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Perea L, Faner R, Chalmers JD, Sibila O. Pathophysiology and genomics of bronchiectasis. Eur Respir Rev 2024; 33:240055. [PMID: 38960613 PMCID: PMC11220622 DOI: 10.1183/16000617.0055-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 05/02/2024] [Indexed: 07/05/2024] Open
Abstract
Bronchiectasis is a complex and heterogeneous inflammatory chronic respiratory disease with an unknown cause in around 30-40% of patients. The presence of airway infection together with chronic inflammation, airway mucociliary dysfunction and lung damage are key components of the vicious vortex model that better describes its pathophysiology. Although bronchiectasis research has significantly increased over the past years and different endotypes have been identified, there are still major gaps in the understanding of the pathophysiology. Genomic approaches may help to identify new endotypes, as has been shown in other chronic airway diseases, such as COPD.Different studies have started to work in this direction, and significant contributions to the understanding of the microbiome and proteome diversity have been made in bronchiectasis in recent years. However, the systematic application of omics approaches to identify new molecular insights into the pathophysiology of bronchiectasis (endotypes) is still limited compared with other respiratory diseases.Given the complexity and diversity of these technologies, this review describes the key components of the pathophysiology of bronchiectasis and how genomics can be applied to increase our knowledge, including the study of new techniques such as proteomics, metabolomics and epigenomics. Furthermore, we propose that the novel concept of trained innate immunity, which is driven by microbiome exposures leading to epigenetic modifications, can complement our current understanding of the vicious vortex. Finally, we discuss the challenges, opportunities and implications of genomics application in clinical practice for better patient stratification into new therapies.
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Affiliation(s)
- Lidia Perea
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Rosa Faner
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
| | - James D Chalmers
- Division of Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - Oriol Sibila
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias M.P. (CIBERES), Barcelona, Spain
- Respiratory Department, Hospital Clínic, University of Barcelona, Barcelona, Spain
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2
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Dunne R, Reguant R, Ramarao-Milne P, Szul P, Sng LM, Lundberg M, Twine NA, Bauer DC. Thresholding Gini variable importance with a single-trained random forest: An empirical Bayes approach. Comput Struct Biotechnol J 2023; 21:4354-4360. [PMID: 37711185 PMCID: PMC10497997 DOI: 10.1016/j.csbj.2023.08.033] [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: 06/04/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Random forests (RFs) are a widely used modelling tool capable of feature selection via a variable importance measure (VIM), however, a threshold is needed to control for false positives. In the absence of a good understanding of the characteristics of VIMs, many current approaches attempt to select features associated to the response by training multiple RFs to generate statistical power via a permutation null, by employing recursive feature elimination, or through a combination of both. However, for high-dimensional datasets these approaches become computationally infeasible. In this paper, we present RFlocalfdr, a statistical approach, built on the empirical Bayes argument of Efron, for thresholding mean decrease in impurity (MDI) importances. It identifies features significantly associated with the response while controlling the false positive rate. Using synthetic data and real-world data in health, we demonstrate that RFlocalfdr has equivalent accuracy to currently published approaches, while being orders of magnitude faster. We show that RFlocalfdr can successfully threshold a dataset of 106 datapoints, establishing its usability for large-scale datasets, like genomics. Furthermore, RFlocalfdr is compatible with any RF implementation that returns a VIM and counts, making it a versatile feature selection tool that reduces false discoveries.
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Affiliation(s)
- Robert Dunne
- Data61, Commonwealth Scientific and Industrial Research Organisation, Sydney, Australia
| | - Roc Reguant
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia
| | - Priya Ramarao-Milne
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia
| | - Piotr Szul
- Data61, Commonwealth Scientific and Industrial Research Organisation, Dutton Park, Australia
| | - Letitia M.F. Sng
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia
| | - Mischa Lundberg
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia
- Diamantina Institute, The University of Queensland, St Lucia, Australia
| | - Natalie A. Twine
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia
- Macquarie University, Applied BioSciences, Faculty of Science and Engineering, Macquarie Park, Australia
| | - Denis C. Bauer
- Transformational Bioinformatics, Commonwealth Scientific and Industrial Research Organisation, Westmead, Australia
- Macquarie University, Applied BioSciences, Faculty of Science and Engineering, Macquarie Park, Australia
- Macquarie University, Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie Park, Australia
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3
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Wu CY, Cilic A, Pak O, Dartsch RC, Wilhelm J, Wujak M, Lo K, Brosien M, Zhang R, Alkoudmani I, Witte B, Pedersen F, Watz H, Voswinckel R, Günther A, Ghofrani HA, Brandes RP, Schermuly RT, Grimminger F, Seeger W, Sommer N, Weissmann N, Hadzic S. CEACAM6 as a Novel Therapeutic Target to Boost HO-1-mediated Antioxidant Defense in COPD. Am J Respir Crit Care Med 2023; 207:1576-1590. [PMID: 37219322 DOI: 10.1164/rccm.202208-1603oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 05/23/2023] [Indexed: 05/24/2023] Open
Abstract
Rationale: Tobacco smoking and air pollution are primary causes of chronic obstructive pulmonary disease (COPD). However, only a minority of smokers develop COPD. The mechanisms underlying the defense against nitrosative/oxidative stress in nonsusceptible smokers to COPD remain largely unresolved. Objectives: To investigate the defense mechanisms against nitrosative/oxidative stress that possibly prevent COPD development or progression. Methods: Four cohorts were investigated: 1) sputum samples (healthy, n = 4; COPD, n = 37), 2) lung tissue samples (healthy, n = 13; smokers without COPD, n = 10; smoker+COPD, n = 17), 3) pulmonary lobectomy tissue samples (no/mild emphysema, n = 6), and 4) blood samples (healthy, n = 6; COPD, n = 18). We screened 3-nitrotyrosine (3-NT) levels, as indication of nitrosative/oxidative stress, in human samples. We established a novel in vitro model of a cigarette smoke extract (CSE)-resistant cell line and studied 3-NT formation, antioxidant capacity, and transcriptomic profiles. Results were validated in lung tissue, isolated primary cells, and an ex vivo model using adeno-associated virus-mediated gene transduction and human precision-cut lung slices. Measurements and Main Results: 3-NT levels correlate with COPD severity of patients. In CSE-resistant cells, nitrosative/oxidative stress upon CSE treatment was attenuated, paralleled by profound upregulation of heme oxygenase-1 (HO-1). We identified carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6) as a negative regulator of HO-1-mediated nitrosative/oxidative stress defense in human alveolar type 2 epithelial cells (hAEC2s). Consistently, inhibition of HO-1 activity in hAEC2s increased the susceptibility toward CSE-induced damage. Epithelium-specific CEACAM6 overexpression increased nitrosative/oxidative stress and cell death in human precision-cut lung slices on CSE treatment. Conclusions: CEACAM6 expression determines the hAEC2 sensitivity to nitrosative/oxidative stress triggering emphysema development/progression in susceptible smokers.
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Affiliation(s)
- Cheng-Yu Wu
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Anis Cilic
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Oleg Pak
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Ruth Charlotte Dartsch
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Jochen Wilhelm
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Magdalena Wujak
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Department of Medicinal Chemistry, Collegium Medicum in Bydgoszcz, Faculty of Pharmacy, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Kevin Lo
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Monika Brosien
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Ruoyu Zhang
- Department of General and Thoracic Surgery, University Hospital of Giessen, Giessen, Germany
| | - Ibrahim Alkoudmani
- Department of General and Thoracic Surgery, University Hospital of Giessen, Giessen, Germany
| | - Biruta Witte
- Department of General and Thoracic Surgery, University Hospital of Giessen, Giessen, Germany
| | - Frauke Pedersen
- Pulmonary Research Institute at LungenClinic Grosshansdorf, Airway Research Center North, DZL, Grosshansdorf, Germany
| | - Henrik Watz
- Pulmonary Research Institute at LungenClinic Grosshansdorf, Airway Research Center North, DZL, Grosshansdorf, Germany
| | | | - Andreas Günther
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Hossein A Ghofrani
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany; and
| | - Ralph T Schermuly
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Friedrich Grimminger
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
| | - Werner Seeger
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
- Institute for Lung Health (ILH), Justus Liebig University Giessen, Giessen, Germany
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
| | - Stefan Hadzic
- Excellence Cluster Cardio-Pulmonary Institute, Universities of Giessen and Marburg Lung Center, member of the German Center for Lung Research (DZL), Justus Liebig University Giessen, Giessen, Germany
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4
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Negewo NA, Gibson PG, Simpson JL, McDonald VM, Baines KJ. Severity of Lung Function Impairment Drives Transcriptional Phenotypes of COPD and Relates to Immune and Metabolic Processes. Int J Chron Obstruct Pulmon Dis 2023; 18:273-287. [PMID: 36942279 PMCID: PMC10024507 DOI: 10.2147/copd.s388297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 02/15/2023] [Indexed: 03/16/2023] Open
Abstract
Purpose This study sought to characterize transcriptional phenotypes of COPD through unsupervised clustering of sputum gene expression profiles, and further investigate mechanisms underlying the characteristics of these clusters. Patients and methods Induced sputum samples were collected from patients with stable COPD (n = 72) and healthy controls (n = 15). Induced sputum was collected for inflammatory cell counts, and RNA extracted. Transcriptional profiles were generated (Illumina Humanref-8 V2) and analyzed by GeneSpring GX14.9.1. Unsupervised hierarchical clustering and differential gene expression analysis were performed, and gene alterations validated in the ECLIPSE dataset (GSE22148). Results We identified 2 main clusters (Cluster 1 [n = 35] and Cluster 2 [n = 37]), which further divided into 4 sub-clusters (Sub-clusters 1.1 [n = 14], 1.2 [n = 21], 2.1 [n = 20] and 2.2 [n = 17]). Compared with Cluster 1, Cluster 2 was associated with significantly lower lung function (p = 0.014), more severe disease (p = 0.009) and breathlessness (p = 0.035), and increased sputum neutrophils (p = 0.031). Sub-cluster 1.1 had significantly higher proportion of people with comorbid cardiovascular disease compared to the other 3 sub-clusters (92.5% vs 57.1%, 50% and 52.9%, p < 0.013). Through supervised analysis we determined that degree of airflow limitation (GOLD stage) was the predominant factor driving gene expression differences in our transcriptional clusters. There were 452 genes (adjusted p < 0.05 and ≥2 fold) altered in GOLD stage 3 and 4 versus 1 and 2, of which 281 (62%) were also found to be significantly expressed between these GOLD stages in the ECLIPSE data set (GSE22148). Differentially expressed genes were largely downregulated in GOLD stages 3 and 4 and connected in 5 networks relating to lipoprotein and cholesterol metabolism; metabolic processes in oxidation/reduction and mitochondrial function; antigen processing and presentation; regulation of complement activation and innate immune responses; and immune and metabolic processes. Conclusion Severity of lung function drives 2 distinct transcriptional phenotypes of COPD and relates to immune and metabolic processes.
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Affiliation(s)
- Netsanet A Negewo
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Peter G Gibson
- Centre of Excellence in Treatable Traits, University of Newcastle, New Lambton Heights, NSW, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia
- Asthma and Breathing Research Centre, Hunter Medical Research Centre, New Lambton Heights, NSW, Australia
| | - Jodie L Simpson
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
| | - Vanessa M McDonald
- Centre of Excellence in Treatable Traits, University of Newcastle, New Lambton Heights, NSW, Australia
- Department of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, NSW, Australia
- Asthma and Breathing Research Centre, Hunter Medical Research Centre, New Lambton Heights, NSW, Australia
- School of Nursing and Midwifery, The University of Newcastle, Callaghan, NSW, Australia
| | - Katherine J Baines
- Immune Health Research Program, Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
- Correspondence: Katherine J Baines, Hunter Medical Research Institute, Level 2 East Wing, Locked Bag 1000, New Lambton Heights, NSW, 2305, Australia, Tel +61 2 40420090, Fax +61 2 40420046, Email
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5
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Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, Richoz N, Ribeiro Orsi A, Mamanova L, Bolt L, Elmentaite R, Pett JP, Huang N, Xu C, He P, Dabrowska M, Pritchard S, Tuck L, Prigmore E, Perera S, Knights A, Oszlanczi A, Hunter A, Vieira SF, Patel M, Lindeboom RGH, Campos LS, Matsuo K, Nakayama T, Yoshida M, Worlock KB, Nikolić MZ, Georgakopoulos N, Mahbubani KT, Saeb-Parsy K, Bayraktar OA, Clatworthy MR, Stegle O, Kumasaka N, Teichmann SA, Meyer KB. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet 2023; 55:66-77. [PMID: 36543915 PMCID: PMC9839452 DOI: 10.1038/s41588-022-01243-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/25/2022] [Indexed: 12/24/2022]
Abstract
Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.
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Affiliation(s)
- Elo Madissoon
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | | | - Nathan Richoz
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Ana Ribeiro Orsi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Rasa Elmentaite
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - J Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Chuan Xu
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Peng He
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Andrew Knights
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Adam Hunter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Sara F Vieira
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Lia S Campos
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | | | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London Hospitals NHS Foundation Trust, London, UK
| | - Nikitas Georgakopoulos
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | | | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Molecular Immunity Unit, University of Cambridge Department of Medicine, MRC Laboratory of Molecular Biology, Francis Crick Ave, Cambridge, UK
| | - Oliver Stegle
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Deutsches Krebsforschungszentrum (DKFZ), Heidelberg, Germany
| | | | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
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6
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Byrd AL, Qu X, Lukyanchuk A, Liu J, Chen F, Naughton KJ, DuCote TJ, Song X, Bowman HC, Zhao Y, Edgin AR, Wang C, Liu J, Brainson CF. Dysregulated Polycomb Repressive Complex 2 contributes to chronic obstructive pulmonary disease by rewiring stem cell fate. Stem Cell Reports 2022; 18:289-304. [PMID: 36525966 PMCID: PMC9860081 DOI: 10.1016/j.stemcr.2022.11.009] [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: 10/26/2021] [Revised: 11/11/2022] [Accepted: 11/14/2022] [Indexed: 12/23/2022] Open
Abstract
Aberrant lung cell differentiation is a hallmark of many lung diseases including chronic obstructive pulmonary disease (COPD). The EZH2-containing Polycomb Repressive Complex 2 (PRC2) regulates embryonic lung stem cell fate, but its role in adult lung is obscure. Histological analysis of patient tissues revealed that loss of PRC2 activity was correlated with aberrant bronchiolar cell differentiation in COPD lung. Histological and single-cell RNA-sequencing analyses showed that loss of EZH2 in mouse lung organoids led to lowered self-renewal capability, increased squamous morphological development, and marked shifts in progenitor cell populations. Evaluation of in vivo models revealed that heterozygosity of Ezh2 in mice with ovalbumin-induced lung inflammation led to epithelial cell differentiation patterns similar to those in COPD lung. We also identified cystathionine-β-synthase as a possible upstream factor for PRC2 destabilization. Our findings suggest that PRC2 is integral to facilitating proper lung stem cell differentiation in humans and mice.
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Affiliation(s)
- Aria L. Byrd
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Xufeng Qu
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA
| | - Alexsandr Lukyanchuk
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Jinpeng Liu
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Fan Chen
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Kassandra J. Naughton
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Tanner J. DuCote
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Xiulong Song
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Hannah C. Bowman
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Yanming Zhao
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Abigail R. Edgin
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Chi Wang
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA,Markey Cancer Center, University of Kentucky, Lexington, KY, USA
| | - Jinze Liu
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, USA,Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Christine Fillmore Brainson
- Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA; Markey Cancer Center, University of Kentucky, Lexington, KY, USA.
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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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Association of childhood BMI trajectory with post-adolescent and adult lung function is mediated by pre-adolescent DNA methylation. Respir Res 2022; 23:194. [PMID: 35906571 PMCID: PMC9335987 DOI: 10.1186/s12931-022-02089-4] [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: 12/09/2021] [Accepted: 06/14/2022] [Indexed: 12/03/2022] Open
Abstract
Background Body mass index (BMI) has been shown to be associated with lung function. Recent findings showed that DNA methylation (DNAm) variation is likely to be a consequence of changes in BMI. However, whether DNAm mediates the association of BMI with lung function is unknown. We examined the mediating role of DNAm on the association of pre-adolescent BMI trajectories with post-adolescent and adulthood lung function (forced expiratory volume (FEV1), forced vital capacity (FVC), and FEV1/FVC). Methods Analyses were undertaken in the Isle of Wight birth cohort (IOWBC). Group-based trajectory modelling was applied to infer latent BMI trajectories from age 1 to 10 years. An R package, ttscreening, was applied to identify CpGs at 10 years potentially associated with BMI trajectories for each sex. Linear regressions were implemented to further screen CpGs for their association with lung function at 18 years. Path analysis, stratified by sex, was applied to each screened CpG to assess its role of mediation. Internal validation was applied to further examine the mediation consistency of the detected CpGs based on lung function at 26 years. Mendelian randomization (MR-base) was used to test possible causal effects of the identified CpGs. Results Two BMI trajectories (high vs. low) were identified. Of the 442,475 CpG sites, 18 CpGs in males and 33 in females passed screening. Eight CpGs in males and 16 CpGs in females (none overlapping) were identified as mediators. For subjects with high BMI trajectory, high DNAm at all CpGs in males were associated with decreased lung function, while 8 CpGs in females were associated with increased lung function at 18 years. At 26 years, 6 CpGs in males and 14 CpGs in females showed the same direction of indirect effects as those at 18 years. DNAm at CpGs cg19088553 (GRIK2) and cg00612625 (HPSE2) showed a potential causal effect on FEV1. Conclusions The effects of BMI trajectory in early childhood on post-adolescence lung function were likely to be mediated by pre-adolescence DNAm in both males and females, but such mediation effects were likely to diminish over time. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02089-4.
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9
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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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10
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Chen L, Zhu D, Huang J, Zhang H, Zhou G, Zhong X. Identification of Hub Genes Associated with COPD Through Integrated Bioinformatics Analysis. Int J Chron Obstruct Pulmon Dis 2022; 17:439-456. [PMID: 35273447 PMCID: PMC8901430 DOI: 10.2147/copd.s353765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 02/20/2022] [Indexed: 12/30/2022] Open
Affiliation(s)
- Lin Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Liuzhou People’s Hospital, LiuZhou, Guangxi, People’s Republic of China
| | - Donglan Zhu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Jinfu Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Hui Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Guang Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
| | - Xiaoning Zhong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, People’s Republic of China
- Correspondence: Xiaoning Zhong, Tel +86 13607881203, Fax +86 771-5356702, Email
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11
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Karim L, Kosmider B, Bahmed K. Mitochondrial ribosomal stress in lung diseases. Am J Physiol Lung Cell Mol Physiol 2021; 322:L507-L517. [PMID: 34873929 DOI: 10.1152/ajplung.00078.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are involved in a variety of critical cellular functions, and their impairment drives cell injury. The mitochondrial ribosome (mitoribosome) is responsible for the protein synthesis of mitochondrial DNA encoded genes. These proteins are involved in oxidative phosphorylation, respiration, and ATP production required in the cell. Mitoribosome components originate from both mitochondrial and nuclear genomes. Their dysfunction can be caused by impaired mitochondrial protein synthesis or mitoribosome misassembly, leading to a decline in mitochondrial translation. This decrease can trigger mitochondrial ribosomal stress and contribute to pulmonary cell injury, death, and diseases. This review focuses on the contribution of the impaired mitoribosome structural components and function to respiratory disease pathophysiology. We present recent findings in the fields of lung cancer, chronic obstructive pulmonary disease, interstitial lung disease, and asthma. We also include reports on the mitoribosome dysfunction in pulmonary hypertension, high altitude pulmonary edema, bacterial and viral infections. Studies of the mitoribosome alterations in respiratory diseases can lead to novel therapeutic targets.
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Affiliation(s)
- Loukmane Karim
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Biomedical Education and Data Science, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
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12
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Green CE, Clarke J, Bicknell R, Turner AM. Pulmonary MicroRNA Changes Alter Angiogenesis in Chronic Obstructive Pulmonary Disease and Lung Cancer. Biomedicines 2021; 9:830. [PMID: 34356894 PMCID: PMC8301412 DOI: 10.3390/biomedicines9070830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/12/2022] Open
Abstract
The pulmonary endothelium is dysfunctional in chronic obstructive pulmonary disease (COPD), a known risk factor for lung cancer. The pulmonary endothelium is altered in emphysema, which is disproportionately affected by cancers. Gene and microRNA expression differs between COPD and non-COPD lung. We hypothesised that the alteration in microRNA expression in the pulmonary endothelium contributes to its dysfunction. A total of 28 patients undergoing pulmonary resection were recruited and endothelial cells were isolated from healthy lung and tumour. MicroRNA expression was compared between COPD and non-COPD patients. Positive findings were confirmed by quantitative polymerase chain reaction (qPCR). Assays assessing angiogenesis and cellular migration were conducted in Human Umbilical Vein Endothelial Cells (n = 3-4) transfected with microRNA mimics and compared to cells transfected with negative control RNA. Expression of miR-181b-3p, miR-429 and miR-23c (all p < 0.05) was increased in COPD. Over-expression of miR-181b-3p was associated with reduced endothelial sprouting (p < 0.05). miR-429 was overexpressed in lung cancer as well and exhibited a reduction in tubular formation. MicroRNA-driven changes in the pulmonary endothelium thus represent a novel mechanism driving emphysema. These processes warrant further study to determine if they may be therapeutic targets in COPD and lung cancer.
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Affiliation(s)
- Clara E. Green
- Institute of Inflammation and Ageing, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Joseph Clarke
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (J.C.); (R.B.)
| | - Roy Bicknell
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK; (J.C.); (R.B.)
| | - Alice M. Turner
- Institute of Applied Health Research, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK;
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13
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Chen XY, Feng PH, Han CL, Jheng YT, Wu CD, Chou HC, Chen YY, Wu SM, Lee KY, Kuo HP, Chung KF, Hsiao TC, Chen KY, Ho SC, Chang TY, Chuang HC. Alveolar epithelial inter-alpha-trypsin inhibitor heavy chain 4 deficiency associated with senescence-regulated apoptosis by air pollution. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 278:116863. [PMID: 33735794 DOI: 10.1016/j.envpol.2021.116863] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/16/2021] [Accepted: 02/27/2021] [Indexed: 06/12/2023]
Abstract
Inter-alpha-trypsin inhibitor heavy chain 4 (ITIH4) is a type II acute-phase protein; however, the role of pulmonary ITIH4 after exposure to air pollution remains unclear. In this study, we investigated the role of ITIH4 in the lungs in response to air pollution. ITIH4 expression in bronchoalveolar lavage fluid (BAL) of 47 healthy human subjects and of Sprague-Dawley rats whole-body exposed to air pollution was determined, and the underlying antiapoptotic and matrix-stabilizing pathways in alveolar epithelial A549 cells induced by diesel exhaust particles (DEPs) as well as ITIH4-knockdown were investigated. We found that an interquartile range (IQR) increase in PM2.5 was associated with a decrease of 2.673 ng/mL in ITIH4, an increase of 1.104 pg/mL of 8-isoprostane, and an increase of 6.918 pg/mL of interleukin (IL)-6 in human BAL. In rats, increases in 8-isoprostane, IL-6, and p53 and a decrease in sirtuin-1 (Sirt1) in the lungs and decreases in ITIH4 in the BAL, lungs, and serum were observed after PM2.5 and gaseous exposure. ITIH4 levels in lung lysates were correlated with levels in BAL samples (r = 0.377, p < 0.01), whereas ITIH4 levels in BAL were correlated with IL-6 levels (r = -0.420, p < 0.01). ITIH4 expression was significantly reduced in alveolar epithelial A549 cells by DEP in a dose-dependent manner. A decrease in Sirt1 and increases in phosphorylated extracellular signal-regulated kinase (p-ERK) and caspase-3 were observed after DEP exposure and ITIH4-knockdown. In conclusion, air pollution decreased ITIH4 expression in the lungs, which was associated with alveolar epithelial cell senescence and apoptosis. ITIH4 could be a vital protein in regulating alveolar cell destruction and its inhibition after exposure to air pollution.
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Affiliation(s)
- Xiao-Yue Chen
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Po-Hao Feng
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Pharmacogenomics and Pharmacoproteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Yu-Teng Jheng
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei, Taiwan
| | - Chih-Da Wu
- Department of Geomatics, National Cheng Kung University, Tainan, Taiwan; National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Hsiu-Chu Chou
- Department of Anatomy and Cell Biology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yi-Ying Chen
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Ming Wu
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Kang-Yun Lee
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Han-Pin Kuo
- Division of Pulmonary Medicine, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Ta-Chih Hsiao
- Graduate Institute of Environmental Engineering, National Taiwan University, Taipei, Taiwan
| | - Kuan-Yuan Chen
- Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Shu-Chuan Ho
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| | - Ta-Yuan Chang
- Department of Occupational Safety and Health, College of Public Health, China Medical University, Taichung, Taiwan
| | - Hsiao-Chi Chuang
- School of Respiratory Therapy, College of Medicine, Taipei Medical University, Taipei, Taiwan; Division of Pulmonary Medicine, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan; Cell Physiology and Molecular Image Research Center, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan.
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14
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Li X, Noell G, Tabib T, Gregory AD, Trejo Bittar HE, Vats R, Kaminski TW, Sembrat J, Snyder ME, Chandra D, Chen K, Zou C, Zhang Y, Sundd P, McDyer JF, Sciurba F, Rojas M, Lafyatis R, Shapiro SD, Faner R, Nyunoya T. Single cell RNA sequencing identifies IGFBP5 and QKI as ciliated epithelial cell genes associated with severe COPD. Respir Res 2021; 22:100. [PMID: 33823868 PMCID: PMC8022543 DOI: 10.1186/s12931-021-01675-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 03/02/2021] [Indexed: 12/11/2022] Open
Abstract
Background Whole lung tissue transcriptomic profiling studies in chronic obstructive pulmonary disease (COPD) have led to the identification of several genes associated with the severity of airflow limitation and/or the presence of emphysema, however, the cell types driving these gene expression signatures remain unidentified. Methods To determine cell specific transcriptomic changes in severe COPD, we conducted single-cell RNA sequencing (scRNA seq) on n = 29,961 cells from the peripheral lung parenchymal tissue of nonsmoking subjects without underlying lung disease (n = 3) and patients with severe COPD (n = 3). The cell type composition and cell specific gene expression signature was assessed. Gene set enrichment analysis (GSEA) was used to identify the specific cell types contributing to the previously reported transcriptomic signatures. Results T-distributed stochastic neighbor embedding and clustering of scRNA seq data revealed a total of 17 distinct populations. Among them, the populations with more differentially expressed genes in cases vs. controls (log fold change >|0.4| and FDR = 0.05) were: monocytes (n = 1499); macrophages (n = 868) and ciliated epithelial cells (n = 590), respectively. Using GSEA, we found that only ciliated and cytotoxic T cells manifested a trend towards enrichment of the previously reported 127 regional emphysema gene signatures (normalized enrichment score [NES] = 1.28 and = 1.33, FDR = 0.085 and = 0.092 respectively). Among the significantly altered genes present in ciliated epithelial cells of the COPD lungs, QKI and IGFBP5 protein levels were also found to be altered in the COPD lungs. Conclusions scRNA seq is useful for identifying transcriptional changes and possibly individual protein levels that may contribute to the development of emphysema in a cell-type specific manner. ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12931-021-01675-2.
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Affiliation(s)
- Xiuying Li
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA.,VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Guillaume Noell
- Centro Investigación Biomedica en Red (CIBERES), Institut D'investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Tracy Tabib
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Alyssa D Gregory
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | | | - Ravi Vats
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tomasz W Kaminski
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Sembrat
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Mark E Snyder
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Divay Chandra
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Kong Chen
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Chunbin Zou
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA.,VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - Yingze Zhang
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Prithu Sundd
- Vascular Medicine Institute, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John F McDyer
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Frank Sciurba
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Mauricio Rojas
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Robert Lafyatis
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Steve D Shapiro
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Rosa Faner
- Centro Investigación Biomedica en Red (CIBERES), Institut D'investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Toru Nyunoya
- Department of Medicine, University of Pittsburgh, NW628 UPMC Montefiore, 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA. .,VA Pittsburgh Healthcare System, Pittsburgh, PA, USA.
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15
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Lee SH, Ahn JR, Go HN, Lee SY, Park MJ, Song KB, Yoon J, Jung S, Cho HJ, Lee E, Yang SI, Hong SJ. Exposure to Polyhexamethylene Guanidine Exacerbates Bronchial Hyperresponsiveness and Lung Inflammation in a Mouse Model of Ovalbumin-Induced Asthma. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2021; 13:655-664. [PMID: 34212551 PMCID: PMC8255342 DOI: 10.4168/aair.2021.13.4.655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 11/22/2020] [Accepted: 11/26/2020] [Indexed: 11/20/2022]
Abstract
Humidifier disinfectants (HDs) exposure has now been associated with acute lung injury and pulmonary fibrosis; polyhexamethylene guanidine (PHMG) has been confirmed to cause severe lung inflammation and fibrosis in mice. Recent evidence also indicates that HDs exposure increases the asthma risk in children, but the underlying mechanisms remain unclear. We aimed to investigate the effects of PHMG exposure on asthma in mice and the potential underlying mechanisms. BALB/c mice were intranasally administered PHMG (0.1 mg/kg/day; 5 days per week) during 2 episodes of ovalbumin (OVA) sensitization and were then challenged with 1% OVA by inhalation. Bronchial hyperresponsiveness (BHR), inflammatory cell influx into bronchoalveolar lavage (BAL) fluid, serum total and OVA-specific immunoglobulin (Ig) E levels, and histopathological changes in the lung were analyzed. The levels of asthma-related cytokines and chemokines were assayed in the lung tissues to evaluate possible mechanisms. Exposure to PHMG following OVA sensitization and challenge significantly enhanced BHR, inflammatory cell counts in BAL fluid, airway inflammation, and total serum IgE levels in the asthma mouse model. In addition, the levels of chemokine ligand (CCL) 11 and serpine F1/pigment epithelium-derived factor (SERPINF1) were significantly elevated in the lungs of these mice compared to those in the control and OVA-treated only groups. Our findings suggest that PHMG can enhance the development of allergic responses and lung inflammation via CCL11- and SERPINF1-induced signaling in a mouse model of asthma.
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Affiliation(s)
- Seung Hwa Lee
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Jae Rin Ahn
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - Han Na Go
- Asan Institute for Life Sciences, University of Ulsan College of Medicine, Seoul, Korea
| | - So Yeon Lee
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min Jee Park
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Kun Baek Song
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jisun Yoon
- Department of Pediatrics, Mediplex Sejong Hospital, Incheon, Korea
| | - Sungsu Jung
- Department of Pediatrics, Pusan National University Yangsan Hospital, Yangsan, Korea
| | - Hyun Ju Cho
- Department of Pediatrics, International St. Mary's hospital, Catholic Kwandong University, Incheon, Korea
| | - Eun Lee
- Department of Pediatrics, Chonnam National University College of Medicine, Gwangju, Korea
| | - Song I Yang
- Department of Pediatrics, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Korea
| | - Soo Jong Hong
- Department of Pediatrics, Childhood Asthma Atopy Center, Humidifier Disinfectant Health Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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16
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Dhamodharan P, Arumugam M. Multiple Gene Expression Dataset Analysis Reveals Toll-Like Receptor Signaling Pathway is Strongly Associated With Chronic Obstructive Pulmonary Disease Pathogenesis. COPD 2020; 17:684-698. [PMID: 32757672 DOI: 10.1080/15412555.2020.1793314] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chronic obstructive pulmonary disease is a complex pulmonary disease that causes airflow obstruction in humans. To identify the core genes in COPD pathogenesis, seven diverse microarray datasets (GSE475, GSE1122, GSE1650, GSE3212, GSE8823, GSE37768, and GSE22148) were downloaded from the gene expression omnibus database. All the datasets were analyzed independently with the R/Bioconductor package to screen the differentially expressed genes (DEGs). The gene ontology and pathway enrichment analysis were performed for the acquired DEGs using DAVID (Database for Annotation, Visualization, and Integrated Discovery). Further protein-protein interaction network was constructed for the DEGs and their potential hub genes and sub-networks were identified using Cytoscape software. From the selected seven datasets, 188 overlapped DEGs were perceived eventually based on considering the repetitive genes between at-least one dataset. Gene Ontology analysis reveals that most of the DEGs were significantly enriched in immune response, inflammatory response, extracellular region, lipid binding, cytokine, and chemokine activity. Moreover, genes from the sub-network analysis were again submitted to the DAVID server to validate the results which uncover the Toll-like receptor signaling pathway was significantly enriched and all the genes present in this pathway were likewise detected as hub genes from Cytoscape software. CXCL9, CXCL10, CXCL11, CCL4, TLR7, and SPP1 hub genes in the toll-like receptor signaling pathway were explored in this study as potential biomarker genes associated with COPD pathogenesis.
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Affiliation(s)
- Pavithra Dhamodharan
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - Mohanapriya Arumugam
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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17
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Porembskaya O, Toropova Y, Tomson V, Lobastov K, Laberko L, Kravchuk V, Saiganov S, Brill A. Pulmonary Artery Thrombosis: A Diagnosis That Strives for Its Independence. Int J Mol Sci 2020; 21:ijms21145086. [PMID: 32708482 PMCID: PMC7404175 DOI: 10.3390/ijms21145086] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
According to a widespread theory, thrombotic masses are not formed in the pulmonary artery (PA) but result from migration of blood clots from the venous system. This concept has prevailed in clinical practice for more than a century. However, a new technologic era has brought forth more diagnostic possibilities, and it has been shown that thrombotic masses in the PA could, in many cases, be found without any obvious source of emboli. Chronic obstructive pulmonary disease, asthma, sickle cell anemia, emergency and elective surgery, viral pneumonia, and other conditions could be complicated by PA thrombosis development without concomitant deep vein thrombosis (DVT). Different pathologies have different causes for local PA thrombotic process. As evidenced by experimental results and clinical observations, endothelial and platelet activation are the crucial mechanisms of this process. Endothelial dysfunction can impair antithrombotic function of the arterial wall through downregulation of endothelial nitric oxide synthase (eNOS) or via stimulation of adhesion receptor expression. Hypoxia, proinflammatory cytokines, or genetic mutations may underlie the procoagulant phenotype of the PA endothelium. Both endotheliocytes and platelets could be activated by protease mediated receptor (PAR)- and receptors for advanced glycation end (RAGE)-dependent mechanisms. Hypoxia, in particular induced by high altitudes, could play a role in thrombotic complications as a trigger of platelet activity. In this review, we discuss potential mechanisms of PA thrombosis in situ.
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Affiliation(s)
- Olga Porembskaya
- Mechnikov North-Western State Medical University, Saint Petersburg 191015, Russia; (V.K.); (S.S.)
- Institute of Experimental Medicine, Saint Petersburg 197376, Russia
- Correspondence: (O.P.); (A.B.); Tel.: +7-92-1310-6629 (O.P.); Tel.: +44-12-1415-8679 (A.B.)
| | - Yana Toropova
- Institute of Experimental Medicine, Almazov National Medical Research Center, Saint Petersburg 197341, Russia;
| | | | - Kirill Lobastov
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; (K.L.); (L.L.)
| | - Leonid Laberko
- Pirogov Russian National Research Medical University, Moscow 117997, Russia; (K.L.); (L.L.)
| | - Viacheslav Kravchuk
- Mechnikov North-Western State Medical University, Saint Petersburg 191015, Russia; (V.K.); (S.S.)
| | - Sergey Saiganov
- Mechnikov North-Western State Medical University, Saint Petersburg 191015, Russia; (V.K.); (S.S.)
| | - Alexander Brill
- Institute of Cardiovascular Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham B152TT, UK
- Department of Pathophysiology, Sechenov First Moscow State Medical University (Sechenov University), Moscow 119991, Russia
- Correspondence: (O.P.); (A.B.); Tel.: +7-92-1310-6629 (O.P.); Tel.: +44-12-1415-8679 (A.B.)
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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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Zhang Z, Wang J, Zheng Z, Chen X, Xu G, Chen S, Liu F, Chen L, Ding M, Yuan L, Li Y, Qian J, Xie X, Deng B, Lu W. A protective polymorphism in MMP16, improved blood gas levels, and chronic obstructive pulmonary diseases: Family and two population-based studies. Hum Mutat 2020; 41:1280-1297. [PMID: 32196811 DOI: 10.1002/humu.24013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/19/2020] [Accepted: 03/13/2020] [Indexed: 12/19/2022]
Abstract
The aberrant expression of matrix metalloproteinases (MMPs) is known to contribute to the pathogenesis of airway remodeling and alveolar disruption in chronic obstructive pulmonary disease (COPD). In the discovery stage, 11 COPD from five families were subjected to whole-genome sequencing, and 21 common polymorphisms in MMPs and TIMPs were identified. These polymorphisms were genotyped in two subsequent verification studies. Of these polymorphisms, c.2392G>A (rs2664370T>C) and c.4158C>A (rs2664369T>G) in MMP16 remained significantly different. Functionally, we found that MMP16 expression was significantly increased in peripheral blood monocytes (PBMCs) from COPD and in cigarette smoke extract-treated 16HBE cells compared with controls. This was also shown by bioinformatics analysis. COPD carrying rs2664370CC showed decreased levels of MMP16 in the plasma and in PBMCs compared with those carrying CT and TT. Treatment with hsa-miR-576-5p mimics led to a greater reduction in luciferase reporter activity in cells transfected with rs2664370CC. Moreover, blood levels of base excess, PCO2 , and PO2 in COPD with rs2664370CC were significantly lower than those with rs2664370CT+TT. Taken together, these results demonstrate that the rs2664370T>C polymorphism in MMP16 protects against the risk of COPD, likely by favoring interaction with hsa-miR-576-5p, leading to reduced MMP16 expression and improved blood gas levels.
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Affiliation(s)
- Zili Zhang
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Jian Wang
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China.,Department of Medicine, Division of Translational and Regenerative Medicine, The University of Arizona, Tucson, Arizona
| | - Zeguang Zheng
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Xindong Chen
- Department of Respiratory Medicine, The First People's Hospital of Lufeng, Lufeng, Guangdong, China
| | - Guihua Xu
- Department of Respiratory Medicine, Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Sifan Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Fei Liu
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Lingdan Chen
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Mingjing Ding
- Department of Respiratory Medicine, Inner Mongolia Autonomous Region People's Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Liang Yuan
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Yuanyuan Li
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Jing Qian
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Xiaohui Xie
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Bingxian Deng
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China
| | - Wenju Lu
- State Key Laboratory of Respiratory Disease, Guangdong Key Laboratory of Vascular Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital, Guangzhou Medical University, Guangdong, Guangzhou, China.,Department of Medicine, Division of Translational and Regenerative Medicine, The University of Arizona, Tucson, Arizona
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20
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Otálora-Otálora BA, Florez M, López-Kleine L, Canas Arboleda A, Grajales Urrego DM, Rojas A. Joint Transcriptomic Analysis of Lung Cancer and Other Lung Diseases. Front Genet 2019; 10:1260. [PMID: 31867044 PMCID: PMC6908522 DOI: 10.3389/fgene.2019.01260] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/14/2019] [Indexed: 12/09/2022] Open
Abstract
Background: Epidemiological and clinical evidence points cancer comorbidity with pulmonary chronic disease. The acquisition of some hallmarks of cancer by cells affected with lung pathologies as a cell adaptive mechanism to a shear stress, suggests that could be associated with the establishment of tumoral processes. Objective: To propose a bioinformatic pipeline for the identification of all deregulated genes and the transcriptional regulators (TFs) that are coexpressed during lung cancer establishment, and therefore could be important for the acquisition of the hallmarks of cancer. Methods: Ten microarray datasets (six of lung cancer, four of lung diseases) comparing normal and diseases-related lung tissue were selected to identify hub differentiated expressed genes (DEGs) in common between lung pathologies and lung cancer, along with transcriptional regulators through the utilization of specialized libraries from R language. DAVID bioinformatics tool for gene enrichment analyses was used to identify genes with experimental evidence associated to tumoral processes and signaling pathways. Coexpression networks of DEGs and TFs in lung cancer establishment were created with Coexnet library, and a survival analysis of the main hub genes was made. Results: Two hundred ten DEGs were identified in common between lung cancer and other lung diseases related to the acquisition of tumoral characteristics, which are coexpressed in a lung cancer network with TFs, suggesting that could be related to the establishment of the tumoral pathology in lung. The comparison of the coexpression networks of lung cancer and other lung diseases allowed the identification of common connectivity patterns (CCPs) with DEGs and TFs correlated to important tumoral processes and signaling pathways, that haven´t been studied to experimentally validate their role in the early stages of lung cancer. Some of the TFs identified showed a correlation between its expression levels and the survival of lung cancer patients. Conclusion: Our findings indicate that lung diseases share genes with lung cancer which are coexpressed in lung cancer, and might be able to explain the epidemiological observations that point to direct and inverse comorbid associations between some chronic lung diseases and lung cancer and represent a complex transcriptomic scenario.
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Affiliation(s)
| | - Mauro Florez
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Liliana López-Kleine
- Departamento de Estadística, Grupo de Investigación en Bioinformática y Biología de sistemas – GiBBS, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | | | - Adriana Rojas
- Instituto de Genética Humana, Facultad de Medicina, Pontificia Universidad Javeriana, Bogotá, Colombia
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21
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Nader CP, Cidem A, Verrills NM, Ammit AJ. Protein phosphatase 2A (PP2A): a key phosphatase in the progression of chronic obstructive pulmonary disease (COPD) to lung cancer. Respir Res 2019; 20:222. [PMID: 31623614 PMCID: PMC6798356 DOI: 10.1186/s12931-019-1192-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 09/20/2019] [Indexed: 02/06/2023] Open
Abstract
Lung cancer (LC) has the highest relative risk of development as a comorbidity of chronic obstructive pulmonary disease (COPD). The molecular mechanisms that mediate chronic inflammation and lung function impairment in COPD have been identified in LC. This suggests the two diseases are more linked than once thought. Emerging data in relation to a key phosphatase, protein phosphatase 2A (PP2A), and its regulatory role in inflammatory and tumour suppression in both disease settings suggests that it may be critical in the progression of COPD to LC. In this review, we uncover the importance of the functional and active PP2A holoenzyme in the context of both diseases. We describe PP2A inactivation via direct and indirect means and explore the actions of two key PP2A endogenous inhibitors, cancerous inhibitor of PP2A (CIP2A) and inhibitor 2 of PP2A (SET), and the role they play in COPD and LC. We explain how dysregulation of PP2A in COPD creates a favourable inflammatory micro-environment and promotes the initiation and progression of tumour pathogenesis. Finally, we highlight PP2A as a druggable target in the treatment of COPD and LC and demonstrate the potential of PP2A re-activation as a strategy to halt COPD disease progression to LC. Although further studies are required to elucidate if PP2A activity in COPD is a causal link for LC progression, studies focused on the potential of PP2A reactivating agents to reduce the risk of LC formation in COPD patients will be pivotal in improving clinical outcomes for both COPD and LC patients in the future.
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Affiliation(s)
- Cassandra P Nader
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Aylin Cidem
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Nicole M Verrills
- School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW, 2308, Australia
- Priority Research Centre for Cancer Research, Innovation & Translation, Faculty of Health & Medicine, Hunter Medical Research Institute, New Lambton Heights, NSW, 2305, Australia
| | - Alaina J Ammit
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, Sydney, NSW, Australia.
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.
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22
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Lin YZ, Zhong XN, Chen X, Liang Y, Zhang H, Zhu DL. Roundabout signaling pathway involved in the pathogenesis of COPD by integrative bioinformatics analysis. Int J Chron Obstruct Pulmon Dis 2019; 14:2145-2162. [PMID: 31571851 PMCID: PMC6756575 DOI: 10.2147/copd.s216050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 08/22/2019] [Indexed: 01/11/2023] Open
Abstract
Purpose To explore the potential mechanism underpinning the development of chronic obstructive pulmonary disease (COPD) and to investigate the role of the Roundabout signaling pathway in COPD. Methods Three microarray datasets (GSE1650, GSE38974 and GSE76925) including 139 cases of severe COPD and 52 cases of normal smokers without carcinoma, were integrated to screen differentially expressed genes (DEGs) using bioinformatics methods. Gene ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway of the DEGs were performed by a DAVID online tool. Finally, a cigarette smoke (CS)- induced emphysema mice model was established, the lung mRNA expression levels of genes associated with Slit guidance ligand 2 (SLIT2) -Roundabout (ROBO) signaling pathway were detected by reverse transcription quantitative polymerase chain reaction (RT-qPCR), and the protein level of SLIT2 was examined by immunohistochemistry staining. Results A total of 315 DEGs were identified in three databases. GO and KEGG pathway analyses suggested that the inflammatory response, extracellular matrix disassembly, immune response, the apoptotic signaling pathway, ubiquitination and the Roundabout signaling pathway all together were involved in the development of COPD. The genes SLIT2 and ROBO2 were decreased in patients with COPD and these decreases were significantly negatively correlated with the disease stages of COPD. Consistently, the mRNA expression levels of SLIT2, ROBO1 and ROBO2, and the protein level of SLIT2 were revealed to be lower in the lungs of CS-induced emphysema mice compared with the air-exposed control mice. In addition, the SLIT2 protein level was negatively associated with alveolar mean linear intercept. Conclusion Integrated bioinformatics analysis may provide novel insights into the complicated pathogenesis of COPD, and to the best of our knowledge, this study is the first to provide evidence to suggest that the Roundabout signaling pathway may be involved in the pathogenesis of COPD.
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Affiliation(s)
- Yuan-Zhen Lin
- Department of Respiratory Medicine, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xiao-Ning Zhong
- Department of Respiratory Medicine, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Xin Chen
- Department of Respiratory Medicine, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Yi Liang
- Department of Respiratory Medicine, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Hui Zhang
- Department of Respiratory Medicine, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
| | - Dong-Lan Zhu
- Department of Respiratory Medicine, The First Affiliated Hospital, Guangxi Medical University, Nanning, Guangxi, People's Republic of China
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23
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Combined Pulmonary Fibrosis and Emphysema: Pulmonary Function Testing and a Pathophysiology Perspective. ACTA ACUST UNITED AC 2019; 55:medicina55090580. [PMID: 31509942 PMCID: PMC6780454 DOI: 10.3390/medicina55090580] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/13/2019] [Accepted: 08/26/2019] [Indexed: 12/24/2022]
Abstract
Combined pulmonary fibrosis and emphysema (CPFE) has been increasingly recognized over the past 10–15 years as a clinical entity characterized by rather severe imaging and gas exchange abnormalities, but often only mild impairment in spirometric and lung volume indices. In this review, we explore the gas exchange and mechanical pathophysiologic abnormalities of pulmonary emphysema, pulmonary fibrosis, and combined emphysema and fibrosis with the goal of understanding how individual pathophysiologic observations in emphysema and fibrosis alone may impact clinical observations on pulmonary function testing (PFT) patterns in patients with CPFE. Lung elastance and lung compliance in patients with CPFE are likely intermediate between those of patients with emphysema and fibrosis alone, suggesting a counter-balancing effect of each individual process. The outcome of combined emphysema and fibrosis results in higher lung volumes overall on PFTs compared to patients with pulmonary fibrosis alone, and the forced expiratory volume in one second (FEV1)/forced vital capacity (FVC) ratio in CPFE patients is generally preserved despite the presence of emphysema on chest computed tomography (CT) imaging. Conversely, there appears to be an additive deleterious effect on gas exchange properties of the lungs, reflecting a loss of normally functioning alveolar capillary units and effective surface area available for gas exchange, and manifested by a uniformly observed severe reduction in the diffusing capacity for carbon monoxide (DLCO). Despite normal or only mildly impaired spirometric and lung volume indices, patients with CPFE are often severely functionally impaired with an overall rather poor prognosis. As chest CT imaging continues to be a frequent imaging modality in patients with cardiopulmonary disease, we expect that patients with a combination of pulmonary emphysema and pulmonary fibrosis will continue to be observed. Understanding the pathophysiology of this combined process and the abnormalities that manifest on PFT testing will likely be helpful to clinicians involved with the care of patients with CPFE.
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24
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Arimura K, Sekine Y, Hiroshima K, Shimizu S, Shibata N, Kondo M, Takeyama K, Tagaya E. PD-L1, FGFR1, PIK3CA, PTEN, and p16 expression in pulmonary emphysema and chronic obstructive pulmonary disease with resected lung squamous cell carcinoma. BMC Pulm Med 2019; 19:169. [PMID: 31481045 PMCID: PMC6724334 DOI: 10.1186/s12890-019-0913-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 08/02/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Emphysema and chronic obstructive pulmonary disease (COPD) are well known independent risk factors for lung cancer. However, the developmental mechanisms between emphysema/COPD and lung cancer remain unknown. The purpose of this study was to evaluate PD-L1, FGFR1, PIK3CA, PTEN, and p16 expression in squamous cell carcinoma (SCC) associated with emphysema/COPD. METHODS A total of 59 patients with squamous cell lung carcinoma (SCC) resected between 2008 and 2012 were retrospectively reviewed. Emphysema was assessed according to the Goddard score. Total severity was divided into none-mild (0-7), moderate (8-15), and severe (≥ 16). Local severity around the existing tumor was divided into no emphysema (0) and presence of emphysema (1-4). COPD severity was based on the Global Initiative for Chronic Obstructive Lung Disease (GOLD) criteria. PD-L1, FGFR1, PIK3CA, PTEN, and p16 expression were evaluated by immunohistochemistry (IHC). Expression level was classified as tumor cells (TC) 3 (≥ 50%), TC2 (5-49%), TC1 (1-4%), or TC0 (< 1%), and as tumor-infiltrating immune cells (IC) 3 (≥ 50%), IC2 (5-49%), IC1 (1-4%), or IC0 (< 1%) for PD-L1. Expression level was compared between none-mild/moderate-severe total emphysema, no/presence of local emphysema, no COPD/COPD, and GOLD 1/GOLD 2, 3. RESULTS PD-L1 expression was significantly correlated with severity of emphysema in TC0, 1, 2 vs. TC3 (P = 0.012). PD-L1 was significantly higher inversely in none-mild emphysema compared to moderate-severe (95% CI, 0.061-5.852, P = 0.045). There were no other significant associations between PD-L1, FGFR1, PIK3CA, PTEN, and p16 expression and total/local severity of emphysema or presence of COPD/GOLD stage. CONCLUSIONS PD-L1 expression in SCC was correlated with severity of emphysema in TC0, 1, 2 vs. TC3 and more frequent in none-mild emphysema than moderate-severe emphysema.
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Affiliation(s)
- Ken Arimura
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan.
| | - Yasuo Sekine
- Departments of Thoracic Surgery, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan.
| | - Kenzo Hiroshima
- Departments of Pathology, Tokyo Women's Medical University Yachiyo Medical Center, Chiba, Japan
| | - Satoru Shimizu
- Departments of Medical Education, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Noriyuki Shibata
- Human and Experimental Pathology and Neuroscience, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Mitsuko Kondo
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Kiyoshi Takeyama
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan
| | - Etsuko Tagaya
- Department of Respiratory Medicine, Tokyo Women's Medical University, Tokyo, Japan
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25
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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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26
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Hu WP, Zeng YY, Zuo YH, Zhang J. Identification of novel candidate genes involved in the progression of emphysema by bioinformatic methods. Int J Chron Obstruct Pulmon Dis 2018; 13:3733-3747. [PMID: 30532529 PMCID: PMC6241693 DOI: 10.2147/copd.s183100] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Purpose By reanalyzing the gene expression profile GSE76925 in the Gene Expression Omnibus database using bioinformatic methods, we attempted to identify novel candidate genes promoting the development of emphysema in patients with COPD. Patients and methods According to the Quantitative CT data in GSE76925, patients were divided into mild emphysema group (%LAA-950<20%, n=12) and severe emphysema group (%LAA-950>50%, n=11). Differentially expressed genes (DEGs) were identified using Agilent GeneSpring GX v11.5 (corrected P-value <0.05 and |Fold Change|>1.3). Known driver genes of COPD were acquired by mining literatures and retrieving databases. Direct protein–protein interaction network (PPi) of DEGs and known driver genes was constructed by STRING.org to screen the DEGs directly interacting with driver genes. In addition, we used STRING.org to obtain the first-layer proteins interacting with DEGs’ products and constructed the indirect PPi of these interaction proteins. By merging the indirect PPi with driver genes’ PPi using Cytoscape v3.6.1, we attempted to discover potential pathways promoting emphysema’s development. Results All the patients had COPD with severe airflow limitation (age=62±8, FEV1%=28±12). A total of 57 DEGs (including 12 pseudogenes) and 135 known driving genes were identified. Direct PPi suggested that GPR65, GNB4, P2RY13, NPSR1, BCR, BAG4, and IMPDH2 were potential pathogenic genes. GPR65 could regulate the response of immune cells to the acidic microenvironment, and NPSR1’s expression on eosinophils was associated with asthma’s severity and IgE level. Indirect merging PPi demonstrated that the interacting network of TP53, IL8, CCR2, HSPA1A, ELANE, PIK3CA was associated with the development of emphysema. IL8, ELANE, and PIK3CA were molecules involved in the pathological mechanisms of emphysema, which also in return proved the role of TP53 in emphysema. Conclusion Candidate genes such as GPR65, NPSR1, and TP53 may be involved in the progression of emphysema.
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Affiliation(s)
- Wei-Ping Hu
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
| | - Ying-Ying Zeng
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
| | - Yi-Hui Zuo
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
| | - Jing Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Shanghai Medical College, Fudan University, Shanghai, China,
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Vishweswaraiah S, George L, Purushothaman N, Ganguly K. A candidate gene identification strategy utilizing mouse to human big-data mining: "3R-tenet" in COPD genetic research. Respir Res 2018; 19:92. [PMID: 29871630 PMCID: PMC5989378 DOI: 10.1186/s12931-018-0795-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research. Electronic supplementary material The online version of this article (10.1186/s12931-018-0795-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Leema George
- SRM Research Institute, SRM University, Chennai, 603203, India
| | - Natarajan Purushothaman
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM University, Chennai, 603203, India
| | - Koustav Ganguly
- SRM Research Institute, SRM University, Chennai, 603203, India. .,Work Environment Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77, Stockholm, Sweden.
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Polverino F, Celli BR, Owen CA. COPD as an endothelial disorder: endothelial injury linking lesions in the lungs and other organs? (2017 Grover Conference Series). Pulm Circ 2018; 8:2045894018758528. [PMID: 29468936 PMCID: PMC5826015 DOI: 10.1177/2045894018758528] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 01/21/2018] [Indexed: 12/27/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by chronic expiratory airflow obstruction that is not fully reversible. COPD patients develop varying degrees of emphysema, small and large airway disease, and various co-morbidities. It has not been clear whether these co-morbidities share common underlying pathogenic processes with the pulmonary lesions. Early research into the pathogenesis of COPD focused on the contributions of injury to the extracellular matrix and pulmonary epithelial cells. More recently, cigarette smoke-induced endothelial dysfunction/injury have been linked to the pulmonary lesions in COPD (especially emphysema) and systemic co-morbidities including atherosclerosis, pulmonary hypertension, and chronic renal injury. Herein, we review the evidence linking endothelial injury to COPD, and the pathways underlying endothelial injury and the "vascular COPD phenotype" including: (1) direct toxic effects of cigarette smoke on endothelial cells; (2) generation of auto-antibodies directed against endothelial cells; (3) vascular inflammation; (4) increased oxidative stress levels in vessels inducing increases in lipid peroxidation and increased activation of the receptor for advanced glycation end-products (RAGE); (5) reduced activation of the anti-oxidant pathways in endothelial cells; (6) increased endothelial cell release of mediators with vasoconstrictor, pro-inflammatory, and remodeling activities (endothelin-1) and reduced endothelial cell expression of mediators that promote vasodilation and homeostasis of endothelial cells (nitric oxide synthase and prostacyclin); and (7) increased endoplasmic reticular stress and the unfolded protein response in endothelial cells. We also review the literature on studies of drugs that inhibit RAGE signaling in other diseases (angiotensin-converting enzyme inhibitors and angiotensin receptor blockers), or vasodilators developed for idiopathic pulmonary arterial hypertension that have been tested on cell culture systems, animal models of COPD, and/or smokers and COPD patients.
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Affiliation(s)
- Francesca Polverino
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Bartolome R. Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | - Caroline A. Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Lovelace Respiratory Research Institute, Albuquerque, NM, USA
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Reinhold D, Morrow JD, Jacobson S, Hu J, Ringel B, Seibold MA, Hersh CP, Kechris KJ, Bowler RP. Meta-analysis of peripheral blood gene expression modules for COPD phenotypes. PLoS One 2017; 12:e0185682. [PMID: 29016655 PMCID: PMC5633174 DOI: 10.1371/journal.pone.0185682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 09/18/2017] [Indexed: 12/22/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) occurs typically in current or former smokers, but only a minority of people with smoking history develops the disease. Besides environmental factors, genetics is an important risk factor for COPD. However, the relationship between genetics, environment and phenotypes is not well understood. Sample sizes for genome-wide expression studies based on lung tissue have been small due to the invasive nature of sample collection. Increasing evidence for the systemic nature of the disease makes blood a good alternative source to study the disease, but there have also been few large-scale blood genomic studies in COPD. Due to the complexity and heterogeneity of COPD, examining groups of interacting genes may have more relevance than identifying individual genes. Therefore, we used Weighted Gene Co-expression Network Analysis to find groups of genes (modules) that are highly connected. However, module definitions may vary between individual data sets. To alleviate this problem, we used a consensus module definition based on two cohorts, COPDGene and ECLIPSE. We studied the relationship between the consensus modules and COPD phenotypes airflow obstruction and emphysema. We also used these consensus module definitions on an independent cohort (TESRA) and performed a meta analysis involving all data sets. We found several modules that are associated with COPD phenotypes, are enriched in functional categories and are overrepresented for cell-type specific genes. Of the 14 consensus modules, three were strongly associated with airflow obstruction (meta p ≤ 0.0002), and two had some association with emphysema (meta p ≤ 0.06); some associations were stronger in the case-control cohorts, and others in the cases-only subcohorts. Gene Ontology terms that were overrepresented included “immune response” and “defense response.” The cell types whose type-specific genes were overrepresented in modules (p < 0.05) included natural killer cells, dendritic cells, and neutrophils. Together, this is the largest investigation of gene blood expression in COPD with 469 cases in COPDGene, ECLIPSE and TESRA combined, with 6267 genes common to all data sets. Additional, we have 42 and 83 controls in COPDGene and ECLIPSE, respectively.
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Affiliation(s)
- Dominik Reinhold
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
- * E-mail:
| | - Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Sean Jacobson
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Junxiao Hu
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Benjamin Ringel
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
| | - Max A. Seibold
- Center for Genes, Environment and Health, Department of Pediatrics, National Jewish Health, Denver, Colorado, United States of America
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States of America
| | - Katerina J. Kechris
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado, United States of America
| | - Russell P. Bowler
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
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Obeidat M, Nie Y, Fishbane N, Li X, Bossé Y, Joubert P, Nickle DC, Hao K, Postma DS, Timens W, Sze MA, Shannon CP, Hollander Z, Ng RT, McManus B, Miller BE, Rennard S, Spira A, Hackett TL, Lam W, Lam S, Faner R, Agusti A, Hogg JC, Sin DD, Paré PD. Integrative Genomics of Emphysema-Associated Genes Reveals Potential Disease Biomarkers. Am J Respir Cell Mol Biol 2017; 57:411-418. [PMID: 28459279 DOI: 10.1165/rcmb.2016-0284oc] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Chronic obstructive pulmonary disease is the third leading cause of death worldwide. Gene expression profiling across multiple regions of the same lung identified genes significantly related to emphysema. We sought to determine whether the lung and epithelial expression of 127 emphysema-related genes was also related to lung function in independent cohorts, and whether any of these genes could be used as biomarkers in the peripheral blood of patients with chronic obstructive pulmonary disease. To that end, we examined whether the expression levels of these genes were under genetic control in lung tissue (n = 1,111). We then determined whether the mRNA levels of these genes in lung tissue (n = 727), small airway epithelial cells (n = 238), and peripheral blood (n = 620) were significantly related to lung function measurements. The expression of 63 of the 127 genes (50%) was under genetic control in lung tissue. The lung and epithelial mRNA expression of a subset of the emphysema-associated genes, including ASRGL1, LPHN2, and EDNRB, was strongly associated with lung function. In peripheral blood, the expression of 40 genes was significantly associated with lung function. Twenty-nine of these genes (73%) were also associated with lung function in lung tissue, but with the opposite direction of effect for 24 of the 29 genes, including those involved in hypoxia and B cell-related responses. The integrative genomics approach uncovered a significant overlap of emphysema genes associations with lung function between lung and blood with opposite directions between the two. These results support the use of peripheral blood to detect disease biomarkers.
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Affiliation(s)
- Ma'en Obeidat
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Yunlong Nie
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Nick Fishbane
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Xuan Li
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Yohan Bossé
- 2 Department of Molecular Medicine.,3 Institut Universitaire de Cardiologie et de Pneumologie de Québec, and
| | - Philippe Joubert
- 3 Institut Universitaire de Cardiologie et de Pneumologie de Québec, and.,4 Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Quebec, Canada
| | - David C Nickle
- 5 Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, Massachusetts
| | - Ke Hao
- 6 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Wim Timens
- 8 Department of Pathology and Medical Biology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Marc A Sze
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Casey P Shannon
- 9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Zsuzsanna Hollander
- 9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Raymond T Ng
- 9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | - Bruce McManus
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,9 Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, British Columbia, Canada
| | | | - Stephen Rennard
- 11 Division of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, Nebraska.,12 Clinical Discovery Unit, Early Clinical Development, AstraZeneca, Cambridge, United Kingdom
| | - Avrum Spira
- 13 Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Tillie-Louise Hackett
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,14 Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wan Lam
- 15 Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Lam
- 15 Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Rosa Faner
- 16 Fundacio Clinic per a la Recerca Biomedica, Barcelona, Spain
| | - Alvar Agusti
- 16 Fundacio Clinic per a la Recerca Biomedica, Barcelona, Spain
| | - James C Hogg
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,17 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Don D Sin
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,18 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter D Paré
- 1 The University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,18 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Olauson H, Mencke R, Hillebrands JL, Larsson TE. Tissue expression and source of circulating αKlotho. Bone 2017; 100:19-35. [PMID: 28323144 DOI: 10.1016/j.bone.2017.03.043] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/16/2022]
Abstract
αKlotho (Klotho), a type I transmembrane protein and a coreceptor for Fibroblast Growth Factor-23, was initially thought to be expressed only in a limited number of tissues, most importantly the kidney, parathyroid gland and choroid plexus. Emerging data may suggest a more ubiquitous Klotho expression pattern which has prompted reevaluation of the restricted Klotho paradigm. Herein we systematically review the evidence for Klotho expression in various tissues and cell types in humans and other mammals, and discuss potential reasons behind existing conflicting data. Based on current literature and tissue expression atlases, we propose a classification of tissues into high, intermediate and low/absent Klotho expression. The functional relevance of Klotho in organs with low expression levels remain uncertain and there is currently limited data on a role for membrane-bound Klotho outside the kidney. Finally, we review the evidence for the tissue source of soluble Klotho, and conclude that the kidney is likely to be the principal source of circulating Klotho in physiology.
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Affiliation(s)
- Hannes Olauson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
| | - Rik Mencke
- Division of Pathology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan-Luuk Hillebrands
- Division of Pathology, Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tobias E Larsson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
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32
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Faner R, Cruz T, Casserras T, López-Giraldo A, Noell G, Coca I, Tal-Singer R, Miller B, Rodriguez-Roisin R, Spira A, Kalko SG, Agustí A. Network Analysis of Lung Transcriptomics Reveals a Distinct B-Cell Signature in Emphysema. Am J Respir Crit Care Med 2017; 193:1242-53. [PMID: 26735770 DOI: 10.1164/rccm.201507-1311oc] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
RATIONALE Chronic obstructive pulmonary disease (COPD) is characterized by chronic airflow limitation caused by a combination of airways disease (bronchiolitis) and parenchymal destruction (emphysema), whose relative proportion varies from patient to patient. OBJECTIVES To explore and contrast the molecular pathogenesis of emphysema and bronchiolitis in COPD. METHODS We used network analysis of lung transcriptomics (Affymetrix arrays) in 70 former smokers with COPD to compare differential expression and gene coexpression in bronchiolitis and emphysema. MEASUREMENTS AND MAIN RESULTS We observed that in emphysema (but not in bronchiolitis) (1) up-regulated genes were enriched in ontologies related to B-cell homing and activation; (2) the immune coexpression network had a central core of B cell-related genes; (3) B-cell recruitment and immunoglobulin transcription genes (CXCL13, CCL19, and POU2AF1) correlated with emphysema severity; (4) there were lymphoid follicles (CD20(+)IgM(+)) with active B cells (phosphorylated nuclear factor-κB p65(+)), proliferation markers (Ki-67(+)), and class-switched B cells (IgG(+)); and (5) both TNFRSF17 mRNA and B cell-activating factor protein were up-regulated. These findings were by and large reproduced in a group of patients with incipient emphysema and when patients with emphysema were matched for the severity of airflow limitation of those with bronchiolitis. CONCLUSIONS Our study identifies enrichment in B cell-related genes in patients with COPD with emphysema that is absent in bronchiolitis. These observations contribute to a better understanding of COPD pathobiology and may open new therapeutic opportunities for patients with COPD.
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Affiliation(s)
- Rosa Faner
- 1 Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain.,2 Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Tamara Cruz
- 1 Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain.,2 Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Teresa Casserras
- 3 Bioinformatics Platform Institut d'investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Alejandra López-Giraldo
- 1 Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain.,2 Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Guillaume Noell
- 2 Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain
| | - Ignacio Coca
- 1 Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain
| | | | | | - Roberto Rodriguez-Roisin
- 1 Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain.,2 Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain.,5 Respiratory Institute, Pulmonary Service, Hospital Clinic, Institut d'investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain; and
| | - Avrum Spira
- 6 Boston University School of Medicine, Boston, Massachusetts
| | - Susana G Kalko
- 3 Bioinformatics Platform Institut d'investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Alvar Agustí
- 1 Fundació Clínic per a la Recerca Biomèdica, Barcelona, Spain.,2 Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Madrid, Spain.,5 Respiratory Institute, Pulmonary Service, Hospital Clinic, Institut d'investigacions Biomèdiques August Pi i Sunyer, University of Barcelona, Barcelona, Spain; and
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33
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Morrow JD, Zhou X, Lao T, Jiang Z, DeMeo DL, Cho MH, Qiu W, Cloonan S, Pinto-Plata V, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Choi AMK, Silverman EK, Hersh CP. Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue. Sci Rep 2017; 7:44232. [PMID: 28287180 PMCID: PMC5347019 DOI: 10.1038/srep44232] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022] Open
Abstract
In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known COPD GWAS gene. Differentially expressed genes showed enrichment for putative interactors of the first three identified COPD GWAS genes IREB2, HHIP, and FAM13A, based on gene sets derived from protein and RNA binding studies, RNA-interference, a murine smoking model, and expression quantitative trait locus analyses. The gene module most highly associated for COPD in Weighted Gene Co-Expression Network Analysis (WGCNA) was enriched for B cell pathways, and shared seventeen genes with a mouse smoking model and twenty genes with previous emphysema studies. As in other common diseases, genes at COPD GWAS loci were not differentially expressed; however, using a combination of network methods, experimental studies and careful phenotype definition, we found differential expression of putative interactors of these genes, and we replicated previous human and mouse microarray results.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Taotao Lao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Zhiqiang Jiang
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Suzanne Cloonan
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - Victor Pinto-Plata
- Department of Critical Care Medicine and Pulmonary Disease, Baystate Medical Center, Springfield, MA, USA
| | - Bartholome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard J Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Augustine M K Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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34
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Fields W, Maione A, Keyser B, Bombick B. Characterization and Application of the VITROCELL VC1 Smoke Exposure System and 3D EpiAirway Models for Toxicological and e-Cigarette Evaluations. ACTA ACUST UNITED AC 2017. [DOI: 10.1089/aivt.2016.0035] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Wanda Fields
- RAI Services Company, Scientific and Regulatory Affairs, Winston-Salem, North Carolina
| | | | - Brian Keyser
- RAI Services Company, Scientific and Regulatory Affairs, Winston-Salem, North Carolina
| | - Betsy Bombick
- RAI Services Company, Scientific and Regulatory Affairs, Winston-Salem, North Carolina
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Green CE, Turner AM. The role of the endothelium in asthma and chronic obstructive pulmonary disease (COPD). Respir Res 2017; 18:20. [PMID: 28100233 PMCID: PMC5241996 DOI: 10.1186/s12931-017-0505-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/13/2017] [Indexed: 01/05/2023] Open
Abstract
COPD and asthma are important chronic inflammatory disorders with a high associated morbidity. Much research has concentrated on the role of inflammatory cells, such as the neutrophil, in these diseases, but relatively little focus has been given to the endothelial tissue, through which inflammatory cells must transmigrate to reach the lung parenchyma and cause damage. There is evidence that there is an abnormal amount of endothelial tissue in COPD and asthma and that this tissue and its’ progenitor cells behave in a dysfunctional manner. This article reviews the evidence of the involvement of pulmonary endothelium in COPD and asthma and potential treatment options for this.
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Affiliation(s)
- Clara E Green
- Centre for Translational Inflammation Research, University of Birmingham, Birmingham, UK.
| | - Alice M Turner
- Centre for Translational Inflammation Research, University of Birmingham, Birmingham, UK
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Scott M, Vallania F, Khatri P. META-ANALYSIS OF CONTINUOUS PHENOTYPES IDENTIFIES A GENE SIGNATURE THAT CORRELATES WITH COPD DISEASE STATUS. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017; 22:266-275. [PMID: 27896981 PMCID: PMC5464998 DOI: 10.1142/9789813207813_0026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The utility of multi-cohort two-class meta-analysis to identify robust differentially expressed gene signatures has been well established. However, many biomedical applications, such as gene signatures of disease progression, require one-class analysis. Here we describe an R package, MetaCorrelator, that can identify a reproducible transcriptional signature that is correlated with a continuous disease phenotype across multiple datasets. We successfully applied this framework to extract a pattern of gene expression that can predict lung function in patients with chronic obstructive pulmonary disease (COPD) in both peripheral blood mononuclear cells (PBMCs) and tissue. Our results point to a disregulation in the oxidation state of the lungs of patients with COPD, as well as underscore the classically recognized inammatory state that underlies this disease.
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Affiliation(s)
- Madeleine Scott
- Stanford Medical School, Stanford University, Stanford, California, USA
| | - Francesco Vallania
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
| | - Purvesh Khatri
- Stanford Institute for Immunity, Transplantation, and Infection, Stanford University, Stanford, California, USA
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, California, USA
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Schumacher FR, Schubert S, Hannus M, Sönnichsen B, Ittrich C, Kreideweiss S, Kurz T, Rippmann JF. RNAi Screen for NRF2 Inducers Identifies Targets That Rescue Primary Lung Epithelial Cells from Cigarette Smoke Induced Radical Stress. PLoS One 2016; 11:e0166352. [PMID: 27832175 PMCID: PMC5104413 DOI: 10.1371/journal.pone.0166352] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 10/27/2016] [Indexed: 12/30/2022] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a highly prevalent condition characterized by inflammation and progressive obstruction of the airways. At present, there is no treatment that suppresses the chronic inflammation of the disease, and COPD patients often succumb to the condition. Excessive oxidative stress caused by smoke inhalation is a major driving force of the disease. The transcription factor NRF2 is a critical player in the battle against oxidative stress and its function is impaired in COPD. Increasing NRF2 activity may therefore be a viable therapeutic option for COPD treatment. We show that down regulation of KEAP1, a NRF2 inhibitor, protects primary human lung epithelial cells from cigarette-smoke-extract (CSE) induced cell death in an established in vitro model of radical stress. To identify new potential drug targets with a similar effect, we performed a siRNA screen of the ‘druggable’ genome using a NRF2 transcriptional reporter cell line. This screen identified multiple genes that when down regulated increased NRF2 transcriptional activity and provided a survival benefit in the in vitro model. Our results suggest that inhibiting components of the ubiquitin-proteasome system will have the strongest effects on NRF2 transcriptional activity by increasing NRF2 levels. We also find that down regulation of the small GTPase Rab28 or the Estrogen Receptor ESRRA provide a survival benefit. Rab28 knockdown increased NRF2 protein levels, indicating that Rab28 may regulate NRF2 proteolysis. Conversely ESRRA down regulation increased NRF2 transcriptional activity without affecting NRF2 levels, suggesting a proteasome-independent mechanism.
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Affiliation(s)
- Frances-Rose Schumacher
- MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Center, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
| | | | | | | | - Carina Ittrich
- Boehringer Ingelheim Pharma GmbH & Co. KG, Research Germany, 8400, Biberach a. d. Riss, Germany
| | - Stefan Kreideweiss
- Boehringer Ingelheim Pharma GmbH & Co. KG, Research Germany, 8400, Biberach a. d. Riss, Germany
| | - Thimo Kurz
- MRC Protein Phosphorylation and Ubiquitylation Unit, The Sir James Black Center, University of Dundee, Dow Street, Dundee, DD1 5EH, United Kingdom
- * E-mail:
| | - Jörg F. Rippmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Research Germany, 8400, Biberach a. d. Riss, Germany
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Kusko RL, Brothers JF, Tedrow J, Pandit K, Huleihel L, Perdomo C, Liu G, Juan-Guardela B, Kass D, Zhang S, Lenburg M, Martinez F, Quackenbush J, Sciurba F, Limper A, Geraci M, Yang I, Schwartz DA, Beane J, Spira A, Kaminski N. Integrated Genomics Reveals Convergent Transcriptomic Networks Underlying Chronic Obstructive Pulmonary Disease and Idiopathic Pulmonary Fibrosis. Am J Respir Crit Care Med 2016; 194:948-960. [PMID: 27104832 PMCID: PMC5067817 DOI: 10.1164/rccm.201510-2026oc] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/27/2016] [Indexed: 12/18/2022] Open
Abstract
RATIONALE Despite shared environmental exposures, idiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease are usually studied in isolation, and the presence of shared molecular mechanisms is unknown. OBJECTIVES We applied an integrative genomic approach to identify convergent transcriptomic pathways in emphysema and IPF. METHODS We defined the transcriptional repertoire of chronic obstructive pulmonary disease, IPF, or normal histology lungs using RNA-seq (n = 87). MEASUREMENTS AND MAIN RESULTS Genes increased in both emphysema and IPF relative to control were enriched for the p53/hypoxia pathway, a finding confirmed in an independent cohort using both gene expression arrays and the nCounter Analysis System (n = 193). Immunohistochemistry confirmed overexpression of HIF1A, MDM2, and NFKBIB members of this pathway in tissues from patients with emphysema or IPF. Using reads aligned across splice junctions, we determined that alternative splicing of p53/hypoxia pathway-associated molecules NUMB and PDGFA occurred more frequently in IPF or emphysema compared with control and validated these findings by quantitative polymerase chain reaction and the nCounter Analysis System on an independent sample set (n = 193). Finally, by integrating parallel microRNA and mRNA-Seq data on the same samples, we identified MIR96 as a key novel regulatory hub in the p53/hypoxia gene-expression network and confirmed that modulation of MIR96 in vitro recapitulates the disease-associated gene-expression network. CONCLUSIONS Our results suggest convergent transcriptional regulatory hubs in diseases as varied phenotypically as chronic obstructive pulmonary disease and IPF and suggest that these hubs may represent shared key responses of the lung to environmental stresses.
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Affiliation(s)
- Rebecca L. Kusko
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - John F. Brothers
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - John Tedrow
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Kusum Pandit
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Luai Huleihel
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Catalina Perdomo
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Gang Liu
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Brenda Juan-Guardela
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
| | - Daniel Kass
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sherry Zhang
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Marc Lenburg
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Fernando Martinez
- Pulmonary & Critical Care Medicine, University of Michigan, Ann Arbor, Michigan
| | - John Quackenbush
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Frank Sciurba
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Mark Geraci
- Pulmonary Sciences and Critical Care Medicine, UC Denver, Denver, Colorado
| | - Ivana Yang
- Pulmonary Sciences and Critical Care Medicine, UC Denver, Denver, Colorado
| | - David A. Schwartz
- Pulmonary Sciences and Critical Care Medicine, UC Denver, Denver, Colorado
| | - Jennifer Beane
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Avrum Spira
- Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts
| | - Naftali Kaminski
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut
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Abstract
Adhesion G protein-coupled receptors (aGPCRs) have a long evolutionary history dating back to very basal unicellular eukaryotes. Almost every vertebrate is equipped with a set of different aGPCRs. Genomic sequence data of several hundred extinct and extant species allows for reconstruction of aGPCR phylogeny in vertebrates and non-vertebrates in general but also provides a detailed view into the recent evolutionary history of human aGPCRs. Mining these sequence sources with bioinformatic tools can unveil many facets of formerly unappreciated aGPCR functions. In this review, we extracted such information from the literature and open public sources and provide insights into the history of aGPCR in humans. This includes comprehensive analyses of signatures of selection, variability of human aGPCR genes, and quantitative traits at human aGPCR loci. As indicated by a large number of genome-wide genotype-phenotype association studies, variations in aGPCR contribute to specific human phenotypes. Our survey demonstrates that aGPCRs are significantly involved in adaptation processes, phenotype variations, and diseases in humans.
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Affiliation(s)
- Peter Kovacs
- Integrated Research and Treatment Center (IFB) AdiposityDiseases, Medical Faculty, University of Leipzig, Liebigstr. 21, Leipzig, 04103, Germany.
| | - Torsten Schöneberg
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, Leipzig, 04103, Germany.
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Liu G, Gradstedt H, Ermert D, Englund E, Singh B, Su YC, Johansson ME, Aspberg A, Agarwal V, Riesbeck K, Blom AM. Moraxella catarrhalis Evades Host Innate Immunity via Targeting Cartilage Oligomeric Matrix Protein. THE JOURNAL OF IMMUNOLOGY 2015; 196:1249-58. [DOI: 10.4049/jimmunol.1502071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 11/23/2015] [Indexed: 12/13/2022]
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Grayson PC, Steiling K, Platt M, Berman JS, Zhang X, Xiao J, Alekseyev YO, Liu G, Monach PA, Kaplan MJ, Spira A, Merkel PA. Defining the nasal transcriptome in granulomatosis with polyangiitis (Wegener's). Arthritis Rheumatol 2015; 67:2233-9. [PMID: 25939343 DOI: 10.1002/art.39185] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/30/2015] [Indexed: 02/02/2023]
Abstract
OBJECTIVE To determine whether disease processes related to granulomatosis with polyangiitis (Wegener's) (GPA) are reflected in gene expression profiles of the nasal mucosa. METHODS Nasal brushings of the inferior turbinate were obtained from 32 patients with GPA (10 with active nasal disease, 13 with prior nasal disease, and 9 with no history of nasal disease) and a composite comparator group with and without inflammatory nasal disease (12 healthy people, 15 with sarcoidosis, and 8 with allergic rhinitis). Differential gene expression was assessed between subgroups of GPA and comparators. RESULTS A total of 339 genes were differentially expressed between the GPA and comparator groups (absolute fold change >1.5; false discovery rate <0.05). Top canonical pathways up-regulated in nasal brushings from patients with GPA included granulocyte adhesion and diapedesis (P = 8.6(-22) ), agranulocyte adhesion and diapedesis (P = 1.3(-14) ), IL10 signaling (P = 3.0(-11) ), LXR/RXR activation (P = 4.3(-11) ), and TREM1 signaling (P = 9.0(-11) ). A set of genes differentially expressed in GPA independently of nasal disease activity status included genes related to epithelial barrier integrity (fibronectin 1, desmosomal proteins) and several matricellular proteins (e.g., osteonectin, osteopontin). Significant overlap of differentially expressed genes was observed between active and prior nasal disease GPA subgroups. Peripheral blood neutrophil and mononuclear gene expression levels associated with GPA were similarly altered in the nasal gene expression profiles of patients with active or prior nasal disease. CONCLUSION Profiling the nasal transcriptome in GPA reveals gene expression signatures related to innate immunity, inflammatory cell chemotaxis, extracellular matrix composition, and epithelial barrier integrity. Thus, airway-based expression profiling is feasible and informative in GPA.
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Affiliation(s)
- Peter C Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland, and Boston University, Boston, Massachusetts
| | | | | | | | | | - Ji Xiao
- Boston University, Boston, Massachusetts
| | | | - Gang Liu
- Boston University, Boston, Massachusetts
| | | | - Mariana J Kaplan
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, Maryland
| | | | - Peter A Merkel
- University of Pennsylvania, Philadelphia, and Boston University, Boston, Massachusetts
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Abd El-Fatah MF, Ghazy MA, Mostafa MS, El-Attar MM, Osman A. Identification of MMP-9 as a biomarker for detecting progression of chronic obstructive pulmonary disease. Biochem Cell Biol 2015; 93:541-7. [PMID: 26291981 DOI: 10.1139/bcb-2015-0073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex immunological disease with multiple pathological features that is primarily induced by smoking together with additional genetic risk factors. COPD is frequently underdiagnosed; forced expiratory volume in the first second (FEV1) is considered to be the main diagnostic measure for COPD, yet it is insufficiently sensitive to monitor disease progression. Biomarkers capable of monitoring COPD progression and severity are needed. In this report, we evaluated matrix metalloproteinase-9 (MMP-9) as an early marker for the detection and staging of COPD, by assessing the mRNA levels of MMP-9 in peripheral blood samples collected from 22 COPD patients, 6 asymptomatic smokers, and 5 healthy controls. Our results demonstrate that the mRNA levels of MMP-9 increased more than two-fold in severe COPD relative to non-COPD smokers or moderate COPD groups. Moreover, in the very severe COPD group, MMP-9 mRNA levels showed a 4-fold increase relative to the non-COPD smokers or the moderate COPD groups, while there was a mild increase (∼40%) when compared to the severe COPD group. Taken together, our results suggest that MMP-9 serves as a biomarker for the grade and severity of COPD.
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Affiliation(s)
- Marwa F Abd El-Fatah
- a Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed A Ghazy
- a Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
| | - Mohamed S Mostafa
- b Poisoning Control Center, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - May M El-Attar
- c Chest Department, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Ahmed Osman
- a Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo 11566, Egypt
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A 7-month cigarette smoke inhalation study in C57BL/6 mice demonstrates reduced lung inflammation and emphysema following smoking cessation or aerosol exposure from a prototypic modified risk tobacco product. Food Chem Toxicol 2015; 80:328-345. [PMID: 25843363 DOI: 10.1016/j.fct.2015.03.009] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Revised: 03/04/2015] [Accepted: 03/10/2015] [Indexed: 01/13/2023]
Abstract
Modified risk tobacco products (MRTP) are designed to reduce smoking-related health risks. A murine model of chronic obstructive pulmonary disease (COPD) was applied to investigate classical toxicology end points plus systems toxicology (transcriptomics and proteomics). C57BL/6 mice were exposed to conventional cigarette smoke (3R4F), fresh air (sham), or a prototypic MRTP (pMRTP) aerosol for up to 7 months, including a cessation group and a switching-to-pMRTP group (2 months of 3R4F exposure followed by fresh air or pMRTP for up to 5 months respectively). 3R4F smoke induced the typical adaptive changes in the airways, as well as inflammation in the lung, associated with emphysematous changes (impaired pulmonary function and alveolar damage). At nicotine-matched exposure concentrations of pMRTP aerosol, no signs of lung inflammation and emphysema were observed. Both the cessation and switching groups showed a similar reversal of inflammatory responses and no progression of initial emphysematous changes. A significant impact on biological processes, including COPD-related inflammation, apoptosis, and proliferation, was identified in 3R4F-exposed, but not in pMRTP-exposed lungs. Smoking cessation or switching reduced these perturbations to near sham-exposed levels. In conclusion, the mouse model indicated retarded disease progression upon cessation or switching to pMRTP which alone had no adverse effects.
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Comprehensive Analysis of Transcriptome Sequencing Data in the Lung Tissues of COPD Subjects. Int J Genomics 2015; 2015:206937. [PMID: 25834810 PMCID: PMC4365374 DOI: 10.1155/2015/206937] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Background and Objectives. Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by airflow limitation. Although airway inflammation and oxidative stress are known to be important in the pathogenesis of COPD, the mechanism underlying airflow obstruction is not fully understood. Gene expression profiling of lung tissue was performed to define the molecular pathways that are dysregulated in COPD. Methods. RNA was isolated from lung tissues obtained from 98 subjects with COPD and 91 control subjects with normal spirometry. The RNA samples were processed with RNA-seq using the HiSeq 2000 system. Genes expressed differentially between the two groups were identified using Student's t-test. Results. After filtering for genes with zero counts and noncoding genes, 16,676 genes were evaluated. A total of 2312 genes were differentially expressed between the lung tissues of COPD and control subjects (false discovery rate corrected q < 0.01). The expression of genes related to oxidative phosphorylation and protein catabolism was reduced and genes related to chromatin modification were dysregulated in lung tissues of COPD subjects. Conclusions. Oxidative phosphorylation, protein degradation, and chromatin modification were the most dysregulated pathways in the lung tissues of COPD subjects. These findings may have clinical and mechanistic implications in COPD.
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Ross CL, Galloway-Phillipps N, Armstrong PC, Mitchell JA, Warner TD, Brearley C, Ito M, Tunstall T, Elkin S, Kon OM, Hansel TT, Paul-Clark MJ. Protocol for a human in vivo model of acute cigarette smoke inhalation challenge in smokers with COPD: monitoring the nasal and systemic immune response using a network biology approach. BMJ Open 2015; 5:e005750. [PMID: 25631307 PMCID: PMC4316420 DOI: 10.1136/bmjopen-2014-005750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
INTRODUCTION Cigarette smoke contributes to a diverse range of diseases including chronic obstructive pulmonary disease (COPD), cardiovascular disorders and many cancers. There currently is a need for human challenge models, to assess the acute effects of a controlled cigarette smoke stimulus, followed by serial sampling of blood and respiratory tissue for advanced molecular profiling. We employ precision sampling of nasal mucosal lining fluid by absorption to permit soluble mediators measurement in eluates. Serial nasal curettage was used for transcriptomic analysis of mucosal tissue. METHODS AND ANALYSIS Three groups of strictly defined patients will be studied: 12 smokers with COPD (GOLD Stage 2) with emphysema, 12 matched smokers with normal lung function and no evidence of emphysema, and 12 matched never smokers with normal spirometry. Patients in the smoking groups are current smokers, and will be given full support to stop smoking immediately after this study. In giving a controlled cigarette smoke stimulus, all patients will have abstained from smoking for 12 h, and will smoke two cigarettes with expiration through the nose in a ventilated chamber. Before and after inhalation of cigarette smoke, a series of samples will be taken from the blood, nasal mucosal lining fluid and nasal tissue by curettage. Analysis of plasma nicotine and metabolites in relation to levels of soluble inflammatory mediators in nasal lining fluid and blood, as well as assessing nasal transcriptomics, ex vivo blood platelet aggregation and leucocyte responses to toll-like receptor agonists will be undertaken. IMPLICATIONS Development of acute cigarette smoke challenge models has promise for the study of molecular effects of smoking in a range of pathological processes. ETHICS AND DISSEMINATION This study was approved by the West London National Research Ethics Committee (12/LO/1101). The study findings will be presented at conferences and will be reported in peer-reviewed journals.
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Affiliation(s)
- Clare L Ross
- Imperial Clinical Respiratory Research Unit (ICRRU) and Biomedical Research Centre (BMRC), Centre for Respiratory Infection (CRI), St Mary's Hospital, Imperial College, London, UK
| | | | - Paul C Armstrong
- William Harvey Research Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, London, UK
| | - Jane A Mitchell
- National Heart and Lung Institute, Imperial College, London, UK
| | - Timothy D Warner
- William Harvey Research Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, London, UK
| | | | - Mari Ito
- Dainippon Sumitomo Pharma Co Ltd, Osaka, Japan
- Department of Molecular Regulation for intractable Diseases, Institute of Medical Science, Tokyo Medical University, Tokyo, Japan
| | - Tanushree Tunstall
- Imperial Clinical Respiratory Research Unit (ICRRU) and Biomedical Research Centre (BMRC), Centre for Respiratory Infection (CRI), St Mary's Hospital, Imperial College, London, UK
| | - Sarah Elkin
- Imperial Clinical Respiratory Research Unit (ICRRU) and Biomedical Research Centre (BMRC), Centre for Respiratory Infection (CRI), St Mary's Hospital, Imperial College, London, UK
| | - Onn Min Kon
- Imperial Clinical Respiratory Research Unit (ICRRU) and Biomedical Research Centre (BMRC), Centre for Respiratory Infection (CRI), St Mary's Hospital, Imperial College, London, UK
| | - Trevor T Hansel
- Imperial Clinical Respiratory Research Unit (ICRRU) and Biomedical Research Centre (BMRC), Centre for Respiratory Infection (CRI), St Mary's Hospital, Imperial College, London, UK
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Stepaniants S, Wang IM, Boie Y, Mortimer J, Kennedy B, Elliott M, Hayashi S, Luo H, Wong J, Loy L, Coulter S, Roberts CJ, Hogg JC, Sin DD, O'Neill G, Crackower M, Morris M, Paré PD, Obeidat M. Genes related to emphysema are enriched for ubiquitination pathways. BMC Pulm Med 2014; 14:187. [PMID: 25432663 PMCID: PMC4280711 DOI: 10.1186/1471-2466-14-187] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 11/19/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Increased small airway resistance and decreased lung elasticity contribute to the airflow limitation in chronic obstructive pulmonary disease (COPD). The lesion that corresponds to loss of lung elasticity is emphysema; the small airway obstruction is due to inflammatory narrowing and obliteration. Despite their convergence in altered physiology, different mechanisms contribute to these processes. The relationships between gene expression and these specific phenotypes may be more revealing than comparison with lung function. METHODS We measured the ratio of alveolar surface area to lung volume (SA/V) in lung tissue from 43 smokers. Two samples from 21 subjects, in which SA/V differed by >49 cm2/mL were profiled to select genes whose expression correlated with SA/V. Significant genes were tested for replication in the 22 remaining subjects. RESULTS The level of expression of 181 transcripts was related to SA/V ( p < 0.05). When these genes were tested in the 22 remaining subjects as a replication, thirty of the 181 genes remained significantly associated with SA/V (P < 0.05) and the direction of association was the same in 164/181. Pathway and network analysis revealed enrichment of genes involved in protein ubiquitination, and western blotting showed altered expression of genes involved in protein ubiquitination in obstructed individuals. CONCLUSION This study implicates modified protein ubiquitination and degradation as a potentially important pathway in the pathogenesis of emphysema.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Peter D Paré
- University of British Columbia Centre for Heart and Lung Innovation, St Paul's Hospital, 1081 Burrard St, Vancouver V6Z 1Y6, BC, Canada.
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Wu X, Sun X, Chen C, Bai C, Wang X. Dynamic gene expressions of peripheral blood mononuclear cells in patients with acute exacerbation of chronic obstructive pulmonary disease: a preliminary study. Crit Care 2014; 18:508. [PMID: 25407108 PMCID: PMC4305227 DOI: 10.1186/s13054-014-0508-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 08/26/2014] [Indexed: 01/09/2023] Open
Abstract
INTRODUCTION Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is a serious event that is responsible for the progress of the disease, increases in medical costs and high mortality. METHODS The aim of the present study was to identify AECOPD-specific biomarkers by evaluating the dynamic gene expression profiling of peripheral blood mononuclear cells (PBMCs) from patients with AECOPD on days 1, 3 and 10 after hospital admission and to compare the derived data with data from healthy controls or patients with stable COPD. RESULTS We found that 14 genes were co-differentially upregulated and 2 downregulated greater than 10-fold in patients with COPD or AECOPD compared with the healthy individuals. Eight co-differentially upregulated genes and six downregulated genes were identified as a panel of AECOPD-specific genes. Downregulation of TCF7 in PBMCs was found to be associated with the severity of COPD. Dynamic changes of Aminolevulinate-delta-synthase 2 and carbonic anhydrase I had similar patterns of Digital Evaluation Score System scores and may serve as potential genes of interest during the course of AECOPD. CONCLUSION Thus, our findings indicate a panel of altered gene expression patterns in PBMCs that can be used as AECOPD-specific dynamic biomarkers to monitor the course of AECOPD.
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Affiliation(s)
- Xiaodan Wu
- Department of Respiratory Medicine, Zhongshan Hospital, Fudan University, Fenglin Rd. No180, 200032, Shanghai, China.
| | - Xiaoru Sun
- Department of Respiratory Medicine, Wenzhou Medical University and The First Hospital, Nanbaixiang, 325000, Wenzhou, China.
| | - Chengshui Chen
- Department of Respiratory Medicine, Wenzhou Medical University and The First Hospital, Nanbaixiang, 325000, Wenzhou, China.
| | - Chunxue Bai
- Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai Respiratory Research Medicine, Fenglin Rd. No 180, 200032, Shanghai, China.
| | - Xiangdong Wang
- Department of Respiratory Medicine, Wenzhou Medical University and The First Hospital, Nanbaixiang, 325000, Wenzhou, China.
- Shanghai Institute of Clinical Bioinformatics, Fudan University Center for Clinical Bioinformatics, Shanghai Respiratory Research Medicine, Fenglin Rd. No 180, 200032, Shanghai, China.
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48
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Hobbs BD, Hersh CP. Integrative genomics of chronic obstructive pulmonary disease. Biochem Biophys Res Commun 2014; 452:276-86. [PMID: 25078622 PMCID: PMC4172635 DOI: 10.1016/j.bbrc.2014.07.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease with both environmental and genetic determinants, the most important of which is cigarette smoking. There is marked heterogeneity in the development of COPD among persons with similar cigarette smoking histories, which is likely partially explained by genetic variation. Genomic approaches such as genomewide association studies and gene expression studies have been used to discover genes and molecular pathways involved in COPD pathogenesis; however, these "first generation" omics studies have limitations. Integrative genomic studies are emerging which can combine genomic datasets to further examine the molecular underpinnings of COPD. Future research in COPD genetics will likely use network-based approaches to integrate multiple genomic data types in order to model the complex molecular interactions involved in COPD pathogenesis. This article reviews the genomic research to date and offers a vision for the future of integrative genomic research in COPD.
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Affiliation(s)
- Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States.
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49
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Voiles L, Lewis DE, Han L, Lupov IP, Lin TL, Robertson MJ, Petrache I, Chang HC. Overexpression of type VI collagen in neoplastic lung tissues. Oncol Rep 2014; 32:1897-904. [PMID: 25176343 PMCID: PMC4203334 DOI: 10.3892/or.2014.3438] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 07/18/2014] [Indexed: 01/19/2023] Open
Abstract
Type VI collagen (COL6), an extracellular matrix protein, is important in maintaining the integrity of lung tissue. An increase in COL6 mRNA and protein deposition was found in the lungs of patients with pulmonary fibrosis, a chronic inflammatory condition with a strong association with lung cancer. In the present study, we demonstrated overexpression of COL6 in the lungs of non-small cell lung cancers. We hypothesized that excessive COL6 in the lung interstitium may exert stimulatory effects on the adjacent cells. In vitro stimulation of monocytes with COL6 resulted in the production of IL-23, which may promote tumor development in an environment of IL-23-mediated lung inflammation, where tissue modeling occurs concurrently with excessive COL6 production. In addition, COL6 was capable of stimulating signaling pathways that activate focal adhesion kinase and extracellular signal-regulated kinase 1/2 in lung epithelial cells, which may also facilitate the development of lung neoplasms. Taken together, our data suggest the potential role of COL6 in promoting lung neoplasia in diseased lungs where COL6 is overexpressed.
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Affiliation(s)
- Larry Voiles
- Department of Biology, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, IN, USA
| | - David E Lewis
- Department of Biology, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, IN, USA
| | - Ling Han
- Department of Biology, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, IN, USA
| | - Ivan P Lupov
- Department of Biology, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, IN, USA
| | - Tsang-Long Lin
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, IN, USA
| | - Michael J Robertson
- The Bone Marrow and Stem Cell Transplantation Program, Lymphoma Program and the Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Irina Petrache
- Division of Pulmonary, Allergy, Critical Care, Occupational and Sleep Medicine, Department of Medicine, Indiana University School of Medicine and the ̔Richard L. Roudebush' VA Medical Center, Indianapolis, IN, USA
| | - Hua-Chen Chang
- Department of Biology, Indiana University-Purdue University Indianapolis School of Science, Indianapolis, IN, USA
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50
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Brandsma CA, van den Berge M, Postma DS, Jonker MR, Brouwer S, Paré PD, Sin DD, Bossé Y, Laviolette M, Karjalainen J, Fehrmann RSN, Nickle DC, Hao K, Spanjer AIR, Timens W, Franke L. A large lung gene expression study identifying fibulin-5 as a novel player in tissue repair in COPD. Thorax 2014; 70:21-32. [PMID: 24990664 DOI: 10.1136/thoraxjnl-2014-205091] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a progressive, incurable lung disease characterised by abnormal tissue repair causing emphysema and small airways fibrosis. Since current therapy cannot modify this abnormal repair, it is crucial to unravel its underlying molecular mechanisms. Unbiased analysis of genome-wide gene expression profiles in lung tissue provides a powerful tool to investigate this. METHODS We performed genome-wide gene expression profiling in 581 lung tissue samples from current and ex-smokers with (n=311) and without COPD (n=270). Subsequently, quantitative PCR, western blot and immunohistochemical analyses were performed to validate our main findings. RESULTS 112 genes were found to be upregulated in patients with COPD compared with controls, whereas 61 genes were downregulated. Among the most upregulated genes were fibulin-5 (FBLN5), elastin (ELN), latent transforming growth factor β binding protein 2 (LTBP2) and microfibrillar associated protein 4 (MFAP4), all implicated in elastogenesis. Our gene expression findings were validated at mRNA and protein level. We demonstrated higher ELN gene expression in COPD lung tissue and similar trends for FBLN5 and MFAP4, and negative correlations with lung function. FBLN5 protein levels were increased in COPD lung tissue and cleaved, possibly non-functional FBLN5 protein was present. Strong coexpression of FBLN5, ELN, LTBP2 and MFAP4 in lung tissue and in silico analysis indicated cofunctionality of these genes. Finally, colocalisation of FBLN5, MFAP4 and LTBP2 with elastic fibres was demonstrated in lung tissue. CONCLUSIONS We identified a clear gene signature for elastogenesis in COPD and propose FBLN5 as a novel player in tissue repair in COPD.
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Affiliation(s)
- Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marnix R Jonker
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Sharon Brouwer
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Peter D Paré
- The University of British Columbia, Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, Canada Respiratory Division, University of British Columbia, Vancouver, Canada
| | - Don D Sin
- The University of British Columbia, Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, Canada Respiratory Division, University of British Columbia, Vancouver, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada Department of Molecular Medicine, Laval University, Québec, Canada
| | - Michel Laviolette
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Juha Karjalainen
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rudolf S N Fehrmann
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Ke Hao
- Merck Research Laboratories, Boston, Massachusetts, USA
| | - Anita I R Spanjer
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands
| | - Wim Timens
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, The Netherlands
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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