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Karp T, Faiz A, van Nijnatten J, Kerstjens HAM, Boudewijn I, Kraft M, Vonk JM, Nawijn MC, Heijink IH, Beghé B, Rabe KF, Papi A, Brightling C, Singh D, van der Molen T, Siddiqui S, Christenson S, Guryev V, van den Berge M. Nasal epithelial gene expression identifies relevant asthma endotypes in the ATLANTIS study. Thorax 2024; 79:905-914. [PMID: 39009441 DOI: 10.1136/thorax-2023-221230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 06/18/2024] [Indexed: 07/17/2024]
Abstract
INTRODUCTION Asthma is an inflammatory airways disease encompassing multiple phenotypes and endotypes. Several studies suggested gene expression in nasal epithelium to serve as a proxy for bronchial epithelium, being a non-invasive approach to investigate lung diseases. We hypothesised that molecular differences in upper airway epithelium reflect asthma-associated differences in the lower airways and are associated with clinical expression of asthma. METHODS We analysed nasal epithelial gene expression data from 369 patients with asthma and 58 non-asthmatic controls from the Assessment of Small Airways Involvement in Asthma study. Unsupervised hierarchical clustering was performed on asthma-associated genes. Asthma-associated gene signatures were replicated in independent cohorts with nasal and bronchial brushes data by comparing Gene Set Variation Analysis scores between asthma patients and non-asthmatic controls. RESULTS We identified 67 higher expressed and 59 lower expressed genes in nasal epithelium from asthma patients compared with controls (false discovery rate<0.05), including CLCA1, CST1 and POSTN, genes well known to reflect asthma in bronchial airway epithelium. Hierarchical clustering revealed several molecular asthma endotypes with distinct clinical characteristics, including an endotype with higher blood and sputum eosinophils, high fractional exhaled nitric oxide, and more severe small airway dysfunction, as reflected by lower forced expiratory flow at 50%. In an independent cohort, we demonstrated that genes higher expressed in the nasal epithelium reflect asthma-associated changes in the lower airways. CONCLUSION Our results show that the nasal epithelial gene expression profile reflects asthma-related processes in the lower airways. We suggest that nasal epithelium may be a useful non-invasive tool to identify asthma endotypes and may advance personalised management of the disease.
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Affiliation(s)
- Tatiana Karp
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Jos van Nijnatten
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Respiratory Bioinformatics and Molecular Biology, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Huib A M Kerstjens
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Ilse Boudewijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Monica Kraft
- Samuel Bronfman Department of Medicine, Icahn School of Medicine, Mount Sinai Medical Center, New York, New York, USA
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Irene H Heijink
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Bianca Beghé
- Department of Respiratory Diseases, University of Modena and Reggio Emilia, Modena, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University Kiel, Kiel and LungenClinic, Grosshansdorf, Germany
| | - Alberto Papi
- Section of Respiratory Medicine, Department of Translational Medicine, University of Ferrara, Ferrara, Italy
| | - Chris Brightling
- The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Dave Singh
- Centre for Respiratory Medicine and Allergy, University of Manchester, Manchester University NHS Foundation Trust, Manchester, UK
| | - Thys van der Molen
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of General Practice and Elderly Care Medicine, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Salman Siddiqui
- Imperial College London National Heart and Lung Institute, London, UK
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine, University of California San Francisco, San Francisco, California, USA
| | - Victor Guryev
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center, Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center, Groningen, The Netherlands
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Buschur KL, Pottinger TD, Vogel-Claussen J, Powell CA, Aguet F, Allen NB, Ardlie K, Bluemke DA, Durda P, Hermann EA, Hoffman EA, Lima JA, Liu Y, Malinsky D, Manichaikul A, Motahari A, Post WS, Prince MR, Rich SS, Rotter JI, Smith BM, Tracy RP, Watson K, Winther HB, Lappalainen T, Barr RG. Peripheral Blood Mononuclear Cell Gene Expression Associated with Pulmonary Microvascular Perfusion: The Multi-Ethnic Study of Atherosclerosis Chronic Obstructive Pulmonary Disease. Ann Am Thorac Soc 2024; 21:884-894. [PMID: 38335160 PMCID: PMC11160125 DOI: 10.1513/annalsats.202305-417oc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 02/09/2024] [Indexed: 02/12/2024] Open
Abstract
Rationale: Chronic obstructive pulmonary disease (COPD) and emphysema are associated with endothelial damage and altered pulmonary microvascular perfusion. The molecular mechanisms underlying these changes are poorly understood in patients, in part because of the inaccessibility of the pulmonary vasculature. Peripheral blood mononuclear cells (PBMCs) interact with the pulmonary endothelium. Objectives: To test the association between gene expression in PBMCs and pulmonary microvascular perfusion in COPD. Methods: The Multi-Ethnic Study of Atherosclerosis (MESA) COPD Study recruited two independent samples of COPD cases and controls with ⩾10 pack-years of smoking history. In both samples, pulmonary microvascular blood flow, pulmonary microvascular blood volume, and mean transit time were assessed on contrast-enhanced magnetic resonance imaging, and PBMC gene expression was assessed by microarray. Additional replication was performed in a third sample with pulmonary microvascular blood volume measures on contrast-enhanced dual-energy computed tomography. Differential expression analyses were adjusted for age, gender, race/ethnicity, educational attainment, height, weight, smoking status, and pack-years of smoking. Results: The 79 participants in the discovery sample had a mean age of 69 ± 6 years, 44% were female, 25% were non-White, 34% were current smokers, and 66% had COPD. There were large PBMC gene expression signatures associated with pulmonary microvascular perfusion traits, with several replicated in the replication sets with magnetic resonance imaging (n = 47) or dual-energy contrast-enhanced computed tomography (n = 157) measures. Many of the identified genes are involved in inflammatory processes, including nuclear factor-κB and chemokine signaling pathways. Conclusions: PBMC gene expression in nuclear factor-κB, inflammatory, and chemokine signaling pathways was associated with pulmonary microvascular perfusion in COPD, potentially offering new targetable candidates for novel therapies.
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Affiliation(s)
| | | | - Jens Vogel-Claussen
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
- Department of Radiology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | | | - Francois Aguet
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Norrina B. Allen
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Kristin Ardlie
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - David A. Bluemke
- Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | | | - Eric A. Hoffman
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - João A.C. Lima
- Division of Cardiology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Yongmei Liu
- Department of Medicine, Duke University Medical Center, Durham, North Carolina
| | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Amin Motahari
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Wendy S. Post
- Division of Cardiology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | | | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California
| | - Benjamin M. Smith
- Department of Medicine
- Research Institute, McGill University Health Center, Montreal, Québec, Canada
| | - Russell P. Tracy
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Karol Watson
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California; and
| | - Hinrich B. Winther
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
| | - Tuuli Lappalainen
- Department of Biostatistics
- Department of Systems Biology, Columbia University Medical Center, New York, New York
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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3
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El-Husseini ZW, Khalenkow D, Lan A, van der Molen T, Brightling C, Papi A, Rabe KF, Siddiqui S, Singh D, Kraft M, Beghe B, van den Berge M, van Gosliga D, Nawijn MC, Rose-John S, Koppelman GH, Gosens R. An epithelial gene signature of trans-IL-6 signaling defines a subgroup of type 2-low asthma. Respir Res 2023; 24:308. [PMID: 38062491 PMCID: PMC10704725 DOI: 10.1186/s12931-023-02617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Asthma is stratified into type 2-high and type 2-low inflammatory phenotypes. Limited success has been achieved in developing drugs that target type 2-low inflammation. Previous studies have linked IL-6 signaling to severe asthma. IL-6 cooperates with soluble-IL-6Rα to activate cell signaling in airway epithelium. OBJECTIVE We sought to study the role of sIL-6Rα amplified IL-6 signaling in airway epithelium and to develop an IL-6+ sIL-6Rα gene signature that may be used to select asthma patients who potentially respond to anti-IL-6 therapy. METHODS Human airway epithelial cells were stimulated with combinations of IL-6, sIL-6Rα, and inhibitors, sgp130 (Olamkicept), and anti-IL-6R (Tocilizumab), to assess effects on pathway activation, epithelial barrier integrity, and gene expression. A gene signature was generated to identify IL-6 high patients using bronchial biopsies and nasal brushes. RESULTS Soluble-IL-6Rα amplified the activation of the IL-6 pathway, shown by the increase of STAT3 phosphorylation and stronger gene induction in airway epithelial cells compared to IL-6 alone. Olamkicept and Tocilizumab inhibited the effect of IL-6 + sIL-6Rα on gene expression. We developed an IL-6 + sIL-6Rα gene signature and observed enrichment of this signature in bronchial biopsies but not nasal brushes from asthma patients compared to healthy controls. An IL-6 + sIL-6Rα gene signature score was associated with lower levels of sputum eosinophils in asthma. CONCLUSION sIL-6Rα amplifies IL-6 signaling in bronchial epithelial cells. Higher local airway IL-6 + sIL-6Rα signaling is observed in asthma patients with low sputum eosinophils.
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Affiliation(s)
- Zaid W El-Husseini
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Dmitry Khalenkow
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Andy Lan
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Thys van der Molen
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Chris Brightling
- Department of Infection, Immunity and Inflammation, Institute for Lung Health, University of Leicester, Leicester, UK
| | - Alberto Papi
- Department of Respiratory Medicine, University of Ferrara, Ferrara, Italy
| | - Klaus F Rabe
- Department of Medicine, Christian Albrechts University Kiel, Kiel and Lungen Clinic Grosshansdorf (Members of the German Center for Lung Research (DZL)), Grosshansdorf, Germany
| | - Salman Siddiqui
- National Heart and Lung Institute, Imperial College and Imperial NIHR Biomedical Research Centre, London, UK
| | - Dave Singh
- Medicines Evaluation Unit, Manchester University NHS Foundation Hospital Trust, University of Manchester, Manchester, UK
| | - Monica Kraft
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Bianca Beghe
- University of Modena and Reggio Emilia, AOU of Modena, Modena, Italy
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Djoke van Gosliga
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | - Martijn C Nawijn
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
- Department of Pathology and Medical Biology, Experimental Pulmonary and Inflammatory Research (EXPIRE), University of Groningen, University Medical Centre Groningen, Groningen, The Netherlands
| | | | - Gerard H Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Reinoud Gosens
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy, University of Groningen, 9713 AV, Groningen, The Netherlands.
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4
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van Nijnatten J, Faiz A, Timens W, Guryev V, Slebos DJ, Klooster K, Hartman JE, Kole T, Choy DF, Chakrabarti A, Grimbaldeston M, Rosenberger CM, Kerstjens H, Brandsma CA, van den Berge M. A bronchial gene signature specific for severe COPD that is retained in the nose. ERJ Open Res 2023; 9:00354-2023. [PMID: 38020574 PMCID: PMC10680034 DOI: 10.1183/23120541.00354-2023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 08/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction A subset of COPD patients develops advanced disease with severe airflow obstruction, hyperinflation and extensive emphysema. We propose that the pathogenesis in these patients differs from mild-moderate COPD and is reflected by bronchial gene expression. The aim of the present study was to identify a unique bronchial epithelial gene signature for severe COPD patients. Methods We obtained RNA sequencing data from bronchial brushes from 123 ex-smokers with severe COPD, 23 with mild-moderate COPD and 23 non-COPD controls. We identified genes specific to severe COPD by comparing severe COPD to non-COPD controls, followed by removing genes that were also differentially expressed between mild-moderate COPD and non-COPD controls. Next, we performed a pathway analysis on these genes and evaluated whether this signature is retained in matched nasal brushings. Results We identified 219 genes uniquely differentially expressed in severe COPD. Interaction network analysis identified VEGFA and FN1 as the key genes with the most interactions. Genes were involved in extracellular matrix regulation, collagen binding and the immune response. Of interest were 10 genes (VEGFA, DCN, SPARC, COL6A2, MGP, CYR61, ANXA6, LGALS1, C1QA and C1QB) directly connected to fibronectin 1 (FN1). Most of these genes were lower expressed in severe COPD and showed the same effect in nasal brushings. Conclusions We found a unique severe COPD bronchial gene signature with key roles for VEGFA and FN1, which was retained in the upper airways. This supports the hypothesis that severe COPD, at least partly, comprises a different pathology and supports the potential for biomarker development based on nasal brushes in COPD.
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Affiliation(s)
- Jos van Nijnatten
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology, Sydney, NSW, Australia
| | - Alen Faiz
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology, Sydney, NSW, Australia
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Victor Guryev
- University of Groningen University Medical Center Groningen, European Research Institute for the Biology of Ageing, Groningen, the Netherlands
| | - Dirk-Jan Slebos
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Karin Klooster
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Jorine E. Hartman
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Tessa Kole
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | | | | | | | | | - Huib Kerstjens
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- These authors contributed equally
| | - Maarten van den Berge
- University of Groningen University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
- University of Groningen University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, the Netherlands
- These authors contributed equally
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Paez R, Kammer MN, Tanner NT, Shojaee S, Heideman BE, Peikert T, Balbach ML, Iams WT, Ning B, Lenburg ME, Mallow C, Yarmus L, Fong KM, Deppen S, Grogan EL, Maldonado F. Update on Biomarkers for the Stratification of Indeterminate Pulmonary Nodules. Chest 2023; 164:1028-1041. [PMID: 37244587 PMCID: PMC10645597 DOI: 10.1016/j.chest.2023.05.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/29/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths. Early detection and diagnosis are critical, as survival decreases with advanced stages. Approximately 1.6 million nodules are incidentally detected every year on chest CT scan images in the United States. This number of nodules identified is likely much larger after accounting for screening-detected nodules. Most of these nodules, whether incidentally or screening detected, are benign. Despite this, many patients undergo unnecessary invasive procedures to rule out cancer because our current stratification approaches are suboptimal, particularly for intermediate probability nodules. Thus, noninvasive strategies are urgently needed. Biomarkers have been developed to assist through the continuum of lung cancer care and include blood protein-based biomarkers, liquid biopsies, quantitative imaging analysis (radiomics), exhaled volatile organic compounds, and bronchial or nasal epithelium genomic classifiers, among others. Although many biomarkers have been developed, few have been integrated into clinical practice as they lack clinical utility studies showing improved patient-centered outcomes. Rapid technologic advances and large network collaborative efforts will continue to drive the discovery and validation of many novel biomarkers. Ultimately, however, randomized clinical utility studies showing improved patient outcomes will be required to bring biomarkers into clinical practice.
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Affiliation(s)
- Rafael Paez
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Michael N Kammer
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Nicole T Tanner
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, Medical University of South Carolina, Charleston, SC
| | - Samira Shojaee
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Brent E Heideman
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Tobias Peikert
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN
| | - Meridith L Balbach
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Wade T Iams
- Department of Medicine, Division of Hematology-Oncology, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Boting Ning
- Department of Medicine, Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, Boston University School of Medicine, Boston, MA
| | - Christopher Mallow
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Miami, Miami, FL
| | - Lonny Yarmus
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University, Baltimore, MD
| | - Kwun M Fong
- University of Queensland Thoracic Research Centre, The Prince Charles Hospital, Brisbane, QLD, Australia
| | - Stephen Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN; Tennessee Valley Healthcare System, Nashville, TN
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN; Vanderbilt-Ingram Cancer Center, Nashville, TN; Tennessee Valley Healthcare System, Nashville, TN
| | - Fabien Maldonado
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN.
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6
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The establishment of COPD organoids to study host-pathogen interaction reveals enhanced viral fitness of SARS-CoV-2 in bronchi. Nat Commun 2022; 13:7635. [PMID: 36496442 PMCID: PMC9735280 DOI: 10.1038/s41467-022-35253-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by airflow limitation and infective exacerbations, however, in-vitro model systems for the study of host-pathogen interaction at the individual level are lacking. Here, we describe the establishment of nasopharyngeal and bronchial organoids from healthy individuals and COPD that recapitulate disease at the individual level. In contrast to healthy organoids, goblet cell hyperplasia and reduced ciliary beat frequency were observed in COPD organoids, hallmark features of the disease. Single-cell transcriptomics uncovered evidence for altered cellular differentiation trajectories in COPD organoids. SARS-CoV-2 infection of COPD organoids revealed more productive replication in bronchi, the key site of infection in severe COVID-19. Viral and bacterial exposure of organoids induced greater pro-inflammatory responses in COPD organoids. In summary, we present an organoid model that recapitulates the in vivo physiological lung microenvironment at the individual level and is amenable to the study of host-pathogen interaction and emerging infectious disease.
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7
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Gregory A, Xu Z, Pratte K, Lee S, Liu C, Chase R, Yun J, Saferali A, Hersh CP, Bowler R, Silverman E, Castaldi PJ, Boueiz A. Clustering-based COPD subtypes have distinct longitudinal outcomes and multi-omics biomarkers. BMJ Open Respir Res 2022; 9:9/1/e001182. [PMID: 35999035 PMCID: PMC9403129 DOI: 10.1136/bmjresp-2021-001182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/31/2022] [Indexed: 11/25/2022] Open
Abstract
Introduction Chronic obstructive pulmonary disease (COPD) can progress across several domains, complicating the identification of the determinants of disease progression. In our previous work, we applied k-means clustering to spirometric and chest radiological measures to identify four COPD-related subtypes: ‘relatively resistant smokers (RRS)’, ‘mild upper lobe-predominant emphysema (ULE)’, ‘airway-predominant disease (AD)’ and ‘severe emphysema (SE)’. In the current study, we examined the associations of these subtypes to longitudinal COPD-related health measures as well as blood transcriptomic and plasma proteomic biomarkers. Methods We included 8266 non-Hispanic white and African-American smokers from the COPDGene study. We used linear regression to investigate cluster associations to 5-year prospective changes in spirometric and radiological measures and to gene expression and protein levels. We used Cox-proportional hazard test to test for cluster associations to prospective exacerbations, comorbidities and mortality. Results The RRS, ULE, AD and SE clusters represented 39%, 15%, 26% and 20% of the studied cohort at baseline, respectively. The SE cluster had the greatest 5-year FEV1 (forced expiratory volume in 1 s) and emphysema progression, and the highest risks of exacerbations, cardiovascular disease and mortality. The AD cluster had the highest diabetes risk. After adjustments, only the SE cluster had an elevated respiratory mortality risk, while the ULE, AD and SE clusters had elevated all-cause mortality risks. These clusters also demonstrated differential protein and gene expression biomarker associations, mostly related to inflammatory and immune processes. Conclusion COPD k-means subtypes demonstrate varying rates of disease progression, prospective comorbidities, mortality and associations to transcriptomic and proteomic biomarkers. These findings emphasise the clinical and biological relevance of these subtypes, which call for more study for translation into clinical practice. Trail registration number NCT00608764.
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Affiliation(s)
- Andrew Gregory
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Zhonghui Xu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Katherine Pratte
- Department of Biostatistics, National Jewish Health, Denver, Colorado, USA
| | - Sool Lee
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Congjian Liu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Robert Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Russell Bowler
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado, USA
| | - Edwin Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,General Medicine and Primary Care, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Adel Boueiz
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA .,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
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8
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Garland LL, Guillen-Rodriguez J, Hsu CH, Davis LE, Szabo E, Husted CR, Liu H, LeClerc A, Alekseyev YO, Liu G, Bauman JE, Spira AE, Beane J, Wojtowicz M, Chow HHS. Clinical Study of Aspirin and Zileuton on Biomarkers of Tobacco-Related Carcinogenesis in Current Smokers. Cancers (Basel) 2022; 14:2893. [PMID: 35740559 PMCID: PMC9221101 DOI: 10.3390/cancers14122893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 12/04/2022] Open
Abstract
The chemopreventive effect of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) on lung cancer risk is supported by epidemiologic and preclinical studies. Zileuton, a 5-lipoxygenase inhibitor, has additive activity with NSAIDs against tobacco carcinogenesis in preclinical models. We hypothesized that cyclooxygenase plus 5-lipoxygenase inhibition would be more effective than a placebo in modulating the nasal epithelium gene signatures of tobacco exposure and lung cancer. We conducted a randomized, double-blinded study of low-dose aspirin plus zileuton vs. double placebo in current smokers to compare the modulating effects on nasal gene expression and arachidonic acid metabolism. In total, 63 participants took aspirin 81 mg daily plus zileuton (Zyflo CR) 600 mg BID or the placebo for 12 weeks. Nasal brushes from the baseline, end-of-intervention, and one-week post intervention were profiled via microarray. Aspirin plus zilueton had minimal effects on the modulation of the nasal or bronchial gene expression signatures of smoking, lung cancer, and COPD but favorably modulated a bronchial gene expression signature of squamous dysplasia. Aspirin plus zileuton suppressed urinary leukotriene but not prostaglandin E2, suggesting shunting through the cyclooxygenase pathway when combined with 5-lipoxygenase inhibition. Continued investigation of leukotriene inhibitors is needed to confirm these findings, understand the long-term effects on the airway epithelium, and identify the safest, optimally dosed agents.
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Affiliation(s)
- Linda L. Garland
- Department of Medicine, University of Arizona, Tucson, AZ 85724, USA;
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (J.G.-R.); (C.-H.H.); (H.-H.S.C.)
| | - José Guillen-Rodriguez
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (J.G.-R.); (C.-H.H.); (H.-H.S.C.)
| | - Chiu-Hsieh Hsu
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (J.G.-R.); (C.-H.H.); (H.-H.S.C.)
| | - Lisa E. Davis
- College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA;
| | - Eva Szabo
- Division of Cancer Prevention, National Cancer Institute, Bethesa, MD 20892, USA; (E.S.); (M.W.)
| | - Christopher R. Husted
- Section of Computational Biomedicine, Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (C.R.H.); (H.L.); (G.L.); (A.E.S.); (J.B.)
| | - Hanqiao Liu
- Section of Computational Biomedicine, Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (C.R.H.); (H.L.); (G.L.); (A.E.S.); (J.B.)
| | - Ashley LeClerc
- Department of Pathology and Laboratory Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (A.L.); (Y.O.A.)
| | - Yuriy O. Alekseyev
- Department of Pathology and Laboratory Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (A.L.); (Y.O.A.)
| | - Gang Liu
- Section of Computational Biomedicine, Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (C.R.H.); (H.L.); (G.L.); (A.E.S.); (J.B.)
| | - Julie E. Bauman
- Department of Medicine, University of Arizona, Tucson, AZ 85724, USA;
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (J.G.-R.); (C.-H.H.); (H.-H.S.C.)
- Division of Hematology/Oncology, Department of Medicine, George Washington (GW) University and GW Cancer Center, Washington, DC 20037, USA
| | - Avrum E. Spira
- Section of Computational Biomedicine, Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (C.R.H.); (H.L.); (G.L.); (A.E.S.); (J.B.)
| | - Jennifer Beane
- Section of Computational Biomedicine, Department of Medicine, School of Medicine, Boston University, Boston, MA 02118, USA; (C.R.H.); (H.L.); (G.L.); (A.E.S.); (J.B.)
| | - Malgorzata Wojtowicz
- Division of Cancer Prevention, National Cancer Institute, Bethesa, MD 20892, USA; (E.S.); (M.W.)
| | - H.-H. Sherry Chow
- University of Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA; (J.G.-R.); (C.-H.H.); (H.-H.S.C.)
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9
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Jo A, Choi TG, Han JY, Tabor MH, Kolliputi N, Lockey RF, Cho SH. Age-Related Increase of Collagen/Fibrin Deposition and High PAI-1 Production in Human Nasal Polyps. Front Pharmacol 2022; 13:845324. [PMID: 35712705 PMCID: PMC9193225 DOI: 10.3389/fphar.2022.845324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Our previous studies showed an age-related increased prevalence of nasal polyps (NP) and reduced production of S100A8/9 in elderly patients with chronic rhinosinusitis with NP (CRSwNP). In this study, we investigated an unbiased age-related gene expression profile in CRSwNP subjects and healthy controls, and further identified the differences in their tissue remodeling. Methods: Microarrays using NP and uncinate tissues from health controls (elderly, age ≥65 vs. non-elderly, age 18-49) were performed, and differentially regulated genes were analyzed. Quantitative real-time PCR (qPCR), Immunostaining, Periodic acid-Schiff (PAS), trichrome staining, Western blot, and ELISA were performed for further investigation. Results: Microarrays identified differentially expressed genes according to disease and age; 278 in NP vs. controls, 75 in non-elderly NP vs. non-elderly controls, and 32 in elderly NP vs. elderly controls. qPCR confirmed that the PLAT gene was downregulated and the SERPINB2 gene upregulated in NP vs. controls. The serous glandular cell-derived antimicrobial protein/peptide-related genes such as BPIFB3, BPIFB2, LPO, and MUC7 were remarkably reduced in NP, regardless of age. SERPINE1 gene (plasminogen activator inhibitor-1, PAI-1) expression was significantly increased in elderly NP versus elderly controls. IHC and western blot confirmed significantly decreased production of MUC7 and LPO in NP versus controls. There was a trend of age-related reduction of submucosal gland cells in normal controls. Trichrome and immunofluorescence staining demonstrated an age-related increase of collagen and fibrin deposition in NP, consistent with increased PAI-1 production. Conclusion: This study demonstrated age-related differential glandular remodeling patterns and fibrosis in NP and normal controls. PAI-1 expression was significantly increased in elderly NP versus elderly controls, suggesting PAI-1 as a potential treatment target in elderly NP.
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Affiliation(s)
- Ara Jo
- Division of Allergy-Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Tae Gyu Choi
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Jung Yeon Han
- Division of Allergy-Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Mark H. Tabor
- Department of Otolaryngology-Head and Neck Surgery, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Narasaiah Kolliputi
- Division of Allergy-Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Richard F. Lockey
- Division of Allergy-Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Seong H. Cho
- Division of Allergy-Immunology, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Division of Allergy-Immunology, James A. Haley Veterans’ Hospital, Tampa, FL, United States
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10
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Faiz A, van den Berge M. Quality over quantity: the importance of collecting relevant samples to understand complex diseases. Eur Respir J 2022; 59:59/5/2200418. [PMID: 35618280 DOI: 10.1183/13993003.00418-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Alen Faiz
- University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, Australia.,University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Dept of Pulmonary Diseases, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Dept of Pulmonary Diseases, Groningen, The Netherlands
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11
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Williams JG, Joshi R, Haslam D, Yehya N, Jones RL, Paranjpe A, Pujato M, Roskin KM, Lahni PM, Wong HR, Varisco BM. Multi-omic characterization of pediatric ARDS via nasal brushings. Respir Res 2022; 23:181. [PMID: 35804409 PMCID: PMC9270778 DOI: 10.1186/s12931-022-02098-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/19/2022] [Indexed: 12/03/2022] Open
Abstract
RATIONALE While nasal brushing transcriptomics can identify disease subtypes in chronic pulmonary diseases, it is unknown whether this is true in pediatric acute respiratory distress syndrome (PARDS). OBJECTIVES Determine whether nasal transcriptomics and methylomics can identify clinically meaningful PARDS subgroups that reflect important pathobiological processes. METHODS Nasal brushings and serum were collected on days 1, 3, 7, and 14 from control and PARDS subjects from two centers. PARDS duration was the primary endpoint. MEASUREMENTS AND MAIN RESULTS Twenty-four control and 39 PARDS subjects were enrolled. Two nasal methylation patterns were identified. Compared to Methyl Subgroup 1, Subgroup 2 had hypomethylation of inflammatory genes and was enriched for immunocompromised subjects. Four transcriptomic patterns were identified with temporal patterns indicating injury, repair, and regeneration. Over time, both inflammatory (Subgroup B) and cell injury (Subgroup D) patterns transitioned to repair (Subgroup A) and eventually homeostasis (Subgroup C). When control specimens were included, they were largely Subgroup C. In comparison with 17 serum biomarkers, the nasal transcriptome was more predictive of prolonged PARDS. Subjects with initial Transcriptomic Subgroup B or D assignment had median PARDS duration of 8 days compared to 2 in A or C (p = 0.02). For predicting PARDS duration ≥ 3 days, nasal transcriptomics was more sensitive and serum biomarkers more specific. CONCLUSIONS PARDS nasal transcriptome may reflect distal lung injury, repair, and regeneration. A combined nasal PCR and serum biomarker assay could be useful for predictive and diagnostic enrichment. Trial registration Clinicaltrials.gov NCT03539783 May 29, 2018.
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Affiliation(s)
- James G. Williams
- grid.239573.90000 0000 9025 8099Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7006, Cincinnati, OH 45229 USA
| | - Rashika Joshi
- grid.239573.90000 0000 9025 8099Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7006, Cincinnati, OH 45229 USA
| | - David Haslam
- grid.239573.90000 0000 9025 8099Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA ,grid.24827.3b0000 0001 2179 9593University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Nadir Yehya
- grid.239552.a0000 0001 0680 8770Critical Care Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA ,grid.261870.a0000 0001 2326 0313Perlman School of Medicine, University of Philadelphia, Philadelphia, PA USA
| | - Rhonda L. Jones
- grid.239573.90000 0000 9025 8099Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7006, Cincinnati, OH 45229 USA
| | - Aditi Paranjpe
- grid.239573.90000 0000 9025 8099Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Mario Pujato
- Production Informatics, AstraZeneca Oncology Division, Gaithersburg, MD USA
| | - Krishna M. Roskin
- grid.24827.3b0000 0001 2179 9593University of Cincinnati College of Medicine, Cincinnati, OH USA ,grid.239573.90000 0000 9025 8099Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH USA
| | - Patrick M. Lahni
- grid.239573.90000 0000 9025 8099Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7006, Cincinnati, OH 45229 USA
| | - Hector R. Wong
- grid.239573.90000 0000 9025 8099Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7006, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593University of Cincinnati College of Medicine, Cincinnati, OH USA
| | - Brian M. Varisco
- grid.239573.90000 0000 9025 8099Critical Care Medicine, Cincinnati Children’s Hospital Medical Center, 3333 Burnet Avenue, MLC 7006, Cincinnati, OH 45229 USA ,grid.24827.3b0000 0001 2179 9593University of Cincinnati College of Medicine, Cincinnati, OH USA
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12
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van den Berge M, Faiz A. Transcriptome Based Signatures: The Future Biomarkers in Obstructive Pulmonary Diseases Such as Asthma and COPD? Am J Respir Crit Care Med 2021; 205:139-140. [PMID: 34793289 PMCID: PMC8787239 DOI: 10.1164/rccm.202110-2353ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonary Diseases, Groningen, Netherlands.,University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, Netherlands;
| | - Alen Faiz
- University of Technology Sydney, 1994, Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, Sydney, New South Wales, Australia
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13
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Ghosh M, Hill CL, Alsudayri A, Lallier SW, Hayes D, Wijeratne S, Tan ZH, Chiang T, Mahoney JE, Carraro G, Stripp BR, Reynolds SD. Repeated injury promotes tracheobronchial tissue stem cell attrition. Stem Cells Transl Med 2021; 10:1696-1713. [PMID: 34546001 PMCID: PMC8641087 DOI: 10.1002/sctm.21-0032] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/20/2022] Open
Abstract
Chronic lung disease has been attributed to stem cell aging and/or exhaustion. We investigated these mechanisms using mouse and human tracheobronchial tissue‐specific stem cells (TSC). In mouse, chromatin labeling and flow cytometry demonstrated that naphthalene (NA) injury activated a subset of TSC. These activated TSC continued to proliferate after the epithelium was repaired and a clone study demonstrated that ~96% of activated TSC underwent terminal differentiation. Despite TSC attrition, epithelial repair after a second NA injury was normal. The second injury accelerated proliferation of previously activated TSC and a nucleotide‐label retention study indicated that the second injury recruited TSC that were quiescent during the first injury. These mouse studies indicate that (a) injury causes selective activation of the TSC pool; (b) activated TSC are predisposed to further proliferation; and (c) the activated state leads to terminal differentiation. In human TSC, repeated proliferation also led to terminal differentiation and depleted the TSC pool. A clone study identified long‐ and short‐lived TSC and showed that short‐lived TSC clones had significantly shorter telomeres than their long‐lived counterparts. The TSC pool was significantly depleted in dyskeratosis congenita donors, who harbor mutations in telomere biology genes. The remaining TSC had short telomeres and short lifespans. Collectively, the mouse and human studies support a model in which epithelial injury increases the biological age of the responding TSC. When applied to chronic lung disease, this model suggests that repeated injury accelerates the biological aging process resulting in abnormal repair and disease initiation.
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Affiliation(s)
- Moumita Ghosh
- Department of Medicine, University of Colorado-Denver, Denver, Colorado, USA
| | - Cynthia L Hill
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Alfahdah Alsudayri
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Scott W Lallier
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Don Hayes
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Saranga Wijeratne
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Zhang Hong Tan
- Center for Regenerative Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Tendy Chiang
- Center for Regenerative Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - John E Mahoney
- Cystic Fibrosis Foundation Therapeutics, Lexington, Massachusetts, USA.,Cystic Fibrosis Foundation, Bethesda, Maryland, USA
| | - Gianni Carraro
- Department of Medicine, Cedars-Sinai Medical Center, Lung and Regenerative Medicine Institutes, Los Angeles, California, USA
| | - Barry R Stripp
- Department of Medicine, Cedars-Sinai Medical Center, Lung and Regenerative Medicine Institutes, Los Angeles, California, USA
| | - Susan D Reynolds
- Center for Perinatal Research, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
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14
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Becker EJ, Faiz A, van den Berge M, Timens W, Hiemstra PS, Clark K, Liu G, Xiao X, Alekseyev YO, O'Connor G, Lam S, Spira A, Lenburg ME, Steiling K. Bronchial gene expression signature associated with rate of subsequent FEV 1 decline in individuals with and at risk of COPD. Thorax 2021; 77:31-39. [PMID: 33972452 DOI: 10.1136/thoraxjnl-2019-214476] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/10/2021] [Accepted: 04/08/2021] [Indexed: 12/25/2022]
Abstract
BACKGROUND COPD is characterised by progressive lung function decline. Leveraging prior work demonstrating bronchial airway COPD-associated gene expression alterations, we sought to determine if there are alterations associated with differences in the rate of FEV1 decline. METHODS We examined gene expression among ever smokers with and without COPD who at baseline had bronchial brushings profiled by Affymetrix microarrays and had longitudinal lung function measurements (n=134; mean follow-up=6.38±2.48 years). Gene expression profiles associated with the rate of FEV1 decline were identified by linear modelling. RESULTS Expression differences in 171 genes were associated with rate of FEV1 decline (false discovery rate <0.05). The FEV1 decline signature was replicated in an independent dataset of bronchial biopsies from patients with COPD (n=46; p=0.018; mean follow-up=6.76±1.32 years). Genes elevated in individuals with more rapid FEV1 decline are significantly enriched among the genes altered by modulation of XBP1 in two independent datasets (Gene Set Enrichment Analysis (GSEA) p<0.05) and are enriched in mucin-related genes (GSEA p<0.05). CONCLUSION We have identified and replicated an airway gene expression signature associated with the rate of FEV1 decline. Aspects of this signature are related to increased expression of XBP1-regulated genes, a transcription factor involved in the unfolded protein response, and genes related to mucin production. Collectively, these data suggest that molecular processes related to the rate of FEV1 decline can be detected in airway epithelium, identify a possible indicator of FEV1 decline and make it possible to detect, in an early phase, ever smokers with and without COPD most at risk of rapid FEV1 decline.
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Affiliation(s)
- Elizabeth J Becker
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology (RBMB), School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia.,Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Centre Groningen, Groningen, The Netherlands
| | - Pieter S Hiemstra
- Department of Pulmonology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kristopher Clark
- Internal Medicine Residency Program, Boston Medical Center, Boston, Massachusetts, USA
| | - Gang Liu
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Xiaohui Xiao
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - George O'Connor
- Division of Pulmonary, Allergy, Sleep, and Critical Care Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Stephen Lam
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Avrum Spira
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Marc E Lenburg
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA.,Bioinformatics Program, Boston University, Boston, Massachusetts, USA.,Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Katrina Steiling
- Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts, USA .,Bioinformatics Program, Boston University, Boston, Massachusetts, USA.,Division of Pulmonary, Allergy, Sleep, and Critical Care Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
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15
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Nasal Epithelial Cell-Based Models for Individualized Study in Cystic Fibrosis. Int J Mol Sci 2021; 22:ijms22094448. [PMID: 33923202 PMCID: PMC8123210 DOI: 10.3390/ijms22094448] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/22/2021] [Accepted: 04/23/2021] [Indexed: 12/11/2022] Open
Abstract
The emergence of highly effective CFTR modulator therapy has led to significant improvements in health care for most patients with cystic fibrosis (CF). For some, however, these therapies remain inaccessible due to the rarity of their individual CFTR variants, or due to a lack of biologic activity of the available therapies for certain variants. One proposed method of addressing this gap is the use of primary human cell-based models, which allow preclinical therapeutic testing and physiologic assessment of relevant tissue at the individual level. Nasal cells represent one such tissue source and have emerged as a powerful model for individual disease study. The ex vivo culture of nasal cells has evolved over time, and modern nasal cell models are beginning to be utilized to predict patient outcomes. This review will discuss both historical and current state-of-the art use of nasal cells for study in CF, with a particular focus on the use of such models to inform personalized patient care.
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16
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Awatade NT, Wong SL, Capraro A, Pandzic E, Slapetova I, Zhong L, Turgutoglu N, Fawcett LK, Whan RM, Jaffe A, Waters SA. Significant functional differences in differentiated Conditionally Reprogrammed (CRC)- and Feeder-free Dual SMAD inhibited-expanded human nasal epithelial cells. J Cyst Fibros 2021; 20:364-371. [PMID: 33414087 DOI: 10.1016/j.jcf.2020.12.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 12/16/2020] [Accepted: 12/20/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Patient-derived airway cells differentiated at Air Liquid Interface (ALI) are valuable models for Cystic fibrosis (CF) precision therapy. Different culture expansion methods have been established to extend expansion capacity of airway basal cells, while retaining functional airway epithelium physiology. Considerable variation in response to CFTR modulators is observed in cultures even within the same CFTR genotype and despite the use of similar ALI culture techniques. We aimed to address culture expansion method impact on differentiation. METHODS Nasal epithelial brushings from 14 individuals (CF=9; non-CF=5) were collected, then equally divided and expanded under conditional reprogramming culture (CRC) and feeder-serum-free "dual-SMAD inhibition" (SMADi) methods. Expanded cells from each culture were differentiated with proprietary PneumaCult™-ALI media. Morphology (Immunofluorescence), global proteomics (LC-MS/MS) and function (barrier integrity, cilia motility, and ion transport) were compared in CRCALI and SMADiALI under basal and CFTR corrector treated (VX-809) conditions. RESULTS No significant difference in the structural morphology or baseline global proteomics profile were observed. Barrier integrity and cilia motility were significantly different, despite no difference in cell junction morphology or cilia abundance. Epithelial Sodium Channels and Calcium-activated Chloride Channel activity did not differ but CFTR mediated chloride currents were significantly reduced in SMADiALI compare to their CRCALI counterparts. CONCLUSION Alteration of cellular physiological function in vitro were more prominent than structural and differentiation potential in airway ALI. Since initial expansion culture conditions significantly influence CFTR activity, this could lead to false conclusions if data from different labs are compared against each other without specific reference ranges.
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Affiliation(s)
- Nikhil T Awatade
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Sharon L Wong
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Alexander Capraro
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Elvis Pandzic
- Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, Australia
| | - Iveta Slapetova
- Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, Australia
| | - Nihan Turgutoglu
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia
| | - Laura K Fawcett
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Renee M Whan
- Biomedical Imaging Facility, University of New South Wales, Sydney, NSW, Australia
| | - Adam Jaffe
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia
| | - Shafagh A Waters
- School of Women's and Children's Health, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia; Molecular and Integrative Cystic Fibrosis Research Centre (miCF_RC), University of New South Wales and Sydney Children's Hospital, Sydney, NSW, Australia; Department of Respiratory Medicine, Sydney Children's Hospital, Sydney, NSW, Australia.
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17
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Fantauzzi MF, Aguiar JA, Tremblay BJM, Mansfield MJ, Yanagihara T, Chandiramohan A, Revill S, Ryu MH, Carlsten C, Ask K, Stämpfli M, Doxey AC, Hirota JA. Expression of endocannabinoid system components in human airway epithelial cells: impact of sex and chronic respiratory disease status. ERJ Open Res 2020; 6:00128-2020. [PMID: 33344628 PMCID: PMC7737429 DOI: 10.1183/23120541.00128-2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/18/2020] [Indexed: 12/12/2022] Open
Abstract
Cannabis smoking is the dominant route of delivery, with the airway epithelium functioning as the site of first contact. The endocannabinoid system is responsible for mediating the physiological effects of inhaled phytocannabinoids. The expression of the endocannabinoid system in the airway epithelium and contribution to normal physiological responses remains to be defined. To begin to address this knowledge gap, a curated dataset of 1090 unique human bronchial brushing gene expression profiles was created. The dataset included 616 healthy subjects, 136 subjects with asthma, and 338 subjects with COPD. A 32-gene endocannabinoid signature was analysed across all samples with sex and disease-specific analyses performed. Immunohistochemistry and immunoblots were performed to probe in situ and in vitro protein expression. CB1, CB2, and TRPV1 protein signal is detectable in human airway epithelial cells in situ and in vitro, justifying examining the downstream endocannabinoid pathway. Sex status was associated with differential expression of 7 of 32 genes. In contrast, disease status was associated with differential expression of 21 of 32 genes in people with asthma and 26 of 32 genes in people with COPD. We confirm at the protein level that TRPV1, the most differentially expressed candidate in our analyses, was upregulated in airway epithelial cells from people with asthma relative to healthy subjects. Our data demonstrate that the endocannabinoid system is expressed in human airway epithelial cells with expression impacted by disease status and minimally by sex. The data suggest that cannabis consumers may have differential physiological responses in the respiratory mucosa.
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Affiliation(s)
- Matthew F Fantauzzi
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | | | | | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Toyoshi Yanagihara
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | - Abiram Chandiramohan
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | - Spencer Revill
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada
| | - Min Hyung Ryu
- Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chris Carlsten
- Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kjetil Ask
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Martin Stämpfli
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Andrew C Doxey
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,Dept of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jeremy A Hirota
- Firestone Institute for Respiratory Health - Division of Respirology, Dept of Medicine, McMaster University, Hamilton, ON, Canada.,McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada.,Dept of Biology, University of Waterloo, Waterloo, ON, Canada.,Division of Respiratory Medicine, Dept of Medicine, University of British Columbia, Vancouver, BC, Canada
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18
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Rathnayake SNH, Hoesein FAAM, Galban CJ, Ten Hacken NHT, Oliver BGG, van den Berge M, Faiz A. Gene expression profiling of bronchial brushes is associated with the level of emphysema measured by computed tomography-based parametric response mapping. Am J Physiol Lung Cell Mol Physiol 2020; 318:L1222-L1228. [PMID: 32320267 DOI: 10.1152/ajplung.00051.2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Parametric response mapping (PRM) is a computed tomography (CT)-based method to phenotype patients with chronic obstructive pulmonary disease (COPD). It is capable of differentiating emphysema-related air trapping with nonemphysematous air trapping (small airway disease), which helps to identify the extent and localization of the disease. Most studies evaluating the gene expression in smokers and COPD patients related this to spirometric measurements, but none have investigated the relationship with CT-based measurements of lung structure. The current study aimed to examine gene expression profiles of brushed bronchial epithelial cells in association with the PRM-defined CT-based measurements of emphysema (PRMEmph) and small airway disease (PRMfSAD). Using the Top Institute Pharma (TIP) study cohort (COPD = 12 and asymptomatic smokers = 32), we identified a gene expression signature of bronchial brushings, which was associated with PRMEmph in the lungs. One hundred thirty-three genes were identified to be associated with PRMEmph. Among the most significantly associated genes, CXCL11 is a potent chemokine involved with CD8+ T cell activation during inflammation in COPD, indicating that it may play an essential role in the development of emphysema. The PRMEmph signature was then replicated in two independent data sets. Pathway analysis showed that the PRMEmph signature is associated with proinflammatory and notch signaling pathways. Together these findings indicate that airway epithelium may play a role in the development of emphysema and/or may act as a biomarker for the presence of emphysema. In contrast, its role in relation to functional small airways disease is less clear.
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Affiliation(s)
- Senani N H Rathnayake
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia.,Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Sydney, New South Wales, Australia
| | - Firdaus A A Mohamed Hoesein
- Division of Heart and Lungs, Department of Respiratory Medicine, University Medical Center, Utrecht University, Utrecht, The Netherlands
| | - Craig J Galban
- Department of Radiology, The University of Michigan, Ann Arbor, Michigan
| | - Nick H T Ten Hacken
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, The University of Groningen, Groningen, The Netherlands.,Department of Pulmonary Diseases, University Medical Center Groningen, The University of Groningen, Groningen, The Netherlands
| | - Brian G G Oliver
- Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Sydney, New South Wales, Australia.,School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, The University of Groningen, Groningen, The Netherlands.,Department of Pulmonary Diseases, University Medical Center Groningen, The University of Groningen, Groningen, The Netherlands
| | - Alen Faiz
- Respiratory Bioinformatics and Molecular Biology, School of Life Sciences, University of Technology Sydney, Sydney, New South Wales, Australia.,Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, The University of Groningen, Groningen, The Netherlands.,Department of Pulmonary Diseases, University Medical Center Groningen, The University of Groningen, Groningen, The Netherlands.,Respiratory Cellular and Molecular Biology, Woolcock Institute of Medical Research, The University of Sydney, Sydney, New South Wales, Australia
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19
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Koopmans T, Hesse L, Nawijn MC, Kumawat K, Menzen MH, Sophie T Bos I, Smits R, Bakker ERM, van den Berge M, Koppelman GH, Guryev V, Gosens R. Smooth-muscle-derived WNT5A augments allergen-induced airway remodelling and Th2 type inflammation. Sci Rep 2020; 10:6754. [PMID: 32317758 PMCID: PMC7174298 DOI: 10.1038/s41598-020-63741-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/06/2020] [Indexed: 12/21/2022] Open
Abstract
Asthma is a heterogeneous disease characterized by chronic inflammation and structural changes in the airways. The airway smooth muscle (ASM) is responsible for airway narrowing and an important source of inflammatory mediators. We and others have previously shown that WNT5A mRNA and protein expression is higher in the ASM of asthmatics compared to healthy controls. Here, we aimed to characterize the functional role of (smooth muscle-derived) WNT5A in asthma. We generated a tet-ON smooth-muscle-specific WNT5A transgenic mouse model, enabling in vivo characterization of smooth-muscle-derived WNT5A in response to ovalbumin. Smooth muscle specific WNT5A overexpression showed a clear trend towards enhanced actin (α-SMA) expression in the ASM in ovalbumin challenged animals, but had no effect on collagen content. WNT5A overexpression in ASM also significantly enhanced the production of the Th2-cytokines IL4 and IL5 in lung tissue after ovalbumin exposure. In line with this, WNT5A increased mucus production, and enhanced eosinophilic infiltration and serum IgE production in ovalbumin-treated animals. In addition, CD4+ T cells of asthma patients and healthy controls were stimulated with WNT5A and changes in gene transcription assessed by RNA-seq. WNT5A promoted expression of 234 genes in human CD4+ T cells, among which the Th2 cytokine IL31 was among the top 5 upregulated genes. IL31 was also upregulated in response to smooth muscle-specific WNT5A overexpression in the mouse. In conclusion, smooth-muscle derived WNT5A augments Th2 type inflammation and remodelling. Our findings imply a pro-inflammatory role for smooth muscle-derived WNT5A in asthma, resulting in increased airway wall inflammation and remodelling.
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Affiliation(s)
- Tim Koopmans
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Laura Hesse
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Experimental Pulmonology and Inflammation Research, Groningen, The Netherlands
| | - Martijn C Nawijn
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Experimental Pulmonology and Inflammation Research, Groningen, The Netherlands
| | - Kuldeep Kumawat
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Mark H Menzen
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - I Sophie T Bos
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands
| | - Ron Smits
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Groningen, The Netherlands
| | - Elvira R M Bakker
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Centre, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children 's Hospital, Groningen, The Netherlands
| | - Victor Guryev
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.,European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands. .,Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, Groningen, The Netherlands.
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20
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Drizik E, Corbett S, Zheng Y, Vermeulen R, Dai Y, Hu W, Ren D, Duan H, Niu Y, Xu J, Fu W, Meliefste K, Zhou B, Zhang X, Yang J, Bassig B, Liu H, Ye M, Liu G, Jia X, Meng T, Bin P, Zhang J, Silverman D, Spira A, Rothman N, Lenburg ME, Lan Q. Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure. ENVIRONMENT INTERNATIONAL 2020; 137:105506. [PMID: 32044442 PMCID: PMC8725607 DOI: 10.1016/j.envint.2020.105506] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/19/2019] [Accepted: 01/17/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Diesel engine exhaust (DEE) exposure causes lung cancer, but the molecular mechanisms by which this occurs are not well understood. OBJECTIVES To assess transcriptomic alterations in nasal epithelium of DEE-exposed factory workers to better understand the cellular and molecular effects of DEE. METHODS Nasal epithelial brushings were obtained from 41 diesel engine factory workers exposed to relatively high levels of DEE (17.2-105.4 μg/m3), and 38 unexposed workers from factories without DEE exposure. mRNA was profiled for gene expression using Affymetrix microarrays. Linear modeling was used to identify differentially expressed genes associated with DEE exposure and interaction effects with current smoking status. Pathway enrichment among differentially expressed genes was assessed using EnrichR. Gene Set Enrichment Analysis (GSEA) was used to compare gene expression patterns between datasets. RESULTS 225 genes had expression associated with DEE exposure after adjusting for smoking status (FDR q < 0.25) and were enriched for genes in pathways related to oxidative stress response, cell cycle pathways such as MAPK/ERK, protein modification, and transmembrane transport. Genes up-regulated in DEE-exposed individuals were enriched among the genes most up-regulated by cigarette smoking in a previously reported bronchial airway smoking dataset. We also found that the DEE signature was enriched among the genes most altered in two previous studies of the effects of acute DEE on PBMC gene expression. An exposure-response relationship was demonstrated between air levels of elemental carbon and the first principal component of the DEE signature. CONCLUSIONS A gene expression signature was identified for workers occupationally exposed to DEE that was altered in an exposure-dependent manner and had some overlap with the effects of smoking and the effects of acute DEE exposure. This is the first study of gene expression in nasal epithelial cells of workers heavily exposed to DEE and provides new insights into the molecular alterations that occur with DEE exposure.
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Affiliation(s)
- E Drizik
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - S Corbett
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Y Zheng
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - R Vermeulen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Y Dai
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - W Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - D Ren
- Chaoyang Center for Disease Control and Prevention, Chaoyang, China
| | - H Duan
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Y Niu
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - J Xu
- Hong Kong University, Hong Kong, China
| | - W Fu
- Chaoyang Center for Disease Control and Prevention, Chaoyang, China
| | - K Meliefste
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - B Zhou
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaohui Zhang
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - J Yang
- Chaoyang Center for Disease Control and Prevention, Chaoyang, China
| | - Bryan Bassig
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Hanqiao Liu
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - M Ye
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Gang Liu
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - X Jia
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - T Meng
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - P Bin
- Key Laboratory of Chemical Safety and Health, National Institute of Occupational, Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - J Zhang
- Nicholas School of the Environment and Duke Global Health Institute, Duke University, Durham, NC, USA; Global Health Research Center, Duke Kunshan University, Kunshan City, Jiangsu Province, China
| | - D Silverman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - A Spira
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA; The Lung Cancer Initiative at Johnson & Johnson, Cambridge, MA, USA
| | - N Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - M E Lenburg
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA; Bioinformatics Program, Boston University, Boston, MA, USA.
| | - Q Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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21
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Kicic A, de Jong E, Ling KM, Nichol K, Anderson D, Wark PAB, Knight DA, Bosco A, Stick SM. Assessing the unified airway hypothesis in children via transcriptional profiling of the airway epithelium. J Allergy Clin Immunol 2020; 145:1562-1573. [PMID: 32113981 DOI: 10.1016/j.jaci.2020.02.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Emerging evidence suggests that disease vulnerability is expressed throughout the airways, the so-called unified airway hypothesis, but the evidence to support this is predominantly indirect. OBJECTIVES We sought to establish the transcriptomic profiles of the upper and lower airways and determine their level of similarity irrespective of airway symptoms (wheeze) and allergy. METHODS We performed RNA sequencing on upper and lower airway epithelial cells from 63 children with or without wheeze and accompanying atopy, using differential gene expression and gene coexpression analyses to determine transcriptional similarity. RESULTS We observed approximately 91% homology in the expressed genes between the 2 sites. When coexpressed genes were grouped into modules relating to biological functions, all were found to be conserved between the 2 regions, resulting in a consensus network containing 16 modules associated with ribosomal function, metabolism, gene expression, mitochondrial activity, and antiviral responses through IFN activity. Although symptom-associated gene expression changes were more prominent in the lower airway, they were reflected in nasal epithelium and included IL-1 receptor like 1, prostaglandin-endoperoxide synthase 1, CCL26, and periostin. Through network analysis we identified a cluster of coexpressed genes associated with atopic wheeze in the lower airway, which could equally distinguish atopic and nonatopic phenotypes in upper airway samples. CONCLUSIONS We show that the upper and lower airways are significantly conserved in their transcriptional composition, and that variations associated with disease are present in both nasal and tracheal epithelium. Findings from this study supporting a unified airway imply that clinical insight regarding the lower airway in health and disease can be gained from studying the nasal epithelium.
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Affiliation(s)
- Anthony Kicic
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia; Occupation and Environment, School of Public Health, Curtin University, Perth, Australia; School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, Australia.
| | - Emma de Jong
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | - Kak-Ming Ling
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia
| | - Kristy Nichol
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, Australia
| | - Denise Anderson
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | - Peter A B Wark
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, Australia
| | - Darryl A Knight
- School of Medicine and Public Health, University of Newcastle, Callaghan, Australia; Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute, Newcastle, Australia; Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Anthony Bosco
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
| | - Stephen M Stick
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia; School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia; Department of Respiratory Medicine, Princess Margaret Hospital for Children, Perth, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Harry Perkins Institute of Medical Research, Nedlands, Australia
| | -
- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia
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- Telethon Kids Institute, Centre for Health Research, The University of Western Australia, Nedlands, Australia; Robinson Research Institute, University of Adelaide, Adelaide, Australia; Hunter Medical Research Institute, Priority Research Centre for Asthma and Respiratory Disease, New Lambton Heights, Australia
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22
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Boudewijn IM, Lan A, Faiz A, Cox CA, Brouwer S, Schokker S, Vroegop SJ, Nawijn MC, Woodruff PG, Christenson SA, Hagedoorn P, Frijlink HW, Choy DF, Brouwer U, Wisman M, Postma DS, Fingleton J, Beasley R, van den Berge M, Guryev V. Nasal gene expression changes with inhaled corticosteroid treatment in asthma. Allergy 2020; 75:191-194. [PMID: 31230369 DOI: 10.1111/all.13952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 06/01/2019] [Accepted: 06/14/2019] [Indexed: 12/15/2022]
Affiliation(s)
- Ilse M. Boudewijn
- Department of Pulmonary Diseases University Medical Center Groningen, University of Groningen Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Andy Lan
- Department of Pulmonary Diseases University Medical Center Groningen, University of Groningen Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pathology, Section Medical Biology, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Alen Faiz
- Department of Pulmonary Diseases University Medical Center Groningen, University of Groningen Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pathology, Section Medical Biology, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Claire A. Cox
- Department of Pulmonary Diseases University Medical Center Groningen, University of Groningen Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Sharon Brouwer
- Department of Pathology, Section Medical Biology, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Siebrig Schokker
- Department of Pulmonary Diseases Martini Hospital Groningen the Netherlands
| | | | - Martijn C. Nawijn
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
- Department of Pathology, Section Medical Biology, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Prescott G. Woodruff
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine University of California San Francisco California USA
- Cardiovascular Research Institute University of California San Francisco California USA
| | - Stephanie A. Christenson
- Department of Medicine, Division of Pulmonary, Critical Care, Allergy, and Sleep Medicine University of California San Francisco California USA
- Cardiovascular Research Institute University of California San Francisco California USA
| | - Paul Hagedoorn
- Department of Pharmaceutical Technology and Biopharmacy University of Groningen Groningen The Netherlands
| | - Henderik W. Frijlink
- Department of Pharmaceutical Technology and Biopharmacy University of Groningen Groningen The Netherlands
| | | | - Uilke Brouwer
- Department of Pathology, Section Medical Biology, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Marissa Wisman
- Department of Pathology, Section Medical Biology, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Dirkje S. Postma
- Department of Pulmonary Diseases University Medical Center Groningen, University of Groningen Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - James Fingleton
- The Medical Research Institute of New Zealand Wellington New Zealand
- The Capital & Coast District Health Board Wellington New Zealand
- Victoria University of Wellington New Zealand
| | - Richard Beasley
- The Medical Research Institute of New Zealand Wellington New Zealand
- The Capital & Coast District Health Board Wellington New Zealand
- Victoria University of Wellington New Zealand
| | - Maarten van den Berge
- Department of Pulmonary Diseases University Medical Center Groningen, University of Groningen Groningen The Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
| | - Victor Guryev
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen University of Groningen Groningen The Netherlands
- European Research Institute for the Biology of Ageing University Medical Center Groningen, University of Groningen Groningen The Netherlands
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23
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Garland LL, Guillen-Rodriguez J, Hsu CH, Yozwiak M, Zhang HH, Alberts DS, Davis LE, Szabo E, Merenstein C, Lel J, Zhang X, Liu H, Liu G, Spira AE, Beane JE, Wojtowicz M, Chow HHS. Effect of Intermittent Versus Continuous Low-Dose Aspirin on Nasal Epithelium Gene Expression in Current Smokers: A Randomized, Double-Blinded Trial. Cancer Prev Res (Phila) 2019; 12:809-820. [PMID: 31451521 PMCID: PMC7485120 DOI: 10.1158/1940-6207.capr-19-0036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 05/23/2019] [Accepted: 08/19/2019] [Indexed: 12/21/2022]
Abstract
A chemopreventive effect of aspirin (ASA) on lung cancer risk is supported by epidemiologic and preclinical studies. We conducted a randomized, double-blinded study in current heavy smokers to compare modulating effects of intermittent versus continuous low-dose ASA on nasal epithelium gene expression and arachidonic acid (ARA) metabolism. Fifty-four participants were randomized to intermittent (ASA 81 mg daily for one week/placebo for one week) or continuous (ASA 81 mg daily) for 12 weeks. Low-dose ASA suppressed urinary prostaglandin E2 metabolite (PGEM; change of -4.55 ± 11.52 from baseline 15.44 ± 13.79 ng/mg creatinine for arms combined, P = 0.02), a surrogate of COX-mediated ARA metabolism, but had minimal effects on nasal gene expression of nasal or bronchial gene-expression signatures associated with smoking, lung cancer, and chronic obstructive pulmonary disease. Suppression of urinary PGEM correlated with favorable changes in a smoking-associated gene signature (P < 0.01). Gene set enrichment analysis (GSEA) showed that ASA intervention led to 1,079 enriched gene sets from the Canonical Pathways within the Molecular Signatures Database. In conclusion, low-dose ASA had minimal effects on known carcinogenesis gene signatures in nasal epithelium of current smokers but results in wide-ranging genomic changes in the nasal epithelium, demonstrating utility of nasal brushings as a surrogate to measure gene-expression responses to chemoprevention. PGEM may serve as a marker for smoking-associated gene-expression changes and systemic inflammation. Future studies should focus on NSAIDs or agent combinations with broader inhibition of pro-inflammatory ARA metabolism to shift gene signatures in an anti-carcinogenic direction.
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Affiliation(s)
| | | | - Chiu-Hsieh Hsu
- University of Arizona Cancer Center, University of Arizona
| | | | | | | | - Lisa E Davis
- University of Arizona Cancer Center, University of Arizona
| | - Eva Szabo
- Division of Cancer Prevention, NCI/NIH, Boston, Massachusetts
| | | | - Julian Lel
- Boston University School of Medicine, Boston, Massachusetts
| | - Xiaohui Zhang
- Boston University School of Medicine, Boston, Massachusetts
| | - Hanqiao Liu
- Boston University School of Medicine, Boston, Massachusetts
| | - Gang Liu
- Boston University School of Medicine, Boston, Massachusetts
| | - Avrum E Spira
- Boston University School of Medicine, Boston, Massachusetts
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24
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Imkamp K, Bernal V, Grzegorzcyk M, Horvatovich P, Vermeulen CJ, Heijink IH, Guryev V, Kerstjens HAM, van den Berge M, Faiz A. Gene network approach reveals co-expression patterns in nasal and bronchial epithelium. Sci Rep 2019; 9:15835. [PMID: 31676779 PMCID: PMC6825243 DOI: 10.1038/s41598-019-50963-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/13/2019] [Indexed: 12/20/2022] Open
Abstract
Nasal gene expression profiling is a new approach to investigate the airway epithelium as a biomarker to study the activity and treatment responses of obstructive pulmonary diseases. We investigated to what extent gene expression profiling of nasal brushings is similar to that of bronchial brushings. We performed genome wide gene expression profiling on matched nasal and bronchial epithelial brushes from 77 respiratory healthy individuals. To investigate differences and similarities among regulatory modules, network analysis was performed on correlated, differentially expressed and smoking-related genes using Gaussian Graphical Models. Between nasal and bronchial brushes, 619 genes were correlated and 1692 genes were differentially expressed (false discovery rate <0.05, |Fold-change|>2). Network analysis of correlated genes showed pro-inflammatory pathways to be similar between the two locations. Focusing on smoking-related genes, cytochrome-P450 pathway related genes were found to be similar, supporting the concept of a detoxifying response to tobacco exposure throughout the airways. In contrast, cilia-related pathways were decreased in nasal compared to bronchial brushes when focusing on differentially expressed genes. Collectively, while there are substantial differences in gene expression between nasal and bronchial brushes, we also found similarities, especially in the response to the external factors such as smoking.
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Affiliation(s)
- Kai Imkamp
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands. .,University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands.
| | - Victor Bernal
- University of Groningen, Bernoulli Institute (JBI), Groningen, The Netherlands.,University of Groningen, Department of Pharmacy, Analytical Biochemistry, Groningen, The Netherlands
| | - Marco Grzegorzcyk
- University of Groningen, Bernoulli Institute (JBI), Groningen, The Netherlands
| | - Peter Horvatovich
- University of Groningen, Department of Pharmacy, Analytical Biochemistry, Groningen, The Netherlands
| | - Cornelis J Vermeulen
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
| | - Irene H Heijink
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, section Medical Biology, Groningen, The Netherlands
| | - Victor Guryev
- University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands.,European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Huib A M Kerstjens
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pathology & Medical Biology, section Medical Biology, Groningen, The Netherlands.,University of Technology Sydney, Respiratory Bioinformatics and Molecular Biology (RBMB), School of life sciences, Sydney, Australia.,Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
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25
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Reyfman PA, Washko GR, Dransfield MT, Spira A, Han MK, Kalhan R. Defining Impaired Respiratory Health. A Paradigm Shift for Pulmonary Medicine. Am J Respir Crit Care Med 2019; 198:440-446. [PMID: 29624449 DOI: 10.1164/rccm.201801-0120pp] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Paul A Reyfman
- 1 Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, and
| | - George R Washko
- 2 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Mark T Dransfield
- 3 Lung Health Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Avrum Spira
- 4 BU-BMC Cancer Center and Division of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts; and
| | - MeiLan K Han
- 5 Division of Pulmonary and Critical Care Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Ravi Kalhan
- 1 Asthma and COPD Program, Division of Pulmonary and Critical Care Medicine, and.,6 Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
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26
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Morrow JD, Chase RP, Parker MM, Glass K, Seo M, Divo M, Owen CA, Castaldi P, DeMeo DL, Silverman EK, Hersh CP. RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD. Respir Res 2019; 20:65. [PMID: 30940135 PMCID: PMC6446359 DOI: 10.1186/s12931-019-1032-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants. METHODS We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance. RESULTS The known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies. CONCLUSIONS Our integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Minseok Seo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Miguel Divo
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
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27
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Jamieson KC, Traves SL, Kooi C, Wiehler S, Dumonceaux CJ, Maciejewski BA, Arnason JW, Michi AN, Leigh R, Proud D. Rhinovirus and Bacteria Synergistically Induce IL-17C Release from Human Airway Epithelial Cells To Promote Neutrophil Recruitment. THE JOURNAL OF IMMUNOLOGY 2018; 202:160-170. [PMID: 30504421 DOI: 10.4049/jimmunol.1800547] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 10/30/2018] [Indexed: 11/19/2022]
Abstract
Virus-bacteria coinfections are associated with more severe exacerbations and increased risk of hospital readmission in patients with chronic obstructive pulmonary disease (COPD). The airway epithelium responds to such infections by releasing proinflammatory and antimicrobial cytokines, including IL-17C. However, the regulation and role of IL-17C is not well understood. In this study, we examine the mechanisms regulating IL-17C production and its potential role in COPD exacerbations. Human bronchial epithelial cells (HBE) obtained from normal, nontransplanted lungs or from brushings of nonsmokers, healthy smokers, or COPD patients were exposed to bacteria and/or human rhinovirus (HRV). RNA and protein were collected for analysis, and signaling pathways were assessed with pharmacological agonists, inhibitors, or small interfering RNAs. HBE were also stimulated with IL-17C to assess function. HRV-bacterial coinfections synergistically induced IL-17C expression. This induction was dependent on HRV replication and required NF-κB-mediated signaling. Synergy was lost in the presence of an inhibitor of the p38 MAP kinase pathway. HBE exposed to IL-17C show increased gene expression of CXCL1, CXCL2, NFKBIZ, and TFRC, and release CXCL1 protein, a neutrophil chemoattractant. Knockdown of IL-17C significantly reduced induction of CXCL1 in response to HRV-bacterial coinfection as well as neutrophil chemotaxis. HBE from healthy smokers release less IL-17C than cells from nonsmokers, but cells from COPD patients release significantly more IL-17C compared with either nonsmokers or healthy smokers. These data suggest that IL-17C may contribute to microbial-induced COPD exacerbations by promoting neutrophil recruitment.
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Affiliation(s)
- Kyla C Jamieson
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and
| | - Suzanne L Traves
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and
| | - Cora Kooi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and.,Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Shahina Wiehler
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and
| | - Curtis J Dumonceaux
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and.,Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Barbara A Maciejewski
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and
| | - Jason W Arnason
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and.,Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - Aubrey N Michi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and
| | - Richard Leigh
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and.,Department of Medicine, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada
| | - David Proud
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4Z6, Canada; and
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28
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Kurokawa M, Koya T, Takeuchi H, Hayashi M, Sakagami T, Ishioka K, Gon Y, Hasegawa T, Kikuchi T. Association of upper and lower airway eosinophilic inflammation with response to omalizumab in patients with severe asthma. J Asthma 2018; 57:71-78. [PMID: 30489179 DOI: 10.1080/02770903.2018.1541357] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background: The anti-immunoglobulin E monoclonal antibody, omalizumab, is used to treat severe asthma and has the potential to ameliorate airway inflammation. However, the effect of omalizumab in ameliorating upper airway inflammation has not been fully elucidated. Objective: We investigated the association of upper and lower airway inflammation with the response to omalizumab treatment. Methods: We used the Global Evaluation of Treatment Effectiveness to assess the efficacy of omalizumab in treating 16 patients with severe asthma. We also investigated the symptom score, short-acting β-agonist inhaler use, pulmonary function, biomarkers, computed tomography scans, and nasal mucosa pathology at omalizumab initiation and after four months of treatment. Results: When the fraction of exhaled nitric oxide (FeNO) and the percentage of sputum eosinophil were used as indicators of lower airway inflammation, positive correlations were found between CD20 B-cell, mast cell, and eosinophil counts in the nasal mucosa. Improved asthma symptoms were observed in 12 of the 16 severe asthma cases. The FeNO and eosinophil levels in the nasal tissue, prior to the administration of omalizumab were predictors of the response to asthma treatment. Conclusions: These findings suggest heterogeneity among people with severe asthma. In addition, the phenotype associated with response to omalizumab, leading to improvement in asthma symptoms, comprises upper airway eosinophilia and high FeNO levels.
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Affiliation(s)
- Makoto Kurokawa
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Toshiyuki Koya
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroyuki Takeuchi
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masachika Hayashi
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Takuro Sakagami
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kojiro Ishioka
- Department of Otolaryngology Head and Neck Surgery, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yasuhiro Gon
- Division of Respiratory Medicine, Department of Internal Medicine, Nihon University of Medicine, Tokyo, Japan
| | - Takashi Hasegawa
- Department of General Medicine, Niigata University Medical and Dental Hospital, Japan, Niigata
| | - Toshiaki Kikuchi
- Department of Respiratory Medicine and Infectious Diseases, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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29
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Sala MA, Balderas-Martínez YI, Buendía-Roldan I, Abdala-Valencia H, Nam K, Jain M, Bhorade S, Bharat A, Reyfman PA, Ridge KM, Pardo A, Sznajder JI, Budinger GRS, Misharin AV, Selman M. Inflammatory pathways are upregulated in the nasal epithelium in patients with idiopathic pulmonary fibrosis. Respir Res 2018; 19:233. [PMID: 30477498 PMCID: PMC6257973 DOI: 10.1186/s12931-018-0932-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by progressive scarring of the lung parenchyma, leading to respiratory failure and death. High resolution computed tomography of the chest is often diagnostic for IPF, but its cost and the risk of radiation exposure limit its use as a screening tool even in patients at high risk for the disease. In patients with lung cancer, investigators have detected transcriptional signatures of disease in airway and nasal epithelial cells distal to the site of disease that are clinically useful as screening tools. Here we assessed the feasibility of distinguishing patients with IPF from age-matched controls through transcriptomic profiling of nasal epithelial curettage samples, which can be safely and repeatedly sampled over the course of a patient's illness. We recruited 10 patients with IPF and 23 age-matched healthy control subjects. Using 3' messenger RNA sequencing (mRNA-seq), we identified 224 differentially expressed genes, most of which were upregulated in patients with IPF compared with controls. Pathway enrichment analysis revealed upregulation of pathways related to immune response and inflammatory signaling in IPF patients compared with controls. These findings support the concept that fibrosis is associated with upregulation of inflammatory pathways across the respiratory epithelium with possible implications for disease detection and pathobiology.
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Affiliation(s)
- Marc A Sala
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | | | - Ivette Buendía-Roldan
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan 4502, CP 14080, Mexico City, Mexico
| | - Hiam Abdala-Valencia
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Kiwon Nam
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Manu Jain
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sangeeta Bhorade
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ankit Bharat
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Paul A Reyfman
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,CONACYT-Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico.,Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan 4502, CP 14080, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Karen M Ridge
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Annie Pardo
- Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
| | - Jacob I Sznajder
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - G R Scott Budinger
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alexander V Misharin
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan 4502, CP 14080, Mexico City, Mexico.
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