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Chioccioli M, Liu S, Magruder S, Tata A, Borriello L, McDonough JE, Konkimalla A, Kim SH, Nouws J, Gonzalez DG, Traub B, Ye X, Yang T, Entenberg DR, Krishnaswamy S, Hendry CE, Kaminski N, Tata PR, Sauler M. Stem cell migration drives lung repair in living mice. Dev Cell 2024; 59:830-840.e4. [PMID: 38377991 PMCID: PMC11003834 DOI: 10.1016/j.devcel.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 06/12/2023] [Accepted: 02/06/2024] [Indexed: 02/22/2024]
Abstract
Tissue repair requires a highly coordinated cellular response to injury. In the lung, alveolar type 2 cells (AT2s) act as stem cells to replenish both themselves and alveolar type 1 cells (AT1s); however, the complex orchestration of stem cell activity after injury is poorly understood. Here, we establish longitudinal imaging of AT2s in murine intact tissues ex vivo and in vivo in order to track their dynamic behavior over time. We discover that a large fraction of AT2s become motile following injury and provide direct evidence for their migration between alveolar units. High-resolution morphokinetic mapping of AT2s further uncovers the emergence of distinct motile phenotypes. Inhibition of AT2 migration via genetic depletion of ArpC3 leads to impaired regeneration of AT2s and AT1s in vivo. Together, our results establish a requirement for stem cell migration between alveolar units and identify properties of stem cell motility at high cellular resolution.
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Affiliation(s)
- Maurizio Chioccioli
- Department of Genetics and Comparative Medicine, Yale University, New Haven, CT 06519, USA; Department of Comparative Medicine, Yale University, New Haven, CT 06519, USA.
| | - Shuyu Liu
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sumner Magruder
- Department of Computer Science, Yale University, New Haven, CT 06511, USA
| | - Aleksandra Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lucia Borriello
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Fox Chase Cancer, Philadelphia, PA 19140, USA
| | - John E McDonough
- Faculty of Health Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Arvind Konkimalla
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA; Medical Scientist Training Program, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sang-Hun Kim
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jessica Nouws
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - David G Gonzalez
- Department of Genetics and Comparative Medicine, Yale University, New Haven, CT 06519, USA
| | - Brian Traub
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA
| | - Xianjun Ye
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA
| | - Tao Yang
- Section of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China
| | - David R Entenberg
- Department of Pathology, Albert Einstein College of Medicine/Montefiore Medical Center, Bronx, NY 10461, USA
| | - Smita Krishnaswamy
- Department of Genetics and Comparative Medicine, Yale University, New Haven, CT 06519, USA; Department of Computer Science, Yale University, New Haven, CT 06511, USA
| | - Caroline E Hendry
- Department of Genetics and Comparative Medicine, Yale University, New Haven, CT 06519, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA
| | - Purushothama Rao Tata
- Department of Cell Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maor Sauler
- Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, CT 06520, USA
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2
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Kerckhof P, Ambrocio GPL, Beeckmans H, Kaes J, Geudens V, Bos S, Willems L, Vermaut A, Vermant M, Goos T, De Fays C, Aversa L, Mohamady Y, Vanstapel A, Orlitová M, Van Slambrouck J, Jin X, Varghese V, Josipovic I, Boone MN, Dupont LJ, Weynand B, Dubbeldam A, Van Raemdonck DE, Ceulemans LJ, Gayan-Ramirez G, De Sadeleer LJ, McDonough JE, Vanaudenaerde BM, Vos R. Ventilatory capacity in CLAD is driven by dysfunctional airway structure. EBioMedicine 2024; 101:105030. [PMID: 38394744 PMCID: PMC10897920 DOI: 10.1016/j.ebiom.2024.105030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Chronic lung allograft dysfunction (CLAD) encompasses three main phenotypes: bronchiolitis obliterans syndrome (BOS), restrictive allograft syndrome (RAS) and a Mixed phenotype combining both pathologies. How the airway structure in its entirety is affected in these phenotypes is still poorly understood. METHODS A detailed analysis of airway morphometry was applied to gain insights on the effects of airway remodelling on the distribution of alveolar ventilation in end-stage CLAD. Ex vivo whole lung μCT and tissue-core μCT scanning of six control, six BOS, three RAS and three Mixed explant lung grafts (9 male, 9 female, 2014-2021, Leuven, Belgium) were used for digital airway reconstruction and calculation of airway dimensions in relation to luminal obstructions. FINDINGS BOS and Mixed explants demonstrated airway obstructions of proximal bronchioles (starting at generation five), while RAS explants particularly had airway obstructions in the most distal bronchioles (generation >12). In BOS and Mixed explants 76% and 84% of bronchioles were obstructed, respectively, while this was 22% in RAS. Bronchiolar obstructions were mainly caused by lymphocytic inflammation of the airway wall or fibrotic remodelling, i.e. constrictive bronchiolitis. Proximal bronchiolectasis and imbalance in distal lung ventilation were present in all CLAD phenotypes and explain poor lung function and deterioration of specific lung function parameters. INTERPRETATION Alterations in the structure of conducting bronchioles revealed CLAD to affect alveolar ventilatory distribution in a regional fashion. The significance of various obstructions, particularly those associated with mucus, is highlighted. FUNDING This research was funded with the National research fund Flanders (G060322N), received by R.V.
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Affiliation(s)
- Pieterjan Kerckhof
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Gene P L Ambrocio
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium; Division of Pulmonary Medicine, Department of Internal Medicine, University of the Philippines - Philippine General Hospital, Manilla, The Philippines
| | - Hanne Beeckmans
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Janne Kaes
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Vincent Geudens
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Saskia Bos
- Newcastle University, Translational and Clinical Research Institute, Newcastle upon Tyne, United Kingdom
| | - Lynn Willems
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Astrid Vermaut
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Marie Vermant
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Charlotte De Fays
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium; Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Lucia Aversa
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Yousry Mohamady
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Arno Vanstapel
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium; Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | - Jan Van Slambrouck
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Xin Jin
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Vimi Varghese
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium; Department of Heart and Lung Transplant, Yashoda Hospitals, Hyderabad, India
| | - Iván Josipovic
- Department of Physics and Astronomy, UGCT, Radiation Physics, Ghent University, Gent, Belgium
| | - Matthieu N Boone
- Department of Physics and Astronomy, UGCT, Radiation Physics, Ghent University, Gent, Belgium
| | - Lieven J Dupont
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Birgit Weynand
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Adriana Dubbeldam
- Department of Radiology, University Hospitals Leuven, Leuven, Belgium
| | | | - Laurens J Ceulemans
- Department of Thoracic Surgery, University Hospitals Leuven, Leuven, Belgium
| | - Ghislaine Gayan-Ramirez
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Laurens J De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium; Cell Circuits in Systems Medicine of Lung Disease (Schiller Lab), Institute of Lung Health and Immunity (LHI) / Comprehensive Pneumology Centre (CPC), German Centre for Lung Research, Helmholtz Zentrum München, München, Germany
| | - John E McDonough
- Department of Medicine, McMaster University, Firestone Institute of Respiratory Health, Hamilton, Canada
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Robin Vos
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.
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Zheng Y, Schupp JC, Adams T, Clair G, Justet A, Ahangari F, Yan X, Hansen P, Carlon M, Cortesi E, Vermant M, Vos R, De Sadeleer LJ, Rosas IO, Pineda R, Sembrat J, Königshoff M, McDonough JE, Vanaudenaerde BM, Wuyts WA, Kaminski N, Ding J. Unagi: Deep Generative Model for Deciphering Cellular Dynamics and In-Silico Drug Discovery in Complex Diseases. Res Sq 2023:rs.3.rs-3676579. [PMID: 38196613 PMCID: PMC10775382 DOI: 10.21203/rs.3.rs-3676579/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Human diseases are characterized by intricate cellular dynamics. Single-cell sequencing provides critical insights, yet a persistent gap remains in computational tools for detailed disease progression analysis and targeted in-silico drug interventions. Here, we introduce UNAGI, a deep generative neural network tailored to analyze time-series single-cell transcriptomic data. This tool captures the complex cellular dynamics underlying disease progression, enhancing drug perturbation modeling and discovery. When applied to a dataset from patients with Idiopathic Pulmonary Fibrosis (IPF), UNAGI learns disease-informed cell embeddings that sharpen our understanding of disease progression, leading to the identification of potential therapeutic drug candidates. Validation via proteomics reveals the accuracy of UNAGI's cellular dynamics analyses, and the use of the Fibrotic Cocktail treated human Precision-cut Lung Slices confirms UNAGI's predictions that Nifedipine, an antihypertensive drug, may have antifibrotic effects on human tissues. UNAGI's versatility extends to other diseases, including a COVID dataset, demonstrating adaptability and confirming its broader applicability in decoding complex cellular dynamics beyond IPF, amplifying its utility in the quest for therapeutic solutions across diverse pathological landscapes.
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Affiliation(s)
- Yumin Zheng
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, Canada
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Jonas C. Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Taylor Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Geremy Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Aurelien Justet
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Paul Hansen
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Marianne Carlon
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Emanuela Cortesi
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Marie Vermant
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Laurens J. De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Ivan O Rosas
- Division of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Ricardo Pineda
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John Sembrat
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Melanie Königshoff
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - John E. McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Wim A. Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism, KU Leuven, Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University, School of Medicine, New Haven, CT, United States
| | - Jun Ding
- Quantitative Life Sciences, Faculty of Medicine & Health Sciences, McGill University, Montreal, QC, Canada
- Meakins-Christie Laboratories, Translational Research in Respiratory Diseases Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
- Mila - Quebec AI Institute, Montreal, QC, Canada
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4
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Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. Correction: iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023; 24:394. [PMID: 37858060 PMCID: PMC10588114 DOI: 10.1186/s12859-023-05523-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023] Open
Affiliation(s)
- Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jiayi Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ningya Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, German Center for Lung Research (DZL), Hannover, Germany
| | - Weimiao Wu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
- Meta Platforms, Inc, Cambridge, USA
| | - John E McDonough
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Geoffrey L Chupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
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5
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de Fays C, Geudens V, Gyselinck I, Kerckhof P, Vermaut A, Goos T, Vermant M, Beeckmans H, Kaes J, Van Slambrouck J, Mohamady Y, Willems L, Aversa L, Cortesi EE, Hooft C, Aerts G, Aelbrecht C, Everaerts S, McDonough JE, De Sadeleer LJ, Gohy S, Ambroise J, Janssens W, Ceulemans LJ, Van Raemdonck D, Vos R, Hackett TL, Hogg JC, Kaminski N, Gayan-Ramirez G, Pilette C, Vanaudenaerde BM. Mucosal immune alterations at the early onset of tissue destruction in chronic obstructive pulmonary disease. Front Immunol 2023; 14:1275845. [PMID: 37915582 PMCID: PMC10616299 DOI: 10.3389/fimmu.2023.1275845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023] Open
Abstract
Rationale COPD is characterized by chronic airway inflammation, small airways changes, with disappearance and obstruction, and also distal/alveolar destruction (emphysema). The chronology by which these three features evolve with altered mucosal immunity remains elusive. This study assessed the mucosal immune defense in human control and end-stage COPD lungs, by detailed microCT and RNA transcriptomic analysis of diversely affected zones. Methods In 11 control (non-used donors) and 11 COPD (end-stage) explant frozen lungs, 4 cylinders/cores were processed per lung for microCT and tissue transcriptomics. MicroCT was used to quantify tissue percentage and alveolar surface density to classify the COPD cores in mild, moderate and severe alveolar destruction groups, as well as to quantify terminal bronchioles in each group. Transcriptomics of each core assessed fold changes in innate and adaptive cells and pathway enrichment score between control and COPD cores. Immunostainings of immune cells were performed for validation. Results In mildly affected zones, decreased defensins and increased mucus production were observed, along CD8+ T cell accumulation and activation of the IgA pathway. In more severely affected zones, CD68+ myeloid antigen-presenting cells, CD4+ T cells and B cells, as well as MHCII and IgA pathway genes were upregulated. In contrast, terminal bronchioles were decreased in all COPD cores. Conclusion Spatial investigation of end-stage COPD lungs show that mucosal defense dysregulation with decreased defensins and increased mucus and IgA responses, start concomitantly with CD8+ T-cell accumulation in mild emphysema zones, where terminal bronchioles are already decreased. In contrast, adaptive Th and B cell activation is observed in areas with more advanced tissue destruction. This study suggests that in COPD innate immune alterations occur early in the tissue destruction process, which affects both the alveoli and the terminal bronchioles, before the onset of an adaptive immune response.
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Affiliation(s)
- Charlotte de Fays
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Vincent Geudens
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Iwein Gyselinck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Pieterjan Kerckhof
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Astrid Vermaut
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Marie Vermant
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Hanne Beeckmans
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Janne Kaes
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Jan Van Slambrouck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Yousry Mohamady
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Lynn Willems
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Lucia Aversa
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Emanuela E. Cortesi
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Charlotte Hooft
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Gitte Aerts
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Stephanie Everaerts
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - John E. McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Laurens J. De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Sophie Gohy
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
- Department of Pneumology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Jerome Ambroise
- Centre de Technologies Moléculaires Appliquées, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Laurens J. Ceulemans
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Dirk Van Raemdonck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Tillie L. Hackett
- Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - James C. Hogg
- Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, United States
| | - Ghislaine Gayan-Ramirez
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
| | - Charles Pilette
- Pole of Pneumology, ENT, and Dermatology, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
- Department of Pneumology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of CHROMETA, KULeuven, Leuven, Belgium
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6
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Liu Y, Zhao J, Adams TS, Wang N, Schupp JC, Wu W, McDonough JE, Chupp GL, Kaminski N, Wang Z, Yan X. iDESC: identifying differential expression in single-cell RNA sequencing data with multiple subjects. BMC Bioinformatics 2023; 24:318. [PMID: 37608264 PMCID: PMC10463720 DOI: 10.1186/s12859-023-05432-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/18/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Single-cell RNA sequencing (scRNA-seq) technology has enabled assessment of transcriptome-wide changes at single-cell resolution. Due to the heterogeneity in environmental exposure and genetic background across subjects, subject effect contributes to the major source of variation in scRNA-seq data with multiple subjects, which severely confounds cell type specific differential expression (DE) analysis. Moreover, dropout events are prevalent in scRNA-seq data, leading to excessive number of zeroes in the data, which further aggravates the challenge in DE analysis. RESULTS We developed iDESC to detect cell type specific DE genes between two groups of subjects in scRNA-seq data. iDESC uses a zero-inflated negative binomial mixed model to consider both subject effect and dropouts. The prevalence of dropout events (dropout rate) was demonstrated to be dependent on gene expression level, which is modeled by pooling information across genes. Subject effect is modeled as a random effect in the log-mean of the negative binomial component. We evaluated and compared the performance of iDESC with eleven existing DE analysis methods. Using simulated data, we demonstrated that iDESC had well-controlled type I error and higher power compared to the existing methods. Applications of those methods with well-controlled type I error to three real scRNA-seq datasets from the same tissue and disease showed that the results of iDESC achieved the best consistency between datasets and the best disease relevance. CONCLUSIONS iDESC was able to achieve more accurate and robust DE analysis results by separating subject effect from disease effect with consideration of dropouts to identify DE genes, suggesting the importance of considering subject effect and dropouts in the DE analysis of scRNA-seq data with multiple subjects.
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Affiliation(s)
- Yunqing Liu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jiayi Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Ningya Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Jonas C Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-Stage and Obstructive Lung Disease Hannover, German Center for Lung Research (DZL), Hannover, Germany
| | - Weimiao Wu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA
- Meta Platforms, Inc, Cambridge, USA
| | - John E McDonough
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Geoffrey L Chupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Zuoheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06520, USA.
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, 06520, USA.
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7
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Geudens V, Van Slambrouck J, Aerts G, Willems L, Goos T, Kaes J, Zajacova A, Gyselinck I, Aelbrecht C, Vermaut A, Beeckmans H, Vermant M, De Fays C, Sacreas A, Aversa L, Orlitova M, Vanstapel A, Josipovic I, Boone MN, McDonough JE, Weynand B, Pilette C, Janssens W, Dupont L, Wuyts WA, Verleden GM, Van Raemdonck DE, Vos R, Gayan-Ramirez G, Ceulemans LJ, Vanaudenaerde BM. COVID-19 progression in hospitalized patients using follow-up in vivo CT and ex vivo microCT. J Thorac Dis 2023; 15:3646-3661. [PMID: 37559650 PMCID: PMC10407474 DOI: 10.21037/jtd-22-1488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/31/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19) which can lead to acute respiratory distress syndrome (ARDS) and evolve to pulmonary fibrosis. Computed tomography (CT) is used to study disease progression and describe radiological patterns in COVID-19 patients. This study aimed to assess disease progression regarding lung volume and density over time on follow-up in vivo chest CT and give a unique look at parenchymal and morphological airway changes in "end-stage" COVID-19 lungs using ex vivo microCT. METHODS Volumes and densities of the lung/lobes of three COVID-19 patients were assessed using follow-up in vivo CT and ex vivo whole lung microCT scans. Airways were quantified by airway segmentations on whole lung microCT and small-partition microCT. As controls, three discarded healthy donor lungs were used. Histology was performed in differently affected regions in the COVID-19 lungs. RESULTS In vivo, COVID-19 lung volumes decreased while density increased over time, mainly in lower lobes as previously shown. Ex vivo COVID-19 lung volumes decreased by 60% and all lobes were smaller compared to controls. Airways were more visible on ex vivo microCT in COVID-19, probably due to fibrosis and increased airway diameter. In addition, small-partition microCT showed more deformation of (small) airway morphology and fibrotic organization in severely affected regions with heterogeneous distributions within the same lung which was confirmed by histology. CONCLUSIONS COVID-19-ARDS and subsequent pulmonary fibrosis alters lung architecture and airway morphology which is described using in vivo CT, ex vivo microCT, and histology.
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Affiliation(s)
- Vincent Geudens
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Jan Van Slambrouck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Gitte Aerts
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Lynn Willems
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Janne Kaes
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Andrea Zajacova
- Prague Lung Transplant Program, Department of Pneumology, Motol University Hospital, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Iwein Gyselinck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Astrid Vermaut
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Hanne Beeckmans
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Marie Vermant
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Charlotte De Fays
- Department of Pneumology, Cliniques Universitaires Saint-Luc, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Annelore Sacreas
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Lucia Aversa
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Michaela Orlitova
- Division of Anesthesiology and Algology, Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Arno Vanstapel
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Ivan Josipovic
- Department of Physics and Astronomy, Centre for X-Ray Tomography (UGCT), Radiation Physics, Ghent University, Gent, Belgium
| | - Matthieu N. Boone
- Department of Physics and Astronomy, Centre for X-Ray Tomography (UGCT), Radiation Physics, Ghent University, Gent, Belgium
| | - John E. McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Birgit Weynand
- Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Charles Pilette
- Department of Pneumology, Cliniques Universitaires Saint-Luc, Institute of Experimental and Clinical Research, Université Catholique de Louvain, Brussels, Belgium
| | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Lieven Dupont
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Wim A. Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Geert M. Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Dirk E. Van Raemdonck
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Ghislaine Gayan-Ramirez
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Laurens J. Ceulemans
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery, BREATHE, Department of Chrometa, KU Leuven, Leuven, Belgium
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8
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Kraven LM, Taylor AR, Molyneaux PL, Maher TM, McDonough JE, Mura M, Yang IV, Schwartz DA, Huang Y, Noth I, Ma SF, Yeo AJ, Fahy WA, Jenkins RG, Wain LV. Cluster analysis of transcriptomic datasets to identify endotypes of idiopathic pulmonary fibrosis. Thorax 2023; 78:551-558. [PMID: 35534152 PMCID: PMC9643664 DOI: 10.1136/thoraxjnl-2021-218563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
BACKGROUND Considerable clinical heterogeneity in idiopathic pulmonary fibrosis (IPF) suggests the existence of multiple disease endotypes. Identifying these endotypes would improve our understanding of the pathogenesis of IPF and could allow for a biomarker-driven personalised medicine approach. We aimed to identify clinically distinct groups of patients with IPF that could represent distinct disease endotypes. METHODS We co-normalised, pooled and clustered three publicly available blood transcriptomic datasets (total 220 IPF cases). We compared clinical traits across clusters and used gene enrichment analysis to identify biological pathways and processes that were over-represented among the genes that were differentially expressed across clusters. A gene-based classifier was developed and validated using three additional independent datasets (total 194 IPF cases). FINDINGS We identified three clusters of patients with IPF with statistically significant differences in lung function (p=0.009) and mortality (p=0.009) between groups. Gene enrichment analysis implicated mitochondrial homeostasis, apoptosis, cell cycle and innate and adaptive immunity in the pathogenesis underlying these groups. We developed and validated a 13-gene cluster classifier that predicted mortality in IPF (high-risk clusters vs low-risk cluster: HR 4.25, 95% CI 2.14 to 8.46, p=3.7×10-5). INTERPRETATION We have identified blood gene expression signatures capable of discerning groups of patients with IPF with significant differences in survival. These clusters could be representative of distinct pathophysiological states, which would support the theory of multiple endotypes of IPF. Although more work must be done to confirm the existence of these endotypes, our classifier could be a useful tool in patient stratification and outcome prediction in IPF.
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Affiliation(s)
- Luke M Kraven
- Department of Health Sciences, University of Leicester, Leicester, UK
- Research & Development, GlaxoSmithKline, Stevenage, UK
| | - Adam R Taylor
- Research & Development, GlaxoSmithKline, Stevenage, UK
| | - Philip L Molyneaux
- Guy's and St Thomas' NHS Foundation Trust, Royal Brompton and Harefield Hospitals, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Toby M Maher
- Guy's and St Thomas' NHS Foundation Trust, Royal Brompton and Harefield Hospitals, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - John E McDonough
- Division of Pulmonary, Critical Care & Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Marco Mura
- Division of Respirology, Western University, London, Ontario, Canada
| | - Ivana V Yang
- Department of Medicine, University of Colorado, Denver, Colorado, USA
| | - David A Schwartz
- Department of Medicine, University of Colorado, Denver, Colorado, USA
| | - Yong Huang
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Imre Noth
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Shwu Fan Ma
- Division of Pulmonary & Critical Care Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Astrid J Yeo
- Research & Development, GlaxoSmithKline, Stevenage, UK
| | | | - R Gisli Jenkins
- National Heart and Lung Institute, Imperial College London, London, UK
- National Institute for Health Research Respiratory Clinical Research Facility, Royal Brompton Hospital, London, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Glenfield Hospital, Leicester, UK
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9
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McDonough JE. Vladeck Redux: Our Endlessly Imperfect American Health Care System. Am J Public Health 2023; 113:477-479. [PMID: 37018695 PMCID: PMC10088951 DOI: 10.2105/ajph.2023.307265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Affiliation(s)
- John E McDonough
- John E. McDonough is a professor of practice at the Harvard T. H. Chan School of Public Health, Boston, MA
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10
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De Man R, McDonough JE, Adams TS, Manning EP, Myers G, Vos R, Ceulemans L, Dupont L, Vanaudenaerde BM, Wuyts WA, Rosas IO, Hagood JS, Ambalavanan N, Niklason L, Hansen KC, Yan X, Kaminski N. A Multi-omic Analysis of the Human Lung Reveals Distinct Cell Specific Aging and Senescence Molecular Programs. bioRxiv 2023:2023.04.19.536722. [PMID: 37131739 PMCID: PMC10153177 DOI: 10.1101/2023.04.19.536722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Age is a major risk factor for lung disease. To understand the mechanisms underlying this association, we characterized the changing cellular, genomic, transcriptional, and epigenetic landscape of lung aging using bulk and single-cell RNAseq (scRNAseq) data. Our analysis revealed age-associated gene networks that reflected hallmarks of aging, including mitochondrial dysfunction, inflammation, and cellular senescence. Cell type deconvolution revealed age-associated changes in the cellular composition of the lung: decreased alveolar epithelial cells and increased fibroblasts and endothelial cells. In the alveolar microenvironment, aging is characterized by decreased AT2B cells and reduced surfactant production, a finding that was validated by scRNAseq and IHC. We showed that a previously reported senescence signature, SenMayo, captures cells expressing canonical senescence markers. SenMayo signature also identified cell-type specific senescence-associated co-expression modules that have distinct molecular functions, including ECM regulation, cell signaling, and damage response pathways. Analysis of somatic mutations showed that burden was highest in lymphocytes and endothelial cells and was associated with high expression of senescence signature. Finally, aging and senescence gene expression modules were associated with differentially methylated regions, with inflammatory markers such as IL1B, IL6R, and TNF being significantly regulated with age. Our findings provide new insights into the mechanisms underlying lung aging and may have implications for the development of interventions to prevent or treat age-related lung diseases.
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Affiliation(s)
- Ruben De Man
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - John E McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Taylor S Adams
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Edward P Manning
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
- VA Connecticut Healthcare System, West Haven, CT, USA
| | - Greg Myers
- Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill
| | - Robin Vos
- Department of Respiratory Medicine, KU Leuven, Leuven, Belgium
| | | | - Lieven Dupont
- Department of Respiratory Medicine, KU Leuven, Leuven, Belgium
| | | | - Wim A Wuyts
- Department of Respiratory Medicine, KU Leuven, Leuven, Belgium
| | - Ivan O Rosas
- Section of Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - James S. Hagood
- Department of Pediatrics (Division of Pulmonology) and Marsico Lung Institute, University of North Carolina at Chapel Hill
| | | | - Laura Niklason
- Department of Anesthesiology, Yale School of Medicine; and Humacyte Global Inc
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | - Xiting Yan
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
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11
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Ahangari F, Price NL, Malik S, Chioccioli M, Bärnthaler T, Adams TS, Kim J, Pradeep SP, Ding S, Cosmos C, Rose KAS, McDonough JE, Aurelien NR, Ibarra G, Omote N, Schupp JC, DeIuliis G, Villalba Nunez JA, Sharma L, Ryu C, Dela Cruz CS, Liu X, Prasse A, Rosas I, Bahal R, Fernández-Hernando C, Kaminski N. microRNA-33 deficiency in macrophages enhances autophagy, improves mitochondrial homeostasis, and protects against lung fibrosis. JCI Insight 2023; 8:e158100. [PMID: 36626225 PMCID: PMC9977502 DOI: 10.1172/jci.insight.158100] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and ultimately fatal disease. Recent findings have shown a marked metabolic reprogramming associated with changes in mitochondrial homeostasis and autophagy during pulmonary fibrosis. The microRNA-33 (miR-33) family of microRNAs (miRNAs) encoded within the introns of sterol regulatory element binding protein (SREBP) genes are master regulators of sterol and fatty acid (FA) metabolism. miR-33 controls macrophage immunometabolic response and enhances mitochondrial biogenesis, FA oxidation, and cholesterol efflux. Here, we show that miR-33 levels are increased in bronchoalveolar lavage (BAL) cells isolated from patients with IPF compared with healthy controls. We demonstrate that specific genetic ablation of miR-33 in macrophages protects against bleomycin-induced pulmonary fibrosis. The absence of miR-33 in macrophages improves mitochondrial homeostasis and increases autophagy while decreasing inflammatory response after bleomycin injury. Notably, pharmacological inhibition of miR-33 in macrophages via administration of anti-miR-33 peptide nucleic acids (PNA-33) attenuates fibrosis in different in vivo and ex vivo mice and human models of pulmonary fibrosis. These studies elucidate a major role of miR-33 in macrophages in the regulation of pulmonary fibrosis and uncover a potentially novel therapeutic approach to treat this disease.
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Affiliation(s)
- Farida Ahangari
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nathan L. Price
- Vascular Biology and Therapeutics Program, Yale Center for Molecular and System Metabolism, Department of Comparative Medicine, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
- Experimental Gerontology Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, Maryland, USA
| | - Shipra Malik
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Maurizio Chioccioli
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Thomas Bärnthaler
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Taylor S. Adams
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jooyoung Kim
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Sai Pallavi Pradeep
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Shuizi Ding
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Carlos Cosmos
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Kadi-Ann S. Rose
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - John E. McDonough
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Nachelle R. Aurelien
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Department of Internal Medicine, Weill Cornell Hospital Medicine, New York, New York, USA
| | - Gabriel Ibarra
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
- Life Span Medical Group, Department of Internal Medicine, Rhode Island Hospital, Providence, Rhode Island, USA
| | - Norihito Omote
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Jonas C. Schupp
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Giuseppe DeIuliis
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Julian A. Villalba Nunez
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lokesh Sharma
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Changwan Ryu
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Charles S. Dela Cruz
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Xinran Liu
- Center for Cellular and Molecular Imaging (CCMI), Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Antje Prasse
- Department of Pneumology, University of Hannover, Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany
| | - Ivan Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Raman Bahal
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, Storrs, Connecticut, USA
| | - Carlos Fernández-Hernando
- Vascular Biology and Therapeutics Program, Yale Center for Molecular and System Metabolism, Department of Comparative Medicine, and Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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12
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De Sadeleer LJ, Verleden SE, Schupp JC, McDonough JE, Goos T, Yserbyt J, Bargagli E, Rottoli P, Kaminski N, Prasse A, Wuyts WA. BAL Transcriptomes Characterize Idiopathic Pulmonary Fibrosis Endotypes With Prognostic Impact. Chest 2022; 161:1576-1588. [PMID: 35063449 PMCID: PMC9424328 DOI: 10.1016/j.chest.2021.12.668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/06/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Given the plethora of pathophysiologic mechanisms described in idiopathic pulmonary fibrosis (IPF), we hypothesize that the mechanisms driving fibrosis in IPF may be different from one patient to another. RESEARCH QUESTION Do IPF endotypes exist and are they associated with outcome? STUDY DESIGN AND METHODS Using a publicly available gene expression dataset retrieved from BAL samples of patients with IPF and control participants (GSE70867), we clustered IPF samples based on a dimension reduction algorithm specifically designed for -omics data, called DDR Tree. After clustering, gene set enrichment analysis was performed for functional annotation, associations with clinical variables and prognosis were investigated, and differences in transcriptional regulation were determined using motif enrichment analysis. The findings were validated in three independent publicly available gene expression datasets retrieved from IPF blood samples. RESULTS One hundred seventy-six IPF samples from three centers were clustered in six IPF clusters, with distinct functional enrichment. Although clinical characteristics did not differ between the clusters, one cluster conferred worse sex-age-physiology score-corrected survival, whereas another showed a numeric trend toward worse survival (P = .08). The first was enriched for increased epithelial and innate and adaptive immunity signatures, whereas the other showed important telomere and mitochondrial dysfunction, loss of proteostasis, and increased myofibroblast signatures. The existence of these two endotypes, including the impact on survival of the immune endotype, was validated in three independent validation cohorts. Finally, we identified transcription factors regulating the expression of endotype-specific survival-associated genes. INTERPRETATION Gene expression-based endotyping in IPF is feasible and can inform clinical evolution. As endotype-specific pathways and survival-associated transcription factors are identified, endotyping may open up the possibility of endotype-tailored therapy.
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Affiliation(s)
- Laurens J De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Unit of Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.
| | - Stijn E Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Antwerp Surgical Training, Anatomy and Research Centre, Antwerp University, Antwerp, Belgium
| | - Jonas C Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT; Department of Pulmonology, Hannover Medical School, Hannover, Germany
| | - John E McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Unit of Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Jonas Yserbyt
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium
| | - Elena Bargagli
- Respiratory Diseases and Lung Transplantation Unit, AOUS and Siena University, Siena, Italy
| | - Paola Rottoli
- Specialization School in Respiratory Diseases, Siena University, Siena, Italy
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT
| | - Antje Prasse
- Department of Pulmonology, Hannover Medical School, Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover, Germany; German Centre for Lung Research, BREATH, Hannover, Germany; Department of Pneumology, University Medical Centre, Freiburg, Germany
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department CHROMETA, KU Leuven, Leuven, Belgium; Unit of Interstitial Lung Diseases, Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
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13
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McDonough JE, Adashi EY. The Center for Medicare and Medicaid Innovation-Toward Value-Based Care. JAMA 2022; 327:1957-1958. [PMID: 35532947 DOI: 10.1001/jama.2022.6927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- John E McDonough
- Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Eli Y Adashi
- The Warren Alpert Medical School, Brown University, Providence, Rhode Island
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14
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Sauler M, McDonough JE, Adams TS, Kothapalli N, Barnthaler T, Werder RB, Schupp JC, Nouws J, Robertson MJ, Coarfa C, Yang T, Chioccioli M, Omote N, Cosme C, Poli S, Ayaub EA, Chu SG, Jensen KH, Gomez JL, Britto CJ, Raredon MSB, Niklason LE, Wilson AA, Timshel PN, Kaminski N, Rosas IO. Characterization of the COPD alveolar niche using single-cell RNA sequencing. Nat Commun 2022; 13:494. [PMID: 35078977 PMCID: PMC8789871 DOI: 10.1038/s41467-022-28062-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 12/14/2021] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, however our understanding of cell specific mechanisms underlying COPD pathobiology remains incomplete. Here, we analyze single-cell RNA sequencing profiles of explanted lung tissue from subjects with advanced COPD or control lungs, and we validate findings using single-cell RNA sequencing of lungs from mice exposed to 10 months of cigarette smoke, RNA sequencing of isolated human alveolar epithelial cells, functional in vitro models, and in situ hybridization and immunostaining of human lung tissue samples. We identify a subpopulation of alveolar epithelial type II cells with transcriptional evidence for aberrant cellular metabolism and reduced cellular stress tolerance in COPD. Using transcriptomic network analyses, we predict capillary endothelial cells are inflamed in COPD, particularly through increased CXCL-motif chemokine signaling. Finally, we detect a high-metallothionein expressing macrophage subpopulation enriched in advanced COPD. Collectively, these findings highlight cell-specific mechanisms involved in the pathobiology of advanced COPD.
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Affiliation(s)
- Maor Sauler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
| | - John E McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA.
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Neeharika Kothapalli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Thomas Barnthaler
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- QIMR Berghofer Medical Research Institute, Herston, QLD, 4006, Australia
| | - Jonas C Schupp
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Respiratory Medicine, Hannover Medical School and Biomedical Research in End-stage and Obstructive Lung Disease Hannover, German Lung Research Center (DZL), Hannover, Germany
| | - Jessica Nouws
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Matthew J Robertson
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Cristian Coarfa
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Tao Yang
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Maurizio Chioccioli
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Norihito Omote
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Carlos Cosme
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Sergio Poli
- Department of Internal Medicine, Mount Sinai Medical Center, Miami, FL, USA
| | - Ehab A Ayaub
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sarah G Chu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Clemente J Britto
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Micha Sam B Raredon
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Medical Scientist Training Program, Yale School of Medicine, New Haven, CT, USA
| | - Laura E Niklason
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, 02118, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Ivan O Rosas
- Pulmonary, Critical Care and Sleep Medicine, Baylor College of Medicine, Houston, TX, USA
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15
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De Sadeleer LJ, McDonough JE, Schupp JC, Yan X, Vanstapel A, Van Herck A, Everaerts S, Geudens V, Sacreas A, Goos T, Aelbrecht C, Nawrot TS, Martens DS, Schols D, Claes S, Verschakelen JA, Verbeken EK, Ackermann M, Decottignies A, Mahieu M, Hackett TL, Hogg JC, Vanaudenaerde BM, Verleden SE, Kaminski N, Wuyts WA. Lung Microenvironments and Disease Progression in Fibrotic Hypersensitivity Pneumonitis. Am J Respir Crit Care Med 2022; 205:60-74. [PMID: 34724391 PMCID: PMC8865586 DOI: 10.1164/rccm.202103-0569oc] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Rationale: Fibrotic hypersensitivity pneumonitis (fHP) is an interstitial lung disease caused by sensitization to an inhaled allergen. Objectives: To identify the molecular determinants associated with progression of fibrosis. Methods: Nine fHP explant lungs and six unused donor lungs (as controls) were systematically sampled (4 samples/lung). According to microcomputed tomography measures, fHP cores were clustered into mild, moderate, and severe fibrosis groups. Gene expression profiles were assessed using weighted gene co-expression network analysis, xCell, gene ontology, and structure enrichment analysis. Gene expression of the prevailing molecular traits was also compared with idiopathic pulmonary fibrosis (IPF). The explant lung findings were evaluated in separate clinical fHP cohorts using tissue, BAL samples, and computed tomography scans. Measurements and Main Results: We found six molecular traits that associated with differential lung involvement. In fHP, extracellular matrix and antigen presentation/sensitization transcriptomic signatures characterized lung zones with only mild structural and histological changes, whereas signatures involved in honeycombing and B cells dominated the transcriptome in the most severely affected lung zones. With increasing disease severity, endothelial function was progressively lost, and progressive disruption in normal cellular homeostatic processes emerged. All six were also found in IPF, with largely similar associations with disease microenvironments. The molecular traits correlated with in vivo disease behavior in a separate clinical fHP cohort. Conclusions: We identified six molecular traits that characterize the morphological progression of fHP and associate with in vivo clinical behavior. Comparing IPF with fHP, the transcriptome landscape was determined considerably by local disease extent rather than by diagnosis alone.
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Affiliation(s)
- Laurens J. De Sadeleer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
| | - John E. McDonough
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Jonas C. Schupp
- Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut;,Department of Respiratory Medicine, Hannover Medical School, Hannover, Germany
| | - Xiting Yan
- Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Arno Vanstapel
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Department of Histopathology, and
| | - Anke Van Herck
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Stephanie Everaerts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
| | - Vincent Geudens
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Annelore Sacreas
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Tinne Goos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
| | - Celine Aelbrecht
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Tim S. Nawrot
- Department of Public Health and Primary Care, and,Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dries S. Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Dominique Schols
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sandra Claes
- Department of Microbiology, Immunology, and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | | | | | - Maximilian Ackermann
- Institute of Functional and Clinical Anatomy, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany;,Institute of Pathology and Molecular Pathology, Helios University Clinic Wuppertal, University of Witten/Herdecke, Wuppertal, Germany
| | - Anabelle Decottignies
- Telomeres Research Group, Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Manon Mahieu
- Telomeres Research Group, Genetic and Epigenetic Alterations of Genomes, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Tillie-Louise Hackett
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - James C. Hogg
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Bart M. Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA)
| | - Stijn E. Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Antwerp Surgical Training, Anatomy and Research Centre, Antwerp University, Antwerp, Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut
| | - Wim A. Wuyts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic Diseases and Metabolism (CHROMETA),,Unit for Interstitial Lung Diseases, Department of Respiratory Diseases
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16
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Ticku S, Barrow J, Fuccillo R, McDonough JE. Oral Health Stakeholders: A Time for Alignment and Action. Milbank Q 2021; 99:882-903. [PMID: 34189771 DOI: 10.1111/1468-0009.12525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Policy Points Since the Surgeon General's report in 2000, multiple stakeholder groups have engaged in advocacy to expand access to oral health coverage, integrate medicine and dentistry, and to improve the dental workforce. Using a stakeholder map across these three policy priorities, we describe how stakeholder groups are shaping the oral health policy landscape in this century. While the stakeholders are numerous, policy has changed little despite invested efforts and resources. To achieve change, multiple movements must coalesce around common goals and messages and a champion must emerge to lead the way. The ongoing COVID-19 pandemic and political changes due to the 2020 elections can open a window of opportunity to unite stakeholders to achieve comprehensive policy change.
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17
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Xu F, Tanabe N, Vasilescu DM, McDonough JE, Coxson HO, Ikezoe K, Kinose D, Ng KW, Verleden SE, Wuyts WA, Vanaudenaerde BM, Verschakelen J, Cooper JD, Lenburg ME, Morshead KB, Abbas AR, Arron JR, Spira A, Hackett TL, Colby TV, Ryerson CJ, Ng RT, Hogg JC. The transition from normal lung anatomy to minimal and established fibrosis in idiopathic pulmonary fibrosis (IPF). EBioMedicine 2021; 66:103325. [PMID: 33862585 PMCID: PMC8054143 DOI: 10.1016/j.ebiom.2021.103325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/12/2021] [Accepted: 03/19/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The transition from normal lung anatomy to minimal and established fibrosis is an important feature of the pathology of idiopathic pulmonary fibrosis (IPF). The purpose of this report is to examine the molecular and cellular mechanisms associated with this transition. METHODS Pre-operative thoracic Multidetector Computed Tomography (MDCT) scans of patients with severe IPF (n = 9) were used to identify regions of minimal(n = 27) and established fibrosis(n = 27). MDCT, Micro-CT, quantitative histology, and next-generation sequencing were used to compare 24 samples from donor controls (n = 4) to minimal and established fibrosis samples. FINDINGS The present results extended earlier reports about the transition from normal lung anatomy to minimal and established fibrosis by showing that there are activations of TGFBI, T cell co-stimulatory genes, and the down-regulation of inhibitory immune-checkpoint genes compared to controls. The expression patterns of these genes indicated activation of a field immune response, which is further supported by the increased infiltration of inflammatory immune cells dominated by lymphocytes that are capable of forming lymphoid follicles. Moreover, fibrosis pathways, mucin secretion, surfactant, TLRs, and cytokine storm-related genes also participate in the transitions from normal lung anatomy to minimal and established fibrosis. INTERPRETATION The transition from normal lung anatomy to minimal and established fibrosis is associated with genes that are involved in the tissue repair processes, the activation of immune responses as well as the increased infiltration of CD4, CD8, B cell lymphocytes, and macrophages. These molecular and cellular events correlate with the development of structural abnormality of IPF and probably contribute to its pathogenesis.
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Affiliation(s)
- Feng Xu
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Naoya Tanabe
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada; Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Dragos M Vasilescu
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - John E McDonough
- Leuven Lung Transplant Unit, KU Leuven and UZ Gasthuisberg, Leuven, Belgium
| | - Harvey O Coxson
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Kohei Ikezoe
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Daisuke Kinose
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada; Division of Respiratory Medicine, Department of Medicine, Shiga University of Medical Science, Shiga, Japan
| | | | - Stijn E Verleden
- Laboratory of Respiratory Diseases, BREATHE, Department of CHROMETA, KU Leuven, Leuven, Belgium
| | - Wim A Wuyts
- Leuven Lung Transplant Unit, KU Leuven and UZ Gasthuisberg, Leuven, Belgium
| | | | - Johny Verschakelen
- Leuven Lung Transplant Unit, KU Leuven and UZ Gasthuisberg, Leuven, Belgium
| | - Joel D Cooper
- Division of Thoracic Surgery, University of Pennsylvania, USA
| | | | | | | | | | - Avrum Spira
- Boston University Medical Center, Boston, MA, USA
| | - Tillie-Louise Hackett
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
| | - Thomas V Colby
- Department of Pathology and Laboratory Medicine, Mayo Clinic Arizona, USA
| | - Christopher J Ryerson
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada; Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Raymond T Ng
- Department of Computer Science, The University of British Columbia, Vancouver, Canada
| | - James C Hogg
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, Canada
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18
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Veith C, Hristova M, Danyal K, Habibovic A, Dustin CM, McDonough JE, Vanaudenaerde BM, Kreuter M, Schneider MA, Kahn N, van Schooten FJ, Boots AW, van der Vliet A. Profibrotic epithelial TGF-β1 signaling involves NOX4-mitochondria cross talk and redox-mediated activation of the tyrosine kinase FYN. Am J Physiol Lung Cell Mol Physiol 2020; 320:L356-L367. [PMID: 33325804 DOI: 10.1152/ajplung.00444.2019] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by a disturbed redox balance and increased production of reactive oxygen species (ROS), which is believed to contribute to epithelial injury and fibrotic lung scarring. The main pulmonary sources of ROS include mitochondria and NADPH oxidases (NOXs), of which the NOX4 isoform has been implicated in IPF. Non-receptor SRC tyrosine kinases (SFK) are important for cellular homeostasis and are often dysregulated in lung diseases. SFK activation by the profibrotic transforming growth factor-β (TGF-β) is thought to contribute to pulmonary fibrosis, but the relevant SFK isoform and its relationship to NOX4 and/or mitochondrial ROS in the context of profibrotic TGF-β signaling is not known. Here, we demonstrate that TGF-β1 can rapidly activate the SRC kinase FYN in human bronchial epithelial cells, which subsequently induces mitochondrial ROS (mtROS) production, genetic damage shown by the DNA damage marker γH2AX, and increased expression of profibrotic genes. Moreover, TGF-β1-induced activation of FYN involves initial activation of NOX4 and direct cysteine oxidation of FYN, and both FYN and mtROS contribute to TGF-β-induced induction of NOX4. NOX4 expression in lung tissues of IPF patients is positively correlated with disease severity, although FYN expression is down-regulated in IPF and does not correlate with disease severity. Collectively, our findings highlight a critical role for FYN in TGF-β1-induced mtROS production, DNA damage response, and induction of profibrotic genes in bronchial epithelial cells, and suggest that altered expression and activation of NOX4 and FYN may contribute to the pathogenesis of pulmonary fibrosis.
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Affiliation(s)
- Carmen Veith
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont.,Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Milena Hristova
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Karamatullah Danyal
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Aida Habibovic
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - Christopher M Dustin
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
| | - John E McDonough
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Michael Kreuter
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Marc A Schneider
- Translational Research Unit, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Nicolas Kahn
- Center for Interstitial and Rare Lung Diseases, Pneumology, Thoraxklinik, Heidelberg University Hospital, Heidelberg, Germany.,Translational Lung Research Center Heidelberg (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Frederik J van Schooten
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Agnes W Boots
- Department of Pharmacology and Toxicology, NUTRIM School of Nutrition, Translational Research and Metabolism, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, The Netherlands
| | - Albert van der Vliet
- Department of Pathology and Laboratory Medicine, Larner College of Medicine, University of Vermont, Burlington, Vermont
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19
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Jolliffe DA, Stefanidis C, Wang Z, Kermani NZ, Dimitrov V, White JH, McDonough JE, Janssens W, Pfeffer P, Griffiths CJ, Bush A, Guo Y, Christenson S, Adcock IM, Chung KF, Thummel KE, Martineau AR. Vitamin D Metabolism Is Dysregulated in Asthma and Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2020; 202:371-382. [PMID: 32186892 DOI: 10.1164/rccm.201909-1867oc] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Rationale: Vitamin D deficiency is common in patients with asthma and chronic obstructive pulmonary disease (COPD). Low 25-hydroxyvitamin D (25[OH]D) levels may represent a cause or a consequence of these conditions.Objectives: To determine whether vitamin D metabolism is altered in asthma or COPD.Methods: We conducted a longitudinal study in 186 adults to determine whether the 25(OH)D response to six oral doses of 3 mg vitamin D3, administered over 1 year, differed between those with asthma or COPD versus control subjects. Serum concentrations of vitamin D3, 25(OH)D3, and 1α,25-dihydroxyvitamin D3 (1α,25[OH]2D3) were determined presupplementation and postsupplementation in 93 adults with asthma, COPD, or neither condition, and metabolite-to-parent compound molar ratios were compared between groups to estimate hydroxylase activity. Additionally, we analyzed 14 datasets to compare expression of 1α,25(OH)2D3-inducible gene expression signatures in clinical samples taken from adults with asthma or COPD versus control subjects.Measurements and Main Results: The mean postsupplementation 25(OH)D increase in participants with asthma (20.9 nmol/L) and COPD (21.5 nmol/L) was lower than in control subjects (39.8 nmol/L; P = 0.001). Compared with control subjects, patients with asthma and COPD had lower molar ratios of 25(OH)D3-to-vitamin D3 and higher molar ratios of 1α,25(OH)2D3-to-25(OH)D3 both presupplementation and postsupplementation (P ≤ 0.005). Intergroup differences in 1α,25(OH)2D3-inducible gene expression signatures were modest and variable if statistically significant.Conclusions: Attenuation of the 25(OH)D response to vitamin D supplementation in asthma and COPD associated with reduced molar ratios of 25(OH)D3-to-vitamin D3 and increased molar ratios of 1α,25(OH)2D3-to-25(OH)D3 in serum, suggesting that vitamin D metabolism is dysregulated in these conditions.
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Affiliation(s)
- David A Jolliffe
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christos Stefanidis
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Zhican Wang
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | | | - Vassil Dimitrov
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | - John H White
- Department of Physiology, McGill University, Montreal, Quebec, Canada
| | | | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery, Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Leuven, Belgium; and
| | - Paul Pfeffer
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Christopher J Griffiths
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
| | - Andrew Bush
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Yike Guo
- Data Science Institute, William Penney Laboratory and
| | - Stephanie Christenson
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California, San Francisco, California
| | - Ian M Adcock
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- National Heart and Lung Institute, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, Seattle, Washington
| | - Adrian R Martineau
- Asthma UK Centre for Applied Research, Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom
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20
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Verleden SE, Kirby M, Everaerts S, Vanstapel A, McDonough JE, Verbeken EK, Braubach P, Boone MN, Aslam D, Verschakelen J, Ceulemans LJ, Neyrinck AP, Van Raemdonck DE, Vos R, Decramer M, Hackett TL, Hogg JC, Janssens W, Verleden GM, Vanaudenaerde BM. Small airway loss in the physiologically ageing lung: a cross-sectional study in unused donor lungs. Lancet Respir Med 2020; 9:167-174. [PMID: 33031747 DOI: 10.1016/s2213-2600(20)30324-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Physiological lung ageing is associated with a gradual decline in dynamic lung volumes and a progressive increase in residual volume due to diminished elastic recoil of the lung, loss of alveolar tissue, and lower chest wall compliance. However, the effects of ageing on the small airways (ie, airways <2·0 mm in diameter) remain largely unknown. By using a combination of ex-vivo conventional CT (resolution 1 mm), whole lung micro-CT (resolution 150 μm), and micro-CT of extracted cores (resolution 10 μm), we aimed to provide a multiresolution assessment of the small airways in lung ageing in a large cohort of never smokers. METHODS For this cross-sectional study, we included donor lungs collected from 32 deceased never-smoking donors (age range 16-83 years). Ex-vivo CT and whole lung high-resolution CT (micro-CT) were used to determine total airway numbers, stratified by airway diameter. Micro-CT was used to assess the number, length, and diameter of terminal bronchioles (ie, the last generation of conducting airways); mean linear intercept; and surface density in four lung tissue cores from each lung, extracted using a uniform sampling approach. Regression β coefficients are calculated using linear regression and polynomial models. FINDINGS Ex-vivo CT analysis showed an age-dependent decrease in the number of airways of diameter 2·0 mm to less than 2·5 mm (β coefficient per decade -0·119, 95% CI -0·193 to -0·045; R2=0·29) and especially in airways smaller than 2·0 mm in diameter (-0·158, -0·233 to -0·084; R2=0·47), between 30 and 80 years of age, but not of the larger (≥2·5 mm) diameter airways (-0·00781, -0·04409 to 0·02848; R2=0·0007). In micro-CT analysis of small airways, the total number of terminal bronchioles per lung increased until the age of 30 years, after which an almost linear decline in the number of terminal bronchioles was observed (β coefficient per decade -2035, 95% CI -2818 to -1252; R2=0·55), accompanied by a non-significant increase in alveolar airspace size (6·44, -0·57 to 13·45, R2=0·10). Moreover, this decrease in terminal bronchioles was associated with the age-related decline of pulmonary function predicted by healthy reference values. INTERPRETATION Loss of terminal bronchioles is an important structural component of age-related decline in pulmonary function of healthy, non-smoking individuals. FUNDING Research Foundation-Flanders, KU Leuven, Parker B Francis Foundation, UGent, Canadian Institutes for Health.
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Affiliation(s)
- Stijn E Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium.
| | - Miranda Kirby
- Department of Physics, Ryerson University, Toronto, ON, Canada
| | - Stephanie Everaerts
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Arno Vanstapel
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - John E McDonough
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Erik K Verbeken
- Department of Imaging and Pathology, KU Leuven, Leuven, Belgium
| | - Peter Braubach
- Institute for Pathology, Hannover Medical School, Hannover, Germany
| | - Matthieu N Boone
- Department of Physics and Astronomy, Radiation Physics-Centre for X-ray Tomography, Ghent University, Ghent, Belgium
| | - Danesh Aslam
- Department of Physics, Ryerson University, Toronto, ON, Canada
| | | | - Laurens J Ceulemans
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Arne P Neyrinck
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Dirk E Van Raemdonck
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Marc Decramer
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Tillie L Hackett
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - James C Hogg
- Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Wim Janssens
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Geert M Verleden
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases and Thoracic Surgery (BREATHE), Department of Chronic diseases, Metabolism and Aging (CHROMETA), KU Leuven, Leuven, Belgium
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21
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McDonough JE. Lost in the ACA: Bit Parts in a Landmark Law. J Health Polit Policy Law 2020; 45:533-545. [PMID: 32186347 DOI: 10.1215/03616878-8255469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The Affordable Care Act (ACA) is a mosaic across a spectrum of health policy domains. The law contains hundreds of smaller and mostly unnoticed reforms aimed at nearly every segment of American health policy. Ten years later, these provisions include successes, failures, and mixed bags, which should be considered in any full assessment of the ACA. This article examines 11 from each of these 3 categories, drawn from 9 of the ACA's 10 titles. These mininarratives deepen recognition that the ACA is our best example of comprehensive health reform and defies simplistic judgments.
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22
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Griffiths CD, Bilawchuk LM, McDonough JE, Jamieson KC, Elawar F, Cen Y, Duan W, Lin C, Song H, Casanova JL, Ogg S, Jensen LD, Thienpont B, Kumar A, Hobman TC, Proud D, Moraes TJ, Marchant DJ. IGF1R is an entry receptor for respiratory syncytial virus. Nature 2020; 583:615-619. [PMID: 32494007 DOI: 10.1038/s41586-020-2369-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 03/25/2020] [Indexed: 11/09/2022]
Abstract
Pneumonia resulting from infection is one of the leading causes of death worldwide. Pulmonary infection by the respiratory syncytial virus (RSV) is a large burden on human health, for which there are few therapeutic options1. RSV targets ciliated epithelial cells in the airways, but how viruses such as RSV interact with receptors on these cells is not understood. Nucleolin is an entry coreceptor for RSV2 and also mediates the cellular entry of influenza, the parainfluenza virus, some enteroviruses and the bacterium that causes tularaemia3,4. Here we show a mechanism of RSV entry into cells in which outside-in signalling, involving binding of the prefusion RSV-F glycoprotein with the insulin-like growth factor-1 receptor, triggers the activation of protein kinase C zeta (PKCζ). This cellular signalling cascade recruits nucleolin from the nuclei of cells to the plasma membrane, where it also binds to RSV-F on virions. We find that inhibiting PKCζ activation prevents the trafficking of nucleolin to RSV particles on airway organoid cultures, and reduces viral replication and pathology in RSV-infected mice. These findings reveal a mechanism of virus entry in which receptor engagement and signal transduction bring the coreceptor to viral particles at the cell surface, and could form the basis of new therapeutics to treat RSV infection.
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Affiliation(s)
- Cameron D Griffiths
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Leanne M Bilawchuk
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - John E McDonough
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Kyla C Jamieson
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Farah Elawar
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Yuchen Cen
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Wenming Duan
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Cindy Lin
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Haeun Song
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, Paris Descartes University, Paris, France
- Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Steven Ogg
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Lionel Dylan Jensen
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Anil Kumar
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - Tom C Hobman
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- Department of Cell Biology, University of Alberta, Edmonton, Alberta, Canada
| | - David Proud
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Theo J Moraes
- Program of Translational Medicine, Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - David J Marchant
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada.
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada.
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Kirby M, Tanabe N, Vasilescu DM, Cooper JD, McDonough JE, Verleden SE, Vanaudenaerde BM, Sin DD, Tan WC, Coxson HO, Hogg JC. Computed Tomography Total Airway Count Is Associated with the Number of Micro-Computed Tomography Terminal Bronchioles. Am J Respir Crit Care Med 2020; 201:613-615. [PMID: 31697561 DOI: 10.1164/rccm.201910-1948le] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Miranda Kirby
- Ryerson UniversityToronto, Canada.,St. Paul's HospitalVancouver, Canada
| | | | | | - Joel D Cooper
- University of PennsylvaniaPhiladelphia, Pennsylvaniaand
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24
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Verleden SE, Tanabe N, McDonough JE, Vasilescu DM, Xu F, Wuyts WA, Piloni D, De Sadeleer L, Willems S, Mai C, Hostens J, Cooper JD, Verbeken EK, Verschakelen J, Galban CJ, Van Raemdonck DE, Colby TV, Decramer M, Verleden GM, Kaminski N, Hackett TL, Vanaudenaerde BM, Hogg JC. Small airways pathology in idiopathic pulmonary fibrosis: a retrospective cohort study. Lancet Respir Med 2020; 8:573-584. [PMID: 32061334 DOI: 10.1016/s2213-2600(19)30356-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND The observation that patients with idiopathic pulmonary fibrosis (IPF) can have higher than normal expiratory flow rates at low lung volumes led to the conclusion that the airways are spared in IPF. This study aimed to re-examine the hypothesis that airways are spared in IPF using a multiresolution imaging protocol that combines multidetector CT (MDCT), with micro-CT and histology. METHODS This was a retrospective cohort study comparing explanted lungs from patients with severe IPF treated by lung transplantation with a cohort of unused donor (control) lungs. The donor control lungs had no known lung disease, comorbidities, or structural lung injury, and were deemed appropriate for transplantation on review of the clinical files. The diagnosis of IPF in the lungs from patients was established by a multidisciplinary consensus committee according to existing guidelines, and was confirmed by video-assisted thoracic surgical biopsy or by pathological examination of the contralateral lung. The control and IPF groups were matched for age, sex, height, and bodyweight. Samples of lung tissue were compared using the multiresolution imaging approach: a cascade of clinical MDCT, micro-CT, and histological imaging. We did two experiments: in experiment 1, all the lungs were randomly sampled; in experiment 2, samples were selected from regions of minimal and established fibrosis. The patients and donors were recruited from the Katholieke Universiteit Leuven (Leuven, Belgium) and the University of Pennsylvania Hospital (Philadelphia, PA, USA). The study took place at the Katholieke Universiteit Leuven, and the University of British Columbia (Vancouver, BC, Canada). FINDINGS Between Oct 5, 2009, and July 22, 2016, explanted lungs from patients with severe IPF (n=11), were compared with a cohort of unused donor (control) lungs (n=10), providing 240 samples of lung tissue for comparison using the multiresolution imaging approach. The MDCT specimen scans show that the number of visible airways located between the ninth generation (control 69 [SD 22] versus patients with IPF 105 [33], p=0·0023) and 14th generation (control 9 [6] versus patients with IPF 49 [28], p<0·0001) of airway branching are increased in patients with IPF, which we show by micro-CT is due to thickening of their walls and distortion of their lumens. The micro-CT analysis showed that compared with healthy (control) lung anatomy (mean 5·6 terminal bronchioles per mL [SD 1·6]), minimal fibrosis in IPF tissue was associated with a 57% loss of the terminal bronchioles (mean 2·4 terminal bronchioles per mL [SD 1·0]; p<0·0001), the appearance of fibroblastic foci, and infiltration of the tissue by inflammatory immune cells capable of forming lymphoid follicles. Established fibrosis in IPF tissue had a similar reduction (66%) in the number of terminal bronchioles (mean 1·9 terminal bronchioles per mL [SD 1·4]; p<0·0001) and was dominated by increased airspace size, Ashcroft fibrosis score, and volume fractions of tissue and collagen. INTERPRETATION Small airways disease is a feature of IPF, with significant loss of terminal bronchioles occuring within regions of minimal fibrosis. On the basis of these findings, we postulate that the small airways could become a potential therapeutic target in IPF. FUNDING Katholieke Universiteit Leuven, US National Institutes of Health, BC Lung Association, and Genentech.
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Affiliation(s)
- Stijn E Verleden
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Naoya Tanabe
- University of British Columbia, Department of Pathology and Center for Heart and Lung Innovation at St Paul's Hospital, Vancouver, BC, Canada; Department of Respiratory Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - John E McDonough
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Dragoş M Vasilescu
- University of British Columbia, Department of Pathology and Center for Heart and Lung Innovation at St Paul's Hospital, Vancouver, BC, Canada
| | - Feng Xu
- University of British Columbia, Department of Pathology and Center for Heart and Lung Innovation at St Paul's Hospital, Vancouver, BC, Canada
| | - Wim A Wuyts
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Davide Piloni
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium; The Respiratory Disease Unit, Fondazione IRCCS Policlinico San Matteo, University of Pavia, Pavia, Italy
| | - Laurens De Sadeleer
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Stijn Willems
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Cindy Mai
- Department of Radiology, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | | | - Joel D Cooper
- Department of Thoracic Surgery University of Pennsylvania, Philadelphia, PA, USA
| | - Erik K Verbeken
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Johny Verschakelen
- Department of Radiology, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Craig J Galban
- Department of Radiology, University of Michigan, Ann Arbor, MI, USA
| | - Dirk E Van Raemdonck
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Thomas V Colby
- Department of Laboratory Medicine and Pathology, Mayo Clinic Arizona, Phoenix, AZ, USA
| | - Marc Decramer
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Geert M Verleden
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care and Sleep Medicine, Yale University, New Haven, CT, USA
| | - Tillie-Louise Hackett
- University of British Columbia, Department of Pathology and Center for Heart and Lung Innovation at St Paul's Hospital, Vancouver, BC, Canada
| | - Bart M Vanaudenaerde
- Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, Katholieke Universiteit Leuven, University Hospitals Leuven, Leuven, Belgium
| | - James C Hogg
- University of British Columbia, Department of Pathology and Center for Heart and Lung Innovation at St Paul's Hospital, Vancouver, BC, Canada.
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25
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McDonough JE, Ahangari F, Li Q, Jain S, Verleden SE, Herazo-Maya J, Vukmirovic M, DeIuliis G, Tzouvelekis A, Tanabe N, Chu F, Yan X, Verschakelen J, Homer RJ, Manatakis DV, Zhang J, Ding J, Maes K, De Sadeleer L, Vos R, Neyrinck A, Benos PV, Bar-Joseph Z, Tantin D, Hogg JC, Vanaudenaerde BM, Wuyts WA, Kaminski N. Transcriptional regulatory model of fibrosis progression in the human lung. JCI Insight 2019; 4:131597. [PMID: 31600171 PMCID: PMC6948862 DOI: 10.1172/jci.insight.131597] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/04/2019] [Indexed: 11/17/2022] Open
Abstract
To develop a systems biology model of fibrosis progression within the human lung we performed RNA sequencing and microRNA analysis on 95 samples obtained from 10 idiopathic pulmonary fibrosis (IPF) and 6 control lungs. Extent of fibrosis in each sample was assessed by microCT-measured alveolar surface density (ASD) and confirmed by histology. Regulatory gene expression networks were identified using linear mixed-effect models and dynamic regulatory events miner (DREM). Differential gene expression analysis identified a core set of genes increased or decreased before fibrosis was histologically evident that continued to change with advanced fibrosis. DREM generated a systems biology model (www.sb.cs.cmu.edu/IPFReg) that identified progressively divergent gene expression tracks with microRNAs and transcription factors that specifically regulate mild or advanced fibrosis. We confirmed model predictions by demonstrating that expression of POU2AF1, previously unassociated with lung fibrosis but proposed by the model as regulator, is increased in B lymphocytes in IPF lungs and that POU2AF1-knockout mice were protected from bleomycin-induced lung fibrosis. Our results reveal distinct regulation of gene expression changes in IPF tissue that remained structurally normal compared with moderate or advanced fibrosis and suggest distinct regulatory mechanisms for each stage.
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Affiliation(s)
- John E. McDonough
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Farida Ahangari
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Qin Li
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Siddhartha Jain
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Stijn E. Verleden
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Jose Herazo-Maya
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Milica Vukmirovic
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Giuseppe DeIuliis
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Argyrios Tzouvelekis
- Division of Immunology, Biomedical Sciences Research Center “Alexander Fleming”, Athens, Greece
| | - Naoya Tanabe
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Fanny Chu
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | - Xiting Yan
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Johny Verschakelen
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robert J. Homer
- Department of Pathology, Yale University School of Medicine, New Haven,Connecticut, USA
- Pathology and Laboratory Medicine Service, VA CT HealthCare System, West Haven, Connecticut, USA
| | - Dimitris V. Manatakis
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Junke Zhang
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jun Ding
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Karen Maes
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Laurens De Sadeleer
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Robin Vos
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Arne Neyrinck
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ziv Bar-Joseph
- Carnegie Mellon University of Computer Science, Pittsburgh, Pennsylvania, USA
| | - Dean Tantin
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - James C. Hogg
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, Canada
| | | | - Wim A. Wuyts
- Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven Belgium
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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Everaerts S, McDonough JE, Verleden SE, Josipovic I, Boone M, Dubbeldam A, Mathyssen C, Serré J, Dupont LJ, Gayan-Ramirez G, Verschakelen J, Hogg JC, Verleden GM, Vanaudenaerde BM, Janssens W. Airway morphometry in COPD with bronchiectasis: a view on all airway generations. Eur Respir J 2019; 54:13993003.02166-2018. [DOI: 10.1183/13993003.02166-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 08/03/2019] [Indexed: 11/05/2022]
Abstract
The pathophysiological processes underlying bronchiectasis in chronic obstructive pulmonary disease (COPD) are not understood. In COPD, both small and large airways are progressively lost. It is currently not known to what extent the different airway generations of patients with COPD and bronchiectasis are involved.COPD explant lungs with bronchiectasis were compared to COPD explant lungs without bronchiectasis and unused donor lungs as controls. In order to investigate all airway generations, a multimodal imaging approach using different resolutions was conducted. Per group, five lungs were frozen (n=15) and underwent computed tomography (CT) imaging for large airway evaluation, with four tissue cores per lung imaged for measurements of the terminal bronchioles. Two additional lungs per group (n=6) were air-dried for lobar microCT images that allow airway segmentation and three-dimensional quantification of the complete airway tree.COPD lungs with bronchiectasis had significantly more airways compared to COPD lungs without bronchiectasis (p<0.001), with large airway numbers similar to control lungs. This difference was present in both upper and lower lobes. Lack of tapering was present (p=0.010) and larger diameters were demonstrated in lower lobes with bronchiectasis (p=0.010). MicroCT analysis of tissue cores showed similar reductions of tissue percentage, surface density and number of terminal bronchioles in both COPD groups compared to control lungs.Although terminal bronchioles were equally reduced in COPD lungs with and without bronchiectasis, significantly more large and small airways were found in COPD lungs with bronchiectasis.
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27
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Vos R, Wuyts WA, Gheysens O, Goffin KE, Schaevers V, Verleden SE, Van Herck A, Sacreas A, Heigl T, McDonough JE, Yserbyt J, Godinas L, Dupont LJ, Neyrinck AP, Van Raemdonck DE, Verbeken EK, Vanaudenaerde BM, Verleden GM. Pirfenidone in restrictive allograft syndrome after lung transplantation: A case series. Am J Transplant 2018; 18:3045-3059. [PMID: 30019840 DOI: 10.1111/ajt.15019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 01/25/2023]
Abstract
Pirfenidone may attenuate the decline of pulmonary function in restrictive allograft syndrome (RAS) after lung transplantation. We retrospectively assessed all lung transplant recipients with RAS who were treated with pirfenidone for at least 3 months (n = 11) in our lung transplant center and report on their long-term outcomes following initiation of pirfenidone. Main outcome parameters included evolution of pulmonary function and overall survival. Pirfenidone appears to attenuate the decline in forced vital capacity and forced expiratory volume in 1 second. Notably, 3 patients were bridged to redo-transplantation with pirfenidone for 11 (5-12) months and are currently alive, while 3 other patients demonstrate long-term stabilization of pulmonary function after 26.6 (range 18.4-46.6) months of treatment. Median overall 3-year survival after RAS diagnosis was 54.5%. Subjective intolerance, mainly anorexia and nausea, necessitating pirfenidone dose de-escalation in 55% of patients, as well as calcineurin dose increase requirements with about 20% are important complications during pirfenidone treatment after lung transplantation. Our findings provide further evidence that pirfenidone appears to be safe and may attenuate the rate of decline in lung function in patients with RAS, but the actual clinical benefit cannot be assessed in the context of this study design and requires further investigation in a larger randomized trial.
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Affiliation(s)
- Robin Vos
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
| | - Wim A Wuyts
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
| | - Olivier Gheysens
- Department of Nuclear Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Karolien E Goffin
- Department of Nuclear Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Veronique Schaevers
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Stijn E Verleden
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Anke Van Herck
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Annelore Sacreas
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Tobias Heigl
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - John E McDonough
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Jonas Yserbyt
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
| | - Laurent Godinas
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
| | - Lieven J Dupont
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
| | - Arne P Neyrinck
- Department of Anesthesiology, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Bart M Vanaudenaerde
- Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
| | - Geert M Verleden
- Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium.,Department of Chronic Diseases, Metabolism & Ageing (CHROMETA), Division of Respiratory Diseases, KU Leuven, Leuven, Belgium
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28
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McDonough JE, Kaminski N, Thienpont B, Hogg JC, Vanaudenaerde BM, Wuyts WA. Gene correlation network analysis to identify regulatory factors in idiopathic pulmonary fibrosis. Thorax 2018; 74:132-140. [PMID: 30366970 PMCID: PMC6467239 DOI: 10.1136/thoraxjnl-2018-211929] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a severe lung disease characterised by extensive pathological changes. The objective for this study was to identify the gene network and regulators underlying disease pathology in IPF and its association with lung function. METHODS Lung Tissue Research Consortium dataset with 262 IPF and control subjects (GSE47460) was randomly divided into two non-overlapping groups for cross-validated differential gene expression analysis. Consensus weighted gene coexpression network analysis identified overlapping coexpressed gene modules between both IPF groups. Modules were correlated with lung function (diffusion capacity, DLCO; forced expiratory volume in 1 s, FEV1; forced vital capacity, FVC) and enrichment analyses used to identify biological function and transcription factors. Module correlation with miRNA data (GSE72967) identified associated regulators. Clinical relevance in IPF was assessed in a peripheral blood gene expression dataset (GSE93606) to identify modules related to survival. RESULTS Correlation network analysis identified 16 modules in IPF. Upregulated modules were associated with cilia, DNA replication and repair, contractile fibres, B-cell and unfolded protein response, and extracellular matrix. Downregulated modules were associated with blood vessels, T-cell and interferon responses, leucocyte activation and degranulation, surfactant metabolism, and cellular metabolic and catabolic processes. Lung function correlated with nine modules (eight with DLCO, five with FVC). Intermodular network of transcription factors and miRNA showed clustering of fibrosis, immune response and contractile modules. The cilia-associated module was able to predict survival (p=0.0097) in an independent peripheral blood IPF cohort. CONCLUSIONS We identified a correlation gene expression network with associated regulators in IPF that provides novel insight into the pathological process of this disease.
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Affiliation(s)
- John E McDonough
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University, New Haven, Connecticut, USA
| | - Bernard Thienpont
- Laboratory for Functional Epigenetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - James C Hogg
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Leuven, Belgium
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29
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McDonough JE, Martens DS, Tanabe N, Ahangari F, Verleden SE, Maes K, Verleden GM, Kaminski N, Hogg JC, Nawrot TS, Wuyts WA, Vanaudenaerde BM. A role for telomere length and chromosomal damage in idiopathic pulmonary fibrosis. Respir Res 2018; 19:132. [PMID: 29986708 PMCID: PMC6038197 DOI: 10.1186/s12931-018-0838-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 07/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis is a fatal lung disease characterized by a progressive formation of fibroblastic foci in the interstitium. This disease is strongly associated with telomere dysfunction but the extent of telomere shortening and consequent chromosomal damage within IPF lungs and with regional disease severity remains unknown. METHODS Explanted IPF lungs (n = 10) were collected from transplant surgeries with six samples per lung analysed to capture the regional heterogeneity ranging from mild to severe disease. Non-used donor lungs (n = 6) were collected as "healthy" controls. Structural changes related to disease severity (microCT surface density), relative telomere length (real-time qPCR), and quantitative histology of chromosomal damage (γ-H2A.X) and extracellular matrix (elastin, total collagen, collagen 1, and collagen 3) were measured. A multivariate linear mixed-effects model controlling for subject was used to identify association of disease severity or fibrotic markers with telomere length and chromosomal damage. RESULTS We observed shorter telomere length (p = 0.001) and increased chromosomal damage (p = 0.018) in IPF lungs compared to controls. In IPF lungs, telomere length was associated with total collagen (p < 0.001) but not with structural changes of disease severity. Chromosomal damage was positively associated with increased elastin (p = 0.006) and negatively with structural disease severity (p = 0.046). Extensive γ-H2A.X staining was also present in airway epithelial cells. CONCLUSIONS Telomere length and chromosomal damage are involved in IPF with regional variation in telomere length and chromosomal damage associated with pathological changes in tissue structure and the extracellular matrix.
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Affiliation(s)
- John E McDonough
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Herestraat 49, O&N I, box 706, B-3000, Leuven, Belgium.
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Naoya Tanabe
- University of British Columbia, Centre for Heart Lung Innovation, Vancouver, BC, Canada
| | - Farida Ahangari
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University, New Haven, CT, USA
| | - Stijn E Verleden
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Herestraat 49, O&N I, box 706, B-3000, Leuven, Belgium
| | - Karen Maes
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Herestraat 49, O&N I, box 706, B-3000, Leuven, Belgium
| | - Geert M Verleden
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Herestraat 49, O&N I, box 706, B-3000, Leuven, Belgium
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University, New Haven, CT, USA
| | - James C Hogg
- University of British Columbia, Centre for Heart Lung Innovation, Vancouver, BC, Canada
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Herestraat 49, O&N I, box 706, B-3000, Leuven, Belgium
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism, and Ageing, KU Leuven, Herestraat 49, O&N I, box 706, B-3000, Leuven, Belgium
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30
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Everaerts S, Lammertyn EJ, Martens DS, De Sadeleer LJ, Maes K, van Batenburg AA, Goldschmeding R, van Moorsel CHM, Dupont LJ, Wuyts WA, Vos R, Gayan-Ramirez G, Kaminski N, Hogg JC, Janssens W, Verleden GM, Nawrot TS, Verleden SE, McDonough JE, Vanaudenaerde BM. The aging lung: tissue telomere shortening in health and disease. Respir Res 2018; 19:95. [PMID: 29751799 PMCID: PMC5948770 DOI: 10.1186/s12931-018-0794-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/27/2018] [Indexed: 11/17/2022] Open
Abstract
Background Telomere shortening has been associated with several lung diseases. However, telomere length is generally measured in peripheral blood leucocytes rather than in lung tissue, where disease occurs. Consequently, telomere dynamics have not been established for the normal human lung nor for diseased lung tissue. We hypothesized an age- and disease-dependent shortening of lung tissue telomeres. Methods At time of (re-)transplantation or autopsy, 70 explant lungs were collected: from unused donors (normal, n = 13) and patients with cystic fibrosis (CF, n = 12), chronic obstructive pulmonary disease (COPD, n = 11), chronic hypersensitivity pneumonitis (cHP, n = 9), bronchiolitis obliterans syndrome (BOS) after prior transplantation (n = 11) and restrictive allograft syndrome (RAS) after prior transplantation (n = 14). Lungs were inflated, frozen and then scanned using CT. Four tissue cores from distinct lung regions were sampled for analysis. Disease severity was evaluated using CT and micro CT imaging. DNA was extracted from the samples and average relative telomere length (RTL) was determined using real-time qPCR. Results The normal lungs showed a decrease in RTL with age (p < 0.0001). Of the diseased lungs, only BOS and RAS showed significant RTL decrease with increasing lung age (p = 0.0220 and p = 0.0272 respectively). Furthermore, we found that RTL showed considerable variability between samples within both normal and diseased lungs. cHP, BOS and RAS lungs had significant shorter RTL in comparison with normal lungs, after adjustment for lung age, sex and BMI (p < 0.0001, p = 0.0051 and p = 0.0301 respectively). When investigating the relation between RTL and regional disease severity in CF, cHP and RAS, no association was found. Conclusion These results show a progressive decline in telomere length with age in normal, BOS and RAS lungs. cHP, BOS and RAS lungs demonstrated shorter RTL compared to normal lungs. Lung tissue RTL does not associate with regional disease severity within the lung. Therefore, tissue RTL does not seem to fully reflect peripheral blood telomere length. Electronic supplementary material The online version of this article (10.1186/s12931-018-0794-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephanie Everaerts
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium.
| | - Elise J Lammertyn
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Laurens J De Sadeleer
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
| | - Karen Maes
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
| | - Aernoud A van Batenburg
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands
| | - Roel Goldschmeding
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Coline H M van Moorsel
- Department of Pulmonology, St Antonius ILD Center of Excellence, St Antonius Hospital, Nieuwegein, the Netherlands.,Division of Heart and Lungs, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Lieven J Dupont
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium.,Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Wim A Wuyts
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium.,Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Robin Vos
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium.,Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Ghislaine Gayan-Ramirez
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
| | - Naftali Kaminski
- Section of Pulmonary, Critical Care, and Sleep Medicine, Yale University, New Haven, CT, USA
| | - James C Hogg
- University of British Columbia James Hogg Research Centre, St. Paul's Hospital, Vancouver, BC, Canada
| | - Wim Janssens
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium.,Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Geert M Verleden
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium.,Department of Respiratory Diseases, University Hospitals Leuven, Leuven, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium.,Department of Public Health & Primary Care, KU Leuven, Leuven, Belgium
| | - Stijn E Verleden
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
| | - John E McDonough
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
| | - Bart M Vanaudenaerde
- Laboratory of Respiratory Diseases, Department of Chronic Diseases, Metabolism & Aging (CHROMETA), KU Leuven, Herestraat 49, O&NI, box 706, B-3000, Leuven, Belgium
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31
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McDonough JE. Our Greedy Health Care System. Am J Public Health 2017; 107:1744-1745. [DOI: 10.2105/ajph.2017.304065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- John E. McDonough
- John E. McDonough is with the Department of Health Policy and Management, Harvard T. H. Chan School of Public Health, Boston, MA
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32
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Suzuki M, Sze MA, Campbell JD, Brothers JF, Lenburg ME, McDonough JE, Elliott WM, Cooper JD, Spira A, Hogg JC. The cellular and molecular determinants of emphysematous destruction in COPD. Sci Rep 2017; 7:9562. [PMID: 28842670 PMCID: PMC5573394 DOI: 10.1038/s41598-017-10126-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/21/2017] [Indexed: 02/06/2023] Open
Abstract
The introduction of microCT has made it possible to show that the terminal bronchioles are narrowed and destroyed before the onset of emphysematous destruction in COPD. This report extends those observations to the cellular and molecular level in the centrilobular phenotype of emphysematous destruction in lungs donated by persons with very severe COPD (n = 4) treated by lung transplantation with unused donor lungs (n = 4) serving as controls. These lung specimens provided companion samples to those previously examined by microCT (n = 61) that we examined using quantitative histology (n = 61) and gene expression profiling (n = 48). The histological analysis showed that remodeling and destruction of the bronchiolar and alveolar tissue is associated with macrophage, CD4, CD8, and B cell infiltration with increased formation of tertiary lymphoid organs. Moreover, gene set enrichment analysis showed that genes known to be expressed by natural killer (NK), lymphoid tissue inducer (LTi), and innate lymphoid cell 1 (ILC1) cells, but not ILC2 or ILC3 cells, were enriched in the expression profiles associated with CD4, CD8, and B cell infiltration. Based on these findings, we postulate that the centrilobular phenotype of emphysematous destruction COPD is driven by a Th1 response activated by infiltrating ILC1, NK, and LTi cells.
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Affiliation(s)
- Masaru Suzuki
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine, and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Respiratory Medicine, Faculty of Medicine and Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Marc A Sze
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine, and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Joshua D Campbell
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John F Brothers
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Marc E Lenburg
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - John E McDonough
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine, and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - W Mark Elliott
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine, and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Joel D Cooper
- Division of Thoracic Surgery, Hospital of the University of Pennsylvania, Philadelphia, PA, USA
| | - Avrum Spira
- Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - James C Hogg
- Centre for Heart Lung Innovation, St. Paul's Hospital, Departments of Medicine, and Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
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33
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Tanabe N, Vasilescu DM, McDonough JE, Kinose D, Suzuki M, Cooper JD, Paré PD, Hogg JC. Micro-Computed Tomography Comparison of Preterminal Bronchioles in Centrilobular and Panlobular Emphysema. Am J Respir Crit Care Med 2017; 195:630-638. [PMID: 27611890 DOI: 10.1164/rccm.201602-0278oc] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
RATIONALE Very little is known about airways that are too small to be visible on thoracic multidetector computed tomography but larger than the terminal bronchioles. OBJECTIVES To examine the structure of preterminal bronchioles located one generation proximal to terminal bronchioles in centrilobular and panlobular emphysema. METHODS Preterminal bronchioles were identified by backtracking from the terminal bronchioles, and their centerlines were established along the entire length of their lumens. Multiple cross-sectional images perpendicular to the centerline were reconstructed to evaluate the bronchiolar wall and lumen, and the alveolar attachments to the outer airway walls in relation to emphysematous destruction in 28 lung samples from six patients with centrilobular emphysema, 20 lung samples from seven patients with panlobular emphysema associated with alpha-1 antitrypsin deficiency, and 47 samples from seven control (donor) lungs. MEASUREMENTS AND MAIN RESULTS The preterminal bronchiolar length, wall volume, total volume (wall + lumen), lumen circularity, and number of alveolar attachments were reduced in both centrilobular and panlobular emphysema compared with control lungs. In contrast, thickening of the wall and narrowing of the lumen were more severe and heterogeneous in centrilobular than in panlobular emphysema. The bronchiolar lumen was narrower in the middle than at both ends, and the decreased number of alveolar attachments was associated with increased wall thickness in centrilobular emphysema. CONCLUSIONS These results provide new information about small airways pathology in centrilobular and panlobular emphysema and show that these changes affect airways that are not visible with thoracic multidetector computed tomography scans but located proximal to the terminal bronchioles in chronic obstructive pulmonary disease.
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Affiliation(s)
- Naoya Tanabe
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dragoş M Vasilescu
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - John E McDonough
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,2 Department of Clinical and Experimental Medicine, Division of Respiratory Diseases, KU Leuven-University of Leuven, Leuven, Belgium
| | - Daisuke Kinose
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Masaru Suzuki
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada.,3 First Department of Medicine, Hokkaido University School of Medicine, Sapporo, Japan; and
| | - Joel D Cooper
- 4 Division of Thoracic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Peter D Paré
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - James C Hogg
- 1 Centre for Heart and Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia, Canada
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34
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McDonough JE. Prospects for Health Care Reform in the U.S. Senate. N Engl J Med 2017; 376:2501-2503. [PMID: 28564552 DOI: 10.1056/nejmp1706433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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McDonough JE. A Consequential Eight Years for Health Care and Public Health. Am J Public Health 2017; 107:24-26. [DOI: 10.2105/ajph.2016.303538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- John E. McDonough
- John E. McDonough is with the Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA
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36
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37
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Affiliation(s)
- John E McDonough
- Department of Health Policy and Management, Harvard School of Public Health, Boston, Massachusetts
| | - David K Jones
- Department of Health Law, Policy, and Management, Boston University School of Public Health, Boston, Massachusetts
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38
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Mai C, Verleden SE, McDonough JE, Willems S, De Wever W, Coolen J, Dubbeldam A, Van Raemdonck DE, Verbeken EK, Verleden GM, Hogg JC, Vanaudenaerde BM, Wuyts WA, Verschakelen JA. Thin-Section CT Features of Idiopathic Pulmonary Fibrosis Correlated with Micro-CT and Histologic Analysis. Radiology 2016; 283:252-263. [PMID: 27715655 DOI: 10.1148/radiol.2016152362] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Purpose To elucidate the underlying lung changes responsible for the computed tomographic (CT) features of idiopathic pulmonary fibrosis (IPF) and to gain insight into the way IPF proceeds through the lungs and progresses over time. Materials and Methods Micro-CT studies of tissue cores obtained from explant lungs were examined and were correlated 1:1 with a CT study obtained immediately before transplantation. Samples for histologic analysis were obtained from selected cores. Results In areas with no or minimal abnormalities on CT images, small areas of increased attenuation located in or near the interlobular septa can be seen on micro-CT studies. In more involved lung areas, the number of opacities increases and opacities enlarge and approach each other along the interlobular septa, causing a fine reticular pattern on CT images. Simultaneously, air-containing structures in and around these opacities arise, corresponding with small cysts on CT images. Honeycombing is caused by a progressive increase in the number and size of these cystic structures and tissue opacities that gradually extend toward the centrilobular region and finally replace the entire lobule. At histologic analysis, the small islands of increased attenuation very likely correspond with fibroblastic foci. Near these fibroblastic foci, an abnormal adjacency of alveolar walls was seen, suggesting alveolar collapse. In later stages, normal lung tissue is replaced by a large amount of young collagen, as seen in patients with advanced fibrosis. Conclusion Fibrosis and cyst formation in patients with IPF seem to start at the periphery of the pulmonary lobule and progressively extend toward the core of this anatomic lung unit. Evidence was found that alveolar collapse might already be present in an early stage when there is only little pulmonary fibrosis. © RSNA, 2016.
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Affiliation(s)
- Cindy Mai
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Stijn E Verleden
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - John E McDonough
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Stijn Willems
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Walter De Wever
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Johan Coolen
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Adriana Dubbeldam
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Dirk E Van Raemdonck
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Eric K Verbeken
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Geert M Verleden
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - James C Hogg
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Bart M Vanaudenaerde
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Wim A Wuyts
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
| | - Johny A Verschakelen
- From the Department of Radiology (C.M., W.D.W., J.C., A.D., J.A.V.), Leuven Lung Transplant Unit (S.E.V., J.E.M., S.W., D.E.V.R., G.M.V., B.M.V., W.A.W.), and Department of Pathology (E.K.V.), UZ Leuven, Herestraat 49, 3000 Leuven, Belgium; and University of British Columbia James Hogg Research Centre, St Paul's Hospital, Vancouver, British Columbia, Canada (J.E.M., J.C.H.)
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Affiliation(s)
- Howard K Koh
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts2Harvard Kennedy School, Cambridge, Massachusetts
| | - Rahul Rajkumar
- Centers for Medicare & Medicaid Services, US Department of Health and Human Services, Bethesda, Maryland4Dr Rajkumar is currently with CareFirst Blue Cross Blue Shield, Baltimore, Maryland
| | - John E McDonough
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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Vercauteren IM, Verleden SE, McDonough JE, Vandermeulen E, Ruttens D, Lammertyn EJ, Bellon H, De Dycker E, Dooms C, Yserbyt J, Verleden GM, Vanaudenaerde BM, Wuyts WA. CYFRA 21.1 in bronchoalveolar lavage of idiopathic pulmonary fibrosis patients. Exp Lung Res 2016; 41:459-65. [PMID: 26381718 DOI: 10.3109/01902148.2015.1073407] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AIM Idiopathic pulmonary fibrosis (IPF) is one of the most aggressive forms of interstitial lung diseases, however, clinically relevant biomarkers of diagnosis or prognosis are lacking. In this study, we investigated the levels of a fragment of Cytokeratin 19 (CYFRA 21.1) in bronchoalveolar lavage (BAL) of IPF patients at time of diagnosis. We further evaluated associations between CYFRA 21.1, pulmonary function evolution, mortality, and BAL cell count. MATERIALS AND METHODS Using the Lumipulse® G1200, CYFRA 21.1 was measured in BAL samples of 81 IPF patients and 9 controls. Based upon the median detected level (1.2 ng/mL) of CYFRA 21.1 in IPF patients, they were subdivided into an IPF CYFRA 21.1 low group (≤ 1.2 ng/mL) and IPF CYFRA 21.1 high group (> 1.2 ng/mL). RESULTS The CYFRA 21.1 levels were significantly higher in BAL of IPF patients compared to controls (P = .0015).Worse survival was observed, but no changes in pulmonary function, for IPF patients with high CYFRA 21.1 levels versus patients with low CYFRA 21.1 levels [P = .030, HR: 0.41, (0.18-0.92)[. The CYFRA 21.1 level correlated with both neutrophils (%: R = 0.60, P < .0001; #: R = 0.47, P < .0001) and eosinophils (%: R = 0.38, P = .0005; #: R = 0.30, P < .0072). CONCLUSIONS CYFRA 21.1 is increased in BAL of IPF patients. IPF patients with a high CYFRA 21.1 concentration have a worse survival. CYFRA 21.1 levels correlate with eosinophils and neutrophils. Further studies are warranted in using CYFRA 21.1 as a biomarker for IPF prognosis.
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Affiliation(s)
- Inge M Vercauteren
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - Stijn E Verleden
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - John E McDonough
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - Elly Vandermeulen
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - David Ruttens
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - Elise J Lammertyn
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - Hannelore Bellon
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - Els De Dycker
- b Department of Pulmonology , University Hospitals Leuven , Leuven , Belgium
| | - Christophe Dooms
- b Department of Pulmonology , University Hospitals Leuven , Leuven , Belgium
| | - Jonas Yserbyt
- b Department of Pulmonology , University Hospitals Leuven , Leuven , Belgium
| | - Geert M Verleden
- b Department of Pulmonology , University Hospitals Leuven , Leuven , Belgium
| | - Bart M Vanaudenaerde
- a Laboratory for Pulmonology, Department of Clinical and Experimental Medicine, KU Leuven , University of Leuven , Leuven , Belgium
| | - Wim A Wuyts
- b Department of Pulmonology , University Hospitals Leuven , Leuven , Belgium
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Boon M, Verleden SE, Bosch B, Lammertyn EJ, McDonough JE, Mai C, Verschakelen J, Kemner-van de Corput M, Tiddens HAW, Proesmans M, Vermeulen FL, Verbeken EK, Cooper J, Van Raemdonck DE, Decramer M, Verleden GM, Hogg JC, Dupont LJ, Vanaudenaerde BM, De Boeck K. Morphometric Analysis of Explant Lungs in Cystic Fibrosis. Am J Respir Crit Care Med 2016; 193:516-26. [DOI: 10.1164/rccm.201507-1281oc] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Affiliation(s)
- John E McDonough
- John E. McDonough is with the Department of Health Policy and Management, Harvard T.H. Chan School of Public Health, Boston, MA
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McDonough JE, Knudsen L, Wright AC, Elliott WM, Ochs M, Hogg JC. Regional differences in alveolar density in the human lung are related to lung height. J Appl Physiol (1985) 2015; 118:1429-34. [PMID: 25882386 DOI: 10.1152/japplphysiol.01017.2014] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The gravity-dependent pleural pressure gradient within the thorax produces regional differences in lung inflation that have a profound effect on the distribution of ventilation within the lung. This study examines the hypothesis that gravitationally induced differences in stress within the thorax also influence alveolar density in terms of the number of alveoli contained per unit volume of lung. To test this hypothesis, we measured the number of alveoli within known volumes of lung located at regular intervals between the apex and base of four normal adult human lungs that were rapidly frozen at a constant transpulmonary pressure, and used microcomputed tomographic imaging to measure alveolar density (number alveoli/mm3) at regular intervals between the lung apex and base. These results show that at total lung capacity, alveolar density in the lung apex is 31.6 ± 3.4 alveoli/mm3, with 15 ± 6% of parenchymal tissue consisting of alveolar duct. The base of the lung had an alveolar density of 21.2 ± 1.6 alveoli/mm3 and alveolar duct volume fraction of 29 ± 6%. The difference in alveolar density can be negated by factoring in the effects of alveolar compression due to the pleural pressure gradient at the base of the lung in vivo and at functional residual capacity.
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Sze MA, Dimitriu PA, Suzuki M, McDonough JE, Campbell JD, Brothers JF, Erb-Downward JR, Huffnagle GB, Hayashi S, Elliott WM, Cooper J, Sin DD, Lenburg ME, Spira A, Mohn WW, Hogg JC. Host Response to the Lung Microbiome in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2015; 192:438-45. [PMID: 25945594 DOI: 10.1164/rccm.201502-0223oc] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
RATIONALE The relatively sparse but diverse microbiome in human lungs may become less diverse in chronic obstructive pulmonary disease (COPD). This article examines the relationship of this microbiome to emphysematous tissue destruction, number of terminal bronchioles, infiltrating inflammatory cells, and host gene expression. METHODS Culture-independent pyrosequencing microbiome analysis was used to examine the V3-V5 regions of bacterial 16S ribosomal DNA in 40 samples of lung from 5 patients with COPD (Global Initiative for Chronic Obstructive Lung Disease [GOLD] stage 4) and 28 samples from 4 donors (controls). A second protocol based on the V1-V3 regions was used to verify the bacterial microbiome results. Within lung tissue samples the microbiome was compared with results of micro-computed tomography, infiltrating inflammatory cells measured by quantitative histology, and host gene expression. MEASUREMENTS AND MAIN RESULTS Ten operational taxonomic units (OTUs) was found sufficient to discriminate between control and GOLD stage 4 lung tissue, which included known pathogens such as Haemophilus influenzae. We also observed a decline in microbial diversity that was associated with emphysematous destruction, remodeling of the bronchiolar and alveolar tissue, and the infiltration of the tissue by CD4(+) T cells. Specific OTUs were also associated with neutrophils, eosinophils, and B-cell infiltration (P < 0.05). The expression profiles of 859 genes and 235 genes were associated with either enrichment or reductions of Firmicutes and Proteobacteria, respectively, at a false discovery rate cutoff of less than 0.1. CONCLUSIONS These results support the hypothesis that there is a host immune response to microorganisms within the lung microbiome that appears to contribute to the pathogenesis of COPD.
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Affiliation(s)
- Marc A Sze
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,2 Department of Medicine
| | - Pedro A Dimitriu
- 3 Department of Microbiology and Immunology, Life Sciences Institute, and
| | - Masaru Suzuki
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - John E McDonough
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,2 Department of Medicine
| | - Josh D Campbell
- 5 Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - John F Brothers
- 5 Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - John R Erb-Downward
- 6 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; and
| | - Gary B Huffnagle
- 6 Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan; and
| | - Shizu Hayashi
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - W Mark Elliott
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,2 Department of Medicine
| | - Joel Cooper
- 7 Department of Cardiovascular and Thoracic Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Don D Sin
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,2 Department of Medicine
| | - Marc E Lenburg
- 5 Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - Avrum Spira
- 5 Division of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - William W Mohn
- 3 Department of Microbiology and Immunology, Life Sciences Institute, and
| | - James C Hogg
- 1 Centre for Heart Lung Innovation, Providence Heart + Lung Institute at St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Verleden SE, Vasilescu DM, McDonough JE, Ruttens D, Vos R, Vandermeulen E, Bellon H, Geenens R, Verbeken EK, Verschakelen J, Van Raemdonck DE, Wuyts WA, Sokolow Y, Knoop C, Cooper JD, Hogg JC, Verleden GM, Vanaudenaerde BM. Linking clinical phenotypes of chronic lung allograft dysfunction to changes in lung structure. Eur Respir J 2015; 46:1430-9. [DOI: 10.1183/09031936.00010615] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/16/2015] [Indexed: 11/05/2022]
Abstract
Chronic lung allograft dysfunction (CLAD) remains the major barrier to long-term success after lung transplantation. This report compares gross and microscopic features of lungs removed from patients receiving a redo-transplant as treatment for CLAD.Lungs donated by patients with either the bronchiolitis obliterans syndrome (BOS) or restrictive allograft syndrome (RAS) phenotype of CLAD and appropriate control lungs (eight per group) were air-inflated, frozen solid and kept frozen while a multi-detector computed tomography (MDCT) was obtained. The lung was then cut into 2-cm thick transverse slices and sampled for micro-CT and histopathology.The MDCT showed reduced lung volume with increased lung weight and density in RAS versus BOS and control (p<0.05). Although pre-terminal bronchioles were obstructed in both phenotypes, RAS lungs showed a reduction of pre-terminal bronchioles (p<0.01). Micro-CT and matched histopathology showed that RAS was associated with reduced numbers of terminal bronchioles/lung compared to BOS and controls (p<0.01), with expansion of the interstitial compartment and obliteration of the alveolar airspaces by fibrous connective tissue.RAS is associated with greater destruction of both pre-terminal and terminal bronchioles. Additionally, the interstitial compartments are expanded and alveolar airspaces are obliterated by accumulation of fibrous connective tissue.
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Slopsema RL, Lin L, Flampouri S, Yeung D, Li Z, McDonough JE, Palta J. Development of a golden beam data set for the commissioning of a proton double-scattering system in a pencil-beam dose calculation algorithm. Med Phys 2015; 41:091710. [PMID: 25186385 DOI: 10.1118/1.4893281] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE The purpose of this investigation is to determine if a single set of beam data, described by a minimal set of equations and fitting variables, can be used to commission different installations of a proton double-scattering system in a commercial pencil-beam dose calculation algorithm. METHODS The beam model parameters required to commission the pencil-beam dose calculation algorithm (virtual and effective SAD, effective source size, and pristine-peak energy spread) are determined for a commercial double-scattering system. These parameters are measured in a first room and parameterized as function of proton energy and nozzle settings by fitting four analytical equations to the measured data. The combination of these equations and fitting values constitutes the golden beam data (GBD). To determine the variation in dose delivery between installations, the same dosimetric properties are measured in two additional rooms at the same facility, as well as in a single room at another facility. The difference between the room-specific measurements and the GBD is evaluated against tolerances that guarantee the 3D dose distribution in each of the rooms matches the GBD-based dose distribution within clinically reasonable limits. The pencil-beam treatment-planning algorithm is commissioned with the GBD. The three-dimensional dose distribution in water is evaluated in the four treatment rooms and compared to the treatment-planning calculated dose distribution. RESULTS The virtual and effective SAD measurements fall between 226 and 257 cm. The effective source size varies between 2.4 and 6.2 cm for the large-field options, and 1.0 and 2.0 cm for the small-field options. The pristine-peak energy spread decreases from 1.05% at the lowest range to 0.6% at the highest. The virtual SAD as well as the effective source size can be accurately described by a linear relationship as function of the inverse of the residual energy. An additional linear correction term as function of RM-step thickness is required for accurate parameterization of the effective SAD. The GBD energy spread is given by a linear function of the exponential of the beam energy. Except for a few outliers, the measured parameters match the GBD within the specified tolerances in all of the four rooms investigated. For a SOBP field with a range of 15 g/cm2 and an air gap of 25 cm, the maximum difference in the 80%-20% lateral penumbra between the GBD-commissioned treatment-planning system and measurements in any of the four rooms is 0.5 mm. CONCLUSIONS The beam model parameters of the double-scattering system can be parameterized with a limited set of equations and parameters. This GBD closely matches the measured dosimetric properties in four different rooms.
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Affiliation(s)
- R L Slopsema
- University of Florida Proton Therapy Institute, 2015 North Jefferson Street, Jacksonville, Florida 32205
| | - L Lin
- Department of Radiation Oncology, University of Pennsylvania, 3400 Civic Boulevard, 2326W TRC, PCAM, Philadelphia, Pennsylvania 19104
| | - S Flampouri
- University of Florida Proton Therapy Institute, 2015 North Jefferson Street, Jacksonville, Florida 32205
| | - D Yeung
- University of Florida Proton Therapy Institute, 2015 North Jefferson Street, Jacksonville, Florida 32205
| | - Z Li
- University of Florida Proton Therapy Institute, 2015 North Jefferson Street, Jacksonville, Florida 32205
| | - J E McDonough
- Department of Radiation Oncology, University of Pennsylvania, 3400 Civic Boulevard, 2326W TRC, PCAM, Philadelphia, Pennsylvania 19104
| | - J Palta
- VCU Massey Cancer Center, Virginia Commonwealth University, 401 College Street, Richmond, Virginia 23298
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48
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Affiliation(s)
- John E McDonough
- Department of Health Policy and Management, Center for Public Health Leadership, Harvard School of Public Health, Boston, Massachusetts
| | - Eli Y Adashi
- Warren Alpert Medical School, Brown University, Providence, Rhode Island
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49
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Affiliation(s)
- John E. McDonough
- Department of Health Policy & Management; Harvard School of Public Health; Boston, MA USA
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50
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Affiliation(s)
- Bruce Donoff
- From the Office of the Dean (B.D.) and the Departments of Oral and Maxillofacial Surgery (B.D.) and Oral Health Policy and Epidemiology (C.A.R.), Harvard School of Dental Medicine; and the Department of Health Policy and Management, Harvard School of Public Health (J.E.M.) - both in Boston
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