investigate the role of rare variants, genome-wide, on IPF risk. Methods: As part of the Trans-Omics for Precision Medicine Program, we sequenced 2,180 cases of IPF. Association testing focused on the aggregated effect of rare variants (minor allele frequency ⩽0.01) within genes or regions. We also identified individual rare variants that are influential within genes and estimated the heritability of IPF on the basis of rare and common variants. Measurements and Main Results: Rare variants in both TERT and RTEL1 were significantly associated with IPF. A single rare variant in each of the TERT and RTEL1 genes was found to consistently influence the aggregated test statistics. There was no significant evidence of association with other previously reported rare variants. The SNP heritability of IPF was estimated to be 32% (SE = 3%). Conclusions: Rare variants within the TERT and RTEL1 genes and well-established common variants have the largest contribution to IPF risk overall. Efforts in risk profiling or the development of therapies for IPF that focus on TERT, RTEL1, common variants, and environmental risk factors are likely to have the largest impact on this complex disease.
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Affiliation(s)
- Anna L. Peljto
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Rachel Z. Blumhagen
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
- National Jewish Health, Denver, Colorado
| | | | - Jonathan Cardwell
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Julia Powers
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Tamera J. Corte
- Royal Prince Alfred Hospital, University of Sydney, Sydney, Australia
| | - Joanne L. Dickinson
- Menzies Institute of Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Ian Glaspole
- Allergy, Asthma and Clinical Immunology Clinic, Alfred Health, Sydney, Australia
| | - Yuben P. Moodley
- Department of Respiratory Medicine, University of Western Australia, Perth, Australia
| | | | - Elisabeth Bendstrup
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Jesper R. Davidsen
- South Danish Center for Interstitial Lung Diseases, Department of Respiratory Medicine, Odense University Hospital, Odense, Denmark
| | | | - Bruno Crestani
- Service de Pneumologie A and
- Université Paris Cité, INSERM, Physiopathologie et Épidémiologie des Maladies Respiratoires, Paris, France
| | | | - Francesco Bonella
- Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Ulrich Costabel
- Center for Interstitial and Rare Lung Diseases, Ruhrlandklinik University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Gunnar Gudmundsson
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
- Department of Respiratory Medicine and Sleep, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Jim Egan
- National Lung Transplantation Centre, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Michael T. Henry
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Michael P. Keane
- St. Vincent’s University Hospital, University College Dublin, Dublin, Ireland
| | - Marcus P. Kennedy
- Department of Respiratory Medicine, Cork University Hospital, Cork, Ireland
| | - Cormac McCarthy
- St. Vincent’s University Hospital, University College Dublin, Dublin, Ireland
| | | | | | | | - Luca Richeldi
- Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Paolo M. Leone
- Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Venerino Poletti
- Department of Diseases of the Thorax, G. B. Morgagni Hospital, Forlì, Italy
- Department of Medical and Surgical Sciences, DIMES University of Bologna, Bologna, Italy
| | - Francesco Puppo
- Department of Internal Medicine, University of Genoa, Genoa, Italy
| | - Sara Tomassetti
- Department of Clinical and Experimental Medicine, Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | - Valentina Luzzi
- Interventional Pulmonology Unit, Careggi University Hospital, Florence, Italy
| | | | - Nesrin Mogulkoc
- Department of Pulmonology, Ege University Hospital, Izmir, Turkey
| | | | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Toby M. Maher
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Keck Medicine of USC, University of Southern California, Los Angeles, California
| | - Philip L. Molyneaux
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Helen Parfrey
- Royal Papworth Hospital NHS Foundation Trust, Cambridge, United Kingdom
| | - Rebecca Braybrooke
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | - Peter D. Jackson
- Department of Pulmonary and Critical Care Medicine, Virginia Commonwealth University, Richmond, Virginia
| | | | - Mary K. Porteous
- Hospital of the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Jason D. Christie
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Harold R. Collard
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Elena E. Foster
- Division of Pulmonary, Critical Care, and Sleep Medicine, School of Medicine, University of California, Davis, Sacramento, California
| | - Kevin F. Gibson
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Marilyn Glassberg
- Division of Pulmonary, Critical Care and Sleep Medicine, College of Medicine, University of Arizona, Phoenix, Arizona
| | - Daniel J. Kass
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - David Lederer
- Regeneron Pharmaceuticals, Inc., Tarrytown, New York
| | - Angela L. Linderholm
- Department of Internal Medicine, University of California, Davis, Davis, California
| | - Jim Loyd
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Sydney B. Montesi
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | | | - Amy J. Palmisciano
- Division of Pulmonary, Critical Care and Sleep Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | - Cristina A. Reichner
- Division of Pulmonary, Critical Care and Sleep Medicine, MedStar Georgetown University Hospital, Washington, DC
| | - Mauricio Rojas
- Division of Pulmonary, Critical Care, and Sleep Medicine, Ohio State University, Columbus, Ohio
| | - Jesse Roman
- Division of Pulmonary, Allergy, and Critical Care, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Neil Schluger
- Columbia University Medical Center, New York, New York
| | - Barry S. Shea
- Division of Pulmonary, Critical Care and Sleep Medicine, Alpert Medical School, Brown University, Providence, Rhode Island
| | | | - Paul J. Wolters
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of California, San Francisco, San Francisco, California
| | - Yingze Zhang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Cecilia M. A. Prele
- Institute for Respiratory Health, University of Western Australia, Perth, Australia
| | - Juan I. Enghelmayer
- Brown University, Providence, Rhode Island
- Hospital de Clínicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Maria Otaola
- Instituto de Rehabilitación Psicofísica de Buenos Aires, Buenos Aires, Argentina
| | - Christopher J. Ryerson
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Martina Sterclova
- Center for Rare Lung Diseases, Department of Respiratory Diseases and Allergy, Aarhus University Hospital, Aarhus, Denmark
| | | | - Marjukka Myllärniemi
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | | | - Haruhiko Furusawa
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Masaki Hirose
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yoshikazu Inoue
- National Hospital Organization Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Yasunari Miyazaki
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken Ohta
- National Hospital Organization Tokyo National Hospital, Tokyo, Japan
| | - Shin Ohta
- Department of Medicine, Showa University, Tokyo, Japan
| | - Tsukasa Okamoto
- Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Dong Soon Kim
- Asan Medical Center, University of Ulsan, Seoul, Republic of Korea
| | - Annie Pardo
- Faculty of Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Alvaro U. Aranda
- Cardiopulmonary Research Center, Alliance Pulmonary Group, Guaynabo, Puerto Rico
| | - Moo Suk Park
- Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jong Sun Park
- Seoul National University Bundang Hospital, Seoul National University, Seongnam, Republic of Korea
| | - Jin Woo Song
- Asan Medical Center, University of Ulsan, Seoul, Republic of Korea
| | | | - Lurdes Planas-Cerezales
- Interstitial Lung Disease Multidisciplinary Unit, University Hospital of Bellvitge, University of Barcelona, Barcelona, Spain
| | | | - Albert V. Smith
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan
| | | | | | - Stephen S. Rich
- Center for Public Health Genomics, and
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Elizabeth C. Oelsner
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - R. Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, New York
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Josee Dupuis
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Quebec, Canada
| | - George O’Connor
- Pulmonary Center, School of Medicine, Boston University, Boston, Massachusetts
| | - Ramachandran S. Vasan
- Boston University and National Heart, Lung, and Blood Institute Framingham Heart Study, Boston, Massachusetts; and
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marvin I. Schwarz
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Mark P. Steele
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Joyce S. Lee
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
| | | | - David A. Schwartz
- Department of Medicine, University of Colorado, Anschutz Medical Campus, Aurora, Colorado
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11
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Yano N, Fedulov AV. Targeted DNA Demethylation: Vectors, Effectors and Perspectives. Biomedicines 2023; 11:biomedicines11051334. [PMID: 37239005 DOI: 10.3390/biomedicines11051334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Aberrant DNA hypermethylation at regulatory cis-elements of particular genes is seen in a plethora of pathological conditions including cardiovascular, neurological, immunological, gastrointestinal and renal diseases, as well as in cancer, diabetes and others. Thus, approaches for experimental and therapeutic DNA demethylation have a great potential to demonstrate mechanistic importance, and even causality of epigenetic alterations, and may open novel avenues to epigenetic cures. However, existing methods based on DNA methyltransferase inhibitors that elicit genome-wide demethylation are not suitable for treatment of diseases with specific epimutations and provide a limited experimental value. Therefore, gene-specific epigenetic editing is a critical approach for epigenetic re-activation of silenced genes. Site-specific demethylation can be achieved by utilizing sequence-dependent DNA-binding molecules such as zinc finger protein array (ZFA), transcription activator-like effector (TALE) and clustered regularly interspaced short palindromic repeat-associated dead Cas9 (CRISPR/dCas9). Synthetic proteins, where these DNA-binding domains are fused with the DNA demethylases such as ten-eleven translocation (Tet) and thymine DNA glycosylase (TDG) enzymes, successfully induced or enhanced transcriptional responsiveness at targeted loci. However, a number of challenges, including the dependence on transgenesis for delivery of the fusion constructs, remain issues to be solved. In this review, we detail current and potential approaches to gene-specific DNA demethylation as a novel epigenetic editing-based therapeutic strategy.
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Affiliation(s)
- Naohiro Yano
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
| | - Alexey V Fedulov
- Department of Surgery, Rhode Island Hospital, Alpert Medical School of Brown University, 593 Eddy Street, Providence, RI 02903, USA
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12
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Liu Y, Wen D, Ho C, Yu L, Zheng D, O'Reilly S, Gao Y, Li Q, Zhang Y. Epigenetics as a versatile regulator of fibrosis. J Transl Med 2023; 21:164. [PMID: 36864460 PMCID: PMC9983257 DOI: 10.1186/s12967-023-04018-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Fibrosis, a process caused by excessive deposition of extracellular matrix (ECM), is a common cause and outcome of organ failure and even death. Researchers have made many efforts to understand the mechanism of fibrogenesis and to develop therapeutic strategies; yet, the outcome remains unsatisfactory. In recent years, advances in epigenetics, including chromatin remodeling, histone modification, DNA methylation, and noncoding RNA (ncRNA), have provided more insights into the fibrotic process and have suggested the possibility of novel therapy for organ fibrosis. In this review, we summarize the current research on the epigenetic mechanisms involved in organ fibrosis and their possible clinical applications.
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Affiliation(s)
- Yangdan Liu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Dongsheng Wen
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Chiakang Ho
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Li Yu
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Danning Zheng
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China
| | | | - Ya Gao
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Qingfeng Li
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
| | - Yifan Zhang
- Department of Plastic & Reconstructive Surgery, School of Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University, 639 Zhizaoju Road, Shanghai, 200011, China.
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13
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Ding D, Gao R, Xue Q, Luan R, Yang J. Genomic Fingerprint Associated with Familial Idiopathic Pulmonary Fibrosis: A Review. Int J Med Sci 2023; 20:329-345. [PMID: 36860670 PMCID: PMC9969503 DOI: 10.7150/ijms.80358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/12/2023] [Indexed: 02/04/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a severe interstitial lung disease; although the recent introduction of two anti-fibrosis drugs, pirfenidone and Nidanib, have resulted in a significant reduction in lung function decline, IPF is still not curable. Approximately 2-20% of patients with IPF have a family history of the disease, which is considered the strongest risk factor for idiopathic interstitial pneumonia. However, the genetic predispositions of familial IPF (f-IPF), a particular type of IPF, remain largely unknown. Genetics affect the susceptibility and progression of f-IPF. Genomic markers are increasingly being recognized for their contribution to disease prognosis and drug therapy outcomes. Existing data suggest that genomics may help identify individuals at risk for f-IPF, accurately classify patients, elucidate key pathways involved in disease pathogenesis, and ultimately develop more effective targeted therapies. Since several genetic variants associated with the disease have been found in f-IPF, this review systematically summarizes the latest progress in the gene spectrum of the f-IPF population and the underlying mechanisms of f-IPF. The genetic susceptibility variation related to the disease phenotype is also illustrated. This review aims to improve the understanding of the IPF pathogenesis and facilitate his early detection.
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Affiliation(s)
- Dongyan Ding
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Rong Gao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Qianfei Xue
- Hospital of Jilin University, Changchun, China
| | - Rumei Luan
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Junling Yang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
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14
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Alonso-Gonzalez A, Tosco-Herrera E, Molina-Molina M, Flores C. Idiopathic pulmonary fibrosis and the role of genetics in the era of precision medicine. Front Med (Lausanne) 2023; 10:1152211. [PMID: 37181377 PMCID: PMC10172674 DOI: 10.3389/fmed.2023.1152211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, rare progressive lung disease, characterized by lung scarring and the irreversible loss of lung function. Two anti-fibrotic drugs, nintedanib and pirfenidone, have been demonstrated to slow down disease progression, although IPF mortality remains a challenge and the patients die after a few years from diagnosis. Rare pathogenic variants in genes that are involved in the surfactant metabolism and telomere maintenance, among others, have a high penetrance and tend to co-segregate with the disease in families. Common recurrent variants in the population with modest effect sizes have been also associated with the disease risk and progression. Genome-wide association studies (GWAS) support at least 23 genetic risk loci, linking the disease pathogenesis with unexpected molecular pathways including cellular adhesion and signaling, wound healing, barrier function, airway clearance, and innate immunity and host defense, besides the surfactant metabolism and telomere biology. As the cost of high-throughput genomic technologies continuously decreases and new technologies and approaches arise, their widespread use by clinicians and researchers is efficiently contributing to a better understanding of the pathogenesis of progressive pulmonary fibrosis. Here we provide an overview of the genetic factors known to be involved in IPF pathogenesis and discuss how they will continue to further advance in this field. We also discuss how genomic technologies could help to further improve IPF diagnosis and prognosis as well as for assessing genetic risk in unaffected relatives. The development and validation of evidence-based guidelines for genetic-based screening of IPF will allow redefining and classifying this disease relying on molecular characteristics and contribute to the implementation of precision medicine approaches.
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Affiliation(s)
- Aitana Alonso-Gonzalez
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Eva Tosco-Herrera
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
| | - Maria Molina-Molina
- Servei de Pneumologia, Laboratori de Pneumologia Experimental, IDIBELL, Barcelona, Spain
- Campus de Bellvitge, Universitat de Barcelona, Barcelona, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Unidad de Investigación, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- *Correspondence: Carlos Flores,
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Tirelli C, Pesenti C, Miozzo M, Mondoni M, Fontana L, Centanni S. The Genetic and Epigenetic Footprint in Idiopathic Pulmonary Fibrosis and Familial Pulmonary Fibrosis: A State-of-the-Art Review. Diagnostics (Basel) 2022; 12:diagnostics12123107. [PMID: 36553114 PMCID: PMC9777399 DOI: 10.3390/diagnostics12123107] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/29/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a rare disease of the lung with a largely unknown etiology and a poor prognosis. Intriguingly, forms of familial pulmonary fibrosis (FPF) have long been known and linked to specific genetic mutations. There is little evidence of the possible role of genetics in the etiology of sporadic IPF. We carried out a non-systematic, narrative literature review aimed at describing the main known genetic and epigenetic mechanisms that are involved in the pathogenesis and prognosis of IPF and FPF. In this review, we highlighted the mutations in classical genes associated with FPF, including those encoding for telomerases (TERT, TERC, PARN, RTEL1), which are also found in about 10-20% of cases of sporadic IPF. In addition to the Mendelian forms, mutations in the genes encoding for the surfactant proteins (SFTPC, SFTPA1, SFTPA2, ABCA3) and polymorphisms of genes for the mucin MUC5B and the Toll-interacting protein TOLLIP are other pathways favoring the fibrogenesis that have been thoroughly explored. Moreover, great attention has been paid to the main epigenetic alterations (DNA methylation, histone modification and non-coding RNA gene silencing) that are emerging to play a role in fibrogenesis. Finally, a gaze on the shared mechanisms between cancer and fibrogenesis, and future perspectives on the genetics of pulmonary fibrosis have been analyzed.
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Affiliation(s)
- Claudio Tirelli
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
- Correspondence:
| | - Chiara Pesenti
- Medical Genetics Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Monica Miozzo
- Medical Genetics Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Michele Mondoni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Laura Fontana
- Medical Genetics Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
| | - Stefano Centanni
- Respiratory Unit, ASST Santi Paolo e Carlo, Department of Health Sciences, University of Milan, 20142 Milan, Italy
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Neatu R, Enekwa I, Thompson DJ, Schwalbe EC, Fois G, Abdelaal G, Veuger S, Frick M, Braubach P, Moschos SA. The Idiopathic Pulmonary Fibrosis-Associated Single Nucleotide Polymorphism RS35705950 Is Transcribed in a MUC5B Promoter Associated Long Non-Coding RNA (AC061979.1). Noncoding RNA 2022; 8:ncrna8060083. [PMID: 36548182 PMCID: PMC9781688 DOI: 10.3390/ncrna8060083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
LncRNAs are involved in regulatory processes in the human genome, including gene expression. The rs35705950 SNP, previously associated with IPF, overlaps with the recently annotated lncRNA AC061979.1, a 1712 nucleotide transcript located within the MUC5B promoter at chromosome 11p15.5. To document the expression pattern of the transcript, we processed 3.9 TBases of publicly available RNA-SEQ data across 27 independent studies involving lung airway epithelial cells. Epithelial lung cells showed expression of this putative pancRNA. The findings were independently validated in cell lines and primary cells. The rs35705950 is found within a conserved region (from fish to primates) within the expressed sequence indicating functional importance. These results implicate the rs35705950-containing AC061979.1 pancRNA as a novel component of the MUC5B expression control minicircuitry.
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Affiliation(s)
- Ruxandra Neatu
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Central Parkway, Newcastle-Upon-Tyne NE1 3BZ, UK
| | - Ifeanyi Enekwa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Dean J. Thompson
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Edward C. Schwalbe
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Giorgio Fois
- Institue of General Physiology, University of Ulm, Albert-Einstein-Allee 11, D89081 Ulm, Germany
| | - Gina Abdelaal
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Stephany Veuger
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
| | - Manfred Frick
- Institue of General Physiology, University of Ulm, Albert-Einstein-Allee 11, D89081 Ulm, Germany
| | - Peter Braubach
- Institute of Pathology, MHH Hannover, 30625 Hannover, Germany
| | - Sterghios A. Moschos
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Ellison Building, Newcastle-Upon-Tyne NE1 8ST, UK
- Correspondence:
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Papiris SA, Kannengiesser C, Borie R, Kolilekas L, Kallieri M, Apollonatou V, Ba I, Nathan N, Bush A, Griese M, Dieude P, Crestani B, Manali ED. Genetics in Idiopathic Pulmonary Fibrosis: A Clinical Perspective. Diagnostics (Basel) 2022; 12:2928. [PMID: 36552935 PMCID: PMC9777433 DOI: 10.3390/diagnostics12122928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/17/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Unraveling the genetic background in a significant proportion of patients with both sporadic and familial IPF provided new insights into the pathogenic pathways of pulmonary fibrosis. AIM The aim of the present study is to overview the clinical significance of genetics in IPF. PERSPECTIVE It is fascinating to realize the so-far underestimated but dynamically increasing impact that genetics has on aspects related to the pathophysiology, accurate and early diagnosis, and treatment and prevention of this devastating disease. Genetics in IPF have contributed as no other in unchaining the disease from the dogma of a "a sporadic entity of the elderly, limited to the lungs" and allowed all scientists, but mostly clinicians, all over the world to consider its many aspects and "faces" in all age groups, including its co-existence with several extra pulmonary conditions from cutaneous albinism to bone-marrow and liver failure. CONCLUSION By providing additional evidence for unsuspected characteristics such as immunodeficiency, impaired mucus, and surfactant and telomere maintenance that very often co-exist through the interaction of common and rare genetic variants in the same patient, genetics have created a generous and pluralistic yet unifying platform that could lead to the understanding of the injurious and pro-fibrotic effects of many seemingly unrelated extrinsic and intrinsic offending factors. The same platform constantly instructs us about our limitations as well as about the heritability, the knowledge and the wisdom that is still missing.
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Affiliation(s)
- Spyros A. Papiris
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Caroline Kannengiesser
- Département de Génétique, APHP Hôpital Bichat, Université de Paris, 75018 Paris, France
- INSERM UMR 1152, Université de Paris, 75018 Paris, France
| | - Raphael Borie
- Service de Pneumologie A, INSERM UMR_1152, Centre de Référence des Maladies Pulmonaires Rares, FHU APOLLO, APHP Hôpital Bichat, Sorbonne Université, 75018 Paris, France
| | - Lykourgos Kolilekas
- 7th Pulmonary Department, Athens Chest Hospital “Sotiria”, 11527 Athens, Greece
| | - Maria Kallieri
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Vasiliki Apollonatou
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Ibrahima Ba
- Département de Génétique, APHP Hôpital Bichat, Université de Paris, 75018 Paris, France
| | - Nadia Nathan
- Peditric Pulmonology Department and Reference Centre for Rare Lung Diseases RespiRare, INSERM UMR_S933 Laboratory of Childhood Genetic Diseases, Armand Trousseau Hospital, Sorbonne University and APHP, 75012 Paris, France
| | - Andrew Bush
- Paediatrics and Paediatric Respirology, Imperial College, Imperial Centre for Paediatrics and Child Health, Royal Brompton Harefield NHS Foundation Trust, London SW3 6NP, UK
| | - Matthias Griese
- Department of Pediatric Pneumology, Dr von Hauner Children’s Hospital, Ludwig-Maximilians-University, German Center for Lung Research, 80337 Munich, Germany
| | - Philippe Dieude
- Department of Rheumatology, INSERM U1152, APHP Hôpital Bichat-Claude Bernard, Université de Paris, 75018 Paris, France
| | - Bruno Crestani
- Service de Pneumologie A, INSERM UMR_1152, Centre de Référence des Maladies Pulmonaires Rares, FHU APOLLO, APHP Hôpital Bichat, Sorbonne Université, 75018 Paris, France
| | - Effrosyni D. Manali
- 2nd Pulmonary Medicine Department, General University Hospital “Attikon”, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece
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18
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Bonham CA, Noth I. Idiopathic Pulmonary Fibrosis Genetic Risk Factors, Function, and Mechanisms? The Concepts Are Starting to Gel. Am J Respir Crit Care Med 2022; 206:1197-1199. [PMID: 36075070 PMCID: PMC9746834 DOI: 10.1164/rccm.202208-1591ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Catherine A Bonham
- Division of Pulmonary & Critical Care Medicine University of Virginia Charlottesville, Virginia
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine University of Virginia Charlottesville, Virginia
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Borie R, Cardwell J, Konigsberg IR, Moore CM, Zhang W, Sasse SK, Gally F, Dobrinskikh E, Walts A, Powers J, Brancato J, Rojas M, Wolters PJ, Brown KK, Blackwell TS, Nakanishi T, Richards JB, Gerber AN, Fingerlin TE, Sachs N, Pulit SL, Zappala Z, Schwartz DA, Yang IV. Colocalization of Gene Expression and DNA Methylation with Genetic Risk Variants Supports Functional Roles of MUC5B and DSP in Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2022; 206:1259-1270. [PMID: 35816432 PMCID: PMC9746850 DOI: 10.1164/rccm.202110-2308oc] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 07/05/2022] [Indexed: 11/16/2022] Open
Abstract
Rationale: Common genetic variants have been associated with idiopathic pulmonary fibrosis (IPF). Objectives: To determine functional relevance of the 10 IPF-associated common genetic variants we previously identified. Methods: We performed expression quantitative trait loci (eQTL) and methylation quantitative trait loci (mQTL) mapping, followed by co-localization of eQTL and mQTL with genetic association signals and functional validation by luciferase reporter assays. Illumina multi-ethnic genotyping arrays, mRNA sequencing, and Illumina 850k methylation arrays were performed on lung tissue of participants with IPF (234 RNA and 345 DNA samples) and non-diseased controls (188 RNA and 202 DNA samples). Measurements and Main Results: Focusing on genetic variants within 10 IPF-associated genetic loci, we identified 27 eQTLs in controls and 24 eQTLs in cases (false-discovery-rate-adjusted P < 0.05). Among these signals, we identified associations of lead variants rs35705950 with expression of MUC5B and rs2076295 with expression of DSP in both cases and controls. mQTL analysis identified CpGs in gene bodies of MUC5B (cg17589883) and DSP (cg08964675) associated with the lead variants in these two loci. We also demonstrated strong co-localization of eQTL/mQTL and genetic signal in MUC5B (rs35705950) and DSP (rs2076295). Functional validation of the mQTL in MUC5B using luciferase reporter assays demonstrates that the CpG resides within a putative internal repressor element. Conclusions: We have established a relationship of the common IPF genetic risk variants rs35705950 and rs2076295 with respective changes in MUC5B and DSP expression and methylation. These results provide additional evidence that both MUC5B and DSP are involved in the etiology of IPF.
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Affiliation(s)
| | | | | | - Camille M. Moore
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
| | | | | | - Fabienne Gally
- Department of Medicine
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | | | | | | | | | - Mauricio Rojas
- Department of Internal Medicine, Ohio State College of Medicine, The Ohio State University, Columbus, Ohio
| | - Paul J. Wolters
- Department of Medicine, University of California, San Francisco, California
| | | | - Timothy S. Blackwell
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Tomoko Nakanishi
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - J. Brent Richards
- Department of Human Genetics, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Canada
| | - Anthony N. Gerber
- Department of Medicine
- Department of Medicine, and
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Tasha E. Fingerlin
- Department of Biostatistics and Bioinformatics and
- Center for Genes, Environment, and Health
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado
| | - Norman Sachs
- Cell Biology, Vertex Pharmaceuticals, San Diego, California; and
| | - Sara L. Pulit
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - Zachary Zappala
- Computational Genomics, Vertex Pharmaceuticals, Boston, Massachusetts
| | - David A. Schwartz
- Department of Medicine
- Department of Microbiology and Immunology, University of Colorado Anschutz Medical Campus; Aurora, Colorado
| | - Ivana V. Yang
- Department of Medicine
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado
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20
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Kurche JS, Stancil IT, Michalski JE, Yang IV, Schwartz DA. Dysregulated Cell-Cell Communication Characterizes Pulmonary Fibrosis. Cells 2022; 11:3319. [PMID: 36291184 PMCID: PMC9600037 DOI: 10.3390/cells11203319] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/04/2022] [Accepted: 10/05/2022] [Indexed: 11/27/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive disease of older adults characterized by fibrotic replacement of functional gas exchange units in the lung. The strongest risk factor for IPF is a genetic variantin the promoter region of the gel-forming mucin, MUC5B. To better understand how the MUC5B variant influences development of fibrosis, we used the NicheNet R package and leveraged publicly available single-cell RNA sequencing data to identify and evaluate how epithelia participating in gas exchange are influenced by ligands expressed in control, MUC5B variant, and fibrotic environments. We observed that loss of type-I alveolar epithelia (AECI) characterizes the single-cell RNA transcriptome in fibrotic lung and validated the pattern of AECI loss using single nuclear RNA sequencing. Examining AECI transcriptomes, we found enrichment of transcriptional signatures for IL6 and AREG, which we have previously shown to mediate aberrant epithelial fluidization in IPF and murine bleomycin models. Moreover, we found that the protease ADAM17, which is upstream of IL6 trans-signaling, was enriched in control MUC5B variant donors. We used immunofluorescence to validate a role for enhanced expression of ADAM17 among MUC5B variants, suggesting involvement in IPF pathogenesis and maintenance.
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Affiliation(s)
- Jonathan S. Kurche
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Rocky Mountain Regional VA Medical Center, Aurora, CO 80045, USA
| | - Ian T. Stancil
- Program in Cellular Biology and Biophysics, Graduate School, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Jacob E. Michalski
- School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Ivana V. Yang
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - David A. Schwartz
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Rocky Mountain Regional VA Medical Center, Aurora, CO 80045, USA
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21
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Partanen JJ, Häppölä P, Zhou W, Lehisto AA, Ainola M, Sutinen E, Allen RJ, Stockwell AD, Leavy OC, Oldham JM, Guillen-Guio B, Cox NJ, Hirbo JB, Schwartz DA, Fingerlin TE, Flores C, Noth I, Yaspan BL, Jenkins RG, Wain LV, Ripatti S, Pirinen M, Laitinen T, Kaarteenaho R, Myllärniemi M, Daly MJ, Koskela JT. Leveraging global multi-ancestry meta-analysis in the study of idiopathic pulmonary fibrosis genetics. CELL GENOMICS 2022; 2:100181. [PMID: 36777997 PMCID: PMC9903787 DOI: 10.1016/j.xgen.2022.100181] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 05/24/2022] [Accepted: 09/07/2022] [Indexed: 04/12/2023]
Abstract
The research of rare and devastating orphan diseases, such as idiopathic pulmonary fibrosis (IPF) has been limited by the rarity of the disease itself. The prognosis is poor-the prevalence of IPF is only approximately four times the incidence, limiting the recruitment of patients to trials and studies of the underlying biology. Global biobanking efforts can dramatically alter the future of IPF research. We describe a large-scale meta-analysis of IPF, with 8,492 patients and 1,355,819 population controls from 13 biobanks around the globe. Finally, we combine this meta-analysis with the largest available meta-analysis of IPF, reaching 11,160 patients and 1,364,410 population controls. We identify seven novel genome-wide significant loci, only one of which would have been identified if the analysis had been limited to European ancestry individuals. We observe notable pleiotropy across IPF susceptibility and severe COVID-19 infection and note an unexplained sex-heterogeneity effect at the strongest IPF locus MUC5B.
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Affiliation(s)
- Juulia J. Partanen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Paavo Häppölä
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wei Zhou
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Arto A. Lehisto
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Mari Ainola
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Eva Sutinen
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Richard J. Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Olivia C. Leavy
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Justin M. Oldham
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
| | | | - Nancy J. Cox
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jibril B. Hirbo
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
| | - Carlos Flores
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Imre Noth
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | - R. Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Matti Pirinen
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - International IPF Genetics Consortium
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Global Biobank Meta-Analysis Initiative (GBMI)
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
- Department of Health Sciences, University of Leicester, Leicester, UK
- Human Genetics, Genentech, South San Francisco, CA, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, University of California, Davis, Sacramento, CA, USA
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Genetic Institute, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Medicine, University of Colorado, Aurora, CO, USA
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Research Unit, Hospital Universitario Ntra. Sra. de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Virginia, Charlottesville, VA, USA
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton and Harefield Hospitals, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
- Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Tarja Laitinen
- Administration Center, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, University of Oulu, Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital, Oulu, Finland
| | - Marjukka Myllärniemi
- Individualized Drug Therapy Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pulmonary Medicine, Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Mark J. Daly
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jukka T. Koskela
- Institute for Molecular Medicine, Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
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22
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Ghanem M, Mailleux AA. Aberrant Multiciliogenesis in Pulmonary Fibrosis: Bystander or Driver of Disease Progression? Am J Respir Cell Mol Biol 2022; 67:142-144. [PMID: 35612966 PMCID: PMC9348563 DOI: 10.1165/rcmb.2022-0201ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Mada Ghanem
- Université Paris Cité, Inserm, PHERE, Paris, France
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23
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Yang XH, Wang FF, Chi XS, Wang XM, Cong JP, Hu Y, Zhang YZ. Disturbance of serum lipid metabolites and potential biomarkers in the Bleomycin model of pulmonary fibrosis in young mice. BMC Pulm Med 2022; 22:176. [PMID: 35509094 PMCID: PMC9066762 DOI: 10.1186/s12890-022-01972-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 04/26/2022] [Indexed: 01/15/2023] Open
Abstract
Background Altered metabolic pathways have recently been considered as potential drivers of idiopathic pulmonary fibrosis (IPF) for the study of drug therapeutic targets. However, our understanding of the metabolite profile during IPF formation is lacking. Methods To comprehensively characterize the metabolic disorders of IPF, a mouse IPF model was constructed by intratracheal injection of bleomycin into C57BL/6J male mice, and lung tissues from IPF mice at 7 days, 14 days, and controls were analyzed by pathology, immunohistochemistry, and Western Blots. Meanwhile, serum metabolite detections were conducted in IPF mice using LC–ESI–MS/MS, KEGG metabolic pathway analysis was applied to the differential metabolites, and biomarkers were screened using machine learning algorithms. Results We analyzed the levels of 1465 metabolites and found that more than one-third of the metabolites were altered during IPF formation. There were 504 and 565 metabolites that differed between M7 and M14 and controls, respectively, while 201 differential metabolites were found between M7 and M14. In IPF mouse sera, about 80% of differential metabolite expression was downregulated. Lipids accounted for more than 80% of the differential metabolite species with down-regulated expression. The KEGG pathway enrichment analysis of differential metabolites was mainly enriched to pathways such as the metabolism of glycerolipids and glycerophospholipids. Eight metabolites were screened by a machine learning random forest model, and receiver operating characteristic curves (ROC) assessed them as ideal diagnostic tools. Conclusions In conclusion, we have identified disturbances in serum lipid metabolism associated with the formation of pulmonary fibrosis, contributing to the understanding of the pathogenesis of pulmonary fibrosis. Supplementary Information The online version contains supplementary material available at 10.1186/s12890-022-01972-6.
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Affiliation(s)
- Xiao-Hui Yang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Fang-Fang Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Xiao-Sa Chi
- Department of Geriatrics, Affiliated Hospital of Qingdao University, Qingdao, 266000, People's Republic of China
| | - Xiao-Meng Wang
- Department of Geriatrics, Affiliated Hospital of Qingdao University, Qingdao, 266000, People's Republic of China
| | - Jin-Peng Cong
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Qingdao University, Qingdao, People's Republic of China
| | - Yi Hu
- Department of Geriatrics, Affiliated Hospital of Qingdao University, Qingdao, 266000, People's Republic of China
| | - Yu-Zhu Zhang
- Department of Geriatrics, Affiliated Hospital of Qingdao University, Qingdao, 266000, People's Republic of China.
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24
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Garcia AN, Casanova NG, Kempf CL, Bermudez T, Valera DG, Song JH, Sun X, Cai H, Moreno-Vinasco L, Gregory T, Oita RC, Hernon VR, Camp SM, Rogers C, Kyubwa EM, Menon N, Axtelle J, Rappaport J, Bime C, Sammani S, Cress AE, Garcia JGN. eNAMPT Is a Novel Damage-associated Molecular Pattern Protein That Contributes to the Severity of Radiation-induced Lung Fibrosis. Am J Respir Cell Mol Biol 2022; 66:497-509. [PMID: 35167418 PMCID: PMC9116358 DOI: 10.1165/rcmb.2021-0357oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 12/17/2021] [Indexed: 11/24/2022] Open
Abstract
The paucity of therapeutic strategies to reduce the severity of radiation-induced lung fibrosis (RILF), a life-threatening complication of intended or accidental ionizing radiation exposure, is a serious unmet need. We evaluated the contribution of eNAMPT (extracellular nicotinamide phosphoribosyltransferase), a damage-associated molecular pattern (DAMP) protein and TLR4 (Toll-like receptor 4) ligand, to the severity of whole-thorax lung irradiation (WTLI)-induced RILF. Wild-type (WT) and Nampt+/- heterozygous C57BL6 mice and nonhuman primates (NHPs, Macaca mulatta) were exposed to a single WTLI dose (9.8 or 10.7 Gy for NHPs, 20 Gy for mice). WT mice received IgG1 (control) or an eNAMPT-neutralizing polyclonal or monoclonal antibody (mAb) intraperitoneally 4 hours after WTLI and weekly thereafter. At 8-12 weeks after WTLI, NAMPT expression was assessed by immunohistochemistry, biochemistry, and plasma biomarker studies. RILF severity was determined by BAL protein/cells, hematoxylin and eosin, and trichrome blue staining and soluble collagen assays. RNA sequencing and bioinformatic analyses identified differentially expressed lung tissue genes/pathways. NAMPT lung tissue expression was increased in both WTLI-exposed WT mice and NHPs. Nampt+/- mice and eNAMPT polyclonal antibody/mAb-treated mice exhibited significantly attenuated WTLI-mediated lung fibrosis with reduced: 1) NAMPT and trichrome blue staining; 2) dysregulated lung tissue expression of smooth muscle actin, p-SMAD2/p-SMAD1/5/9, TGF-β, TSP1 (thrombospondin-1), NOX4, IL-1β, and NRF2; 3) plasma eNAMPT and IL-1β concentrations; and 4) soluble collagen. Multiple WTLI-induced dysregulated differentially expressed lung tissue genes/pathways with known tissue fibrosis involvement were each rectified in mice receiving eNAMPT mAbs.The eNAMPT/TLR4 inflammatory network is essentially involved in radiation pathobiology, with eNAMPT neutralization an effective therapeutic strategy to reduce RILF severity.
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Affiliation(s)
| | | | | | | | | | | | | | - Hua Cai
- Department of Anesthesiology, University of California Los Angeles, Los Angeles, California
| | | | | | | | | | | | | | | | | | | | - Jay Rappaport
- Tulane National Primate Research Center, New Orleans, Louisiana
| | | | | | - Anne E. Cress
- Department of Cell and Molecular Medicine, University of Arizona Health Sciences, Tucson, Arizona
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25
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Singh S, Natalini JG, Segal LN. Lung microbial-host interface through the lens of multi-omics. Mucosal Immunol 2022; 15:837-845. [PMID: 35794200 PMCID: PMC9391302 DOI: 10.1038/s41385-022-00541-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/23/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023]
Abstract
In recent years, our understanding of the microbial world within us has been revolutionized by the use of culture-independent techniques. The use of multi-omic approaches can now not only comprehensively characterize the microbial environment but also evaluate its functional aspects and its relationship with the host immune response. Advances in bioinformatics have enabled high throughput and in-depth analyses of transcripts, proteins and metabolites and enormously expanded our understanding of the role of the human microbiome in different conditions. Such investigations of the lower airways have specific challenges but as the field develops, new approaches will be facilitated. In this review, we focus on how integrative multi-omics can advance our understanding of the microbial environment and its effects on the host immune tone in the lungs.
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Affiliation(s)
- Shivani Singh
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Jake G. Natalini
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY,NYU Langone Lung Transplant Institute, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
| | - Leopoldo N. Segal
- Division of Pulmonary, Critical Care, and Sleep Medicine, New York University Grossman School of Medicine, NYU Langone Health, New York, NY
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26
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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27
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Abstract
Pulmonary fibrosis, a kind of terminal pathological changes in the lung, is caused by aberrant wound healing, deposition of extracellular matrix (ECM), and eventually replacement of lung parenchyma by ECM. Pulmonary fibrosis induced by acute lung injury and some diseases is reversible under treatment. While idiopathic pulmonary fibrosis is persistent and irreversible even after treatment. Currently, the pathogenesis of irreversible pulmonary fibrosis is not fully elucidated. The known factors associated with the development of irreversible fibrosis include apoptosis resistance of (myo)fibroblasts, dysfunction of pulmonary vessel, cell mitochondria and autophagy, aberrant epithelia hyperplasia and lipid metabolism disorder. In this review, other than a brief introduction of reversible pulmonary fibrosis, we focus on the underlying pathogenesis of irreversible pulmonary fibrosis from the above aspects as well as preclinical disease models, and also suggest directions for future studies.
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Affiliation(s)
- Qing Yang Yu
- 1State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xiao Xiao Tang
- 1State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,2Guangzhou Laboratory, Bio-island, Guangzhou, China
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28
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Avci E, Sarvari P, Savai R, Seeger W, Pullamsetti SS. Epigenetic Mechanisms in Parenchymal Lung Diseases: Bystanders or Therapeutic Targets? Int J Mol Sci 2022; 23:ijms23010546. [PMID: 35008971 PMCID: PMC8745712 DOI: 10.3390/ijms23010546] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 12/28/2021] [Accepted: 12/30/2021] [Indexed: 12/17/2022] Open
Abstract
Epigenetic responses due to environmental changes alter chromatin structure, which in turn modifies the phenotype, gene expression profile, and activity of each cell type that has a role in the pathophysiology of a disease. Pulmonary diseases are one of the major causes of death in the world, including lung cancer, idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD), pulmonary hypertension (PH), lung tuberculosis, pulmonary embolism, and asthma. Several lines of evidence indicate that epigenetic modifications may be one of the main factors to explain the increasing incidence and prevalence of lung diseases including IPF and COPD. Interestingly, isolated fibroblasts and smooth muscle cells from patients with pulmonary diseases such as IPF and PH that were cultured ex vivo maintained the disease phenotype. The cells often show a hyper-proliferative, apoptosis-resistant phenotype with increased expression of extracellular matrix (ECM) and activated focal adhesions suggesting the presence of an epigenetically imprinted phenotype. Moreover, many abnormalities observed in molecular processes in IPF patients are shown to be epigenetically regulated, such as innate immunity, cellular senescence, and apoptotic cell death. DNA methylation, histone modification, and microRNA regulation constitute the most common epigenetic modification mechanisms.
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MESH Headings
- Animals
- Biomarkers
- Combined Modality Therapy
- DNA Methylation
- Diagnosis, Differential
- Disease Management
- Disease Susceptibility
- Epigenesis, Genetic
- Gene Expression Regulation
- Histones/metabolism
- Humans
- Idiopathic Pulmonary Fibrosis/diagnosis
- Idiopathic Pulmonary Fibrosis/etiology
- Idiopathic Pulmonary Fibrosis/metabolism
- Idiopathic Pulmonary Fibrosis/therapy
- Lung Diseases, Interstitial/diagnosis
- Lung Diseases, Interstitial/etiology
- Lung Diseases, Interstitial/metabolism
- Lung Diseases, Interstitial/therapy
- Pulmonary Disease, Chronic Obstructive/diagnosis
- Pulmonary Disease, Chronic Obstructive/etiology
- Pulmonary Disease, Chronic Obstructive/metabolism
- Pulmonary Disease, Chronic Obstructive/therapy
- Treatment Outcome
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Affiliation(s)
- Edibe Avci
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
| | - Pouya Sarvari
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
| | - Rajkumar Savai
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
- Department of Internal Medicine, Justus Liebig University, 35392 Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Werner Seeger
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
- Department of Internal Medicine, Justus Liebig University, 35392 Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University, 35392 Giessen, Germany
| | - Soni S. Pullamsetti
- Department of Lung Development and Remodeling, Max-Planck Institute for Heart and Lung Research, Parkstrasse 1, 61231 Bad Nauheim, Germany; (E.A.); (P.S.); (R.S.); (W.S.)
- Department of Internal Medicine, Justus Liebig University, 35392 Giessen, Germany
- Correspondence: ; Tel.: +49-603-270-5380; Fax: +49-603-270-5385
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29
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Wu X, Li W, Luo Z, Chen Y. The minor T allele of the MUC5B promoter rs35705950 associated with susceptibility to idiopathic pulmonary fibrosis: a meta-analysis. Sci Rep 2021; 11:24007. [PMID: 34907291 PMCID: PMC8671516 DOI: 10.1038/s41598-021-03533-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 12/06/2021] [Indexed: 11/09/2022] Open
Abstract
MUC5B promoter rs35705950 T/G gene polymorphism has been associated with the risk of IPF, but the influence of this relationship varies among different populations. In the past 2 years, there were new clinical studies with different results, but none of them reached unified conclusions. Therefore, this study further included the latest case-control studies, integrated their results and carried out meta-analysis on them to draw reliable conclusions. PubMed, EMBASE, CNKI, Wanfang database and VIP Chinese science were searched by a computer to collect the related literatures of MUC5B gene polymorphism and IPF susceptibility published before June 15, 2021. The first author, year of publication, diagnostic criteria and gene frequency were extracted after screened them. Forest plot was drawn and the trial sequential analysis (TSA) was carried out to confirm the stability of the meta-analysis results. Registration number: CRD42021272940. A total of 24 case-control studies (13 studies on the Caucasian, 7 studies on the Asian and 4 studies on the mixed population), and a total of 6749 IPF patients and 13,898 healthy controls were included in this study. The T vs.G, TT vs. GG, GT vs. GG, GT + TT vs. GG and TT vs. GG + GT genetic models of MUC5B promoter rs35705950 T/G polymorphism were associated with IPF risk in all populations, and the effect values were ([OR] 4.12, 95% CI [3.64, 4.67]), ([OR] 10.12, 95% CI [7.06, 14.49]), ([OR] 4.84, 95% CI [3.85, 6.08]), ([OR] 4.84, 95% CI [3.79, 6.19]) and ([OR] 5.11, 95% CI [4.02, 6.49]), respectively. The results of TSA confirmed the stability of the results. Subgroup analysis showed that T vs.G, TT vs. GG, GT vs. GG, GT + TT vs. GG and TT vs. GG + GT genetic models of MUC5B polymorphism were associated with IPF risk in Caucasian population. The effect values were ([OR] 4.50, 95% CI [3.93, 5.16]), ([OR] 10.98, 95% CI [7.59, 15.89]), ([OR] 6.27, 95% CI [5.37, 7.32]), ([OR] 6.30, 95% CI [5.19, 7.64]) and ([OR] 5.15, 95% CI [4.01, 6.61]), respectively. Similar results were also found in Asian and mixed populations. The association strength of the minor T allele in the Caucasian was more significant than that of the Asian population ([OR] 4.50 vs. [OR] 2.39), and the association strength of all genetic models carrying "T" was more significant than that of the Asian population ([OR] 10.98 vs. [OR] 4.29). In Caucasian, Asian and mixed populations, T minor allele carriers were more likely to be susceptible to pulmonary fibrosis, and TT genotype carriers were more likely to be susceptible to IPF than GT genotype carriers. The association between IPF and Caucasian population with minor T allele and all "T" genetic model was more significant than that of Asian population.
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Affiliation(s)
- Xiaozheng Wu
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Wen Li
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Zhenliang Luo
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China
| | - Yunzhi Chen
- Department of Preclinical Medicine, Guizhou University of Traditional Chinese Medicine, Guiyang, 510025, China.
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30
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van Moorsel CHM, van der Vis JJ, Duckworth A, Scotton CJ, Benschop C, Ellinghaus D, Ruven HJT, Quanjel MJR, Grutters JC. The MUC5B Promoter Polymorphism Associates With Severe COVID-19 in the European Population. Front Med (Lausanne) 2021; 8:668024. [PMID: 34888316 PMCID: PMC8650310 DOI: 10.3389/fmed.2021.668024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 10/22/2021] [Indexed: 01/11/2023] Open
Abstract
Background: Diversity in response on exposure to severe acute respiratory syndrome coronavirus 2 may be related to the innate immune response in the elderly. The mucin MUC5B is an important component of the innate immune response and expression levels are associated with the MUC5B promoter polymorphism, rs35705950. The high expressing T-allele is a risk allele for the non-infectious aging lung disease idiopathic pulmonary fibrosis (IPF). We investigated if MUC5B rs35705950 associates with severe COVID-19. Methods: In this retrospective candidate gene case-control study we recruited 108 Dutch patients (69% male, median age 66 years, 77% white) requiring hospitalization for COVID-19 (22% ICU stay, 24% died). For validation, genotypes were obtained from the UK-Biobank (n = 436, 57% male, median age 70 years, 27% died), for replication data from the severe COVID-19 GWAS group from Italy (n = 835) and Spain (n = 775) was used, each with a control cohort (n = 356,735, n = 1,255, n = 950, respectively). MUC5B association analysis was performed including adjustment for age and sex. Results: The rs35705950 T-allele frequency was significantly lower in Dutch white patients (n = 83) than in controls (0.04 vs. 0.10; p = 0.02). This was validated in the UK biobank cohort (0.08 vs. 0.11; p = 0.001). While age and sex differed significantly between cases and control, comparable results were obtained with age and sex as confounding variables in a multivariate analysis. The association was replicated in the Italian (p = 0.04), and Spanish (p = 0.03) case-control cohorts. Meta-analysis showed a negative association for the T-allele with COVID-19 (OR = 0.75 (CI: 0.67–0.85); p = 6.63 × 10−6). Conclusions: This study shows that carriage of the T-allele of MUC5B rs35705950 confers protection from development of severe COVID-19. Because the T-allele is a known risk allele for IPF, this study provides further evidence for the existence of trade-offs between optimal mucin expression levels in the aging lung.
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Affiliation(s)
- Coline H M van Moorsel
- Department of Pulmonology, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands.,Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
| | - Joanne J van der Vis
- Department of Pulmonology, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands.,Department of Clinical Chemistry, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands
| | - Anna Duckworth
- College of Medicine & Health, Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
| | - Chris J Scotton
- College of Medicine & Health, Institute of Biomedical & Clinical Science, University of Exeter, Exeter, United Kingdom
| | - Claudia Benschop
- Department of Pulmonology, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands.,Department of Medical Microbiology and Immunology, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands
| | - David Ellinghaus
- Genetics and Bioinformatics Group, Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, University of Copenhagen, Copenhagen, Denmark
| | - Henk J T Ruven
- Department of Clinical Chemistry, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands
| | - Marian J R Quanjel
- Department of Pulmonology, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands
| | - Jan C Grutters
- Department of Pulmonology, St Antonius ILD Center of Excellence, St. Antonius Hospital, Nieuwegein, Netherlands.,Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, Netherlands
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31
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Konigsberg IR, Borie R, Walts AD, Cardwell J, Rojas M, Metzger F, Hauck SM, Fingerlin TE, Yang IV, Schwartz DA. Molecular Signatures of Idiopathic Pulmonary Fibrosis. Am J Respir Cell Mol Biol 2021; 65:430-441. [PMID: 34038697 PMCID: PMC8525208 DOI: 10.1165/rcmb.2020-0546oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/24/2021] [Indexed: 11/24/2022] Open
Abstract
Molecular patterns and pathways in idiopathic pulmonary fibrosis (IPF) have been extensively investigated, but few studies have assimilated multiomic platforms to provide an integrative understanding of molecular patterns that are relevant in IPF. Herein, we combine the coding and noncoding transcriptomes, DNA methylomes, and proteomes from IPF and healthy lung tissue to identify molecules and pathways associated with this disease. RNA sequencing, Illumina MethylationEPIC array, and liquid chromatography-mass spectrometry proteomic data were collected on lung tissue from 24 subjects with IPF and 14 control subjects. Significant differential features were identified by using linear models adjusting for age and sex, inflation, and bias when appropriate. Data Integration Analysis for Biomarker Discovery Using a Latent Component Method for Omics Studies was used for integrative multiomic analysis. We identified 4,643 differentially expressed transcripts aligning to 3,439 genes, 998 differentially abundant proteins, 2,500 differentially methylated regions, and 1,269 differentially expressed long noncoding RNAs (lncRNAs) that were significant after correcting for multiple tests (false discovery rate < 0.05). Unsupervised hierarchical clustering using 20 coding mRNA, protein, methylation, and lncRNA features with the highest loadings on the top latent variable from the four data sets demonstrates perfect separation of IPF and control lungs. Our analysis confirmed previously validated molecules and pathways known to be dysregulated in disease and implicated novel molecular features as potential drivers and modifiers of disease. For example, 4 proteins, 18 differentially methylated regions, and 10 lncRNAs were found to have strong correlations (|r| > 0.8) with MMP7 (matrix metalloproteinase 7). Therefore, by using a system biology approach, we have identified novel molecular relationships in IPF.
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Affiliation(s)
- Iain R. Konigsberg
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - Raphael Borie
- Department of Medicine, Bichat Hospital, Paris, France
| | - Avram D. Walts
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - Jonathan Cardwell
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - Mauricio Rojas
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Fabian Metzger
- Research Unit for Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany; and
| | - Stefanie M. Hauck
- Research Unit for Protein Science, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany; and
| | - Tasha E. Fingerlin
- Department of Immunology and Genomic Medicine and Center for Genes, Environment and Health, National Jewish Health, Denver, Colorado
| | - Ivana V. Yang
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
| | - David A. Schwartz
- Department of Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado
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A Closer Look at the Role of Anti-CCP Antibodies in the Pathogenesis of Rheumatoid Arthritis-Associated Interstitial Lung Disease and Bronchiectasis. Rheumatol Ther 2021; 8:1463-1475. [PMID: 34449068 PMCID: PMC8572256 DOI: 10.1007/s40744-021-00362-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 08/13/2021] [Indexed: 12/20/2022] Open
Abstract
Rheumatoid arthritis (RA) is an articular disease with extra-articular manifestations. Pulmonary manifestations are not uncommon and can involve all compartments of the lungs with airway disease in the form of bronchiectasis or bronchiolitis, interstitial lung disease (ILD), pleural effusions and parenchymal lung nodules. The pulmonary features may present synchronously or after the articular disease, but, importantly, it may be the first presentation in 10% of patients in the absence of articular symptoms. Here we discuss the pathogenesis of RA lung involvement, particularly interstitial lung disease and bronchiectasis, focusing on the role anti-CCP antibodies (ACPAs). We highlight the complex interplay among genetic, environmental and immune factors. Furthermore, we explore the relationship of citrullination and smoking as well as the concept of interstitial pneumonia with autoimmune features (IPAF), where patients do not have evidence of another known cause of interstitial pneumonia and have incomplete features of connective tissue disease (CTD). We surmise that the frequency and titers of rheumatoid factor (RF) and ACPAs are increased in bronchiectasis and RA-bronchiectasis compared to RA patients without lung disease. ACPA is associated with more severe disease in both RA-ILD and RA-bronchiectasis even in the absence of articular symptoms. There is no clear prediction of development of articular RA with high ACPA levels in the context of positive ACPA and ILD; however, in RA-bronchiectasis, patients with positive antibodies can develop RA within a year after diagnosis of bronchiectasis. Though the primary focus of this narrative is to highlight the role of ACPA in pathogenesis and clinical practice, we also discuss the current treatment options and trials in RA-ILD and RA-bronchiectasis. Currently, there are no clear treatment guidelines. The treatments are now focusing on using a combination of immunosuppression and antifibrotic agents. Combination treatment targets both the fibrotic and inflammatory components of the disease process. Further studies are needed to identify the use of ACPA as a biomarker to tailor the treatment in RA-ILD and RA-bronchiectasis.
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Li FJ, Surolia R, Li H, Wang Z, Liu G, Kulkarni T, Massicano AVF, Mobley JA, Mondal S, de Andrade JA, Coonrod SA, Thompson PR, Wille K, Lapi SE, Athar M, Thannickal VJ, Carter AB, Antony VB. Citrullinated vimentin mediates development and progression of lung fibrosis. Sci Transl Med 2021; 13:13/585/eaba2927. [PMID: 33731433 DOI: 10.1126/scitranslmed.aba2927] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 07/06/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022]
Abstract
The mechanisms by which environmental exposures contribute to the pathogenesis of lung fibrosis are unclear. Here, we demonstrate an increase in cadmium (Cd) and carbon black (CB), common components of cigarette smoke (CS) and environmental particulate matter (PM), in lung tissue from subjects with idiopathic pulmonary fibrosis (IPF). Cd concentrations were directly proportional to citrullinated vimentin (Cit-Vim) amounts in lung tissue of subjects with IPF. Cit-Vim amounts were higher in subjects with IPF, especially smokers, which correlated with lung function and were associated with disease manifestations. Cd/CB induced the secretion of Cit-Vim in an Akt1- and peptidylarginine deiminase 2 (PAD2)-dependent manner. Cit-Vim mediated fibroblast invasion in a 3D ex vivo model of human pulmospheres that resulted in higher expression of CD26, collagen, and α-SMA. Cit-Vim activated NF-κB in a TLR4-dependent fashion and induced the production of active TGF-β1, CTGF, and IL-8 along with higher surface expression of TLR4 in lung fibroblasts. To corroborate ex vivo findings, mice treated with Cit-Vim, but not Vim, independently developed a similar pattern of fibrotic tissue remodeling, which was TLR4 dependent. Moreover, wild-type mice, but not PAD2-/- and TLR4 mutant (MUT) mice, exposed to Cd/CB generated high amounts of Cit-Vim, in both plasma and bronchoalveolar lavage fluid, and developed lung fibrosis in a stereotypic manner. Together, these studies support a role for Cit-Vim as a damage-associated molecular pattern molecule (DAMP) that is generated by lung macrophages in response to environmental Cd/CB exposure. Furthermore, PAD2 might represent a promising target to attenuate Cd/CB-induced fibrosis.
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Affiliation(s)
- Fu Jun Li
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ranu Surolia
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Huashi Li
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Zheng Wang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Gang Liu
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Tejaswini Kulkarni
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adriana V F Massicano
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - James A Mobley
- Department of Surgery, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Santanu Mondal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Joao A de Andrade
- Vanderbilt Lung Institute, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Scott A Coonrod
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Paul R Thompson
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Keith Wille
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Suzanne E Lapi
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Mohammad Athar
- Department of Dermatology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Victor J Thannickal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Birmingham VA Medical Center, Birmingham, AL 35294, USA
| | - A Brent Carter
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.,Birmingham VA Medical Center, Birmingham, AL 35294, USA
| | - Veena B Antony
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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Dobrinskikh E, Estrella AM, Hennessy CE, Hara N, Schwarz MI, Kurche JS, Yang IV, Schwartz DA. Genes, other than Muc5b, play a role in bleomycin-induced lung fibrosis. Am J Physiol Lung Cell Mol Physiol 2021; 321:L440-L450. [PMID: 34160296 PMCID: PMC8410112 DOI: 10.1152/ajplung.00615.2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is an incurable genetic disease that affects 5 million people worldwide. The gain-of-function MUC5B promoter variant rs35705950 is the dominant genetic risk factor for IPF, yet has a low penetrance. This raises the possibility that other genes and transcripts affect the penetrance of MUC5B. Previously, we have shown that the concentration of Muc5b in bronchoalveolar epithelia is directly associated with the extent and persistence of bleomycin-induced lung fibrosis in mice. In this study, we investigated whether bleomycin-induced lung injury is Muc5b dependent in genetically divergent strains of mice. Specifically, mice from the eight Diversity Outbred (DO) founders were phenotyped for Muc5b expression and lung fibrosis 3 wk after intratracheal bleomycin administration. Although we identified strains with low Muc5b expression and minimal lung fibrosis (CAST/EiJ and PWK/PhJ) and strains with high Muc5b expression and extensive lung fibrosis (NZO/H1LtJ and WSB/EiJ), there also were strains that did not demonstrate a clear relationship between Muc5b expression and lung fibrosis (129S1/SvlmJ, NOD/ShiLtJ, and C57BL/6J, A/J). Hierarchical clustering suggests that other factors may work in concert with or potentially independent of Muc5b to promote bleomycin-induced lung injury and fibrosis. This study suggests that these strains and their recombinant inbred crosses may prove helpful in identifying the genes and transcripts that interact with Muc5b and cause lung fibrosis.
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Affiliation(s)
- Evgenia Dobrinskikh
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Alani M Estrella
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Corinne E Hennessy
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Naoko Hara
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Marvin I Schwarz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - Ivana V Yang
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado.,Department of Immunology, University of Colorado School of Medicine, Aurora, Colorado
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Furukawa H, Oka S, Higuchi T, Shimada K, Hashimoto A, Matsui T, Tohma S. Biomarkers for interstitial lung disease and acute-onset diffuse interstitial lung disease in rheumatoid arthritis. Ther Adv Musculoskelet Dis 2021; 13:1759720X211022506. [PMID: 34211592 PMCID: PMC8216360 DOI: 10.1177/1759720x211022506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/11/2021] [Indexed: 12/31/2022] Open
Abstract
Interstitial lung disease (ILD) is frequently a complication of rheumatoid arthritis (RA) as an extra-articular manifestation which has a poor prognosis. Acute-onset diffuse ILD (AoDILD) occasionally occurs in RA and includes acute exacerbation of ILD, drug-induced ILD, and Pneumocystis pneumonia. AoDILD also confers a poor prognosis in RA. Previously-established biomarkers for ILD include Krebs von den lungen-6 and surfactant protein-D originally defined in patients with idiopathic pulmonary fibrosis; the sensitivity of these markers for RA-associated ILD (RA-ILD) is low. Although many studies on ILD markers have been performed in idiopathic pulmonary fibrosis, only a few validation studies in RA-ILD or AoDILD have been reported. Biomarkers for RA-ILD and AoDILD are thus still required. Recently, genomic, cytokine, antibody, and metabolomic profiles of RA-ILD or AoDILD have been investigated with the aim of improving biomarkers. In this review, we summarize current preliminary data on these potential biomarkers for RA-ILD or AoDILD. The development of biomarkers on RA-ILD has only just begun. When validated, such candidate biomarkers will provide valuable information on pathogenesis, prognosis, and drug responses in RA-ILD in future.
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Affiliation(s)
- Hiroshi Furukawa
- Department of Rheumatology, National Hospital Organization Tokyo National Hospital, 3-1-1 Takeoka, Kiyose 204-8585, Japan
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
| | - Shomi Oka
- Department of Rheumatology, National Hospital Organization Tokyo National Hospital, Kiyose, Japan
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
| | - Takashi Higuchi
- Department of Rheumatology, National Hospital Organization Tokyo National Hospital, Kiyose, Japan
- Department of Nephrology, Ushiku Aiwa General Hospital, Ushiku, Japan
| | - Kota Shimada
- Department of Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
- Department of Rheumatic Diseases, Tokyo Metropolitan Tama Medical Center, Fuchu, Japan
| | - Atsushi Hashimoto
- Department of Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
- Department of Internal Medicine, Sagami Seikyou Hospital, Minami-ku, Sagamihara, Japan
| | - Toshihiro Matsui
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
- Department of Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
| | - Shigeto Tohma
- Department of Rheumatology, National Hospital Organization Tokyo National Hospital, Kiyose, Japan
- Clinical Research Center for Allergy and Rheumatology, National Hospital Organization Sagamihara National Hospital, Minami-ku, Sagamihara, Japan
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Rostami MR, Bradic M. The derepression of transposable elements in lung cells is associated with the inflammatory response and gene activation in idiopathic pulmonary fibrosis. Mob DNA 2021; 12:14. [PMID: 34108012 PMCID: PMC8191028 DOI: 10.1186/s13100-021-00241-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 04/26/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Transposable elements (TEs) are repetitive sequences of viral origin that compose almost half of the human genome. These elements are tightly controlled within cells, and if activated, they can cause changes in both gene regulation and immune viral responses that have been associated with several chronic inflammatory diseases in humans. As oxidants are potent activators of TEs, and because oxidative injury is a major risk factor in relation to idiopathic pulmonary fibrosis (IPF), we hypothesized that TEs might be involved in the regulation of gene expression and so contribute to inflammation in cases of IPF. IPF is a fatal lung disease that involves the gradual replacement of the alveolar tissue with fibrotic scars as well as the accumulation of inflammatory cells in the lower respiratory tract. Although IPF is known to occur as a result of the complex interaction between age, environmental risk factors (i.e., oxidative stress) and genetics, the relative contributions of these factors to the disease remain unclear. To determine whether TEs are associated with IPF, we compared the transcriptional profiles of the genes and TEs of lung cells obtained from both healthy donors and IPF patients. RESULTS We quantified TE and gene expression levels using a published bulk RNA-seq dataset containing 24 subjects (16 donors and eight IPF patients), including three lung-cell types per subject, as well as an scRNA-seq dataset concerning 16 subjects (eight donors and eight IPF patients). We found evidence of TE dysregulation in the alveolar type II lung cells and alveolar macrophages of the IPF patients. In addition, the activation of the LINE1 family of elements in IPF is associated with the increased expression of TE cellular regulators (MOV10, IFI16, SAMHD1, and APOBECG3), interferon-stimulating genes (ISG15, IFI6, IFI27, IFI44, and OAS1), chemokines (CX3CL1 and CXCL9), and interleukins (IL15RA). We also propose that TE derepression might be involved in the regulation of previously reported IPF candidate genes (MUC5B, CHL1, SPP1, and MMP7). CONCLUSION Based on our findings, we propose that TE derepression plays an important role in the regulation of gene expression and can also prompt both the recruitment of inflammatory processes and the disruption of the immunological balance, which can lead to chronic inflammation in IPF.
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Affiliation(s)
- Mahboubeh R Rostami
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA
| | - Martina Bradic
- Department of Genetic Medicine, Weill Cornell Medical College, 1300 York Avenue, Box 164, New York, NY, 10065, USA.
- Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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It's in the (Epi)genetics: Effects of DNA Methylation on Gene Expression in Atopic Asthma? Chest 2021; 158:1799-1801. [PMID: 33160517 DOI: 10.1016/j.chest.2020.07.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022] Open
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Biondini D, Cocconcelli E, Bernardinello N, Lorenzoni G, Rigobello C, Lococo S, Castelli G, Baraldo S, Cosio MG, Gregori D, Saetta M, Balestro E, Spagnolo P. Prognostic role of MUC5B rs35705950 genotype in patients with idiopathic pulmonary fibrosis (IPF) on antifibrotic treatment. Respir Res 2021; 22:98. [PMID: 33794872 PMCID: PMC8017848 DOI: 10.1186/s12931-021-01694-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/24/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND A common variant located in the promoter region of MUC5B (rs35705950) is the strongest risk factor for sporadic and familiar IPF, as well as a predictor of outcome. However, there are no data on the effect of MUC5B rs35705950 genotype on the prognosis of IPF patients on antifibrotic treatment. The aim of this study is to determine, in a phenotypically well-characterized population of patients with IPF treated with antifibrotics, the impact of MUC5B rs35705950 genotype on disease progression and survival. METHODS 88 IPF patients on antifibrotic treatment were followed-up from 2014 until transplantation, death or end of follow-up (December 2019). Disease progression was defined as a forced vital capacity (FVC) loss ≥ 5% per year. All patients were genotyped for MUC5B rs35705950 by PCR amplification and Sanger sequencing. RESULTS Out of 88 patients, 61 (69%) carried the mutant T allele (TT or TG) and 27 (31%) did not (GG). Carriage of the MUC5B rs35705950 T allele was not associated with a faster decline in FVC. Conversely, at the end of the follow-up, overall survival in carriers of the TT/TG genotype was longer compared to that of the GG genotype carriers. FVC (L) at baseline and time to respiratory failure at rest were independent predictors of worse prognosis. CONCLUSIONS In IPF patients on antifibrotic treatment, carriage of the MUC5B rs35705950 T allele is associated with longer survival, highlighting the usefulness of MUC5B genetic data in clinical decision making.
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Affiliation(s)
- Davide Biondini
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Elisabetta Cocconcelli
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Nicol Bernardinello
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Giulia Lorenzoni
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac Thoracic Vascular Sciences and Public Health, University of Padova, 35128, Padova, Italy
| | - Chiara Rigobello
- Department of Women's and Children's Health, University of Padova, 35128, Padova, Italy
| | - Sara Lococo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Gioele Castelli
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Simonetta Baraldo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Manuel G Cosio
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy.,Meakins Christie Laboratories, Respiratory Division, McGill University, Montreal, Canada
| | - Dario Gregori
- Unit of Biostatistics, Epidemiology and Public Health, Department of Cardiac Thoracic Vascular Sciences and Public Health, University of Padova, 35128, Padova, Italy
| | - Marina Saetta
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Elisabetta Balestro
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy
| | - Paolo Spagnolo
- Respiratory Disease Unit, Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, Via Giustiniani 2, 35128, Padova, Italy.
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Bonella F, Campo I, Zorzetto M, Boerner E, Ohshimo S, Theegarten D, Taube C, Costabel U. Potential clinical utility of MUC5B und TOLLIP single nucleotide polymorphisms (SNPs) in the management of patients with IPF. Orphanet J Rare Dis 2021; 16:111. [PMID: 33639995 PMCID: PMC7913255 DOI: 10.1186/s13023-021-01750-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/16/2021] [Indexed: 11/26/2022] Open
Abstract
Background Genetic variants of TOLLIP and MUC5B, both on chromosome 11, have been reported to be associated with the development and/or prognosis of idiopathic pulmonary fibrosis (IPF). This retrospective study was conducted to investigate the association of MUC5B and TOLLIP SNPs with disease outcome in IPF. 62 IPF patients and 50 healthy controls (HC) from our Institution were genotyped for SNPs within MUC5B (rs35705950) and TOLLIP (rs3750920 and rs5743890). Correlation of SNPs genotypes with survival, acute exacerbation (AE) or disease progression (defined as a decline of ≥ 5% in FVC and or ≥ 10% in DLco in one year) was investigated. Results The MUC5B rs35705950 minor allele (T) was more frequent in IPF subjects than in HC (35% vs 9% p < 0.001). TOLLIP SNPs alleles and genotype distribution did not differ between IPF and HC and did not vary according to gender, age, BMI and lung functional impairment at baseline. The minor allele (C) in TOLLIP rs5743890 was associated with worse survival and with disease progression in all performed analyses. The MUC5B rs35705950 or the TOLLIP rs3750920 minor allele, were not associated with disease progression or AE.
Conclusion We confirm that the minor allele of MUC5B rs35705950 is associated with IPF. The minor allele of TOLLIP rs5743890 appears to be a predictor of worse survival and more rapid disease progression, therefore being of potential utility to stratify IPF patients at baseline.
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Affiliation(s)
- Francesco Bonella
- Center for Interstitial and Rare Lung Diseases, Pneumology Department, Ruhrlandklinik University Hospital, University of Duisburg-Essen, 45239, Essen, Germany.
| | - Ilaria Campo
- SC Pneumologia - Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Michele Zorzetto
- Clinical Chemistry Laboratory, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Eda Boerner
- Center for Interstitial and Rare Lung Diseases, Pneumology Department, Ruhrlandklinik University Hospital, University of Duisburg-Essen, 45239, Essen, Germany
| | - Shinichiro Ohshimo
- Department of Emergency and Critical Care Medicine, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Dirk Theegarten
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Christian Taube
- Center for Interstitial and Rare Lung Diseases, Pneumology Department, Ruhrlandklinik University Hospital, University of Duisburg-Essen, 45239, Essen, Germany
| | - Ulrich Costabel
- Center for Interstitial and Rare Lung Diseases, Pneumology Department, Ruhrlandklinik University Hospital, University of Duisburg-Essen, 45239, Essen, Germany
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40
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Gally F, Sasse SK, Kurche JS, Gruca MA, Cardwell JH, Okamoto T, Chu HW, Hou X, Poirion OB, Buchanan J, Preissl S, Ren B, Colgan SP, Dowell RD, Yang IV, Schwartz DA, Gerber AN. The MUC5B-associated variant rs35705950 resides within an enhancer subject to lineage- and disease-dependent epigenetic remodeling. JCI Insight 2021; 6:144294. [PMID: 33320836 PMCID: PMC7934873 DOI: 10.1172/jci.insight.144294] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/09/2020] [Indexed: 12/19/2022] Open
Abstract
The G/T transversion rs35705950, located approximately 3 kb upstream of the MUC5B start site, is the cardinal risk factor for idiopathic pulmonary fibrosis (IPF). Here, we investigate the function and chromatin structure of this –3 kb region and provide evidence that it functions as a classically defined enhancer subject to epigenetic programming. We use nascent transcript analysis to show that RNA polymerase II loads within 10 bp of the G/T transversion site, definitively establishing enhancer function for the region. By integrating Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) analysis of fresh and cultured human airway epithelial cells with nuclease sensitivity data, we demonstrate that this region is in accessible chromatin that affects the expression of MUC5B. Through applying paired single-nucleus RNA- and ATAC-seq to frozen tissue from IPF lungs, we extend these findings directly to disease, with results indicating that epigenetic programming of the –3 kb enhancer in IPF occurs in both MUC5B-expressing and nonexpressing lineages. In aggregate, our results indicate that the MUC5B-associated variant rs35705950 resides within an enhancer that is subject to epigenetic remodeling and contributes to pathologic misexpression in IPF.
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Affiliation(s)
- Fabienne Gally
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Sarah K Sasse
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Jonathan S Kurche
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Margaret A Gruca
- BioFrontiers Institute, University of Colorado-Boulder (CU Boulder), Boulder, Colorado, USA
| | | | - Tsukasa Okamoto
- Department of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Respiratory Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hong W Chu
- Department of Medicine, National Jewish Health, Denver, Colorado, USA
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Olivier B Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Justin Buchanan
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA
| | - Bing Ren
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, California, USA.,Ludwig Institute for Cancer Research, La Jolla, California, USA
| | - Sean P Colgan
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Robin D Dowell
- BioFrontiers Institute, University of Colorado-Boulder (CU Boulder), Boulder, Colorado, USA.,Molecular, Cellular and Developmental Biology, and.,Computer Science, CU Boulder, Boulder, Colorado, USA
| | - Ivana V Yang
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado, Aurora, Colorado, USA
| | - Anthony N Gerber
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, Colorado, USA.,Department of Medicine, University of Colorado, Aurora, Colorado, USA.,Department of Medicine, National Jewish Health, Denver, Colorado, USA
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41
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Michalski JE, Schwartz DA. Genetic Risk Factors for Idiopathic Pulmonary Fibrosis: Insights into Immunopathogenesis. J Inflamm Res 2021; 13:1305-1318. [PMID: 33447070 PMCID: PMC7801923 DOI: 10.2147/jir.s280958] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 12/18/2020] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis is an etiologically complex interstitial lung disease characterized by progressive scarring of the lungs with a subsequent decline in lung function. While much of the pathogenesis of IPF still remains unclear, it is now understood that genetic variation accounts for at least one-third of the risk of developing the disease. The single-most validated and most significant risk factor, genetic or otherwise, is a gain-of-function promoter variant in the MUC5B gene. While the functional impact of these IPF risk variants at the cellular and tissue levels are areas of active investigation, there is a growing body of evidence that these genetic variants may influence disease pathogenesis through modulation of innate immune processes.
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Affiliation(s)
- Jacob E Michalski
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
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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:sciadv.abb6075. [PMID: 33277324 PMCID: PMC7775789 DOI: 10.1126/sciadv.abb6075] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [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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43
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Lou HQ, Huang CX, Li GY, Li P, Zhang SM, Li HG, Han L, Bao MH. The Association between MUC5B Rs35705950 and Risks of Idiopathic Interstitial Pneumonia, Systemic Sclerosis Interstitial Lung Disease, and Familial Interstitial Pneumonia: A Meta-Analysis. IRANIAN JOURNAL OF PUBLIC HEALTH 2020; 49:2240-2250. [PMID: 34178730 PMCID: PMC8215073 DOI: 10.18502/ijph.v49i12.4801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background: Interstitial lung disease (ILD) is a category of chronic lung diseases with more than 200 subtypes. Idiopathic interstitial pneumonia (IIP), systemic sclerosis (SSc) ILD, and familial interstitial pneumonia (FIP) are three major groups of lung diseases with different causes or with unknown causes. Mucin5B (MUC5B) belongs to the mucin family, which contribute to the lubricating and viscoelastic properties of the whole saliva, normal lung mucus, and cervical mucus. The association between MUC5B rs35705950 and ILDs risks has been widely studied. However, the results were inconclusive and inconsistent. Methods: In the present meta-analysis, the database PubMed, Embase, Cochrane Central Register of Controlled Trials, CNKI and Chinese Biomedical Literature Database were searched till Aug 20th, 2018. Overall 16 publications with 28 studies, 76345 cases and 18402 controls were included. Results: The results indicated a significant increase of overall IIP risk for TT genotype and T allele of the rs35705950 in all genetic models (TT vs GG, OR=9.11; TT vs GT+TT, OR=5.80; GT+TT vs GG, OR=4.34; T vs G, OR=4.03. P<0.0001). Subgroup analysis by subtypes of IIP revealed higher risks of TT genotype and T allele for IPF and iNSIP (P<0.05). A significant increase of FIP risk was also found for the TT genotype and T allele of the rs35705950 (TT vs GG, OR=17.08; GT+TT vs GG, OR=6.02; T vs G, OR=1.64.P<0.05). Conclusion: No significant relations existed between the rs35705950 and SSc-ILD risks. MUC5B rs35705950 might be a predictor for the susceptibility of IIP and FIP.
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Affiliation(s)
- Huai-Qing Lou
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China.,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410007, China
| | - Chun-Xia Huang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Science, Changsha Medical University, Changsha, Hunan, 410007, China
| | - Guang-Yi Li
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Ping Li
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Shou-Ming Zhang
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China
| | - Hai-Gang Li
- Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China
| | - Li Han
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Physiology, School of Basic Medical Science, Central South University, Changsha, Hunan, 410007, China
| | - Mei-Hua Bao
- Department of Physiology and Pathophysiology, Science Research Center, School of Basic Medical Science, Changsha Medical University, Changsha, 410219, China.,Department of Pharmacology, School of Pharmaceutical Science, Changsha Medical University, Changsha, 410219, China
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44
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Dobrinskikh E, Yang IV. Unraveling the role of MUC5B in idiopathic interstitial pneumonias (IIPs). Thorax 2020; 75:830. [DOI: 10.1136/thoraxjnl-2020-215406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 06/28/2020] [Indexed: 11/04/2022]
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45
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Stock CJ, Conti C, Montero-Fernandez Á, Caramori G, Molyneaux PL, George PM, Kokosi M, Kouranos V, Maher TM, Chua F, Rice A, Denton CP, Nicholson AG, Wells A, Sestini P, Renzoni EA. Interaction between the promoter MUC5B polymorphism and mucin expression: is there a difference according to ILD subtype? Thorax 2020; 75:901-903. [PMID: 32580994 DOI: 10.1136/thoraxjnl-2020-214579] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 05/18/2020] [Accepted: 05/26/2020] [Indexed: 12/23/2022]
Abstract
The MUC5B promoter variant rs35705950 is associated with idiopathic pulmonary fibrosis (IPF). MUC5B glycoprotein is overexpressed in IPF lungs. We examined immunohistochemical expression of MUC5B in different interstitial lung disease patterns according to rs35705950 T-allele carriage. We observed increased expression of MUC5B in T-allele carriers in both distal airways and honeycomb cysts in patients with IPF (n=23), but no difference in MUC5B expression according to T-carrier status in the distal airways of patients with idiopathic non-specific interstitial pneumonitis (n=17), in scleroderma-associated non-specific interstitial pneumonitis (n=15) or in control lungs (n=20), suggesting that tissue overexpression in MUC5B rs35705950 T-carriers is specific to IPF.
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Affiliation(s)
- Carmel J Stock
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Caterina Conti
- Respiratory Unit ASST, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Ángeles Montero-Fernandez
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Gaetano Caramori
- UOC di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Philip L Molyneaux
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Peter M George
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Maria Kokosi
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Vaslis Kouranos
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Toby M Maher
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Felix Chua
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Alexandra Rice
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Christopher P Denton
- Centre for Rheumatology and Connective Tissue Diseases, University College London Medical School, London, UK
| | - Andrew G Nicholson
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Athol Wells
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
| | - Piersante Sestini
- Department of Medical and Surgical Sciences and Neurosciences, University of Siena, Siena, Toscana, Italy
| | - Elisabetta A Renzoni
- Interstitial Lung Disease Unit, Royal Brompton and Harefield NHS Foundation Trust/ National Heart and Lung Institute, Imperial College, London, UK
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46
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DNA Methylation in Chronic Obstructive Pulmonary Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1255:83-98. [PMID: 32949392 DOI: 10.1007/978-981-15-4494-1_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a lung disease affected by both genetic and environmental factors. Therefore, the role of epigenetics in the pathogenesis of COPD has attracted much attention. As one of the three epigenetic mechanisms, DNA methylation has been extensively studied in COPD. The present review aims at overviewing the effect of DNA methylation on etiology, pathogenesis, pathophysiological changes, and complications of COPD. The clarification of aberrant methylation of target genes, which play important roles in the initiation and progression of COPD, will provide new disease-specific biomarker and targets for early diagnosis and therapy.
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47
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Paudel KR, Dharwal V, Patel VK, Galvao I, Wadhwa R, Malyla V, Shen SS, Budden KF, Hansbro NG, Vaughan A, Yang IA, Kohonen-Corish MRJ, Bebawy M, Dua K, Hansbro PM. Role of Lung Microbiome in Innate Immune Response Associated With Chronic Lung Diseases. Front Med (Lausanne) 2020; 7:554. [PMID: 33043031 PMCID: PMC7530186 DOI: 10.3389/fmed.2020.00554] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), lung fibrosis, and lung cancer, pose a huge socio-economic burden on society and are one of the leading causes of death worldwide. In the past, culture-dependent techniques could not detect bacteria in the lungs, therefore the lungs were considered a sterile environment. However, the development of culture-independent techniques, particularly 16S rRNA sequencing, allowed for the detection of commensal microbes in the lung and with further investigation, their roles in disease have since emerged. In healthy individuals, the predominant commensal microbes are of phylum Firmicutes and Bacteroidetes, including those of the genera Veillonella and Prevotella. In contrast, pathogenic microbes (Haemophilus, Streptococcus, Klebsiella, Pseudomonas) are often associated with lung diseases. There is growing evidence that microbial metabolites, structural components, and toxins from pathogenic and opportunistic bacteria have the capacity to stimulate both innate and adaptive immune responses, and therefore can contribute to the pathogenesis of lung diseases. Here we review the multiple mechanisms that are altered by pathogenic microbiomes in asthma, COPD, lung cancer, and lung fibrosis. Furthermore, we focus on the recent exciting advancements in therapies that can be used to restore altered microbiomes in the lungs.
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Affiliation(s)
- Keshav Raj Paudel
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Vivek Dharwal
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Vyoma K Patel
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Izabela Galvao
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Ridhima Wadhwa
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Vamshikrishna Malyla
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Sj Sijie Shen
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Kurtis F Budden
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Nicole G Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Annalicia Vaughan
- Faculty of Medicine, Thoracic Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Ian A Yang
- Faculty of Medicine, Thoracic Research Centre, The University of Queensland, Brisbane, QLD, Australia.,Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Maija R J Kohonen-Corish
- Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.,School of Medicine, Western Sydney University, Sydney, NSW, Australia.,St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Mary Bebawy
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia
| | - Kamal Dua
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M Hansbro
- Centre for Inflammation, Centenary Institute, Sydney, NSW, Australia.,Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.,Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, The University of Newcastle, Newcastle, NSW, Australia
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48
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Iyer GR, Samajder S, Zubeda S, S DSN, Mali V, Pv SK, Sharma A, Abbas NZ, Bora NS, Narravula A, Hasan Q. Infectivity and Progression of COVID-19 Based on Selected Host Candidate Gene Variants. Front Genet 2020; 11:861. [PMID: 33101356 PMCID: PMC7500201 DOI: 10.3389/fgene.2020.00861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/15/2020] [Indexed: 12/30/2022] Open
Abstract
Introduction: Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) has spread around the globe. Susceptibility has been associated with age, biological sex, and other prior existing health conditions. However, host genes are involved in viral infectivity and pathogenicity, and polymorphisms in these could be responsible for the interethnic/interindividual variability observed in infection and progression of COVID-19. Materials and Methods: Clinical exome data of 103 individuals was analyzed to identify sequence variants in five selected candidate genes: ACE2, TMPRSS2, CD209, IFITM3, and MUC5B to assess their prevalence and role to understand the COVID-19 infectivity and progression in our population. Results: A total of 497 polymorphisms were identified in the five selected genes in the exomes analyzed. Thirty-eight polymorphisms identified in our cohort have been reported earlier in literature and have functional significance or association with health conditions. These variants were classified into three groups: protective, susceptible, and responsible for comorbidities. Discussion and Conclusion: The two polymorphisms described in literature as risk inducing are rs35705950 in MUC5B gene and TMPRSS2 haplotype (rs463727, rs34624090, rs55964536, rs734056, rs4290734, rs34783969, rs11702475, rs35899679, and rs35041537) were absent in our cohort explaining the slower infectivity of the disease in this part of India. The 38 functional variants identified can be used as a predisposition panel for the COVID-19 infectivity and progression and stratify individuals as "high or low risk," which would help in planning appropriate surveillance and management protocols. A larger study from different regions of India is warranted to validate these results.
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Affiliation(s)
- Gayatri R Iyer
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India.,Department of Genetics, Osmania University, Hyderabad, India
| | - Sayani Samajder
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Syeda Zubeda
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | | | - Vishakha Mali
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Sharath Krishnan Pv
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Anuradha Sharma
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | | | | | - Amulya Narravula
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
| | - Qurratulain Hasan
- Department of Genetics and Molecular Medicine, Kamineni Hospitals, Hyderabad, India
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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: 54] [Impact Index Per Article: 13.5] [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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50
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Dai Y, Wang W, Yu Y, Hu S. Rheumatoid arthritis-associated interstitial lung disease: an overview of epidemiology, pathogenesis and management. Clin Rheumatol 2020; 40:1211-1220. [PMID: 32794076 DOI: 10.1007/s10067-020-05320-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/16/2020] [Accepted: 08/04/2020] [Indexed: 12/29/2022]
Abstract
Interstitial lung disease (ILD) accounts for the major cause of morbidity and mortality in rheumatoid arthritis (RA). However, little is known of the pathogenesis, diagnosis and treatment of RA-associated ILD. In this review, we describe our present understanding and ongoing research in RA-ILD. Its aetiology does appear to associate with anti-cyclic citrullinated peptide antibodies, MUC5B mutation and smoking. Another focus of this article is on recent diagnostic methods in RA-ILD. Compared with other methods, high-resolution computed tomography (HRCT) imaging is a main method for the evaluation of ILD in RA patients. Pulmonary function is better suited for assessing progression. An important topic relates to therapeutic intervention. Disease-modifying anti-rheumatic drugs (DMARDs) in RA lack strong evidence in the onset or worsening of ILD. The available literature support that methotrexate, leflunomide, abatacept and rituximab play beneficial roles in the prevention and treatment of RA-ILD.
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Affiliation(s)
- Yujie Dai
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 JieFang Road, Wuhan, HuBei, China.,Department of Nephrology and Rheumatology, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Weina Wang
- Department of Respiration, Puai Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yikai Yu
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 JieFang Road, Wuhan, HuBei, China.
| | - Shaoxian Hu
- Department of Rheumatology and Immunology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 JieFang Road, Wuhan, HuBei, China.
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